Starting phenix.real_space_refine on Thu May 15 22:42:00 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9dwm_47255/05_2025/9dwm_47255.cif Found real_map, /net/cci-nas-00/data/ceres_data/9dwm_47255/05_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/9dwm_47255/05_2025/9dwm_47255.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9dwm_47255/05_2025/9dwm_47255.map" model { file = "/net/cci-nas-00/data/ceres_data/9dwm_47255/05_2025/9dwm_47255.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9dwm_47255/05_2025/9dwm_47255.cif" } resolution = 4.2 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 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-filer2/raid1/xp/phenix/phenix-dev-5687/modules/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: {'GLN:plan1': 6, 'ASP:plan': 4, 'TYR:plan': 3, 'ASN:plan1': 1, 'HIS:plan': 2, 'PHE:plan': 4, 'GLU:plan': 7, 'ARG:plan': 14} 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: {'GLN:plan1': 2, 'HIS:plan': 1, 'TYR:plan': 4, 'ASN:plan1': 2, 'ASP:plan': 3, 'PHE:plan': 2, 'GLU:plan': 4, 'ARG:plan': 10} 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: {'GLN:plan1': 4, 'ASP:plan': 2, 'TYR:plan': 3, 'ASN:plan1': 6, 'HIS:plan': 2, 'PHE:plan': 1, 'GLU:plan': 6, 'ARG:plan': 11} 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: {'GLN:plan1': 2, 'HIS:plan': 3, 'TYR:plan': 5, 'ASN:plan1': 3, 'ASP:plan': 2, 'PHE:plan': 2, 'GLU:plan': 6, 'ARG:plan': 6} 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: {'GLN:plan1': 6, 'ASP:plan': 4, 'TYR:plan': 3, 'ASN:plan1': 1, 'HIS:plan': 2, 'PHE:plan': 4, 'GLU:plan': 7, 'ARG:plan': 14} 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: {'GLN:plan1': 2, 'HIS:plan': 1, 'TYR:plan': 4, 'ASN:plan1': 2, 'ASP:plan': 3, 'PHE:plan': 2, 'GLU:plan': 4, 'ARG:plan': 10} 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: {'GLN:plan1': 4, 'ASP:plan': 2, 'TYR:plan': 3, 'ASN:plan1': 6, 'HIS:plan': 2, 'PHE:plan': 1, 'GLU:plan': 6, 'ARG:plan': 10} 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: {'GLN:plan1': 2, 'ARG:plan': 5, 'TYR:plan': 5, 'ASN:plan1': 3, 'ASP:plan': 2, 'PHE:plan': 2, 'GLU:plan': 6, 'HIS:plan': 3} 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: {'GLN:plan1': 11, 'ARG:plan': 18, 'TYR:plan': 12, 'ASN:plan1': 12, 'TRP:plan': 1, 'HIS:plan': 9, 'PHE:plan': 14, 'GLU:plan': 26, 'ASP:plan': 21} Unresolved non-hydrogen planarities: 559 Time building chain proxies: 7.48, per 1000 atoms: 0.67 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: 2.98 Conformation dependent library (CDL) restraints added in 1.2 seconds 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: 5.28 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: 5.01 Time building geometry restraints manager: 3.43 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: 1.800 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.090 Construct map_model_manager: 0.010 Extract box with map and model: 0.490 Check model and map are aligned: 0.080 Set scattering table: 0.120 Process input model: 32.850 Find NCS groups from input model: 0.290 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.060 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.870 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 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 TRP 0.000 0.000 TRP L 325 PHE 0.000 0.000 PHE A 67 TYR 0.000 0.000 TYR A 41 Details of bonding type rmsd hydrogen bonds : bond 0.11862 ( 894) hydrogen bonds : angle 4.31793 ( 2291) covalent geometry : bond 0.00479 (11883) covalent geometry : angle 0.61223 (17523) *********************** 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 : 0.722 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 16 average time/residue: 0.1007 time to fit residues: 3.9535 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 : 0.795 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 108 optimal weight: 40.0000 chunk 97 optimal weight: 40.0000 chunk 54 optimal weight: 3.9990 chunk 33 optimal weight: 7.9990 chunk 65 optimal weight: 20.0000 chunk 52 optimal weight: 5.9990 chunk 101 optimal weight: 2.9990 chunk 39 optimal weight: 20.0000 chunk 61 optimal weight: 6.9990 chunk 75 optimal weight: 6.9990 chunk 117 optimal weight: 30.0000 overall best weight: 5.3990 ------------------------------------------------------------------------------- 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 = 0.3432 r_free = 0.3432 target = 0.059174 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.2795 r_free = 0.2795 target = 0.034953 restraints weight = 124347.320| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 70)----------------| | r_work = 0.2811 r_free = 0.2811 target = 0.035415 restraints weight = 69096.225| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 65)----------------| | r_work = 0.2820 r_free = 0.2820 target = 0.035681 restraints weight = 46978.158| |-----------------------------------------------------------------------------| r_work (final): 0.2742 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8743 moved from start: 0.0592 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.037 11883 Z= 0.285 Angle : 0.585 7.564 17523 Z= 0.374 Chirality : 0.037 0.136 2149 Planarity : 0.003 0.014 1344 Dihedral : 30.289 140.039 4184 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 10.97 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.35 (0.27), residues: 1045 helix: 2.38 (0.19), residues: 719 sheet: 2.89 (0.83), residues: 35 loop : -0.79 (0.37), residues: 291 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP L 325 PHE 0.000 0.000 PHE A 67 TYR 0.000 0.000 TYR A 41 Details of bonding type rmsd hydrogen bonds : bond 0.05873 ( 894) hydrogen bonds : angle 3.89425 ( 2291) covalent geometry : bond 0.00572 (11883) covalent geometry : angle 0.58502 (17523) *********************** 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 : 0.767 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 16 average time/residue: 0.1037 time to fit residues: 4.2610 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 : 0.762 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 105 optimal weight: 20.0000 chunk 53 optimal weight: 5.9990 chunk 27 optimal weight: 5.9990 chunk 128 optimal weight: 0.0570 chunk 33 optimal weight: 8.9990 chunk 106 optimal weight: 30.0000 chunk 26 optimal weight: 6.9990 chunk 59 optimal weight: 10.0000 chunk 97 optimal weight: 40.0000 chunk 40 optimal weight: 6.9990 chunk 6 optimal weight: 2.9990 overall best weight: 4.4106 ------------------------------------------------------------------------------- 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 = 0.3440 r_free = 0.3440 target = 0.059371 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.2804 r_free = 0.2804 target = 0.035123 restraints weight = 125298.203| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 53)----------------| | r_work = 0.2821 r_free = 0.2821 target = 0.035578 restraints weight = 68947.898| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.2832 r_free = 0.2832 target = 0.035894 restraints weight = 46660.251| |-----------------------------------------------------------------------------| r_work (final): 0.2751 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8740 moved from start: 0.0693 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= 0.233 Angle : 0.553 7.098 17523 Z= 0.353 Chirality : 0.036 0.150 2149 Planarity : 0.002 0.009 1344 Dihedral : 30.282 138.121 4184 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 9.25 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.70 (0.27), residues: 1045 helix: 2.70 (0.19), residues: 717 sheet: 2.78 (0.85), residues: 35 loop : -0.77 (0.38), residues: 293 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP L 325 PHE 0.000 0.000 PHE A 67 TYR 0.000 0.000 TYR A 41 Details of bonding type rmsd hydrogen bonds : bond 0.05647 ( 894) hydrogen bonds : angle 3.61057 ( 2291) covalent geometry : bond 0.00465 (11883) covalent geometry : angle 0.55332 (17523) *********************** 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 : 0.678 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 16 average time/residue: 0.0979 time to fit residues: 3.8757 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 : 0.796 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 26 optimal weight: 30.0000 chunk 108 optimal weight: 50.0000 chunk 28 optimal weight: 30.0000 chunk 95 optimal weight: 10.0000 chunk 29 optimal weight: 10.0000 chunk 107 optimal weight: 9.9990 chunk 73 optimal weight: 7.9990 chunk 2 optimal weight: 20.0000 chunk 66 optimal weight: 10.0000 chunk 15 optimal weight: 4.9990 chunk 9 optimal weight: 7.9990 overall best weight: 8.1992 ------------------------------------------------------------------------------- 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 = 0.3393 r_free = 0.3393 target = 0.057671 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.2844 r_free = 0.2844 target = 0.035029 restraints weight = 142743.416| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 70)----------------| | r_work = 0.2863 r_free = 0.2863 target = 0.035586 restraints weight = 75316.186| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.2876 r_free = 0.2876 target = 0.035941 restraints weight = 48791.376| |-----------------------------------------------------------------------------| r_work (final): 0.2693 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8795 moved from start: 0.2183 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.060 11883 Z= 0.409 Angle : 0.681 6.877 17523 Z= 0.433 Chirality : 0.043 0.175 2149 Planarity : 0.003 0.011 1344 Dihedral : 30.677 137.212 4184 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 15.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.78 % Favored : 95.22 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.40 (0.26), residues: 1045 helix: 1.70 (0.19), residues: 719 sheet: 1.81 (0.80), residues: 35 loop : -1.16 (0.38), residues: 291 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP L 325 PHE 0.000 0.000 PHE A 67 TYR 0.000 0.000 TYR A 41 Details of bonding type rmsd hydrogen bonds : bond 0.08422 ( 894) hydrogen bonds : angle 4.63379 ( 2291) covalent geometry : bond 0.00832 (11883) covalent geometry : angle 0.68068 (17523) *********************** 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 : 0.792 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 16 average time/residue: 0.0964 time to fit residues: 4.2407 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 : 0.776 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 86 optimal weight: 5.9990 chunk 75 optimal weight: 4.9990 chunk 56 optimal weight: 9.9990 chunk 73 optimal weight: 6.9990 chunk 119 optimal weight: 4.9990 chunk 51 optimal weight: 20.0000 chunk 17 optimal weight: 10.0000 chunk 96 optimal weight: 10.0000 chunk 115 optimal weight: 50.0000 chunk 10 optimal weight: 2.9990 chunk 50 optimal weight: 10.0000 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 = 0.3415 r_free = 0.3415 target = 0.060031 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.2876 r_free = 0.2876 target = 0.036543 restraints weight = 134501.906| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 55)----------------| | r_work = 0.2895 r_free = 0.2895 target = 0.037119 restraints weight = 72487.221| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.2908 r_free = 0.2908 target = 0.037493 restraints weight = 47595.043| |-----------------------------------------------------------------------------| r_work (final): 0.2723 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8779 moved from start: 0.2138 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= 0.275 Angle : 0.584 6.009 17523 Z= 0.373 Chirality : 0.037 0.148 2149 Planarity : 0.003 0.010 1344 Dihedral : 30.490 141.011 4184 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 10.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.64 % Favored : 96.36 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.96 (0.27), residues: 1045 helix: 2.24 (0.19), residues: 718 sheet: 1.36 (0.82), residues: 35 loop : -1.18 (0.38), residues: 292 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP L 325 PHE 0.000 0.000 PHE A 67 TYR 0.000 0.000 TYR A 41 Details of bonding type rmsd hydrogen bonds : bond 0.06210 ( 894) hydrogen bonds : angle 3.81048 ( 2291) covalent geometry : bond 0.00559 (11883) covalent geometry : angle 0.58400 (17523) *********************** 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 : 0.716 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 16 average time/residue: 0.0969 time to fit residues: 3.9699 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 : 0.873 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 72 optimal weight: 8.9990 chunk 90 optimal weight: 5.9990 chunk 18 optimal weight: 0.9980 chunk 93 optimal weight: 7.9990 chunk 0 optimal weight: 40.0000 chunk 81 optimal weight: 7.9990 chunk 122 optimal weight: 30.0000 chunk 79 optimal weight: 8.9990 chunk 74 optimal weight: 7.9990 chunk 78 optimal weight: 7.9990 chunk 114 optimal weight: 30.0000 overall best weight: 6.1988 ------------------------------------------------------------------------------- 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 = 0.3397 r_free = 0.3397 target = 0.057771 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.2855 r_free = 0.2855 target = 0.035252 restraints weight = 140454.423| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 62)----------------| | r_work = 0.2875 r_free = 0.2875 target = 0.035824 restraints weight = 73946.468| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.2888 r_free = 0.2888 target = 0.036183 restraints weight = 47868.159| |-----------------------------------------------------------------------------| r_work (final): 0.2707 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8781 moved from start: 0.2501 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.051 11883 Z= 0.324 Angle : 0.619 6.035 17523 Z= 0.396 Chirality : 0.039 0.147 2149 Planarity : 0.003 0.011 1344 Dihedral : 30.529 142.737 4184 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 13.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.98 % Favored : 95.02 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.52 (0.27), residues: 1045 helix: 1.93 (0.19), residues: 721 sheet: 0.99 (0.84), residues: 35 loop : -1.45 (0.38), residues: 289 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP L 325 PHE 0.000 0.000 PHE A 67 TYR 0.000 0.000 TYR A 41 Details of bonding type rmsd hydrogen bonds : bond 0.07759 ( 894) hydrogen bonds : angle 4.20989 ( 2291) covalent geometry : bond 0.00659 (11883) covalent geometry : angle 0.61875 (17523) *********************** 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 : 0.712 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 16 average time/residue: 0.1002 time to fit residues: 4.0411 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 : 0.729 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 116 optimal weight: 50.0000 chunk 39 optimal weight: 20.0000 chunk 60 optimal weight: 20.0000 chunk 80 optimal weight: 6.9990 chunk 4 optimal weight: 20.0000 chunk 36 optimal weight: 1.9990 chunk 95 optimal weight: 10.0000 chunk 74 optimal weight: 6.9990 chunk 96 optimal weight: 10.0000 chunk 105 optimal weight: 20.0000 chunk 56 optimal weight: 10.0000 overall best weight: 7.1994 ------------------------------------------------------------------------------- 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 = 0.3392 r_free = 0.3392 target = 0.057393 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.2753 r_free = 0.2753 target = 0.033703 restraints weight = 127897.531| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 53)----------------| | r_work = 0.2769 r_free = 0.2769 target = 0.034154 restraints weight = 69482.985| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 56)----------------| | r_work = 0.2778 r_free = 0.2778 target = 0.034439 restraints weight = 46873.234| |-----------------------------------------------------------------------------| r_work (final): 0.2751 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8796 moved from start: 0.3283 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.052 11883 Z= 0.354 Angle : 0.654 6.178 17523 Z= 0.416 Chirality : 0.041 0.170 2149 Planarity : 0.003 0.012 1344 Dihedral : 30.757 142.186 4184 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 14.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.26 % Favored : 94.74 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.13 (0.27), residues: 1045 helix: 1.70 (0.19), residues: 715 sheet: 0.58 (1.01), residues: 29 loop : -1.62 (0.36), residues: 301 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP L 325 PHE 0.000 0.000 PHE A 67 TYR 0.000 0.000 TYR A 41 Details of bonding type rmsd hydrogen bonds : bond 0.07969 ( 894) hydrogen bonds : angle 4.49887 ( 2291) covalent geometry : bond 0.00722 (11883) covalent geometry : angle 0.65445 (17523) *********************** 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 : 0.787 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 16 average time/residue: 0.0977 time to fit residues: 4.0020 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 : 0.771 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 121 optimal weight: 5.9990 chunk 22 optimal weight: 30.0000 chunk 115 optimal weight: 40.0000 chunk 108 optimal weight: 50.0000 chunk 45 optimal weight: 9.9990 chunk 15 optimal weight: 9.9990 chunk 30 optimal weight: 10.0000 chunk 18 optimal weight: 0.3980 chunk 79 optimal weight: 7.9990 chunk 128 optimal weight: 5.9990 chunk 122 optimal weight: 20.0000 overall best weight: 6.0788 ------------------------------------------------------------------------------- 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 = 0.3405 r_free = 0.3405 target = 0.057761 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.2784 r_free = 0.2784 target = 0.034420 restraints weight = 128254.374| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 65)----------------| | r_work = 0.2789 r_free = 0.2789 target = 0.034597 restraints weight = 73678.241| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.2800 r_free = 0.2800 target = 0.034892 restraints weight = 50567.053| |-----------------------------------------------------------------------------| r_work (final): 0.2713 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8759 moved from start: 0.3359 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= 0.311 Angle : 0.610 5.460 17523 Z= 0.388 Chirality : 0.039 0.155 2149 Planarity : 0.003 0.010 1344 Dihedral : 30.574 144.135 4184 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 11.86 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.40 (0.27), residues: 1045 helix: 1.97 (0.19), residues: 715 sheet: 0.30 (1.01), residues: 29 loop : -1.64 (0.36), residues: 301 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP L 325 PHE 0.000 0.000 PHE A 67 TYR 0.000 0.000 TYR A 41 Details of bonding type rmsd hydrogen bonds : bond 0.06847 ( 894) hydrogen bonds : angle 4.13104 ( 2291) covalent geometry : bond 0.00632 (11883) covalent geometry : angle 0.60999 (17523) *********************** 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 : 0.823 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 16 average time/residue: 0.1015 time to fit residues: 4.1784 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 : 0.768 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 42 optimal weight: 5.9990 chunk 46 optimal weight: 7.9990 chunk 72 optimal weight: 8.9990 chunk 110 optimal weight: 6.9990 chunk 6 optimal weight: 20.0000 chunk 66 optimal weight: 8.9990 chunk 119 optimal weight: 20.0000 chunk 54 optimal weight: 2.9990 chunk 69 optimal weight: 4.9990 chunk 30 optimal weight: 10.0000 chunk 19 optimal weight: 5.9990 overall best weight: 5.3990 ------------------------------------------------------------------------------- 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 = 0.3408 r_free = 0.3408 target = 0.057776 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.2787 r_free = 0.2787 target = 0.034425 restraints weight = 128065.254| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 54)----------------| | r_work = 0.2797 r_free = 0.2797 target = 0.034734 restraints weight = 72797.156| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.2808 r_free = 0.2808 target = 0.034983 restraints weight = 50386.113| |-----------------------------------------------------------------------------| r_work (final): 0.2722 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8763 moved from start: 0.3552 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.043 11883 Z= 0.282 Angle : 0.596 5.427 17523 Z= 0.380 Chirality : 0.038 0.144 2149 Planarity : 0.003 0.010 1344 Dihedral : 30.541 142.666 4184 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 11.03 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.60 (0.27), residues: 1045 helix: 2.15 (0.19), residues: 721 sheet: 0.46 (1.10), residues: 26 loop : -1.74 (0.36), residues: 298 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP L 325 PHE 0.000 0.000 PHE A 67 TYR 0.000 0.000 TYR A 41 Details of bonding type rmsd hydrogen bonds : bond 0.06654 ( 894) hydrogen bonds : angle 3.98580 ( 2291) covalent geometry : bond 0.00574 (11883) covalent geometry : angle 0.59641 (17523) *********************** 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 : 0.710 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 16 average time/residue: 0.1099 time to fit residues: 4.1231 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 : 0.720 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 11 optimal weight: 20.0000 chunk 77 optimal weight: 6.9990 chunk 128 optimal weight: 0.0010 chunk 109 optimal weight: 50.0000 chunk 118 optimal weight: 4.9990 chunk 76 optimal weight: 6.9990 chunk 117 optimal weight: 9.9990 chunk 49 optimal weight: 7.9990 chunk 27 optimal weight: 5.9990 chunk 75 optimal weight: 6.9990 chunk 14 optimal weight: 0.7980 overall best weight: 3.7592 ------------------------------------------------------------------------------- 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 = 0.3419 r_free = 0.3419 target = 0.058264 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.2810 r_free = 0.2810 target = 0.034952 restraints weight = 127281.152| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 68)----------------| | r_work = 0.2823 r_free = 0.2823 target = 0.035329 restraints weight = 72490.479| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.2834 r_free = 0.2834 target = 0.035606 restraints weight = 50014.922| |-----------------------------------------------------------------------------| r_work (final): 0.2750 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8739 moved from start: 0.3509 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 11883 Z= 0.219 Angle : 0.552 5.152 17523 Z= 0.351 Chirality : 0.036 0.151 2149 Planarity : 0.002 0.010 1344 Dihedral : 30.433 142.836 4184 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 8.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.88 % Favored : 95.12 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.22 (0.28), residues: 1045 helix: 2.69 (0.20), residues: 721 sheet: 0.08 (1.90), residues: 12 loop : -1.59 (0.36), residues: 312 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP L 325 PHE 0.000 0.000 PHE A 67 TYR 0.000 0.000 TYR A 41 Details of bonding type rmsd hydrogen bonds : bond 0.05263 ( 894) hydrogen bonds : angle 3.51154 ( 2291) covalent geometry : bond 0.00444 (11883) covalent geometry : angle 0.55188 (17523) ********************** 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 : 0.769 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 16 average time/residue: 0.0998 time to fit residues: 4.1281 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 : 0.690 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 33 optimal weight: 9.9990 chunk 96 optimal weight: 10.0000 chunk 123 optimal weight: 40.0000 chunk 100 optimal weight: 50.0000 chunk 104 optimal weight: 40.0000 chunk 51 optimal weight: 20.0000 chunk 85 optimal weight: 7.9990 chunk 127 optimal weight: 50.0000 chunk 102 optimal weight: 50.0000 chunk 29 optimal weight: 20.0000 chunk 40 optimal weight: 8.9990 overall best weight: 11.3994 ------------------------------------------------------------------------------- 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 = 0.3375 r_free = 0.3375 target = 0.058125 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.2792 r_free = 0.2792 target = 0.034309 restraints weight = 135235.978| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.2805 r_free = 0.2805 target = 0.034753 restraints weight = 69620.629| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 20)----------------| | r_work = 0.2819 r_free = 0.2819 target = 0.035065 restraints weight = 45264.125| |-----------------------------------------------------------------------------| r_work (final): 0.2666 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8838 moved from start: 0.4344 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.011 0.078 11883 Z= 0.525 Angle : 0.775 6.038 17523 Z= 0.496 Chirality : 0.047 0.222 2149 Planarity : 0.004 0.014 1344 Dihedral : 30.914 143.181 4184 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 21.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.66 % Favored : 92.34 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.22 (0.26), residues: 1045 helix: 0.98 (0.19), residues: 706 sheet: 0.61 (2.06), residues: 10 loop : -1.68 (0.34), residues: 329 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP L 325 PHE 0.000 0.000 PHE A 67 TYR 0.000 0.000 TYR A 41 Details of bonding type rmsd hydrogen bonds : bond 0.10445 ( 894) hydrogen bonds : angle 5.40788 ( 2291) covalent geometry : bond 0.01063 (11883) covalent geometry : angle 0.77523 (17523) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4056.71 seconds wall clock time: 70 minutes 51.35 seconds (4251.35 seconds total)