Starting phenix.real_space_refine on Fri Jul 3 19:55:52 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7x3w_32995/07_2026/7x3w_32995.cif Found real_map, /net/cci-nas-00/data/ceres_data/7x3w_32995/07_2026/7x3w_32995.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7x3w_32995/07_2026/7x3w_32995.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7x3w_32995/07_2026/7x3w_32995.map" restraint_files = "/net/cci-nas-00/data/ceres_data/7x3w_32995/07_2026/7x3w_32995.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7x3w_32995/07_2026/7x3w_32995.cif" model { file = "/net/cci-nas-00/data/ceres_data/7x3w_32995/07_2026/7x3w_32995.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7x3w_32995/07_2026/7x3w_32995.cif" } resolution = 3.1 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= 0.001 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs 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: 8 Type Number sf(0) Gaussians P 294 5.49 5 Mg 1 5.21 5 S 25 5.16 5 Be 1 3.05 5 C 9257 2.51 5 N 2959 2.21 5 O 3594 1.98 5 F 3 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 43 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 16134 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 801 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 801 Classifications: {'peptide': 98} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 4, 'TRANS': 93} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "B" Number of atoms: 707 Number of conformers: 1 Conformer: "" Number of residues, atoms: 88, 707 Classifications: {'peptide': 88} Link IDs: {'PTRANS': 1, 'TRANS': 86} Chain: "C" Number of atoms: 811 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 811 Classifications: {'peptide': 107} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 5, 'TRANS': 101} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 12 Chain: "D" Number of atoms: 717 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 717 Classifications: {'peptide': 93} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 2, 'TRANS': 90} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 8 Chain: "E" Number of atoms: 779 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 779 Classifications: {'peptide': 95} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 3, 'TRANS': 91} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "F" Number of atoms: 632 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 632 Classifications: {'peptide': 80} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 1, 'TRANS': 78} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "G" Number of atoms: 815 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 815 Classifications: {'peptide': 107} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 5, 'TRANS': 101} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 8 Chain: "H" Number of atoms: 725 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 725 Classifications: {'peptide': 93} Link IDs: {'PTRANS': 2, 'TRANS': 90} Chain: "I" Number of atoms: 2978 Number of conformers: 1 Conformer: "" Number of residues, atoms: 146, 2978 Classifications: {'DNA': 146} Link IDs: {'rna3p': 145} Chain: "J" Number of atoms: 3008 Number of conformers: 1 Conformer: "" Number of residues, atoms: 146, 3008 Classifications: {'DNA': 146} Link IDs: {'rna3p': 145} Chain: "K" Number of atoms: 4129 Number of conformers: 1 Conformer: "" Number of residues, atoms: 504, 4129 Classifications: {'peptide': 504} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 18, 'TRANS': 485} Chain breaks: 3 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "K" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Unusual residues: {' MG': 1, 'ADP': 1, 'BEF': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Time building chain proxies: 3.57, per 1000 atoms: 0.22 Number of scatterers: 16134 At special positions: 0 Unit cell: (109.332, 127.735, 150.467, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 8 Type Number sf(0) S 25 16.00 P 294 15.00 Mg 1 11.99 F 3 9.00 O 3594 8.00 N 2959 7.00 C 9257 6.00 Be 1 4.00 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=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 1.43 Conformation dependent library (CDL) restraints added in 557.9 milliseconds 2482 Ramachandran restraints generated. 1241 Oldfield, 0 Emsley, 1241 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2392 Finding SS restraints... Secondary structure from input PDB file: 60 helices and 11 sheets defined 66.2% alpha, 4.6% beta 144 base pairs and 259 stacking pairs defined. Time for finding SS restraints: 2.38 Creating SS restraints... Processing helix chain 'A' and resid 44 through 57 Processing helix chain 'A' and resid 63 through 76 Processing helix chain 'A' and resid 85 through 114 Processing helix chain 'A' and resid 120 through 132 Processing helix chain 'B' and resid 24 through 29 Processing helix chain 'B' and resid 30 through 42 Processing helix chain 'B' and resid 49 through 76 removed outlier: 3.568A pdb=" N GLU B 53 " --> pdb=" O LEU B 49 " (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 36 Processing helix chain 'C' and resid 46 through 73 Processing helix chain 'C' and resid 79 through 90 Processing helix chain 'C' and resid 90 through 97 Processing helix chain 'C' and resid 112 through 116 Processing helix chain 'D' and resid 34 through 46 Processing helix chain 'D' and resid 52 through 81 Processing helix chain 'D' and resid 87 through 99 Processing helix chain 'D' and resid 101 through 121 removed outlier: 3.819A pdb=" N LYS D 105 " --> pdb=" O GLY D 101 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N HIS D 106 " --> pdb=" O GLU D 102 " (cutoff:3.500A) Processing helix chain 'E' and resid 45 through 57 Processing helix chain 'E' and resid 63 through 76 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 Processing helix chain 'F' and resid 30 through 42 Processing helix chain 'F' and resid 49 through 76 removed outlier: 3.672A pdb=" N GLU F 53 " --> pdb=" O LEU F 49 " (cutoff:3.500A) Processing helix chain 'F' and resid 82 through 94 removed outlier: 3.505A pdb=" N VAL F 86 " --> pdb=" O THR F 82 " (cutoff:3.500A) Processing helix chain 'G' and resid 16 through 22 Processing helix chain 'G' and resid 26 through 37 Processing helix chain 'G' and resid 46 through 73 Processing helix chain 'G' and resid 79 through 90 Processing helix chain 'G' and resid 90 through 97 Processing helix chain 'H' and resid 34 through 46 Processing helix chain 'H' and resid 52 through 81 removed outlier: 3.541A pdb=" N MET H 56 " --> pdb=" O SER H 52 " (cutoff:3.500A) Processing helix chain 'H' and resid 87 through 99 Processing helix chain 'H' and resid 101 through 121 Processing helix chain 'K' and resid 102 through 113 removed outlier: 3.687A pdb=" N HIS K 111 " --> pdb=" O LYS K 107 " (cutoff:3.500A) Processing helix chain 'K' and resid 117 through 125 Processing helix chain 'K' and resid 132 through 143 removed outlier: 3.671A pdb=" N VAL K 136 " --> pdb=" O LYS K 132 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N VAL K 139 " --> pdb=" O GLN K 135 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N LEU K 140 " --> pdb=" O VAL K 136 " (cutoff:3.500A) Processing helix chain 'K' and resid 197 through 214 Processing helix chain 'K' and resid 226 through 241 Processing helix chain 'K' and resid 253 through 255 No H-bonds generated for 'chain 'K' and resid 253 through 255' Processing helix chain 'K' and resid 256 through 268 removed outlier: 3.655A pdb=" N TRP K 260 " --> pdb=" O THR K 256 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N LEU K 261 " --> pdb=" O LEU K 257 " (cutoff:3.500A) Processing helix chain 'K' and resid 279 through 294 removed outlier: 3.568A pdb=" N LEU K 286 " --> pdb=" O GLU K 282 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N LEU K 291 " --> pdb=" O ILE K 287 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N LEU K 292 " --> pdb=" O GLN K 288 " (cutoff:3.500A) Processing helix chain 'K' and resid 302 through 309 removed outlier: 3.828A pdb=" N ILE K 306 " --> pdb=" O SER K 302 " (cutoff:3.500A) removed outlier: 4.213A pdb=" N ILE K 307 " --> pdb=" O TYR K 303 " (cutoff:3.500A) Processing helix chain 'K' and resid 309 through 315 removed outlier: 3.754A pdb=" N LYS K 315 " --> pdb=" O SER K 311 " (cutoff:3.500A) Processing helix chain 'K' and resid 327 through 331 removed outlier: 3.571A pdb=" N LYS K 330 " --> pdb=" O HIS K 327 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N ASN K 331 " --> pdb=" O ARG K 328 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 327 through 331' Processing helix chain 'K' and resid 334 through 341 Processing helix chain 'K' and resid 359 through 368 Processing helix chain 'K' and resid 371 through 376 Processing helix chain 'K' and resid 379 through 390 removed outlier: 3.602A pdb=" N PHE K 385 " --> pdb=" O PHE K 381 " (cutoff:3.500A) removed outlier: 6.369A pdb=" N SER K 387 " --> pdb=" O ASP K 383 " (cutoff:3.500A) removed outlier: 8.375A pdb=" N GLU K 388 " --> pdb=" O TRP K 384 " (cutoff:3.500A) removed outlier: 4.311A pdb=" N SER K 389 " --> pdb=" O PHE K 385 " (cutoff:3.500A) Processing helix chain 'K' and resid 397 through 406 removed outlier: 3.895A pdb=" N LEU K 401 " --> pdb=" O ILE K 397 " (cutoff:3.500A) Processing helix chain 'K' and resid 434 through 446 removed outlier: 4.117A pdb=" N LYS K 439 " --> pdb=" O SER K 435 " (cutoff:3.500A) removed outlier: 4.170A pdb=" N TRP K 440 " --> pdb=" O MET K 436 " (cutoff:3.500A) Processing helix chain 'K' and resid 467 through 478 Processing helix chain 'K' and resid 479 through 483 removed outlier: 3.519A pdb=" N PHE K 482 " --> pdb=" O PRO K 479 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N ASP K 483 " --> pdb=" O TYR K 480 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 479 through 483' Processing helix chain 'K' and resid 494 through 501 removed outlier: 4.316A pdb=" N VAL K 498 " --> pdb=" O ASP K 494 " (cutoff:3.500A) Processing helix chain 'K' and resid 501 through 518 removed outlier: 4.052A pdb=" N GLN K 505 " --> pdb=" O ALA K 501 " (cutoff:3.500A) removed outlier: 4.463A pdb=" N VAL K 506 " --> pdb=" O ALA K 502 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N GLU K 516 " --> pdb=" O LYS K 512 " (cutoff:3.500A) Processing helix chain 'K' and resid 527 through 542 Processing helix chain 'K' and resid 554 through 566 removed outlier: 3.799A pdb=" N ILE K 558 " --> pdb=" O HIS K 554 " (cutoff:3.500A) Processing helix chain 'K' and resid 601 through 610 Processing helix chain 'K' and resid 631 through 657 removed outlier: 4.081A pdb=" N LYS K 635 " --> pdb=" O SER K 631 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N ASP K 647 " --> pdb=" O LYS K 643 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N LEU K 649 " --> pdb=" O ARG K 645 " (cutoff:3.500A) removed outlier: 5.380A pdb=" N VAL K 650 " --> pdb=" O LEU K 646 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N ARG K 655 " --> pdb=" O ILE K 651 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N THR K 656 " --> pdb=" O GLN K 652 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 118 through 119 Processing sheet with id=AA2, first strand: chain 'B' and resid 96 through 98 removed outlier: 6.644A 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: 7.211A pdb=" N ARG C 42 " --> pdb=" O ILE D 86 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'C' and resid 77 through 78 Processing sheet with id=AA5, first strand: chain 'C' and resid 100 through 102 removed outlier: 6.568A pdb=" N THR C 101 " --> pdb=" O TYR F 98 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'E' and resid 118 through 119 Processing sheet with id=AA7, first strand: chain 'G' and resid 42 through 43 removed outlier: 7.311A pdb=" N ARG G 42 " --> pdb=" O ILE H 86 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'G' and resid 77 through 78 Processing sheet with id=AA9, first strand: chain 'K' and resid 218 through 219 Processing sheet with id=AB1, first strand: chain 'K' and resid 273 through 275 removed outlier: 5.802A pdb=" N PHE K 274 " --> pdb=" O ILE K 300 " (cutoff:3.500A) removed outlier: 6.591A pdb=" N LEU K 249 " --> pdb=" O ILE K 322 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'K' and resid 424 through 432 removed outlier: 6.641A pdb=" N LYS K 425 " --> pdb=" O VAL K 623 " (cutoff:3.500A) removed outlier: 7.827A pdb=" N ARG K 625 " --> pdb=" O LYS K 425 " (cutoff:3.500A) removed outlier: 6.400A pdb=" N LEU K 427 " --> pdb=" O ARG K 625 " (cutoff:3.500A) removed outlier: 7.244A pdb=" N VAL K 627 " --> pdb=" O LEU K 427 " (cutoff:3.500A) removed outlier: 5.759A pdb=" N LEU K 429 " --> pdb=" O VAL K 627 " (cutoff:3.500A) removed outlier: 6.466A pdb=" N ASP K 629 " --> pdb=" O LEU K 429 " (cutoff:3.500A) removed outlier: 6.718A pdb=" N VAL K 431 " --> pdb=" O ASP K 629 " (cutoff:3.500A) removed outlier: 7.073A pdb=" N VAL K 593 " --> pdb=" O PHE K 624 " (cutoff:3.500A) removed outlier: 7.882A pdb=" N LEU K 626 " --> pdb=" O VAL K 593 " (cutoff:3.500A) removed outlier: 6.847A pdb=" N LEU K 595 " --> pdb=" O LEU K 626 " (cutoff:3.500A) removed outlier: 8.636A pdb=" N THR K 628 " --> pdb=" O LEU K 595 " (cutoff:3.500A) removed outlier: 6.246A pdb=" N LEU K 522 " --> pdb=" O VAL K 594 " (cutoff:3.500A) removed outlier: 8.298A pdb=" N LEU K 576 " --> pdb=" O VAL K 521 " (cutoff:3.500A) removed outlier: 5.954A pdb=" N ILE K 523 " --> pdb=" O LEU K 576 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 572 hydrogen bonds defined for protein. 1695 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 368 hydrogen bonds 732 hydrogen bond angles 0 basepair planarities 144 basepair parallelities 259 stacking parallelities Total time for adding SS restraints: 3.81 Time building geometry restraints manager: 1.91 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2845 1.33 - 1.45: 5316 1.45 - 1.57: 8227 1.57 - 1.69: 585 1.69 - 1.81: 46 Bond restraints: 17019 Sorted by residual: bond pdb=" F2 BEF K1202 " pdb="BE BEF K1202 " ideal model delta sigma weight residual 1.476 1.706 -0.230 2.00e-02 2.50e+03 1.33e+02 bond pdb=" F1 BEF K1202 " pdb="BE BEF K1202 " ideal model delta sigma weight residual 1.476 1.704 -0.228 2.00e-02 2.50e+03 1.30e+02 bond pdb=" F3 BEF K1202 " pdb="BE BEF K1202 " ideal model delta sigma weight residual 1.476 1.691 -0.215 2.00e-02 2.50e+03 1.15e+02 bond pdb=" C3' DT I 89 " pdb=" O3' DT I 89 " ideal model delta sigma weight residual 1.435 1.381 0.054 1.30e-02 5.92e+03 1.72e+01 bond pdb=" C3' DG J 68 " pdb=" O3' DG J 68 " ideal model delta sigma weight residual 1.435 1.383 0.052 1.30e-02 5.92e+03 1.61e+01 ... (remaining 17014 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.10: 24182 4.10 - 8.21: 64 8.21 - 12.31: 2 12.31 - 16.41: 1 16.41 - 20.51: 1 Bond angle restraints: 24250 Sorted by residual: angle pdb=" F1 BEF K1202 " pdb="BE BEF K1202 " pdb=" F3 BEF K1202 " ideal model delta sigma weight residual 120.12 99.61 20.51 3.00e+00 1.11e-01 4.68e+01 angle pdb=" F2 BEF K1202 " pdb="BE BEF K1202 " pdb=" F3 BEF K1202 " ideal model delta sigma weight residual 119.96 104.96 15.00 3.00e+00 1.11e-01 2.50e+01 angle pdb=" N3 DT I 145 " pdb=" C4 DT I 145 " pdb=" O4 DT I 145 " ideal model delta sigma weight residual 119.90 122.72 -2.82 6.00e-01 2.78e+00 2.21e+01 angle pdb=" N3 DT I 32 " pdb=" C4 DT I 32 " pdb=" O4 DT I 32 " ideal model delta sigma weight residual 119.90 122.64 -2.74 6.00e-01 2.78e+00 2.08e+01 angle pdb=" N3 DT I 15 " pdb=" C4 DT I 15 " pdb=" O4 DT I 15 " ideal model delta sigma weight residual 119.90 122.63 -2.73 6.00e-01 2.78e+00 2.06e+01 ... (remaining 24245 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 31.84: 7842 31.84 - 63.67: 1626 63.67 - 95.51: 37 95.51 - 127.34: 0 127.34 - 159.18: 4 Dihedral angle restraints: 9509 sinusoidal: 5817 harmonic: 3692 Sorted by residual: dihedral pdb=" C5' ADP K1201 " pdb=" O5' ADP K1201 " pdb=" PA ADP K1201 " pdb=" O2A ADP K1201 " ideal model delta sinusoidal sigma weight residual 300.00 160.16 139.84 1 2.00e+01 2.50e-03 4.23e+01 dihedral pdb=" O1B ADP K1201 " pdb=" O3A ADP K1201 " pdb=" PB ADP K1201 " pdb=" PA ADP K1201 " ideal model delta sinusoidal sigma weight residual -60.00 -153.84 93.84 1 2.00e+01 2.50e-03 2.56e+01 dihedral pdb=" CA ASN K 359 " pdb=" C ASN K 359 " pdb=" N LEU K 360 " pdb=" CA LEU K 360 " ideal model delta harmonic sigma weight residual 180.00 157.36 22.64 0 5.00e+00 4.00e-02 2.05e+01 ... (remaining 9506 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.041: 1640 0.041 - 0.083: 769 0.083 - 0.124: 287 0.124 - 0.166: 53 0.166 - 0.207: 4 Chirality restraints: 2753 Sorted by residual: chirality pdb=" C3' DG J 52 " pdb=" C4' DG J 52 " pdb=" O3' DG J 52 " pdb=" C2' DG J 52 " both_signs ideal model delta sigma weight residual False -2.73 -2.52 -0.21 2.00e-01 2.50e+01 1.07e+00 chirality pdb=" C3' DT J 51 " pdb=" C4' DT J 51 " pdb=" O3' DT J 51 " pdb=" C2' DT J 51 " both_signs ideal model delta sigma weight residual False -2.73 -2.55 -0.18 2.00e-01 2.50e+01 7.82e-01 chirality pdb=" C3' DA I 97 " pdb=" C4' DA I 97 " pdb=" O3' DA I 97 " pdb=" C2' DA I 97 " both_signs ideal model delta sigma weight residual False -2.73 -2.56 -0.17 2.00e-01 2.50e+01 7.55e-01 ... (remaining 2750 not shown) Planarity restraints: 2063 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR B 88 " 0.021 2.00e-02 2.50e+03 2.57e-02 1.33e+01 pdb=" CG TYR B 88 " -0.062 2.00e-02 2.50e+03 pdb=" CD1 TYR B 88 " 0.028 2.00e-02 2.50e+03 pdb=" CD2 TYR B 88 " 0.013 2.00e-02 2.50e+03 pdb=" CE1 TYR B 88 " -0.009 2.00e-02 2.50e+03 pdb=" CE2 TYR B 88 " 0.006 2.00e-02 2.50e+03 pdb=" CZ TYR B 88 " 0.003 2.00e-02 2.50e+03 pdb=" OH TYR B 88 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR D 80 " 0.026 2.00e-02 2.50e+03 1.74e-02 6.04e+00 pdb=" CG TYR D 80 " -0.039 2.00e-02 2.50e+03 pdb=" CD1 TYR D 80 " 0.001 2.00e-02 2.50e+03 pdb=" CD2 TYR D 80 " -0.002 2.00e-02 2.50e+03 pdb=" CE1 TYR D 80 " -0.002 2.00e-02 2.50e+03 pdb=" CE2 TYR D 80 " 0.001 2.00e-02 2.50e+03 pdb=" CZ TYR D 80 " 0.014 2.00e-02 2.50e+03 pdb=" OH TYR D 80 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU H 99 " -0.041 5.00e-02 4.00e+02 6.14e-02 6.03e+00 pdb=" N PRO H 100 " 0.106 5.00e-02 4.00e+02 pdb=" CA PRO H 100 " -0.032 5.00e-02 4.00e+02 pdb=" CD PRO H 100 " -0.034 5.00e-02 4.00e+02 ... (remaining 2060 not shown) Histogram of nonbonded interaction distances: 1.83 - 2.45: 58 2.45 - 3.06: 10279 3.06 - 3.67: 26095 3.67 - 4.29: 41325 4.29 - 4.90: 60540 Nonbonded interactions: 138297 Sorted by model distance: nonbonded pdb=" O3B ADP K1201 " pdb="MG MG K1203 " model vdw 1.833 2.170 nonbonded pdb=" N LYS K 227 " pdb="MG MG K1203 " model vdw 1.946 2.250 nonbonded pdb=" N THR K 228 " pdb="MG MG K1203 " model vdw 2.010 2.250 nonbonded pdb=" NZ LYS K 314 " pdb=" O GLU K 342 " model vdw 2.104 3.120 nonbonded pdb=" OG1 THR K 228 " pdb=" O3B ADP K1201 " model vdw 2.124 3.040 ... (remaining 138292 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 40 through 134) selection = chain 'E' } ncs_group { reference = (chain 'B' and ((resid 23 and (name N or name CA or name C or name O or name CB \ )) or resid 24 through 101)) selection = (chain 'F' and resid 23 through 101) } ncs_group { reference = (chain 'C' and (resid 12 through 73 or (resid 74 and (name N or name CA or name \ C or name O or name CB )) or resid 75 through 118)) selection = (chain 'G' and ((resid 12 through 14 and (name N or name CA or name C or name O \ or name CB )) or resid 15 through 35 or (resid 36 and (name N or name CA or name \ C or name O or name CB )) or resid 37 through 118)) } ncs_group { reference = chain 'D' selection = (chain 'H' and (resid 29 through 30 or (resid 31 and (name N or name CA or name \ C or name O or name CB )) or resid 32 through 53 or (resid 54 through 55 and (na \ me N or name CA or name C or name O or name CB )) or resid 56 through 121)) } 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.290 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.280 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 17.880 Find NCS groups from input model: 0.170 Set up NCS constraints: 0.030 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: 23.150 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8713 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 : 0.012 0.899 17020 Z= 1.023 Angle : 0.874 20.515 24250 Z= 0.676 Chirality : 0.053 0.207 2753 Planarity : 0.004 0.061 2063 Dihedral : 25.400 159.177 7117 Min Nonbonded Distance : 1.833 Molprobity Statistics. All-atom Clashscore : 10.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.48 % Favored : 94.52 % Rotamer: Outliers : 0.00 % Allowed : 0.19 % Favored : 99.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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 are not related in a simple way. whole: -0.00 (0.24), residues: 1241 helix: 1.11 (0.19), residues: 782 sheet: -1.75 (0.68), residues: 57 loop : -1.97 (0.30), residues: 402 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG C 32 TYR 0.062 0.003 TYR B 88 PHE 0.032 0.003 PHE G 25 TRP 0.027 0.003 TRP K 364 HIS 0.011 0.002 HIS B 18 Details of bonding type rmsd/Z covalent geometry : bond 0.00996 / 0.76 (17019) covalent geometry : angle 0.87360 / 0.68 (24250) hydrogen bonds : bond 0.09247 / 6.18 ( 940) hydrogen bonds : angle 4.18286 / 3.14 ( 2427) Misc. bond : bond 0.89903 / 47.32 ( 1) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2482 Ramachandran restraints generated. 1241 Oldfield, 0 Emsley, 1241 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2482 Ramachandran restraints generated. 1241 Oldfield, 0 Emsley, 1241 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 159 time to evaluate : 0.498 Fit side-chains revert: symmetry clash REVERT: E 56 LYS cc_start: 0.8764 (ttmt) cc_final: 0.8541 (mttt) REVERT: K 369 PHE cc_start: 0.6774 (m-80) cc_final: 0.5935 (t80) outliers start: 0 outliers final: 0 residues processed: 159 average time/residue: 0.1642 time to fit residues: 36.8879 Evaluate side-chains 138 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 138 time to evaluate : 0.488 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 98 optimal weight: 10.0000 chunk 107 optimal weight: 20.0000 chunk 10 optimal weight: 0.6980 chunk 66 optimal weight: 0.6980 chunk 130 optimal weight: 8.9990 chunk 124 optimal weight: 2.9990 chunk 103 optimal weight: 0.9980 chunk 77 optimal weight: 7.9990 chunk 122 optimal weight: 0.8980 chunk 91 optimal weight: 6.9990 chunk 149 optimal weight: 5.9990 overall best weight: 1.2582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... F 93 GLN G 110 ASN ** K 437 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 554 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3709 r_free = 0.3709 target = 0.091748 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.3039 r_free = 0.3039 target = 0.058917 restraints weight = 45512.679| |-----------------------------------------------------------------------------| r_work (start): 0.2971 rms_B_bonded: 2.03 r_work: 0.2804 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work: 0.2681 rms_B_bonded: 4.45 restraints_weight: 0.2500 r_work (final): 0.2681 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8908 moved from start: 0.0710 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 17020 Z= 0.190 Angle : 0.695 8.617 24250 Z= 0.388 Chirality : 0.049 0.277 2753 Planarity : 0.005 0.061 2063 Dihedral : 29.604 160.145 4594 Min Nonbonded Distance : 1.954 Molprobity Statistics. All-atom Clashscore : 7.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.87 % Favored : 96.13 % Rotamer: Outliers : 0.46 % Allowed : 4.54 % Favored : 95.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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 are not related in a simple way. whole: 0.26 (0.24), residues: 1241 helix: 1.31 (0.19), residues: 786 sheet: -1.46 (0.70), residues: 57 loop : -1.93 (0.30), residues: 398 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG K 411 TYR 0.023 0.002 TYR B 88 PHE 0.014 0.002 PHE K 408 TRP 0.026 0.002 TRP K 206 HIS 0.007 0.001 HIS K 554 Details of bonding type rmsd/Z covalent geometry : bond 0.00381 / 0.19 (17019) covalent geometry : angle 0.69506 / 0.39 (24250) hydrogen bonds : bond 0.05922 / 3.74 ( 940) hydrogen bonds : angle 3.62257 / 2.65 ( 2427) Misc. bond : bond 0.00882 / 0.46 ( 1) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2482 Ramachandran restraints generated. 1241 Oldfield, 0 Emsley, 1241 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2482 Ramachandran restraints generated. 1241 Oldfield, 0 Emsley, 1241 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 156 time to evaluate : 0.415 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 24 ASP cc_start: 0.8119 (t0) cc_final: 0.7903 (t0) REVERT: B 93 GLN cc_start: 0.8594 (mt0) cc_final: 0.8365 (mt0) REVERT: D 90 GLU cc_start: 0.8506 (mp0) cc_final: 0.8189 (mp0) REVERT: G 68 ASN cc_start: 0.8831 (m-40) cc_final: 0.8455 (m-40) REVERT: G 92 GLU cc_start: 0.9145 (mm-30) cc_final: 0.8921 (mp0) REVERT: G 112 GLN cc_start: 0.8855 (mm-40) cc_final: 0.8550 (mm110) REVERT: K 369 PHE cc_start: 0.6483 (m-80) cc_final: 0.5782 (t80) outliers start: 5 outliers final: 3 residues processed: 158 average time/residue: 0.1612 time to fit residues: 36.2722 Evaluate side-chains 143 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 140 time to evaluate : 0.481 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 110 ASN Chi-restraints excluded: chain E residue 124 ILE Chi-restraints excluded: chain K residue 321 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 146 optimal weight: 3.9990 chunk 95 optimal weight: 8.9990 chunk 26 optimal weight: 0.1980 chunk 143 optimal weight: 8.9990 chunk 134 optimal weight: 1.9990 chunk 8 optimal weight: 2.9990 chunk 22 optimal weight: 0.7980 chunk 56 optimal weight: 2.9990 chunk 127 optimal weight: 9.9990 chunk 1 optimal weight: 0.7980 chunk 107 optimal weight: 3.9990 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 68 GLN B 93 GLN G 110 ASN H 92 GLN K 500 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3706 r_free = 0.3706 target = 0.091488 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 74)----------------| | r_work = 0.3017 r_free = 0.3017 target = 0.057885 restraints weight = 46713.178| |-----------------------------------------------------------------------------| r_work (start): 0.2961 rms_B_bonded: 2.10 r_work: 0.2791 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work: 0.2669 rms_B_bonded: 4.61 restraints_weight: 0.2500 r_work (final): 0.2669 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8910 moved from start: 0.0969 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 17020 Z= 0.189 Angle : 0.651 7.026 24250 Z= 0.369 Chirality : 0.047 0.272 2753 Planarity : 0.005 0.049 2063 Dihedral : 29.517 159.309 4594 Min Nonbonded Distance : 1.934 Molprobity Statistics. All-atom Clashscore : 6.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.03 % Favored : 95.97 % Rotamer: Outliers : 1.02 % Allowed : 6.57 % Favored : 92.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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 are not related in a simple way. whole: 0.53 (0.24), residues: 1241 helix: 1.54 (0.19), residues: 786 sheet: -1.31 (0.71), residues: 57 loop : -1.87 (0.30), residues: 398 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 76 TYR 0.018 0.002 TYR F 51 PHE 0.014 0.002 PHE G 25 TRP 0.016 0.002 TRP K 206 HIS 0.012 0.001 HIS K 402 Details of bonding type rmsd/Z covalent geometry : bond 0.00379 / 0.19 (17019) covalent geometry : angle 0.65098 / 0.37 (24250) hydrogen bonds : bond 0.05572 / 3.57 ( 940) hydrogen bonds : angle 3.46962 / 2.52 ( 2427) Misc. bond : bond 0.00302 / 0.16 ( 1) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2482 Ramachandran restraints generated. 1241 Oldfield, 0 Emsley, 1241 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2482 Ramachandran restraints generated. 1241 Oldfield, 0 Emsley, 1241 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 147 time to evaluate : 0.492 Fit side-chains revert: symmetry clash REVERT: B 24 ASP cc_start: 0.8207 (t0) cc_final: 0.7914 (t0) REVERT: D 90 GLU cc_start: 0.8620 (mp0) cc_final: 0.8345 (mp0) REVERT: G 92 GLU cc_start: 0.9188 (mm-30) cc_final: 0.8928 (mp0) outliers start: 11 outliers final: 7 residues processed: 153 average time/residue: 0.1556 time to fit residues: 34.0721 Evaluate side-chains 144 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 137 time to evaluate : 0.448 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 LYS Chi-restraints excluded: chain A residue 68 GLN Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain C residue 110 ASN Chi-restraints excluded: chain C residue 113 SER Chi-restraints excluded: chain K residue 306 ILE Chi-restraints excluded: chain K residue 321 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 133 optimal weight: 9.9990 chunk 0 optimal weight: 5.9990 chunk 46 optimal weight: 0.6980 chunk 104 optimal weight: 0.4980 chunk 100 optimal weight: 10.0000 chunk 21 optimal weight: 1.9990 chunk 123 optimal weight: 8.9990 chunk 98 optimal weight: 10.0000 chunk 13 optimal weight: 0.6980 chunk 3 optimal weight: 0.7980 chunk 91 optimal weight: 10.0000 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 68 GLN G 68 ASN G 110 ASN K 317 ASN ** K 437 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 526 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3718 r_free = 0.3718 target = 0.092006 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 74)----------------| | r_work = 0.3035 r_free = 0.3035 target = 0.058539 restraints weight = 46144.455| |-----------------------------------------------------------------------------| r_work (start): 0.2981 rms_B_bonded: 2.09 r_work: 0.2812 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work: 0.2687 rms_B_bonded: 4.64 restraints_weight: 0.2500 r_work (final): 0.2687 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8899 moved from start: 0.1200 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 17020 Z= 0.155 Angle : 0.620 8.546 24250 Z= 0.353 Chirality : 0.045 0.274 2753 Planarity : 0.004 0.046 2063 Dihedral : 29.424 158.563 4594 Min Nonbonded Distance : 1.953 Molprobity Statistics. All-atom Clashscore : 7.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.11 % Favored : 95.89 % Rotamer: Outliers : 0.65 % Allowed : 7.31 % Favored : 92.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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 are not related in a simple way. whole: 0.84 (0.25), residues: 1241 helix: 1.77 (0.19), residues: 786 sheet: -1.11 (0.73), residues: 57 loop : -1.73 (0.31), residues: 398 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG G 71 TYR 0.014 0.001 TYR F 51 PHE 0.012 0.001 PHE A 67 TRP 0.016 0.002 TRP K 206 HIS 0.004 0.001 HIS K 402 Details of bonding type rmsd/Z covalent geometry : bond 0.00297 / 0.15 (17019) covalent geometry : angle 0.61972 / 0.35 (24250) hydrogen bonds : bond 0.05095 / 3.24 ( 940) hydrogen bonds : angle 3.31058 / 2.40 ( 2427) Misc. bond : bond 0.00084 / 0.04 ( 1) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2482 Ramachandran restraints generated. 1241 Oldfield, 0 Emsley, 1241 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2482 Ramachandran restraints generated. 1241 Oldfield, 0 Emsley, 1241 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 149 time to evaluate : 0.447 Fit side-chains revert: symmetry clash REVERT: B 24 ASP cc_start: 0.8192 (t0) cc_final: 0.7858 (t0) REVERT: C 113 SER cc_start: 0.9258 (OUTLIER) cc_final: 0.8915 (p) REVERT: D 90 GLU cc_start: 0.8617 (mp0) cc_final: 0.8335 (mp0) REVERT: G 92 GLU cc_start: 0.9157 (mm-30) cc_final: 0.8929 (mp0) REVERT: K 433 MET cc_start: 0.6686 (tmm) cc_final: 0.6346 (tmm) REVERT: K 609 MET cc_start: 0.8019 (mpp) cc_final: 0.7816 (mpp) outliers start: 7 outliers final: 4 residues processed: 151 average time/residue: 0.1521 time to fit residues: 33.1657 Evaluate side-chains 147 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 142 time to evaluate : 0.454 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain C residue 110 ASN Chi-restraints excluded: chain C residue 113 SER Chi-restraints excluded: chain E residue 76 GLN Chi-restraints excluded: chain K residue 321 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 15 optimal weight: 2.9990 chunk 142 optimal weight: 0.2980 chunk 81 optimal weight: 9.9990 chunk 91 optimal weight: 8.9990 chunk 104 optimal weight: 10.0000 chunk 105 optimal weight: 6.9990 chunk 14 optimal weight: 0.6980 chunk 95 optimal weight: 10.0000 chunk 23 optimal weight: 4.9990 chunk 130 optimal weight: 9.9990 chunk 46 optimal weight: 0.5980 overall best weight: 1.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 104 GLN G 110 ASN ** K 437 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3700 r_free = 0.3700 target = 0.091026 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 75)----------------| | r_work = 0.3007 r_free = 0.3007 target = 0.057466 restraints weight = 46326.265| |-----------------------------------------------------------------------------| r_work (start): 0.2951 rms_B_bonded: 2.10 r_work: 0.2779 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work: 0.2654 rms_B_bonded: 4.67 restraints_weight: 0.2500 r_work (final): 0.2654 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8926 moved from start: 0.1173 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 17020 Z= 0.235 Angle : 0.658 7.124 24250 Z= 0.367 Chirality : 0.047 0.265 2753 Planarity : 0.005 0.048 2063 Dihedral : 29.518 159.066 4594 Min Nonbonded Distance : 1.961 Molprobity Statistics. All-atom Clashscore : 6.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.35 % Favored : 95.65 % Rotamer: Outliers : 1.11 % Allowed : 7.69 % Favored : 91.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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 are not related in a simple way. whole: 0.80 (0.25), residues: 1241 helix: 1.73 (0.19), residues: 787 sheet: -1.06 (0.73), residues: 57 loop : -1.76 (0.31), residues: 397 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 131 TYR 0.014 0.002 TYR C 57 PHE 0.019 0.002 PHE G 25 TRP 0.018 0.002 TRP K 206 HIS 0.004 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00493 / 0.24 (17019) covalent geometry : angle 0.65763 / 0.37 (24250) hydrogen bonds : bond 0.05761 / 3.71 ( 940) hydrogen bonds : angle 3.37765 / 2.45 ( 2427) Misc. bond : bond 0.00053 / 0.03 ( 1) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2482 Ramachandran restraints generated. 1241 Oldfield, 0 Emsley, 1241 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2482 Ramachandran restraints generated. 1241 Oldfield, 0 Emsley, 1241 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 144 time to evaluate : 0.523 Fit side-chains revert: symmetry clash REVERT: C 113 SER cc_start: 0.9238 (OUTLIER) cc_final: 0.8889 (p) REVERT: D 90 GLU cc_start: 0.8666 (mp0) cc_final: 0.8405 (mp0) REVERT: G 92 GLU cc_start: 0.9223 (mm-30) cc_final: 0.8920 (mp0) outliers start: 12 outliers final: 8 residues processed: 148 average time/residue: 0.1514 time to fit residues: 32.5940 Evaluate side-chains 148 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 139 time to evaluate : 0.589 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 LYS Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain C residue 110 ASN Chi-restraints excluded: chain C residue 113 SER Chi-restraints excluded: chain E residue 124 ILE Chi-restraints excluded: chain K residue 306 ILE Chi-restraints excluded: chain K residue 321 ILE Chi-restraints excluded: chain K residue 401 LEU Chi-restraints excluded: chain K residue 632 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 92 optimal weight: 7.9990 chunk 24 optimal weight: 0.8980 chunk 0 optimal weight: 4.9990 chunk 67 optimal weight: 0.6980 chunk 141 optimal weight: 7.9990 chunk 127 optimal weight: 10.0000 chunk 86 optimal weight: 10.0000 chunk 91 optimal weight: 8.9990 chunk 121 optimal weight: 2.9990 chunk 110 optimal weight: 4.9990 chunk 129 optimal weight: 1.9990 overall best weight: 2.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... G 110 ASN K 317 ASN ** K 437 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3690 r_free = 0.3690 target = 0.090611 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.2992 r_free = 0.2992 target = 0.056925 restraints weight = 46282.995| |-----------------------------------------------------------------------------| r_work (start): 0.2937 rms_B_bonded: 2.13 r_work: 0.2763 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work: 0.2638 rms_B_bonded: 4.68 restraints_weight: 0.2500 r_work (final): 0.2638 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8937 moved from start: 0.1210 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.049 17020 Z= 0.267 Angle : 0.693 13.031 24250 Z= 0.380 Chirality : 0.048 0.269 2753 Planarity : 0.005 0.047 2063 Dihedral : 29.597 159.035 4594 Min Nonbonded Distance : 1.984 Molprobity Statistics. All-atom Clashscore : 7.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.83 % Favored : 95.17 % Rotamer: Outliers : 1.02 % Allowed : 8.80 % Favored : 90.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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 are not related in a simple way. whole: 0.69 (0.25), residues: 1241 helix: 1.63 (0.19), residues: 794 sheet: -1.04 (0.73), residues: 57 loop : -1.81 (0.31), residues: 390 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 131 TYR 0.015 0.002 TYR C 57 PHE 0.022 0.002 PHE G 25 TRP 0.020 0.002 TRP K 206 HIS 0.004 0.001 HIS K 554 Details of bonding type rmsd/Z covalent geometry : bond 0.00567 / 0.27 (17019) covalent geometry : angle 0.69252 / 0.38 (24250) hydrogen bonds : bond 0.05992 / 3.87 ( 940) hydrogen bonds : angle 3.45477 / 2.50 ( 2427) Misc. bond : bond 0.00041 / 0.02 ( 1) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2482 Ramachandran restraints generated. 1241 Oldfield, 0 Emsley, 1241 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2482 Ramachandran restraints generated. 1241 Oldfield, 0 Emsley, 1241 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 138 time to evaluate : 0.494 Fit side-chains revert: symmetry clash REVERT: B 24 ASP cc_start: 0.8053 (t0) cc_final: 0.7788 (t0) REVERT: B 88 TYR cc_start: 0.9244 (m-10) cc_final: 0.8943 (m-80) REVERT: C 113 SER cc_start: 0.9283 (OUTLIER) cc_final: 0.8940 (p) REVERT: D 90 GLU cc_start: 0.8721 (mp0) cc_final: 0.8466 (mp0) REVERT: G 35 ARG cc_start: 0.9002 (OUTLIER) cc_final: 0.8145 (ttp80) REVERT: G 92 GLU cc_start: 0.9192 (mm-30) cc_final: 0.8968 (mp0) REVERT: H 65 ASP cc_start: 0.9217 (t70) cc_final: 0.8901 (t0) outliers start: 11 outliers final: 7 residues processed: 144 average time/residue: 0.1578 time to fit residues: 32.4236 Evaluate side-chains 147 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 138 time to evaluate : 0.503 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain C residue 110 ASN Chi-restraints excluded: chain C residue 113 SER Chi-restraints excluded: chain E residue 124 ILE Chi-restraints excluded: chain G residue 35 ARG Chi-restraints excluded: chain K residue 139 VAL Chi-restraints excluded: chain K residue 306 ILE Chi-restraints excluded: chain K residue 321 ILE Chi-restraints excluded: chain K residue 632 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 120 optimal weight: 6.9990 chunk 69 optimal weight: 0.5980 chunk 35 optimal weight: 0.7980 chunk 4 optimal weight: 0.7980 chunk 39 optimal weight: 0.8980 chunk 64 optimal weight: 1.9990 chunk 92 optimal weight: 7.9990 chunk 3 optimal weight: 0.9980 chunk 50 optimal weight: 1.9990 chunk 9 optimal weight: 0.3980 chunk 118 optimal weight: 6.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... G 110 ASN ** K 437 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3716 r_free = 0.3716 target = 0.091823 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3043 r_free = 0.3043 target = 0.058934 restraints weight = 46037.270| |-----------------------------------------------------------------------------| r_work (start): 0.2976 rms_B_bonded: 2.06 r_work: 0.2809 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work: 0.2686 rms_B_bonded: 4.52 restraints_weight: 0.2500 r_work (final): 0.2686 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8903 moved from start: 0.1347 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 17020 Z= 0.141 Angle : 0.636 12.311 24250 Z= 0.356 Chirality : 0.046 0.274 2753 Planarity : 0.004 0.043 2063 Dihedral : 29.485 158.185 4594 Min Nonbonded Distance : 1.997 Molprobity Statistics. All-atom Clashscore : 7.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.35 % Favored : 95.65 % Rotamer: Outliers : 0.83 % Allowed : 8.80 % Favored : 90.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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 are not related in a simple way. whole: 0.87 (0.25), residues: 1241 helix: 1.76 (0.19), residues: 794 sheet: -1.00 (0.74), residues: 57 loop : -1.73 (0.31), residues: 390 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG K 547 TYR 0.018 0.001 TYR B 88 PHE 0.009 0.001 PHE K 274 TRP 0.020 0.002 TRP K 206 HIS 0.005 0.001 HIS K 554 Details of bonding type rmsd/Z covalent geometry : bond 0.00264 / 0.14 (17019) covalent geometry : angle 0.63570 / 0.36 (24250) hydrogen bonds : bond 0.05142 / 3.27 ( 940) hydrogen bonds : angle 3.29346 / 2.37 ( 2427) Misc. bond : bond 0.00036 / 0.02 ( 1) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2482 Ramachandran restraints generated. 1241 Oldfield, 0 Emsley, 1241 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2482 Ramachandran restraints generated. 1241 Oldfield, 0 Emsley, 1241 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 145 time to evaluate : 0.500 Fit side-chains revert: symmetry clash REVERT: B 24 ASP cc_start: 0.7977 (t0) cc_final: 0.7670 (t0) REVERT: B 84 MET cc_start: 0.9118 (tpp) cc_final: 0.8836 (tpp) REVERT: B 88 TYR cc_start: 0.9206 (m-10) cc_final: 0.8976 (m-80) REVERT: C 113 SER cc_start: 0.9225 (OUTLIER) cc_final: 0.8889 (p) REVERT: D 90 GLU cc_start: 0.8667 (mp0) cc_final: 0.8415 (mp0) REVERT: G 35 ARG cc_start: 0.8955 (OUTLIER) cc_final: 0.8086 (ttp80) REVERT: G 92 GLU cc_start: 0.9143 (mm-30) cc_final: 0.8936 (mp0) REVERT: H 65 ASP cc_start: 0.9202 (t70) cc_final: 0.8887 (t0) outliers start: 9 outliers final: 5 residues processed: 149 average time/residue: 0.1498 time to fit residues: 32.0648 Evaluate side-chains 144 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 137 time to evaluate : 0.479 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain C residue 110 ASN Chi-restraints excluded: chain C residue 113 SER Chi-restraints excluded: chain G residue 35 ARG Chi-restraints excluded: chain K residue 139 VAL Chi-restraints excluded: chain K residue 321 ILE Chi-restraints excluded: chain K residue 476 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 34 optimal weight: 0.1980 chunk 58 optimal weight: 0.6980 chunk 46 optimal weight: 0.7980 chunk 18 optimal weight: 1.9990 chunk 81 optimal weight: 10.0000 chunk 124 optimal weight: 8.9990 chunk 131 optimal weight: 0.9980 chunk 33 optimal weight: 0.5980 chunk 146 optimal weight: 3.9990 chunk 7 optimal weight: 0.6980 chunk 31 optimal weight: 0.6980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 113 HIS C 104 GLN F 93 GLN G 110 ASN ** K 437 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3735 r_free = 0.3735 target = 0.092684 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.3073 r_free = 0.3073 target = 0.060091 restraints weight = 46322.738| |-----------------------------------------------------------------------------| r_work (start): 0.3005 rms_B_bonded: 2.05 r_work: 0.2842 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work: 0.2719 rms_B_bonded: 4.52 restraints_weight: 0.2500 r_work (final): 0.2719 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8880 moved from start: 0.1596 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 17020 Z= 0.129 Angle : 0.589 9.918 24250 Z= 0.338 Chirality : 0.043 0.272 2753 Planarity : 0.004 0.043 2063 Dihedral : 29.238 157.852 4594 Min Nonbonded Distance : 2.052 Molprobity Statistics. All-atom Clashscore : 7.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.11 % Favored : 95.89 % Rotamer: Outliers : 1.20 % Allowed : 8.70 % Favored : 90.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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 are not related in a simple way. whole: 1.15 (0.25), residues: 1241 helix: 1.99 (0.19), residues: 794 sheet: -0.97 (0.73), residues: 57 loop : -1.64 (0.31), residues: 390 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG G 71 TYR 0.018 0.001 TYR B 51 PHE 0.010 0.001 PHE E 67 TRP 0.025 0.002 TRP K 206 HIS 0.003 0.001 HIS K 554 Details of bonding type rmsd/Z covalent geometry : bond 0.00228 / 0.13 (17019) covalent geometry : angle 0.58851 / 0.34 (24250) hydrogen bonds : bond 0.04651 / 2.97 ( 940) hydrogen bonds : angle 3.16081 / 2.28 ( 2427) Misc. bond : bond 0.00045 / 0.02 ( 1) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2482 Ramachandran restraints generated. 1241 Oldfield, 0 Emsley, 1241 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2482 Ramachandran restraints generated. 1241 Oldfield, 0 Emsley, 1241 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 145 time to evaluate : 0.322 Fit side-chains revert: symmetry clash REVERT: B 24 ASP cc_start: 0.8045 (t0) cc_final: 0.7696 (t0) REVERT: C 113 SER cc_start: 0.9143 (OUTLIER) cc_final: 0.8845 (p) REVERT: D 90 GLU cc_start: 0.8655 (mp0) cc_final: 0.8380 (mp0) REVERT: G 92 GLU cc_start: 0.9158 (mm-30) cc_final: 0.8880 (mp0) REVERT: H 65 ASP cc_start: 0.9162 (t70) cc_final: 0.8899 (t0) outliers start: 13 outliers final: 7 residues processed: 150 average time/residue: 0.1303 time to fit residues: 28.4302 Evaluate side-chains 145 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 137 time to evaluate : 0.483 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 110 ASN Chi-restraints excluded: chain C residue 113 SER Chi-restraints excluded: chain K residue 139 VAL Chi-restraints excluded: chain K residue 306 ILE Chi-restraints excluded: chain K residue 311 SER Chi-restraints excluded: chain K residue 321 ILE Chi-restraints excluded: chain K residue 476 CYS Chi-restraints excluded: chain K residue 632 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 96 optimal weight: 8.9990 chunk 51 optimal weight: 0.8980 chunk 55 optimal weight: 0.8980 chunk 5 optimal weight: 0.5980 chunk 42 optimal weight: 0.9980 chunk 4 optimal weight: 0.9990 chunk 60 optimal weight: 1.9990 chunk 49 optimal weight: 0.5980 chunk 146 optimal weight: 0.0770 chunk 19 optimal weight: 2.9990 chunk 9 optimal weight: 20.0000 overall best weight: 0.6138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... G 110 ASN ** K 437 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3739 r_free = 0.3739 target = 0.092881 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3079 r_free = 0.3079 target = 0.060342 restraints weight = 46507.919| |-----------------------------------------------------------------------------| r_work (start): 0.3011 rms_B_bonded: 2.06 r_work: 0.2848 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work: 0.2726 rms_B_bonded: 4.53 restraints_weight: 0.2500 r_work (final): 0.2726 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8875 moved from start: 0.1737 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 17020 Z= 0.134 Angle : 0.587 8.014 24250 Z= 0.337 Chirality : 0.043 0.271 2753 Planarity : 0.004 0.058 2063 Dihedral : 29.187 157.412 4594 Min Nonbonded Distance : 2.056 Molprobity Statistics. All-atom Clashscore : 7.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.11 % Favored : 95.89 % Rotamer: Outliers : 0.93 % Allowed : 9.54 % Favored : 89.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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 are not related in a simple way. whole: 1.26 (0.25), residues: 1241 helix: 2.05 (0.19), residues: 794 sheet: -0.83 (0.74), residues: 57 loop : -1.54 (0.31), residues: 390 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 76 TYR 0.020 0.002 TYR B 88 PHE 0.010 0.001 PHE K 369 TRP 0.019 0.002 TRP K 206 HIS 0.007 0.001 HIS K 402 Details of bonding type rmsd/Z covalent geometry : bond 0.00242 / 0.13 (17019) covalent geometry : angle 0.58697 / 0.34 (24250) hydrogen bonds : bond 0.04575 / 2.92 ( 940) hydrogen bonds : angle 3.14860 / 2.27 ( 2427) Misc. bond : bond 0.00040 / 0.02 ( 1) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2482 Ramachandran restraints generated. 1241 Oldfield, 0 Emsley, 1241 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2482 Ramachandran restraints generated. 1241 Oldfield, 0 Emsley, 1241 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 144 time to evaluate : 0.521 Fit side-chains REVERT: B 24 ASP cc_start: 0.8029 (t0) cc_final: 0.7660 (t0) REVERT: C 113 SER cc_start: 0.9043 (OUTLIER) cc_final: 0.8783 (p) REVERT: D 90 GLU cc_start: 0.8647 (mp0) cc_final: 0.8378 (mp0) REVERT: G 35 ARG cc_start: 0.8907 (OUTLIER) cc_final: 0.8047 (ttp80) REVERT: H 30 ARG cc_start: 0.7209 (mtt-85) cc_final: 0.6950 (ttm170) REVERT: H 65 ASP cc_start: 0.9176 (t70) cc_final: 0.8912 (t0) outliers start: 10 outliers final: 5 residues processed: 148 average time/residue: 0.1502 time to fit residues: 32.1047 Evaluate side-chains 145 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 138 time to evaluate : 0.495 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 113 SER Chi-restraints excluded: chain G residue 35 ARG Chi-restraints excluded: chain K residue 139 VAL Chi-restraints excluded: chain K residue 311 SER Chi-restraints excluded: chain K residue 321 ILE Chi-restraints excluded: chain K residue 401 LEU Chi-restraints excluded: chain K residue 632 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 91 optimal weight: 10.0000 chunk 29 optimal weight: 0.6980 chunk 71 optimal weight: 1.9990 chunk 40 optimal weight: 0.6980 chunk 52 optimal weight: 0.4980 chunk 133 optimal weight: 10.0000 chunk 116 optimal weight: 0.6980 chunk 10 optimal weight: 0.9980 chunk 21 optimal weight: 2.9990 chunk 17 optimal weight: 1.9990 chunk 135 optimal weight: 10.0000 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 104 GLN G 110 ASN ** K 437 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3701 r_free = 0.3701 target = 0.092254 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.2988 r_free = 0.2988 target = 0.057700 restraints weight = 46396.492| |-----------------------------------------------------------------------------| r_work (start): 0.2931 rms_B_bonded: 2.20 r_work: 0.2754 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work: 0.2628 rms_B_bonded: 4.86 restraints_weight: 0.2500 r_work (final): 0.2628 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8868 moved from start: 0.1827 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 17020 Z= 0.138 Angle : 0.595 15.573 24250 Z= 0.337 Chirality : 0.043 0.270 2753 Planarity : 0.004 0.043 2063 Dihedral : 29.160 157.201 4594 Min Nonbonded Distance : 2.069 Molprobity Statistics. All-atom Clashscore : 7.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.11 % Favored : 95.89 % Rotamer: Outliers : 0.83 % Allowed : 9.63 % Favored : 89.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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 are not related in a simple way. whole: 1.27 (0.25), residues: 1241 helix: 2.00 (0.19), residues: 800 sheet: -0.77 (0.74), residues: 57 loop : -1.45 (0.32), residues: 384 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 131 TYR 0.013 0.001 TYR B 51 PHE 0.008 0.001 PHE E 67 TRP 0.020 0.002 TRP K 206 HIS 0.009 0.001 HIS D 79 Details of bonding type rmsd/Z covalent geometry : bond 0.00256 / 0.14 (17019) covalent geometry : angle 0.59509 / 0.34 (24250) hydrogen bonds : bond 0.04529 / 2.89 ( 940) hydrogen bonds : angle 3.13276 / 2.26 ( 2427) Misc. bond : bond 0.00041 / 0.02 ( 1) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2482 Ramachandran restraints generated. 1241 Oldfield, 0 Emsley, 1241 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2482 Ramachandran restraints generated. 1241 Oldfield, 0 Emsley, 1241 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 144 time to evaluate : 0.489 Fit side-chains REVERT: B 24 ASP cc_start: 0.8028 (t0) cc_final: 0.7646 (t0) REVERT: C 113 SER cc_start: 0.8956 (OUTLIER) cc_final: 0.8711 (p) REVERT: D 90 GLU cc_start: 0.8793 (mp0) cc_final: 0.8460 (mp0) REVERT: G 35 ARG cc_start: 0.9053 (OUTLIER) cc_final: 0.8254 (ttp80) REVERT: G 90 ASP cc_start: 0.8618 (t70) cc_final: 0.8370 (t0) REVERT: G 91 GLU cc_start: 0.8260 (pm20) cc_final: 0.7975 (pm20) REVERT: G 92 GLU cc_start: 0.9196 (mp0) cc_final: 0.8766 (mp0) REVERT: H 65 ASP cc_start: 0.9279 (t70) cc_final: 0.8968 (t0) outliers start: 9 outliers final: 5 residues processed: 149 average time/residue: 0.1596 time to fit residues: 33.9532 Evaluate side-chains 147 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 140 time to evaluate : 0.382 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 113 SER Chi-restraints excluded: chain G residue 35 ARG Chi-restraints excluded: chain K residue 139 VAL Chi-restraints excluded: chain K residue 223 MET Chi-restraints excluded: chain K residue 311 SER Chi-restraints excluded: chain K residue 321 ILE Chi-restraints excluded: chain K residue 632 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 128 optimal weight: 5.9990 chunk 145 optimal weight: 1.9990 chunk 143 optimal weight: 10.0000 chunk 116 optimal weight: 2.9990 chunk 35 optimal weight: 0.8980 chunk 52 optimal weight: 1.9990 chunk 7 optimal weight: 0.5980 chunk 127 optimal weight: 6.9990 chunk 62 optimal weight: 3.9990 chunk 132 optimal weight: 2.9990 chunk 137 optimal weight: 0.8980 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 104 GLN G 110 ASN ** K 437 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3724 r_free = 0.3724 target = 0.092212 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3056 r_free = 0.3056 target = 0.059413 restraints weight = 46279.634| |-----------------------------------------------------------------------------| r_work (start): 0.2987 rms_B_bonded: 2.07 r_work: 0.2822 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work: 0.2699 rms_B_bonded: 4.50 restraints_weight: 0.2500 r_work (final): 0.2699 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8895 moved from start: 0.1772 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 17020 Z= 0.175 Angle : 0.617 12.690 24250 Z= 0.346 Chirality : 0.044 0.265 2753 Planarity : 0.004 0.042 2063 Dihedral : 29.228 157.477 4594 Min Nonbonded Distance : 2.056 Molprobity Statistics. All-atom Clashscore : 7.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.27 % Favored : 95.73 % Rotamer: Outliers : 0.74 % Allowed : 9.91 % Favored : 89.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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 are not related in a simple way. whole: 1.20 (0.25), residues: 1241 helix: 1.99 (0.19), residues: 791 sheet: -0.66 (0.75), residues: 57 loop : -1.55 (0.31), residues: 393 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG F 92 TYR 0.013 0.001 TYR C 57 PHE 0.013 0.002 PHE K 385 TRP 0.020 0.002 TRP K 384 HIS 0.005 0.001 HIS D 79 Details of bonding type rmsd/Z covalent geometry : bond 0.00353 / 0.17 (17019) covalent geometry : angle 0.61686 / 0.35 (24250) hydrogen bonds : bond 0.04960 / 3.17 ( 940) hydrogen bonds : angle 3.21380 / 2.31 ( 2427) Misc. bond : bond 0.00032 / 0.02 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5389.74 seconds wall clock time: 92 minutes 33.87 seconds (5553.87 seconds total)