Starting phenix.real_space_refine on Fri Jul 3 15:41:25 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9njb_49478/07_2026/9njb_49478.cif Found real_map, /net/cci-nas-00/data/ceres_data/9njb_49478/07_2026/9njb_49478.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.15 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9njb_49478/07_2026/9njb_49478.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9njb_49478/07_2026/9njb_49478.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9njb_49478/07_2026/9njb_49478.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9njb_49478/07_2026/9njb_49478.map" } resolution = 2.15 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.008 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 6 5.49 5 Mg 2 5.21 5 S 63 5.16 5 C 9073 2.51 5 N 2453 2.21 5 O 2813 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 24 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 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: 1.03 Conformation dependent library (CDL) restraints added in 650.3 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: 0.34 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: 1.97 Time building geometry restraints manager: 1.36 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: 3.190 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.220 Check model and map are aligned: 0.040 Set scattering table: 0.020 Process input model: 13.040 Find NCS groups from input model: 0.360 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.280 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.180 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8818 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 14650 Z= 0.135 Angle : 0.503 7.868 19866 Z= 0.285 Chirality : 0.049 0.566 2333 Planarity : 0.005 0.212 2551 Dihedral : 16.549 128.825 5546 Min Nonbonded Distance : 2.080 Molprobity Statistics. All-atom Clashscore : 4.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.51 % Favored : 98.49 % Rotamer: Outliers : 1.46 % Allowed : 15.76 % Favored : 82.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.43 (0.20), residues: 1851 helix: 1.14 (0.18), residues: 724 sheet: 1.37 (0.26), residues: 437 loop : 0.65 (0.25), residues: 690 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 617 TYR 0.011 0.001 TYR A 427 PHE 0.011 0.001 PHE A 545 TRP 0.005 0.001 TRP C 184 HIS 0.003 0.001 HIS B 304 Details of bonding type rmsd/Z covalent geometry : bond 0.00256 / 0.14 (14650) covalent geometry : angle 0.50325 / 0.29 (19866) hydrogen bonds : bond 0.20498 / 13.44 ( 854) hydrogen bonds : angle 7.60748 / 5.45 ( 2394) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3702 Ramachandran restraints generated. 1851 Oldfield, 0 Emsley, 1851 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3702 Ramachandran restraints generated. 1851 Oldfield, 0 Emsley, 1851 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 1580 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 130 time to evaluate : 0.444 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: 0.7605 time to fit residues: 121.5019 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 : 0.482 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 116 TYR Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 355 GLU Chi-restraints excluded: chain A residue 365 THR Chi-restraints excluded: chain A residue 642 VAL Chi-restraints excluded: chain A residue 646 THR Chi-restraints excluded: chain B residue 141 LEU Chi-restraints excluded: chain B residue 206 ARG Chi-restraints excluded: chain B residue 365 THR Chi-restraints excluded: chain B residue 372 CYS Chi-restraints excluded: chain B residue 448 LEU Chi-restraints excluded: chain B residue 528 ARG Chi-restraints excluded: chain B residue 610 VAL Chi-restraints excluded: chain C residue 56 LEU Chi-restraints excluded: chain C residue 379 THR Chi-restraints excluded: chain C residue 412 ILE Chi-restraints excluded: chain C residue 448 LEU Chi-restraints excluded: chain C residue 525 GLU Chi-restraints excluded: chain C residue 572 MET Chi-restraints excluded: chain C residue 664 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 98 optimal weight: 9.9990 chunk 107 optimal weight: 0.0470 chunk 10 optimal weight: 5.9990 chunk 66 optimal weight: 3.9990 chunk 130 optimal weight: 10.0000 chunk 124 optimal weight: 2.9990 chunk 103 optimal weight: 3.9990 chunk 77 optimal weight: 2.9990 chunk 122 optimal weight: 5.9990 chunk 91 optimal weight: 3.9990 chunk 149 optimal weight: 1.9990 overall best weight: 2.4086 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 115 ASN C 658 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3687 r_free = 0.3687 target = 0.114606 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.088003 restraints weight = 20742.549| |-----------------------------------------------------------------------------| r_work (start): 0.3262 rms_B_bonded: 2.12 r_work: 0.3128 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.3014 rms_B_bonded: 4.11 restraints_weight: 0.2500 r_work (final): 0.3014 ------------------------------------------------------------------------------- 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 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3010 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8889 moved from start: 0.0847 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.048 14650 Z= 0.253 Angle : 0.574 6.881 19866 Z= 0.317 Chirality : 0.046 0.153 2333 Planarity : 0.004 0.047 2551 Dihedral : 8.705 127.313 2112 Min Nonbonded Distance : 2.078 Molprobity Statistics. All-atom Clashscore : 4.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.57 % Favored : 98.43 % Rotamer: Outliers : 3.04 % Allowed : 14.49 % 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: 1.86 (0.20), residues: 1851 helix: 1.79 (0.18), residues: 734 sheet: 1.53 (0.25), residues: 442 loop : 0.53 (0.25), residues: 675 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 617 TYR 0.022 0.002 TYR C 334 PHE 0.021 0.002 PHE A 545 TRP 0.003 0.001 TRP C 184 HIS 0.008 0.001 HIS C 658 Details of bonding type rmsd/Z covalent geometry : bond 0.00556 / 0.25 (14650) covalent geometry : angle 0.57383 / 0.32 (19866) hydrogen bonds : bond 0.06964 / 4.64 ( 854) hydrogen bonds : angle 5.72712 / 4.14 ( 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 171 residues out of total 1580 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 123 time to evaluate : 0.570 Fit side-chains revert: symmetry clash REVERT: A 56 LEU cc_start: 0.8704 (OUTLIER) cc_final: 0.8442 (mp) REVERT: A 96 MET cc_start: 0.8397 (OUTLIER) cc_final: 0.7699 (ttm) REVERT: A 103 ARG cc_start: 0.8606 (mtm110) cc_final: 0.8403 (mtp-110) REVERT: A 424 MET cc_start: 0.8903 (ptp) cc_final: 0.8320 (ppp) REVERT: A 617 ARG cc_start: 0.7873 (mmm160) cc_final: 0.7505 (mmm160) REVERT: A 645 GLU cc_start: 0.7694 (tp30) cc_final: 0.7373 (mm-30) REVERT: B 50 ASP cc_start: 0.8705 (OUTLIER) cc_final: 0.8462 (t0) REVERT: B 89 LYS cc_start: 0.8699 (OUTLIER) cc_final: 0.8385 (pttm) REVERT: B 444 ASN cc_start: 0.7811 (m110) cc_final: 0.7528 (m-40) REVERT: B 445 ARG cc_start: 0.7857 (mtt180) cc_final: 0.6807 (ptt180) REVERT: B 446 ARG cc_start: 0.8014 (ttp80) cc_final: 0.7613 (tmm-80) REVERT: B 471 ARG cc_start: 0.8604 (ttp80) cc_final: 0.8075 (ttm110) REVERT: C 96 MET cc_start: 0.8154 (OUTLIER) cc_final: 0.6536 (ttp) REVERT: C 250 LYS cc_start: 0.8620 (OUTLIER) cc_final: 0.8321 (tmtp) REVERT: C 412 ILE cc_start: 0.6626 (OUTLIER) cc_final: 0.6213 (mm) REVERT: C 523 GLU cc_start: 0.6443 (tp30) cc_final: 0.6094 (tp30) REVERT: C 525 GLU cc_start: 0.8620 (OUTLIER) cc_final: 0.8113 (pm20) REVERT: C 616 LYS cc_start: 0.8476 (ptpp) cc_final: 0.7825 (ptmt) REVERT: C 643 ASP cc_start: 0.8403 (t0) cc_final: 0.8034 (m-30) outliers start: 48 outliers final: 14 residues processed: 158 average time/residue: 0.7100 time to fit residues: 121.3902 Evaluate side-chains 146 residues out of total 1580 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 124 time to evaluate : 0.482 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 LEU Chi-restraints excluded: chain A residue 96 MET Chi-restraints excluded: chain A residue 116 TYR Chi-restraints excluded: chain A residue 283 ILE Chi-restraints excluded: chain A residue 365 THR Chi-restraints excluded: chain B residue 50 ASP 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 365 THR Chi-restraints excluded: chain B residue 448 LEU Chi-restraints excluded: chain B residue 606 VAL Chi-restraints excluded: chain C residue 96 MET Chi-restraints excluded: chain C residue 188 VAL Chi-restraints excluded: chain C residue 230 GLU Chi-restraints excluded: chain C residue 250 LYS Chi-restraints excluded: chain C residue 372 CYS Chi-restraints excluded: chain C residue 412 ILE Chi-restraints excluded: chain C residue 483 SER Chi-restraints excluded: chain C residue 525 GLU Chi-restraints excluded: chain C residue 591 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 167 optimal weight: 5.9990 chunk 118 optimal weight: 0.9990 chunk 126 optimal weight: 1.9990 chunk 23 optimal weight: 3.9990 chunk 161 optimal weight: 0.9990 chunk 6 optimal weight: 3.9990 chunk 133 optimal weight: 0.7980 chunk 148 optimal weight: 3.9990 chunk 89 optimal weight: 0.6980 chunk 179 optimal weight: 1.9990 chunk 41 optimal weight: 0.6980 overall best weight: 0.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.3719 r_free = 0.3719 target = 0.116993 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.090478 restraints weight = 20709.212| |-----------------------------------------------------------------------------| r_work (start): 0.3301 rms_B_bonded: 2.14 r_work: 0.3168 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.3056 rms_B_bonded: 4.15 restraints_weight: 0.2500 r_work (final): 0.3056 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3054 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3054 r_free = 0.3054 target_work(ls_wunit_k1) = 0.075 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3054 r_free = 0.3054 target_work(ls_wunit_k1) = 0.075 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3054 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8851 moved from start: 0.0983 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= 0.141 Angle : 0.488 7.710 19866 Z= 0.268 Chirality : 0.044 0.130 2333 Planarity : 0.004 0.049 2551 Dihedral : 7.719 129.230 2083 Min Nonbonded Distance : 2.083 Molprobity Statistics. All-atom Clashscore : 4.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.46 % Favored : 98.54 % Rotamer: Outliers : 2.85 % Allowed : 15.13 % Favored : 82.03 % 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: 2.06 (0.18), residues: 740 sheet: 1.42 (0.25), residues: 442 loop : 0.59 (0.26), residues: 669 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 617 TYR 0.019 0.001 TYR C 334 PHE 0.017 0.001 PHE A 545 TRP 0.005 0.001 TRP C 184 HIS 0.002 0.001 HIS C 426 Details of bonding type rmsd/Z covalent geometry : bond 0.00288 / 0.14 (14650) covalent geometry : angle 0.48814 / 0.27 (19866) hydrogen bonds : bond 0.05725 / 3.81 ( 854) hydrogen bonds : angle 5.28482 / 3.83 ( 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 171 residues out of total 1580 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 126 time to evaluate : 0.590 Fit side-chains revert: symmetry clash REVERT: A 103 ARG cc_start: 0.8560 (mtm180) cc_final: 0.8334 (mtp-110) REVERT: A 424 MET cc_start: 0.8798 (ptp) cc_final: 0.8273 (ppp) REVERT: A 645 GLU cc_start: 0.7708 (tp30) cc_final: 0.7370 (mm-30) REVERT: B 50 ASP cc_start: 0.8727 (OUTLIER) cc_final: 0.8485 (t0) REVERT: B 444 ASN cc_start: 0.7734 (m110) cc_final: 0.7444 (m-40) REVERT: B 445 ARG cc_start: 0.7769 (mtt180) cc_final: 0.6673 (ptt180) REVERT: B 446 ARG cc_start: 0.7889 (ttp80) cc_final: 0.7540 (tmm-80) REVERT: B 471 ARG cc_start: 0.8559 (ttp80) cc_final: 0.8050 (ttm110) REVERT: C 126 LYS cc_start: 0.8612 (OUTLIER) cc_final: 0.8388 (ttmt) REVERT: C 250 LYS cc_start: 0.8584 (OUTLIER) cc_final: 0.8312 (tmtp) REVERT: C 346 GLU cc_start: 0.8221 (tp30) cc_final: 0.7890 (tp30) REVERT: C 412 ILE cc_start: 0.6657 (OUTLIER) cc_final: 0.6185 (mm) REVERT: C 445 ARG cc_start: 0.7774 (OUTLIER) cc_final: 0.7073 (mtm180) REVERT: C 446 ARG cc_start: 0.8603 (mtm180) cc_final: 0.8313 (mtm-85) REVERT: C 616 LYS cc_start: 0.8573 (ptpp) cc_final: 0.7959 (ptmt) REVERT: C 643 ASP cc_start: 0.8375 (t0) cc_final: 0.8038 (m-30) outliers start: 45 outliers final: 16 residues processed: 159 average time/residue: 0.6765 time to fit residues: 116.7690 Evaluate side-chains 143 residues out of total 1580 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 122 time to evaluate : 0.513 ------------------------------------------------------------------------------- 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 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 266 THR Chi-restraints excluded: chain B residue 284 VAL Chi-restraints excluded: chain B residue 301 ASP Chi-restraints excluded: chain B residue 448 LEU Chi-restraints excluded: chain B residue 606 VAL Chi-restraints excluded: chain B residue 610 VAL Chi-restraints excluded: chain C residue 126 LYS Chi-restraints excluded: chain C residue 250 LYS Chi-restraints excluded: chain C residue 257 GLN Chi-restraints excluded: chain C residue 372 CYS Chi-restraints excluded: chain C residue 379 THR Chi-restraints excluded: chain C residue 412 ILE Chi-restraints excluded: chain C residue 441 THR Chi-restraints excluded: chain C residue 445 ARG Chi-restraints excluded: chain C residue 483 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 126 optimal weight: 7.9990 chunk 99 optimal weight: 3.9990 chunk 43 optimal weight: 6.9990 chunk 120 optimal weight: 9.9990 chunk 149 optimal weight: 5.9990 chunk 151 optimal weight: 5.9990 chunk 1 optimal weight: 4.9990 chunk 160 optimal weight: 0.6980 chunk 39 optimal weight: 0.4980 chunk 34 optimal weight: 4.9990 chunk 101 optimal weight: 0.9990 overall best weight: 2.2386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 426 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3697 r_free = 0.3697 target = 0.115333 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.088587 restraints weight = 20715.085| |-----------------------------------------------------------------------------| r_work (start): 0.3270 rms_B_bonded: 2.12 r_work: 0.3143 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.3033 rms_B_bonded: 4.06 restraints_weight: 0.2500 r_work (final): 0.3033 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3025 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3025 r_free = 0.3025 target_work(ls_wunit_k1) = 0.073 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3025 r_free = 0.3025 target_work(ls_wunit_k1) = 0.073 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (11 function evaluations) r_final: 0.3025 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8862 moved from start: 0.1099 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 14650 Z= 0.229 Angle : 0.542 6.940 19866 Z= 0.296 Chirality : 0.045 0.149 2333 Planarity : 0.004 0.052 2551 Dihedral : 7.678 128.938 2079 Min Nonbonded Distance : 2.114 Molprobity Statistics. All-atom Clashscore : 5.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.57 % Favored : 98.43 % Rotamer: Outliers : 3.10 % Allowed : 15.19 % Favored : 81.71 % 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: 1.92 (0.20), residues: 1851 helix: 1.99 (0.18), residues: 738 sheet: 1.39 (0.25), residues: 443 loop : 0.49 (0.26), residues: 670 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 617 TYR 0.020 0.002 TYR C 334 PHE 0.019 0.002 PHE A 545 TRP 0.003 0.001 TRP C 184 HIS 0.003 0.001 HIS A 658 Details of bonding type rmsd/Z covalent geometry : bond 0.00507 / 0.23 (14650) covalent geometry : angle 0.54211 / 0.30 (19866) hydrogen bonds : bond 0.06033 / 4.00 ( 854) hydrogen bonds : angle 5.30159 / 3.83 ( 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 173 residues out of total 1580 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 124 time to evaluate : 0.650 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 96 MET cc_start: 0.8381 (OUTLIER) cc_final: 0.7674 (ttm) REVERT: A 239 GLN cc_start: 0.8148 (OUTLIER) cc_final: 0.7850 (pm20) REVERT: A 355 GLU cc_start: 0.8546 (OUTLIER) cc_final: 0.7966 (mt-10) REVERT: A 424 MET cc_start: 0.8877 (ptp) cc_final: 0.8279 (ppp) REVERT: A 645 GLU cc_start: 0.7704 (tp30) cc_final: 0.7367 (mm-30) REVERT: B 50 ASP cc_start: 0.8740 (OUTLIER) cc_final: 0.8498 (t0) REVERT: B 89 LYS cc_start: 0.8658 (OUTLIER) cc_final: 0.8360 (pttm) REVERT: B 444 ASN cc_start: 0.7798 (m110) cc_final: 0.7498 (m-40) REVERT: B 445 ARG cc_start: 0.7846 (mtt180) cc_final: 0.6697 (ptt180) REVERT: B 446 ARG cc_start: 0.7946 (ttp80) cc_final: 0.7567 (tmm-80) REVERT: B 471 ARG cc_start: 0.8562 (ttp80) cc_final: 0.8013 (ttm110) REVERT: C 126 LYS cc_start: 0.8629 (OUTLIER) cc_final: 0.8409 (ttmt) REVERT: C 412 ILE cc_start: 0.6641 (OUTLIER) cc_final: 0.6261 (mm) REVERT: C 445 ARG cc_start: 0.7861 (OUTLIER) cc_final: 0.7157 (mtm180) REVERT: C 523 GLU cc_start: 0.6349 (tp30) cc_final: 0.6103 (tp30) REVERT: C 525 GLU cc_start: 0.8631 (OUTLIER) cc_final: 0.8151 (pm20) REVERT: C 616 LYS cc_start: 0.8575 (ptpp) cc_final: 0.7953 (ptmt) REVERT: C 643 ASP cc_start: 0.8358 (t0) cc_final: 0.8035 (m-30) outliers start: 49 outliers final: 24 residues processed: 161 average time/residue: 0.7262 time to fit residues: 126.6150 Evaluate side-chains 151 residues out of total 1580 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 118 time to evaluate : 0.511 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 96 MET Chi-restraints excluded: chain A residue 116 TYR Chi-restraints excluded: chain A residue 239 GLN Chi-restraints excluded: chain A residue 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 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 372 CYS Chi-restraints excluded: chain B residue 448 LEU Chi-restraints excluded: chain B residue 517 THR Chi-restraints excluded: chain B residue 587 GLN Chi-restraints excluded: chain B residue 606 VAL Chi-restraints excluded: chain B residue 610 VAL Chi-restraints excluded: chain B residue 645 GLU Chi-restraints excluded: chain C residue 126 LYS Chi-restraints excluded: chain C residue 188 VAL Chi-restraints excluded: chain C residue 230 GLU Chi-restraints excluded: chain C residue 257 GLN Chi-restraints excluded: chain C residue 342 VAL Chi-restraints excluded: chain C residue 372 CYS Chi-restraints excluded: chain C residue 412 ILE Chi-restraints excluded: chain C residue 441 THR Chi-restraints excluded: chain C residue 445 ARG Chi-restraints excluded: chain C residue 448 LEU Chi-restraints excluded: chain C residue 483 SER Chi-restraints excluded: chain C residue 525 GLU Chi-restraints excluded: chain C residue 528 ARG Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 155 optimal weight: 4.9990 chunk 35 optimal weight: 0.9980 chunk 86 optimal weight: 0.6980 chunk 6 optimal weight: 4.9990 chunk 61 optimal weight: 8.9990 chunk 3 optimal weight: 6.9990 chunk 111 optimal weight: 4.9990 chunk 94 optimal weight: 2.9990 chunk 176 optimal weight: 0.7980 chunk 87 optimal weight: 0.0870 chunk 60 optimal weight: 0.9980 overall best weight: 0.7158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 426 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 658 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3727 r_free = 0.3727 target = 0.117546 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.091676 restraints weight = 20687.685| |-----------------------------------------------------------------------------| r_work (start): 0.3320 rms_B_bonded: 2.08 r_work: 0.3195 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.3087 rms_B_bonded: 4.03 restraints_weight: 0.2500 r_work (final): 0.3087 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3078 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3078 r_free = 0.3078 target_work(ls_wunit_k1) = 0.076 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3078 r_free = 0.3078 target_work(ls_wunit_k1) = 0.076 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3078 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8820 moved from start: 0.1190 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 14650 Z= 0.133 Angle : 0.481 6.348 19866 Z= 0.262 Chirality : 0.043 0.133 2333 Planarity : 0.004 0.049 2551 Dihedral : 7.490 130.189 2079 Min Nonbonded Distance : 2.125 Molprobity Statistics. All-atom Clashscore : 5.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.73 % Favored : 98.27 % Rotamer: Outliers : 2.66 % Allowed : 16.20 % 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: 2.07 (0.20), residues: 1851 helix: 2.18 (0.18), residues: 740 sheet: 1.35 (0.25), residues: 447 loop : 0.57 (0.26), residues: 664 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 617 TYR 0.019 0.001 TYR C 334 PHE 0.021 0.001 PHE A 663 TRP 0.006 0.001 TRP C 184 HIS 0.003 0.001 HIS C 426 Details of bonding type rmsd/Z covalent geometry : bond 0.00278 / 0.13 (14650) covalent geometry : angle 0.48051 / 0.26 (19866) hydrogen bonds : bond 0.05034 / 3.35 ( 854) hydrogen bonds : angle 4.99542 / 3.62 ( 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 174 residues out of total 1580 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 132 time to evaluate : 0.573 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 103 ARG cc_start: 0.8618 (mtp-110) cc_final: 0.8303 (mmm-85) REVERT: A 239 GLN cc_start: 0.8088 (OUTLIER) cc_final: 0.7765 (pm20) REVERT: A 355 GLU cc_start: 0.8499 (OUTLIER) cc_final: 0.7853 (mt-10) REVERT: A 424 MET cc_start: 0.8768 (ptp) cc_final: 0.8228 (ppp) REVERT: A 445 ARG cc_start: 0.8236 (mtt180) cc_final: 0.6955 (ptt-90) REVERT: A 645 GLU cc_start: 0.7717 (tp30) cc_final: 0.7367 (mm-30) REVERT: B 50 ASP cc_start: 0.8735 (OUTLIER) cc_final: 0.8489 (t0) REVERT: B 103 ARG cc_start: 0.8079 (OUTLIER) cc_final: 0.7376 (mtp85) REVERT: B 444 ASN cc_start: 0.7684 (m110) cc_final: 0.7399 (m-40) REVERT: B 445 ARG cc_start: 0.7720 (mtt180) cc_final: 0.6573 (ptt180) REVERT: B 446 ARG cc_start: 0.7863 (ttp80) cc_final: 0.7507 (tmm-80) REVERT: B 471 ARG cc_start: 0.8498 (ttp80) cc_final: 0.7916 (ttm110) REVERT: C 346 GLU cc_start: 0.8169 (tp30) cc_final: 0.7842 (tp30) REVERT: C 412 ILE cc_start: 0.6700 (OUTLIER) cc_final: 0.6362 (mm) REVERT: C 445 ARG cc_start: 0.7805 (OUTLIER) cc_final: 0.7075 (mtm180) REVERT: C 446 ARG cc_start: 0.8585 (mtm-85) cc_final: 0.8257 (mtm-85) REVERT: C 523 GLU cc_start: 0.6439 (tp30) cc_final: 0.6040 (tp30) REVERT: C 525 GLU cc_start: 0.8618 (OUTLIER) cc_final: 0.8100 (pm20) REVERT: C 616 LYS cc_start: 0.8577 (ptpp) cc_final: 0.8007 (ptpt) REVERT: C 643 ASP cc_start: 0.8324 (t0) cc_final: 0.8023 (m-30) outliers start: 42 outliers final: 17 residues processed: 163 average time/residue: 0.7326 time to fit residues: 129.3166 Evaluate side-chains 149 residues out of total 1580 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 125 time to evaluate : 0.581 ------------------------------------------------------------------------------- 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 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 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 257 GLN Chi-restraints excluded: chain C residue 372 CYS Chi-restraints excluded: chain C residue 412 ILE Chi-restraints excluded: chain C residue 441 THR Chi-restraints excluded: chain C residue 445 ARG Chi-restraints excluded: chain C residue 483 SER Chi-restraints excluded: chain C residue 525 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 10 optimal weight: 2.9990 chunk 114 optimal weight: 1.9990 chunk 149 optimal weight: 5.9990 chunk 35 optimal weight: 1.9990 chunk 33 optimal weight: 4.9990 chunk 76 optimal weight: 5.9990 chunk 125 optimal weight: 6.9990 chunk 17 optimal weight: 0.9980 chunk 30 optimal weight: 4.9990 chunk 126 optimal weight: 5.9990 chunk 12 optimal weight: 4.9990 overall best weight: 2.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 155 ASN ** C 426 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3685 r_free = 0.3685 target = 0.114564 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.087931 restraints weight = 20735.912| |-----------------------------------------------------------------------------| r_work (start): 0.3260 rms_B_bonded: 2.13 r_work: 0.3128 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.3015 rms_B_bonded: 4.09 restraints_weight: 0.2500 r_work (final): 0.3015 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3011 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3011 r_free = 0.3011 target_work(ls_wunit_k1) = 0.073 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3011 r_free = 0.3011 target_work(ls_wunit_k1) = 0.073 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3011 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8888 moved from start: 0.1255 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.052 14650 Z= 0.258 Angle : 0.571 7.231 19866 Z= 0.311 Chirality : 0.046 0.158 2333 Planarity : 0.005 0.052 2551 Dihedral : 7.669 129.665 2079 Min Nonbonded Distance : 2.133 Molprobity Statistics. All-atom Clashscore : 5.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.73 % Favored : 98.27 % Rotamer: Outliers : 3.04 % Allowed : 16.20 % Favored : 80.76 % 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: 1.92 (0.20), residues: 1851 helix: 2.01 (0.18), residues: 738 sheet: 1.37 (0.25), residues: 445 loop : 0.48 (0.26), residues: 668 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C 617 TYR 0.020 0.002 TYR C 427 PHE 0.022 0.002 PHE A 663 TRP 0.004 0.001 TRP B 184 HIS 0.003 0.001 HIS A 658 Details of bonding type rmsd/Z covalent geometry : bond 0.00575 / 0.26 (14650) covalent geometry : angle 0.57072 / 0.31 (19866) hydrogen bonds : bond 0.06056 / 4.01 ( 854) hydrogen bonds : angle 5.24045 / 3.78 ( 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 174 residues out of total 1580 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 126 time to evaluate : 0.370 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 96 MET cc_start: 0.8423 (OUTLIER) cc_final: 0.7727 (ttm) REVERT: A 239 GLN cc_start: 0.8126 (OUTLIER) cc_final: 0.7846 (pm20) REVERT: A 355 GLU cc_start: 0.8543 (OUTLIER) cc_final: 0.7961 (mt-10) REVERT: A 424 MET cc_start: 0.8850 (ptp) cc_final: 0.8297 (ppp) REVERT: A 645 GLU cc_start: 0.7718 (tp30) cc_final: 0.7375 (mm-30) REVERT: B 50 ASP cc_start: 0.8717 (OUTLIER) cc_final: 0.8481 (t0) REVERT: B 89 LYS cc_start: 0.8718 (OUTLIER) cc_final: 0.8431 (pttm) REVERT: B 103 ARG cc_start: 0.8174 (OUTLIER) cc_final: 0.7496 (mtp85) REVERT: B 346 GLU cc_start: 0.8031 (pp20) cc_final: 0.7454 (tm-30) REVERT: B 375 ASP cc_start: 0.8407 (OUTLIER) cc_final: 0.8185 (t0) REVERT: B 444 ASN cc_start: 0.7908 (m110) cc_final: 0.7600 (m110) REVERT: B 445 ARG cc_start: 0.7831 (mtt180) cc_final: 0.6713 (ptt180) REVERT: B 446 ARG cc_start: 0.7979 (ttp80) cc_final: 0.7587 (tmm-80) REVERT: B 471 ARG cc_start: 0.8577 (ttp80) cc_final: 0.8052 (ttm110) REVERT: C 412 ILE cc_start: 0.6723 (OUTLIER) cc_final: 0.6393 (mm) REVERT: C 445 ARG cc_start: 0.7903 (OUTLIER) cc_final: 0.7136 (mtm180) REVERT: C 446 ARG cc_start: 0.8670 (mtm-85) cc_final: 0.8436 (mtm-85) REVERT: C 523 GLU cc_start: 0.6474 (tp30) cc_final: 0.6158 (tp30) REVERT: C 525 GLU cc_start: 0.8617 (OUTLIER) cc_final: 0.8099 (pm20) REVERT: C 616 LYS cc_start: 0.8627 (ptpp) cc_final: 0.8063 (ptpt) REVERT: C 643 ASP cc_start: 0.8381 (t0) cc_final: 0.8040 (m-30) outliers start: 48 outliers final: 23 residues processed: 161 average time/residue: 0.7146 time to fit residues: 124.6295 Evaluate side-chains 158 residues out of total 1580 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 125 time to evaluate : 0.501 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 96 MET Chi-restraints excluded: chain A residue 116 TYR Chi-restraints excluded: chain A residue 239 GLN Chi-restraints excluded: chain A residue 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 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 372 CYS Chi-restraints excluded: chain B residue 375 ASP Chi-restraints excluded: chain B residue 448 LEU Chi-restraints excluded: chain B residue 517 THR Chi-restraints excluded: chain B residue 587 GLN Chi-restraints excluded: chain B residue 606 VAL Chi-restraints excluded: chain B residue 610 VAL Chi-restraints excluded: chain B residue 645 GLU Chi-restraints excluded: chain C residue 188 VAL Chi-restraints excluded: chain C residue 230 GLU Chi-restraints excluded: chain C residue 257 GLN Chi-restraints excluded: chain C residue 372 CYS Chi-restraints excluded: chain C residue 412 ILE Chi-restraints excluded: chain C residue 441 THR Chi-restraints excluded: chain C residue 445 ARG Chi-restraints excluded: chain C residue 448 LEU Chi-restraints excluded: chain C residue 483 SER Chi-restraints excluded: chain C residue 525 GLU Chi-restraints excluded: chain C residue 528 ARG Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 144 optimal weight: 0.8980 chunk 98 optimal weight: 3.9990 chunk 44 optimal weight: 4.9990 chunk 99 optimal weight: 0.9980 chunk 64 optimal weight: 0.9990 chunk 118 optimal weight: 2.9990 chunk 164 optimal weight: 0.5980 chunk 50 optimal weight: 2.9990 chunk 137 optimal weight: 3.9990 chunk 108 optimal weight: 4.9990 chunk 18 optimal weight: 0.8980 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 426 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3718 r_free = 0.3718 target = 0.116968 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.090690 restraints weight = 20539.941| |-----------------------------------------------------------------------------| r_work (start): 0.3305 rms_B_bonded: 2.10 r_work: 0.3179 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.3069 rms_B_bonded: 4.07 restraints_weight: 0.2500 r_work (final): 0.3069 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3064 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3064 r_free = 0.3064 target_work(ls_wunit_k1) = 0.076 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3064 r_free = 0.3064 target_work(ls_wunit_k1) = 0.076 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3064 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8832 moved from start: 0.1277 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 14650 Z= 0.141 Angle : 0.495 6.016 19866 Z= 0.270 Chirality : 0.044 0.152 2333 Planarity : 0.004 0.050 2551 Dihedral : 7.497 131.059 2079 Min Nonbonded Distance : 2.106 Molprobity Statistics. All-atom Clashscore : 5.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.73 % Favored : 98.27 % Rotamer: Outliers : 2.53 % Allowed : 16.52 % Favored : 80.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.06 (0.20), residues: 1851 helix: 2.20 (0.18), residues: 740 sheet: 1.31 (0.24), residues: 448 loop : 0.55 (0.26), residues: 663 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 0.027 0.001 PHE A 663 TRP 0.005 0.001 TRP C 184 HIS 0.004 0.001 HIS C 658 Details of bonding type rmsd/Z covalent geometry : bond 0.00294 / 0.14 (14650) covalent geometry : angle 0.49492 / 0.27 (19866) hydrogen bonds : bond 0.05131 / 3.42 ( 854) hydrogen bonds : angle 4.98902 / 3.61 ( 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 165 residues out of total 1580 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 125 time to evaluate : 0.566 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 239 GLN cc_start: 0.8048 (OUTLIER) cc_final: 0.7721 (pm20) REVERT: A 355 GLU cc_start: 0.8498 (OUTLIER) cc_final: 0.7854 (mt-10) REVERT: A 424 MET cc_start: 0.8782 (ptp) cc_final: 0.8239 (ppp) REVERT: A 645 GLU cc_start: 0.7723 (tp30) cc_final: 0.7371 (mm-30) REVERT: B 50 ASP cc_start: 0.8736 (OUTLIER) cc_final: 0.8491 (t0) REVERT: B 103 ARG cc_start: 0.8070 (OUTLIER) cc_final: 0.7362 (mtp85) REVERT: B 444 ASN cc_start: 0.7756 (m110) cc_final: 0.7429 (m-40) REVERT: B 445 ARG cc_start: 0.7754 (mtt180) cc_final: 0.6607 (ptt180) REVERT: B 446 ARG cc_start: 0.7888 (ttp80) cc_final: 0.7508 (tmm-80) REVERT: B 471 ARG cc_start: 0.8500 (ttp80) cc_final: 0.7967 (ttm110) REVERT: C 120 GLU cc_start: 0.6701 (OUTLIER) cc_final: 0.6461 (mt-10) REVERT: C 346 GLU cc_start: 0.8195 (tp30) cc_final: 0.7859 (tp30) REVERT: C 412 ILE cc_start: 0.6640 (OUTLIER) cc_final: 0.6305 (mm) REVERT: C 445 ARG cc_start: 0.7819 (OUTLIER) cc_final: 0.6981 (mtm180) REVERT: C 446 ARG cc_start: 0.8608 (mtm180) cc_final: 0.8370 (mtm-85) REVERT: C 523 GLU cc_start: 0.6555 (tp30) cc_final: 0.6250 (tp30) REVERT: C 525 GLU cc_start: 0.8609 (OUTLIER) cc_final: 0.8079 (pm20) REVERT: C 616 LYS cc_start: 0.8603 (ptpp) cc_final: 0.8019 (ptpt) REVERT: C 643 ASP cc_start: 0.8356 (t0) cc_final: 0.8029 (m-30) REVERT: C 664 ILE cc_start: 0.7303 (OUTLIER) cc_final: 0.7017 (mp) outliers start: 40 outliers final: 18 residues processed: 156 average time/residue: 0.7440 time to fit residues: 125.8853 Evaluate side-chains 151 residues out of total 1580 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 124 time to evaluate : 0.448 ------------------------------------------------------------------------------- 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 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 103 ARG Chi-restraints excluded: chain B residue 141 LEU Chi-restraints excluded: chain B residue 188 VAL Chi-restraints excluded: chain B residue 284 VAL Chi-restraints excluded: chain B residue 372 CYS Chi-restraints excluded: chain B residue 448 LEU Chi-restraints excluded: chain B residue 517 THR Chi-restraints excluded: chain B residue 587 GLN Chi-restraints excluded: chain B residue 606 VAL Chi-restraints excluded: chain B residue 610 VAL Chi-restraints excluded: chain B residue 645 GLU Chi-restraints excluded: chain C residue 120 GLU Chi-restraints excluded: chain C residue 257 GLN Chi-restraints excluded: chain C residue 372 CYS Chi-restraints excluded: chain C residue 412 ILE Chi-restraints excluded: chain C residue 441 THR Chi-restraints excluded: chain C residue 445 ARG Chi-restraints excluded: chain C residue 483 SER Chi-restraints excluded: chain C residue 525 GLU Chi-restraints excluded: chain C residue 664 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 27 optimal weight: 0.9980 chunk 83 optimal weight: 3.9990 chunk 51 optimal weight: 4.9990 chunk 91 optimal weight: 0.6980 chunk 71 optimal weight: 0.0030 chunk 21 optimal weight: 3.9990 chunk 11 optimal weight: 5.9990 chunk 158 optimal weight: 4.9990 chunk 29 optimal weight: 6.9990 chunk 182 optimal weight: 3.9990 chunk 109 optimal weight: 0.7980 overall best weight: 1.2992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 426 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 658 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3713 r_free = 0.3713 target = 0.116470 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.090369 restraints weight = 20568.616| |-----------------------------------------------------------------------------| r_work (start): 0.3298 rms_B_bonded: 2.08 r_work: 0.3173 rms_B_bonded: 2.54 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: 0.3057 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3057 r_free = 0.3057 target_work(ls_wunit_k1) = 0.075 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3057 r_free = 0.3057 target_work(ls_wunit_k1) = 0.075 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3057 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8838 moved from start: 0.1300 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 14650 Z= 0.164 Angle : 0.504 6.205 19866 Z= 0.274 Chirality : 0.044 0.134 2333 Planarity : 0.004 0.049 2551 Dihedral : 7.474 130.628 2079 Min Nonbonded Distance : 2.066 Molprobity Statistics. All-atom Clashscore : 5.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.62 % Favored : 98.38 % Rotamer: Outliers : 2.47 % Allowed : 16.65 % 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: 2.11 (0.20), residues: 1851 helix: 2.24 (0.18), residues: 740 sheet: 1.35 (0.25), residues: 447 loop : 0.57 (0.26), residues: 664 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 0.005 0.001 TRP C 184 HIS 0.002 0.001 HIS C 658 Details of bonding type rmsd/Z covalent geometry : bond 0.00356 / 0.16 (14650) covalent geometry : angle 0.50427 / 0.27 (19866) hydrogen bonds : bond 0.05208 / 3.46 ( 854) hydrogen bonds : angle 4.97256 / 3.59 ( 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 167 residues out of total 1580 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 128 time to evaluate : 0.584 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 239 GLN cc_start: 0.8028 (OUTLIER) cc_final: 0.7710 (pm20) REVERT: A 355 GLU cc_start: 0.8505 (OUTLIER) cc_final: 0.7854 (mt-10) REVERT: A 424 MET cc_start: 0.8777 (ptp) cc_final: 0.8239 (ppp) REVERT: A 645 GLU cc_start: 0.7714 (tp30) cc_final: 0.7365 (mm-30) REVERT: B 50 ASP cc_start: 0.8721 (OUTLIER) cc_final: 0.8476 (t0) REVERT: B 103 ARG cc_start: 0.8075 (OUTLIER) cc_final: 0.7398 (mtp85) REVERT: B 346 GLU cc_start: 0.7956 (pp20) cc_final: 0.7375 (tm-30) REVERT: B 444 ASN cc_start: 0.7745 (m110) cc_final: 0.7441 (m110) REVERT: B 445 ARG cc_start: 0.7801 (mtt180) cc_final: 0.6629 (ptt180) REVERT: B 446 ARG cc_start: 0.7899 (ttp80) cc_final: 0.7514 (tmm-80) REVERT: B 471 ARG cc_start: 0.8517 (ttp80) cc_final: 0.7978 (ttm110) REVERT: C 120 GLU cc_start: 0.6686 (OUTLIER) cc_final: 0.6403 (mt-10) REVERT: C 346 GLU cc_start: 0.8177 (tp30) cc_final: 0.7844 (tp30) REVERT: C 412 ILE cc_start: 0.6629 (OUTLIER) cc_final: 0.6290 (mm) REVERT: C 445 ARG cc_start: 0.7804 (OUTLIER) cc_final: 0.6958 (mtm180) REVERT: C 446 ARG cc_start: 0.8607 (mtm180) cc_final: 0.8354 (mtm-85) REVERT: C 523 GLU cc_start: 0.6590 (tp30) cc_final: 0.6280 (tp30) REVERT: C 525 GLU cc_start: 0.8598 (OUTLIER) cc_final: 0.8066 (pm20) REVERT: C 616 LYS cc_start: 0.8606 (ptpp) cc_final: 0.8014 (ptpt) REVERT: C 643 ASP cc_start: 0.8349 (t0) cc_final: 0.8025 (m-30) REVERT: C 664 ILE cc_start: 0.7298 (OUTLIER) cc_final: 0.7002 (mp) outliers start: 39 outliers final: 21 residues processed: 159 average time/residue: 0.7252 time to fit residues: 124.8998 Evaluate side-chains 154 residues out of total 1580 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 124 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 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 103 ARG Chi-restraints excluded: chain B residue 141 LEU Chi-restraints excluded: chain B residue 188 VAL Chi-restraints excluded: chain B residue 284 VAL Chi-restraints excluded: chain B residue 372 CYS Chi-restraints excluded: chain B residue 448 LEU Chi-restraints excluded: chain B residue 517 THR Chi-restraints excluded: chain B residue 587 GLN Chi-restraints excluded: chain B residue 606 VAL Chi-restraints excluded: chain B residue 610 VAL Chi-restraints excluded: chain B residue 645 GLU Chi-restraints excluded: chain C residue 120 GLU Chi-restraints excluded: chain C residue 188 VAL Chi-restraints excluded: chain C residue 257 GLN Chi-restraints excluded: chain C residue 342 VAL Chi-restraints excluded: chain C residue 372 CYS Chi-restraints excluded: chain C residue 412 ILE Chi-restraints excluded: chain C residue 441 THR Chi-restraints excluded: chain C residue 445 ARG Chi-restraints excluded: chain C residue 483 SER Chi-restraints excluded: chain C residue 525 GLU Chi-restraints excluded: chain C residue 607 VAL Chi-restraints excluded: chain C residue 664 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 56 optimal weight: 1.9990 chunk 29 optimal weight: 3.9990 chunk 142 optimal weight: 0.8980 chunk 85 optimal weight: 1.9990 chunk 43 optimal weight: 1.9990 chunk 99 optimal weight: 4.9990 chunk 96 optimal weight: 4.9990 chunk 7 optimal weight: 3.9990 chunk 25 optimal weight: 0.7980 chunk 80 optimal weight: 2.9990 chunk 89 optimal weight: 3.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 426 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3708 r_free = 0.3708 target = 0.116353 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.089778 restraints weight = 20608.247| |-----------------------------------------------------------------------------| r_work (start): 0.3291 rms_B_bonded: 2.12 r_work: 0.3165 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.3056 rms_B_bonded: 4.06 restraints_weight: 0.2500 r_work (final): 0.3056 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3047 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3047 r_free = 0.3047 target_work(ls_wunit_k1) = 0.074 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3047 r_free = 0.3047 target_work(ls_wunit_k1) = 0.074 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3047 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8844 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 : 0.004 0.039 14650 Z= 0.181 Angle : 0.524 7.282 19866 Z= 0.285 Chirality : 0.044 0.168 2333 Planarity : 0.004 0.050 2551 Dihedral : 7.460 130.834 2079 Min Nonbonded Distance : 2.018 Molprobity Statistics. All-atom Clashscore : 5.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.51 % Favored : 98.49 % Rotamer: Outliers : 2.22 % Allowed : 16.90 % 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: 2.11 (0.20), residues: 1851 helix: 2.22 (0.18), residues: 741 sheet: 1.39 (0.24), residues: 447 loop : 0.55 (0.26), residues: 663 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A 103 TYR 0.019 0.002 TYR C 334 PHE 0.038 0.001 PHE A 663 TRP 0.004 0.001 TRP C 184 HIS 0.002 0.001 HIS A 658 Details of bonding type rmsd/Z covalent geometry : bond 0.00395 / 0.18 (14650) covalent geometry : angle 0.52412 / 0.28 (19866) hydrogen bonds : bond 0.05323 / 3.53 ( 854) hydrogen bonds : angle 4.99336 / 3.61 ( 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 162 residues out of total 1580 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 127 time to evaluate : 0.584 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 116 TYR cc_start: 0.4632 (OUTLIER) cc_final: 0.4202 (m-10) REVERT: A 239 GLN cc_start: 0.8049 (OUTLIER) cc_final: 0.7723 (pm20) REVERT: A 355 GLU cc_start: 0.8514 (OUTLIER) cc_final: 0.7863 (mt-10) REVERT: A 424 MET cc_start: 0.8788 (ptp) cc_final: 0.8240 (ppp) REVERT: A 645 GLU cc_start: 0.7718 (tp30) cc_final: 0.7369 (mm-30) REVERT: B 50 ASP cc_start: 0.8738 (OUTLIER) cc_final: 0.8496 (t0) REVERT: B 103 ARG cc_start: 0.8092 (OUTLIER) cc_final: 0.7407 (mtp85) REVERT: B 322 GLU cc_start: 0.7824 (pm20) cc_final: 0.7520 (pm20) REVERT: B 346 GLU cc_start: 0.7973 (pp20) cc_final: 0.7393 (tm-30) REVERT: B 444 ASN cc_start: 0.7799 (m110) cc_final: 0.7491 (m110) REVERT: B 445 ARG cc_start: 0.7817 (mtt180) cc_final: 0.6645 (ptt180) REVERT: B 446 ARG cc_start: 0.7935 (ttp80) cc_final: 0.7551 (tmm-80) REVERT: B 471 ARG cc_start: 0.8518 (ttp80) cc_final: 0.7986 (ttm110) REVERT: C 120 GLU cc_start: 0.6721 (OUTLIER) cc_final: 0.6431 (mt-10) REVERT: C 346 GLU cc_start: 0.8184 (tp30) cc_final: 0.7845 (tp30) REVERT: C 412 ILE cc_start: 0.6621 (OUTLIER) cc_final: 0.6295 (mm) REVERT: C 445 ARG cc_start: 0.7812 (OUTLIER) cc_final: 0.6958 (mtm180) REVERT: C 446 ARG cc_start: 0.8629 (mtm180) cc_final: 0.8372 (mtm-85) REVERT: C 523 GLU cc_start: 0.6628 (tp30) cc_final: 0.6320 (tp30) REVERT: C 525 GLU cc_start: 0.8602 (OUTLIER) cc_final: 0.8089 (pm20) REVERT: C 616 LYS cc_start: 0.8610 (ptpp) cc_final: 0.8020 (ptpt) REVERT: C 643 ASP cc_start: 0.8359 (t0) cc_final: 0.8026 (m-30) REVERT: C 664 ILE cc_start: 0.7293 (OUTLIER) cc_final: 0.6999 (mp) outliers start: 35 outliers final: 20 residues processed: 155 average time/residue: 0.6894 time to fit residues: 116.1244 Evaluate side-chains 155 residues out of total 1580 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 125 time to evaluate : 0.431 ------------------------------------------------------------------------------- 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 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 103 ARG Chi-restraints excluded: chain B residue 141 LEU Chi-restraints excluded: chain B residue 188 VAL Chi-restraints excluded: chain B residue 284 VAL Chi-restraints excluded: chain B residue 372 CYS Chi-restraints excluded: chain B residue 448 LEU Chi-restraints excluded: chain B residue 517 THR Chi-restraints excluded: chain B residue 587 GLN Chi-restraints excluded: chain B residue 606 VAL Chi-restraints excluded: chain B residue 610 VAL Chi-restraints excluded: chain B residue 645 GLU Chi-restraints excluded: chain C residue 120 GLU Chi-restraints excluded: chain C residue 188 VAL Chi-restraints excluded: chain C residue 257 GLN Chi-restraints excluded: chain C residue 342 VAL Chi-restraints excluded: chain C residue 372 CYS Chi-restraints excluded: chain C residue 412 ILE Chi-restraints excluded: chain C residue 441 THR Chi-restraints excluded: chain C residue 445 ARG Chi-restraints excluded: chain C residue 483 SER Chi-restraints excluded: chain C residue 525 GLU Chi-restraints excluded: chain C residue 607 VAL Chi-restraints excluded: chain C residue 664 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 8 optimal weight: 1.9990 chunk 168 optimal weight: 0.0020 chunk 144 optimal weight: 3.9990 chunk 164 optimal weight: 0.6980 chunk 49 optimal weight: 5.9990 chunk 145 optimal weight: 1.9990 chunk 92 optimal weight: 0.9990 chunk 113 optimal weight: 1.9990 chunk 52 optimal weight: 1.9990 chunk 160 optimal weight: 0.7980 chunk 112 optimal weight: 4.9990 overall best weight: 0.8992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 426 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 658 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3723 r_free = 0.3723 target = 0.117292 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.091563 restraints weight = 20468.648| |-----------------------------------------------------------------------------| r_work (start): 0.3316 rms_B_bonded: 2.06 r_work: 0.3191 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.3083 rms_B_bonded: 4.01 restraints_weight: 0.2500 r_work (final): 0.3083 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3076 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3076 r_free = 0.3076 target_work(ls_wunit_k1) = 0.076 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3076 r_free = 0.3076 target_work(ls_wunit_k1) = 0.076 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3076 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8823 moved from start: 0.1336 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 14650 Z= 0.139 Angle : 0.496 6.577 19866 Z= 0.269 Chirality : 0.043 0.134 2333 Planarity : 0.004 0.047 2551 Dihedral : 7.335 131.160 2079 Min Nonbonded Distance : 1.985 Molprobity Statistics. All-atom Clashscore : 5.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.78 % Favored : 98.22 % Rotamer: Outliers : 2.03 % Allowed : 17.15 % 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: 2.17 (0.20), residues: 1851 helix: 2.34 (0.19), residues: 735 sheet: 1.34 (0.24), residues: 450 loop : 0.58 (0.26), residues: 666 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 103 TYR 0.019 0.001 TYR C 334 PHE 0.040 0.001 PHE A 663 TRP 0.006 0.001 TRP C 184 HIS 0.002 0.001 HIS B 288 Details of bonding type rmsd/Z covalent geometry : bond 0.00294 / 0.14 (14650) covalent geometry : angle 0.49550 / 0.27 (19866) hydrogen bonds : bond 0.04909 / 3.27 ( 854) hydrogen bonds : angle 4.87138 / 3.52 ( 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 161 residues out of total 1580 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 129 time to evaluate : 0.623 Fit side-chains revert: symmetry clash REVERT: A 292 MET cc_start: 0.8396 (tmm) cc_final: 0.8118 (tmm) REVERT: A 355 GLU cc_start: 0.8486 (OUTLIER) cc_final: 0.7842 (mt-10) REVERT: A 424 MET cc_start: 0.8766 (ptp) cc_final: 0.8224 (ppp) REVERT: A 617 ARG cc_start: 0.7778 (mmm160) cc_final: 0.7096 (ttm110) REVERT: A 645 GLU cc_start: 0.7720 (tp30) cc_final: 0.7464 (mm-30) REVERT: B 50 ASP cc_start: 0.8723 (OUTLIER) cc_final: 0.8478 (t0) REVERT: B 96 MET cc_start: 0.8407 (OUTLIER) cc_final: 0.8068 (tpp) REVERT: B 103 ARG cc_start: 0.8059 (OUTLIER) cc_final: 0.7381 (mtp85) REVERT: B 346 GLU cc_start: 0.7976 (pp20) cc_final: 0.7394 (tm-30) REVERT: B 444 ASN cc_start: 0.7721 (m110) cc_final: 0.7414 (m-40) REVERT: B 445 ARG cc_start: 0.7776 (mtt180) cc_final: 0.6627 (ptt180) REVERT: B 446 ARG cc_start: 0.7886 (ttp80) cc_final: 0.7509 (tmm-80) REVERT: B 471 ARG cc_start: 0.8512 (ttp80) cc_final: 0.7978 (ttm110) REVERT: C 120 GLU cc_start: 0.6713 (OUTLIER) cc_final: 0.6440 (mt-10) REVERT: C 346 GLU cc_start: 0.8192 (tp30) cc_final: 0.7853 (tp30) REVERT: C 412 ILE cc_start: 0.6540 (OUTLIER) cc_final: 0.6246 (mm) REVERT: C 445 ARG cc_start: 0.7769 (OUTLIER) cc_final: 0.6913 (mtm180) REVERT: C 446 ARG cc_start: 0.8603 (mtm180) cc_final: 0.8345 (mtm-85) REVERT: C 523 GLU cc_start: 0.6603 (tp30) cc_final: 0.6283 (tp30) REVERT: C 525 GLU cc_start: 0.8595 (OUTLIER) cc_final: 0.8065 (pm20) REVERT: C 616 LYS cc_start: 0.8610 (ptpp) cc_final: 0.8013 (ptpt) REVERT: C 643 ASP cc_start: 0.8334 (t0) cc_final: 0.8020 (m-30) REVERT: C 664 ILE cc_start: 0.7298 (OUTLIER) cc_final: 0.7022 (mp) outliers start: 32 outliers final: 18 residues processed: 153 average time/residue: 0.7702 time to fit residues: 127.5732 Evaluate side-chains 151 residues out of total 1580 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 124 time to evaluate : 0.568 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 96 MET 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 284 VAL Chi-restraints excluded: chain B residue 372 CYS Chi-restraints excluded: chain B residue 448 LEU Chi-restraints excluded: chain B residue 517 THR Chi-restraints excluded: chain B residue 587 GLN Chi-restraints excluded: chain B residue 606 VAL Chi-restraints excluded: chain B residue 610 VAL Chi-restraints excluded: chain B residue 645 GLU Chi-restraints excluded: chain C residue 120 GLU Chi-restraints excluded: chain C residue 188 VAL Chi-restraints excluded: chain C residue 257 GLN Chi-restraints excluded: chain C residue 372 CYS Chi-restraints excluded: chain C residue 412 ILE Chi-restraints excluded: chain C residue 441 THR Chi-restraints excluded: chain C residue 445 ARG Chi-restraints excluded: chain C residue 483 SER Chi-restraints excluded: chain C residue 525 GLU Chi-restraints excluded: chain C residue 607 VAL Chi-restraints excluded: chain C residue 664 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 182 optimal weight: 6.9990 chunk 65 optimal weight: 1.9990 chunk 53 optimal weight: 0.9990 chunk 61 optimal weight: 6.9990 chunk 34 optimal weight: 5.9990 chunk 63 optimal weight: 1.9990 chunk 25 optimal weight: 1.9990 chunk 72 optimal weight: 3.9990 chunk 68 optimal weight: 0.8980 chunk 129 optimal weight: 5.9990 chunk 113 optimal weight: 2.9990 overall best weight: 1.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 658 HIS ** C 426 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3710 r_free = 0.3710 target = 0.116341 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.089913 restraints weight = 20567.244| |-----------------------------------------------------------------------------| r_work (start): 0.3291 rms_B_bonded: 2.10 r_work: 0.3165 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.3057 rms_B_bonded: 4.04 restraints_weight: 0.2500 r_work (final): 0.3057 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3052 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3052 r_free = 0.3052 target_work(ls_wunit_k1) = 0.075 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3052 r_free = 0.3052 target_work(ls_wunit_k1) = 0.075 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3052 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8844 moved from start: 0.1315 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= 0.183 Angle : 0.527 6.945 19866 Z= 0.286 Chirality : 0.044 0.136 2333 Planarity : 0.004 0.050 2551 Dihedral : 7.332 131.075 2077 Min Nonbonded Distance : 1.933 Molprobity Statistics. All-atom Clashscore : 5.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.51 % Favored : 98.49 % Rotamer: Outliers : 2.22 % Allowed : 16.90 % 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: 2.13 (0.20), residues: 1851 helix: 2.25 (0.18), residues: 742 sheet: 1.41 (0.24), residues: 447 loop : 0.54 (0.26), residues: 662 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 103 TYR 0.019 0.002 TYR C 334 PHE 0.039 0.001 PHE A 663 TRP 0.003 0.001 TRP C 184 HIS 0.003 0.001 HIS A 658 Details of bonding type rmsd/Z covalent geometry : bond 0.00401 / 0.18 (14650) covalent geometry : angle 0.52745 / 0.29 (19866) hydrogen bonds : bond 0.05287 / 3.51 ( 854) hydrogen bonds : angle 4.96857 / 3.59 ( 2394) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6313.94 seconds wall clock time: 108 minutes 1.90 seconds (6481.90 seconds total)