Starting phenix.real_space_refine on Thu Sep 18 03:32:29 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9dwm_47255/09_2025/9dwm_47255.cif Found real_map, /net/cci-nas-00/data/ceres_data/9dwm_47255/09_2025/9dwm_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_47255/09_2025/9dwm_47255.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9dwm_47255/09_2025/9dwm_47255.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9dwm_47255/09_2025/9dwm_47255.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9dwm_47255/09_2025/9dwm_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-2.0-5805/lib/python3.9/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: 3.26, per 1000 atoms: 0.29 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: 1.19 Conformation dependent library (CDL) restraints added in 557.0 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 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: 2.47 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: 2.60 Time building geometry restraints manager: 1.53 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=" P DA I 69 " pdb=" OP1 DA I 69 " ideal model delta sigma weight residual 1.480 1.521 -0.041 2.00e-02 2.50e+03 4.17e+00 bond pdb=" P DT J 7 " pdb=" OP1 DT J 7 " ideal model delta sigma weight residual 1.480 1.519 -0.039 2.00e-02 2.50e+03 3.78e+00 bond pdb=" P DT J 7 " pdb=" OP2 DT J 7 " ideal model delta sigma weight residual 1.480 1.518 -0.038 2.00e-02 2.50e+03 3.65e+00 bond pdb=" P DC I 110 " pdb=" OP2 DC I 110 " ideal model delta sigma weight residual 1.480 1.518 -0.038 2.00e-02 2.50e+03 3.53e+00 ... (remaining 11878 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.60: 16957 1.60 - 3.20: 526 3.20 - 4.81: 24 4.81 - 6.41: 9 6.41 - 8.01: 7 Bond angle restraints: 17523 Sorted by residual: angle pdb=" O3' DA J 6 " pdb=" P DT J 7 " pdb=" O5' DT J 7 " ideal model delta sigma weight residual 104.00 109.55 -5.55 1.50e+00 4.44e-01 1.37e+01 angle pdb=" C3' DA J 6 " pdb=" O3' DA J 6 " pdb=" P DT J 7 " ideal model delta sigma weight residual 120.20 125.69 -5.49 1.50e+00 4.44e-01 1.34e+01 angle pdb=" C4' DA J 19 " pdb=" C3' DA J 19 " pdb=" O3' DA J 19 " ideal model delta sigma weight residual 110.00 114.81 -4.81 1.50e+00 4.44e-01 1.03e+01 angle pdb=" C1' DA J 19 " pdb=" N9 DA J 19 " pdb=" C8 DA J 19 " ideal model delta sigma weight residual 127.05 131.77 -4.72 1.50e+00 4.44e-01 9.90e+00 angle pdb=" O3' DC I 109 " pdb=" P DC I 110 " pdb=" O5' DC I 110 " ideal model delta sigma weight residual 104.00 99.31 4.69 1.50e+00 4.44e-01 9.76e+00 ... (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 - 0.129: 2143 0.129 - 0.259: 2 0.259 - 0.388: 0 0.388 - 0.517: 1 0.517 - 0.647: 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 2.35 -2.99 -0.65 2.00e-01 2.50e+01 1.05e+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 2.35 -2.93 -0.58 2.00e-01 2.50e+01 8.41e+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 2.35 -2.91 -0.57 2.00e-01 2.50e+01 7.99e+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: 3.320 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: 0.180 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 15.810 Find NCS groups from input model: 0.110 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.010 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.490 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.040 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8790 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 : 0.005 0.121 11883 Z= 0.234 Angle : 0.612 8.008 17523 Z= 0.373 Chirality : 0.045 0.647 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 aren 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 covalent geometry : bond 0.00479 (11883) covalent geometry : angle 0.61223 (17523) hydrogen bonds : bond 0.11862 ( 894) hydrogen bonds : angle 4.31793 ( 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 : 0.287 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 16 average time/residue: 0.0516 time to fit residues: 1.9082 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=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: 6.9990 chunk 122 optimal weight: 50.0000 chunk 91 optimal weight: 8.9990 chunk 55 optimal weight: 5.9990 chunk 35 optimal weight: 40.0000 overall best weight: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.062375 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.2796 r_free = 0.2796 target = 0.036490 restraints weight = 124164.769| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 61)----------------| | r_work = 0.2814 r_free = 0.2814 target = 0.036985 restraints weight = 71358.986| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 54)----------------| | r_work = 0.2823 r_free = 0.2823 target = 0.037310 restraints weight = 49470.349| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.2828 r_free = 0.2828 target = 0.037422 restraints weight = 39367.079| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 54)----------------| | r_work = 0.2829 r_free = 0.2829 target = 0.037593 restraints weight = 35099.902| |-----------------------------------------------------------------------------| r_work (final): 0.2745 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8750 moved from start: 0.0570 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.036 11883 Z= 0.277 Angle : 0.581 7.580 17523 Z= 0.371 Chirality : 0.037 0.135 2149 Planarity : 0.003 0.014 1344 Dihedral : 30.289 140.071 4184 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 10.56 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 aren not related in a simple way. whole: 2.39 (0.27), residues: 1045 helix: 2.42 (0.19), residues: 719 sheet: 2.90 (0.83), residues: 35 loop : -0.78 (0.37), 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 covalent geometry : bond 0.00556 (11883) covalent geometry : angle 0.58075 (17523) hydrogen bonds : bond 0.05766 ( 894) hydrogen bonds : angle 3.86687 ( 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 : 0.325 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 16 average time/residue: 0.0453 time to fit residues: 1.7678 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 : 0.309 ------------------------------------------------------------------------------- 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: 8.9990 chunk 28 optimal weight: 30.0000 chunk 5 optimal weight: 6.9990 chunk 73 optimal weight: 7.9990 chunk 11 optimal weight: 20.0000 chunk 4 optimal weight: 5.9990 chunk 98 optimal weight: 7.9990 chunk 36 optimal weight: 0.9990 chunk 124 optimal weight: 9.9990 chunk 24 optimal weight: 9.9990 overall best weight: 5.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.058890 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.2785 r_free = 0.2785 target = 0.034662 restraints weight = 125867.017| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 53)----------------| | r_work = 0.2800 r_free = 0.2800 target = 0.035093 restraints weight = 68859.914| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 65)----------------| | r_work = 0.2811 r_free = 0.2811 target = 0.035392 restraints weight = 46659.548| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 55)----------------| | r_work = 0.2817 r_free = 0.2817 target = 0.035596 restraints weight = 36714.885| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.2820 r_free = 0.2820 target = 0.035689 restraints weight = 32106.349| |-----------------------------------------------------------------------------| r_work (final): 0.2744 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8750 moved from start: 0.0889 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.044 11883 Z= 0.301 Angle : 0.591 6.906 17523 Z= 0.378 Chirality : 0.038 0.152 2149 Planarity : 0.003 0.010 1344 Dihedral : 30.282 138.145 4184 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 11.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.02 % Favored : 95.98 % 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 aren not related in a simple way. whole: 2.21 (0.27), residues: 1045 helix: 2.31 (0.19), residues: 716 sheet: 2.67 (0.85), residues: 35 loop : -0.88 (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 covalent geometry : bond 0.00611 (11883) covalent geometry : angle 0.59086 (17523) hydrogen bonds : bond 0.06812 ( 894) hydrogen bonds : angle 3.95433 ( 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 : 0.272 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 16 average time/residue: 0.0496 time to fit residues: 1.8615 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 31 optimal weight: 2.9990 chunk 116 optimal weight: 9.9990 chunk 35 optimal weight: 30.0000 chunk 74 optimal weight: 6.9990 chunk 77 optimal weight: 6.9990 chunk 100 optimal weight: 9.9990 chunk 22 optimal weight: 30.0000 chunk 36 optimal weight: 1.9990 chunk 114 optimal weight: 50.0000 chunk 117 optimal weight: 20.0000 chunk 44 optimal weight: 10.0000 overall best weight: 5.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.058689 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.2782 r_free = 0.2782 target = 0.034519 restraints weight = 126996.146| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.2797 r_free = 0.2797 target = 0.034938 restraints weight = 69259.002| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.2809 r_free = 0.2809 target = 0.035256 restraints weight = 46673.480| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.2815 r_free = 0.2815 target = 0.035462 restraints weight = 36789.355| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 46)----------------| | r_work = 0.2817 r_free = 0.2817 target = 0.035560 restraints weight = 31950.203| |-----------------------------------------------------------------------------| r_work (final): 0.2791 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8757 moved from start: 0.1458 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.042 11883 Z= 0.296 Angle : 0.595 5.733 17523 Z= 0.380 Chirality : 0.038 0.136 2149 Planarity : 0.003 0.011 1344 Dihedral : 30.340 136.037 4184 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 10.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.11 % Favored : 95.89 % 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 aren not related in a simple way. whole: 2.14 (0.27), residues: 1045 helix: 2.29 (0.19), residues: 718 sheet: 2.08 (0.83), residues: 35 loop : -0.98 (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 covalent geometry : bond 0.00602 (11883) covalent geometry : angle 0.59477 (17523) hydrogen bonds : bond 0.06158 ( 894) hydrogen bonds : angle 3.95006 ( 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 : 0.288 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 16 average time/residue: 0.0530 time to fit residues: 1.9726 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 102 optimal weight: 5.9990 chunk 118 optimal weight: 0.5980 chunk 119 optimal weight: 30.0000 chunk 10 optimal weight: 6.9990 chunk 75 optimal weight: 5.9990 chunk 100 optimal weight: 20.0000 chunk 9 optimal weight: 0.2980 chunk 52 optimal weight: 4.9990 chunk 39 optimal weight: 20.0000 chunk 56 optimal weight: 8.9990 chunk 57 optimal weight: 20.0000 overall best weight: 3.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.059127 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.2815 r_free = 0.2815 target = 0.035332 restraints weight = 124355.408| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 61)----------------| | r_work = 0.2822 r_free = 0.2822 target = 0.035516 restraints weight = 69488.452| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 55)----------------| | r_work = 0.2833 r_free = 0.2833 target = 0.035815 restraints weight = 46822.432| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.2839 r_free = 0.2839 target = 0.035999 restraints weight = 36958.268| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.2843 r_free = 0.2843 target = 0.036124 restraints weight = 32249.471| |-----------------------------------------------------------------------------| r_work (final): 0.2762 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8714 moved from start: 0.1482 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 11883 Z= 0.214 Angle : 0.544 5.647 17523 Z= 0.345 Chirality : 0.036 0.144 2149 Planarity : 0.002 0.010 1344 Dihedral : 30.321 137.449 4184 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 9.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % 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 aren not related in a simple way. whole: 2.81 (0.27), residues: 1045 helix: 2.90 (0.19), residues: 722 sheet: 1.80 (0.83), residues: 35 loop : -1.01 (0.39), residues: 288 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 covalent geometry : bond 0.00435 (11883) covalent geometry : angle 0.54406 (17523) hydrogen bonds : bond 0.04844 ( 894) hydrogen bonds : angle 3.34335 ( 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 : 0.255 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 16 average time/residue: 0.0515 time to fit residues: 1.9095 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 ------------------------------------------------------------------------------- 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: 0.0020 chunk 24 optimal weight: 10.0000 chunk 65 optimal weight: 20.0000 chunk 15 optimal weight: 9.9990 chunk 128 optimal weight: 40.0000 chunk 70 optimal weight: 10.0000 chunk 85 optimal weight: 7.9990 chunk 7 optimal weight: 10.0000 chunk 6 optimal weight: 0.9990 chunk 1 optimal weight: 8.9990 chunk 45 optimal weight: 2.9990 overall best weight: 4.1996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.059031 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.2811 r_free = 0.2811 target = 0.035246 restraints weight = 125436.106| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 62)----------------| | r_work = 0.2819 r_free = 0.2819 target = 0.035418 restraints weight = 70165.614| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 64)----------------| | r_work = 0.2830 r_free = 0.2830 target = 0.035756 restraints weight = 47278.579| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 54)----------------| | r_work = 0.2836 r_free = 0.2836 target = 0.035907 restraints weight = 37141.876| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 49)----------------| | r_work = 0.2840 r_free = 0.2840 target = 0.036037 restraints weight = 32367.346| |-----------------------------------------------------------------------------| r_work (final): 0.2761 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8717 moved from start: 0.1510 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= 0.234 Angle : 0.548 5.154 17523 Z= 0.349 Chirality : 0.036 0.140 2149 Planarity : 0.002 0.010 1344 Dihedral : 30.293 137.774 4184 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 9.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % 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 aren not related in a simple way. whole: 2.82 (0.27), residues: 1045 helix: 2.93 (0.19), residues: 722 sheet: 1.75 (0.83), residues: 35 loop : -1.04 (0.39), residues: 288 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 covalent geometry : bond 0.00479 (11883) covalent geometry : angle 0.54782 (17523) hydrogen bonds : bond 0.04948 ( 894) hydrogen bonds : angle 3.41466 ( 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 : 0.265 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 16 average time/residue: 0.0389 time to fit residues: 1.4938 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 : 0.197 ------------------------------------------------------------------------------- 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: 10.0000 chunk 68 optimal weight: 20.0000 chunk 78 optimal weight: 7.9990 chunk 5 optimal weight: 10.0000 chunk 110 optimal weight: 0.9990 chunk 109 optimal weight: 8.9990 chunk 43 optimal weight: 3.9990 chunk 105 optimal weight: 30.0000 chunk 20 optimal weight: 10.0000 chunk 91 optimal weight: 10.0000 chunk 14 optimal weight: 9.9990 overall best weight: 6.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.057873 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.2852 r_free = 0.2852 target = 0.035163 restraints weight = 140726.842| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 64)----------------| | r_work = 0.2871 r_free = 0.2871 target = 0.035724 restraints weight = 74759.060| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.2884 r_free = 0.2884 target = 0.036095 restraints weight = 48352.127| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 45)----------------| | r_work = 0.2893 r_free = 0.2893 target = 0.036340 restraints weight = 36084.915| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.2897 r_free = 0.2897 target = 0.036454 restraints weight = 29744.004| |-----------------------------------------------------------------------------| r_work (final): 0.2720 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8767 moved from start: 0.2370 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.047 11883 Z= 0.317 Angle : 0.626 5.861 17523 Z= 0.398 Chirality : 0.039 0.150 2149 Planarity : 0.003 0.010 1344 Dihedral : 30.536 139.276 4184 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 12.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.07 % Favored : 94.93 % 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 aren not related in a simple way. whole: 1.98 (0.27), residues: 1045 helix: 2.29 (0.19), residues: 719 sheet: 1.26 (0.84), residues: 35 loop : -1.27 (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 covalent geometry : bond 0.00647 (11883) covalent geometry : angle 0.62555 (17523) hydrogen bonds : bond 0.07235 ( 894) hydrogen bonds : angle 4.15611 ( 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 : 0.215 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 16 average time/residue: 0.0484 time to fit residues: 1.8345 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 74 optimal weight: 6.9990 chunk 2 optimal weight: 9.9990 chunk 83 optimal weight: 10.0000 chunk 113 optimal weight: 50.0000 chunk 121 optimal weight: 50.0000 chunk 96 optimal weight: 10.0000 chunk 17 optimal weight: 20.0000 chunk 42 optimal weight: 5.9990 chunk 80 optimal weight: 7.9990 chunk 54 optimal weight: 2.9990 chunk 104 optimal weight: 10.0000 overall best weight: 6.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.057655 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2780 r_free = 0.2780 target = 0.034368 restraints weight = 127054.085| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 64)----------------| | r_work = 0.2785 r_free = 0.2785 target = 0.034514 restraints weight = 73612.909| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.2795 r_free = 0.2795 target = 0.034775 restraints weight = 50512.981| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 59)----------------| | r_work = 0.2800 r_free = 0.2800 target = 0.034990 restraints weight = 40416.938| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.2802 r_free = 0.2802 target = 0.035038 restraints weight = 35405.290| |-----------------------------------------------------------------------------| r_work (final): 0.2721 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8757 moved from start: 0.3107 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.050 11883 Z= 0.326 Angle : 0.629 5.811 17523 Z= 0.400 Chirality : 0.039 0.156 2149 Planarity : 0.003 0.011 1344 Dihedral : 30.622 144.319 4184 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 12.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.11 % Favored : 95.89 % 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 aren not related in a simple way. whole: 1.44 (0.27), residues: 1045 helix: 1.94 (0.19), residues: 715 sheet: 0.79 (1.03), residues: 29 loop : -1.51 (0.36), residues: 301 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 covalent geometry : bond 0.00662 (11883) covalent geometry : angle 0.62903 (17523) hydrogen bonds : bond 0.07284 ( 894) hydrogen bonds : angle 4.24790 ( 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 : 0.276 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 16 average time/residue: 0.0472 time to fit residues: 1.7739 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 ------------------------------------------------------------------------------- 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: 6.9990 chunk 20 optimal weight: 8.9990 chunk 92 optimal weight: 6.9990 chunk 39 optimal weight: 20.0000 chunk 89 optimal weight: 5.9990 chunk 126 optimal weight: 0.8980 chunk 63 optimal weight: 0.6980 chunk 29 optimal weight: 20.0000 chunk 25 optimal weight: 9.9990 chunk 52 optimal weight: 5.9990 chunk 49 optimal weight: 0.9980 overall best weight: 2.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.060549 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.2893 r_free = 0.2893 target = 0.037026 restraints weight = 134931.082| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.2914 r_free = 0.2914 target = 0.037655 restraints weight = 72078.588| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.2926 r_free = 0.2926 target = 0.038060 restraints weight = 47027.690| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.2934 r_free = 0.2934 target = 0.038289 restraints weight = 35268.146| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.2939 r_free = 0.2939 target = 0.038463 restraints weight = 29384.812| |-----------------------------------------------------------------------------| r_work (final): 0.2761 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8730 moved from start: 0.2941 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 11883 Z= 0.192 Angle : 0.539 4.960 17523 Z= 0.342 Chirality : 0.036 0.152 2149 Planarity : 0.002 0.010 1344 Dihedral : 30.365 142.404 4184 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 8.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.92 % Favored : 96.08 % 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 aren not related in a simple way. whole: 2.57 (0.28), residues: 1045 helix: 2.92 (0.20), residues: 722 sheet: 0.68 (1.03), residues: 29 loop : -1.50 (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 covalent geometry : bond 0.00388 (11883) covalent geometry : angle 0.53903 (17523) hydrogen bonds : bond 0.04683 ( 894) hydrogen bonds : angle 3.24453 ( 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 : 0.278 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 16 average time/residue: 0.0453 time to fit residues: 1.7254 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 : 0.227 ------------------------------------------------------------------------------- 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: 9.9990 chunk 8 optimal weight: 10.0000 chunk 57 optimal weight: 0.9990 chunk 97 optimal weight: 50.0000 chunk 83 optimal weight: 10.0000 chunk 46 optimal weight: 10.0000 chunk 124 optimal weight: 40.0000 chunk 37 optimal weight: 20.0000 chunk 110 optimal weight: 7.9990 chunk 77 optimal weight: 7.9990 overall best weight: 7.3992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.057517 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.2772 r_free = 0.2772 target = 0.034227 restraints weight = 129134.286| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 58)----------------| | r_work = 0.2777 r_free = 0.2777 target = 0.034326 restraints weight = 74105.192| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 72)----------------| | r_work = 0.2787 r_free = 0.2787 target = 0.034640 restraints weight = 51193.188| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.2791 r_free = 0.2791 target = 0.034718 restraints weight = 40564.582| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.2795 r_free = 0.2795 target = 0.034814 restraints weight = 36311.677| |-----------------------------------------------------------------------------| r_work (final): 0.2711 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8770 moved from start: 0.3347 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.053 11883 Z= 0.362 Angle : 0.644 5.604 17523 Z= 0.411 Chirality : 0.040 0.170 2149 Planarity : 0.003 0.011 1344 Dihedral : 30.503 143.147 4184 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 14.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.22 % Favored : 93.78 % 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 aren not related in a simple way. whole: 1.54 (0.27), residues: 1045 helix: 2.04 (0.19), residues: 720 sheet: 0.62 (1.03), residues: 29 loop : -1.60 (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 covalent geometry : bond 0.00738 (11883) covalent geometry : angle 0.64365 (17523) hydrogen bonds : bond 0.07783 ( 894) hydrogen bonds : angle 4.39754 ( 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 : 0.264 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 16 average time/residue: 0.0498 time to fit residues: 1.7950 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 ------------------------------------------------------------------------------- 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: 8.9990 chunk 52 optimal weight: 1.9990 chunk 67 optimal weight: 5.9990 chunk 69 optimal weight: 20.0000 chunk 116 optimal weight: 50.0000 chunk 128 optimal weight: 40.0000 chunk 30 optimal weight: 10.0000 chunk 51 optimal weight: 0.0870 chunk 10 optimal weight: 0.9990 chunk 12 optimal weight: 20.0000 chunk 80 optimal weight: 6.9990 overall best weight: 3.2166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.060202 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.2884 r_free = 0.2884 target = 0.036806 restraints weight = 136830.292| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 61)----------------| | r_work = 0.2905 r_free = 0.2905 target = 0.037444 restraints weight = 72841.704| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.2919 r_free = 0.2919 target = 0.037813 restraints weight = 47708.373| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.2928 r_free = 0.2928 target = 0.038077 restraints weight = 35926.510| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.2931 r_free = 0.2931 target = 0.038172 restraints weight = 29678.367| |-----------------------------------------------------------------------------| r_work (final): 0.2752 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8740 moved from start: 0.3187 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 11883 Z= 0.203 Angle : 0.543 5.133 17523 Z= 0.345 Chirality : 0.036 0.152 2149 Planarity : 0.002 0.010 1344 Dihedral : 30.360 141.903 4184 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 8.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.92 % Favored : 96.08 % 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 aren not related in a simple way. whole: 2.48 (0.28), residues: 1045 helix: 2.85 (0.19), residues: 722 sheet: 0.62 (1.03), residues: 29 loop : -1.55 (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 covalent geometry : bond 0.00411 (11883) covalent geometry : angle 0.54325 (17523) hydrogen bonds : bond 0.04947 ( 894) hydrogen bonds : angle 3.37378 ( 2291) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2812.87 seconds wall clock time: 48 minutes 35.12 seconds (2915.12 seconds total)