Starting phenix.real_space_refine on Thu Aug 6 10:43:02 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9njb_49478/08_2026/9njb_49478.cif Found real_map, /net/cci-nas-00/data/ceres_data/9njb_49478/08_2026/9njb_49478.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.15 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9njb_49478/08_2026/9njb_49478.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9njb_49478/08_2026/9njb_49478.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9njb_49478/08_2026/9njb_49478.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9njb_49478/08_2026/9njb_49478.map" } resolution = 2.15 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= 0.008 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: 6 Type Number sf(0) Gaussians P 6 5.49 5 Mg 2 5.21 5 S 63 5.16 5 C 9073 2.51 5 N 2453 2.21 5 O 2813 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 24 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 14410 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 4760 Number of conformers: 1 Conformer: "" Number of residues, atoms: 620, 4760 Classifications: {'peptide': 620} Link IDs: {'PTRANS': 31, 'TRANS': 588} Chain breaks: 1 Chain: "B" Number of atoms: 4728 Number of conformers: 1 Conformer: "" Number of residues, atoms: 618, 4728 Classifications: {'peptide': 618} Link IDs: {'PTRANS': 31, 'TRANS': 586} Chain breaks: 1 Chain: "C" Number of atoms: 4779 Number of conformers: 1 Conformer: "" Number of residues, atoms: 623, 4779 Classifications: {'peptide': 623} Link IDs: {'PTRANS': 31, 'TRANS': 591} Chain: "D" Number of atoms: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 126 Classifications: {'RNA': 6} Modifications used: {'rna2p_pyr': 1, 'rna3p_pur': 3, 'rna3p_pyr': 2} Link IDs: {'rna2p': 1, 'rna3p': 4} Chain: "A" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 5 Unusual residues: {'SO4': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 5 Unusual residues: {'SO4': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 6 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 6 Unusual residues: {' MG': 1, 'SO4': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Residues with excluded nonbonded symmetry interactions: 2 residue: pdb="MG MG C 902 " occ=0.60 residue: pdb="MG MG D 101 " occ=0.40 Time building chain proxies: 3.34, per 1000 atoms: 0.23 Number of scatterers: 14410 At special positions: 0 Unit cell: (105.75, 109.134, 107.442, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 63 16.00 P 6 15.00 Mg 2 11.99 O 2813 8.00 N 2453 7.00 C 9073 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.13 Conformation dependent library (CDL) restraints added in 633.2 milliseconds 3702 Ramachandran restraints generated. 1851 Oldfield, 0 Emsley, 1851 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3466 Finding SS restraints... Secondary structure from input PDB file: 60 helices and 13 sheets defined 43.5% alpha, 22.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.39 Creating SS restraints... Processing helix chain 'A' and resid 114 through 118 Processing helix chain 'A' and resid 124 through 139 Processing helix chain 'A' and resid 140 through 142 No H-bonds generated for 'chain 'A' and resid 140 through 142' Processing helix chain 'A' and resid 164 through 180 removed outlier: 4.140A pdb=" N LEU A 168 " --> pdb=" O GLU A 164 " (cutoff:3.500A) Processing helix chain 'A' and resid 205 through 210 Processing helix chain 'A' and resid 222 through 224 No H-bonds generated for 'chain 'A' and resid 222 through 224' Processing helix chain 'A' and resid 237 through 266 removed outlier: 3.681A pdb=" N GLN A 254 " --> pdb=" O LYS A 250 " (cutoff:3.500A) Processing helix chain 'A' and resid 280 through 300 removed outlier: 3.695A pdb=" N LYS A 289 " --> pdb=" O LYS A 285 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N LEU A 290 " --> pdb=" O TYR A 286 " (cutoff:3.500A) removed outlier: 5.945A pdb=" N GLU A 293 " --> pdb=" O LYS A 289 " (cutoff:3.500A) removed outlier: 5.545A pdb=" N ARG A 294 " --> pdb=" O LEU A 290 " (cutoff:3.500A) Processing helix chain 'A' and resid 305 through 328 removed outlier: 4.751A pdb=" N GLU A 322 " --> pdb=" O LEU A 318 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N GLN A 323 " --> pdb=" O ASP A 319 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N GLU A 326 " --> pdb=" O GLU A 322 " (cutoff:3.500A) Processing helix chain 'A' and resid 332 through 356 removed outlier: 3.541A pdb=" N ILE A 337 " --> pdb=" O PRO A 333 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N VAL A 352 " --> pdb=" O PHE A 348 " (cutoff:3.500A) Processing helix chain 'A' and resid 401 through 406 Processing helix chain 'A' and resid 409 through 416 Processing helix chain 'A' and resid 430 through 435 Processing helix chain 'A' and resid 445 through 459 Processing helix chain 'A' and resid 482 through 499 Processing helix chain 'A' and resid 534 through 540 Processing helix chain 'A' and resid 567 through 593 removed outlier: 3.559A pdb=" N THR A 592 " --> pdb=" O ILE A 588 " (cutoff:3.500A) Processing helix chain 'A' and resid 613 through 622 removed outlier: 4.466A pdb=" N ALA A 618 " --> pdb=" O LEU A 614 " (cutoff:3.500A) removed outlier: 4.909A pdb=" N LYS A 619 " --> pdb=" O SER A 615 " (cutoff:3.500A) Processing helix chain 'A' and resid 625 through 635 Processing helix chain 'A' and resid 653 through 668 removed outlier: 3.517A pdb=" N GLU A 666 " --> pdb=" O ASP A 662 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N ILE A 667 " --> pdb=" O PHE A 663 " (cutoff:3.500A) Processing helix chain 'B' and resid 124 through 139 Processing helix chain 'B' and resid 140 through 142 No H-bonds generated for 'chain 'B' and resid 140 through 142' Processing helix chain 'B' and resid 164 through 180 removed outlier: 4.127A pdb=" N LEU B 168 " --> pdb=" O GLU B 164 " (cutoff:3.500A) Processing helix chain 'B' and resid 205 through 211 removed outlier: 3.697A pdb=" N SER B 211 " --> pdb=" O LYS B 207 " (cutoff:3.500A) Processing helix chain 'B' and resid 237 through 266 removed outlier: 3.698A pdb=" N GLN B 254 " --> pdb=" O LYS B 250 " (cutoff:3.500A) Processing helix chain 'B' and resid 280 through 300 removed outlier: 3.696A pdb=" N TYR B 286 " --> pdb=" O GLU B 282 " (cutoff:3.500A) removed outlier: 5.457A pdb=" N GLU B 293 " --> pdb=" O LYS B 289 " (cutoff:3.500A) removed outlier: 5.321A pdb=" N ARG B 294 " --> pdb=" O LEU B 290 " (cutoff:3.500A) Processing helix chain 'B' and resid 305 through 328 removed outlier: 4.135A pdb=" N GLU B 322 " --> pdb=" O LEU B 318 " (cutoff:3.500A) removed outlier: 4.955A pdb=" N GLN B 323 " --> pdb=" O ASP B 319 " (cutoff:3.500A) Processing helix chain 'B' and resid 332 through 356 removed outlier: 3.522A pdb=" N PHE B 340 " --> pdb=" O ILE B 336 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N VAL B 352 " --> pdb=" O PHE B 348 " (cutoff:3.500A) Processing helix chain 'B' and resid 401 through 405 Processing helix chain 'B' and resid 409 through 417 Processing helix chain 'B' and resid 430 through 435 Processing helix chain 'B' and resid 444 through 459 Processing helix chain 'B' and resid 460 through 462 No H-bonds generated for 'chain 'B' and resid 460 through 462' Processing helix chain 'B' and resid 482 through 499 Processing helix chain 'B' and resid 534 through 540 Processing helix chain 'B' and resid 567 through 593 removed outlier: 3.732A pdb=" N THR B 592 " --> pdb=" O ILE B 588 " (cutoff:3.500A) Processing helix chain 'B' and resid 616 through 622 Processing helix chain 'B' and resid 625 through 635 Processing helix chain 'B' and resid 653 through 668 Processing helix chain 'C' and resid 117 through 122 Processing helix chain 'C' and resid 124 through 139 Processing helix chain 'C' and resid 164 through 180 removed outlier: 4.183A pdb=" N LEU C 168 " --> pdb=" O GLU C 164 " (cutoff:3.500A) Processing helix chain 'C' and resid 205 through 210 Processing helix chain 'C' and resid 237 through 267 removed outlier: 3.815A pdb=" N GLN C 254 " --> pdb=" O LYS C 250 " (cutoff:3.500A) Processing helix chain 'C' and resid 280 through 288 Processing helix chain 'C' and resid 291 through 300 Processing helix chain 'C' and resid 305 through 328 removed outlier: 3.856A pdb=" N GLU C 322 " --> pdb=" O LEU C 318 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N GLN C 323 " --> pdb=" O ASP C 319 " (cutoff:3.500A) Processing helix chain 'C' and resid 332 through 356 removed outlier: 3.876A pdb=" N VAL C 352 " --> pdb=" O PHE C 348 " (cutoff:3.500A) Processing helix chain 'C' and resid 401 through 406 removed outlier: 3.792A pdb=" N GLY C 405 " --> pdb=" O LEU C 402 " (cutoff:3.500A) Processing helix chain 'C' and resid 413 through 417 Processing helix chain 'C' and resid 430 through 434 Processing helix chain 'C' and resid 444 through 459 Processing helix chain 'C' and resid 460 through 462 No H-bonds generated for 'chain 'C' and resid 460 through 462' Processing helix chain 'C' and resid 483 through 499 Processing helix chain 'C' and resid 534 through 541 Processing helix chain 'C' and resid 567 through 593 removed outlier: 3.523A pdb=" N VAL C 571 " --> pdb=" O PRO C 567 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N THR C 592 " --> pdb=" O ILE C 588 " (cutoff:3.500A) Processing helix chain 'C' and resid 613 through 615 No H-bonds generated for 'chain 'C' and resid 613 through 615' Processing helix chain 'C' and resid 616 through 622 Processing helix chain 'C' and resid 625 through 636 Processing helix chain 'C' and resid 653 through 667 Processing sheet with id=AA1, first strand: chain 'A' and resid 47 through 51 removed outlier: 6.434A pdb=" N ALA A 79 " --> pdb=" O LEU A 157 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 199 through 202 removed outlier: 3.994A pdb=" N ILE A 195 " --> pdb=" O LEU A 214 " (cutoff:3.500A) removed outlier: 4.517A pdb=" N LEU A 214 " --> pdb=" O ILE A 195 " (cutoff:3.500A) removed outlier: 6.729A pdb=" N ASN A 215 " --> pdb=" O ALA A 231 " (cutoff:3.500A) removed outlier: 4.278A pdb=" N ALA A 231 " --> pdb=" O ASN A 215 " (cutoff:3.500A) removed outlier: 6.843A pdb=" N VAL A 217 " --> pdb=" O LEU A 229 " (cutoff:3.500A) removed outlier: 4.411A pdb=" N LEU A 229 " --> pdb=" O VAL A 217 " (cutoff:3.500A) removed outlier: 6.636A pdb=" N ALA A 219 " --> pdb=" O VAL A 227 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N GLN A 225 " --> pdb=" O ALA A 221 " (cutoff:3.500A) removed outlier: 7.010A pdb=" N VAL A 227 " --> pdb=" O ILE A 561 " (cutoff:3.500A) removed outlier: 4.268A pdb=" N ILE A 561 " --> pdb=" O VAL A 227 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N LEU A 229 " --> pdb=" O ALA A 559 " (cutoff:3.500A) removed outlier: 4.415A pdb=" N THR A 555 " --> pdb=" O ALA A 233 " (cutoff:3.500A) removed outlier: 4.275A pdb=" N MET A 543 " --> pdb=" O LEU A 513 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N LEU A 513 " --> pdb=" O MET A 543 " (cutoff:3.500A) removed outlier: 7.202A pdb=" N ALA A 510 " --> pdb=" O THR A 531 " (cutoff:3.500A) removed outlier: 5.070A pdb=" N THR A 531 " --> pdb=" O ALA A 510 " (cutoff:3.500A) removed outlier: 6.256A pdb=" N GLY A 512 " --> pdb=" O LEU A 529 " (cutoff:3.500A) removed outlier: 4.610A pdb=" N LEU A 529 " --> pdb=" O GLY A 512 " (cutoff:3.500A) removed outlier: 6.550A pdb=" N VAL A 514 " --> pdb=" O TYR A 527 " (cutoff:3.500A) removed outlier: 4.399A pdb=" N TYR A 527 " --> pdb=" O VAL A 514 " (cutoff:3.500A) removed outlier: 6.913A pdb=" N LYS A 516 " --> pdb=" O GLU A 525 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 370 through 374 removed outlier: 6.305A pdb=" N GLN A 392 " --> pdb=" O LEU A 477 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 606 through 611 Processing sheet with id=AA5, first strand: chain 'B' and resid 47 through 51 removed outlier: 6.336A pdb=" N ALA B 79 " --> pdb=" O LEU B 157 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N LEU B 156 " --> pdb=" O ARG B 103 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 199 through 202 removed outlier: 4.117A pdb=" N ILE B 195 " --> pdb=" O LEU B 214 " (cutoff:3.500A) removed outlier: 4.573A pdb=" N LEU B 214 " --> pdb=" O ILE B 195 " (cutoff:3.500A) removed outlier: 6.184A pdb=" N ALA B 221 " --> pdb=" O ILE B 226 " (cutoff:3.500A) removed outlier: 5.780A pdb=" N ILE B 226 " --> pdb=" O ALA B 221 " (cutoff:3.500A) removed outlier: 6.837A pdb=" N VAL B 227 " --> pdb=" O ILE B 561 " (cutoff:3.500A) removed outlier: 4.230A pdb=" N ILE B 561 " --> pdb=" O VAL B 227 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N LEU B 229 " --> pdb=" O ALA B 559 " (cutoff:3.500A) removed outlier: 4.425A pdb=" N THR B 555 " --> pdb=" O ALA B 233 " (cutoff:3.500A) removed outlier: 4.398A pdb=" N MET B 543 " --> pdb=" O LEU B 513 " (cutoff:3.500A) removed outlier: 4.129A pdb=" N LEU B 513 " --> pdb=" O MET B 543 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N ASP B 526 " --> pdb=" O LYS B 516 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 370 through 374 removed outlier: 6.252A pdb=" N GLN B 392 " --> pdb=" O LEU B 477 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 606 through 611 Processing sheet with id=AA9, first strand: chain 'C' and resid 47 through 51 removed outlier: 6.364A pdb=" N ALA C 79 " --> pdb=" O LEU C 157 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N LEU C 156 " --> pdb=" O ARG C 103 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 106 through 107 Processing sheet with id=AB2, first strand: chain 'C' and resid 199 through 202 removed outlier: 3.990A pdb=" N ILE C 195 " --> pdb=" O LEU C 214 " (cutoff:3.500A) removed outlier: 4.618A pdb=" N LEU C 214 " --> pdb=" O ILE C 195 " (cutoff:3.500A) removed outlier: 6.123A pdb=" N ALA C 221 " --> pdb=" O ILE C 226 " (cutoff:3.500A) removed outlier: 5.830A pdb=" N ILE C 226 " --> pdb=" O ALA C 221 " (cutoff:3.500A) removed outlier: 7.264A pdb=" N VAL C 227 " --> pdb=" O ILE C 561 " (cutoff:3.500A) removed outlier: 4.581A pdb=" N ILE C 561 " --> pdb=" O VAL C 227 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N LEU C 229 " --> pdb=" O ALA C 559 " (cutoff:3.500A) removed outlier: 4.402A pdb=" N THR C 555 " --> pdb=" O ALA C 233 " (cutoff:3.500A) removed outlier: 4.210A pdb=" N MET C 543 " --> pdb=" O LEU C 513 " (cutoff:3.500A) removed outlier: 4.143A pdb=" N LEU C 513 " --> pdb=" O MET C 543 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N ASP C 526 " --> pdb=" O LYS C 516 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 370 through 374 removed outlier: 6.150A pdb=" N GLN C 392 " --> pdb=" O LEU C 477 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 606 through 611 854 hydrogen bonds defined for protein. 2394 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.42 Time building geometry restraints manager: 1.53 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 4776 1.34 - 1.46: 2876 1.46 - 1.58: 6888 1.58 - 1.70: 11 1.70 - 1.82: 99 Bond restraints: 14650 Sorted by residual: bond pdb=" N ILE C 412 " pdb=" CA ILE C 412 " ideal model delta sigma weight residual 1.458 1.494 -0.036 9.00e-03 1.23e+04 1.61e+01 bond pdb=" N GLN C 410 " pdb=" CA GLN C 410 " ideal model delta sigma weight residual 1.459 1.489 -0.030 1.21e-02 6.83e+03 6.23e+00 bond pdb=" N SER C 408 " pdb=" CA SER C 408 " ideal model delta sigma weight residual 1.459 1.489 -0.030 1.24e-02 6.50e+03 5.87e+00 bond pdb=" P A D 2 " pdb=" O5' A D 2 " ideal model delta sigma weight residual 1.593 1.615 -0.022 1.00e-02 1.00e+04 4.92e+00 bond pdb=" N ARG C 139 " pdb=" CA ARG C 139 " ideal model delta sigma weight residual 1.461 1.481 -0.020 9.20e-03 1.18e+04 4.62e+00 ... (remaining 14645 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.57: 19535 1.57 - 3.15: 252 3.15 - 4.72: 61 4.72 - 6.29: 12 6.29 - 7.87: 6 Bond angle restraints: 19866 Sorted by residual: angle pdb=" C VAL C 411 " pdb=" N ILE C 412 " pdb=" CA ILE C 412 " ideal model delta sigma weight residual 123.16 117.23 5.93 1.06e+00 8.90e-01 3.12e+01 angle pdb=" C3' U D 5 " pdb=" C2' U D 5 " pdb=" C1' U D 5 " ideal model delta sigma weight residual 101.50 97.21 4.29 8.00e-01 1.56e+00 2.87e+01 angle pdb=" C3' A D 2 " pdb=" O3' A D 2 " pdb=" P U D 3 " ideal model delta sigma weight residual 119.70 124.90 -5.20 1.20e+00 6.94e-01 1.88e+01 angle pdb=" CA ILE C 412 " pdb=" C ILE C 412 " pdb=" O ILE C 412 " ideal model delta sigma weight residual 120.80 116.95 3.85 8.90e-01 1.26e+00 1.87e+01 angle pdb=" CA ILE C 412 " pdb=" C ILE C 412 " pdb=" N THR C 413 " ideal model delta sigma weight residual 117.15 120.44 -3.29 7.80e-01 1.64e+00 1.77e+01 ... (remaining 19861 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 25.77: 8423 25.77 - 51.53: 487 51.53 - 77.30: 80 77.30 - 103.06: 21 103.06 - 128.83: 1 Dihedral angle restraints: 9012 sinusoidal: 3640 harmonic: 5372 Sorted by residual: dihedral pdb=" CA LYS B 407 " pdb=" C LYS B 407 " pdb=" N SER B 408 " pdb=" CA SER B 408 " ideal model delta harmonic sigma weight residual 180.00 161.47 18.53 0 5.00e+00 4.00e-02 1.37e+01 dihedral pdb=" CA ASP A 420 " pdb=" C ASP A 420 " pdb=" N LYS A 421 " pdb=" CA LYS A 421 " ideal model delta harmonic sigma weight residual 180.00 162.27 17.73 0 5.00e+00 4.00e-02 1.26e+01 dihedral pdb=" CA TYR A 116 " pdb=" C TYR A 116 " pdb=" N LEU A 117 " pdb=" CA LEU A 117 " ideal model delta harmonic sigma weight residual 180.00 162.30 17.70 0 5.00e+00 4.00e-02 1.25e+01 ... (remaining 9009 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.113: 2299 0.113 - 0.227: 29 0.227 - 0.340: 0 0.340 - 0.453: 1 0.453 - 0.566: 4 Chirality restraints: 2333 Sorted by residual: chirality pdb=" P A D 2 " pdb=" OP1 A D 2 " pdb=" OP2 A D 2 " pdb=" O5' A D 2 " both_signs ideal model delta sigma weight residual True 2.41 -2.98 -0.57 2.00e-01 2.50e+01 8.02e+00 chirality pdb=" P U D 5 " pdb=" OP1 U D 5 " pdb=" OP2 U D 5 " pdb=" O5' U D 5 " both_signs ideal model delta sigma weight residual True 2.41 -2.93 -0.52 2.00e-01 2.50e+01 6.86e+00 chirality pdb=" P C D 4 " pdb=" OP1 C D 4 " pdb=" OP2 C D 4 " pdb=" O5' C D 4 " both_signs ideal model delta sigma weight residual True 2.41 -2.88 -0.47 2.00e-01 2.50e+01 5.50e+00 ... (remaining 2330 not shown) Planarity restraints: 2551 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG C 132 " 0.474 9.50e-02 1.11e+02 2.12e-01 2.76e+01 pdb=" NE ARG C 132 " -0.029 2.00e-02 2.50e+03 pdb=" CZ ARG C 132 " -0.003 2.00e-02 2.50e+03 pdb=" NH1 ARG C 132 " -0.004 2.00e-02 2.50e+03 pdb=" NH2 ARG C 132 " 0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LYS C 407 " 0.011 2.00e-02 2.50e+03 2.14e-02 4.58e+00 pdb=" C LYS C 407 " -0.037 2.00e-02 2.50e+03 pdb=" O LYS C 407 " 0.014 2.00e-02 2.50e+03 pdb=" N SER C 408 " 0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL C 411 " 0.009 2.00e-02 2.50e+03 1.84e-02 3.40e+00 pdb=" C VAL C 411 " -0.032 2.00e-02 2.50e+03 pdb=" O VAL C 411 " 0.012 2.00e-02 2.50e+03 pdb=" N ILE C 412 " 0.011 2.00e-02 2.50e+03 ... (remaining 2548 not shown) Histogram of nonbonded interaction distances: 2.08 - 2.64: 29 2.64 - 3.21: 13049 3.21 - 3.77: 22548 3.77 - 4.34: 32435 4.34 - 4.90: 52035 Nonbonded interactions: 120096 Sorted by model distance: nonbonded pdb=" OD2 ASP C 544 " pdb="MG MG C 902 " model vdw 2.080 2.170 nonbonded pdb="MG MG C 902 " pdb="MG MG D 101 " model vdw 2.402 1.300 nonbonded pdb=" O ASP C 409 " pdb=" N THR C 413 " model vdw 2.462 3.120 nonbonded pdb=" N GLU A 322 " pdb=" OE1 GLU A 322 " model vdw 2.558 3.120 nonbonded pdb=" O ASP A 375 " pdb=" OD1 ASP A 375 " model vdw 2.559 3.040 ... (remaining 120091 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 46 through 115 or resid 121 through 901)) selection = (chain 'B' and (resid 46 through 440 or resid 444 through 901)) selection = (chain 'C' and (resid 46 through 115 or resid 121 through 440 or resid 444 throu \ gh 901)) } 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=0.40 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: 3.230 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: 0.370 Check model and map are aligned: 0.060 Set scattering table: 0.070 Process input model: 13.800 Find NCS groups from input model: 0.400 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: 0.010 Load rotamer database and sin/cos tables:9.270 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.250 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8818 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 : 0.003 0.037 14650 Z= 0.139 Angle : 0.502 7.868 19866 Z= 0.287 Chirality : 0.049 0.566 2333 Planarity : 0.005 0.212 2551 Dihedral : 16.549 128.825 5546 Min Nonbonded Distance : 2.080 Molprobity Statistics. All-atom Clashscore : 4.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.51 % Favored : 98.49 % Rotamer: Outliers : 1.46 % Allowed : 15.76 % Favored : 82.78 % 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: 1.43 (0.20), residues: 1851 helix: 1.14 (0.18), residues: 724 sheet: 1.37 (0.26), residues: 437 loop : 0.65 (0.25), residues: 690 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 617 TYR 0.011 0.001 TYR A 427 PHE 0.011 0.001 PHE A 545 TRP 0.005 0.001 TRP C 184 HIS 0.003 0.001 HIS B 304 Details of bonding type rmsd/Z covalent geometry : bond 0.00256 / 0.14 (14650) covalent geometry : angle 0.50210 / 0.29 (19866) hydrogen bonds : bond 0.20498 / 13.44 ( 854) hydrogen bonds : angle 7.60748 / 5.45 ( 2394) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3702 Ramachandran restraints generated. 1851 Oldfield, 0 Emsley, 1851 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3702 Ramachandran restraints generated. 1851 Oldfield, 0 Emsley, 1851 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 1580 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 130 time to evaluate : 0.445 Fit side-chains revert: symmetry clash REVERT: A 103 ARG cc_start: 0.8615 (mtm110) cc_final: 0.8338 (mmm-85) REVERT: A 355 GLU cc_start: 0.8558 (OUTLIER) cc_final: 0.8014 (mt-10) REVERT: A 424 MET cc_start: 0.9002 (ptp) cc_final: 0.8285 (ppp) REVERT: A 572 MET cc_start: 0.9096 (mmt) cc_final: 0.8779 (mmt) REVERT: A 645 GLU cc_start: 0.7674 (tp30) cc_final: 0.7342 (mm-30) REVERT: B 444 ASN cc_start: 0.7883 (m110) cc_final: 0.7607 (m-40) REVERT: B 445 ARG cc_start: 0.7736 (mtt180) cc_final: 0.7015 (mtp-110) REVERT: B 446 ARG cc_start: 0.7950 (ttp80) cc_final: 0.7564 (tmm-80) REVERT: B 471 ARG cc_start: 0.8627 (ttp80) cc_final: 0.8033 (ttm110) REVERT: B 526 ASP cc_start: 0.7854 (t0) cc_final: 0.7583 (t0) REVERT: B 528 ARG cc_start: 0.8836 (OUTLIER) cc_final: 0.8381 (mmt-90) REVERT: C 56 LEU cc_start: 0.9108 (OUTLIER) cc_final: 0.8812 (mp) REVERT: C 346 GLU cc_start: 0.8283 (tp30) cc_final: 0.7842 (tp30) REVERT: C 412 ILE cc_start: 0.7132 (OUTLIER) cc_final: 0.6670 (mm) REVERT: C 525 GLU cc_start: 0.8538 (OUTLIER) cc_final: 0.8019 (pm20) REVERT: C 616 LYS cc_start: 0.8291 (ptpp) cc_final: 0.7765 (ptmt) REVERT: C 617 ARG cc_start: 0.8134 (ptm-80) cc_final: 0.7764 (ttt-90) REVERT: C 643 ASP cc_start: 0.8384 (t0) cc_final: 0.8012 (m-30) REVERT: C 664 ILE cc_start: 0.7116 (OUTLIER) cc_final: 0.6881 (mp) outliers start: 23 outliers final: 14 residues processed: 148 average time/residue: 0.7183 time to fit residues: 114.8409 Evaluate side-chains 142 residues out of total 1580 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 122 time to evaluate : 0.504 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 116 TYR Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 355 GLU Chi-restraints excluded: chain A residue 365 THR Chi-restraints excluded: chain A residue 642 VAL Chi-restraints excluded: chain A residue 646 THR Chi-restraints excluded: chain B residue 141 LEU Chi-restraints excluded: chain B residue 206 ARG Chi-restraints excluded: chain B residue 365 THR Chi-restraints excluded: chain B residue 372 CYS Chi-restraints excluded: chain B residue 448 LEU Chi-restraints excluded: chain B residue 528 ARG Chi-restraints excluded: chain B residue 610 VAL Chi-restraints excluded: chain C residue 56 LEU Chi-restraints excluded: chain C residue 379 THR Chi-restraints excluded: chain C residue 412 ILE Chi-restraints excluded: chain C residue 448 LEU Chi-restraints excluded: chain C residue 525 GLU Chi-restraints excluded: chain C residue 572 MET Chi-restraints excluded: chain C residue 664 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 98 optimal weight: 9.9990 chunk 107 optimal weight: 0.0470 chunk 10 optimal weight: 5.9990 chunk 66 optimal weight: 3.9990 chunk 130 optimal weight: 10.0000 chunk 124 optimal weight: 2.9990 chunk 103 optimal weight: 3.9990 chunk 77 optimal weight: 2.9990 chunk 122 optimal weight: 5.9990 chunk 91 optimal weight: 3.9990 chunk 149 optimal weight: 1.9990 overall best weight: 2.4086 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 115 ASN C 658 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3687 r_free = 0.3687 target = 0.114568 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3286 r_free = 0.3286 target = 0.088023 restraints weight = 20741.899| |-----------------------------------------------------------------------------| r_work (start): 0.3263 rms_B_bonded: 2.11 r_work: 0.3129 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.3015 rms_B_bonded: 4.11 restraints_weight: 0.2500 r_work (final): 0.3015 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3010 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3010 r_free = 0.3010 target_work(ls_wunit_k1) = 0.073 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3010 r_free = 0.3010 target_work(ls_wunit_k1) = 0.073 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3010 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8890 moved from start: 0.0818 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 14650 Z= 0.250 Angle : 0.574 6.704 19866 Z= 0.317 Chirality : 0.046 0.153 2333 Planarity : 0.004 0.047 2551 Dihedral : 8.644 124.166 2112 Min Nonbonded Distance : 2.078 Molprobity Statistics. All-atom Clashscore : 4.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.57 % Favored : 98.43 % Rotamer: Outliers : 2.85 % Allowed : 14.75 % Favored : 82.41 % 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: 1.87 (0.20), residues: 1851 helix: 1.80 (0.18), residues: 733 sheet: 1.55 (0.25), residues: 442 loop : 0.53 (0.25), residues: 676 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 617 TYR 0.021 0.002 TYR C 334 PHE 0.020 0.002 PHE A 545 TRP 0.003 0.001 TRP C 184 HIS 0.007 0.001 HIS C 658 Details of bonding type rmsd/Z covalent geometry : bond 0.00545 / 0.25 (14650) covalent geometry : angle 0.57369 / 0.32 (19866) hydrogen bonds : bond 0.07042 / 4.69 ( 854) hydrogen bonds : angle 5.76197 / 4.17 ( 2394) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3702 Ramachandran restraints generated. 1851 Oldfield, 0 Emsley, 1851 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3702 Ramachandran restraints generated. 1851 Oldfield, 0 Emsley, 1851 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 1580 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 122 time to evaluate : 0.506 Fit side-chains revert: symmetry clash REVERT: A 56 LEU cc_start: 0.8702 (OUTLIER) cc_final: 0.8437 (mp) REVERT: A 96 MET cc_start: 0.8388 (OUTLIER) cc_final: 0.7695 (ttm) REVERT: A 103 ARG cc_start: 0.8603 (mtm110) cc_final: 0.8397 (mtp-110) REVERT: A 424 MET cc_start: 0.8899 (ptp) cc_final: 0.8321 (ppp) REVERT: A 617 ARG cc_start: 0.7863 (mmm160) cc_final: 0.7494 (mmm160) REVERT: A 645 GLU cc_start: 0.7690 (tp30) cc_final: 0.7367 (mm-30) REVERT: B 50 ASP cc_start: 0.8704 (OUTLIER) cc_final: 0.8461 (t0) REVERT: B 206 ARG cc_start: 0.8135 (OUTLIER) cc_final: 0.7922 (mtp-110) REVERT: B 444 ASN cc_start: 0.7807 (m110) cc_final: 0.7529 (m-40) REVERT: B 445 ARG cc_start: 0.7840 (mtt180) cc_final: 0.6818 (ptt180) REVERT: B 446 ARG cc_start: 0.8025 (ttp80) cc_final: 0.7618 (tmm-80) REVERT: B 471 ARG cc_start: 0.8606 (ttp80) cc_final: 0.8076 (ttm110) REVERT: C 96 MET cc_start: 0.8146 (OUTLIER) cc_final: 0.6533 (ttp) REVERT: C 250 LYS cc_start: 0.8621 (OUTLIER) cc_final: 0.8305 (tmtp) REVERT: C 412 ILE cc_start: 0.6680 (OUTLIER) cc_final: 0.6258 (mm) REVERT: C 523 GLU cc_start: 0.6454 (tp30) cc_final: 0.6102 (tp30) REVERT: C 525 GLU cc_start: 0.8606 (OUTLIER) cc_final: 0.8105 (pm20) REVERT: C 616 LYS cc_start: 0.8465 (ptpp) cc_final: 0.7813 (ptmt) REVERT: C 643 ASP cc_start: 0.8404 (t0) cc_final: 0.8032 (m-30) outliers start: 45 outliers final: 15 residues processed: 156 average time/residue: 0.7040 time to fit residues: 118.8766 Evaluate side-chains 146 residues out of total 1580 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 123 time to evaluate : 0.333 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 LEU Chi-restraints excluded: chain A residue 96 MET Chi-restraints excluded: chain A residue 116 TYR Chi-restraints excluded: chain A residue 283 ILE Chi-restraints excluded: chain A residue 365 THR Chi-restraints excluded: chain A residue 646 THR Chi-restraints excluded: chain A residue 663 PHE Chi-restraints excluded: chain B residue 50 ASP Chi-restraints excluded: chain B residue 103 ARG Chi-restraints excluded: chain B residue 188 VAL Chi-restraints excluded: chain B residue 206 ARG Chi-restraints excluded: chain B residue 266 THR Chi-restraints excluded: chain B residue 365 THR Chi-restraints excluded: chain B residue 448 LEU Chi-restraints excluded: chain B residue 606 VAL Chi-restraints excluded: chain C residue 96 MET Chi-restraints excluded: chain C residue 230 GLU Chi-restraints excluded: chain C residue 250 LYS Chi-restraints excluded: chain C residue 372 CYS Chi-restraints excluded: chain C residue 412 ILE Chi-restraints excluded: chain C residue 483 SER Chi-restraints excluded: chain C residue 525 GLU Chi-restraints excluded: chain C residue 591 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 167 optimal weight: 5.9990 chunk 118 optimal weight: 4.9990 chunk 126 optimal weight: 1.9990 chunk 23 optimal weight: 4.9990 chunk 161 optimal weight: 0.6980 chunk 6 optimal weight: 4.9990 chunk 133 optimal weight: 0.8980 chunk 148 optimal weight: 3.9990 chunk 89 optimal weight: 0.7980 chunk 179 optimal weight: 0.9980 chunk 41 optimal weight: 0.2980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 426 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 658 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3724 r_free = 0.3724 target = 0.117331 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.090954 restraints weight = 20715.054| |-----------------------------------------------------------------------------| r_work (start): 0.3311 rms_B_bonded: 2.13 r_work: 0.3179 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.3066 rms_B_bonded: 4.15 restraints_weight: 0.2500 r_work (final): 0.3066 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3064 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3064 r_free = 0.3064 target_work(ls_wunit_k1) = 0.075 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3064 r_free = 0.3064 target_work(ls_wunit_k1) = 0.075 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3064 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8841 moved from start: 0.0989 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 14650 Z= 0.135 Angle : 0.482 7.513 19866 Z= 0.264 Chirality : 0.043 0.131 2333 Planarity : 0.004 0.048 2551 Dihedral : 7.700 125.719 2088 Min Nonbonded Distance : 2.092 Molprobity Statistics. All-atom Clashscore : 5.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.51 % Favored : 98.49 % Rotamer: Outliers : 2.72 % Allowed : 15.38 % Favored : 81.90 % 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: 2.04 (0.20), residues: 1851 helix: 2.08 (0.18), residues: 740 sheet: 1.42 (0.25), residues: 442 loop : 0.59 (0.26), residues: 669 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 617 TYR 0.019 0.001 TYR C 334 PHE 0.017 0.001 PHE A 545 TRP 0.005 0.001 TRP C 184 HIS 0.002 0.001 HIS B 304 Details of bonding type rmsd/Z covalent geometry : bond 0.00275 / 0.14 (14650) covalent geometry : angle 0.48214 / 0.26 (19866) hydrogen bonds : bond 0.05594 / 3.72 ( 854) hydrogen bonds : angle 5.23195 / 3.79 ( 2394) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3702 Ramachandran restraints generated. 1851 Oldfield, 0 Emsley, 1851 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3702 Ramachandran restraints generated. 1851 Oldfield, 0 Emsley, 1851 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 1580 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 127 time to evaluate : 0.473 Fit side-chains revert: symmetry clash REVERT: A 103 ARG cc_start: 0.8585 (mtm180) cc_final: 0.8373 (mtp-110) REVERT: A 424 MET cc_start: 0.8800 (ptp) cc_final: 0.8262 (ppp) REVERT: A 645 GLU cc_start: 0.7707 (tp30) cc_final: 0.7372 (mm-30) REVERT: B 50 ASP cc_start: 0.8715 (OUTLIER) cc_final: 0.8470 (t0) REVERT: B 206 ARG cc_start: 0.8045 (OUTLIER) cc_final: 0.7654 (mtp-110) REVERT: B 444 ASN cc_start: 0.7715 (m110) cc_final: 0.7425 (m-40) REVERT: B 445 ARG cc_start: 0.7762 (mtt180) cc_final: 0.6645 (ptt180) REVERT: B 446 ARG cc_start: 0.7882 (ttp80) cc_final: 0.7528 (tmm-80) REVERT: B 471 ARG cc_start: 0.8533 (ttp80) cc_final: 0.8029 (ttm110) REVERT: C 126 LYS cc_start: 0.8612 (OUTLIER) cc_final: 0.8387 (ttmt) REVERT: C 250 LYS cc_start: 0.8586 (OUTLIER) cc_final: 0.8301 (tmtp) REVERT: C 346 GLU cc_start: 0.8222 (tp30) cc_final: 0.7896 (tp30) REVERT: C 412 ILE cc_start: 0.6688 (OUTLIER) cc_final: 0.6203 (mm) REVERT: C 445 ARG cc_start: 0.7735 (OUTLIER) cc_final: 0.7003 (mtm180) REVERT: C 616 LYS cc_start: 0.8568 (ptpp) cc_final: 0.7950 (ptmt) REVERT: C 643 ASP cc_start: 0.8371 (t0) cc_final: 0.8035 (m-30) outliers start: 43 outliers final: 18 residues processed: 160 average time/residue: 0.6574 time to fit residues: 113.7804 Evaluate side-chains 145 residues out of total 1580 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 121 time to evaluate : 0.476 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 116 TYR Chi-restraints excluded: chain A residue 365 THR Chi-restraints excluded: chain A residue 642 VAL Chi-restraints excluded: chain A residue 663 PHE Chi-restraints excluded: chain B residue 50 ASP Chi-restraints excluded: chain B residue 56 LEU Chi-restraints excluded: chain B residue 103 ARG Chi-restraints excluded: chain B residue 188 VAL Chi-restraints excluded: chain B residue 206 ARG Chi-restraints excluded: chain B residue 284 VAL Chi-restraints excluded: chain B residue 301 ASP Chi-restraints excluded: chain B residue 448 LEU Chi-restraints excluded: chain B residue 606 VAL Chi-restraints excluded: chain B residue 610 VAL Chi-restraints excluded: chain C residue 126 LYS Chi-restraints excluded: chain C residue 188 VAL Chi-restraints excluded: chain C residue 250 LYS Chi-restraints excluded: chain C residue 257 GLN Chi-restraints excluded: chain C residue 372 CYS Chi-restraints excluded: chain C residue 379 THR Chi-restraints excluded: chain C residue 412 ILE Chi-restraints excluded: chain C residue 441 THR Chi-restraints excluded: chain C residue 445 ARG Chi-restraints excluded: chain C residue 483 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 126 optimal weight: 7.9990 chunk 99 optimal weight: 3.9990 chunk 43 optimal weight: 7.9990 chunk 120 optimal weight: 9.9990 chunk 149 optimal weight: 5.9990 chunk 151 optimal weight: 3.9990 chunk 1 optimal weight: 4.9990 chunk 160 optimal weight: 3.9990 chunk 39 optimal weight: 0.0060 chunk 34 optimal weight: 3.9990 chunk 101 optimal weight: 0.9990 overall best weight: 2.6004 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 658 HIS ** C 426 HIS ** 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 = 0.3687 r_free = 0.3687 target = 0.114659 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.087859 restraints weight = 20718.168| |-----------------------------------------------------------------------------| r_work (start): 0.3259 rms_B_bonded: 2.12 r_work: 0.3131 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.3022 rms_B_bonded: 4.03 restraints_weight: 0.2500 r_work (final): 0.3022 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3013 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3013 r_free = 0.3013 target_work(ls_wunit_k1) = 0.073 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3013 r_free = 0.3013 target_work(ls_wunit_k1) = 0.073 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3013 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8873 moved from start: 0.1145 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.058 14650 Z= 0.265 Angle : 0.580 7.364 19866 Z= 0.316 Chirality : 0.047 0.157 2333 Planarity : 0.005 0.053 2551 Dihedral : 7.737 125.777 2083 Min Nonbonded Distance : 2.125 Molprobity Statistics. All-atom Clashscore : 5.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.67 % Favored : 98.33 % Rotamer: Outliers : 3.29 % Allowed : 15.19 % Favored : 81.52 % 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: 1.85 (0.20), residues: 1851 helix: 1.90 (0.18), residues: 737 sheet: 1.42 (0.25), residues: 441 loop : 0.45 (0.25), residues: 673 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG C 617 TYR 0.020 0.002 TYR C 334 PHE 0.034 0.002 PHE A 663 TRP 0.004 0.002 TRP B 184 HIS 0.004 0.001 HIS A 658 Details of bonding type rmsd/Z covalent geometry : bond 0.00596 / 0.27 (14650) covalent geometry : angle 0.58037 / 0.32 (19866) hydrogen bonds : bond 0.06279 / 4.16 ( 854) hydrogen bonds : angle 5.36646 / 3.87 ( 2394) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3702 Ramachandran restraints generated. 1851 Oldfield, 0 Emsley, 1851 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3702 Ramachandran restraints generated. 1851 Oldfield, 0 Emsley, 1851 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 1580 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 122 time to evaluate : 0.583 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 96 MET cc_start: 0.8452 (OUTLIER) cc_final: 0.7735 (ttm) REVERT: A 239 GLN cc_start: 0.8163 (OUTLIER) cc_final: 0.7872 (pm20) REVERT: A 355 GLU cc_start: 0.8545 (OUTLIER) cc_final: 0.7953 (mt-10) REVERT: A 424 MET cc_start: 0.8884 (ptp) cc_final: 0.8275 (ppp) REVERT: A 645 GLU cc_start: 0.7701 (tp30) cc_final: 0.7382 (mm-30) REVERT: B 50 ASP cc_start: 0.8731 (OUTLIER) cc_final: 0.8491 (t0) REVERT: B 89 LYS cc_start: 0.8671 (OUTLIER) cc_final: 0.8372 (pttm) REVERT: B 346 GLU cc_start: 0.8045 (pp20) cc_final: 0.7416 (tm-30) REVERT: B 444 ASN cc_start: 0.7829 (m110) cc_final: 0.7525 (m-40) REVERT: B 445 ARG cc_start: 0.7844 (mtt180) cc_final: 0.6700 (ptt180) REVERT: B 446 ARG cc_start: 0.7962 (ttp80) cc_final: 0.7580 (tmm-80) REVERT: B 471 ARG cc_start: 0.8577 (ttp80) cc_final: 0.8020 (ttm110) REVERT: C 126 LYS cc_start: 0.8616 (OUTLIER) cc_final: 0.8397 (ttmt) REVERT: C 250 LYS cc_start: 0.8636 (OUTLIER) cc_final: 0.8376 (ttmp) REVERT: C 412 ILE cc_start: 0.6718 (OUTLIER) cc_final: 0.6358 (mm) REVERT: C 445 ARG cc_start: 0.7853 (OUTLIER) cc_final: 0.7115 (mtm180) REVERT: C 523 GLU cc_start: 0.6376 (tp30) cc_final: 0.6116 (tp30) REVERT: C 525 GLU cc_start: 0.8624 (OUTLIER) cc_final: 0.8110 (pm20) REVERT: C 528 ARG cc_start: 0.8947 (OUTLIER) cc_final: 0.7429 (mmt90) REVERT: C 616 LYS cc_start: 0.8586 (ptpp) cc_final: 0.7968 (ptmt) REVERT: C 643 ASP cc_start: 0.8357 (t0) cc_final: 0.8024 (m-30) outliers start: 52 outliers final: 26 residues processed: 162 average time/residue: 0.6816 time to fit residues: 119.7598 Evaluate side-chains 155 residues out of total 1580 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 118 time to evaluate : 0.448 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 96 MET Chi-restraints excluded: chain A residue 116 TYR Chi-restraints excluded: chain A residue 239 GLN Chi-restraints excluded: chain A residue 285 LYS Chi-restraints excluded: chain A residue 355 GLU Chi-restraints excluded: chain A residue 365 THR Chi-restraints excluded: chain A residue 642 VAL Chi-restraints excluded: chain A residue 646 THR Chi-restraints excluded: chain B residue 50 ASP Chi-restraints excluded: chain B residue 56 LEU Chi-restraints excluded: chain B residue 89 LYS Chi-restraints excluded: chain B residue 103 ARG Chi-restraints excluded: chain B residue 123 THR Chi-restraints excluded: chain B residue 188 VAL Chi-restraints excluded: chain B residue 266 THR Chi-restraints excluded: chain B residue 284 VAL Chi-restraints excluded: chain B residue 372 CYS Chi-restraints excluded: chain B residue 448 LEU Chi-restraints excluded: chain B residue 517 THR Chi-restraints excluded: chain B residue 587 GLN Chi-restraints excluded: chain B residue 606 VAL Chi-restraints excluded: chain B residue 610 VAL Chi-restraints excluded: chain B residue 645 GLU Chi-restraints excluded: chain C residue 126 LYS Chi-restraints excluded: chain C residue 188 VAL Chi-restraints excluded: chain C residue 230 GLU Chi-restraints excluded: chain C residue 250 LYS Chi-restraints excluded: chain C residue 257 GLN Chi-restraints excluded: chain C residue 342 VAL Chi-restraints excluded: chain C residue 372 CYS Chi-restraints excluded: chain C residue 412 ILE Chi-restraints excluded: chain C residue 441 THR Chi-restraints excluded: chain C residue 445 ARG Chi-restraints excluded: chain C residue 448 LEU Chi-restraints excluded: chain C residue 483 SER Chi-restraints excluded: chain C residue 525 GLU Chi-restraints excluded: chain C residue 528 ARG Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 155 optimal weight: 3.9990 chunk 35 optimal weight: 0.8980 chunk 86 optimal weight: 0.4980 chunk 6 optimal weight: 3.9990 chunk 61 optimal weight: 0.0040 chunk 3 optimal weight: 5.9990 chunk 111 optimal weight: 4.9990 chunk 94 optimal weight: 0.0980 chunk 176 optimal weight: 0.7980 chunk 87 optimal weight: 4.9990 chunk 60 optimal weight: 0.3980 overall best weight: 0.3592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 115 ASN ** C 426 HIS ** 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 = 0.3738 r_free = 0.3738 target = 0.118391 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.092669 restraints weight = 20647.060| |-----------------------------------------------------------------------------| r_work (start): 0.3335 rms_B_bonded: 2.07 r_work: 0.3211 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.3103 rms_B_bonded: 4.03 restraints_weight: 0.2500 r_work (final): 0.3103 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3096 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3096 r_free = 0.3096 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3096 r_free = 0.3096 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (7 function evaluations) r_final: 0.3096 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8804 moved from start: 0.1249 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 14650 Z= 0.119 Angle : 0.475 6.604 19866 Z= 0.257 Chirality : 0.043 0.139 2333 Planarity : 0.004 0.049 2551 Dihedral : 7.355 127.385 2079 Min Nonbonded Distance : 2.119 Molprobity Statistics. All-atom Clashscore : 5.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.73 % Favored : 98.27 % Rotamer: Outliers : 2.53 % Allowed : 16.27 % Favored : 81.20 % 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: 2.05 (0.20), residues: 1851 helix: 2.19 (0.18), residues: 739 sheet: 1.28 (0.24), residues: 450 loop : 0.57 (0.26), residues: 662 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 617 TYR 0.019 0.001 TYR C 334 PHE 0.018 0.001 PHE B 545 TRP 0.007 0.001 TRP B 184 HIS 0.004 0.001 HIS C 658 Details of bonding type rmsd/Z covalent geometry : bond 0.00241 / 0.12 (14650) covalent geometry : angle 0.47496 / 0.26 (19866) hydrogen bonds : bond 0.04788 / 3.20 ( 854) hydrogen bonds : angle 4.92339 / 3.57 ( 2394) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3702 Ramachandran restraints generated. 1851 Oldfield, 0 Emsley, 1851 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3702 Ramachandran restraints generated. 1851 Oldfield, 0 Emsley, 1851 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 1580 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 136 time to evaluate : 0.576 Fit side-chains revert: symmetry clash REVERT: A 103 ARG cc_start: 0.8595 (mtp-110) cc_final: 0.8295 (mmm-85) REVERT: A 239 GLN cc_start: 0.8026 (OUTLIER) cc_final: 0.7688 (pm20) REVERT: A 355 GLU cc_start: 0.8484 (OUTLIER) cc_final: 0.7863 (mt-10) REVERT: A 424 MET cc_start: 0.8732 (ptp) cc_final: 0.8217 (ppp) REVERT: A 445 ARG cc_start: 0.8230 (mtt180) cc_final: 0.6950 (ptt-90) REVERT: A 645 GLU cc_start: 0.7722 (tp30) cc_final: 0.7369 (mm-30) REVERT: B 50 ASP cc_start: 0.8723 (OUTLIER) cc_final: 0.8476 (t0) REVERT: B 103 ARG cc_start: 0.8034 (OUTLIER) cc_final: 0.7329 (mtp85) REVERT: B 206 ARG cc_start: 0.7967 (OUTLIER) cc_final: 0.7515 (mtp-110) REVERT: B 444 ASN cc_start: 0.7654 (m110) cc_final: 0.7369 (m-40) REVERT: B 445 ARG cc_start: 0.7699 (mtt180) cc_final: 0.6521 (ptt180) REVERT: B 446 ARG cc_start: 0.7845 (ttp80) cc_final: 0.7468 (tmm-80) REVERT: B 471 ARG cc_start: 0.8497 (ttp80) cc_final: 0.7911 (ttm110) REVERT: C 346 GLU cc_start: 0.8202 (tp30) cc_final: 0.7871 (tp30) REVERT: C 412 ILE cc_start: 0.6599 (OUTLIER) cc_final: 0.6236 (mm) REVERT: C 445 ARG cc_start: 0.7723 (OUTLIER) cc_final: 0.6971 (mtm180) REVERT: C 523 GLU cc_start: 0.6570 (tp30) cc_final: 0.6259 (tp30) REVERT: C 525 GLU cc_start: 0.8612 (OUTLIER) cc_final: 0.8117 (pm20) REVERT: C 616 LYS cc_start: 0.8549 (ptpp) cc_final: 0.7984 (ptpt) REVERT: C 643 ASP cc_start: 0.8325 (t0) cc_final: 0.7993 (m-30) outliers start: 40 outliers final: 13 residues processed: 165 average time/residue: 0.6623 time to fit residues: 118.2362 Evaluate side-chains 145 residues out of total 1580 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 124 time to evaluate : 0.600 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 116 TYR Chi-restraints excluded: chain A residue 239 GLN Chi-restraints excluded: chain A residue 355 GLU Chi-restraints excluded: chain A residue 365 THR Chi-restraints excluded: chain A residue 642 VAL Chi-restraints excluded: chain B residue 50 ASP Chi-restraints excluded: chain B residue 56 LEU Chi-restraints excluded: chain B residue 103 ARG Chi-restraints excluded: chain B residue 206 ARG Chi-restraints excluded: chain B residue 284 VAL Chi-restraints excluded: chain B residue 448 LEU Chi-restraints excluded: chain B residue 610 VAL Chi-restraints excluded: chain C residue 188 VAL Chi-restraints excluded: chain C residue 257 GLN Chi-restraints excluded: chain C residue 372 CYS Chi-restraints excluded: chain C residue 412 ILE Chi-restraints excluded: chain C residue 441 THR Chi-restraints excluded: chain C residue 445 ARG Chi-restraints excluded: chain C residue 483 SER Chi-restraints excluded: chain C residue 525 GLU Chi-restraints excluded: chain C residue 607 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 10 optimal weight: 3.9990 chunk 114 optimal weight: 2.9990 chunk 149 optimal weight: 5.9990 chunk 35 optimal weight: 1.9990 chunk 33 optimal weight: 4.9990 chunk 76 optimal weight: 5.9990 chunk 125 optimal weight: 7.9990 chunk 17 optimal weight: 0.4980 chunk 30 optimal weight: 3.9990 chunk 126 optimal weight: 2.9990 chunk 12 optimal weight: 4.9990 overall best weight: 2.4988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 426 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 658 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3689 r_free = 0.3689 target = 0.114797 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.088191 restraints weight = 20740.370| |-----------------------------------------------------------------------------| r_work (start): 0.3265 rms_B_bonded: 2.13 r_work: 0.3132 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.3019 rms_B_bonded: 4.11 restraints_weight: 0.2500 r_work (final): 0.3019 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3015 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3015 r_free = 0.3015 target_work(ls_wunit_k1) = 0.073 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3015 r_free = 0.3015 target_work(ls_wunit_k1) = 0.073 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3015 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8885 moved from start: 0.1275 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.053 14650 Z= 0.251 Angle : 0.564 7.031 19866 Z= 0.307 Chirality : 0.046 0.158 2333 Planarity : 0.004 0.051 2551 Dihedral : 7.527 127.079 2079 Min Nonbonded Distance : 2.120 Molprobity Statistics. All-atom Clashscore : 5.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.67 % Favored : 98.33 % Rotamer: Outliers : 3.29 % Allowed : 16.08 % Favored : 80.63 % 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: 1.96 (0.20), residues: 1851 helix: 2.04 (0.18), residues: 738 sheet: 1.36 (0.25), residues: 447 loop : 0.52 (0.26), residues: 666 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 617 TYR 0.020 0.002 TYR C 334 PHE 0.026 0.002 PHE A 663 TRP 0.004 0.001 TRP B 184 HIS 0.003 0.001 HIS A 658 Details of bonding type rmsd/Z covalent geometry : bond 0.00560 / 0.25 (14650) covalent geometry : angle 0.56414 / 0.31 (19866) hydrogen bonds : bond 0.05923 / 3.92 ( 854) hydrogen bonds : angle 5.19149 / 3.74 ( 2394) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3702 Ramachandran restraints generated. 1851 Oldfield, 0 Emsley, 1851 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3702 Ramachandran restraints generated. 1851 Oldfield, 0 Emsley, 1851 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 1580 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 125 time to evaluate : 0.561 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 206 ARG cc_start: 0.8387 (OUTLIER) cc_final: 0.7584 (ttp-110) REVERT: A 239 GLN cc_start: 0.8119 (OUTLIER) cc_final: 0.7826 (pm20) REVERT: A 355 GLU cc_start: 0.8535 (OUTLIER) cc_final: 0.7956 (mt-10) REVERT: A 424 MET cc_start: 0.8842 (ptp) cc_final: 0.8294 (ppp) REVERT: A 645 GLU cc_start: 0.7712 (tp30) cc_final: 0.7370 (mm-30) REVERT: B 50 ASP cc_start: 0.8703 (OUTLIER) cc_final: 0.8466 (t0) REVERT: B 89 LYS cc_start: 0.8703 (OUTLIER) cc_final: 0.8488 (pmtt) REVERT: B 103 ARG cc_start: 0.8151 (OUTLIER) cc_final: 0.7464 (mtp85) REVERT: B 206 ARG cc_start: 0.8129 (OUTLIER) cc_final: 0.7671 (mtp-110) REVERT: B 346 GLU cc_start: 0.8023 (pp20) cc_final: 0.7429 (tm-30) REVERT: B 444 ASN cc_start: 0.7893 (m110) cc_final: 0.7589 (m110) REVERT: B 445 ARG cc_start: 0.7855 (mtt180) cc_final: 0.6713 (ptt180) REVERT: B 446 ARG cc_start: 0.7980 (ttp80) cc_final: 0.7591 (tmm-80) REVERT: B 471 ARG cc_start: 0.8586 (ttp80) cc_final: 0.8056 (ttm110) REVERT: C 120 GLU cc_start: 0.6676 (OUTLIER) cc_final: 0.6400 (mt-10) REVERT: C 250 LYS cc_start: 0.8604 (OUTLIER) cc_final: 0.8296 (tmtp) REVERT: C 412 ILE cc_start: 0.6695 (OUTLIER) cc_final: 0.6374 (mm) REVERT: C 445 ARG cc_start: 0.7884 (OUTLIER) cc_final: 0.7132 (mtm180) REVERT: C 523 GLU cc_start: 0.6571 (tp30) cc_final: 0.6258 (tp30) REVERT: C 525 GLU cc_start: 0.8608 (OUTLIER) cc_final: 0.8087 (pm20) REVERT: C 616 LYS cc_start: 0.8612 (ptpp) cc_final: 0.8034 (ptpt) REVERT: C 643 ASP cc_start: 0.8388 (t0) cc_final: 0.8043 (m-30) outliers start: 52 outliers final: 21 residues processed: 162 average time/residue: 0.6895 time to fit residues: 120.9867 Evaluate side-chains 156 residues out of total 1580 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 123 time to evaluate : 0.573 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 116 TYR Chi-restraints excluded: chain A residue 206 ARG Chi-restraints excluded: chain A residue 239 GLN Chi-restraints excluded: chain A residue 355 GLU Chi-restraints excluded: chain A residue 365 THR Chi-restraints excluded: chain A residue 642 VAL Chi-restraints excluded: chain B residue 50 ASP Chi-restraints excluded: chain B residue 56 LEU Chi-restraints excluded: chain B residue 89 LYS Chi-restraints excluded: chain B residue 103 ARG Chi-restraints excluded: chain B residue 141 LEU Chi-restraints excluded: chain B residue 188 VAL Chi-restraints excluded: chain B residue 206 ARG Chi-restraints excluded: chain B residue 266 THR Chi-restraints excluded: chain B residue 284 VAL Chi-restraints excluded: chain B residue 372 CYS Chi-restraints excluded: chain B residue 448 LEU Chi-restraints excluded: chain B residue 517 THR Chi-restraints excluded: chain B residue 587 GLN Chi-restraints excluded: chain B residue 606 VAL Chi-restraints excluded: chain B residue 610 VAL Chi-restraints excluded: chain B residue 645 GLU Chi-restraints excluded: chain C residue 120 GLU Chi-restraints excluded: chain C residue 188 VAL Chi-restraints excluded: chain C residue 230 GLU Chi-restraints excluded: chain C residue 250 LYS Chi-restraints excluded: chain C residue 372 CYS Chi-restraints excluded: chain C residue 412 ILE Chi-restraints excluded: chain C residue 441 THR Chi-restraints excluded: chain C residue 445 ARG Chi-restraints excluded: chain C residue 483 SER Chi-restraints excluded: chain C residue 525 GLU Chi-restraints excluded: chain C residue 607 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 144 optimal weight: 0.8980 chunk 98 optimal weight: 2.9990 chunk 44 optimal weight: 4.9990 chunk 99 optimal weight: 0.9990 chunk 64 optimal weight: 4.9990 chunk 118 optimal weight: 0.8980 chunk 164 optimal weight: 0.9990 chunk 50 optimal weight: 3.9990 chunk 137 optimal weight: 0.9980 chunk 108 optimal weight: 3.9990 chunk 18 optimal weight: 0.9990 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 426 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3719 r_free = 0.3719 target = 0.117062 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.090737 restraints weight = 20498.738| |-----------------------------------------------------------------------------| r_work (start): 0.3306 rms_B_bonded: 2.11 r_work: 0.3179 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.3069 rms_B_bonded: 4.06 restraints_weight: 0.2500 r_work (final): 0.3069 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3062 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3062 r_free = 0.3062 target_work(ls_wunit_k1) = 0.075 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3062 r_free = 0.3062 target_work(ls_wunit_k1) = 0.075 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3062 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8832 moved from start: 0.1282 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 14650 Z= 0.144 Angle : 0.496 5.816 19866 Z= 0.270 Chirality : 0.044 0.156 2333 Planarity : 0.004 0.049 2551 Dihedral : 7.366 128.042 2079 Min Nonbonded Distance : 2.089 Molprobity Statistics. All-atom Clashscore : 5.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.73 % Favored : 98.27 % Rotamer: Outliers : 2.66 % Allowed : 16.46 % Favored : 80.89 % 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: 2.07 (0.20), residues: 1851 helix: 2.20 (0.18), residues: 740 sheet: 1.33 (0.25), residues: 448 loop : 0.55 (0.26), residues: 663 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 617 TYR 0.019 0.001 TYR C 334 PHE 0.031 0.001 PHE A 663 TRP 0.005 0.001 TRP C 184 HIS 0.002 0.001 HIS C 426 Details of bonding type rmsd/Z covalent geometry : bond 0.00304 / 0.14 (14650) covalent geometry : angle 0.49615 / 0.27 (19866) hydrogen bonds : bond 0.05096 / 3.39 ( 854) hydrogen bonds : angle 4.95793 / 3.59 ( 2394) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3702 Ramachandran restraints generated. 1851 Oldfield, 0 Emsley, 1851 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3702 Ramachandran restraints generated. 1851 Oldfield, 0 Emsley, 1851 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 1580 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 127 time to evaluate : 0.563 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 103 ARG cc_start: 0.8574 (mtp-110) cc_final: 0.8371 (mmm-85) REVERT: A 239 GLN cc_start: 0.8030 (OUTLIER) cc_final: 0.7705 (pm20) REVERT: A 355 GLU cc_start: 0.8510 (OUTLIER) cc_final: 0.7873 (mt-10) REVERT: A 424 MET cc_start: 0.8784 (ptp) cc_final: 0.8236 (ppp) REVERT: A 645 GLU cc_start: 0.7710 (tp30) cc_final: 0.7357 (mm-30) REVERT: B 50 ASP cc_start: 0.8728 (OUTLIER) cc_final: 0.8481 (t0) REVERT: B 103 ARG cc_start: 0.8071 (OUTLIER) cc_final: 0.7378 (mtp85) REVERT: B 206 ARG cc_start: 0.8032 (OUTLIER) cc_final: 0.7562 (mtp-110) REVERT: B 346 GLU cc_start: 0.7945 (pp20) cc_final: 0.7353 (tm-30) REVERT: B 444 ASN cc_start: 0.7760 (m110) cc_final: 0.7433 (m-40) REVERT: B 445 ARG cc_start: 0.7793 (mtt180) cc_final: 0.6619 (ptt180) REVERT: B 446 ARG cc_start: 0.7886 (ttp80) cc_final: 0.7503 (tmm-80) REVERT: B 471 ARG cc_start: 0.8530 (ttp80) cc_final: 0.7996 (ttm110) REVERT: C 250 LYS cc_start: 0.8568 (OUTLIER) cc_final: 0.8262 (tmtp) REVERT: C 346 GLU cc_start: 0.8182 (tp30) cc_final: 0.7847 (tp30) REVERT: C 412 ILE cc_start: 0.6601 (OUTLIER) cc_final: 0.6257 (mm) REVERT: C 445 ARG cc_start: 0.7763 (OUTLIER) cc_final: 0.6992 (mtm180) REVERT: C 523 GLU cc_start: 0.6545 (tp30) cc_final: 0.6242 (tp30) REVERT: C 525 GLU cc_start: 0.8596 (OUTLIER) cc_final: 0.8064 (pm20) REVERT: C 616 LYS cc_start: 0.8607 (ptpp) cc_final: 0.8013 (ptpt) REVERT: C 643 ASP cc_start: 0.8346 (t0) cc_final: 0.8029 (m-30) outliers start: 42 outliers final: 22 residues processed: 162 average time/residue: 0.6535 time to fit residues: 114.7528 Evaluate side-chains 156 residues out of total 1580 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 125 time to evaluate : 0.566 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 116 TYR Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 119 ARG Chi-restraints excluded: chain A residue 239 GLN Chi-restraints excluded: chain A residue 355 GLU Chi-restraints excluded: chain A residue 365 THR Chi-restraints excluded: chain A residue 642 VAL Chi-restraints excluded: chain B residue 50 ASP Chi-restraints excluded: chain B residue 56 LEU Chi-restraints excluded: chain B residue 103 ARG Chi-restraints excluded: chain B residue 141 LEU Chi-restraints excluded: chain B residue 188 VAL Chi-restraints excluded: chain B residue 206 ARG Chi-restraints excluded: chain B residue 284 VAL Chi-restraints excluded: chain B residue 372 CYS Chi-restraints excluded: chain B residue 448 LEU Chi-restraints excluded: chain B residue 517 THR Chi-restraints excluded: chain B residue 587 GLN Chi-restraints excluded: chain B residue 606 VAL Chi-restraints excluded: chain B residue 610 VAL Chi-restraints excluded: chain B residue 645 GLU Chi-restraints excluded: chain C residue 188 VAL Chi-restraints excluded: chain C residue 250 LYS Chi-restraints excluded: chain C residue 257 GLN Chi-restraints excluded: chain C residue 372 CYS Chi-restraints excluded: chain C residue 412 ILE Chi-restraints excluded: chain C residue 441 THR Chi-restraints excluded: chain C residue 445 ARG Chi-restraints excluded: chain C residue 483 SER Chi-restraints excluded: chain C residue 525 GLU Chi-restraints excluded: chain C residue 607 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 27 optimal weight: 0.9980 chunk 83 optimal weight: 3.9990 chunk 51 optimal weight: 4.9990 chunk 91 optimal weight: 3.9990 chunk 71 optimal weight: 0.0470 chunk 21 optimal weight: 3.9990 chunk 11 optimal weight: 7.9990 chunk 158 optimal weight: 6.9990 chunk 29 optimal weight: 6.9990 chunk 182 optimal weight: 4.9990 chunk 109 optimal weight: 0.2980 overall best weight: 1.8682 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 426 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 658 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3699 r_free = 0.3699 target = 0.115638 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.089069 restraints weight = 20543.273| |-----------------------------------------------------------------------------| r_work (start): 0.3280 rms_B_bonded: 2.12 r_work: 0.3147 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.3034 rms_B_bonded: 4.11 restraints_weight: 0.2500 r_work (final): 0.3034 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3030 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3030 r_free = 0.3030 target_work(ls_wunit_k1) = 0.074 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3030 r_free = 0.3030 target_work(ls_wunit_k1) = 0.074 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (17 function evaluations) r_final: 0.3030 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8872 moved from start: 0.1306 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 14650 Z= 0.204 Angle : 0.536 6.715 19866 Z= 0.291 Chirality : 0.045 0.142 2333 Planarity : 0.004 0.051 2551 Dihedral : 7.438 128.016 2079 Min Nonbonded Distance : 2.032 Molprobity Statistics. All-atom Clashscore : 5.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.51 % Favored : 98.49 % Rotamer: Outliers : 2.59 % Allowed : 16.46 % Favored : 80.95 % 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: 2.05 (0.20), residues: 1851 helix: 2.16 (0.18), residues: 740 sheet: 1.35 (0.24), residues: 448 loop : 0.55 (0.26), residues: 663 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 118 TYR 0.020 0.002 TYR C 334 PHE 0.033 0.002 PHE A 663 TRP 0.003 0.001 TRP C 184 HIS 0.003 0.001 HIS A 658 Details of bonding type rmsd/Z covalent geometry : bond 0.00448 / 0.20 (14650) covalent geometry : angle 0.53567 / 0.29 (19866) hydrogen bonds : bond 0.05539 / 3.67 ( 854) hydrogen bonds : angle 5.06043 / 3.65 ( 2394) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3702 Ramachandran restraints generated. 1851 Oldfield, 0 Emsley, 1851 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3702 Ramachandran restraints generated. 1851 Oldfield, 0 Emsley, 1851 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 1580 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 125 time to evaluate : 0.573 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 355 GLU cc_start: 0.8533 (OUTLIER) cc_final: 0.7884 (mt-10) REVERT: A 424 MET cc_start: 0.8799 (ptp) cc_final: 0.8263 (ppp) REVERT: A 645 GLU cc_start: 0.7728 (tp30) cc_final: 0.7379 (mm-30) REVERT: B 50 ASP cc_start: 0.8699 (OUTLIER) cc_final: 0.8461 (t0) REVERT: B 89 LYS cc_start: 0.8718 (OUTLIER) cc_final: 0.8374 (pttm) REVERT: B 103 ARG cc_start: 0.8099 (OUTLIER) cc_final: 0.7424 (mtp85) REVERT: B 206 ARG cc_start: 0.8113 (OUTLIER) cc_final: 0.7652 (mtp-110) REVERT: B 346 GLU cc_start: 0.7992 (pp20) cc_final: 0.7421 (tm-30) REVERT: B 444 ASN cc_start: 0.7879 (m110) cc_final: 0.7577 (m110) REVERT: B 445 ARG cc_start: 0.7834 (mtt180) cc_final: 0.6708 (ptt180) REVERT: B 446 ARG cc_start: 0.7963 (ttp80) cc_final: 0.7584 (tmm-80) REVERT: B 471 ARG cc_start: 0.8561 (ttp80) cc_final: 0.8044 (ttm110) REVERT: C 120 GLU cc_start: 0.6792 (OUTLIER) cc_final: 0.6534 (mt-10) REVERT: C 346 GLU cc_start: 0.8219 (tp30) cc_final: 0.7877 (tp30) REVERT: C 412 ILE cc_start: 0.6643 (OUTLIER) cc_final: 0.6334 (mm) REVERT: C 445 ARG cc_start: 0.7847 (OUTLIER) cc_final: 0.7087 (mtm180) REVERT: C 523 GLU cc_start: 0.6664 (tp30) cc_final: 0.6350 (tp30) REVERT: C 525 GLU cc_start: 0.8600 (OUTLIER) cc_final: 0.8069 (pm20) REVERT: C 616 LYS cc_start: 0.8610 (ptpp) cc_final: 0.8024 (ptpt) REVERT: C 643 ASP cc_start: 0.8388 (t0) cc_final: 0.8044 (m-30) REVERT: C 664 ILE cc_start: 0.7236 (OUTLIER) cc_final: 0.6961 (mp) outliers start: 41 outliers final: 22 residues processed: 157 average time/residue: 0.7016 time to fit residues: 119.2256 Evaluate side-chains 158 residues out of total 1580 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 126 time to evaluate : 0.384 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 116 TYR Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 206 ARG Chi-restraints excluded: chain A residue 355 GLU Chi-restraints excluded: chain A residue 365 THR Chi-restraints excluded: chain A residue 642 VAL Chi-restraints excluded: chain B residue 50 ASP Chi-restraints excluded: chain B residue 56 LEU Chi-restraints excluded: chain B residue 89 LYS Chi-restraints excluded: chain B residue 103 ARG Chi-restraints excluded: chain B residue 141 LEU Chi-restraints excluded: chain B residue 188 VAL Chi-restraints excluded: chain B residue 206 ARG Chi-restraints excluded: chain B residue 284 VAL Chi-restraints excluded: chain B residue 372 CYS Chi-restraints excluded: chain B residue 448 LEU Chi-restraints excluded: chain B residue 517 THR Chi-restraints excluded: chain B residue 587 GLN Chi-restraints excluded: chain B residue 606 VAL Chi-restraints excluded: chain B residue 610 VAL Chi-restraints excluded: chain B residue 645 GLU Chi-restraints excluded: chain C residue 120 GLU Chi-restraints excluded: chain C residue 188 VAL Chi-restraints excluded: chain C residue 257 GLN Chi-restraints excluded: chain C residue 372 CYS Chi-restraints excluded: chain C residue 412 ILE Chi-restraints excluded: chain C residue 441 THR Chi-restraints excluded: chain C residue 445 ARG Chi-restraints excluded: chain C residue 483 SER Chi-restraints excluded: chain C residue 525 GLU Chi-restraints excluded: chain C residue 607 VAL Chi-restraints excluded: chain C residue 664 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 56 optimal weight: 0.9980 chunk 29 optimal weight: 3.9990 chunk 142 optimal weight: 1.9990 chunk 85 optimal weight: 0.1980 chunk 43 optimal weight: 3.9990 chunk 99 optimal weight: 4.9990 chunk 96 optimal weight: 3.9990 chunk 7 optimal weight: 0.0050 chunk 25 optimal weight: 0.5980 chunk 80 optimal weight: 0.9980 chunk 89 optimal weight: 0.0570 overall best weight: 0.3712 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 426 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3744 r_free = 0.3744 target = 0.118717 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.093151 restraints weight = 20572.746| |-----------------------------------------------------------------------------| r_work (start): 0.3342 rms_B_bonded: 2.06 r_work: 0.3218 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.3110 rms_B_bonded: 4.02 restraints_weight: 0.2500 r_work (final): 0.3110 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3103 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3103 r_free = 0.3103 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3103 r_free = 0.3103 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3103 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8800 moved from start: 0.1390 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 14650 Z= 0.116 Angle : 0.484 6.459 19866 Z= 0.262 Chirality : 0.043 0.169 2333 Planarity : 0.004 0.048 2551 Dihedral : 7.229 127.936 2079 Min Nonbonded Distance : 2.017 Molprobity Statistics. All-atom Clashscore : 5.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.78 % Favored : 98.22 % Rotamer: Outliers : 2.15 % Allowed : 16.71 % Favored : 81.14 % 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: 2.16 (0.20), residues: 1851 helix: 2.33 (0.19), residues: 741 sheet: 1.33 (0.25), residues: 446 loop : 0.56 (0.26), residues: 664 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 617 TYR 0.019 0.001 TYR C 334 PHE 0.040 0.001 PHE A 663 TRP 0.008 0.002 TRP B 184 HIS 0.002 0.001 HIS C 426 Details of bonding type rmsd/Z covalent geometry : bond 0.00236 / 0.12 (14650) covalent geometry : angle 0.48390 / 0.26 (19866) hydrogen bonds : bond 0.04545 / 3.03 ( 854) hydrogen bonds : angle 4.77639 / 3.46 ( 2394) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3702 Ramachandran restraints generated. 1851 Oldfield, 0 Emsley, 1851 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3702 Ramachandran restraints generated. 1851 Oldfield, 0 Emsley, 1851 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 1580 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 127 time to evaluate : 0.555 Fit side-chains revert: symmetry clash REVERT: A 292 MET cc_start: 0.8372 (tmm) cc_final: 0.8110 (tmm) REVERT: A 355 GLU cc_start: 0.8497 (OUTLIER) cc_final: 0.7876 (mt-10) REVERT: A 424 MET cc_start: 0.8737 (ptp) cc_final: 0.8223 (ppp) REVERT: A 645 GLU cc_start: 0.7721 (tp30) cc_final: 0.7365 (mm-30) REVERT: B 50 ASP cc_start: 0.8726 (OUTLIER) cc_final: 0.8479 (t0) REVERT: B 103 ARG cc_start: 0.8031 (OUTLIER) cc_final: 0.7615 (mmm160) REVERT: B 206 ARG cc_start: 0.7993 (OUTLIER) cc_final: 0.7521 (mtp-110) REVERT: B 346 GLU cc_start: 0.7966 (pp20) cc_final: 0.7385 (tm-30) REVERT: B 444 ASN cc_start: 0.7644 (m110) cc_final: 0.7326 (m-40) REVERT: B 445 ARG cc_start: 0.7749 (mtt180) cc_final: 0.6577 (ptt180) REVERT: B 446 ARG cc_start: 0.7844 (ttp80) cc_final: 0.7479 (tmm-80) REVERT: B 471 ARG cc_start: 0.8492 (ttp80) cc_final: 0.7908 (ttm110) REVERT: C 118 ARG cc_start: 0.7998 (mmm-85) cc_final: 0.7729 (mtp-110) REVERT: C 120 GLU cc_start: 0.6722 (OUTLIER) cc_final: 0.6489 (mt-10) REVERT: C 346 GLU cc_start: 0.8210 (tp30) cc_final: 0.7880 (tp30) REVERT: C 412 ILE cc_start: 0.6487 (OUTLIER) cc_final: 0.6172 (mm) REVERT: C 445 ARG cc_start: 0.7717 (OUTLIER) cc_final: 0.6907 (mtm180) REVERT: C 523 GLU cc_start: 0.6579 (tp30) cc_final: 0.6274 (tp30) REVERT: C 525 GLU cc_start: 0.8587 (OUTLIER) cc_final: 0.8060 (pm20) REVERT: C 616 LYS cc_start: 0.8545 (ptpp) cc_final: 0.7948 (ptpt) REVERT: C 643 ASP cc_start: 0.8332 (t0) cc_final: 0.8020 (m-30) REVERT: C 664 ILE cc_start: 0.7258 (OUTLIER) cc_final: 0.6985 (mp) outliers start: 34 outliers final: 18 residues processed: 154 average time/residue: 0.6893 time to fit residues: 115.1526 Evaluate side-chains 152 residues out of total 1580 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 125 time to evaluate : 0.440 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 116 TYR Chi-restraints excluded: chain A residue 355 GLU Chi-restraints excluded: chain A residue 365 THR Chi-restraints excluded: chain A residue 642 VAL Chi-restraints excluded: chain B residue 50 ASP Chi-restraints excluded: chain B residue 56 LEU Chi-restraints excluded: chain B residue 103 ARG Chi-restraints excluded: chain B residue 141 LEU Chi-restraints excluded: chain B residue 206 ARG Chi-restraints excluded: chain B residue 284 VAL Chi-restraints excluded: chain B residue 372 CYS Chi-restraints excluded: chain B residue 448 LEU Chi-restraints excluded: chain B residue 517 THR Chi-restraints excluded: chain B residue 587 GLN Chi-restraints excluded: chain B residue 610 VAL Chi-restraints excluded: chain B residue 645 GLU Chi-restraints excluded: chain C residue 120 GLU Chi-restraints excluded: chain C residue 188 VAL Chi-restraints excluded: chain C residue 257 GLN Chi-restraints excluded: chain C residue 372 CYS Chi-restraints excluded: chain C residue 412 ILE Chi-restraints excluded: chain C residue 441 THR Chi-restraints excluded: chain C residue 445 ARG Chi-restraints excluded: chain C residue 483 SER Chi-restraints excluded: chain C residue 525 GLU Chi-restraints excluded: chain C residue 607 VAL Chi-restraints excluded: chain C residue 664 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 8 optimal weight: 4.9990 chunk 168 optimal weight: 0.0270 chunk 144 optimal weight: 1.9990 chunk 164 optimal weight: 0.0980 chunk 49 optimal weight: 5.9990 chunk 145 optimal weight: 0.7980 chunk 92 optimal weight: 0.4980 chunk 113 optimal weight: 2.9990 chunk 52 optimal weight: 1.9990 chunk 160 optimal weight: 2.9990 chunk 112 optimal weight: 3.9990 overall best weight: 0.6840 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 155 ASN B 658 HIS ** C 426 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 658 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3736 r_free = 0.3736 target = 0.118301 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.092620 restraints weight = 20489.936| |-----------------------------------------------------------------------------| r_work (start): 0.3334 rms_B_bonded: 2.07 r_work: 0.3211 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.3103 rms_B_bonded: 4.03 restraints_weight: 0.2500 r_work (final): 0.3103 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3095 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3095 r_free = 0.3095 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3095 r_free = 0.3095 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3095 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8805 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 : 0.003 0.036 14650 Z= 0.126 Angle : 0.484 6.737 19866 Z= 0.262 Chirality : 0.043 0.131 2333 Planarity : 0.004 0.046 2551 Dihedral : 7.190 127.044 2079 Min Nonbonded Distance : 1.994 Molprobity Statistics. All-atom Clashscore : 5.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.67 % Favored : 98.33 % Rotamer: Outliers : 1.77 % Allowed : 17.15 % Favored : 81.08 % 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: 2.23 (0.20), residues: 1851 helix: 2.39 (0.18), residues: 742 sheet: 1.35 (0.24), residues: 449 loop : 0.60 (0.26), residues: 660 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 617 TYR 0.019 0.001 TYR C 334 PHE 0.040 0.001 PHE A 663 TRP 0.006 0.001 TRP C 184 HIS 0.002 0.001 HIS B 288 Details of bonding type rmsd/Z covalent geometry : bond 0.00268 / 0.13 (14650) covalent geometry : angle 0.48405 / 0.26 (19866) hydrogen bonds : bond 0.04577 / 3.04 ( 854) hydrogen bonds : angle 4.73986 / 3.43 ( 2394) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3702 Ramachandran restraints generated. 1851 Oldfield, 0 Emsley, 1851 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3702 Ramachandran restraints generated. 1851 Oldfield, 0 Emsley, 1851 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 1580 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 127 time to evaluate : 0.481 Fit side-chains revert: symmetry clash REVERT: A 96 MET cc_start: 0.8596 (OUTLIER) cc_final: 0.7290 (tpt) REVERT: A 103 ARG cc_start: 0.8529 (mtp-110) cc_final: 0.8195 (mmm-85) REVERT: A 292 MET cc_start: 0.8367 (tmm) cc_final: 0.8104 (tmm) REVERT: A 424 MET cc_start: 0.8761 (ptp) cc_final: 0.8241 (ppp) REVERT: A 445 ARG cc_start: 0.8206 (mtt180) cc_final: 0.6873 (ptt-90) REVERT: A 645 GLU cc_start: 0.7709 (tp30) cc_final: 0.7375 (mm-30) REVERT: B 50 ASP cc_start: 0.8725 (OUTLIER) cc_final: 0.8490 (t0) REVERT: B 103 ARG cc_start: 0.8049 (OUTLIER) cc_final: 0.7628 (mmm160) REVERT: B 206 ARG cc_start: 0.8019 (OUTLIER) cc_final: 0.7540 (mtp-110) REVERT: B 346 GLU cc_start: 0.7987 (pp20) cc_final: 0.7392 (tm-30) REVERT: B 444 ASN cc_start: 0.7645 (m110) cc_final: 0.7330 (m-40) REVERT: B 445 ARG cc_start: 0.7759 (mtt180) cc_final: 0.6578 (ptt180) REVERT: B 446 ARG cc_start: 0.7858 (ttp80) cc_final: 0.7494 (tmm-80) REVERT: B 471 ARG cc_start: 0.8493 (ttp80) cc_final: 0.7902 (ttm110) REVERT: C 118 ARG cc_start: 0.7998 (mmm-85) cc_final: 0.7713 (mtp-110) REVERT: C 120 GLU cc_start: 0.6715 (OUTLIER) cc_final: 0.6426 (mt-10) REVERT: C 346 GLU cc_start: 0.8191 (tp30) cc_final: 0.7844 (tp30) REVERT: C 412 ILE cc_start: 0.6491 (OUTLIER) cc_final: 0.6189 (mm) REVERT: C 445 ARG cc_start: 0.7716 (OUTLIER) cc_final: 0.6900 (mtm180) REVERT: C 523 GLU cc_start: 0.6594 (tp30) cc_final: 0.6277 (tp30) REVERT: C 525 GLU cc_start: 0.8590 (OUTLIER) cc_final: 0.8063 (pm20) REVERT: C 616 LYS cc_start: 0.8553 (ptpp) cc_final: 0.7958 (ptpt) REVERT: C 643 ASP cc_start: 0.8289 (t0) cc_final: 0.7994 (m-30) REVERT: C 664 ILE cc_start: 0.7269 (OUTLIER) cc_final: 0.6996 (mp) outliers start: 28 outliers final: 15 residues processed: 149 average time/residue: 0.6652 time to fit residues: 107.2251 Evaluate side-chains 144 residues out of total 1580 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 120 time to evaluate : 0.549 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 96 MET Chi-restraints excluded: chain A residue 116 TYR Chi-restraints excluded: chain A residue 365 THR Chi-restraints excluded: chain A residue 642 VAL Chi-restraints excluded: chain B residue 50 ASP Chi-restraints excluded: chain B residue 56 LEU Chi-restraints excluded: chain B residue 103 ARG Chi-restraints excluded: chain B residue 141 LEU Chi-restraints excluded: chain B residue 206 ARG Chi-restraints excluded: chain B residue 284 VAL Chi-restraints excluded: chain B residue 372 CYS Chi-restraints excluded: chain B residue 448 LEU Chi-restraints excluded: chain B residue 517 THR Chi-restraints excluded: chain B residue 610 VAL Chi-restraints excluded: chain B residue 645 GLU Chi-restraints excluded: chain C residue 120 GLU Chi-restraints excluded: chain C residue 188 VAL Chi-restraints excluded: chain C residue 257 GLN Chi-restraints excluded: chain C residue 372 CYS Chi-restraints excluded: chain C residue 412 ILE Chi-restraints excluded: chain C residue 441 THR Chi-restraints excluded: chain C residue 445 ARG Chi-restraints excluded: chain C residue 525 GLU Chi-restraints excluded: chain C residue 664 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 182 optimal weight: 7.9990 chunk 65 optimal weight: 5.9990 chunk 53 optimal weight: 0.7980 chunk 61 optimal weight: 7.9990 chunk 34 optimal weight: 5.9990 chunk 63 optimal weight: 3.9990 chunk 25 optimal weight: 0.8980 chunk 72 optimal weight: 2.9990 chunk 68 optimal weight: 4.9990 chunk 129 optimal weight: 6.9990 chunk 113 optimal weight: 0.0000 overall best weight: 1.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 658 HIS ** C 426 HIS ** 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 = 0.3708 r_free = 0.3708 target = 0.116165 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.089793 restraints weight = 20627.602| |-----------------------------------------------------------------------------| r_work (start): 0.3290 rms_B_bonded: 2.09 r_work: 0.3165 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.3056 rms_B_bonded: 4.04 restraints_weight: 0.2500 r_work (final): 0.3056 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3047 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3047 r_free = 0.3047 target_work(ls_wunit_k1) = 0.074 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3047 r_free = 0.3047 target_work(ls_wunit_k1) = 0.074 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3047 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8845 moved from start: 0.1353 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 14650 Z= 0.193 Angle : 0.534 7.234 19866 Z= 0.289 Chirality : 0.045 0.141 2333 Planarity : 0.004 0.050 2551 Dihedral : 7.328 126.896 2079 Min Nonbonded Distance : 1.932 Molprobity Statistics. All-atom Clashscore : 5.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.62 % Favored : 98.38 % Rotamer: Outliers : 1.90 % Allowed : 17.09 % Favored : 81.01 % 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: 2.18 (0.20), residues: 1851 helix: 2.29 (0.18), residues: 742 sheet: 1.40 (0.24), residues: 448 loop : 0.59 (0.26), residues: 661 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 617 TYR 0.019 0.002 TYR C 334 PHE 0.043 0.002 PHE A 663 TRP 0.003 0.001 TRP C 184 HIS 0.003 0.001 HIS A 658 Details of bonding type rmsd/Z covalent geometry : bond 0.00427 / 0.19 (14650) covalent geometry : angle 0.53432 / 0.29 (19866) hydrogen bonds : bond 0.05312 / 3.52 ( 854) hydrogen bonds : angle 4.94584 / 3.57 ( 2394) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5937.98 seconds wall clock time: 101 minutes 33.63 seconds (6093.63 seconds total)