Starting phenix.real_space_refine on Thu May 15 13:07:12 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9dwk_47253/05_2025/9dwk_47253.cif Found real_map, /net/cci-nas-00/data/ceres_data/9dwk_47253/05_2025/9dwk_47253.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9dwk_47253/05_2025/9dwk_47253.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9dwk_47253/05_2025/9dwk_47253.map" model { file = "/net/cci-nas-00/data/ceres_data/9dwk_47253/05_2025/9dwk_47253.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9dwk_47253/05_2025/9dwk_47253.cif" } resolution = 4.3 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= 0.000 sd= 0.002 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 3861 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 249 5.49 5 C 5548 2.51 5 N 2015 2.21 5 O 2563 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: 10375 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 467 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 467 Classifications: {'peptide': 94} Incomplete info: {'truncation_to_alanine': 81} Link IDs: {'PTRANS': 3, 'TRANS': 90} Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 316 Unresolved non-hydrogen angles: 397 Unresolved non-hydrogen dihedrals: 257 Unresolved non-hydrogen chiralities: 28 Planarities with less than four sites: {'GLN:plan1': 6, 'HIS:plan': 1, 'TYR:plan': 3, 'ASN:plan1': 1, 'ASP:plan': 4, 'PHE:plan': 4, 'GLU:plan': 7, 'ARG:plan': 13} Unresolved non-hydrogen planarities: 182 Chain: "B" Number of atoms: 392 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 392 Classifications: {'peptide': 80} Incomplete info: {'truncation_to_alanine': 66} Link IDs: {'PTRANS': 1, 'TRANS': 78} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 257 Unresolved non-hydrogen angles: 326 Unresolved non-hydrogen dihedrals: 207 Unresolved non-hydrogen chiralities: 28 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': 11} Unresolved non-hydrogen planarities: 139 Chain: "C" Number of atoms: 516 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 516 Classifications: {'peptide': 105} Incomplete info: {'truncation_to_alanine': 83} Link IDs: {'PTRANS': 5, 'TRANS': 99} Unresolved chain link angles: 5 Unresolved non-hydrogen bonds: 306 Unresolved non-hydrogen angles: 388 Unresolved non-hydrogen dihedrals: 244 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: "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: 477 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 477 Classifications: {'peptide': 96} Incomplete info: {'truncation_to_alanine': 83} Link IDs: {'PTRANS': 3, 'TRANS': 92} Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 325 Unresolved non-hydrogen angles: 409 Unresolved non-hydrogen dihedrals: 266 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': 13} Unresolved non-hydrogen planarities: 187 Chain: "F" Number of atoms: 407 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 407 Classifications: {'peptide': 83} Incomplete info: {'truncation_to_alanine': 69} Link IDs: {'PTRANS': 1, 'TRANS': 81} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 269 Unresolved non-hydrogen angles: 340 Unresolved non-hydrogen dihedrals: 217 Unresolved non-hydrogen chiralities: 29 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': 12} Unresolved non-hydrogen planarities: 144 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: 455 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 455 Classifications: {'peptide': 92} Incomplete info: {'truncation_to_alanine': 79} Link IDs: {'PTRANS': 2, 'TRANS': 89} Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 276 Unresolved non-hydrogen angles: 349 Unresolved non-hydrogen dihedrals: 230 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: "I" Number of atoms: 2144 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 2144 Classifications: {'DNA': 105} Link IDs: {'rna3p': 104} Chain: "J" Number of atoms: 2579 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 2579 Classifications: {'DNA': 125} Link IDs: {'rna3p': 124} Chain: "K" Number of atoms: 384 Number of conformers: 1 Conformer: "" Number of residues, atoms: 19, 384 Classifications: {'DNA': 19} Modifications used: {'p5*END': 1} Link IDs: {'rna3p': 18} Chain: "L" Number of atoms: 1593 Number of conformers: 1 Conformer: "" Number of residues, atoms: 323, 1593 Classifications: {'peptide': 323} Incomplete info: {'truncation_to_alanine': 284} Link IDs: {'CIS': 1, 'PTRANS': 13, 'TRANS': 308} Chain breaks: 1 Unresolved chain link angles: 13 Unresolved non-hydrogen bonds: 1047 Unresolved non-hydrogen angles: 1320 Unresolved non-hydrogen dihedrals: 876 Unresolved non-hydrogen chiralities: 84 Planarities with less than four sites: {'GLN:plan1': 12, '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: 563 Time building chain proxies: 10.93, per 1000 atoms: 1.05 Number of scatterers: 10375 At special positions: 0 Unit cell: (101.258, 117.018, 149.326, 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 249 15.00 O 2563 8.00 N 2015 7.00 C 5548 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: 2.61 Conformation dependent library (CDL) restraints added in 1.1 seconds 2096 Ramachandran restraints generated. 1048 Oldfield, 0 Emsley, 1048 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1992 Finding SS restraints... Secondary structure from input PDB file: 51 helices and 10 sheets defined 69.2% alpha, 4.7% beta 124 base pairs and 207 stacking pairs defined. Time for finding SS restraints: 4.93 Creating SS restraints... Processing helix chain 'A' and resid 44 through 57 Processing helix chain 'A' and resid 63 through 77 removed outlier: 3.651A pdb=" N ASP A 77 " --> pdb=" O GLU A 73 " (cutoff:3.500A) Processing helix chain 'A' and resid 85 through 114 Processing helix chain 'A' and resid 120 through 131 Processing helix chain 'B' and resid 24 through 29 removed outlier: 3.587A pdb=" N ILE B 29 " --> pdb=" O ILE B 26 " (cutoff:3.500A) Processing helix chain 'B' and resid 30 through 41 Processing helix chain 'B' and resid 49 through 76 removed outlier: 3.524A pdb=" N GLU B 53 " --> pdb=" O LEU B 49 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N ARG B 55 " --> pdb=" O TYR B 51 " (cutoff:3.500A) removed outlier: 3.965A 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 26 through 37 removed outlier: 3.731A pdb=" N VAL C 30 " --> pdb=" O PRO C 26 " (cutoff:3.500A) Processing helix chain 'C' and resid 45 through 74 removed outlier: 4.019A pdb=" N VAL C 49 " --> pdb=" O ALA C 45 " (cutoff:3.500A) Processing helix chain 'C' and resid 79 through 90 Processing helix chain 'C' and resid 90 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 103 through 122 removed outlier: 3.542A pdb=" N ALA D 107 " --> pdb=" O PRO D 103 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N VAL D 111 " --> pdb=" O ALA D 107 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N SER D 112 " --> pdb=" O LYS D 108 " (cutoff:3.500A) Processing helix chain 'E' and resid 50 through 57 Processing helix chain 'E' and resid 63 through 79 removed outlier: 3.620A pdb=" N ASP E 77 " --> pdb=" O GLU E 73 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N PHE E 78 " --> pdb=" O ILE E 74 " (cutoff:3.500A) Processing helix chain 'E' and resid 85 through 114 Processing helix chain 'E' and resid 120 through 132 Processing helix chain 'F' and resid 25 through 29 removed outlier: 3.515A 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 49 through 76 removed outlier: 3.643A pdb=" N GLU F 53 " --> pdb=" O LEU F 49 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N ASP F 68 " --> pdb=" O ASN F 64 " (cutoff:3.500A) Processing helix chain 'F' and resid 82 through 93 Processing helix chain 'G' and resid 17 through 22 Processing helix chain 'G' and resid 26 through 37 Processing helix chain 'G' and resid 45 through 73 removed outlier: 3.920A pdb=" N VAL G 49 " --> pdb=" O ALA G 45 " (cutoff:3.500A) Processing helix chain 'G' and resid 79 through 90 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 124 Processing helix chain 'L' and resid 12 through 29 Processing helix chain 'L' and resid 32 through 49 removed outlier: 4.304A pdb=" N ALA L 38 " --> pdb=" O HIS L 34 " (cutoff:3.500A) Processing helix chain 'L' and resid 55 through 61 removed outlier: 3.578A 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 90 Processing helix chain 'L' and resid 91 through 102 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 147 removed outlier: 3.547A pdb=" N GLU L 147 " --> pdb=" O PHE L 143 " (cutoff:3.500A) Processing helix chain 'L' and resid 152 through 170 Processing helix chain 'L' and resid 209 through 221 Processing helix chain 'L' and resid 261 through 274 removed outlier: 4.649A pdb=" N TYR L 266 " --> pdb=" O LYS L 262 " (cutoff:3.500A) removed outlier: 5.416A pdb=" N CYS L 267 " --> pdb=" O ASP L 263 " (cutoff:3.500A) removed outlier: 3.835A 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 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: 6.958A 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 98 removed outlier: 6.866A 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: 7.129A 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 'E' and resid 83 through 84 removed outlier: 7.007A pdb=" N ARG E 83 " --> pdb=" O VAL F 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'E' and resid 118 through 119 Processing sheet with id=AA6, first strand: chain 'G' and resid 42 through 43 removed outlier: 6.586A pdb=" N ARG G 42 " --> pdb=" O ILE H 89 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'G' and resid 77 through 78 Processing sheet with id=AA8, first strand: chain 'L' and resid 150 through 151 Processing sheet with id=AA9, first strand: chain 'L' and resid 174 through 178 removed outlier: 4.829A pdb=" N ASP L 192 " --> pdb=" O CYS L 178 " (cutoff:3.500A) removed outlier: 6.291A pdb=" N MET L 191 " --> pdb=" O ASP L 256 " (cutoff:3.500A) removed outlier: 7.775A pdb=" N ARG L 258 " --> pdb=" O MET L 191 " (cutoff:3.500A) removed outlier: 6.597A pdb=" N VAL L 193 " --> pdb=" O ARG L 258 " (cutoff:3.500A) removed outlier: 7.463A pdb=" N ILE L 260 " --> pdb=" O VAL L 193 " (cutoff:3.500A) removed outlier: 6.232A pdb=" N LEU L 195 " --> pdb=" O ILE L 260 " (cutoff:3.500A) removed outlier: 6.620A pdb=" N VAL L 238 " --> pdb=" O THR L 227 " (cutoff:3.500A) removed outlier: 5.388A pdb=" N THR L 227 " --> pdb=" O VAL L 238 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'L' and resid 291 through 293 536 hydrogen bonds defined for protein. 1581 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 321 hydrogen bonds 638 hydrogen bond angles 0 basepair planarities 124 basepair parallelities 207 stacking parallelities Total time for adding SS restraints: 4.70 Time building geometry restraints manager: 3.06 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: 1317 1.29 - 1.38: 2613 1.38 - 1.46: 2305 1.46 - 1.54: 4171 1.54 - 1.62: 579 Bond restraints: 10985 Sorted by residual: bond pdb=" P DT K 108 " pdb=" OP3 DT K 108 " ideal model delta sigma weight residual 1.480 1.611 -0.131 2.00e-02 2.50e+03 4.31e+01 bond pdb=" P DC K 118 " pdb=" OP1 DC K 118 " ideal model delta sigma weight residual 1.480 1.525 -0.045 2.00e-02 2.50e+03 5.14e+00 bond pdb=" P DC I 80 " pdb=" OP1 DC I 80 " ideal model delta sigma weight residual 1.480 1.521 -0.041 2.00e-02 2.50e+03 4.22e+00 bond pdb=" P DG J 145 " pdb=" OP2 DG J 145 " 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 K 117 " pdb=" OP2 DT K 117 " ideal model delta sigma weight residual 1.480 1.520 -0.040 2.00e-02 2.50e+03 3.98e+00 ... (remaining 10980 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.52: 15537 1.52 - 3.04: 533 3.04 - 4.56: 36 4.56 - 6.08: 15 6.08 - 7.59: 15 Bond angle restraints: 16136 Sorted by residual: angle pdb=" O3' DT K 117 " pdb=" P DC K 118 " pdb=" O5' DC K 118 " ideal model delta sigma weight residual 104.00 97.62 6.38 1.50e+00 4.44e-01 1.81e+01 angle pdb=" O3' DT K 117 " pdb=" C3' DT K 117 " pdb=" C2' DT K 117 " ideal model delta sigma weight residual 111.50 105.76 5.74 1.50e+00 4.44e-01 1.46e+01 angle pdb=" O3' DC I 79 " pdb=" C3' DC I 79 " pdb=" C2' DC I 79 " ideal model delta sigma weight residual 111.50 105.93 5.57 1.50e+00 4.44e-01 1.38e+01 angle pdb=" O3' DC I 79 " pdb=" P DC I 80 " pdb=" O5' DC I 80 " ideal model delta sigma weight residual 104.00 108.79 -4.79 1.50e+00 4.44e-01 1.02e+01 angle pdb=" C3' DC I 79 " pdb=" O3' DC I 79 " pdb=" P DC I 80 " ideal model delta sigma weight residual 120.20 124.62 -4.42 1.50e+00 4.44e-01 8.67e+00 ... (remaining 16131 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 28.59: 4307 28.59 - 57.17: 1257 57.17 - 85.76: 164 85.76 - 114.34: 1 114.34 - 142.93: 2 Dihedral angle restraints: 5731 sinusoidal: 2681 harmonic: 3050 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 77.07 142.93 1 3.50e+01 8.16e-04 1.41e+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 85.89 134.11 1 3.50e+01 8.16e-04 1.33e+01 dihedral pdb=" CA PRO H 103 " pdb=" C PRO H 103 " pdb=" N GLY H 104 " pdb=" CA GLY H 104 " ideal model delta harmonic sigma weight residual -180.00 -162.25 -17.75 0 5.00e+00 4.00e-02 1.26e+01 ... (remaining 5728 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.126: 1979 0.126 - 0.253: 2 0.253 - 0.379: 0 0.379 - 0.505: 1 0.505 - 0.632: 10 Chirality restraints: 1992 Sorted by residual: chirality pdb=" P DT I 2 " pdb=" OP1 DT I 2 " pdb=" OP2 DT I 2 " pdb=" O5' DT I 2 " both_signs ideal model delta sigma weight residual True 2.35 -2.98 -0.63 2.00e-01 2.50e+01 9.98e+00 chirality pdb=" P DC K 116 " pdb=" OP1 DC K 116 " pdb=" OP2 DC K 116 " pdb=" O5' DC K 116 " both_signs ideal model delta sigma weight residual True 2.35 -2.95 -0.61 2.00e-01 2.50e+01 9.17e+00 chirality pdb=" P DC I 80 " pdb=" OP1 DC I 80 " pdb=" OP2 DC I 80 " pdb=" O5' DC I 80 " both_signs ideal model delta sigma weight residual True 2.35 -2.92 -0.58 2.00e-01 2.50e+01 8.37e+00 ... (remaining 1989 not shown) Planarity restraints: 1307 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' DC I 80 " 0.027 2.00e-02 2.50e+03 1.38e-02 4.28e+00 pdb=" N1 DC I 80 " -0.013 2.00e-02 2.50e+03 pdb=" C2 DC I 80 " 0.001 2.00e-02 2.50e+03 pdb=" O2 DC I 80 " -0.014 2.00e-02 2.50e+03 pdb=" N3 DC I 80 " 0.004 2.00e-02 2.50e+03 pdb=" C4 DC I 80 " -0.004 2.00e-02 2.50e+03 pdb=" N4 DC I 80 " 0.019 2.00e-02 2.50e+03 pdb=" C5 DC I 80 " -0.015 2.00e-02 2.50e+03 pdb=" C6 DC I 80 " -0.005 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DA I 39 " -0.026 2.00e-02 2.50e+03 1.10e-02 3.30e+00 pdb=" N9 DA I 39 " 0.021 2.00e-02 2.50e+03 pdb=" C8 DA I 39 " 0.008 2.00e-02 2.50e+03 pdb=" N7 DA I 39 " -0.000 2.00e-02 2.50e+03 pdb=" C5 DA I 39 " -0.002 2.00e-02 2.50e+03 pdb=" C6 DA I 39 " -0.004 2.00e-02 2.50e+03 pdb=" N6 DA I 39 " -0.008 2.00e-02 2.50e+03 pdb=" N1 DA I 39 " 0.001 2.00e-02 2.50e+03 pdb=" C2 DA I 39 " 0.001 2.00e-02 2.50e+03 pdb=" N3 DA I 39 " 0.007 2.00e-02 2.50e+03 pdb=" C4 DA I 39 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DT I 88 " 0.018 2.00e-02 2.50e+03 9.34e-03 2.18e+00 pdb=" N1 DT I 88 " -0.021 2.00e-02 2.50e+03 pdb=" C2 DT I 88 " -0.003 2.00e-02 2.50e+03 pdb=" O2 DT I 88 " -0.004 2.00e-02 2.50e+03 pdb=" N3 DT I 88 " 0.002 2.00e-02 2.50e+03 pdb=" C4 DT I 88 " 0.003 2.00e-02 2.50e+03 pdb=" O4 DT I 88 " 0.007 2.00e-02 2.50e+03 pdb=" C5 DT I 88 " 0.002 2.00e-02 2.50e+03 pdb=" C7 DT I 88 " -0.006 2.00e-02 2.50e+03 pdb=" C6 DT I 88 " 0.001 2.00e-02 2.50e+03 ... (remaining 1304 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.76: 1968 2.76 - 3.30: 9773 3.30 - 3.83: 21836 3.83 - 4.37: 21532 4.37 - 4.90: 30040 Nonbonded interactions: 85149 Sorted by model distance: nonbonded pdb=" O ARG E 83 " pdb=" N VAL F 81 " model vdw 2.231 3.120 nonbonded pdb=" N2 DG J 38 " pdb=" O2 DC K 110 " model vdw 2.310 2.496 nonbonded pdb=" N VAL A 117 " pdb=" OP2 DG I 71 " model vdw 2.319 3.120 nonbonded pdb=" O ARG A 83 " pdb=" N VAL B 81 " model vdw 2.340 3.120 nonbonded pdb=" N TYR E 41 " pdb=" OP1 DC I 84 " model vdw 2.355 3.120 ... (remaining 85144 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' and resid 41 through 133) selection = (chain 'E' and resid 41 through 133) } ncs_group { reference = chain 'B' selection = (chain 'F' and resid 22 through 101) } ncs_group { reference = (chain 'C' and resid 16 through 117) selection = chain 'G' } ncs_group { reference = (chain 'D' and resid 33 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: 29.090 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.080 Construct map_model_manager: 0.020 Extract box with map and model: 0.880 Check model and map are aligned: 0.060 Set scattering table: 0.110 Process input model: 35.040 Find NCS groups from input model: 0.250 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.810 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 68.380 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8913 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 0.131 10985 Z= 0.256 Angle : 0.661 7.594 16136 Z= 0.397 Chirality : 0.056 0.632 1992 Planarity : 0.003 0.014 1307 Dihedral : 30.863 142.931 3739 Min Nonbonded Distance : 2.231 Molprobity Statistics. All-atom Clashscore : 7.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.05 % Favored : 98.95 % 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: 2.01 (0.26), residues: 1048 helix: 1.83 (0.19), residues: 717 sheet: 2.21 (0.93), residues: 29 loop : 0.13 (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 0.12123 ( 857) hydrogen bonds : angle 4.39653 ( 2219) covalent geometry : bond 0.00514 (10985) covalent geometry : angle 0.66149 (16136) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2096 Ramachandran restraints generated. 1048 Oldfield, 0 Emsley, 1048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2096 Ramachandran restraints generated. 1048 Oldfield, 0 Emsley, 1048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 16 residues out of total 905 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 16 time to evaluate : 0.684 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 16 average time/residue: 0.0928 time to fit residues: 3.7044 Evaluate side-chains 16 residues out of total 905 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 16 time to evaluate : 0.759 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 107 optimal weight: 6.9990 chunk 96 optimal weight: 5.9990 chunk 53 optimal weight: 20.0000 chunk 32 optimal weight: 20.0000 chunk 64 optimal weight: 30.0000 chunk 51 optimal weight: 3.9990 chunk 99 optimal weight: 40.0000 chunk 38 optimal weight: 6.9990 chunk 60 optimal weight: 0.8980 chunk 74 optimal weight: 10.0000 chunk 115 optimal weight: 60.0000 overall best weight: 4.9788 ------------------------------------------------------------------------------- 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 = 0.3066 r_free = 0.3066 target = 0.040556 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.2486 r_free = 0.2486 target = 0.023760 restraints weight = 149234.874| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.2503 r_free = 0.2503 target = 0.024225 restraints weight = 95936.081| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.2515 r_free = 0.2515 target = 0.024539 restraints weight = 71053.641| |-----------------------------------------------------------------------------| r_work (final): 0.2473 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8968 moved from start: 0.0751 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 10985 Z= 0.222 Angle : 0.535 6.728 16136 Z= 0.341 Chirality : 0.036 0.126 1992 Planarity : 0.002 0.012 1307 Dihedral : 30.754 143.379 3739 Min Nonbonded Distance : 2.053 Molprobity Statistics. All-atom Clashscore : 9.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % 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: 2.98 (0.27), residues: 1048 helix: 2.64 (0.19), residues: 730 sheet: 2.21 (0.89), residues: 29 loop : 0.20 (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 0.05343 ( 857) hydrogen bonds : angle 3.34491 ( 2219) covalent geometry : bond 0.00442 (10985) covalent geometry : angle 0.53459 (16136) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2096 Ramachandran restraints generated. 1048 Oldfield, 0 Emsley, 1048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2096 Ramachandran restraints generated. 1048 Oldfield, 0 Emsley, 1048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 16 residues out of total 905 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 16 time to evaluate : 0.763 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 16 average time/residue: 0.0927 time to fit residues: 3.8486 Evaluate side-chains 16 residues out of total 905 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 16 time to evaluate : 0.722 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 68 optimal weight: 7.9990 chunk 96 optimal weight: 6.9990 chunk 11 optimal weight: 30.0000 chunk 100 optimal weight: 50.0000 chunk 109 optimal weight: 50.0000 chunk 64 optimal weight: 30.0000 chunk 49 optimal weight: 7.9990 chunk 51 optimal weight: 0.6980 chunk 93 optimal weight: 10.0000 chunk 66 optimal weight: 20.0000 chunk 26 optimal weight: 50.0000 overall best weight: 6.7390 ------------------------------------------------------------------------------- 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 = 0.2979 r_free = 0.2979 target = 0.038606 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.2411 r_free = 0.2411 target = 0.021760 restraints weight = 161040.383| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.2436 r_free = 0.2436 target = 0.022362 restraints weight = 90111.006| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.2453 r_free = 0.2453 target = 0.022799 restraints weight = 61860.139| |-----------------------------------------------------------------------------| r_work (final): 0.2480 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7981 moved from start: 0.2117 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.038 10985 Z= 0.281 Angle : 0.566 7.558 16136 Z= 0.360 Chirality : 0.038 0.131 1992 Planarity : 0.003 0.012 1307 Dihedral : 31.083 144.808 3739 Min Nonbonded Distance : 1.937 Molprobity Statistics. All-atom Clashscore : 12.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % 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: 3.16 (0.27), residues: 1048 helix: 2.82 (0.19), residues: 732 sheet: 1.41 (0.88), residues: 29 loop : 0.22 (0.39), residues: 287 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 0.05887 ( 857) hydrogen bonds : angle 3.43178 ( 2219) covalent geometry : bond 0.00567 (10985) covalent geometry : angle 0.56567 (16136) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2096 Ramachandran restraints generated. 1048 Oldfield, 0 Emsley, 1048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2096 Ramachandran restraints generated. 1048 Oldfield, 0 Emsley, 1048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 16 residues out of total 905 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 16 time to evaluate : 0.814 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 16 average time/residue: 0.1079 time to fit residues: 4.3652 Evaluate side-chains 16 residues out of total 905 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 16 time to evaluate : 0.788 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 50 optimal weight: 0.9990 chunk 74 optimal weight: 10.0000 chunk 22 optimal weight: 20.0000 chunk 33 optimal weight: 20.0000 chunk 68 optimal weight: 7.9990 chunk 0 optimal weight: 50.0000 chunk 88 optimal weight: 8.9990 chunk 30 optimal weight: 20.0000 chunk 70 optimal weight: 20.0000 chunk 64 optimal weight: 20.0000 chunk 82 optimal weight: 20.0000 overall best weight: 9.5994 ------------------------------------------------------------------------------- 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 = 0.2923 r_free = 0.2923 target = 0.036853 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.2358 r_free = 0.2358 target = 0.020563 restraints weight = 161537.515| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.2382 r_free = 0.2382 target = 0.021101 restraints weight = 91309.760| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.2398 r_free = 0.2398 target = 0.021497 restraints weight = 63004.605| |-----------------------------------------------------------------------------| r_work (final): 0.2424 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7931 moved from start: 0.3829 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.055 10985 Z= 0.381 Angle : 0.664 8.156 16136 Z= 0.420 Chirality : 0.041 0.165 1992 Planarity : 0.003 0.014 1307 Dihedral : 31.961 142.879 3739 Min Nonbonded Distance : 1.892 Molprobity Statistics. All-atom Clashscore : 20.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % 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: 2.16 (0.26), residues: 1048 helix: 2.08 (0.19), residues: 735 sheet: 2.38 (1.27), residues: 14 loop : -0.23 (0.37), 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 0.08773 ( 857) hydrogen bonds : angle 4.33773 ( 2219) covalent geometry : bond 0.00771 (10985) covalent geometry : angle 0.66374 (16136) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2096 Ramachandran restraints generated. 1048 Oldfield, 0 Emsley, 1048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2096 Ramachandran restraints generated. 1048 Oldfield, 0 Emsley, 1048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 16 residues out of total 905 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 16 time to evaluate : 0.753 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 16 average time/residue: 0.0945 time to fit residues: 3.8874 Evaluate side-chains 16 residues out of total 905 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 16 time to evaluate : 0.799 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 43 optimal weight: 20.0000 chunk 14 optimal weight: 8.9990 chunk 97 optimal weight: 40.0000 chunk 93 optimal weight: 10.0000 chunk 30 optimal weight: 9.9990 chunk 78 optimal weight: 7.9990 chunk 79 optimal weight: 6.9990 chunk 125 optimal weight: 30.0000 chunk 0 optimal weight: 40.0000 chunk 72 optimal weight: 10.0000 chunk 5 optimal weight: 9.9990 overall best weight: 8.7990 ------------------------------------------------------------------------------- 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 = 0.2974 r_free = 0.2974 target = 0.037502 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.2399 r_free = 0.2399 target = 0.021676 restraints weight = 155645.334| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.2415 r_free = 0.2415 target = 0.022075 restraints weight = 100993.616| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.2426 r_free = 0.2426 target = 0.022334 restraints weight = 75643.755| |-----------------------------------------------------------------------------| r_work (final): 0.2378 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9033 moved from start: 0.4167 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.047 10985 Z= 0.341 Angle : 0.622 6.340 16136 Z= 0.394 Chirality : 0.039 0.162 1992 Planarity : 0.003 0.012 1307 Dihedral : 31.880 143.380 3739 Min Nonbonded Distance : 1.910 Molprobity Statistics. All-atom Clashscore : 17.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % 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: 2.32 (0.26), residues: 1048 helix: 2.31 (0.19), residues: 738 sheet: 0.28 (1.06), residues: 24 loop : -0.42 (0.39), residues: 286 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 0.07765 ( 857) hydrogen bonds : angle 4.02623 ( 2219) covalent geometry : bond 0.00685 (10985) covalent geometry : angle 0.62158 (16136) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2096 Ramachandran restraints generated. 1048 Oldfield, 0 Emsley, 1048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2096 Ramachandran restraints generated. 1048 Oldfield, 0 Emsley, 1048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 16 residues out of total 905 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 16 time to evaluate : 1.021 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 16 average time/residue: 0.1013 time to fit residues: 4.1545 Evaluate side-chains 16 residues out of total 905 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 16 time to evaluate : 0.760 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 82 optimal weight: 20.0000 chunk 63 optimal weight: 0.7980 chunk 92 optimal weight: 10.0000 chunk 100 optimal weight: 30.0000 chunk 61 optimal weight: 10.0000 chunk 72 optimal weight: 10.0000 chunk 75 optimal weight: 10.0000 chunk 113 optimal weight: 40.0000 chunk 54 optimal weight: 9.9990 chunk 51 optimal weight: 30.0000 chunk 20 optimal weight: 9.9990 overall best weight: 8.1592 ------------------------------------------------------------------------------- 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 = 0.2965 r_free = 0.2965 target = 0.037297 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.2401 r_free = 0.2401 target = 0.021662 restraints weight = 157799.233| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.2418 r_free = 0.2418 target = 0.022056 restraints weight = 102194.301| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.2428 r_free = 0.2428 target = 0.022321 restraints weight = 76597.854| |-----------------------------------------------------------------------------| r_work (final): 0.2378 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9021 moved from start: 0.4849 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.045 10985 Z= 0.327 Angle : 0.617 6.488 16136 Z= 0.389 Chirality : 0.039 0.146 1992 Planarity : 0.003 0.013 1307 Dihedral : 31.995 142.801 3739 Min Nonbonded Distance : 1.923 Molprobity Statistics. All-atom Clashscore : 17.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.91 % Favored : 96.09 % 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: 2.56 (0.27), residues: 1048 helix: 2.58 (0.19), residues: 734 sheet: -0.40 (1.20), residues: 20 loop : -0.48 (0.38), residues: 294 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 0.07675 ( 857) hydrogen bonds : angle 4.03173 ( 2219) covalent geometry : bond 0.00659 (10985) covalent geometry : angle 0.61674 (16136) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2096 Ramachandran restraints generated. 1048 Oldfield, 0 Emsley, 1048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2096 Ramachandran restraints generated. 1048 Oldfield, 0 Emsley, 1048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 16 residues out of total 905 (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: 0.0953 time to fit residues: 3.9133 Evaluate side-chains 16 residues out of total 905 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 16 time to evaluate : 0.750 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 92 optimal weight: 10.0000 chunk 56 optimal weight: 9.9990 chunk 30 optimal weight: 20.0000 chunk 27 optimal weight: 0.7980 chunk 46 optimal weight: 0.8980 chunk 31 optimal weight: 0.9990 chunk 98 optimal weight: 9.9990 chunk 87 optimal weight: 8.9990 chunk 72 optimal weight: 10.0000 chunk 94 optimal weight: 10.0000 chunk 105 optimal weight: 2.9990 overall best weight: 2.9386 ------------------------------------------------------------------------------- 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 = 0.3014 r_free = 0.3014 target = 0.038923 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2461 r_free = 0.2461 target = 0.023078 restraints weight = 155373.556| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.2478 r_free = 0.2478 target = 0.023546 restraints weight = 96453.743| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 50)----------------| | r_work = 0.2490 r_free = 0.2490 target = 0.023844 restraints weight = 69542.570| |-----------------------------------------------------------------------------| r_work (final): 0.2441 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8939 moved from start: 0.4646 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 10985 Z= 0.164 Angle : 0.529 5.279 16136 Z= 0.331 Chirality : 0.036 0.122 1992 Planarity : 0.002 0.010 1307 Dihedral : 31.462 142.781 3739 Min Nonbonded Distance : 1.993 Molprobity Statistics. All-atom Clashscore : 10.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.10 % Favored : 97.90 % 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: 3.71 (0.28), residues: 1048 helix: 3.54 (0.19), residues: 739 sheet: -0.43 (1.02), residues: 24 loop : -0.40 (0.40), residues: 285 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 0.04299 ( 857) hydrogen bonds : angle 3.06012 ( 2219) covalent geometry : bond 0.00329 (10985) covalent geometry : angle 0.52941 (16136) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2096 Ramachandran restraints generated. 1048 Oldfield, 0 Emsley, 1048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2096 Ramachandran restraints generated. 1048 Oldfield, 0 Emsley, 1048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 16 residues out of total 905 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 16 time to evaluate : 0.812 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 16 average time/residue: 0.1022 time to fit residues: 4.2352 Evaluate side-chains 16 residues out of total 905 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 16 time to evaluate : 0.755 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 76 optimal weight: 10.0000 chunk 0 optimal weight: 40.0000 chunk 108 optimal weight: 20.0000 chunk 39 optimal weight: 5.9990 chunk 48 optimal weight: 0.8980 chunk 6 optimal weight: 10.0000 chunk 58 optimal weight: 7.9990 chunk 118 optimal weight: 40.0000 chunk 40 optimal weight: 40.0000 chunk 34 optimal weight: 20.0000 chunk 4 optimal weight: 30.0000 overall best weight: 6.9792 ------------------------------------------------------------------------------- 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 = 0.2929 r_free = 0.2929 target = 0.037256 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.2391 r_free = 0.2391 target = 0.021303 restraints weight = 164064.257| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.2417 r_free = 0.2417 target = 0.021906 restraints weight = 91943.109| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.2433 r_free = 0.2433 target = 0.022318 restraints weight = 62167.453| |-----------------------------------------------------------------------------| r_work (final): 0.2458 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7765 moved from start: 0.4916 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.039 10985 Z= 0.282 Angle : 0.577 5.814 16136 Z= 0.366 Chirality : 0.038 0.124 1992 Planarity : 0.002 0.013 1307 Dihedral : 31.667 142.328 3739 Min Nonbonded Distance : 1.939 Molprobity Statistics. All-atom Clashscore : 15.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.72 % Favored : 96.28 % 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: 3.28 (0.27), residues: 1048 helix: 3.24 (0.19), residues: 737 sheet: -0.58 (1.03), residues: 24 loop : -0.58 (0.39), residues: 287 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 0.06352 ( 857) hydrogen bonds : angle 3.61102 ( 2219) covalent geometry : bond 0.00566 (10985) covalent geometry : angle 0.57744 (16136) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2096 Ramachandran restraints generated. 1048 Oldfield, 0 Emsley, 1048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2096 Ramachandran restraints generated. 1048 Oldfield, 0 Emsley, 1048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 16 residues out of total 905 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 16 time to evaluate : 0.725 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 16 average time/residue: 0.0963 time to fit residues: 3.8793 Evaluate side-chains 16 residues out of total 905 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 16 time to evaluate : 0.823 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 53 optimal weight: 20.0000 chunk 13 optimal weight: 9.9990 chunk 72 optimal weight: 10.0000 chunk 50 optimal weight: 0.9990 chunk 87 optimal weight: 8.9990 chunk 98 optimal weight: 50.0000 chunk 52 optimal weight: 3.9990 chunk 24 optimal weight: 5.9990 chunk 106 optimal weight: 7.9990 chunk 90 optimal weight: 8.9990 chunk 96 optimal weight: 9.9990 overall best weight: 5.5990 ------------------------------------------------------------------------------- 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 = 0.2987 r_free = 0.2987 target = 0.038073 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.2431 r_free = 0.2431 target = 0.022368 restraints weight = 157130.714| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 56)----------------| | r_work = 0.2450 r_free = 0.2450 target = 0.022816 restraints weight = 98028.792| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.2462 r_free = 0.2462 target = 0.023121 restraints weight = 71535.819| |-----------------------------------------------------------------------------| r_work (final): 0.2410 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8972 moved from start: 0.5002 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.031 10985 Z= 0.240 Angle : 0.556 5.494 16136 Z= 0.350 Chirality : 0.037 0.122 1992 Planarity : 0.002 0.013 1307 Dihedral : 31.571 142.796 3739 Min Nonbonded Distance : 1.965 Molprobity Statistics. All-atom Clashscore : 12.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % 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: 3.34 (0.27), residues: 1048 helix: 3.30 (0.19), residues: 739 sheet: -0.73 (1.02), residues: 24 loop : -0.63 (0.39), residues: 285 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 0.05657 ( 857) hydrogen bonds : angle 3.41924 ( 2219) covalent geometry : bond 0.00484 (10985) covalent geometry : angle 0.55625 (16136) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2096 Ramachandran restraints generated. 1048 Oldfield, 0 Emsley, 1048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2096 Ramachandran restraints generated. 1048 Oldfield, 0 Emsley, 1048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 16 residues out of total 905 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 16 time to evaluate : 0.679 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 16 average time/residue: 0.0918 time to fit residues: 3.6812 Evaluate side-chains 16 residues out of total 905 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 16 time to evaluate : 0.691 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 15 optimal weight: 20.0000 chunk 80 optimal weight: 10.0000 chunk 124 optimal weight: 0.9980 chunk 32 optimal weight: 9.9990 chunk 28 optimal weight: 0.6980 chunk 112 optimal weight: 0.0870 chunk 102 optimal weight: 20.0000 chunk 42 optimal weight: 0.9990 chunk 41 optimal weight: 5.9990 chunk 52 optimal weight: 0.7980 chunk 90 optimal weight: 10.0000 overall best weight: 0.7160 ------------------------------------------------------------------------------- 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 = 0.3062 r_free = 0.3062 target = 0.040510 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.2534 r_free = 0.2534 target = 0.024774 restraints weight = 149728.715| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 55)----------------| | r_work = 0.2553 r_free = 0.2553 target = 0.025280 restraints weight = 92554.275| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.2566 r_free = 0.2566 target = 0.025604 restraints weight = 66513.192| |-----------------------------------------------------------------------------| r_work (final): 0.2512 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8888 moved from start: 0.5029 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 10985 Z= 0.132 Angle : 0.504 3.891 16136 Z= 0.316 Chirality : 0.036 0.123 1992 Planarity : 0.002 0.012 1307 Dihedral : 30.834 141.760 3739 Min Nonbonded Distance : 2.041 Molprobity Statistics. All-atom Clashscore : 7.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % 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: 4.20 (0.28), residues: 1048 helix: 3.98 (0.19), residues: 739 sheet: -0.78 (0.95), residues: 26 loop : -0.38 (0.39), residues: 283 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 0.03157 ( 857) hydrogen bonds : angle 2.52814 ( 2219) covalent geometry : bond 0.00265 (10985) covalent geometry : angle 0.50397 (16136) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2096 Ramachandran restraints generated. 1048 Oldfield, 0 Emsley, 1048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2096 Ramachandran restraints generated. 1048 Oldfield, 0 Emsley, 1048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 16 residues out of total 905 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 16 time to evaluate : 0.692 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 16 average time/residue: 0.0918 time to fit residues: 3.7240 Evaluate side-chains 16 residues out of total 905 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 16 time to evaluate : 0.829 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 63 optimal weight: 5.9990 chunk 124 optimal weight: 10.0000 chunk 13 optimal weight: 20.0000 chunk 94 optimal weight: 10.0000 chunk 92 optimal weight: 10.0000 chunk 47 optimal weight: 30.0000 chunk 34 optimal weight: 9.9990 chunk 12 optimal weight: 10.0000 chunk 110 optimal weight: 10.0000 chunk 19 optimal weight: 0.9990 chunk 116 optimal weight: 30.0000 overall best weight: 7.3994 ------------------------------------------------------------------------------- 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 = 0.2934 r_free = 0.2934 target = 0.037472 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.2404 r_free = 0.2404 target = 0.021608 restraints weight = 162945.770| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.2429 r_free = 0.2429 target = 0.022216 restraints weight = 90625.625| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.2446 r_free = 0.2446 target = 0.022644 restraints weight = 61284.231| |-----------------------------------------------------------------------------| r_work (final): 0.2470 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7769 moved from start: 0.5083 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.042 10985 Z= 0.291 Angle : 0.562 5.170 16136 Z= 0.359 Chirality : 0.037 0.125 1992 Planarity : 0.002 0.014 1307 Dihedral : 31.305 141.692 3739 Min Nonbonded Distance : 1.945 Molprobity Statistics. All-atom Clashscore : 14.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.53 % Favored : 96.47 % 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: 3.62 (0.27), residues: 1048 helix: 3.53 (0.19), residues: 739 sheet: -0.53 (1.05), residues: 24 loop : -0.59 (0.39), residues: 285 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 0.06163 ( 857) hydrogen bonds : angle 3.38586 ( 2219) covalent geometry : bond 0.00583 (10985) covalent geometry : angle 0.56246 (16136) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9573.30 seconds wall clock time: 166 minutes 51.57 seconds (10011.57 seconds total)