Starting phenix.real_space_refine on Wed Mar 4 19:43:07 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7x3w_32995/03_2026/7x3w_32995.cif Found real_map, /net/cci-nas-00/data/ceres_data/7x3w_32995/03_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_32995/03_2026/7x3w_32995.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7x3w_32995/03_2026/7x3w_32995.map" model { file = "/net/cci-nas-00/data/ceres_data/7x3w_32995/03_2026/7x3w_32995.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7x3w_32995/03_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-5986/lib/python3.9/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: 3.26, per 1000 atoms: 0.20 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: 1.53 Conformation dependent library (CDL) restraints added in 357.0 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: 2.41 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: 3.58 Time building geometry restraints manager: 1.94 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=" CA ARG F 95 " pdb=" CB ARG F 95 " ideal model delta sigma weight residual 1.528 1.473 0.056 2.61e-02 1.47e+03 4.57e+00 bond pdb=" CG LEU E 82 " pdb=" CD2 LEU E 82 " ideal model delta sigma weight residual 1.521 1.463 0.058 3.30e-02 9.18e+02 3.12e+00 ... (remaining 17014 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.10: 24187 4.10 - 8.21: 59 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=" CB MET B 84 " pdb=" CG MET B 84 " pdb=" SD MET B 84 " ideal model delta sigma weight residual 112.70 123.95 -11.25 3.00e+00 1.11e-01 1.41e+01 angle pdb=" C LEU K 340 " pdb=" N ARG K 341 " pdb=" CA ARG K 341 " ideal model delta sigma weight residual 121.94 115.15 6.79 2.00e+00 2.50e-01 1.15e+01 angle pdb=" CA MET K 433 " pdb=" CB MET K 433 " pdb=" CG MET K 433 " ideal model delta sigma weight residual 114.10 119.99 -5.89 2.00e+00 2.50e-01 8.68e+00 ... (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 - 0.031: 1354 0.031 - 0.061: 913 0.061 - 0.092: 366 0.092 - 0.123: 92 0.123 - 0.153: 28 Chirality restraints: 2753 Sorted by residual: chirality pdb=" CA LEU E 65 " pdb=" N LEU E 65 " pdb=" C LEU E 65 " pdb=" CB LEU E 65 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.15 2.00e-01 2.50e+01 5.88e-01 chirality pdb=" CG LEU B 22 " pdb=" CB LEU B 22 " pdb=" CD1 LEU B 22 " pdb=" CD2 LEU B 22 " both_signs ideal model delta sigma weight residual False -2.59 -2.44 -0.15 2.00e-01 2.50e+01 5.39e-01 chirality pdb=" CB ILE K 558 " pdb=" CA ILE K 558 " pdb=" CG1 ILE K 558 " pdb=" CG2 ILE K 558 " both_signs ideal model delta sigma weight residual False 2.64 2.50 0.14 2.00e-01 2.50e+01 5.11e-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: 3.050 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: 0.020 Extract box with map and model: 0.260 Check model and map are aligned: 0.060 Set scattering table: 0.040 Process input model: 16.860 Find NCS groups from input model: 0.140 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.090 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.560 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8534 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= 0.808 Angle : 0.771 20.515 24250 Z= 0.439 Chirality : 0.046 0.153 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 covalent geometry : bond 0.00949 (17019) covalent geometry : angle 0.77063 (24250) hydrogen bonds : bond 0.09247 ( 940) hydrogen bonds : angle 4.18286 ( 2427) Misc. bond : bond 0.89903 ( 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 : 0.359 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: 0.1532 time to fit residues: 34.1363 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 : 0.467 ------------------------------------------------------------------------------- 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: 2.9990 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: 1.9990 chunk 122 optimal weight: 0.8980 chunk 91 optimal weight: 1.9990 chunk 149 optimal weight: 5.9990 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 93 GLN F 93 GLN G 110 ASN ** K 437 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 500 ASN K 554 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3722 r_free = 0.3722 target = 0.092466 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3045 r_free = 0.3045 target = 0.059083 restraints weight = 45826.200| |-----------------------------------------------------------------------------| r_work (start): 0.2994 rms_B_bonded: 2.14 r_work: 0.2823 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work: 0.2698 rms_B_bonded: 4.63 restraints_weight: 0.2500 r_work (final): 0.2698 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8807 moved from start: 0.1027 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 17020 Z= 0.195 Angle : 0.601 8.860 24250 Z= 0.346 Chirality : 0.037 0.140 2753 Planarity : 0.004 0.053 2063 Dihedral : 28.869 158.006 4594 Min Nonbonded Distance : 1.951 Molprobity Statistics. All-atom Clashscore : 7.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.87 % Favored : 96.13 % Rotamer: Outliers : 0.56 % Allowed : 4.35 % Favored : 95.09 % 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: 0.53 (0.24), residues: 1241 helix: 1.56 (0.19), residues: 787 sheet: -1.45 (0.69), residues: 57 loop : -1.88 (0.30), residues: 397 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG K 614 TYR 0.027 0.002 TYR B 88 PHE 0.014 0.002 PHE G 25 TRP 0.022 0.002 TRP K 206 HIS 0.004 0.001 HIS K 554 Details of bonding type rmsd covalent geometry : bond 0.00435 (17019) covalent geometry : angle 0.60078 (24250) hydrogen bonds : bond 0.04804 ( 940) hydrogen bonds : angle 3.37664 ( 2427) Misc. bond : bond 0.00010 ( 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 165 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 159 time to evaluate : 0.474 Fit side-chains revert: symmetry clash REVERT: A 59 GLU cc_start: 0.8877 (pm20) cc_final: 0.8641 (pm20) REVERT: B 24 ASP cc_start: 0.8222 (t0) cc_final: 0.7963 (t0) REVERT: B 88 TYR cc_start: 0.9214 (m-80) cc_final: 0.8916 (m-80) REVERT: C 113 SER cc_start: 0.9285 (m) cc_final: 0.8993 (p) REVERT: D 90 GLU cc_start: 0.8596 (mp0) cc_final: 0.8271 (mp0) REVERT: K 609 MET cc_start: 0.7942 (mpp) cc_final: 0.7623 (mpp) outliers start: 6 outliers final: 3 residues processed: 160 average time/residue: 0.1505 time to fit residues: 34.3080 Evaluate side-chains 141 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 138 time to evaluate : 0.467 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 LYS Chi-restraints excluded: chain C residue 110 ASN 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: 0.4980 chunk 95 optimal weight: 2.9990 chunk 26 optimal weight: 1.9990 chunk 143 optimal weight: 3.9990 chunk 134 optimal weight: 0.9980 chunk 8 optimal weight: 1.9990 chunk 22 optimal weight: 0.9990 chunk 56 optimal weight: 2.9990 chunk 127 optimal weight: 1.9990 chunk 1 optimal weight: 0.7980 chunk 107 optimal weight: 10.0000 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 GLN G 68 ASN G 110 ASN H 92 GLN ** 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 = 0.3723 r_free = 0.3723 target = 0.092284 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3042 r_free = 0.3042 target = 0.058836 restraints weight = 46760.509| |-----------------------------------------------------------------------------| r_work (start): 0.2989 rms_B_bonded: 2.13 r_work: 0.2818 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work: 0.2693 rms_B_bonded: 4.69 restraints_weight: 0.2500 r_work (final): 0.2693 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8807 moved from start: 0.1320 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 17020 Z= 0.189 Angle : 0.568 6.086 24250 Z= 0.331 Chirality : 0.036 0.140 2753 Planarity : 0.004 0.048 2063 Dihedral : 28.773 157.619 4594 Min Nonbonded Distance : 2.025 Molprobity Statistics. All-atom Clashscore : 6.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.95 % Favored : 96.05 % Rotamer: Outliers : 1.02 % Allowed : 5.93 % Favored : 93.06 % 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: 0.89 (0.25), residues: 1241 helix: 1.84 (0.19), residues: 788 sheet: -1.24 (0.70), residues: 57 loop : -1.77 (0.30), residues: 396 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG G 71 TYR 0.018 0.001 TYR B 88 PHE 0.013 0.001 PHE G 25 TRP 0.015 0.002 TRP K 364 HIS 0.004 0.001 HIS K 402 Details of bonding type rmsd covalent geometry : bond 0.00424 (17019) covalent geometry : angle 0.56803 (24250) hydrogen bonds : bond 0.04571 ( 940) hydrogen bonds : angle 3.21634 ( 2427) Misc. bond : bond 0.00063 ( 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 163 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 152 time to evaluate : 0.558 Fit side-chains revert: symmetry clash REVERT: B 24 ASP cc_start: 0.8147 (t0) cc_final: 0.7769 (t0) REVERT: B 88 TYR cc_start: 0.9247 (m-80) cc_final: 0.8977 (m-80) REVERT: C 113 SER cc_start: 0.9251 (m) cc_final: 0.8969 (p) REVERT: D 90 GLU cc_start: 0.8627 (mp0) cc_final: 0.8310 (mp0) REVERT: G 92 GLU cc_start: 0.9156 (mm-30) cc_final: 0.8868 (mp0) REVERT: H 65 ASP cc_start: 0.9201 (t70) cc_final: 0.8947 (t0) REVERT: K 223 MET cc_start: 0.1767 (ppp) cc_final: 0.1463 (ppp) outliers start: 11 outliers final: 6 residues processed: 157 average time/residue: 0.1478 time to fit residues: 32.9957 Evaluate side-chains 143 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 137 time to evaluate : 0.347 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 E residue 76 GLN 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: 7.9990 chunk 0 optimal weight: 4.9990 chunk 46 optimal weight: 0.6980 chunk 104 optimal weight: 4.9990 chunk 100 optimal weight: 7.9990 chunk 21 optimal weight: 2.9990 chunk 123 optimal weight: 10.0000 chunk 98 optimal weight: 3.9990 chunk 13 optimal weight: 0.8980 chunk 3 optimal weight: 0.5980 chunk 91 optimal weight: 2.9990 overall best weight: 1.6384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 GLN G 110 ASN ** K 437 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 526 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3706 r_free = 0.3706 target = 0.091440 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3017 r_free = 0.3017 target = 0.057937 restraints weight = 46234.269| |-----------------------------------------------------------------------------| r_work (start): 0.2962 rms_B_bonded: 2.10 r_work: 0.2790 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work: 0.2666 rms_B_bonded: 4.64 restraints_weight: 0.2500 r_work (final): 0.2666 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8825 moved from start: 0.1316 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.043 17020 Z= 0.248 Angle : 0.594 7.118 24250 Z= 0.344 Chirality : 0.038 0.136 2753 Planarity : 0.004 0.048 2063 Dihedral : 28.876 157.913 4594 Min Nonbonded Distance : 2.026 Molprobity Statistics. All-atom Clashscore : 6.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.11 % Favored : 95.89 % Rotamer: Outliers : 0.65 % Allowed : 7.41 % Favored : 91.94 % 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: 0.89 (0.25), residues: 1241 helix: 1.80 (0.19), residues: 794 sheet: -1.11 (0.72), residues: 57 loop : -1.76 (0.31), residues: 390 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG G 71 TYR 0.015 0.002 TYR F 51 PHE 0.017 0.002 PHE G 25 TRP 0.017 0.002 TRP K 364 HIS 0.004 0.001 HIS K 478 Details of bonding type rmsd covalent geometry : bond 0.00565 (17019) covalent geometry : angle 0.59355 (24250) hydrogen bonds : bond 0.05046 ( 940) hydrogen bonds : angle 3.29539 ( 2427) Misc. bond : bond 0.00027 ( 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 150 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 143 time to evaluate : 0.480 Fit side-chains REVERT: B 88 TYR cc_start: 0.9289 (m-10) cc_final: 0.8855 (m-80) REVERT: C 113 SER cc_start: 0.9260 (m) cc_final: 0.8962 (p) REVERT: D 90 GLU cc_start: 0.8683 (mp0) cc_final: 0.8389 (mp0) REVERT: H 65 ASP cc_start: 0.9218 (t70) cc_final: 0.8962 (t0) outliers start: 7 outliers final: 5 residues processed: 147 average time/residue: 0.1453 time to fit residues: 30.6055 Evaluate side-chains 141 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 136 time to evaluate : 0.477 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain C residue 110 ASN Chi-restraints excluded: chain E residue 124 ILE Chi-restraints excluded: chain K residue 306 ILE 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: 0.9990 chunk 142 optimal weight: 4.9990 chunk 81 optimal weight: 2.9990 chunk 91 optimal weight: 2.9990 chunk 104 optimal weight: 0.0010 chunk 105 optimal weight: 1.9990 chunk 14 optimal weight: 0.5980 chunk 95 optimal weight: 2.9990 chunk 23 optimal weight: 3.9990 chunk 130 optimal weight: 0.6980 chunk 46 optimal weight: 0.9990 overall best weight: 0.6590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 104 GLN G 110 ASN K 317 ASN ** K 437 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3725 r_free = 0.3725 target = 0.092404 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3043 r_free = 0.3043 target = 0.059010 restraints weight = 46277.702| |-----------------------------------------------------------------------------| r_work (start): 0.2989 rms_B_bonded: 2.07 r_work: 0.2817 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work: 0.2691 rms_B_bonded: 4.65 restraints_weight: 0.2500 r_work (final): 0.2691 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8807 moved from start: 0.1465 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 17020 Z= 0.160 Angle : 0.568 14.001 24250 Z= 0.329 Chirality : 0.036 0.135 2753 Planarity : 0.004 0.043 2063 Dihedral : 28.837 157.560 4594 Min Nonbonded Distance : 2.024 Molprobity Statistics. All-atom Clashscore : 6.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.03 % Favored : 95.97 % Rotamer: Outliers : 0.74 % Allowed : 7.96 % Favored : 91.30 % 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: 1.05 (0.25), residues: 1241 helix: 1.92 (0.19), residues: 794 sheet: -1.04 (0.72), residues: 57 loop : -1.68 (0.31), residues: 390 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG K 614 TYR 0.015 0.001 TYR B 51 PHE 0.010 0.001 PHE A 67 TRP 0.017 0.001 TRP K 206 HIS 0.005 0.001 HIS K 478 Details of bonding type rmsd covalent geometry : bond 0.00351 (17019) covalent geometry : angle 0.56764 (24250) hydrogen bonds : bond 0.04577 ( 940) hydrogen bonds : angle 3.17077 ( 2427) Misc. bond : bond 0.00035 ( 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 153 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 145 time to evaluate : 0.480 Fit side-chains REVERT: B 88 TYR cc_start: 0.9209 (m-10) cc_final: 0.8889 (m-80) REVERT: C 113 SER cc_start: 0.9253 (m) cc_final: 0.8963 (p) REVERT: D 90 GLU cc_start: 0.8634 (mp0) cc_final: 0.8348 (mp0) REVERT: G 92 GLU cc_start: 0.9114 (mm-30) cc_final: 0.8861 (mp0) REVERT: H 65 ASP cc_start: 0.9206 (t70) cc_final: 0.8875 (t0) outliers start: 8 outliers final: 6 residues processed: 147 average time/residue: 0.1424 time to fit residues: 30.1593 Evaluate side-chains 143 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 137 time to evaluate : 0.476 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain C residue 110 ASN 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 476 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 92 optimal weight: 2.9990 chunk 24 optimal weight: 1.9990 chunk 0 optimal weight: 5.9990 chunk 67 optimal weight: 1.9990 chunk 141 optimal weight: 10.0000 chunk 127 optimal weight: 0.0670 chunk 86 optimal weight: 5.9990 chunk 91 optimal weight: 2.9990 chunk 121 optimal weight: 1.9990 chunk 110 optimal weight: 6.9990 chunk 129 optimal weight: 3.9990 overall best weight: 1.8126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 104 GLN F 75 HIS G 110 ASN ** K 437 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3701 r_free = 0.3701 target = 0.091201 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.3006 r_free = 0.3006 target = 0.057543 restraints weight = 46400.922| |-----------------------------------------------------------------------------| r_work (start): 0.2952 rms_B_bonded: 2.10 r_work: 0.2777 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work: 0.2651 rms_B_bonded: 4.69 restraints_weight: 0.2500 r_work (final): 0.2651 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8842 moved from start: 0.1417 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.043 17020 Z= 0.268 Angle : 0.603 9.041 24250 Z= 0.349 Chirality : 0.039 0.135 2753 Planarity : 0.004 0.046 2063 Dihedral : 28.923 157.588 4594 Min Nonbonded Distance : 1.991 Molprobity Statistics. All-atom Clashscore : 7.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.59 % Favored : 95.41 % Rotamer: Outliers : 1.39 % Allowed : 8.24 % 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: 1.04 (0.25), residues: 1241 helix: 1.92 (0.19), residues: 788 sheet: -0.87 (0.74), residues: 57 loop : -1.70 (0.30), residues: 396 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 55 TYR 0.018 0.002 TYR D 80 PHE 0.017 0.002 PHE G 25 TRP 0.025 0.002 TRP K 206 HIS 0.004 0.001 HIS K 478 Details of bonding type rmsd covalent geometry : bond 0.00610 (17019) covalent geometry : angle 0.60289 (24250) hydrogen bonds : bond 0.05195 ( 940) hydrogen bonds : angle 3.29441 ( 2427) Misc. bond : bond 0.00008 ( 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 159 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 144 time to evaluate : 0.487 Fit side-chains REVERT: B 24 ASP cc_start: 0.8272 (t0) cc_final: 0.7825 (t0) REVERT: B 88 TYR cc_start: 0.9302 (m-10) cc_final: 0.8924 (m-80) REVERT: C 113 SER cc_start: 0.9286 (m) cc_final: 0.8985 (p) REVERT: D 90 GLU cc_start: 0.8676 (OUTLIER) cc_final: 0.8415 (mp0) REVERT: G 35 ARG cc_start: 0.8984 (OUTLIER) cc_final: 0.8111 (ttp80) REVERT: G 92 GLU cc_start: 0.9156 (mm-30) cc_final: 0.8878 (mp0) REVERT: H 65 ASP cc_start: 0.9229 (t70) cc_final: 0.8963 (t0) outliers start: 15 outliers final: 8 residues processed: 153 average time/residue: 0.1485 time to fit residues: 32.3565 Evaluate side-chains 150 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 140 time to evaluate : 0.395 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain C residue 110 ASN Chi-restraints excluded: chain D residue 90 GLU 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 321 ILE Chi-restraints excluded: chain K residue 401 LEU Chi-restraints excluded: chain K residue 476 CYS 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: 10.0000 chunk 69 optimal weight: 1.9990 chunk 35 optimal weight: 2.9990 chunk 4 optimal weight: 0.5980 chunk 39 optimal weight: 0.6980 chunk 64 optimal weight: 0.9990 chunk 92 optimal weight: 1.9990 chunk 3 optimal weight: 0.8980 chunk 50 optimal weight: 1.9990 chunk 9 optimal weight: 1.9990 chunk 118 optimal weight: 3.9990 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3712 r_free = 0.3712 target = 0.091670 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3024 r_free = 0.3024 target = 0.058229 restraints weight = 46137.008| |-----------------------------------------------------------------------------| r_work (start): 0.2968 rms_B_bonded: 2.06 r_work: 0.2797 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work: 0.2674 rms_B_bonded: 4.61 restraints_weight: 0.2500 r_work (final): 0.2674 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8816 moved from start: 0.1502 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 17020 Z= 0.188 Angle : 0.586 8.539 24250 Z= 0.339 Chirality : 0.037 0.146 2753 Planarity : 0.004 0.045 2063 Dihedral : 28.909 157.474 4594 Min Nonbonded Distance : 1.998 Molprobity Statistics. All-atom Clashscore : 7.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.19 % Favored : 95.81 % Rotamer: Outliers : 0.93 % Allowed : 8.98 % 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: 1.10 (0.25), residues: 1241 helix: 1.96 (0.19), residues: 788 sheet: -0.80 (0.74), residues: 57 loop : -1.65 (0.31), residues: 396 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG K 614 TYR 0.019 0.001 TYR D 80 PHE 0.011 0.001 PHE G 25 TRP 0.020 0.002 TRP K 206 HIS 0.003 0.001 HIS F 75 Details of bonding type rmsd covalent geometry : bond 0.00419 (17019) covalent geometry : angle 0.58576 (24250) hydrogen bonds : bond 0.04922 ( 940) hydrogen bonds : angle 3.22140 ( 2427) Misc. bond : bond 0.00016 ( 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 150 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 140 time to evaluate : 0.487 Fit side-chains REVERT: B 24 ASP cc_start: 0.8241 (t0) cc_final: 0.8003 (t0) REVERT: B 88 TYR cc_start: 0.9231 (m-10) cc_final: 0.8927 (m-80) REVERT: C 113 SER cc_start: 0.9268 (m) cc_final: 0.8973 (p) REVERT: D 90 GLU cc_start: 0.8653 (OUTLIER) cc_final: 0.8397 (mp0) REVERT: G 35 ARG cc_start: 0.8970 (OUTLIER) cc_final: 0.8093 (ttp80) REVERT: G 92 GLU cc_start: 0.9115 (mm-30) cc_final: 0.8890 (mp0) REVERT: H 65 ASP cc_start: 0.9220 (t70) cc_final: 0.8888 (t0) outliers start: 10 outliers final: 8 residues processed: 145 average time/residue: 0.1468 time to fit residues: 30.3615 Evaluate side-chains 145 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 135 time to evaluate : 0.447 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain C residue 110 ASN Chi-restraints excluded: chain D residue 90 GLU 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 321 ILE Chi-restraints excluded: chain K residue 401 LEU Chi-restraints excluded: chain K residue 476 CYS Chi-restraints excluded: chain K residue 632 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 34 optimal weight: 0.8980 chunk 58 optimal weight: 0.6980 chunk 46 optimal weight: 0.6980 chunk 18 optimal weight: 0.9980 chunk 81 optimal weight: 2.9990 chunk 124 optimal weight: 0.8980 chunk 131 optimal weight: 0.9990 chunk 33 optimal weight: 0.9990 chunk 146 optimal weight: 9.9990 chunk 7 optimal weight: 0.9980 chunk 31 optimal weight: 0.6980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 113 HIS C 104 GLN G 110 ASN ** K 437 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3726 r_free = 0.3726 target = 0.092298 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3054 r_free = 0.3054 target = 0.059393 restraints weight = 46231.251| |-----------------------------------------------------------------------------| r_work (start): 0.2988 rms_B_bonded: 2.05 r_work: 0.2823 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work: 0.2701 rms_B_bonded: 4.50 restraints_weight: 0.2500 r_work (final): 0.2701 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8796 moved from start: 0.1622 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 17020 Z= 0.166 Angle : 0.565 7.667 24250 Z= 0.329 Chirality : 0.036 0.141 2753 Planarity : 0.004 0.043 2063 Dihedral : 28.808 157.392 4594 Min Nonbonded Distance : 2.013 Molprobity Statistics. All-atom Clashscore : 7.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.19 % Favored : 95.81 % Rotamer: Outliers : 0.83 % Allowed : 9.26 % Favored : 89.91 % 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: 2.05 (0.19), residues: 788 sheet: -0.79 (0.75), residues: 57 loop : -1.63 (0.31), residues: 396 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG K 614 TYR 0.020 0.001 TYR D 80 PHE 0.009 0.001 PHE A 67 TRP 0.032 0.002 TRP K 206 HIS 0.002 0.001 HIS K 478 Details of bonding type rmsd covalent geometry : bond 0.00366 (17019) covalent geometry : angle 0.56450 (24250) hydrogen bonds : bond 0.04527 ( 940) hydrogen bonds : angle 3.15086 ( 2427) Misc. bond : bond 0.00023 ( 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 150 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 141 time to evaluate : 0.514 Fit side-chains REVERT: C 113 SER cc_start: 0.9229 (m) cc_final: 0.8966 (p) REVERT: D 90 GLU cc_start: 0.8658 (OUTLIER) cc_final: 0.8396 (mp0) REVERT: G 35 ARG cc_start: 0.8947 (OUTLIER) cc_final: 0.8063 (ttp80) REVERT: G 92 GLU cc_start: 0.9097 (mm-30) cc_final: 0.8893 (mp0) REVERT: H 65 ASP cc_start: 0.9207 (t70) cc_final: 0.8936 (t0) outliers start: 9 outliers final: 6 residues processed: 145 average time/residue: 0.1434 time to fit residues: 29.7582 Evaluate side-chains 147 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 139 time to evaluate : 0.446 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain C residue 110 ASN Chi-restraints excluded: chain D residue 90 GLU 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 321 ILE Chi-restraints excluded: chain K residue 401 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 96 optimal weight: 2.9990 chunk 51 optimal weight: 0.6980 chunk 55 optimal weight: 1.9990 chunk 5 optimal weight: 0.5980 chunk 42 optimal weight: 0.9990 chunk 4 optimal weight: 1.9990 chunk 60 optimal weight: 0.8980 chunk 49 optimal weight: 0.5980 chunk 146 optimal weight: 9.9990 chunk 19 optimal weight: 2.9990 chunk 9 optimal weight: 9.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.092254 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 73)----------------| | r_work = 0.2983 r_free = 0.2983 target = 0.057515 restraints weight = 46808.933| |-----------------------------------------------------------------------------| r_work (start): 0.2927 rms_B_bonded: 2.23 r_work: 0.2747 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work: 0.2620 rms_B_bonded: 4.90 restraints_weight: 0.2500 r_work (final): 0.2620 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8789 moved from start: 0.1800 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 17020 Z= 0.162 Angle : 0.555 8.830 24250 Z= 0.323 Chirality : 0.035 0.147 2753 Planarity : 0.004 0.044 2063 Dihedral : 28.624 157.109 4594 Min Nonbonded Distance : 2.046 Molprobity Statistics. All-atom Clashscore : 7.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.03 % Favored : 95.97 % Rotamer: Outliers : 0.74 % Allowed : 9.63 % Favored : 89.63 % 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: 1.34 (0.25), residues: 1241 helix: 2.14 (0.19), residues: 788 sheet: -0.72 (0.75), residues: 57 loop : -1.55 (0.31), residues: 396 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 76 TYR 0.037 0.002 TYR D 80 PHE 0.009 0.001 PHE A 67 TRP 0.021 0.002 TRP K 206 HIS 0.009 0.001 HIS D 79 Details of bonding type rmsd covalent geometry : bond 0.00360 (17019) covalent geometry : angle 0.55523 (24250) hydrogen bonds : bond 0.04276 ( 940) hydrogen bonds : angle 3.10484 ( 2427) Misc. bond : bond 0.00031 ( 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 156 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 148 time to evaluate : 0.370 Fit side-chains revert: symmetry clash REVERT: C 113 SER cc_start: 0.9122 (m) cc_final: 0.8863 (p) REVERT: D 90 GLU cc_start: 0.8818 (OUTLIER) cc_final: 0.8499 (mp0) REVERT: G 35 ARG cc_start: 0.9039 (OUTLIER) cc_final: 0.8226 (ttp80) REVERT: G 92 GLU cc_start: 0.9239 (mm-30) cc_final: 0.8932 (mp0) REVERT: H 65 ASP cc_start: 0.9320 (t70) cc_final: 0.8942 (t0) outliers start: 8 outliers final: 5 residues processed: 151 average time/residue: 0.1400 time to fit residues: 30.4421 Evaluate side-chains 148 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 141 time to evaluate : 0.476 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 90 GLU Chi-restraints excluded: chain E residue 124 ILE Chi-restraints excluded: chain G residue 35 ARG Chi-restraints excluded: chain K residue 223 MET 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 91 optimal weight: 2.9990 chunk 29 optimal weight: 0.7980 chunk 71 optimal weight: 1.9990 chunk 40 optimal weight: 0.0470 chunk 52 optimal weight: 1.9990 chunk 133 optimal weight: 0.0070 chunk 116 optimal weight: 2.9990 chunk 10 optimal weight: 0.6980 chunk 21 optimal weight: 1.9990 chunk 17 optimal weight: 3.9990 chunk 135 optimal weight: 5.9990 overall best weight: 0.7098 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 104 GLN K 121 HIS ** 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 = 0.3706 r_free = 0.3706 target = 0.092589 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.2998 r_free = 0.2998 target = 0.058092 restraints weight = 46373.779| |-----------------------------------------------------------------------------| r_work (start): 0.2942 rms_B_bonded: 2.19 r_work: 0.2764 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work: 0.2637 rms_B_bonded: 4.82 restraints_weight: 0.2500 r_work (final): 0.2637 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8761 moved from start: 0.2030 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 17020 Z= 0.157 Angle : 0.556 9.747 24250 Z= 0.321 Chirality : 0.035 0.140 2753 Planarity : 0.004 0.045 2063 Dihedral : 28.505 156.438 4594 Min Nonbonded Distance : 2.070 Molprobity Statistics. All-atom Clashscore : 7.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.03 % Favored : 95.97 % Rotamer: Outliers : 0.56 % Allowed : 10.46 % Favored : 88.98 % 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: 1.47 (0.25), residues: 1241 helix: 2.24 (0.19), residues: 787 sheet: -0.60 (0.75), residues: 57 loop : -1.48 (0.31), residues: 397 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG K 341 TYR 0.012 0.001 TYR C 57 PHE 0.012 0.001 PHE K 369 TRP 0.027 0.002 TRP K 384 HIS 0.007 0.001 HIS K 402 Details of bonding type rmsd covalent geometry : bond 0.00347 (17019) covalent geometry : angle 0.55592 (24250) hydrogen bonds : bond 0.04119 ( 940) hydrogen bonds : angle 3.05614 ( 2427) Misc. bond : bond 0.00039 ( 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 152 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 146 time to evaluate : 0.426 Fit side-chains REVERT: B 88 TYR cc_start: 0.9247 (m-80) cc_final: 0.8946 (m-80) REVERT: C 113 SER cc_start: 0.9068 (m) cc_final: 0.8825 (p) REVERT: D 90 GLU cc_start: 0.8810 (OUTLIER) cc_final: 0.8424 (mp0) REVERT: G 35 ARG cc_start: 0.9060 (OUTLIER) cc_final: 0.8251 (ttp80) REVERT: G 92 GLU cc_start: 0.9181 (mm-30) cc_final: 0.8929 (mp0) REVERT: H 65 ASP cc_start: 0.9296 (t70) cc_final: 0.8895 (t0) REVERT: K 476 CYS cc_start: 0.8076 (t) cc_final: 0.7834 (t) outliers start: 6 outliers final: 4 residues processed: 150 average time/residue: 0.1355 time to fit residues: 29.3985 Evaluate side-chains 148 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 142 time to evaluate : 0.424 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 90 GLU 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 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: 7.9990 chunk 145 optimal weight: 1.9990 chunk 143 optimal weight: 10.0000 chunk 116 optimal weight: 1.9990 chunk 35 optimal weight: 0.6980 chunk 52 optimal weight: 2.9990 chunk 7 optimal weight: 0.7980 chunk 127 optimal weight: 7.9990 chunk 62 optimal weight: 4.9990 chunk 132 optimal weight: 0.7980 chunk 137 optimal weight: 5.9990 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 121 HIS ** 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 = 0.3685 r_free = 0.3685 target = 0.091527 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 73)----------------| | r_work = 0.2964 r_free = 0.2964 target = 0.056723 restraints weight = 46602.764| |-----------------------------------------------------------------------------| r_work (start): 0.2907 rms_B_bonded: 2.20 r_work: 0.2727 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work: 0.2600 rms_B_bonded: 4.81 restraints_weight: 0.2500 r_work (final): 0.2600 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8791 moved from start: 0.1913 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 17020 Z= 0.208 Angle : 0.582 9.499 24250 Z= 0.334 Chirality : 0.037 0.141 2753 Planarity : 0.004 0.043 2063 Dihedral : 28.643 156.608 4594 Min Nonbonded Distance : 2.023 Molprobity Statistics. All-atom Clashscore : 7.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.03 % Favored : 95.97 % Rotamer: Outliers : 0.93 % Allowed : 10.28 % Favored : 88.80 % 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: 1.33 (0.25), residues: 1241 helix: 2.12 (0.19), residues: 792 sheet: -0.53 (0.76), residues: 57 loop : -1.57 (0.31), residues: 392 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG K 614 TYR 0.012 0.001 TYR C 57 PHE 0.014 0.001 PHE K 369 TRP 0.023 0.002 TRP K 206 HIS 0.003 0.001 HIS D 79 Details of bonding type rmsd covalent geometry : bond 0.00471 (17019) covalent geometry : angle 0.58186 (24250) hydrogen bonds : bond 0.04659 ( 940) hydrogen bonds : angle 3.14888 ( 2427) Misc. bond : bond 0.00027 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5291.93 seconds wall clock time: 90 minutes 31.48 seconds (5431.48 seconds total)