Starting phenix.real_space_refine on Fri Jul 3 10:34:36 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9dwm_47255/07_2026/9dwm_47255.cif Found real_map, /net/cci-nas-00/data/ceres_data/9dwm_47255/07_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 { model { file = "/net/cci-nas-00/data/ceres_data/9dwm_47255/07_2026/9dwm_47255.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9dwm_47255/07_2026/9dwm_47255.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9dwm_47255/07_2026/9dwm_47255.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9dwm_47255/07_2026/9dwm_47255.map" } 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-dev-6108/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: 2.32, per 1000 atoms: 0.21 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: 0.69 Conformation dependent library (CDL) restraints added in 299.7 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: 1.39 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: 2.07 Time building geometry restraints manager: 0.94 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: 16373 1.60 - 3.20: 1084 3.20 - 4.81: 50 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=" 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 angle pdb=" O4' DT J 96 " pdb=" C4' DT J 96 " pdb=" C3' DT J 96 " ideal model delta sigma weight residual 106.00 103.08 2.92 6.00e-01 2.78e+00 2.37e+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: 2.260 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.030 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: 11.540 Find NCS groups from input model: 0.090 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: 0.000 Load rotamer database and sin/cos tables:1.280 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.520 ------------------------------------------------------------------------------- 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 : 0.780 8.008 17523 Z= 0.720 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 0.78010 / 0.72 (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 : 0.226 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 16 average time/residue: 0.0495 time to fit residues: 1.7347 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 : 0.264 ------------------------------------------------------------------------------- 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 = 0.059476 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2810 r_free = 0.2810 target = 0.035720 restraints weight = 124439.071| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 65)----------------| | r_work = 0.2813 r_free = 0.2813 target = 0.035576 restraints weight = 75024.792| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.2824 r_free = 0.2824 target = 0.035895 restraints weight = 50460.998| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 56)----------------| | r_work = 0.2832 r_free = 0.2832 target = 0.036147 restraints weight = 39657.056| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 18)----------------| | r_work = 0.2834 r_free = 0.2834 target = 0.036202 restraints weight = 34263.809| |-----------------------------------------------------------------------------| r_work (final): 0.2759 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8814 moved from start: 0.0517 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= 0.222 Angle : 0.639 7.276 17523 Z= 0.412 Chirality : 0.046 0.215 2149 Planarity : 0.003 0.014 1344 Dihedral : 30.497 142.803 4184 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 10.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % 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: 2.45 (0.27), residues: 1045 helix: 2.45 (0.19), residues: 719 sheet: 2.91 (0.84), residues: 35 loop : -0.75 (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 0.00296 / 0.22 (11883) covalent geometry : angle 0.63910 / 0.41 (17523) hydrogen bonds : bond 0.06246 / 4.75 ( 894) hydrogen bonds : angle 4.03901 / 3.14 ( 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 : 0.272 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 16 average time/residue: 0.0477 time to fit residues: 1.7840 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=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: 9.9990 chunk 4 optimal weight: 7.9990 chunk 98 optimal weight: 6.9990 chunk 36 optimal weight: 1.9990 chunk 124 optimal weight: 40.0000 chunk 24 optimal weight: 7.9990 overall best weight: 6.9990 ------------------------------------------------------------------------------- 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 = 0.3426 r_free = 0.3426 target = 0.058949 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.2791 r_free = 0.2791 target = 0.034979 restraints weight = 125807.612| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 65)----------------| | r_work = 0.2798 r_free = 0.2798 target = 0.035137 restraints weight = 69236.243| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.2810 r_free = 0.2810 target = 0.035502 restraints weight = 46700.094| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.2817 r_free = 0.2817 target = 0.035657 restraints weight = 36505.019| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 61)----------------| | r_work = 0.2819 r_free = 0.2819 target = 0.035782 restraints weight = 31934.287| |-----------------------------------------------------------------------------| r_work (final): 0.2744 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8839 moved from start: 0.0727 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= 0.267 Angle : 0.687 6.869 17523 Z= 0.436 Chirality : 0.047 0.195 2149 Planarity : 0.003 0.013 1344 Dihedral : 30.541 141.292 4184 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 13.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % 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: 1.92 (0.26), residues: 1045 helix: 2.05 (0.19), residues: 716 sheet: 2.74 (0.84), residues: 35 loop : -0.91 (0.37), 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 0.00357 / 0.27 (11883) covalent geometry : angle 0.68709 / 0.44 (17523) hydrogen bonds : bond 0.06935 / 5.29 ( 894) hydrogen bonds : angle 4.36245 / 3.41 ( 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 : 0.255 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 16 average time/residue: 0.0413 time to fit residues: 1.5884 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 : 0.240 ------------------------------------------------------------------------------- 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: 1.9990 chunk 116 optimal weight: 40.0000 chunk 35 optimal weight: 40.0000 chunk 74 optimal weight: 20.0000 chunk 77 optimal weight: 20.0000 chunk 100 optimal weight: 2.9990 chunk 22 optimal weight: 30.0000 chunk 36 optimal weight: 0.9980 chunk 114 optimal weight: 30.0000 chunk 117 optimal weight: 40.0000 chunk 44 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 = 0.3419 r_free = 0.3419 target = 0.058552 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.2771 r_free = 0.2771 target = 0.034294 restraints weight = 126449.063| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 55)----------------| | r_work = 0.2785 r_free = 0.2785 target = 0.034712 restraints weight = 68724.590| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 69)----------------| | r_work = 0.2795 r_free = 0.2795 target = 0.034998 restraints weight = 46328.766| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.2799 r_free = 0.2799 target = 0.035104 restraints weight = 36490.766| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 52)----------------| | r_work = 0.2804 r_free = 0.2804 target = 0.035291 restraints weight = 32600.513| |-----------------------------------------------------------------------------| r_work (final): 0.2779 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8869 moved from start: 0.1439 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= 0.259 Angle : 0.657 6.599 17523 Z= 0.424 Chirality : 0.045 0.202 2149 Planarity : 0.003 0.013 1344 Dihedral : 30.741 140.173 4184 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 14.42 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: 1.28 (0.26), residues: 1045 helix: 1.58 (0.19), residues: 719 sheet: 2.03 (0.83), residues: 35 loop : -1.13 (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 0.00337 / 0.26 (11883) covalent geometry : angle 0.65719 / 0.42 (17523) hydrogen bonds : bond 0.07921 / 6.06 ( 894) hydrogen bonds : angle 4.38264 / 3.43 ( 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 : 0.263 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 16 average time/residue: 0.0473 time to fit residues: 1.7388 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 : 0.255 ------------------------------------------------------------------------------- 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: 2.9990 chunk 118 optimal weight: 50.0000 chunk 119 optimal weight: 20.0000 chunk 10 optimal weight: 0.9990 chunk 75 optimal weight: 20.0000 chunk 100 optimal weight: 9.9990 chunk 9 optimal weight: 6.9990 chunk 52 optimal weight: 1.9990 chunk 39 optimal weight: 30.0000 chunk 56 optimal weight: 9.9990 chunk 57 optimal weight: 20.0000 overall best weight: 4.5990 ------------------------------------------------------------------------------- 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 = 0.3432 r_free = 0.3432 target = 0.059025 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2799 r_free = 0.2799 target = 0.035028 restraints weight = 124360.013| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 53)----------------| | r_work = 0.2809 r_free = 0.2809 target = 0.035269 restraints weight = 68744.314| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 58)----------------| | r_work = 0.2819 r_free = 0.2819 target = 0.035552 restraints weight = 46163.226| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 51)----------------| | r_work = 0.2826 r_free = 0.2826 target = 0.035733 restraints weight = 36158.307| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 55)----------------| | r_work = 0.2830 r_free = 0.2830 target = 0.035862 restraints weight = 31468.268| |-----------------------------------------------------------------------------| r_work (final): 0.2805 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8832 moved from start: 0.1419 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= 0.197 Angle : 0.599 6.995 17523 Z= 0.385 Chirality : 0.044 0.186 2149 Planarity : 0.002 0.010 1344 Dihedral : 30.741 137.127 4184 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 9.97 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: 2.08 (0.27), residues: 1045 helix: 2.32 (0.19), residues: 718 sheet: 1.66 (0.79), residues: 35 loop : -1.15 (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 0.00248 / 0.20 (11883) covalent geometry : angle 0.59871 / 0.38 (17523) hydrogen bonds : bond 0.05703 / 4.34 ( 894) hydrogen bonds : angle 3.74101 / 2.93 ( 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 : 0.262 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 16 average time/residue: 0.0426 time to fit residues: 1.5389 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 102 optimal weight: 7.9990 chunk 24 optimal weight: 8.9990 chunk 65 optimal weight: 20.0000 chunk 15 optimal weight: 9.9990 chunk 128 optimal weight: 50.0000 chunk 70 optimal weight: 50.0000 chunk 85 optimal weight: 30.0000 chunk 7 optimal weight: 6.9990 chunk 6 optimal weight: 2.9990 chunk 1 optimal weight: 8.9990 chunk 45 optimal weight: 1.9990 overall best weight: 5.7990 ------------------------------------------------------------------------------- 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 = 0.3426 r_free = 0.3426 target = 0.058747 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.2785 r_free = 0.2785 target = 0.034575 restraints weight = 125825.701| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.2806 r_free = 0.2806 target = 0.035107 restraints weight = 68208.177| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 62)----------------| | r_work = 0.2813 r_free = 0.2813 target = 0.035368 restraints weight = 46081.331| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.2819 r_free = 0.2819 target = 0.035532 restraints weight = 36188.362| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 54)----------------| | r_work = 0.2821 r_free = 0.2821 target = 0.035609 restraints weight = 31496.152| |-----------------------------------------------------------------------------| r_work (final): 0.2795 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8850 moved from start: 0.1535 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= 0.219 Angle : 0.619 7.111 17523 Z= 0.397 Chirality : 0.044 0.182 2149 Planarity : 0.003 0.011 1344 Dihedral : 30.736 139.439 4184 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 11.86 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: 1.95 (0.27), residues: 1045 helix: 2.24 (0.19), residues: 718 sheet: 1.58 (0.80), residues: 35 loop : -1.26 (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 0.00283 / 0.22 (11883) covalent geometry : angle 0.61902 / 0.40 (17523) hydrogen bonds : bond 0.06855 / 5.23 ( 894) hydrogen bonds : angle 3.97492 / 3.11 ( 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 : 0.252 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 16 average time/residue: 0.0485 time to fit residues: 1.8328 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 : 0.264 ------------------------------------------------------------------------------- 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: 30.0000 chunk 68 optimal weight: 20.0000 chunk 78 optimal weight: 20.0000 chunk 5 optimal weight: 9.9990 chunk 110 optimal weight: 6.9990 chunk 109 optimal weight: 6.9990 chunk 43 optimal weight: 5.9990 chunk 105 optimal weight: 40.0000 chunk 20 optimal weight: 5.9990 chunk 91 optimal weight: 30.0000 chunk 14 optimal weight: 8.9990 overall best weight: 6.9990 ------------------------------------------------------------------------------- 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 = 0.3410 r_free = 0.3410 target = 0.058233 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.2866 r_free = 0.2866 target = 0.035555 restraints weight = 139282.487| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 69)----------------| | r_work = 0.2886 r_free = 0.2886 target = 0.036137 restraints weight = 72828.246| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.2899 r_free = 0.2899 target = 0.036467 restraints weight = 46995.433| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 46)----------------| | r_work = 0.2907 r_free = 0.2907 target = 0.036730 restraints weight = 35216.488| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.2912 r_free = 0.2912 target = 0.036858 restraints weight = 29152.654| |-----------------------------------------------------------------------------| r_work (final): 0.2732 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8856 moved from start: 0.1792 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.020 11883 Z= 0.255 Angle : 0.652 7.287 17523 Z= 0.419 Chirality : 0.045 0.194 2149 Planarity : 0.003 0.013 1344 Dihedral : 30.786 140.932 4184 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 14.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.40 % Favored : 95.60 % 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: 1.40 (0.27), residues: 1045 helix: 1.80 (0.19), residues: 721 sheet: 1.34 (0.82), residues: 35 loop : -1.40 (0.38), residues: 289 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 0.00333 / 0.26 (11883) covalent geometry : angle 0.65215 / 0.42 (17523) hydrogen bonds : bond 0.07796 / 5.95 ( 894) hydrogen bonds : angle 4.28304 / 3.35 ( 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 : 0.271 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 16 average time/residue: 0.0483 time to fit residues: 1.8104 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 : 0.208 ------------------------------------------------------------------------------- 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: 20.0000 chunk 2 optimal weight: 10.0000 chunk 83 optimal weight: 50.0000 chunk 113 optimal weight: 8.9990 chunk 121 optimal weight: 50.0000 chunk 96 optimal weight: 40.0000 chunk 17 optimal weight: 9.9990 chunk 42 optimal weight: 0.6980 chunk 80 optimal weight: 20.0000 chunk 54 optimal weight: 3.9990 chunk 104 optimal weight: 30.0000 overall best weight: 6.7390 ------------------------------------------------------------------------------- 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 = 0.058117 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.2862 r_free = 0.2862 target = 0.035471 restraints weight = 139905.945| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 66)----------------| | r_work = 0.2882 r_free = 0.2882 target = 0.036036 restraints weight = 72979.214| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.2895 r_free = 0.2895 target = 0.036407 restraints weight = 47161.130| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 51)----------------| | r_work = 0.2902 r_free = 0.2902 target = 0.036643 restraints weight = 35047.837| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.2907 r_free = 0.2907 target = 0.036764 restraints weight = 28973.915| |-----------------------------------------------------------------------------| r_work (final): 0.2728 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8855 moved from start: 0.2142 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= 0.249 Angle : 0.647 7.348 17523 Z= 0.414 Chirality : 0.045 0.205 2149 Planarity : 0.003 0.012 1344 Dihedral : 30.890 140.396 4184 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 12.28 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: 1.39 (0.27), residues: 1045 helix: 1.84 (0.19), residues: 719 sheet: 1.19 (0.86), residues: 35 loop : -1.50 (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 0.00328 / 0.25 (11883) covalent geometry : angle 0.64747 / 0.41 (17523) hydrogen bonds : bond 0.07328 / 5.58 ( 894) hydrogen bonds : angle 4.22269 / 3.30 ( 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 : 0.193 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 16 average time/residue: 0.0465 time to fit residues: 1.6477 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 : 0.161 ------------------------------------------------------------------------------- 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: 8.9990 chunk 92 optimal weight: 20.0000 chunk 39 optimal weight: 20.0000 chunk 89 optimal weight: 20.0000 chunk 126 optimal weight: 0.3980 chunk 63 optimal weight: 0.7980 chunk 29 optimal weight: 20.0000 chunk 25 optimal weight: 20.0000 chunk 52 optimal weight: 4.9990 chunk 49 optimal weight: 6.9990 overall best weight: 4.4386 ------------------------------------------------------------------------------- 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 = 0.3420 r_free = 0.3420 target = 0.058580 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.2878 r_free = 0.2878 target = 0.035776 restraints weight = 137901.086| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.2899 r_free = 0.2899 target = 0.036371 restraints weight = 72594.047| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.2912 r_free = 0.2912 target = 0.036756 restraints weight = 46813.126| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 53)----------------| | r_work = 0.2920 r_free = 0.2920 target = 0.037006 restraints weight = 34810.681| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 21)----------------| | r_work = 0.2925 r_free = 0.2925 target = 0.037123 restraints weight = 28644.278| |-----------------------------------------------------------------------------| r_work (final): 0.2750 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8833 moved from start: 0.2142 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= 0.186 Angle : 0.590 7.340 17523 Z= 0.378 Chirality : 0.043 0.211 2149 Planarity : 0.002 0.010 1344 Dihedral : 30.845 141.055 4184 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 9.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.83 % Favored : 96.17 % 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: 2.16 (0.27), residues: 1045 helix: 2.52 (0.19), residues: 716 sheet: 1.08 (0.87), residues: 35 loop : -1.41 (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 0.00235 / 0.19 (11883) covalent geometry : angle 0.58956 / 0.38 (17523) hydrogen bonds : bond 0.05715 / 4.34 ( 894) hydrogen bonds : angle 3.68534 / 2.89 ( 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 : 0.283 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 16 average time/residue: 0.0462 time to fit residues: 1.7876 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 : 0.264 ------------------------------------------------------------------------------- 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: 20.0000 chunk 20 optimal weight: 5.9990 chunk 8 optimal weight: 7.9990 chunk 57 optimal weight: 2.9990 chunk 97 optimal weight: 40.0000 chunk 83 optimal weight: 50.0000 chunk 46 optimal weight: 9.9990 chunk 124 optimal weight: 30.0000 chunk 37 optimal weight: 20.0000 chunk 110 optimal weight: 2.9990 chunk 77 optimal weight: 20.0000 overall best weight: 5.9990 ------------------------------------------------------------------------------- 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 = 0.3406 r_free = 0.3406 target = 0.058106 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.2864 r_free = 0.2864 target = 0.035429 restraints weight = 141108.961| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.2886 r_free = 0.2886 target = 0.036031 restraints weight = 74114.856| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 68)----------------| | r_work = 0.2897 r_free = 0.2897 target = 0.036387 restraints weight = 47844.098| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.2905 r_free = 0.2905 target = 0.036619 restraints weight = 35515.011| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.2910 r_free = 0.2910 target = 0.036730 restraints weight = 29317.468| |-----------------------------------------------------------------------------| r_work (final): 0.2732 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8850 moved from start: 0.2318 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.018 11883 Z= 0.225 Angle : 0.623 7.523 17523 Z= 0.398 Chirality : 0.044 0.218 2149 Planarity : 0.003 0.012 1344 Dihedral : 30.839 143.229 4184 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 11.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.84 % Favored : 94.16 % 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: 1.82 (0.27), residues: 1045 helix: 2.23 (0.19), residues: 716 sheet: 1.88 (0.94), residues: 29 loop : -1.51 (0.38), residues: 300 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 0.00292 / 0.23 (11883) covalent geometry : angle 0.62297 / 0.40 (17523) hydrogen bonds : bond 0.07269 / 5.54 ( 894) hydrogen bonds : angle 4.06038 / 3.18 ( 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 : 0.274 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 16 average time/residue: 0.0494 time to fit residues: 1.8389 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 : 0.265 ------------------------------------------------------------------------------- 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: 10.0000 chunk 52 optimal weight: 0.9990 chunk 67 optimal weight: 7.9990 chunk 69 optimal weight: 20.0000 chunk 116 optimal weight: 50.0000 chunk 128 optimal weight: 6.9990 chunk 30 optimal weight: 9.9990 chunk 51 optimal weight: 1.9990 chunk 10 optimal weight: 1.9990 chunk 12 optimal weight: 20.0000 chunk 80 optimal weight: 30.0000 overall best weight: 3.9990 ------------------------------------------------------------------------------- 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 = 0.3420 r_free = 0.3420 target = 0.060192 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.2880 r_free = 0.2880 target = 0.036668 restraints weight = 136034.367| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.2900 r_free = 0.2900 target = 0.037270 restraints weight = 72408.777| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.2913 r_free = 0.2913 target = 0.037651 restraints weight = 47338.636| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 59)----------------| | r_work = 0.2921 r_free = 0.2921 target = 0.037908 restraints weight = 35541.959| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.2926 r_free = 0.2926 target = 0.038050 restraints weight = 29552.279| |-----------------------------------------------------------------------------| r_work (final): 0.2745 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8844 moved from start: 0.2322 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= 0.182 Angle : 0.586 7.410 17523 Z= 0.376 Chirality : 0.043 0.222 2149 Planarity : 0.002 0.011 1344 Dihedral : 30.810 142.006 4184 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 9.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.21 % Favored : 95.79 % 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: 2.27 (0.27), residues: 1045 helix: 2.63 (0.19), residues: 716 sheet: 1.95 (0.97), residues: 29 loop : -1.51 (0.37), residues: 300 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 0.00227 / 0.18 (11883) covalent geometry : angle 0.58562 / 0.38 (17523) hydrogen bonds : bond 0.05847 / 4.45 ( 894) hydrogen bonds : angle 3.63229 / 2.85 ( 2291) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2515.71 seconds wall clock time: 43 minutes 34.71 seconds (2614.71 seconds total)