Starting phenix.real_space_refine on Thu Jun 12 07:53:14 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9dwm_47255/06_2025/9dwm_47255.cif Found real_map, /net/cci-nas-00/data/ceres_data/9dwm_47255/06_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_47255/06_2025/9dwm_47255.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9dwm_47255/06_2025/9dwm_47255.map" model { file = "/net/cci-nas-00/data/ceres_data/9dwm_47255/06_2025/9dwm_47255.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9dwm_47255/06_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-5710/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: 6.84, per 1000 atoms: 0.61 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: 2.96 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: 5.58 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: 4.77 Time building geometry restraints manager: 3.22 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: 1.850 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: 0.420 Check model and map are aligned: 0.080 Set scattering table: 0.090 Process input model: 32.270 Find NCS groups from input model: 0.230 Set up NCS constraints: 0.050 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:3.080 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.180 ------------------------------------------------------------------------------- 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 : 0.695 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 16 average time/residue: 0.1002 time to fit residues: 3.9517 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=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 = 59)----------------| | r_work = 0.2794 r_free = 0.2794 target = 0.034943 restraints weight = 124347.320| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 53)----------------| | r_work = 0.2811 r_free = 0.2811 target = 0.035397 restraints weight = 69132.910| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 66)----------------| | r_work = 0.2820 r_free = 0.2820 target = 0.035683 restraints weight = 47205.780| |-----------------------------------------------------------------------------| 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 : 0.785 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 16 average time/residue: 0.0999 time to fit residues: 4.0079 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 : 0.812 ------------------------------------------------------------------------------- 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 = 55)----------------| | r_work = 0.2804 r_free = 0.2804 target = 0.035123 restraints weight = 125298.203| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.2821 r_free = 0.2821 target = 0.035588 restraints weight = 68878.711| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 50)----------------| | r_work = 0.2832 r_free = 0.2832 target = 0.035900 restraints weight = 46555.520| |-----------------------------------------------------------------------------| r_work (final): 0.2749 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8741 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 : 0.722 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 16 average time/residue: 0.0979 time to fit residues: 3.9582 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 : 0.733 ------------------------------------------------------------------------------- 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: 6.9990 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: 7.5992 ------------------------------------------------------------------------------- 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 = 0.057831 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 74)----------------| | r_work = 0.2847 r_free = 0.2847 target = 0.035068 restraints weight = 142120.626| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 63)----------------| | r_work = 0.2866 r_free = 0.2866 target = 0.035638 restraints weight = 74844.458| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 64)----------------| | r_work = 0.2878 r_free = 0.2878 target = 0.035998 restraints weight = 48292.864| |-----------------------------------------------------------------------------| r_work (final): 0.2695 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8792 moved from start: 0.2133 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.053 11883 Z= 0.367 Angle : 0.666 6.402 17523 Z= 0.423 Chirality : 0.042 0.158 2149 Planarity : 0.003 0.010 1344 Dihedral : 30.637 137.419 4184 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 15.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.69 % Favored : 95.31 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.10 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.44 (0.26), residues: 1045 helix: 1.73 (0.19), residues: 719 sheet: 1.81 (0.80), residues: 35 loop : -1.14 (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 0.08685 ( 894) hydrogen bonds : angle 4.49339 ( 2291) covalent geometry : bond 0.00753 (11883) covalent geometry : angle 0.66568 (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 : 0.693 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 16 average time/residue: 0.0990 time to fit residues: 3.9973 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 : 0.698 ------------------------------------------------------------------------------- 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: 6.9990 chunk 75 optimal weight: 5.9990 chunk 56 optimal weight: 7.9990 chunk 73 optimal weight: 6.9990 chunk 119 optimal weight: 50.0000 chunk 51 optimal weight: 20.0000 chunk 17 optimal weight: 9.9990 chunk 96 optimal weight: 10.0000 chunk 115 optimal weight: 50.0000 chunk 10 optimal weight: 2.9990 chunk 50 optimal weight: 9.9990 overall best weight: 6.1990 ------------------------------------------------------------------------------- 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 = 0.3406 r_free = 0.3406 target = 0.059717 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 77)----------------| | r_work = 0.2867 r_free = 0.2867 target = 0.036273 restraints weight = 134964.319| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 57)----------------| | r_work = 0.2886 r_free = 0.2886 target = 0.036851 restraints weight = 72798.416| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.2898 r_free = 0.2898 target = 0.037212 restraints weight = 48062.084| |-----------------------------------------------------------------------------| r_work (final): 0.2712 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8790 moved from start: 0.2306 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= 0.306 Angle : 0.607 6.056 17523 Z= 0.387 Chirality : 0.039 0.150 2149 Planarity : 0.003 0.010 1344 Dihedral : 30.572 141.426 4184 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 11.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.73 % Favored : 96.27 % 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: 1.93 (0.19), residues: 721 sheet: 1.30 (0.82), residues: 35 loop : -1.24 (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 0.06863 ( 894) hydrogen bonds : angle 4.06155 ( 2291) covalent geometry : bond 0.00624 (11883) covalent geometry : angle 0.60679 (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 : 0.796 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 16 average time/residue: 0.0879 time to fit residues: 3.6731 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 : 0.735 ------------------------------------------------------------------------------- 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: 7.9990 chunk 90 optimal weight: 6.9990 chunk 18 optimal weight: 0.3980 chunk 93 optimal weight: 7.9990 chunk 0 optimal weight: 40.0000 chunk 81 optimal weight: 6.9990 chunk 122 optimal weight: 50.0000 chunk 79 optimal weight: 7.9990 chunk 74 optimal weight: 7.9990 chunk 78 optimal weight: 6.9990 chunk 114 optimal weight: 2.9990 overall best weight: 4.8788 ------------------------------------------------------------------------------- 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 = 0.3411 r_free = 0.3411 target = 0.059903 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.2872 r_free = 0.2872 target = 0.036470 restraints weight = 136137.300| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.2895 r_free = 0.2895 target = 0.037094 restraints weight = 73039.321| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 58)----------------| | r_work = 0.2907 r_free = 0.2907 target = 0.037484 restraints weight = 47838.943| |-----------------------------------------------------------------------------| r_work (final): 0.2723 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8773 moved from start: 0.2524 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 11883 Z= 0.262 Angle : 0.579 5.660 17523 Z= 0.368 Chirality : 0.037 0.151 2149 Planarity : 0.002 0.010 1344 Dihedral : 30.429 143.038 4184 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 10.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.40 % Favored : 95.60 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.10 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 2.13 (0.27), residues: 1045 helix: 2.45 (0.19), residues: 716 sheet: 1.05 (0.91), residues: 33 loop : -1.28 (0.37), residues: 296 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 0.06014 ( 894) hydrogen bonds : angle 3.70664 ( 2291) covalent geometry : bond 0.00533 (11883) covalent geometry : angle 0.57938 (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 : 0.804 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 16 average time/residue: 0.1017 time to fit residues: 4.2012 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 : 0.808 ------------------------------------------------------------------------------- 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: 10.0000 chunk 39 optimal weight: 20.0000 chunk 60 optimal weight: 20.0000 chunk 80 optimal weight: 8.9990 chunk 4 optimal weight: 20.0000 chunk 36 optimal weight: 4.9990 chunk 95 optimal weight: 10.0000 chunk 74 optimal weight: 7.9990 chunk 96 optimal weight: 10.0000 chunk 105 optimal weight: 6.9990 chunk 56 optimal weight: 10.0000 overall best weight: 7.7992 ------------------------------------------------------------------------------- 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 = 0.3403 r_free = 0.3403 target = 0.057435 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.2788 r_free = 0.2788 target = 0.034295 restraints weight = 128264.666| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 66)----------------| | r_work = 0.2791 r_free = 0.2791 target = 0.034481 restraints weight = 73848.344| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.2801 r_free = 0.2801 target = 0.034781 restraints weight = 51313.750| |-----------------------------------------------------------------------------| r_work (final): 0.2715 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8768 moved from start: 0.3235 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.058 11883 Z= 0.385 Angle : 0.676 6.151 17523 Z= 0.431 Chirality : 0.042 0.177 2149 Planarity : 0.003 0.011 1344 Dihedral : 30.701 141.962 4184 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 15.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.93 % Favored : 94.07 % 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: 1.06 (0.26), residues: 1045 helix: 1.62 (0.19), residues: 714 sheet: 0.71 (1.01), residues: 29 loop : -1.58 (0.36), residues: 302 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 0.08431 ( 894) hydrogen bonds : angle 4.69371 ( 2291) covalent geometry : bond 0.00788 (11883) covalent geometry : angle 0.67583 (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 : 0.714 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 16 average time/residue: 0.0988 time to fit residues: 4.0175 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 : 0.818 ------------------------------------------------------------------------------- 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: 40.0000 chunk 22 optimal weight: 30.0000 chunk 115 optimal weight: 30.0000 chunk 108 optimal weight: 9.9990 chunk 45 optimal weight: 6.9990 chunk 15 optimal weight: 9.9990 chunk 30 optimal weight: 10.0000 chunk 18 optimal weight: 0.9990 chunk 79 optimal weight: 7.9990 chunk 128 optimal weight: 7.9990 chunk 122 optimal weight: 20.0000 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 = 0.3400 r_free = 0.3400 target = 0.057586 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.2777 r_free = 0.2777 target = 0.034290 restraints weight = 128663.330| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 54)----------------| | r_work = 0.2781 r_free = 0.2781 target = 0.034429 restraints weight = 73698.790| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.2791 r_free = 0.2791 target = 0.034652 restraints weight = 50799.014| |-----------------------------------------------------------------------------| r_work (final): 0.2703 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8766 moved from start: 0.3393 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= 0.339 Angle : 0.637 5.488 17523 Z= 0.406 Chirality : 0.040 0.165 2149 Planarity : 0.003 0.011 1344 Dihedral : 30.655 144.249 4184 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 13.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.74 % Favored : 94.26 % 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: 1.10 (0.27), residues: 1045 helix: 1.67 (0.19), residues: 717 sheet: 0.44 (1.00), residues: 29 loop : -1.61 (0.36), residues: 299 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 0.07545 ( 894) hydrogen bonds : angle 4.37036 ( 2291) covalent geometry : bond 0.00689 (11883) covalent geometry : angle 0.63698 (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 : 0.715 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 16 average time/residue: 0.0977 time to fit residues: 3.9728 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 ------------------------------------------------------------------------------- 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: 8.9990 chunk 72 optimal weight: 8.9990 chunk 110 optimal weight: 6.9990 chunk 6 optimal weight: 20.0000 chunk 66 optimal weight: 4.9990 chunk 119 optimal weight: 50.0000 chunk 54 optimal weight: 3.9990 chunk 69 optimal weight: 1.9990 chunk 30 optimal weight: 10.0000 chunk 19 optimal weight: 6.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- 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 = 0.3414 r_free = 0.3414 target = 0.058032 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2798 r_free = 0.2798 target = 0.034789 restraints weight = 127696.536| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 59)----------------| | r_work = 0.2805 r_free = 0.2805 target = 0.034943 restraints weight = 73328.596| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.2815 r_free = 0.2815 target = 0.035202 restraints weight = 50114.166| |-----------------------------------------------------------------------------| r_work (final): 0.2728 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8742 moved from start: 0.3366 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 11883 Z= 0.257 Angle : 0.577 5.353 17523 Z= 0.367 Chirality : 0.037 0.150 2149 Planarity : 0.002 0.010 1344 Dihedral : 30.518 143.304 4184 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 10.26 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: 1.75 (0.27), residues: 1045 helix: 2.25 (0.19), residues: 721 sheet: 0.43 (1.00), residues: 29 loop : -1.63 (0.37), residues: 295 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 0.06142 ( 894) hydrogen bonds : angle 3.81605 ( 2291) covalent geometry : bond 0.00524 (11883) covalent geometry : angle 0.57714 (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 : 0.721 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 16 average time/residue: 0.1019 time to fit residues: 4.0521 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 : 0.743 ------------------------------------------------------------------------------- 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: 0.1980 chunk 109 optimal weight: 50.0000 chunk 118 optimal weight: 4.9990 chunk 76 optimal weight: 6.9990 chunk 117 optimal weight: 20.0000 chunk 49 optimal weight: 3.9990 chunk 27 optimal weight: 6.9990 chunk 75 optimal weight: 6.9990 chunk 14 optimal weight: 0.8980 overall best weight: 3.4186 ------------------------------------------------------------------------------- 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 = 0.3418 r_free = 0.3418 target = 0.060185 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.2888 r_free = 0.2888 target = 0.036860 restraints weight = 136836.189| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 69)----------------| | r_work = 0.2907 r_free = 0.2907 target = 0.037471 restraints weight = 72966.626| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.2921 r_free = 0.2921 target = 0.037851 restraints weight = 47655.334| |-----------------------------------------------------------------------------| r_work (final): 0.2742 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8747 moved from start: 0.3381 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 11883 Z= 0.206 Angle : 0.543 5.033 17523 Z= 0.345 Chirality : 0.036 0.149 2149 Planarity : 0.002 0.010 1344 Dihedral : 30.352 143.072 4184 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 8.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.40 % Favored : 95.60 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.10 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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 (0.28), residues: 1045 helix: 2.95 (0.20), residues: 725 sheet: 0.33 (1.03), residues: 29 loop : -1.56 (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 0.04831 ( 894) hydrogen bonds : angle 3.29778 ( 2291) covalent geometry : bond 0.00416 (11883) covalent geometry : angle 0.54331 (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 : 0.788 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 16 average time/residue: 0.0982 time to fit residues: 4.0656 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 : 0.733 ------------------------------------------------------------------------------- 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: 10.0000 chunk 96 optimal weight: 10.0000 chunk 123 optimal weight: 30.0000 chunk 100 optimal weight: 50.0000 chunk 104 optimal weight: 5.9990 chunk 51 optimal weight: 20.0000 chunk 85 optimal weight: 8.9990 chunk 127 optimal weight: 40.0000 chunk 102 optimal weight: 0.0470 chunk 29 optimal weight: 20.0000 chunk 40 optimal weight: 10.0000 overall best weight: 7.0090 ------------------------------------------------------------------------------- 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 = 0.3379 r_free = 0.3379 target = 0.058831 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.2844 r_free = 0.2844 target = 0.035766 restraints weight = 136930.363| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.2863 r_free = 0.2863 target = 0.036346 restraints weight = 73925.083| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.2876 r_free = 0.2876 target = 0.036727 restraints weight = 48793.766| |-----------------------------------------------------------------------------| r_work (final): 0.2693 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8797 moved from start: 0.3831 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= 0.350 Angle : 0.644 5.830 17523 Z= 0.410 Chirality : 0.040 0.167 2149 Planarity : 0.003 0.011 1344 Dihedral : 30.613 142.718 4184 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 13.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.70 % Favored : 93.30 % 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: 1.49 (0.27), residues: 1045 helix: 2.03 (0.19), residues: 721 sheet: 0.28 (1.93), residues: 12 loop : -1.58 (0.35), 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 0.07922 ( 894) hydrogen bonds : angle 4.42714 ( 2291) covalent geometry : bond 0.00711 (11883) covalent geometry : angle 0.64417 (17523) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4356.26 seconds wall clock time: 75 minutes 9.04 seconds (4509.04 seconds total)