Starting phenix.real_space_refine on Thu Feb 5 03:22:22 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9njb_49478/02_2026/9njb_49478.cif Found real_map, /net/cci-nas-00/data/ceres_data/9njb_49478/02_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/9njb_49478/02_2026/9njb_49478.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9njb_49478/02_2026/9njb_49478.map" model { file = "/net/cci-nas-00/data/ceres_data/9njb_49478/02_2026/9njb_49478.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9njb_49478/02_2026/9njb_49478.cif" } 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-2.0-5952/lib/python3.9/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: 3.27, 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: 1.19 Conformation dependent library (CDL) restraints added in 588.9 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: 0.67 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: 2.29 Time building geometry restraints manager: 1.57 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=" 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 bond pdb=" N VAL C 411 " pdb=" CA VAL C 411 " ideal model delta sigma weight residual 1.461 1.484 -0.023 1.19e-02 7.06e+03 3.84e+00 ... (remaining 14645 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.57: 19530 1.57 - 3.15: 255 3.15 - 4.72: 64 4.72 - 6.29: 11 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=" 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=" 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 1.00e+00 1.00e+00 1.84e+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 angle pdb=" C GLN C 410 " pdb=" CA GLN C 410 " pdb=" CB GLN C 410 " ideal model delta sigma weight residual 110.79 117.54 -6.75 1.66e+00 3.63e-01 1.65e+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: 2296 0.113 - 0.227: 32 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: 3.080 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.220 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 13.780 Find NCS groups from input model: 0.310 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:6.980 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.500 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8606 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= 0.134 Angle : 0.503 7.868 19866 Z= 0.284 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 covalent geometry : bond 0.00256 (14650) covalent geometry : angle 0.50325 (19866) hydrogen bonds : bond 0.20498 ( 854) hydrogen bonds : angle 7.60748 ( 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 : 0.386 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: 0.7506 time to fit residues: 119.5936 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 : 0.543 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: B 115 ASN ** C 426 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 658 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3685 r_free = 0.3685 target = 0.114440 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.087945 restraints weight = 20740.419| |-----------------------------------------------------------------------------| r_work (start): 0.3262 rms_B_bonded: 2.11 r_work: 0.3128 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.3015 rms_B_bonded: 4.10 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 = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3010 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8681 moved from start: 0.0860 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.046 14650 Z= 0.251 Angle : 0.566 6.788 19866 Z= 0.313 Chirality : 0.046 0.146 2333 Planarity : 0.004 0.043 2551 Dihedral : 8.692 127.639 2112 Min Nonbonded Distance : 2.077 Molprobity Statistics. All-atom Clashscore : 4.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.57 % Favored : 98.43 % Rotamer: Outliers : 2.85 % Allowed : 14.68 % Favored : 82.47 % 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: 1.89 (0.20), residues: 1851 helix: 1.83 (0.18), residues: 735 sheet: 1.53 (0.25), residues: 442 loop : 0.54 (0.26), residues: 674 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 617 TYR 0.019 0.002 TYR C 427 PHE 0.019 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 covalent geometry : bond 0.00557 (14650) covalent geometry : angle 0.56591 (19866) hydrogen bonds : bond 0.06980 ( 854) hydrogen bonds : angle 5.69709 ( 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 168 residues out of total 1580 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 123 time to evaluate : 0.445 Fit side-chains revert: symmetry clash REVERT: A 56 LEU cc_start: 0.8700 (OUTLIER) cc_final: 0.8436 (mp) REVERT: A 89 LYS cc_start: 0.8072 (OUTLIER) cc_final: 0.7790 (pptt) REVERT: A 96 MET cc_start: 0.8410 (OUTLIER) cc_final: 0.7751 (ttm) REVERT: A 103 ARG cc_start: 0.8607 (mtm110) cc_final: 0.8397 (mtp-110) REVERT: A 424 MET cc_start: 0.8898 (ptp) cc_final: 0.8317 (ppp) REVERT: A 617 ARG cc_start: 0.7871 (mmm160) cc_final: 0.7497 (mmm160) REVERT: A 645 GLU cc_start: 0.7716 (tp30) cc_final: 0.7390 (mm-30) REVERT: B 50 ASP cc_start: 0.8703 (OUTLIER) cc_final: 0.8462 (t0) REVERT: B 206 ARG cc_start: 0.8125 (OUTLIER) cc_final: 0.7878 (mtp-110) REVERT: B 444 ASN cc_start: 0.7821 (m110) cc_final: 0.7540 (m-40) REVERT: B 445 ARG cc_start: 0.7849 (mtt180) cc_final: 0.6840 (ptt180) REVERT: B 446 ARG cc_start: 0.8010 (ttp80) cc_final: 0.7616 (tmm-80) REVERT: B 471 ARG cc_start: 0.8600 (ttp80) cc_final: 0.8087 (ttm110) REVERT: C 96 MET cc_start: 0.8155 (OUTLIER) cc_final: 0.6537 (ttp) REVERT: C 412 ILE cc_start: 0.6710 (OUTLIER) cc_final: 0.6294 (mm) REVERT: C 523 GLU cc_start: 0.6546 (tp30) cc_final: 0.6240 (tp30) REVERT: C 525 GLU cc_start: 0.8615 (OUTLIER) cc_final: 0.8107 (pm20) REVERT: C 616 LYS cc_start: 0.8479 (ptpp) cc_final: 0.7831 (ptmt) REVERT: C 643 ASP cc_start: 0.8399 (t0) cc_final: 0.8031 (m-30) outliers start: 45 outliers final: 13 residues processed: 156 average time/residue: 0.7629 time to fit residues: 128.0377 Evaluate side-chains 142 residues out of total 1580 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 121 time to evaluate : 0.616 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 LEU Chi-restraints excluded: chain A residue 89 LYS 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 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 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 372 CYS Chi-restraints excluded: chain C residue 412 ILE Chi-restraints excluded: chain C residue 441 THR 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: 0.9980 chunk 126 optimal weight: 4.9990 chunk 23 optimal weight: 4.9990 chunk 161 optimal weight: 0.9990 chunk 6 optimal weight: 4.9990 chunk 133 optimal weight: 3.9990 chunk 148 optimal weight: 3.9990 chunk 89 optimal weight: 0.9990 chunk 179 optimal weight: 0.6980 chunk 41 optimal weight: 8.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3704 r_free = 0.3704 target = 0.115931 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.089392 restraints weight = 20751.480| |-----------------------------------------------------------------------------| r_work (start): 0.3284 rms_B_bonded: 2.13 r_work: 0.3152 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.3039 rms_B_bonded: 4.13 restraints_weight: 0.2500 r_work (final): 0.3039 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3035 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3035 r_free = 0.3035 target_work(ls_wunit_k1) = 0.074 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3035 r_free = 0.3035 target_work(ls_wunit_k1) = 0.074 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3035 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8656 moved from start: 0.1068 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 14650 Z= 0.179 Angle : 0.515 8.165 19866 Z= 0.281 Chirality : 0.044 0.136 2333 Planarity : 0.004 0.049 2551 Dihedral : 7.835 130.123 2086 Min Nonbonded Distance : 2.107 Molprobity Statistics. All-atom Clashscore : 4.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.40 % Favored : 98.60 % Rotamer: Outliers : 3.42 % Allowed : 14.81 % Favored : 81.77 % 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: 1.95 (0.20), residues: 1851 helix: 1.98 (0.18), residues: 740 sheet: 1.41 (0.25), residues: 443 loop : 0.55 (0.26), residues: 668 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 617 TYR 0.020 0.002 TYR C 334 PHE 0.019 0.001 PHE A 545 TRP 0.004 0.001 TRP C 184 HIS 0.002 0.001 HIS C 426 Details of bonding type rmsd covalent geometry : bond 0.00384 (14650) covalent geometry : angle 0.51520 (19866) hydrogen bonds : bond 0.05785 ( 854) hydrogen bonds : angle 5.26346 ( 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 178 residues out of total 1580 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 124 time to evaluate : 0.600 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 56 LEU cc_start: 0.8647 (OUTLIER) cc_final: 0.8441 (mp) REVERT: A 89 LYS cc_start: 0.8084 (OUTLIER) cc_final: 0.7827 (pptt) REVERT: A 103 ARG cc_start: 0.8580 (mtm180) cc_final: 0.8339 (mmm-85) REVERT: A 239 GLN cc_start: 0.8105 (OUTLIER) cc_final: 0.7807 (pm20) REVERT: A 355 GLU cc_start: 0.8539 (OUTLIER) cc_final: 0.7938 (mt-10) REVERT: A 424 MET cc_start: 0.8837 (ptp) cc_final: 0.8291 (ppp) REVERT: A 645 GLU cc_start: 0.7718 (tp30) cc_final: 0.7377 (mm-30) REVERT: B 50 ASP cc_start: 0.8711 (OUTLIER) cc_final: 0.8471 (t0) REVERT: B 89 LYS cc_start: 0.8688 (OUTLIER) cc_final: 0.8392 (pttm) REVERT: B 206 ARG cc_start: 0.8107 (OUTLIER) cc_final: 0.7683 (mtp-110) REVERT: B 444 ASN cc_start: 0.7815 (m110) cc_final: 0.7511 (m-40) REVERT: B 445 ARG cc_start: 0.7843 (mtt180) cc_final: 0.6726 (ptt180) REVERT: B 446 ARG cc_start: 0.7919 (ttp80) cc_final: 0.7565 (tmm-80) REVERT: B 471 ARG cc_start: 0.8562 (ttp80) cc_final: 0.8047 (ttm110) REVERT: C 153 LEU cc_start: 0.9213 (OUTLIER) cc_final: 0.9012 (mt) REVERT: C 412 ILE cc_start: 0.6763 (OUTLIER) cc_final: 0.6388 (mm) REVERT: C 445 ARG cc_start: 0.7869 (OUTLIER) cc_final: 0.7130 (mtm180) REVERT: C 446 ARG cc_start: 0.8595 (mtm180) cc_final: 0.8283 (mtm-85) REVERT: C 616 LYS cc_start: 0.8550 (ptpp) cc_final: 0.7935 (ptmt) REVERT: C 643 ASP cc_start: 0.8380 (t0) cc_final: 0.8042 (m-30) outliers start: 54 outliers final: 23 residues processed: 165 average time/residue: 0.7769 time to fit residues: 138.1737 Evaluate side-chains 153 residues out of total 1580 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 120 time to evaluate : 0.422 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 LEU Chi-restraints excluded: chain A residue 89 LYS 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 663 PHE 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 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 301 ASP 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 B residue 610 VAL Chi-restraints excluded: chain B residue 645 GLU Chi-restraints excluded: chain C residue 153 LEU Chi-restraints excluded: chain C residue 188 VAL Chi-restraints excluded: chain C residue 230 GLU 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: 6.9990 chunk 99 optimal weight: 3.9990 chunk 43 optimal weight: 0.0060 chunk 120 optimal weight: 1.9990 chunk 149 optimal weight: 5.9990 chunk 151 optimal weight: 3.9990 chunk 1 optimal weight: 0.0970 chunk 160 optimal weight: 3.9990 chunk 39 optimal weight: 0.2980 chunk 34 optimal weight: 1.9990 chunk 101 optimal weight: 0.9980 overall best weight: 0.6796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.3732 r_free = 0.3732 target = 0.117986 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.091926 restraints weight = 20668.096| |-----------------------------------------------------------------------------| r_work (start): 0.3325 rms_B_bonded: 2.09 r_work: 0.3200 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.3092 rms_B_bonded: 4.04 restraints_weight: 0.2500 r_work (final): 0.3092 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3085 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3085 r_free = 0.3085 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3085 r_free = 0.3085 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3085 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8599 moved from start: 0.1197 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 : 0.475 7.300 19866 Z= 0.258 Chirality : 0.043 0.134 2333 Planarity : 0.004 0.049 2551 Dihedral : 7.530 130.047 2083 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 4.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.67 % Favored : 98.33 % Rotamer: Outliers : 2.97 % Allowed : 15.70 % Favored : 81.33 % 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: 2.11 (0.20), residues: 1851 helix: 2.21 (0.18), residues: 739 sheet: 1.36 (0.25), residues: 446 loop : 0.60 (0.26), residues: 666 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 0.017 0.001 PHE B 545 TRP 0.005 0.001 TRP C 184 HIS 0.003 0.001 HIS C 658 Details of bonding type rmsd covalent geometry : bond 0.00258 (14650) covalent geometry : angle 0.47536 (19866) hydrogen bonds : bond 0.04875 ( 854) hydrogen bonds : angle 4.96484 ( 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 182 residues out of total 1580 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 135 time to evaluate : 0.586 Fit side-chains revert: symmetry clash REVERT: A 239 GLN cc_start: 0.8025 (OUTLIER) cc_final: 0.7731 (pm20) REVERT: A 424 MET cc_start: 0.8753 (ptp) cc_final: 0.8231 (ppp) REVERT: A 645 GLU cc_start: 0.7725 (tp30) cc_final: 0.7376 (mm-30) REVERT: B 50 ASP cc_start: 0.8731 (OUTLIER) cc_final: 0.8483 (t0) REVERT: B 103 ARG cc_start: 0.8068 (OUTLIER) cc_final: 0.7366 (mtp85) REVERT: B 206 ARG cc_start: 0.8012 (OUTLIER) cc_final: 0.7550 (mtp-110) REVERT: B 444 ASN cc_start: 0.7638 (m110) cc_final: 0.7352 (m-40) REVERT: B 445 ARG cc_start: 0.7742 (mtt180) cc_final: 0.6588 (ptt180) REVERT: B 446 ARG cc_start: 0.7859 (ttp80) cc_final: 0.7498 (tmm-80) REVERT: B 471 ARG cc_start: 0.8518 (ttp80) cc_final: 0.7932 (ttm110) REVERT: C 250 LYS cc_start: 0.8507 (OUTLIER) cc_final: 0.8211 (tmtp) REVERT: C 346 GLU cc_start: 0.8206 (tp30) cc_final: 0.7850 (tp30) REVERT: C 412 ILE cc_start: 0.6607 (OUTLIER) cc_final: 0.6214 (mm) REVERT: C 445 ARG cc_start: 0.7749 (OUTLIER) cc_final: 0.7004 (mtm180) REVERT: C 523 GLU cc_start: 0.6498 (tp30) cc_final: 0.6203 (tp30) REVERT: C 525 GLU cc_start: 0.8625 (OUTLIER) cc_final: 0.8073 (pm20) REVERT: C 527 TYR cc_start: 0.8953 (p90) cc_final: 0.8748 (p90) REVERT: C 616 LYS cc_start: 0.8582 (ptpp) cc_final: 0.8002 (ptpt) REVERT: C 643 ASP cc_start: 0.8326 (t0) cc_final: 0.7992 (m-30) outliers start: 47 outliers final: 16 residues processed: 169 average time/residue: 0.8147 time to fit residues: 148.1786 Evaluate side-chains 150 residues out of total 1580 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 126 time to evaluate : 0.602 ------------------------------------------------------------------------------- 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 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 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 365 THR 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 606 VAL Chi-restraints excluded: chain B residue 610 VAL Chi-restraints excluded: chain C residue 81 MET 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 445 ARG Chi-restraints excluded: chain C residue 525 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 155 optimal weight: 0.4980 chunk 35 optimal weight: 0.6980 chunk 86 optimal weight: 0.7980 chunk 6 optimal weight: 4.9990 chunk 61 optimal weight: 9.9990 chunk 3 optimal weight: 4.9990 chunk 111 optimal weight: 3.9990 chunk 94 optimal weight: 0.9980 chunk 176 optimal weight: 0.8980 chunk 87 optimal weight: 0.4980 chunk 60 optimal weight: 10.0000 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 155 ASN B 115 ASN ** 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 = 0.3737 r_free = 0.3737 target = 0.118267 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.092467 restraints weight = 20742.138| |-----------------------------------------------------------------------------| r_work (start): 0.3333 rms_B_bonded: 2.08 r_work: 0.3210 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.3102 rms_B_bonded: 4.06 restraints_weight: 0.2500 r_work (final): 0.3102 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3094 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3094 r_free = 0.3094 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3094 r_free = 0.3094 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3094 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8590 moved from start: 0.1296 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= 0.124 Angle : 0.472 6.374 19866 Z= 0.256 Chirality : 0.043 0.130 2333 Planarity : 0.004 0.048 2551 Dihedral : 7.428 129.468 2083 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 4.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.62 % Favored : 98.38 % Rotamer: Outliers : 2.97 % Allowed : 15.82 % 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: 2.20 (0.20), residues: 1851 helix: 2.32 (0.19), residues: 740 sheet: 1.36 (0.25), residues: 450 loop : 0.63 (0.26), residues: 661 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 617 TYR 0.019 0.001 TYR C 334 PHE 0.017 0.001 PHE A 545 TRP 0.005 0.001 TRP A 184 HIS 0.002 0.001 HIS B 288 Details of bonding type rmsd covalent geometry : bond 0.00259 (14650) covalent geometry : angle 0.47171 (19866) hydrogen bonds : bond 0.04648 ( 854) hydrogen bonds : angle 4.83444 ( 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 175 residues out of total 1580 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 128 time to evaluate : 0.551 Fit side-chains revert: symmetry clash REVERT: A 103 ARG cc_start: 0.8569 (mtp-110) cc_final: 0.8270 (mmm-85) REVERT: A 239 GLN cc_start: 0.7972 (OUTLIER) cc_final: 0.7660 (pm20) REVERT: A 424 MET cc_start: 0.8730 (ptp) cc_final: 0.8232 (ppp) REVERT: A 445 ARG cc_start: 0.8213 (mtt180) cc_final: 0.6919 (ptt-90) REVERT: A 645 GLU cc_start: 0.7718 (tp30) cc_final: 0.7370 (mm-30) REVERT: B 50 ASP cc_start: 0.8726 (OUTLIER) cc_final: 0.8490 (t0) REVERT: B 89 LYS cc_start: 0.8633 (OUTLIER) cc_final: 0.8349 (pttm) REVERT: B 103 ARG cc_start: 0.8063 (OUTLIER) cc_final: 0.7347 (mtp85) REVERT: B 444 ASN cc_start: 0.7666 (m110) cc_final: 0.7399 (m-40) REVERT: B 445 ARG cc_start: 0.7716 (mtt180) cc_final: 0.6526 (ptt180) REVERT: B 446 ARG cc_start: 0.7843 (ttp80) cc_final: 0.7487 (tmm-80) REVERT: B 471 ARG cc_start: 0.8506 (ttp80) cc_final: 0.7936 (ttm110) REVERT: C 250 LYS cc_start: 0.8512 (OUTLIER) cc_final: 0.8209 (tmtp) REVERT: C 346 GLU cc_start: 0.8217 (tp30) cc_final: 0.7852 (tp30) REVERT: C 412 ILE cc_start: 0.6635 (OUTLIER) cc_final: 0.6323 (mm) REVERT: C 446 ARG cc_start: 0.8590 (mtm-85) cc_final: 0.8333 (mtm180) REVERT: C 523 GLU cc_start: 0.6601 (tp30) cc_final: 0.6361 (tp30) REVERT: C 525 GLU cc_start: 0.8615 (OUTLIER) cc_final: 0.8120 (pm20) REVERT: C 527 TYR cc_start: 0.8946 (p90) cc_final: 0.8681 (p90) REVERT: C 616 LYS cc_start: 0.8577 (ptpp) cc_final: 0.7999 (ptpt) REVERT: C 643 ASP cc_start: 0.8300 (t0) cc_final: 0.7976 (m-30) outliers start: 47 outliers final: 22 residues processed: 163 average time/residue: 0.7416 time to fit residues: 130.3428 Evaluate side-chains 152 residues out of total 1580 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 123 time to evaluate : 0.667 ------------------------------------------------------------------------------- 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 365 THR Chi-restraints excluded: chain A residue 372 CYS 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 188 VAL Chi-restraints excluded: chain B residue 266 THR Chi-restraints excluded: chain B residue 284 VAL 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 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 C residue 81 MET 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 448 LEU Chi-restraints excluded: chain C residue 525 GLU Chi-restraints excluded: chain C residue 543 MET 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: 3.9990 chunk 76 optimal weight: 6.9990 chunk 125 optimal weight: 7.9990 chunk 17 optimal weight: 5.9990 chunk 30 optimal weight: 3.9990 chunk 126 optimal weight: 0.9990 chunk 12 optimal weight: 0.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3695 r_free = 0.3695 target = 0.115127 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.088995 restraints weight = 20675.082| |-----------------------------------------------------------------------------| r_work (start): 0.3276 rms_B_bonded: 2.07 r_work: 0.3149 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.3040 rms_B_bonded: 4.00 restraints_weight: 0.2500 r_work (final): 0.3040 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3031 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3031 r_free = 0.3031 target_work(ls_wunit_k1) = 0.074 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3031 r_free = 0.3031 target_work(ls_wunit_k1) = 0.074 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3031 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8650 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 : 0.005 0.049 14650 Z= 0.231 Angle : 0.548 7.125 19866 Z= 0.297 Chirality : 0.045 0.152 2333 Planarity : 0.004 0.053 2551 Dihedral : 7.545 129.755 2079 Min Nonbonded Distance : 2.075 Molprobity Statistics. All-atom Clashscore : 5.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.73 % Favored : 98.27 % Rotamer: Outliers : 3.04 % Allowed : 15.82 % 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: 2.03 (0.20), residues: 1851 helix: 2.13 (0.18), residues: 739 sheet: 1.39 (0.25), residues: 445 loop : 0.53 (0.26), residues: 667 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 617 TYR 0.019 0.002 TYR C 334 PHE 0.030 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 covalent geometry : bond 0.00515 (14650) covalent geometry : angle 0.54788 (19866) hydrogen bonds : bond 0.05800 ( 854) hydrogen bonds : angle 5.14140 ( 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 173 residues out of total 1580 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 125 time to evaluate : 0.596 Fit side-chains revert: symmetry clash REVERT: A 56 LEU cc_start: 0.8640 (OUTLIER) cc_final: 0.8404 (mp) REVERT: A 96 MET cc_start: 0.8376 (OUTLIER) cc_final: 0.7681 (ttm) REVERT: A 239 GLN cc_start: 0.8089 (OUTLIER) cc_final: 0.7806 (pm20) REVERT: A 355 GLU cc_start: 0.8486 (OUTLIER) cc_final: 0.7859 (mt-10) REVERT: A 424 MET cc_start: 0.8843 (ptp) cc_final: 0.8278 (ppp) REVERT: A 645 GLU cc_start: 0.7709 (tp30) cc_final: 0.7361 (mm-30) REVERT: B 50 ASP cc_start: 0.8730 (OUTLIER) cc_final: 0.8491 (t0) REVERT: B 89 LYS cc_start: 0.8667 (OUTLIER) cc_final: 0.8371 (pttm) REVERT: B 103 ARG cc_start: 0.8149 (OUTLIER) cc_final: 0.7453 (mtp85) REVERT: B 322 GLU cc_start: 0.7793 (pm20) cc_final: 0.7477 (pm20) REVERT: B 346 GLU cc_start: 0.7994 (pp20) cc_final: 0.7408 (tm-30) REVERT: B 444 ASN cc_start: 0.7846 (m110) cc_final: 0.7537 (m110) REVERT: B 445 ARG cc_start: 0.7850 (mtt180) cc_final: 0.6692 (ptt180) REVERT: B 446 ARG cc_start: 0.7942 (ttp80) cc_final: 0.7550 (tmm-80) REVERT: B 471 ARG cc_start: 0.8549 (ttp80) cc_final: 0.8013 (ttm110) REVERT: C 153 LEU cc_start: 0.9218 (OUTLIER) cc_final: 0.9011 (mt) REVERT: C 250 LYS cc_start: 0.8613 (OUTLIER) cc_final: 0.8353 (ttmp) REVERT: C 346 GLU cc_start: 0.8189 (tp30) cc_final: 0.7833 (tp30) REVERT: C 412 ILE cc_start: 0.6723 (OUTLIER) cc_final: 0.6423 (mm) REVERT: C 446 ARG cc_start: 0.8644 (mtm-85) cc_final: 0.8407 (mtm-85) REVERT: C 523 GLU cc_start: 0.6628 (tp30) cc_final: 0.6413 (tp30) REVERT: C 525 GLU cc_start: 0.8612 (OUTLIER) cc_final: 0.8103 (pm20) REVERT: C 616 LYS cc_start: 0.8600 (ptpp) cc_final: 0.8007 (ptpt) REVERT: C 643 ASP cc_start: 0.8337 (t0) cc_final: 0.8024 (m-30) outliers start: 48 outliers final: 23 residues processed: 164 average time/residue: 0.7851 time to fit residues: 139.1509 Evaluate side-chains 159 residues out of total 1580 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 125 time to evaluate : 0.599 ------------------------------------------------------------------------------- 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 117 LEU 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 141 LEU 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 365 THR 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 C residue 153 LEU 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 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 525 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 144 optimal weight: 0.9980 chunk 98 optimal weight: 9.9990 chunk 44 optimal weight: 5.9990 chunk 99 optimal weight: 2.9990 chunk 64 optimal weight: 5.9990 chunk 118 optimal weight: 0.0670 chunk 164 optimal weight: 0.2980 chunk 50 optimal weight: 3.9990 chunk 137 optimal weight: 2.9990 chunk 108 optimal weight: 3.9990 chunk 18 optimal weight: 1.9990 overall best weight: 1.2722 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3713 r_free = 0.3713 target = 0.116648 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.090271 restraints weight = 20532.659| |-----------------------------------------------------------------------------| r_work (start): 0.3297 rms_B_bonded: 2.10 r_work: 0.3171 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.3063 rms_B_bonded: 4.04 restraints_weight: 0.2500 r_work (final): 0.3063 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3058 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3058 r_free = 0.3058 target_work(ls_wunit_k1) = 0.075 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3058 r_free = 0.3058 target_work(ls_wunit_k1) = 0.075 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3058 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8625 moved from start: 0.1266 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= 0.161 Angle : 0.504 6.320 19866 Z= 0.274 Chirality : 0.044 0.178 2333 Planarity : 0.004 0.051 2551 Dihedral : 7.403 131.200 2079 Min Nonbonded Distance : 2.022 Molprobity Statistics. All-atom Clashscore : 5.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.57 % Favored : 98.43 % Rotamer: Outliers : 2.66 % Allowed : 16.33 % 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: 2.11 (0.20), residues: 1851 helix: 2.24 (0.18), residues: 740 sheet: 1.39 (0.25), residues: 443 loop : 0.54 (0.26), residues: 668 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 617 TYR 0.019 0.002 TYR C 334 PHE 0.032 0.001 PHE A 663 TRP 0.004 0.001 TRP C 184 HIS 0.004 0.001 HIS C 658 Details of bonding type rmsd covalent geometry : bond 0.00347 (14650) covalent geometry : angle 0.50362 (19866) hydrogen bonds : bond 0.05190 ( 854) hydrogen bonds : angle 4.97006 ( 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 172 residues out of total 1580 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 130 time to evaluate : 0.567 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 103 ARG cc_start: 0.8534 (mtp-110) cc_final: 0.8270 (mmm-85) REVERT: A 239 GLN cc_start: 0.8008 (OUTLIER) cc_final: 0.7713 (pm20) REVERT: A 424 MET cc_start: 0.8801 (ptp) cc_final: 0.8239 (ppp) REVERT: A 445 ARG cc_start: 0.8220 (mtt180) cc_final: 0.6947 (ptt-90) REVERT: A 645 GLU cc_start: 0.7711 (tp30) cc_final: 0.7361 (mm-30) REVERT: B 50 ASP cc_start: 0.8717 (OUTLIER) cc_final: 0.8475 (t0) REVERT: B 103 ARG cc_start: 0.8079 (OUTLIER) cc_final: 0.7410 (mtp85) REVERT: B 346 GLU cc_start: 0.7954 (pp20) cc_final: 0.7364 (tm-30) REVERT: B 444 ASN cc_start: 0.7749 (m110) cc_final: 0.7429 (m-40) REVERT: B 445 ARG cc_start: 0.7799 (mtt180) cc_final: 0.6628 (ptt180) REVERT: B 446 ARG cc_start: 0.7912 (ttp80) cc_final: 0.7532 (tmm-80) REVERT: B 471 ARG cc_start: 0.8517 (ttp80) cc_final: 0.7929 (ttm110) REVERT: C 120 GLU cc_start: 0.6705 (OUTLIER) cc_final: 0.6413 (mt-10) REVERT: C 346 GLU cc_start: 0.8178 (tp30) cc_final: 0.7832 (tp30) REVERT: C 412 ILE cc_start: 0.6663 (OUTLIER) cc_final: 0.6345 (mm) REVERT: C 446 ARG cc_start: 0.8606 (mtm180) cc_final: 0.8365 (mtm-85) REVERT: C 523 GLU cc_start: 0.6638 (tp30) cc_final: 0.6424 (tp30) REVERT: C 525 GLU cc_start: 0.8594 (OUTLIER) cc_final: 0.8069 (pm20) REVERT: C 616 LYS cc_start: 0.8592 (ptpp) cc_final: 0.7992 (ptpt) REVERT: C 643 ASP cc_start: 0.8346 (t0) cc_final: 0.8021 (m-30) REVERT: C 664 ILE cc_start: 0.7315 (OUTLIER) cc_final: 0.7032 (mp) outliers start: 42 outliers final: 20 residues processed: 164 average time/residue: 0.7810 time to fit residues: 137.8476 Evaluate side-chains 150 residues out of total 1580 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 123 time to evaluate : 0.652 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 116 TYR Chi-restraints excluded: chain A residue 119 ARG Chi-restraints excluded: chain A residue 239 GLN 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 188 VAL Chi-restraints excluded: chain B residue 266 THR Chi-restraints excluded: chain B residue 284 VAL 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 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 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 525 GLU Chi-restraints excluded: chain C residue 607 VAL Chi-restraints excluded: chain C residue 664 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 27 optimal weight: 5.9990 chunk 83 optimal weight: 3.9990 chunk 51 optimal weight: 0.4980 chunk 91 optimal weight: 4.9990 chunk 71 optimal weight: 0.4980 chunk 21 optimal weight: 3.9990 chunk 11 optimal weight: 4.9990 chunk 158 optimal weight: 3.9990 chunk 29 optimal weight: 0.6980 chunk 182 optimal weight: 10.0000 chunk 109 optimal weight: 0.7980 overall best weight: 1.2982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 658 HIS ** C 426 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 658 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3713 r_free = 0.3713 target = 0.116661 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.090253 restraints weight = 20491.485| |-----------------------------------------------------------------------------| r_work (start): 0.3298 rms_B_bonded: 2.10 r_work: 0.3172 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.3064 rms_B_bonded: 4.03 restraints_weight: 0.2500 r_work (final): 0.3064 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3059 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3059 r_free = 0.3059 target_work(ls_wunit_k1) = 0.075 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3059 r_free = 0.3059 target_work(ls_wunit_k1) = 0.075 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3059 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8624 moved from start: 0.1304 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 14650 Z= 0.164 Angle : 0.507 6.345 19866 Z= 0.275 Chirality : 0.044 0.139 2333 Planarity : 0.004 0.050 2551 Dihedral : 7.359 131.340 2079 Min Nonbonded Distance : 1.974 Molprobity Statistics. All-atom Clashscore : 5.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.57 % Favored : 98.43 % Rotamer: Outliers : 2.22 % Allowed : 16.71 % 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: 2.13 (0.20), residues: 1851 helix: 2.26 (0.18), residues: 741 sheet: 1.41 (0.25), residues: 442 loop : 0.54 (0.26), residues: 668 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 617 TYR 0.019 0.002 TYR C 334 PHE 0.036 0.001 PHE A 663 TRP 0.004 0.001 TRP C 184 HIS 0.002 0.001 HIS B 288 Details of bonding type rmsd covalent geometry : bond 0.00355 (14650) covalent geometry : angle 0.50733 (19866) hydrogen bonds : bond 0.05164 ( 854) hydrogen bonds : angle 4.94665 ( 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 163 residues out of total 1580 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 128 time to evaluate : 0.605 Fit side-chains REVERT: A 103 ARG cc_start: 0.8531 (mtp-110) cc_final: 0.8253 (mmm-85) REVERT: A 239 GLN cc_start: 0.8002 (OUTLIER) cc_final: 0.7704 (pm20) REVERT: A 355 GLU cc_start: 0.8513 (OUTLIER) cc_final: 0.7908 (mt-10) REVERT: A 424 MET cc_start: 0.8799 (ptp) cc_final: 0.8244 (ppp) REVERT: A 445 ARG cc_start: 0.8228 (mtt180) cc_final: 0.6944 (ptt-90) REVERT: A 645 GLU cc_start: 0.7715 (tp30) cc_final: 0.7370 (mm-30) REVERT: B 50 ASP cc_start: 0.8732 (OUTLIER) cc_final: 0.8490 (t0) REVERT: B 103 ARG cc_start: 0.8067 (OUTLIER) cc_final: 0.7388 (mtp85) REVERT: B 346 GLU cc_start: 0.7960 (pp20) cc_final: 0.7365 (tm-30) REVERT: B 444 ASN cc_start: 0.7755 (m110) cc_final: 0.7430 (m-40) REVERT: B 445 ARG cc_start: 0.7810 (mtt180) cc_final: 0.6626 (ptt180) REVERT: B 446 ARG cc_start: 0.7912 (ttp80) cc_final: 0.7534 (tmm-80) REVERT: B 471 ARG cc_start: 0.8528 (ttp80) cc_final: 0.7923 (ttm110) REVERT: C 120 GLU cc_start: 0.6717 (OUTLIER) cc_final: 0.6430 (mt-10) REVERT: C 346 GLU cc_start: 0.8173 (tp30) cc_final: 0.7836 (tp30) REVERT: C 412 ILE cc_start: 0.6601 (OUTLIER) cc_final: 0.6310 (mm) REVERT: C 446 ARG cc_start: 0.8617 (mtm180) cc_final: 0.8364 (mtm-85) REVERT: C 525 GLU cc_start: 0.8602 (OUTLIER) cc_final: 0.8080 (pm20) REVERT: C 616 LYS cc_start: 0.8592 (ptpp) cc_final: 0.7988 (ptpt) REVERT: C 643 ASP cc_start: 0.8346 (t0) cc_final: 0.8017 (m-30) REVERT: C 664 ILE cc_start: 0.7270 (OUTLIER) cc_final: 0.6986 (mp) outliers start: 35 outliers final: 19 residues processed: 153 average time/residue: 0.8113 time to fit residues: 133.4970 Evaluate side-chains 148 residues out of total 1580 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 121 time to evaluate : 0.586 ------------------------------------------------------------------------------- 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 188 VAL Chi-restraints excluded: chain B residue 266 THR Chi-restraints excluded: chain B residue 284 VAL 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 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 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 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: 1.9990 chunk 29 optimal weight: 3.9990 chunk 142 optimal weight: 1.9990 chunk 85 optimal weight: 2.9990 chunk 43 optimal weight: 5.9990 chunk 99 optimal weight: 4.9990 chunk 96 optimal weight: 3.9990 chunk 7 optimal weight: 7.9990 chunk 25 optimal weight: 0.9980 chunk 80 optimal weight: 0.8980 chunk 89 optimal weight: 1.9990 overall best weight: 1.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3706 r_free = 0.3706 target = 0.115943 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.089928 restraints weight = 20661.041| |-----------------------------------------------------------------------------| r_work (start): 0.3292 rms_B_bonded: 2.07 r_work: 0.3160 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.3049 rms_B_bonded: 4.05 restraints_weight: 0.2500 r_work (final): 0.3049 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3046 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3046 r_free = 0.3046 target_work(ls_wunit_k1) = 0.074 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3046 r_free = 0.3046 target_work(ls_wunit_k1) = 0.074 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3046 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8637 moved from start: 0.1295 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 14650 Z= 0.184 Angle : 0.528 6.825 19866 Z= 0.286 Chirality : 0.044 0.170 2333 Planarity : 0.004 0.051 2551 Dihedral : 7.371 131.584 2079 Min Nonbonded Distance : 1.900 Molprobity Statistics. All-atom Clashscore : 5.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.67 % Favored : 98.33 % Rotamer: Outliers : 2.03 % Allowed : 16.90 % 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: 2.11 (0.20), residues: 1851 helix: 2.26 (0.18), residues: 735 sheet: 1.39 (0.25), residues: 443 loop : 0.54 (0.26), residues: 673 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 617 TYR 0.019 0.002 TYR C 334 PHE 0.041 0.001 PHE A 663 TRP 0.003 0.001 TRP C 184 HIS 0.002 0.001 HIS A 658 Details of bonding type rmsd covalent geometry : bond 0.00403 (14650) covalent geometry : angle 0.52800 (19866) hydrogen bonds : bond 0.05344 ( 854) hydrogen bonds : angle 4.99155 ( 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 157 residues out of total 1580 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 125 time to evaluate : 0.513 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 103 ARG cc_start: 0.8540 (mtp-110) cc_final: 0.8252 (mmm-85) REVERT: A 355 GLU cc_start: 0.8503 (OUTLIER) cc_final: 0.7904 (mt-10) REVERT: A 424 MET cc_start: 0.8821 (ptp) cc_final: 0.8262 (ppp) REVERT: A 645 GLU cc_start: 0.7730 (tp30) cc_final: 0.7384 (mm-30) REVERT: B 50 ASP cc_start: 0.8751 (OUTLIER) cc_final: 0.8509 (t0) REVERT: B 103 ARG cc_start: 0.8092 (OUTLIER) cc_final: 0.7415 (mtp85) REVERT: B 346 GLU cc_start: 0.7971 (pp20) cc_final: 0.7385 (tm-30) REVERT: B 444 ASN cc_start: 0.7810 (m110) cc_final: 0.7500 (m110) REVERT: B 445 ARG cc_start: 0.7842 (mtt180) cc_final: 0.6706 (ptt180) REVERT: B 446 ARG cc_start: 0.7945 (ttp80) cc_final: 0.7562 (tmm-80) REVERT: B 471 ARG cc_start: 0.8528 (ttp80) cc_final: 0.7988 (ttm110) REVERT: C 120 GLU cc_start: 0.6717 (OUTLIER) cc_final: 0.6442 (mt-10) REVERT: C 346 GLU cc_start: 0.8197 (tp30) cc_final: 0.7853 (tp30) REVERT: C 412 ILE cc_start: 0.6627 (OUTLIER) cc_final: 0.6345 (mm) REVERT: C 446 ARG cc_start: 0.8612 (mtm180) cc_final: 0.8339 (mtm-85) REVERT: C 523 GLU cc_start: 0.6492 (tp30) cc_final: 0.6287 (tp30) REVERT: C 525 GLU cc_start: 0.8618 (OUTLIER) cc_final: 0.8096 (pm20) REVERT: C 616 LYS cc_start: 0.8585 (ptpp) cc_final: 0.7993 (ptpt) REVERT: C 643 ASP cc_start: 0.8366 (t0) cc_final: 0.8032 (m-30) REVERT: C 664 ILE cc_start: 0.7249 (OUTLIER) cc_final: 0.6969 (mp) outliers start: 32 outliers final: 21 residues processed: 150 average time/residue: 0.7593 time to fit residues: 122.6410 Evaluate side-chains 150 residues out of total 1580 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 122 time to evaluate : 0.573 ------------------------------------------------------------------------------- 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 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 266 THR Chi-restraints excluded: chain B residue 284 VAL 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 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 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: 3.9990 chunk 168 optimal weight: 0.5980 chunk 144 optimal weight: 3.9990 chunk 164 optimal weight: 0.0570 chunk 49 optimal weight: 5.9990 chunk 145 optimal weight: 0.7980 chunk 92 optimal weight: 0.6980 chunk 113 optimal weight: 0.9980 chunk 52 optimal weight: 1.9990 chunk 160 optimal weight: 0.9990 chunk 112 optimal weight: 3.9990 overall best weight: 0.6298 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 658 HIS ** C 426 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 658 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3740 r_free = 0.3740 target = 0.118670 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.092493 restraints weight = 20465.117| |-----------------------------------------------------------------------------| r_work (start): 0.3334 rms_B_bonded: 2.10 r_work: 0.3211 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.3103 rms_B_bonded: 4.07 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 = 0.46 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 = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3096 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8588 moved from start: 0.1416 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 14650 Z= 0.123 Angle : 0.492 6.661 19866 Z= 0.266 Chirality : 0.043 0.131 2333 Planarity : 0.004 0.047 2551 Dihedral : 7.164 131.165 2079 Min Nonbonded Distance : 1.862 Molprobity Statistics. All-atom Clashscore : 5.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.94 % Favored : 98.06 % Rotamer: Outliers : 1.71 % Allowed : 17.41 % 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: 2.27 (0.20), residues: 1851 helix: 2.46 (0.19), residues: 735 sheet: 1.40 (0.25), residues: 445 loop : 0.60 (0.26), residues: 671 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 0.043 0.001 PHE A 663 TRP 0.007 0.001 TRP B 184 HIS 0.002 0.001 HIS B 288 Details of bonding type rmsd covalent geometry : bond 0.00261 (14650) covalent geometry : angle 0.49232 (19866) hydrogen bonds : bond 0.04545 ( 854) hydrogen bonds : angle 4.74642 ( 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 156 residues out of total 1580 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 129 time to evaluate : 0.425 Fit side-chains revert: symmetry clash REVERT: A 103 ARG cc_start: 0.8505 (mtp-110) cc_final: 0.8263 (mmm-85) REVERT: A 292 MET cc_start: 0.8384 (tmm) cc_final: 0.8109 (tmm) REVERT: A 424 MET cc_start: 0.8757 (ptp) cc_final: 0.8226 (ppp) REVERT: A 445 ARG cc_start: 0.8195 (mtt180) cc_final: 0.6922 (ptt-90) REVERT: A 645 GLU cc_start: 0.7721 (tp30) cc_final: 0.7376 (mm-30) REVERT: B 50 ASP cc_start: 0.8728 (OUTLIER) cc_final: 0.8481 (t0) REVERT: B 96 MET cc_start: 0.7500 (ttm) cc_final: 0.6879 (tmm) REVERT: B 103 ARG cc_start: 0.8030 (OUTLIER) cc_final: 0.7622 (mmm160) REVERT: B 346 GLU cc_start: 0.7954 (pp20) cc_final: 0.7360 (tm-30) REVERT: B 444 ASN cc_start: 0.7658 (m110) cc_final: 0.7338 (m-40) REVERT: B 445 ARG cc_start: 0.7760 (mtt180) cc_final: 0.6597 (ptt180) REVERT: B 446 ARG cc_start: 0.7862 (ttp80) cc_final: 0.7494 (tmm-80) REVERT: B 471 ARG cc_start: 0.8496 (ttp80) cc_final: 0.7898 (ttm110) REVERT: C 346 GLU cc_start: 0.8220 (tp30) cc_final: 0.7862 (tp30) REVERT: C 412 ILE cc_start: 0.6512 (OUTLIER) cc_final: 0.6215 (mm) REVERT: C 446 ARG cc_start: 0.8593 (mtm180) cc_final: 0.8340 (mtm-85) REVERT: C 523 GLU cc_start: 0.6485 (tp30) cc_final: 0.6274 (tp30) REVERT: C 525 GLU cc_start: 0.8614 (OUTLIER) cc_final: 0.8076 (pm20) REVERT: C 616 LYS cc_start: 0.8575 (ptpp) cc_final: 0.7970 (ptpt) REVERT: C 643 ASP cc_start: 0.8319 (t0) cc_final: 0.8006 (m-30) REVERT: C 664 ILE cc_start: 0.7226 (OUTLIER) cc_final: 0.6963 (mp) outliers start: 27 outliers final: 19 residues processed: 149 average time/residue: 0.7281 time to fit residues: 117.2312 Evaluate side-chains 146 residues out of total 1580 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 122 time to evaluate : 0.595 ------------------------------------------------------------------------------- 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 284 VAL 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 517 THR 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 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 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 182 optimal weight: 8.9990 chunk 65 optimal weight: 5.9990 chunk 53 optimal weight: 4.9990 chunk 61 optimal weight: 9.9990 chunk 34 optimal weight: 5.9990 chunk 63 optimal weight: 3.9990 chunk 25 optimal weight: 0.9990 chunk 72 optimal weight: 4.9990 chunk 68 optimal weight: 4.9990 chunk 129 optimal weight: 4.9990 chunk 113 optimal weight: 0.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 155 ASN B 658 HIS ** C 426 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3684 r_free = 0.3684 target = 0.114461 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3286 r_free = 0.3286 target = 0.087788 restraints weight = 20655.779| |-----------------------------------------------------------------------------| r_work (start): 0.3256 rms_B_bonded: 2.10 r_work: 0.3128 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.3020 rms_B_bonded: 4.02 restraints_weight: 0.2500 r_work (final): 0.3020 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3012 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3012 r_free = 0.3012 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 = 0.3012 r_free = 0.3012 target_work(ls_wunit_k1) = 0.073 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3012 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8667 moved from start: 0.1346 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.057 14650 Z= 0.306 Angle : 0.615 8.043 19866 Z= 0.333 Chirality : 0.048 0.181 2333 Planarity : 0.005 0.051 2551 Dihedral : 7.486 131.649 2079 Min Nonbonded Distance : 1.737 Molprobity Statistics. All-atom Clashscore : 5.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.94 % Favored : 98.06 % Rotamer: Outliers : 2.09 % Allowed : 17.09 % Favored : 80.82 % 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: 1.95 (0.20), residues: 1851 helix: 2.09 (0.18), residues: 733 sheet: 1.31 (0.24), residues: 453 loop : 0.49 (0.26), residues: 665 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 617 TYR 0.022 0.002 TYR C 427 PHE 0.040 0.002 PHE A 663 TRP 0.007 0.002 TRP B 184 HIS 0.005 0.001 HIS A 243 Details of bonding type rmsd covalent geometry : bond 0.00686 (14650) covalent geometry : angle 0.61481 (19866) hydrogen bonds : bond 0.06147 ( 854) hydrogen bonds : angle 5.20144 ( 2394) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6507.52 seconds wall clock time: 111 minutes 14.93 seconds (6674.93 seconds total)