Starting phenix.real_space_refine on Thu Sep 18 02:05:39 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9dwk_47253/09_2025/9dwk_47253.cif Found real_map, /net/cci-nas-00/data/ceres_data/9dwk_47253/09_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 { model { file = "/net/cci-nas-00/data/ceres_data/9dwk_47253/09_2025/9dwk_47253.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9dwk_47253/09_2025/9dwk_47253.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9dwk_47253/09_2025/9dwk_47253.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9dwk_47253/09_2025/9dwk_47253.map" } resolution = 4.3 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 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-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/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: {'TYR:plan': 3, 'ARG:plan': 13, 'GLU:plan': 7, 'GLN:plan1': 6, 'PHE:plan': 4, 'ASP:plan': 4, 'ASN:plan1': 1, 'HIS:plan': 1} 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: {'ARG:plan': 11, 'ASP:plan': 3, 'ASN:plan1': 2, 'GLN:plan1': 2, 'TYR:plan': 4, 'GLU:plan': 4, 'PHE:plan': 2, 'HIS:plan': 1} 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: {'ARG:plan': 10, 'GLN:plan1': 4, 'PHE:plan': 1, 'HIS:plan': 2, 'ASN:plan1': 6, 'TYR:plan': 3, 'GLU:plan': 6, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 151 Chain: "D" Number of atoms: 460 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 460 Classifications: {'peptide': 93} Incomplete info: {'truncation_to_alanine': 80} Link IDs: {'PTRANS': 2, 'TRANS': 90} Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 277 Unresolved non-hydrogen angles: 350 Unresolved non-hydrogen dihedrals: 231 Unresolved non-hydrogen chiralities: 27 Planarities with less than four sites: {'ARG:plan': 6, 'GLU:plan': 6, 'TYR:plan': 5, 'GLN:plan1': 2, 'HIS:plan': 3, 'ASP:plan': 2, 'ASN:plan1': 3, 'PHE:plan': 2} Unresolved non-hydrogen planarities: 139 Chain: "E" Number of atoms: 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: {'HIS:plan': 2, 'ARG:plan': 13, 'TYR:plan': 3, 'GLU:plan': 7, 'GLN:plan1': 6, 'PHE:plan': 4, 'ASP:plan': 4, 'ASN:plan1': 1} 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: {'ARG:plan': 12, 'ASP:plan': 3, 'ASN:plan1': 2, 'GLN:plan1': 2, 'TYR:plan': 4, 'GLU:plan': 4, 'PHE:plan': 2, 'HIS:plan': 1} 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: {'ARG:plan': 10, 'GLN:plan1': 4, 'PHE:plan': 1, 'HIS:plan': 2, 'ASN:plan1': 6, 'TYR:plan': 3, 'GLU:plan': 6, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 151 Chain: "H" Number of atoms: 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: {'ARG:plan': 6, 'GLU:plan': 6, 'TYR:plan': 5, 'GLN:plan1': 2, 'HIS:plan': 3, 'ASP:plan': 2, 'ASN:plan1': 3, 'PHE:plan': 2} Unresolved non-hydrogen planarities: 139 Chain: "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: {'ASN:plan1': 12, 'ASP:plan': 21, 'GLU:plan': 26, 'PHE:plan': 14, 'GLN:plan1': 12, 'HIS:plan': 9, 'TYR:plan': 12, 'ARG:plan': 18, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 563 Time building chain proxies: 2.77, per 1000 atoms: 0.27 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: 1.11 Conformation dependent library (CDL) restraints added in 329.3 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 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: 1.80 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: 2.21 Time building geometry restraints manager: 1.44 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: 21.270 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.040 Construct map_model_manager: 0.000 Extract box with map and model: 1.070 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 12.680 Find NCS groups from input model: 0.080 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.400 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.640 ------------------------------------------------------------------------------- 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.01 (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 TYR 0.000 0.000 TYR A 41 PHE 0.000 0.000 PHE A 67 TRP 0.000 0.000 TRP L 325 Details of bonding type rmsd covalent geometry : bond 0.00514 (10985) covalent geometry : angle 0.66149 (16136) hydrogen bonds : bond 0.12123 ( 857) hydrogen bonds : angle 4.39653 ( 2219) *********************** 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 : 0.404 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 16 average time/residue: 0.0479 time to fit residues: 1.8227 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 : 0.300 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 108 optimal weight: 0.6980 chunk 49 optimal weight: 9.9990 chunk 97 optimal weight: 50.0000 chunk 113 optimal weight: 50.0000 chunk 53 optimal weight: 20.0000 chunk 5 optimal weight: 10.0000 chunk 33 optimal weight: 0.7980 chunk 123 optimal weight: 50.0000 chunk 65 optimal weight: 2.9990 chunk 62 optimal weight: 5.9990 chunk 51 optimal weight: 3.9990 overall best weight: 2.8986 ------------------------------------------------------------------------------- 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 = 0.3083 r_free = 0.3083 target = 0.041175 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.2507 r_free = 0.2507 target = 0.024265 restraints weight = 148075.106| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 57)----------------| | r_work = 0.2525 r_free = 0.2525 target = 0.024748 restraints weight = 94597.468| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.2537 r_free = 0.2537 target = 0.025081 restraints weight = 69728.250| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.2544 r_free = 0.2544 target = 0.025308 restraints weight = 56832.546| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.2549 r_free = 0.2549 target = 0.025428 restraints weight = 49840.778| |-----------------------------------------------------------------------------| r_work (final): 0.2509 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8914 moved from start: 0.0998 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 10985 Z= 0.165 Angle : 0.503 6.551 16136 Z= 0.321 Chirality : 0.036 0.152 1992 Planarity : 0.002 0.011 1307 Dihedral : 30.564 142.263 3739 Min Nonbonded Distance : 2.051 Molprobity Statistics. All-atom Clashscore : 8.27 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 3.21 (0.27), residues: 1048 helix: 2.84 (0.19), residues: 731 sheet: 2.33 (0.89), residues: 29 loop : 0.19 (0.37), residues: 288 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.000 0.000 TYR A 41 PHE 0.000 0.000 PHE A 67 TRP 0.000 0.000 TRP L 325 Details of bonding type rmsd covalent geometry : bond 0.00330 (10985) covalent geometry : angle 0.50350 (16136) hydrogen bonds : bond 0.04001 ( 857) hydrogen bonds : angle 2.97036 ( 2219) *********************** 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 : 0.251 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 16 average time/residue: 0.0412 time to fit residues: 1.5314 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 : 0.284 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 69 optimal weight: 20.0000 chunk 94 optimal weight: 10.0000 chunk 7 optimal weight: 3.9990 chunk 113 optimal weight: 7.9990 chunk 111 optimal weight: 50.0000 chunk 6 optimal weight: 20.0000 chunk 47 optimal weight: 30.0000 chunk 23 optimal weight: 40.0000 chunk 124 optimal weight: 40.0000 chunk 12 optimal weight: 8.9990 chunk 31 optimal weight: 20.0000 overall best weight: 10.1994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2940 r_free = 0.2940 target = 0.037367 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.2366 r_free = 0.2366 target = 0.020760 restraints weight = 161894.198| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.2390 r_free = 0.2390 target = 0.021305 restraints weight = 92190.938| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 54)----------------| | r_work = 0.2406 r_free = 0.2406 target = 0.021704 restraints weight = 63724.959| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 51)----------------| | r_work = 0.2417 r_free = 0.2417 target = 0.021976 restraints weight = 49299.310| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.2424 r_free = 0.2424 target = 0.022141 restraints weight = 41375.030| |-----------------------------------------------------------------------------| r_work (final): 0.2451 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7967 moved from start: 0.2819 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.056 10985 Z= 0.405 Angle : 0.659 8.007 16136 Z= 0.421 Chirality : 0.042 0.165 1992 Planarity : 0.003 0.014 1307 Dihedral : 31.570 146.286 3739 Min Nonbonded Distance : 1.886 Molprobity Statistics. All-atom Clashscore : 20.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.10 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.36 (0.26), residues: 1048 helix: 2.18 (0.19), residues: 736 sheet: 1.89 (0.96), residues: 23 loop : -0.02 (0.39), residues: 289 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.000 0.000 TYR A 41 PHE 0.000 0.000 PHE A 67 TRP 0.000 0.000 TRP L 325 Details of bonding type rmsd covalent geometry : bond 0.00815 (10985) covalent geometry : angle 0.65857 (16136) hydrogen bonds : bond 0.08733 ( 857) hydrogen bonds : angle 4.19971 ( 2219) *********************** 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 : 0.276 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 16 average time/residue: 0.0484 time to fit residues: 1.7735 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 : 0.291 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 3 optimal weight: 7.9990 chunk 98 optimal weight: 9.9990 chunk 102 optimal weight: 40.0000 chunk 23 optimal weight: 30.0000 chunk 61 optimal weight: 40.0000 chunk 35 optimal weight: 0.9980 chunk 77 optimal weight: 7.9990 chunk 42 optimal weight: 0.9980 chunk 50 optimal weight: 0.9990 chunk 76 optimal weight: 6.9990 chunk 89 optimal weight: 8.9990 overall best weight: 3.5986 ------------------------------------------------------------------------------- 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 = 0.3037 r_free = 0.3037 target = 0.039567 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.2463 r_free = 0.2463 target = 0.023121 restraints weight = 152783.585| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.2480 r_free = 0.2480 target = 0.023574 restraints weight = 97747.543| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.2492 r_free = 0.2492 target = 0.023878 restraints weight = 72336.838| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 45)----------------| | r_work = 0.2500 r_free = 0.2500 target = 0.024083 restraints weight = 59296.214| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.2504 r_free = 0.2504 target = 0.024186 restraints weight = 52011.617| |-----------------------------------------------------------------------------| r_work (final): 0.2454 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8961 moved from start: 0.2529 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.024 10985 Z= 0.188 Angle : 0.526 7.092 16136 Z= 0.332 Chirality : 0.036 0.123 1992 Planarity : 0.002 0.012 1307 Dihedral : 31.010 143.332 3739 Min Nonbonded Distance : 1.989 Molprobity Statistics. All-atom Clashscore : 10.45 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 3.56 (0.27), residues: 1048 helix: 3.21 (0.19), residues: 737 sheet: 1.34 (0.94), residues: 29 loop : 0.06 (0.40), residues: 282 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.000 0.000 TYR A 41 PHE 0.000 0.000 PHE A 67 TRP 0.000 0.000 TRP L 325 Details of bonding type rmsd covalent geometry : bond 0.00376 (10985) covalent geometry : angle 0.52644 (16136) hydrogen bonds : bond 0.04937 ( 857) hydrogen bonds : angle 3.08126 ( 2219) *********************** 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 : 0.267 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 16 average time/residue: 0.0409 time to fit residues: 1.4892 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 : 0.244 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 11 optimal weight: 30.0000 chunk 67 optimal weight: 20.0000 chunk 29 optimal weight: 30.0000 chunk 115 optimal weight: 50.0000 chunk 126 optimal weight: 20.0000 chunk 101 optimal weight: 8.9990 chunk 2 optimal weight: 30.0000 chunk 35 optimal weight: 3.9990 chunk 104 optimal weight: 10.0000 chunk 38 optimal weight: 30.0000 chunk 98 optimal weight: 30.0000 overall best weight: 12.5996 ------------------------------------------------------------------------------- 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 = 0.2905 r_free = 0.2905 target = 0.036238 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.2337 r_free = 0.2337 target = 0.020128 restraints weight = 165659.221| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.2360 r_free = 0.2360 target = 0.020651 restraints weight = 94361.837| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 52)----------------| | r_work = 0.2375 r_free = 0.2375 target = 0.021018 restraints weight = 65097.355| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 49)----------------| | r_work = 0.2385 r_free = 0.2385 target = 0.021267 restraints weight = 50574.634| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.2391 r_free = 0.2391 target = 0.021418 restraints weight = 42785.530| |-----------------------------------------------------------------------------| r_work (final): 0.2378 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9084 moved from start: 0.4126 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.070 10985 Z= 0.505 Angle : 0.733 7.195 16136 Z= 0.471 Chirality : 0.046 0.192 1992 Planarity : 0.004 0.014 1307 Dihedral : 32.089 145.071 3739 Min Nonbonded Distance : 1.861 Molprobity Statistics. All-atom Clashscore : 26.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.01 % Favored : 95.99 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.10 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.70 (0.26), residues: 1048 helix: 1.74 (0.18), residues: 735 sheet: 2.46 (1.32), residues: 14 loop : -0.42 (0.38), residues: 299 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.000 0.000 TYR A 41 PHE 0.000 0.000 PHE A 67 TRP 0.000 0.000 TRP L 325 Details of bonding type rmsd covalent geometry : bond 0.01010 (10985) covalent geometry : angle 0.73315 (16136) hydrogen bonds : bond 0.10785 ( 857) hydrogen bonds : angle 4.78600 ( 2219) *********************** 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 : 0.237 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 16 average time/residue: 0.0513 time to fit residues: 1.8474 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 : 0.283 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 86 optimal weight: 4.9990 chunk 80 optimal weight: 7.9990 chunk 94 optimal weight: 10.0000 chunk 46 optimal weight: 8.9990 chunk 121 optimal weight: 50.0000 chunk 40 optimal weight: 3.9990 chunk 63 optimal weight: 0.9990 chunk 25 optimal weight: 0.6980 chunk 33 optimal weight: 20.0000 chunk 112 optimal weight: 50.0000 chunk 118 optimal weight: 50.0000 overall best weight: 3.7388 ------------------------------------------------------------------------------- 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 = 0.3013 r_free = 0.3013 target = 0.038803 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.2448 r_free = 0.2448 target = 0.022699 restraints weight = 155483.244| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 56)----------------| | r_work = 0.2465 r_free = 0.2465 target = 0.023149 restraints weight = 96505.644| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.2477 r_free = 0.2477 target = 0.023434 restraints weight = 70367.677| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.2485 r_free = 0.2485 target = 0.023657 restraints weight = 57480.593| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.2489 r_free = 0.2489 target = 0.023764 restraints weight = 50319.581| |-----------------------------------------------------------------------------| r_work (final): 0.2437 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8948 moved from start: 0.3638 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= 0.193 Angle : 0.546 5.640 16136 Z= 0.343 Chirality : 0.036 0.128 1992 Planarity : 0.002 0.013 1307 Dihedral : 31.441 142.737 3739 Min Nonbonded Distance : 1.979 Molprobity Statistics. All-atom Clashscore : 10.77 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 3.33 (0.27), residues: 1048 helix: 3.12 (0.19), residues: 738 sheet: 0.25 (0.92), residues: 29 loop : -0.19 (0.40), residues: 281 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.000 0.000 TYR A 41 PHE 0.000 0.000 PHE A 67 TRP 0.000 0.000 TRP L 325 Details of bonding type rmsd covalent geometry : bond 0.00383 (10985) covalent geometry : angle 0.54565 (16136) hydrogen bonds : bond 0.05041 ( 857) hydrogen bonds : angle 3.27982 ( 2219) *********************** 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 : 0.230 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 16 average time/residue: 0.0453 time to fit residues: 1.7595 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 : 0.220 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 124 optimal weight: 0.0070 chunk 14 optimal weight: 20.0000 chunk 103 optimal weight: 50.0000 chunk 28 optimal weight: 0.7980 chunk 44 optimal weight: 30.0000 chunk 71 optimal weight: 20.0000 chunk 3 optimal weight: 0.7980 chunk 6 optimal weight: 20.0000 chunk 4 optimal weight: 30.0000 chunk 1 optimal weight: 20.0000 chunk 10 optimal weight: 10.0000 overall best weight: 6.3206 ------------------------------------------------------------------------------- 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 = 0.2993 r_free = 0.2993 target = 0.038159 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.2419 r_free = 0.2419 target = 0.022177 restraints weight = 154991.361| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 58)----------------| | r_work = 0.2436 r_free = 0.2436 target = 0.022608 restraints weight = 97398.081| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.2448 r_free = 0.2448 target = 0.022902 restraints weight = 71654.051| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.2455 r_free = 0.2455 target = 0.023062 restraints weight = 58469.588| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 47)----------------| | r_work = 0.2459 r_free = 0.2459 target = 0.023202 restraints weight = 51812.289| |-----------------------------------------------------------------------------| r_work (final): 0.2413 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8964 moved from start: 0.4005 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.035 10985 Z= 0.265 Angle : 0.563 5.193 16136 Z= 0.357 Chirality : 0.037 0.130 1992 Planarity : 0.002 0.012 1307 Dihedral : 31.485 142.318 3739 Min Nonbonded Distance : 1.944 Molprobity Statistics. All-atom Clashscore : 14.10 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 3.23 (0.27), residues: 1048 helix: 3.07 (0.19), residues: 742 sheet: 0.11 (1.00), residues: 24 loop : -0.33 (0.40), residues: 282 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.000 0.000 TYR A 41 PHE 0.000 0.000 PHE A 67 TRP 0.000 0.000 TRP L 325 Details of bonding type rmsd covalent geometry : bond 0.00530 (10985) covalent geometry : angle 0.56283 (16136) hydrogen bonds : bond 0.05964 ( 857) hydrogen bonds : angle 3.52298 ( 2219) *********************** 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 : 0.309 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 16 average time/residue: 0.0493 time to fit residues: 1.8364 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 : 0.286 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 111 optimal weight: 50.0000 chunk 23 optimal weight: 40.0000 chunk 68 optimal weight: 40.0000 chunk 35 optimal weight: 30.0000 chunk 37 optimal weight: 7.9990 chunk 80 optimal weight: 10.0000 chunk 88 optimal weight: 10.0000 chunk 107 optimal weight: 60.0000 chunk 94 optimal weight: 10.0000 chunk 9 optimal weight: 20.0000 chunk 96 optimal weight: 7.9990 overall best weight: 9.1996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2954 r_free = 0.2954 target = 0.037009 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.2373 r_free = 0.2373 target = 0.021261 restraints weight = 157627.554| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.2390 r_free = 0.2390 target = 0.021652 restraints weight = 102418.314| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.2401 r_free = 0.2401 target = 0.021910 restraints weight = 76811.996| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.2407 r_free = 0.2407 target = 0.022055 restraints weight = 63483.144| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 46)----------------| | r_work = 0.2412 r_free = 0.2412 target = 0.022179 restraints weight = 56628.152| |-----------------------------------------------------------------------------| r_work (final): 0.2375 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9012 moved from start: 0.4854 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.051 10985 Z= 0.367 Angle : 0.647 6.198 16136 Z= 0.412 Chirality : 0.040 0.163 1992 Planarity : 0.003 0.013 1307 Dihedral : 31.935 143.828 3739 Min Nonbonded Distance : 1.905 Molprobity Statistics. All-atom Clashscore : 19.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.29 % Favored : 95.71 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.10 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.33 (0.26), residues: 1048 helix: 2.38 (0.18), residues: 740 sheet: -0.40 (1.15), residues: 20 loop : -0.57 (0.39), residues: 288 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.000 0.000 TYR A 41 PHE 0.000 0.000 PHE A 67 TRP 0.000 0.000 TRP L 325 Details of bonding type rmsd covalent geometry : bond 0.00738 (10985) covalent geometry : angle 0.64727 (16136) hydrogen bonds : bond 0.08535 ( 857) hydrogen bonds : angle 4.30154 ( 2219) *********************** 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 : 0.204 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 16 average time/residue: 0.0460 time to fit residues: 1.7248 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 : 0.287 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 51 optimal weight: 30.0000 chunk 30 optimal weight: 10.0000 chunk 11 optimal weight: 0.0030 chunk 31 optimal weight: 0.9980 chunk 28 optimal weight: 20.0000 chunk 101 optimal weight: 50.0000 chunk 103 optimal weight: 50.0000 chunk 44 optimal weight: 8.9990 chunk 65 optimal weight: 5.9990 chunk 95 optimal weight: 5.9990 chunk 21 optimal weight: 5.9990 overall best weight: 3.7996 ------------------------------------------------------------------------------- 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 = 0.3004 r_free = 0.3004 target = 0.038586 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.2444 r_free = 0.2444 target = 0.022713 restraints weight = 153800.960| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.2462 r_free = 0.2462 target = 0.023166 restraints weight = 96062.602| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.2474 r_free = 0.2474 target = 0.023478 restraints weight = 70292.293| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.2481 r_free = 0.2481 target = 0.023646 restraints weight = 56953.058| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 49)----------------| | r_work = 0.2486 r_free = 0.2486 target = 0.023784 restraints weight = 50244.937| |-----------------------------------------------------------------------------| r_work (final): 0.2438 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8932 moved from start: 0.4603 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.025 10985 Z= 0.188 Angle : 0.541 4.713 16136 Z= 0.340 Chirality : 0.036 0.122 1992 Planarity : 0.002 0.011 1307 Dihedral : 31.433 142.741 3739 Min Nonbonded Distance : 1.979 Molprobity Statistics. All-atom Clashscore : 11.60 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 3.48 (0.27), residues: 1048 helix: 3.38 (0.19), residues: 739 sheet: -0.71 (0.99), residues: 24 loop : -0.49 (0.39), residues: 285 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.000 0.000 TYR A 41 PHE 0.000 0.000 PHE A 67 TRP 0.000 0.000 TRP L 325 Details of bonding type rmsd covalent geometry : bond 0.00373 (10985) covalent geometry : angle 0.54111 (16136) hydrogen bonds : bond 0.04956 ( 857) hydrogen bonds : angle 3.26436 ( 2219) *********************** 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 : 0.339 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 16 average time/residue: 0.0420 time to fit residues: 1.5953 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 : 0.289 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 45 optimal weight: 0.5980 chunk 17 optimal weight: 30.0000 chunk 98 optimal weight: 10.0000 chunk 15 optimal weight: 20.0000 chunk 63 optimal weight: 1.9990 chunk 64 optimal weight: 8.9990 chunk 71 optimal weight: 30.0000 chunk 93 optimal weight: 10.0000 chunk 124 optimal weight: 20.0000 chunk 82 optimal weight: 20.0000 chunk 87 optimal weight: 10.0000 overall best weight: 6.3192 ------------------------------------------------------------------------------- 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 = 0.2985 r_free = 0.2985 target = 0.037956 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.2423 r_free = 0.2423 target = 0.022200 restraints weight = 155698.064| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 56)----------------| | r_work = 0.2440 r_free = 0.2440 target = 0.022635 restraints weight = 97815.024| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.2452 r_free = 0.2452 target = 0.022910 restraints weight = 71726.732| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 51)----------------| | r_work = 0.2459 r_free = 0.2459 target = 0.023104 restraints weight = 58827.652| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.2463 r_free = 0.2463 target = 0.023210 restraints weight = 51856.684| |-----------------------------------------------------------------------------| r_work (final): 0.2416 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8963 moved from start: 0.4704 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 10985 Z= 0.269 Angle : 0.561 5.177 16136 Z= 0.357 Chirality : 0.037 0.123 1992 Planarity : 0.002 0.012 1307 Dihedral : 31.419 142.112 3739 Min Nonbonded Distance : 1.946 Molprobity Statistics. All-atom Clashscore : 14.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.82 % Favored : 96.18 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.10 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 3.26 (0.27), residues: 1048 helix: 3.23 (0.19), residues: 737 sheet: -0.86 (0.99), residues: 24 loop : -0.58 (0.39), residues: 287 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.000 0.000 TYR A 41 PHE 0.000 0.000 PHE A 67 TRP 0.000 0.000 TRP L 325 Details of bonding type rmsd covalent geometry : bond 0.00543 (10985) covalent geometry : angle 0.56111 (16136) hydrogen bonds : bond 0.06508 ( 857) hydrogen bonds : angle 3.50349 ( 2219) ********************** 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 : 0.222 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 16 average time/residue: 0.0476 time to fit residues: 1.7611 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 : 0.221 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 6 optimal weight: 20.0000 chunk 5 optimal weight: 5.9990 chunk 105 optimal weight: 8.9990 chunk 35 optimal weight: 0.9990 chunk 37 optimal weight: 6.9990 chunk 103 optimal weight: 50.0000 chunk 10 optimal weight: 20.0000 chunk 95 optimal weight: 5.9990 chunk 17 optimal weight: 20.0000 chunk 87 optimal weight: 10.0000 chunk 110 optimal weight: 30.0000 overall best weight: 5.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2990 r_free = 0.2990 target = 0.038116 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.2428 r_free = 0.2428 target = 0.022345 restraints weight = 154444.033| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 58)----------------| | r_work = 0.2446 r_free = 0.2446 target = 0.022788 restraints weight = 96726.711| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 51)----------------| | r_work = 0.2457 r_free = 0.2457 target = 0.023082 restraints weight = 70894.551| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.2465 r_free = 0.2465 target = 0.023245 restraints weight = 57894.438| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.2469 r_free = 0.2469 target = 0.023373 restraints weight = 51172.325| |-----------------------------------------------------------------------------| r_work (final): 0.2422 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8952 moved from start: 0.4773 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= 0.242 Angle : 0.554 4.915 16136 Z= 0.351 Chirality : 0.037 0.121 1992 Planarity : 0.002 0.012 1307 Dihedral : 31.458 142.116 3739 Min Nonbonded Distance : 1.954 Molprobity Statistics. All-atom Clashscore : 12.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.63 % Favored : 96.37 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.10 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 3.36 (0.27), residues: 1048 helix: 3.31 (0.19), residues: 739 sheet: -0.93 (0.98), residues: 24 loop : -0.57 (0.39), residues: 285 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.000 0.000 TYR A 41 PHE 0.000 0.000 PHE A 67 TRP 0.000 0.000 TRP L 325 Details of bonding type rmsd covalent geometry : bond 0.00482 (10985) covalent geometry : angle 0.55381 (16136) hydrogen bonds : bond 0.05506 ( 857) hydrogen bonds : angle 3.44992 ( 2219) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4979.19 seconds wall clock time: 84 minutes 57.40 seconds (5097.40 seconds total)