Starting phenix.real_space_refine on Sun Aug 24 07:56:23 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9b6q_44274/08_2025/9b6q_44274.cif Found real_map, /net/cci-nas-00/data/ceres_data/9b6q_44274/08_2025/9b6q_44274.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.77 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9b6q_44274/08_2025/9b6q_44274.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9b6q_44274/08_2025/9b6q_44274.map" model { file = "/net/cci-nas-00/data/ceres_data/9b6q_44274/08_2025/9b6q_44274.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9b6q_44274/08_2025/9b6q_44274.cif" } resolution = 2.77 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 ------------------------------------------------------------------------------- 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= 1.000 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: 4 Type Number sf(0) Gaussians S 69 5.16 5 C 11830 2.51 5 N 3253 2.21 5 O 3613 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 88 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 18765 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 3129 Number of conformers: 1 Conformer: "" Number of residues, atoms: 395, 3129 Classifications: {'peptide': 395} Link IDs: {'PCIS': 1, 'PTRANS': 29, 'TRANS': 364} Chain breaks: 3 Chain: "B" Number of atoms: 1367 Number of conformers: 1 Conformer: "" Number of residues, atoms: 176, 1367 Classifications: {'peptide': 176} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 164} Chain breaks: 1 Chain: "C" Number of atoms: 3981 Number of conformers: 1 Conformer: "" Number of residues, atoms: 498, 3981 Classifications: {'peptide': 498} Link IDs: {'PCIS': 1, 'PTRANS': 32, 'TRANS': 464} Chain breaks: 2 Chain: "D" Number of atoms: 3129 Number of conformers: 1 Conformer: "" Number of residues, atoms: 395, 3129 Classifications: {'peptide': 395} Link IDs: {'PCIS': 1, 'PTRANS': 29, 'TRANS': 364} Chain breaks: 3 Chain: "E" Number of atoms: 1367 Number of conformers: 1 Conformer: "" Number of residues, atoms: 176, 1367 Classifications: {'peptide': 176} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 164} Chain breaks: 1 Chain: "F" Number of atoms: 3981 Number of conformers: 1 Conformer: "" Number of residues, atoms: 498, 3981 Classifications: {'peptide': 498} Link IDs: {'PCIS': 1, 'PTRANS': 32, 'TRANS': 464} Chain breaks: 2 Chain: "H" Number of atoms: 1008 Number of conformers: 1 Conformer: "" Number of residues, atoms: 130, 1008 Classifications: {'peptide': 130} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 125} Chain: "L" Number of atoms: 803 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 803 Classifications: {'peptide': 111} Link IDs: {'PTRANS': 8, 'TRANS': 102} Time building chain proxies: 3.55, per 1000 atoms: 0.19 Number of scatterers: 18765 At special positions: 0 Unit cell: (155.397, 127.143, 96.396, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 69 16.00 O 3613 8.00 N 3253 7.00 C 11830 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS H 41 " - pdb=" SG CYS H 115 " distance=2.03 Simple disulfide: pdb=" SG CYS L 42 " - pdb=" SG CYS L 109 " distance=2.03 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: 1.57 Conformation dependent library (CDL) restraints added in 657.5 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 4678 Ramachandran restraints generated. 2339 Oldfield, 0 Emsley, 2339 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4366 Finding SS restraints... Secondary structure from input PDB file: 34 helices and 51 sheets defined 7.9% alpha, 15.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.46 Creating SS restraints... Processing helix chain 'A' and resid 288 through 293 removed outlier: 4.147A pdb=" N HIS A 292 " --> pdb=" O ARG A 288 " (cutoff:3.500A) Processing helix chain 'A' and resid 396 through 400 Processing helix chain 'A' and resid 554 through 556 No H-bonds generated for 'chain 'A' and resid 554 through 556' Processing helix chain 'A' and resid 563 through 569 removed outlier: 4.304A pdb=" N THR A 568 " --> pdb=" O GLU A 565 " (cutoff:3.500A) Processing helix chain 'B' and resid 431 through 435 removed outlier: 3.700A pdb=" N LEU B 435 " --> pdb=" O LEU B 432 " (cutoff:3.500A) Processing helix chain 'B' and resid 492 through 496 Processing helix chain 'B' and resid 563 through 569 removed outlier: 4.026A pdb=" N THR B 568 " --> pdb=" O GLU B 565 " (cutoff:3.500A) Processing helix chain 'C' and resid 262 through 266 Processing helix chain 'C' and resid 269 through 273 Processing helix chain 'C' and resid 288 through 293 removed outlier: 4.159A pdb=" N HIS C 292 " --> pdb=" O ARG C 288 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 304 removed outlier: 3.974A pdb=" N ASN C 304 " --> pdb=" O ARG C 300 " (cutoff:3.500A) Processing helix chain 'C' and resid 396 through 400 Processing helix chain 'C' and resid 431 through 435 removed outlier: 4.082A pdb=" N LEU C 435 " --> pdb=" O LEU C 432 " (cutoff:3.500A) Processing helix chain 'C' and resid 492 through 496 Processing helix chain 'C' and resid 554 through 556 No H-bonds generated for 'chain 'C' and resid 554 through 556' Processing helix chain 'C' and resid 563 through 569 removed outlier: 4.204A pdb=" N THR C 568 " --> pdb=" O GLU C 565 " (cutoff:3.500A) Processing helix chain 'D' and resid 269 through 273 Processing helix chain 'D' and resid 288 through 292 Processing helix chain 'D' and resid 355 through 359 removed outlier: 3.548A pdb=" N SER D 358 " --> pdb=" O VAL D 355 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N ALA D 359 " --> pdb=" O LEU D 356 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 355 through 359' Processing helix chain 'D' and resid 396 through 400 removed outlier: 3.775A pdb=" N PHE D 400 " --> pdb=" O LEU D 397 " (cutoff:3.500A) Processing helix chain 'D' and resid 492 through 496 Processing helix chain 'D' and resid 563 through 569 removed outlier: 4.040A pdb=" N THR D 568 " --> pdb=" O GLU D 565 " (cutoff:3.500A) Processing helix chain 'E' and resid 492 through 496 Processing helix chain 'E' and resid 563 through 567 Processing helix chain 'F' and resid 252 through 256 Processing helix chain 'F' and resid 263 through 266 Processing helix chain 'F' and resid 288 through 293 removed outlier: 4.176A pdb=" N HIS F 292 " --> pdb=" O ARG F 288 " (cutoff:3.500A) Processing helix chain 'F' and resid 294 through 304 removed outlier: 3.617A pdb=" N ASN F 304 " --> pdb=" O ARG F 300 " (cutoff:3.500A) Processing helix chain 'F' and resid 355 through 359 removed outlier: 3.766A pdb=" N SER F 358 " --> pdb=" O VAL F 355 " (cutoff:3.500A) removed outlier: 4.171A pdb=" N ALA F 359 " --> pdb=" O LEU F 356 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 355 through 359' Processing helix chain 'F' and resid 396 through 400 Processing helix chain 'F' and resid 492 through 496 Processing helix chain 'H' and resid 81 through 84 Processing helix chain 'H' and resid 106 through 110 removed outlier: 3.549A pdb=" N THR H 110 " --> pdb=" O SER H 107 " (cutoff:3.500A) Processing helix chain 'L' and resid 100 through 104 Processing sheet with id=AA1, first strand: chain 'A' and resid 240 through 249 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 240 through 249 current: chain 'A' and resid 335 through 336 No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 258 through 261 Processing sheet with id=AA3, first strand: chain 'A' and resid 479 through 480 removed outlier: 6.375A pdb=" N ILE A 479 " --> pdb=" O VAL A 606 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'A' and resid 483 through 484 Processing sheet with id=AA5, first strand: chain 'A' and resid 488 through 490 Processing sheet with id=AA6, first strand: chain 'A' and resid 514 through 517 removed outlier: 4.083A pdb=" N GLY C 578 " --> pdb=" O VAL C 596 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 542 through 544 Processing sheet with id=AA8, first strand: chain 'A' and resid 593 through 596 removed outlier: 4.003A pdb=" N GLY A 578 " --> pdb=" O VAL A 596 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 619 through 621 removed outlier: 6.119A pdb=" N ALA A 620 " --> pdb=" O MET A 640 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'A' and resid 627 through 628 removed outlier: 6.406A pdb=" N ILE C 479 " --> pdb=" O VAL C 606 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 445 through 449 removed outlier: 5.761A pdb=" N LEU B 447 " --> pdb=" O SER B 464 " (cutoff:3.500A) removed outlier: 6.487A pdb=" N SER B 464 " --> pdb=" O LEU B 447 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 479 through 480 removed outlier: 6.318A pdb=" N ILE B 479 " --> pdb=" O VAL B 606 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N MET B 605 " --> pdb=" O PHE C 629 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 483 through 484 Processing sheet with id=AB5, first strand: chain 'B' and resid 488 through 490 Processing sheet with id=AB6, first strand: chain 'B' and resid 593 through 596 removed outlier: 3.942A pdb=" N GLY B 578 " --> pdb=" O VAL B 596 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 231 through 235 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 238 through 249 current: chain 'C' and resid 335 through 336 Processing sheet with id=AB8, first strand: chain 'C' and resid 258 through 261 Processing sheet with id=AB9, first strand: chain 'C' and resid 427 through 428 removed outlier: 6.327A pdb=" N ALA C 427 " --> pdb=" O ARG C 734 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB9 Processing sheet with id=AC1, first strand: chain 'C' and resid 445 through 451 removed outlier: 6.676A pdb=" N LYS C 462 " --> pdb=" O SER C 448 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N THR C 450 " --> pdb=" O THR C 460 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 483 through 484 Processing sheet with id=AC3, first strand: chain 'C' and resid 488 through 490 Processing sheet with id=AC4, first strand: chain 'C' and resid 542 through 544 Processing sheet with id=AC5, first strand: chain 'C' and resid 619 through 621 Processing sheet with id=AC6, first strand: chain 'D' and resid 240 through 249 WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 240 through 249 current: chain 'D' and resid 335 through 336 No H-bonds generated for sheet with id=AC6 Processing sheet with id=AC7, first strand: chain 'D' and resid 258 through 261 Processing sheet with id=AC8, first strand: chain 'D' and resid 383 through 384 Processing sheet with id=AC9, first strand: chain 'D' and resid 479 through 480 removed outlier: 6.368A pdb=" N ILE D 479 " --> pdb=" O VAL D 606 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC9 Processing sheet with id=AD1, first strand: chain 'D' and resid 483 through 484 Processing sheet with id=AD2, first strand: chain 'D' and resid 488 through 490 Processing sheet with id=AD3, first strand: chain 'D' and resid 514 through 517 removed outlier: 3.932A pdb=" N GLY F 578 " --> pdb=" O VAL F 596 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'D' and resid 542 through 544 Processing sheet with id=AD5, first strand: chain 'D' and resid 553 through 554 removed outlier: 4.042A pdb=" N THR F 450 " --> pdb=" O THR F 460 " (cutoff:3.500A) removed outlier: 6.576A pdb=" N LYS F 462 " --> pdb=" O SER F 448 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'D' and resid 593 through 596 removed outlier: 4.051A pdb=" N GLY D 578 " --> pdb=" O VAL D 596 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'D' and resid 619 through 621 removed outlier: 6.152A pdb=" N ALA D 620 " --> pdb=" O MET D 640 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD7 Processing sheet with id=AD8, first strand: chain 'D' and resid 627 through 629 removed outlier: 3.907A pdb=" N MET F 605 " --> pdb=" O PHE D 629 " (cutoff:3.500A) removed outlier: 6.463A pdb=" N ILE F 479 " --> pdb=" O VAL F 606 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'E' and resid 445 through 451 removed outlier: 5.571A pdb=" N LEU E 447 " --> pdb=" O SER E 464 " (cutoff:3.500A) removed outlier: 6.407A pdb=" N SER E 464 " --> pdb=" O LEU E 447 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N ILE E 451 " --> pdb=" O THR E 460 " (cutoff:3.500A) removed outlier: 5.830A pdb=" N THR E 460 " --> pdb=" O ILE E 451 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'E' and resid 479 through 480 removed outlier: 6.277A pdb=" N ILE E 479 " --> pdb=" O VAL E 606 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'E' and resid 483 through 484 Processing sheet with id=AE3, first strand: chain 'E' and resid 488 through 490 Processing sheet with id=AE4, first strand: chain 'E' and resid 593 through 596 removed outlier: 4.145A pdb=" N GLY E 578 " --> pdb=" O VAL E 596 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'F' and resid 231 through 235 WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 238 through 249 current: chain 'F' and resid 335 through 336 Processing sheet with id=AE6, first strand: chain 'F' and resid 258 through 261 Processing sheet with id=AE7, first strand: chain 'F' and resid 427 through 428 removed outlier: 6.245A pdb=" N ALA F 427 " --> pdb=" O ARG F 734 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE7 Processing sheet with id=AE8, first strand: chain 'F' and resid 483 through 484 Processing sheet with id=AE9, first strand: chain 'F' and resid 488 through 490 Processing sheet with id=AF1, first strand: chain 'F' and resid 542 through 544 Processing sheet with id=AF2, first strand: chain 'F' and resid 619 through 621 Processing sheet with id=AF3, first strand: chain 'H' and resid 22 through 25 Processing sheet with id=AF4, first strand: chain 'H' and resid 29 through 31 WARNING: can't find start of bonding for strands! previous: chain 'H' and resid 29 through 31 current: chain 'H' and resid 64 through 70 WARNING: can't find start of bonding for strands! previous: chain 'H' and resid 77 through 79 current: chain 'H' and resid 138 through 139 Processing sheet with id=AF5, first strand: chain 'L' and resid 24 through 25 Processing sheet with id=AF6, first strand: chain 'L' and resid 29 through 32 WARNING: can't find start of bonding for strands! previous: chain 'L' and resid 29 through 32 current: chain 'L' and resid 66 through 69 WARNING: can't find start of bonding for strands! previous: chain 'L' and resid 66 through 69 current: chain 'L' and resid 118 through 121 No H-bonds generated for sheet with id=AF6 240 hydrogen bonds defined for protein. 462 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.49 Time building geometry restraints manager: 2.05 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 4886 1.33 - 1.45: 4159 1.45 - 1.57: 10139 1.57 - 1.69: 0 1.69 - 1.81: 120 Bond restraints: 19304 Sorted by residual: bond pdb=" C ILE L 69 " pdb=" O ILE L 69 " ideal model delta sigma weight residual 1.236 1.212 0.023 1.01e-02 9.80e+03 5.28e+00 bond pdb=" CA SER E 425 " pdb=" C SER E 425 " ideal model delta sigma weight residual 1.531 1.498 0.033 1.46e-02 4.69e+03 5.25e+00 bond pdb=" C GLN B 458 " pdb=" O GLN B 458 " ideal model delta sigma weight residual 1.234 1.207 0.027 1.19e-02 7.06e+03 5.02e+00 bond pdb=" CA GLN B 458 " pdb=" C GLN B 458 " ideal model delta sigma weight residual 1.525 1.499 0.026 1.29e-02 6.01e+03 4.09e+00 bond pdb=" C TYR D 399 " pdb=" N PHE D 400 " ideal model delta sigma weight residual 1.335 1.268 0.067 3.59e-02 7.76e+02 3.44e+00 ... (remaining 19299 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.68: 25735 2.68 - 5.36: 481 5.36 - 8.04: 48 8.04 - 10.72: 15 10.72 - 13.40: 7 Bond angle restraints: 26286 Sorted by residual: angle pdb=" N VAL H 121 " pdb=" CA VAL H 121 " pdb=" C VAL H 121 " ideal model delta sigma weight residual 110.72 120.61 -9.89 1.01e+00 9.80e-01 9.60e+01 angle pdb=" N THR C 492 " pdb=" CA THR C 492 " pdb=" C THR C 492 " ideal model delta sigma weight residual 109.59 97.02 12.57 1.47e+00 4.63e-01 7.31e+01 angle pdb=" N THR H 50 " pdb=" CA THR H 50 " pdb=" C THR H 50 " ideal model delta sigma weight residual 111.28 119.44 -8.16 1.09e+00 8.42e-01 5.60e+01 angle pdb=" N ASP H 137 " pdb=" CA ASP H 137 " pdb=" C ASP H 137 " ideal model delta sigma weight residual 111.36 119.41 -8.05 1.09e+00 8.42e-01 5.45e+01 angle pdb=" N ASP A 551 " pdb=" CA ASP A 551 " pdb=" C ASP A 551 " ideal model delta sigma weight residual 108.90 120.80 -11.90 1.63e+00 3.76e-01 5.33e+01 ... (remaining 26281 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.12: 10851 17.12 - 34.23: 357 34.23 - 51.35: 65 51.35 - 68.46: 12 68.46 - 85.58: 17 Dihedral angle restraints: 11302 sinusoidal: 4460 harmonic: 6842 Sorted by residual: dihedral pdb=" CA TYR F 484 " pdb=" C TYR F 484 " pdb=" N ARG F 485 " pdb=" CA ARG F 485 " ideal model delta harmonic sigma weight residual -180.00 -156.51 -23.49 0 5.00e+00 4.00e-02 2.21e+01 dihedral pdb=" CA TYR D 484 " pdb=" C TYR D 484 " pdb=" N ARG D 485 " pdb=" CA ARG D 485 " ideal model delta harmonic sigma weight residual 180.00 -158.53 -21.47 0 5.00e+00 4.00e-02 1.84e+01 dihedral pdb=" CA LEU D 256 " pdb=" C LEU D 256 " pdb=" N TYR D 257 " pdb=" CA TYR D 257 " ideal model delta harmonic sigma weight residual 180.00 158.60 21.40 0 5.00e+00 4.00e-02 1.83e+01 ... (remaining 11299 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.086: 2363 0.086 - 0.172: 316 0.172 - 0.259: 29 0.259 - 0.345: 11 0.345 - 0.431: 1 Chirality restraints: 2720 Sorted by residual: chirality pdb=" CA TYR C 706 " pdb=" N TYR C 706 " pdb=" C TYR C 706 " pdb=" CB TYR C 706 " both_signs ideal model delta sigma weight residual False 2.51 2.08 0.43 2.00e-01 2.50e+01 4.64e+00 chirality pdb=" CA THR C 492 " pdb=" N THR C 492 " pdb=" C THR C 492 " pdb=" CB THR C 492 " both_signs ideal model delta sigma weight residual False 2.53 2.85 -0.32 2.00e-01 2.50e+01 2.56e+00 chirality pdb=" CA ASP H 137 " pdb=" N ASP H 137 " pdb=" C ASP H 137 " pdb=" CB ASP H 137 " both_signs ideal model delta sigma weight residual False 2.51 2.20 0.31 2.00e-01 2.50e+01 2.42e+00 ... (remaining 2717 not shown) Planarity restraints: 3496 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA PHE F 422 " 0.013 2.00e-02 2.50e+03 2.64e-02 6.94e+00 pdb=" C PHE F 422 " -0.046 2.00e-02 2.50e+03 pdb=" O PHE F 422 " 0.017 2.00e-02 2.50e+03 pdb=" N HIS F 423 " 0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA TYR H 124 " 0.012 2.00e-02 2.50e+03 2.44e-02 5.96e+00 pdb=" C TYR H 124 " -0.042 2.00e-02 2.50e+03 pdb=" O TYR H 124 " 0.016 2.00e-02 2.50e+03 pdb=" N TYR H 125 " 0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASP D 657 " 0.033 5.00e-02 4.00e+02 5.00e-02 4.00e+00 pdb=" N PRO D 658 " -0.086 5.00e-02 4.00e+02 pdb=" CA PRO D 658 " 0.026 5.00e-02 4.00e+02 pdb=" CD PRO D 658 " 0.027 5.00e-02 4.00e+02 ... (remaining 3493 not shown) Histogram of nonbonded interaction distances: 1.80 - 2.42: 55 2.42 - 3.04: 11586 3.04 - 3.66: 28934 3.66 - 4.28: 46712 4.28 - 4.90: 75948 Nonbonded interactions: 163235 Sorted by model distance: nonbonded pdb=" NH1 ARG D 312 " pdb=" OE1 GLU D 684 " model vdw 1.798 3.120 nonbonded pdb=" OH TYR A 399 " pdb=" OD2 ASP F 297 " model vdw 2.106 3.040 nonbonded pdb=" NH2 ARG A 485 " pdb=" OG SER A 576 " model vdw 2.139 3.120 nonbonded pdb=" OH TYR D 415 " pdb=" O HIS D 642 " model vdw 2.157 3.040 nonbonded pdb=" OD2 ASP E 441 " pdb=" NH1 ARG F 550 " model vdw 2.181 3.120 ... (remaining 163230 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' selection = chain 'D' } ncs_group { reference = chain 'B' selection = chain 'E' } ncs_group { reference = chain 'C' selection = chain 'F' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.410 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.310 Check model and map are aligned: 0.070 Set scattering table: 0.040 Process input model: 15.470 Find NCS groups from input model: 0.190 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:8.420 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.960 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8454 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 : 0.006 0.070 19306 Z= 0.293 Angle : 0.916 13.403 26290 Z= 0.552 Chirality : 0.060 0.431 2720 Planarity : 0.005 0.050 3496 Dihedral : 10.148 85.576 6930 Min Nonbonded Distance : 1.798 Molprobity Statistics. All-atom Clashscore : 11.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 0.54 % Allowed : 2.29 % Favored : 97.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.75 % 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 aren not related in a simple way. whole: -1.40 (0.14), residues: 2339 helix: -4.29 (0.25), residues: 92 sheet: -0.80 (0.16), residues: 672 loop : -0.75 (0.13), residues: 1575 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.002 ARG C 734 TYR 0.026 0.003 TYR A 252 PHE 0.026 0.003 PHE C 534 TRP 0.026 0.003 TRP F 281 HIS 0.017 0.003 HIS D 290 Details of bonding type rmsd covalent geometry : bond 0.00594 (19304) covalent geometry : angle 0.91568 (26286) SS BOND : bond 0.00272 ( 2) SS BOND : angle 1.44600 ( 4) hydrogen bonds : bond 0.22422 ( 240) hydrogen bonds : angle 8.92975 ( 462) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4678 Ramachandran restraints generated. 2339 Oldfield, 0 Emsley, 2339 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4678 Ramachandran restraints generated. 2339 Oldfield, 0 Emsley, 2339 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 334 residues out of total 2052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 323 time to evaluate : 0.740 Fit side-chains REVERT: A 588 GLN cc_start: 0.7664 (mp10) cc_final: 0.7377 (mm-40) REVERT: A 590 GLN cc_start: 0.7460 (mt0) cc_final: 0.7219 (mt0) REVERT: B 533 ARG cc_start: 0.7865 (ptt-90) cc_final: 0.7593 (ptp90) REVERT: D 370 ASP cc_start: 0.7196 (m-30) cc_final: 0.6760 (m-30) REVERT: D 373 MET cc_start: 0.8750 (ttt) cc_final: 0.8511 (ttt) REVERT: D 474 GLN cc_start: 0.7888 (mt0) cc_final: 0.7680 (tp40) REVERT: E 514 ARG cc_start: 0.7998 (mtm180) cc_final: 0.6441 (mmt180) REVERT: H 118 ASP cc_start: 0.8050 (t0) cc_final: 0.7797 (t70) REVERT: L 100 GLN cc_start: 0.7937 (OUTLIER) cc_final: 0.7636 (mt0) outliers start: 11 outliers final: 7 residues processed: 331 average time/residue: 0.8377 time to fit residues: 303.8768 Evaluate side-chains 199 residues out of total 2052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 191 time to evaluate : 0.769 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 491 THR Chi-restraints excluded: chain H residue 75 ASP Chi-restraints excluded: chain H residue 102 LEU Chi-restraints excluded: chain H residue 136 MET Chi-restraints excluded: chain L residue 21 GLN Chi-restraints excluded: chain L residue 23 VAL Chi-restraints excluded: chain L residue 55 ASN Chi-restraints excluded: chain L residue 100 GLN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 216 optimal weight: 9.9990 chunk 98 optimal weight: 9.9990 chunk 194 optimal weight: 4.9990 chunk 227 optimal weight: 10.0000 chunk 107 optimal weight: 8.9990 chunk 10 optimal weight: 0.8980 chunk 66 optimal weight: 1.9990 chunk 130 optimal weight: 6.9990 chunk 124 optimal weight: 10.0000 chunk 103 optimal weight: 9.9990 chunk 200 optimal weight: 8.9990 overall best weight: 4.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 253 ASN A 259 GLN ** A 290 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 337 ASN A 474 GLN A 519 ASN A 624 HIS A 646 GLN A 651 ASN B 430 GLN B 458 GLN B 512 ASN B 608 GLN C 321 GLN C 387 GLN C 419 ASN C 452 ASN C 497 ASN C 552 ASN C 608 GLN C 646 GLN C 651 ASN C 673 GLN C 700 GLN C 704 ASN D 259 GLN ** D 262 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 290 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 343 GLN D 412 GLN D 552 ASN D 588 GLN D 599 GLN D 646 GLN D 651 ASN D 673 GLN E 452 ASN E 599 GLN F 254 ASN F 403 GLN F 497 ASN F 585 GLN F 590 GLN F 608 GLN F 646 GLN F 651 ASN F 673 GLN F 700 GLN F 710 ASN H 81 GLN H 120 ASN H 129 ASN L 26 GLN L 117 ASN Total number of N/Q/H flips: 51 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3037 r_free = 0.3037 target = 0.091815 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2834 r_free = 0.2834 target = 0.079608 restraints weight = 29968.516| |-----------------------------------------------------------------------------| r_work (start): 0.2835 rms_B_bonded: 1.38 r_work: 0.2758 rms_B_bonded: 1.76 restraints_weight: 0.5000 r_work: 0.2663 rms_B_bonded: 3.02 restraints_weight: 0.2500 r_work (final): 0.2663 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8648 moved from start: 0.1508 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 19306 Z= 0.181 Angle : 0.623 9.711 26290 Z= 0.328 Chirality : 0.046 0.146 2720 Planarity : 0.005 0.051 3496 Dihedral : 6.591 85.729 2586 Min Nonbonded Distance : 2.567 Molprobity Statistics. All-atom Clashscore : 5.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.62 % Favored : 98.38 % Rotamer: Outliers : 2.34 % Allowed : 6.87 % Favored : 90.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.75 % 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 aren not related in a simple way. whole: -0.92 (0.15), residues: 2339 helix: -3.42 (0.40), residues: 92 sheet: -0.60 (0.17), residues: 646 loop : -0.39 (0.14), residues: 1601 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 514 TYR 0.017 0.002 TYR F 701 PHE 0.022 0.002 PHE H 83 TRP 0.014 0.002 TRP F 281 HIS 0.013 0.002 HIS C 290 Details of bonding type rmsd covalent geometry : bond 0.00416 (19304) covalent geometry : angle 0.62264 (26286) SS BOND : bond 0.00422 ( 2) SS BOND : angle 1.21804 ( 4) hydrogen bonds : bond 0.03965 ( 240) hydrogen bonds : angle 6.67788 ( 462) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4678 Ramachandran restraints generated. 2339 Oldfield, 0 Emsley, 2339 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4678 Ramachandran restraints generated. 2339 Oldfield, 0 Emsley, 2339 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 242 residues out of total 2052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 194 time to evaluate : 0.810 Fit side-chains REVERT: A 485 ARG cc_start: 0.8578 (OUTLIER) cc_final: 0.7145 (ttm170) REVERT: A 588 GLN cc_start: 0.7791 (mp10) cc_final: 0.7371 (mm-40) REVERT: A 590 GLN cc_start: 0.7773 (mt0) cc_final: 0.7480 (mt0) REVERT: B 500 GLU cc_start: 0.7698 (OUTLIER) cc_final: 0.6650 (tm-30) REVERT: B 533 ARG cc_start: 0.7814 (ptt-90) cc_final: 0.7554 (ptt180) REVERT: C 416 GLU cc_start: 0.8181 (OUTLIER) cc_final: 0.7854 (tp30) REVERT: C 641 LYS cc_start: 0.8744 (ttmm) cc_final: 0.8456 (mmmm) REVERT: D 370 ASP cc_start: 0.7261 (m-30) cc_final: 0.6790 (m-30) REVERT: D 373 MET cc_start: 0.8781 (ttt) cc_final: 0.8518 (ttt) REVERT: D 474 GLN cc_start: 0.8223 (mt0) cc_final: 0.7486 (tp40) REVERT: D 532 ASP cc_start: 0.7550 (OUTLIER) cc_final: 0.7315 (p0) REVERT: E 485 ARG cc_start: 0.8534 (OUTLIER) cc_final: 0.7041 (ttm170) REVERT: E 514 ARG cc_start: 0.7986 (mtm180) cc_final: 0.5821 (tpt170) REVERT: F 235 LEU cc_start: 0.8368 (OUTLIER) cc_final: 0.8069 (mp) REVERT: F 529 GLU cc_start: 0.7742 (OUTLIER) cc_final: 0.7326 (tt0) REVERT: F 550 ARG cc_start: 0.8492 (OUTLIER) cc_final: 0.7365 (mtm180) REVERT: F 654 VAL cc_start: 0.7964 (t) cc_final: 0.7729 (m) REVERT: F 725 ARG cc_start: 0.8450 (OUTLIER) cc_final: 0.8117 (pmm-80) REVERT: H 57 ARG cc_start: 0.8794 (OUTLIER) cc_final: 0.7542 (ptm160) REVERT: H 118 ASP cc_start: 0.8446 (t0) cc_final: 0.8205 (t70) REVERT: L 100 GLN cc_start: 0.8053 (OUTLIER) cc_final: 0.7562 (mp10) outliers start: 48 outliers final: 14 residues processed: 225 average time/residue: 0.8455 time to fit residues: 209.4167 Evaluate side-chains 196 residues out of total 2052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 171 time to evaluate : 0.827 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 431 SER Chi-restraints excluded: chain A residue 485 ARG Chi-restraints excluded: chain B residue 500 GLU Chi-restraints excluded: chain C residue 238 ARG Chi-restraints excluded: chain C residue 339 THR Chi-restraints excluded: chain C residue 416 GLU Chi-restraints excluded: chain D residue 531 GLU Chi-restraints excluded: chain D residue 532 ASP Chi-restraints excluded: chain D residue 660 THR Chi-restraints excluded: chain E residue 485 ARG Chi-restraints excluded: chain E residue 580 VAL Chi-restraints excluded: chain F residue 235 LEU Chi-restraints excluded: chain F residue 529 GLU Chi-restraints excluded: chain F residue 550 ARG Chi-restraints excluded: chain F residue 703 SER Chi-restraints excluded: chain F residue 725 ARG Chi-restraints excluded: chain H residue 56 VAL Chi-restraints excluded: chain H residue 57 ARG Chi-restraints excluded: chain H residue 75 ASP Chi-restraints excluded: chain H residue 82 ARG Chi-restraints excluded: chain H residue 102 LEU Chi-restraints excluded: chain H residue 136 MET Chi-restraints excluded: chain L residue 23 VAL Chi-restraints excluded: chain L residue 100 GLN Chi-restraints excluded: chain L residue 115 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 225 optimal weight: 10.0000 chunk 70 optimal weight: 10.0000 chunk 177 optimal weight: 20.0000 chunk 32 optimal weight: 2.9990 chunk 194 optimal weight: 10.0000 chunk 190 optimal weight: 0.9990 chunk 205 optimal weight: 10.0000 chunk 102 optimal weight: 8.9990 chunk 3 optimal weight: 9.9990 chunk 61 optimal weight: 9.9990 chunk 193 optimal weight: 0.1980 overall best weight: 4.6388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 290 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 474 GLN A 592 GLN B 428 HIS C 428 HIS ** D 262 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 290 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 552 ASN D 588 GLN F 254 ASN F 585 GLN H 129 ASN L 73 ASN L 117 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3026 r_free = 0.3026 target = 0.090972 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2824 r_free = 0.2824 target = 0.078874 restraints weight = 30196.035| |-----------------------------------------------------------------------------| r_work (start): 0.2823 rms_B_bonded: 1.38 r_work: 0.2745 rms_B_bonded: 1.77 restraints_weight: 0.5000 r_work: 0.2650 rms_B_bonded: 3.03 restraints_weight: 0.2500 r_work (final): 0.2650 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8663 moved from start: 0.1807 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 19306 Z= 0.170 Angle : 0.578 9.252 26290 Z= 0.302 Chirality : 0.044 0.138 2720 Planarity : 0.004 0.063 3496 Dihedral : 6.063 78.599 2580 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 4.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 2.34 % Allowed : 7.80 % Favored : 89.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.75 % 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 aren not related in a simple way. whole: -0.76 (0.15), residues: 2339 helix: -3.39 (0.41), residues: 92 sheet: -0.48 (0.18), residues: 641 loop : -0.28 (0.14), residues: 1606 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 514 TYR 0.017 0.002 TYR C 701 PHE 0.020 0.002 PHE H 83 TRP 0.013 0.002 TRP E 509 HIS 0.012 0.002 HIS F 290 Details of bonding type rmsd covalent geometry : bond 0.00391 (19304) covalent geometry : angle 0.57757 (26286) SS BOND : bond 0.00404 ( 2) SS BOND : angle 1.24786 ( 4) hydrogen bonds : bond 0.03496 ( 240) hydrogen bonds : angle 6.27446 ( 462) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4678 Ramachandran restraints generated. 2339 Oldfield, 0 Emsley, 2339 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4678 Ramachandran restraints generated. 2339 Oldfield, 0 Emsley, 2339 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 232 residues out of total 2052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 184 time to evaluate : 0.958 Fit side-chains REVERT: A 485 ARG cc_start: 0.8570 (OUTLIER) cc_final: 0.8001 (ttm170) REVERT: A 588 GLN cc_start: 0.7833 (mp10) cc_final: 0.7376 (mm110) REVERT: A 590 GLN cc_start: 0.7775 (mt0) cc_final: 0.7457 (mt0) REVERT: B 485 ARG cc_start: 0.8355 (OUTLIER) cc_final: 0.7823 (ttm170) REVERT: B 533 ARG cc_start: 0.7843 (ptt-90) cc_final: 0.7579 (ptt180) REVERT: C 399 TYR cc_start: 0.7329 (t80) cc_final: 0.7106 (t80) REVERT: C 641 LYS cc_start: 0.8727 (ttmm) cc_final: 0.8464 (mmmm) REVERT: D 370 ASP cc_start: 0.7431 (m-30) cc_final: 0.6938 (m-30) REVERT: D 384 ASP cc_start: 0.8136 (t0) cc_final: 0.7789 (t0) REVERT: D 474 GLN cc_start: 0.8247 (mt0) cc_final: 0.7506 (tp40) REVERT: D 532 ASP cc_start: 0.7603 (OUTLIER) cc_final: 0.7369 (p0) REVERT: E 485 ARG cc_start: 0.8540 (OUTLIER) cc_final: 0.6961 (ttm170) REVERT: E 514 ARG cc_start: 0.8016 (mtm180) cc_final: 0.5831 (tpt170) REVERT: F 529 GLU cc_start: 0.7797 (OUTLIER) cc_final: 0.7421 (tt0) REVERT: F 550 ARG cc_start: 0.8488 (OUTLIER) cc_final: 0.7388 (mtm180) REVERT: F 588 GLN cc_start: 0.8056 (mp10) cc_final: 0.7757 (mp10) REVERT: F 654 VAL cc_start: 0.7896 (t) cc_final: 0.7683 (m) REVERT: F 725 ARG cc_start: 0.8412 (OUTLIER) cc_final: 0.8075 (pmm-80) REVERT: H 57 ARG cc_start: 0.8784 (OUTLIER) cc_final: 0.7582 (ptm160) REVERT: H 106 ARG cc_start: 0.7586 (mpt-90) cc_final: 0.7384 (mpt-90) REVERT: H 118 ASP cc_start: 0.8460 (t0) cc_final: 0.8231 (t70) REVERT: L 100 GLN cc_start: 0.8008 (OUTLIER) cc_final: 0.7547 (mt0) outliers start: 48 outliers final: 22 residues processed: 215 average time/residue: 0.8136 time to fit residues: 193.1676 Evaluate side-chains 202 residues out of total 2052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 171 time to evaluate : 0.767 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 485 ARG Chi-restraints excluded: chain B residue 469 SER Chi-restraints excluded: chain B residue 485 ARG Chi-restraints excluded: chain B residue 500 GLU Chi-restraints excluded: chain C residue 238 ARG Chi-restraints excluded: chain C residue 348 SER Chi-restraints excluded: chain D residue 531 GLU Chi-restraints excluded: chain D residue 532 ASP Chi-restraints excluded: chain D residue 551 ASP Chi-restraints excluded: chain D residue 660 THR Chi-restraints excluded: chain E residue 449 LYS Chi-restraints excluded: chain E residue 485 ARG Chi-restraints excluded: chain E residue 491 THR Chi-restraints excluded: chain E residue 540 SER Chi-restraints excluded: chain E residue 580 VAL Chi-restraints excluded: chain F residue 529 GLU Chi-restraints excluded: chain F residue 550 ARG Chi-restraints excluded: chain F residue 725 ARG Chi-restraints excluded: chain H residue 23 VAL Chi-restraints excluded: chain H residue 56 VAL Chi-restraints excluded: chain H residue 57 ARG Chi-restraints excluded: chain H residue 75 ASP Chi-restraints excluded: chain H residue 82 ARG Chi-restraints excluded: chain H residue 102 LEU Chi-restraints excluded: chain H residue 136 MET Chi-restraints excluded: chain L residue 23 VAL Chi-restraints excluded: chain L residue 33 THR Chi-restraints excluded: chain L residue 38 VAL Chi-restraints excluded: chain L residue 39 THR Chi-restraints excluded: chain L residue 100 GLN Chi-restraints excluded: chain L residue 115 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 116 optimal weight: 5.9990 chunk 77 optimal weight: 9.9990 chunk 57 optimal weight: 20.0000 chunk 227 optimal weight: 10.0000 chunk 158 optimal weight: 20.0000 chunk 153 optimal weight: 10.0000 chunk 122 optimal weight: 20.0000 chunk 88 optimal weight: 9.9990 chunk 50 optimal weight: 3.9990 chunk 51 optimal weight: 10.0000 chunk 58 optimal weight: 5.9990 overall best weight: 7.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 290 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 474 GLN C 590 GLN ** D 290 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 588 GLN F 254 ASN ** F 262 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 585 GLN L 26 GLN L 117 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2996 r_free = 0.2996 target = 0.089168 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2792 r_free = 0.2792 target = 0.077087 restraints weight = 30202.572| |-----------------------------------------------------------------------------| r_work (start): 0.2795 rms_B_bonded: 1.37 r_work: 0.2716 rms_B_bonded: 1.75 restraints_weight: 0.5000 r_work: 0.2621 rms_B_bonded: 3.00 restraints_weight: 0.2500 r_work (final): 0.2621 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8687 moved from start: 0.2006 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.045 19306 Z= 0.239 Angle : 0.628 9.731 26290 Z= 0.330 Chirality : 0.047 0.140 2720 Planarity : 0.005 0.057 3496 Dihedral : 6.335 79.408 2580 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 4.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 2.78 % Allowed : 7.80 % Favored : 89.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.75 % 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 aren not related in a simple way. whole: -0.89 (0.16), residues: 2339 helix: -3.52 (0.41), residues: 92 sheet: -0.62 (0.18), residues: 607 loop : -0.35 (0.14), residues: 1640 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C 485 TYR 0.021 0.002 TYR C 701 PHE 0.016 0.002 PHE C 286 TRP 0.015 0.002 TRP E 509 HIS 0.015 0.002 HIS F 290 Details of bonding type rmsd covalent geometry : bond 0.00558 (19304) covalent geometry : angle 0.62739 (26286) SS BOND : bond 0.00525 ( 2) SS BOND : angle 1.34168 ( 4) hydrogen bonds : bond 0.03686 ( 240) hydrogen bonds : angle 6.35140 ( 462) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4678 Ramachandran restraints generated. 2339 Oldfield, 0 Emsley, 2339 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4678 Ramachandran restraints generated. 2339 Oldfield, 0 Emsley, 2339 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 236 residues out of total 2052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 179 time to evaluate : 0.806 Fit side-chains REVERT: A 485 ARG cc_start: 0.8700 (OUTLIER) cc_final: 0.7583 (ttm170) REVERT: A 564 GLU cc_start: 0.7127 (pp20) cc_final: 0.6926 (pp20) REVERT: A 588 GLN cc_start: 0.7776 (mp10) cc_final: 0.7384 (mm110) REVERT: A 590 GLN cc_start: 0.7761 (mt0) cc_final: 0.7454 (mt0) REVERT: B 449 LYS cc_start: 0.8780 (OUTLIER) cc_final: 0.8424 (ttpp) REVERT: B 485 ARG cc_start: 0.8476 (OUTLIER) cc_final: 0.7530 (ttm170) REVERT: B 533 ARG cc_start: 0.7802 (ptt-90) cc_final: 0.7443 (ptt-90) REVERT: C 485 ARG cc_start: 0.8788 (OUTLIER) cc_final: 0.8448 (ttm170) REVERT: C 550 ARG cc_start: 0.8447 (OUTLIER) cc_final: 0.8165 (mtp85) REVERT: C 641 LYS cc_start: 0.8744 (ttmm) cc_final: 0.8440 (mmmm) REVERT: D 370 ASP cc_start: 0.7321 (m-30) cc_final: 0.6805 (m-30) REVERT: D 384 ASP cc_start: 0.8142 (t0) cc_final: 0.7823 (t0) REVERT: D 474 GLN cc_start: 0.8291 (mt0) cc_final: 0.7523 (tp40) REVERT: D 532 ASP cc_start: 0.7761 (OUTLIER) cc_final: 0.7491 (p0) REVERT: E 485 ARG cc_start: 0.8633 (OUTLIER) cc_final: 0.7146 (ttm170) REVERT: E 514 ARG cc_start: 0.8044 (mtm180) cc_final: 0.6143 (mmt180) REVERT: F 259 GLN cc_start: 0.8839 (OUTLIER) cc_final: 0.7929 (tt0) REVERT: F 529 GLU cc_start: 0.7805 (OUTLIER) cc_final: 0.7230 (tt0) REVERT: F 550 ARG cc_start: 0.8548 (OUTLIER) cc_final: 0.7458 (mtm180) REVERT: F 654 VAL cc_start: 0.7925 (t) cc_final: 0.7692 (m) REVERT: F 725 ARG cc_start: 0.8473 (OUTLIER) cc_final: 0.8220 (pmm-80) REVERT: H 57 ARG cc_start: 0.8895 (OUTLIER) cc_final: 0.7593 (ptm160) REVERT: H 118 ASP cc_start: 0.8531 (t0) cc_final: 0.8304 (t70) REVERT: L 100 GLN cc_start: 0.8039 (OUTLIER) cc_final: 0.7578 (mt0) outliers start: 57 outliers final: 33 residues processed: 220 average time/residue: 0.8114 time to fit residues: 196.9249 Evaluate side-chains 218 residues out of total 2052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 172 time to evaluate : 0.773 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 239 VAL Chi-restraints excluded: chain A residue 430 GLN Chi-restraints excluded: chain A residue 431 SER Chi-restraints excluded: chain A residue 485 ARG Chi-restraints excluded: chain B residue 449 LYS Chi-restraints excluded: chain B residue 469 SER Chi-restraints excluded: chain B residue 485 ARG Chi-restraints excluded: chain B residue 500 GLU Chi-restraints excluded: chain C residue 238 ARG Chi-restraints excluded: chain C residue 290 HIS Chi-restraints excluded: chain C residue 314 ASN Chi-restraints excluded: chain C residue 348 SER Chi-restraints excluded: chain C residue 485 ARG Chi-restraints excluded: chain C residue 499 SER Chi-restraints excluded: chain C residue 550 ARG Chi-restraints excluded: chain D residue 531 GLU Chi-restraints excluded: chain D residue 532 ASP Chi-restraints excluded: chain D residue 551 ASP Chi-restraints excluded: chain D residue 660 THR Chi-restraints excluded: chain E residue 449 LYS Chi-restraints excluded: chain E residue 485 ARG Chi-restraints excluded: chain E residue 491 THR Chi-restraints excluded: chain E residue 540 SER Chi-restraints excluded: chain E residue 580 VAL Chi-restraints excluded: chain F residue 235 LEU Chi-restraints excluded: chain F residue 239 VAL Chi-restraints excluded: chain F residue 259 GLN Chi-restraints excluded: chain F residue 529 GLU Chi-restraints excluded: chain F residue 550 ARG Chi-restraints excluded: chain F residue 703 SER Chi-restraints excluded: chain F residue 725 ARG Chi-restraints excluded: chain H residue 23 VAL Chi-restraints excluded: chain H residue 56 VAL Chi-restraints excluded: chain H residue 57 ARG Chi-restraints excluded: chain H residue 75 ASP Chi-restraints excluded: chain H residue 82 ARG Chi-restraints excluded: chain H residue 101 GLU Chi-restraints excluded: chain H residue 102 LEU Chi-restraints excluded: chain H residue 136 MET Chi-restraints excluded: chain L residue 22 SER Chi-restraints excluded: chain L residue 23 VAL Chi-restraints excluded: chain L residue 33 THR Chi-restraints excluded: chain L residue 38 VAL Chi-restraints excluded: chain L residue 39 THR Chi-restraints excluded: chain L residue 100 GLN Chi-restraints excluded: chain L residue 115 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 129 optimal weight: 9.9990 chunk 83 optimal weight: 0.6980 chunk 76 optimal weight: 10.0000 chunk 107 optimal weight: 6.9990 chunk 147 optimal weight: 7.9990 chunk 87 optimal weight: 0.9980 chunk 18 optimal weight: 0.4980 chunk 24 optimal weight: 7.9990 chunk 45 optimal weight: 8.9990 chunk 192 optimal weight: 6.9990 chunk 89 optimal weight: 5.9990 overall best weight: 3.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 290 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 474 GLN ** D 262 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 290 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 588 GLN F 254 ASN ** F 262 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 585 GLN L 117 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3028 r_free = 0.3028 target = 0.091145 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2826 r_free = 0.2826 target = 0.078971 restraints weight = 30017.584| |-----------------------------------------------------------------------------| r_work (start): 0.2825 rms_B_bonded: 1.38 r_work: 0.2747 rms_B_bonded: 1.77 restraints_weight: 0.5000 r_work: 0.2651 rms_B_bonded: 3.03 restraints_weight: 0.2500 r_work (final): 0.2651 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8662 moved from start: 0.2128 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 19306 Z= 0.124 Angle : 0.522 7.936 26290 Z= 0.273 Chirality : 0.042 0.136 2720 Planarity : 0.004 0.038 3496 Dihedral : 5.782 75.511 2580 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 4.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 2.19 % Allowed : 8.72 % Favored : 89.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.75 % 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 aren not related in a simple way. whole: -0.73 (0.16), residues: 2339 helix: -3.50 (0.40), residues: 99 sheet: -0.46 (0.18), residues: 621 loop : -0.24 (0.14), residues: 1619 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 514 TYR 0.014 0.001 TYR C 701 PHE 0.012 0.001 PHE H 83 TRP 0.012 0.001 TRP E 509 HIS 0.007 0.001 HIS F 290 Details of bonding type rmsd covalent geometry : bond 0.00284 (19304) covalent geometry : angle 0.52231 (26286) SS BOND : bond 0.00331 ( 2) SS BOND : angle 1.01350 ( 4) hydrogen bonds : bond 0.02957 ( 240) hydrogen bonds : angle 5.86286 ( 462) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4678 Ramachandran restraints generated. 2339 Oldfield, 0 Emsley, 2339 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4678 Ramachandran restraints generated. 2339 Oldfield, 0 Emsley, 2339 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 223 residues out of total 2052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 178 time to evaluate : 0.782 Fit side-chains REVERT: A 485 ARG cc_start: 0.8516 (OUTLIER) cc_final: 0.7806 (ttm170) REVERT: A 564 GLU cc_start: 0.7103 (pp20) cc_final: 0.6858 (pp20) REVERT: A 588 GLN cc_start: 0.7846 (mp10) cc_final: 0.7454 (mm-40) REVERT: A 590 GLN cc_start: 0.7790 (mt0) cc_final: 0.7443 (mt0) REVERT: A 641 LYS cc_start: 0.8644 (OUTLIER) cc_final: 0.8340 (mttt) REVERT: B 449 LYS cc_start: 0.8791 (OUTLIER) cc_final: 0.8344 (ttpp) REVERT: B 485 ARG cc_start: 0.8352 (OUTLIER) cc_final: 0.7963 (ttm170) REVERT: B 500 GLU cc_start: 0.7695 (OUTLIER) cc_final: 0.6832 (tm-30) REVERT: B 533 ARG cc_start: 0.7804 (ptt-90) cc_final: 0.7474 (ptt-90) REVERT: C 641 LYS cc_start: 0.8711 (ttmm) cc_final: 0.8473 (mmmm) REVERT: D 370 ASP cc_start: 0.7425 (m-30) cc_final: 0.6975 (m-30) REVERT: D 474 GLN cc_start: 0.8263 (mt0) cc_final: 0.7526 (tp40) REVERT: D 532 ASP cc_start: 0.7715 (OUTLIER) cc_final: 0.7491 (p0) REVERT: E 514 ARG cc_start: 0.8035 (mtm180) cc_final: 0.5816 (tpt170) REVERT: F 258 LYS cc_start: 0.8327 (mtmt) cc_final: 0.7395 (mmpt) REVERT: F 550 ARG cc_start: 0.8536 (OUTLIER) cc_final: 0.7448 (mtm180) REVERT: F 654 VAL cc_start: 0.7869 (t) cc_final: 0.7629 (m) REVERT: H 57 ARG cc_start: 0.8822 (OUTLIER) cc_final: 0.7637 (ptm160) REVERT: H 118 ASP cc_start: 0.8466 (t0) cc_final: 0.8251 (t70) REVERT: H 136 MET cc_start: 0.8901 (OUTLIER) cc_final: 0.8666 (ptp) REVERT: L 100 GLN cc_start: 0.7995 (OUTLIER) cc_final: 0.7602 (mt0) outliers start: 45 outliers final: 18 residues processed: 208 average time/residue: 0.8299 time to fit residues: 190.1504 Evaluate side-chains 199 residues out of total 2052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 171 time to evaluate : 0.801 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 430 GLN Chi-restraints excluded: chain A residue 485 ARG Chi-restraints excluded: chain A residue 641 LYS Chi-restraints excluded: chain B residue 449 LYS Chi-restraints excluded: chain B residue 469 SER Chi-restraints excluded: chain B residue 485 ARG Chi-restraints excluded: chain B residue 500 GLU Chi-restraints excluded: chain C residue 238 ARG Chi-restraints excluded: chain C residue 314 ASN Chi-restraints excluded: chain D residue 532 ASP Chi-restraints excluded: chain D residue 660 THR Chi-restraints excluded: chain E residue 449 LYS Chi-restraints excluded: chain E residue 491 THR Chi-restraints excluded: chain E residue 580 VAL Chi-restraints excluded: chain F residue 239 VAL Chi-restraints excluded: chain F residue 550 ARG Chi-restraints excluded: chain H residue 23 VAL Chi-restraints excluded: chain H residue 56 VAL Chi-restraints excluded: chain H residue 57 ARG Chi-restraints excluded: chain H residue 75 ASP Chi-restraints excluded: chain H residue 82 ARG Chi-restraints excluded: chain H residue 101 GLU Chi-restraints excluded: chain H residue 102 LEU Chi-restraints excluded: chain H residue 136 MET Chi-restraints excluded: chain L residue 23 VAL Chi-restraints excluded: chain L residue 39 THR Chi-restraints excluded: chain L residue 100 GLN Chi-restraints excluded: chain L residue 115 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 107 optimal weight: 0.0270 chunk 117 optimal weight: 8.9990 chunk 33 optimal weight: 20.0000 chunk 153 optimal weight: 20.0000 chunk 139 optimal weight: 7.9990 chunk 126 optimal weight: 10.0000 chunk 115 optimal weight: 7.9990 chunk 188 optimal weight: 0.0050 chunk 162 optimal weight: 10.0000 chunk 192 optimal weight: 10.0000 chunk 152 optimal weight: 10.0000 overall best weight: 5.0058 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 290 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 290 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 430 GLN D 588 GLN F 254 ASN ** F 262 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 585 GLN F 673 GLN H 129 ASN L 117 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3009 r_free = 0.3009 target = 0.089942 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2806 r_free = 0.2806 target = 0.077846 restraints weight = 29769.816| |-----------------------------------------------------------------------------| r_work (start): 0.2804 rms_B_bonded: 1.36 r_work: 0.2726 rms_B_bonded: 1.74 restraints_weight: 0.5000 r_work: 0.2630 rms_B_bonded: 2.98 restraints_weight: 0.2500 r_work (final): 0.2630 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8676 moved from start: 0.2188 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 19306 Z= 0.177 Angle : 0.561 8.491 26290 Z= 0.294 Chirality : 0.044 0.136 2720 Planarity : 0.004 0.048 3496 Dihedral : 5.945 74.671 2580 Min Nonbonded Distance : 2.562 Molprobity Statistics. All-atom Clashscore : 4.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 2.73 % Allowed : 8.33 % Favored : 88.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.75 % 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 aren not related in a simple way. whole: -0.68 (0.16), residues: 2339 helix: -3.48 (0.43), residues: 92 sheet: -0.43 (0.19), residues: 621 loop : -0.21 (0.15), residues: 1626 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C 485 TYR 0.018 0.002 TYR C 701 PHE 0.014 0.002 PHE H 83 TRP 0.014 0.002 TRP E 509 HIS 0.011 0.002 HIS F 290 Details of bonding type rmsd covalent geometry : bond 0.00410 (19304) covalent geometry : angle 0.56093 (26286) SS BOND : bond 0.00403 ( 2) SS BOND : angle 1.05694 ( 4) hydrogen bonds : bond 0.03230 ( 240) hydrogen bonds : angle 5.98083 ( 462) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4678 Ramachandran restraints generated. 2339 Oldfield, 0 Emsley, 2339 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4678 Ramachandran restraints generated. 2339 Oldfield, 0 Emsley, 2339 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 233 residues out of total 2052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 177 time to evaluate : 0.781 Fit side-chains REVERT: A 474 GLN cc_start: 0.6934 (mp10) cc_final: 0.6632 (tp-100) REVERT: A 485 ARG cc_start: 0.8607 (OUTLIER) cc_final: 0.8018 (ttm170) REVERT: A 564 GLU cc_start: 0.7078 (pp20) cc_final: 0.6789 (pp20) REVERT: A 588 GLN cc_start: 0.7822 (mp10) cc_final: 0.7396 (mm110) REVERT: A 590 GLN cc_start: 0.7793 (mt0) cc_final: 0.7443 (mt0) REVERT: A 641 LYS cc_start: 0.8652 (OUTLIER) cc_final: 0.8347 (mttt) REVERT: B 449 LYS cc_start: 0.8800 (OUTLIER) cc_final: 0.8444 (ttpp) REVERT: B 485 ARG cc_start: 0.8440 (OUTLIER) cc_final: 0.7853 (ttm170) REVERT: B 533 ARG cc_start: 0.7761 (ptt-90) cc_final: 0.7433 (ptt-90) REVERT: C 271 ASP cc_start: 0.8145 (m-30) cc_final: 0.7918 (m-30) REVERT: C 550 ARG cc_start: 0.8450 (mtp85) cc_final: 0.8094 (mtp85) REVERT: C 641 LYS cc_start: 0.8691 (ttmm) cc_final: 0.8447 (mmmm) REVERT: D 314 ASN cc_start: 0.8292 (OUTLIER) cc_final: 0.7762 (m-40) REVERT: D 370 ASP cc_start: 0.7403 (m-30) cc_final: 0.6965 (m-30) REVERT: D 474 GLN cc_start: 0.8271 (mt0) cc_final: 0.7529 (tp40) REVERT: D 532 ASP cc_start: 0.7759 (OUTLIER) cc_final: 0.7548 (p0) REVERT: E 514 ARG cc_start: 0.8056 (mtm180) cc_final: 0.5819 (tpt170) REVERT: F 258 LYS cc_start: 0.8348 (mtmt) cc_final: 0.7407 (mmpt) REVERT: F 529 GLU cc_start: 0.7875 (OUTLIER) cc_final: 0.7472 (tt0) REVERT: F 550 ARG cc_start: 0.8549 (OUTLIER) cc_final: 0.7450 (mtm180) REVERT: F 654 VAL cc_start: 0.7887 (t) cc_final: 0.7648 (m) REVERT: F 725 ARG cc_start: 0.8436 (OUTLIER) cc_final: 0.8118 (pmm-80) REVERT: H 57 ARG cc_start: 0.8853 (OUTLIER) cc_final: 0.7617 (ptm160) REVERT: H 118 ASP cc_start: 0.8482 (t0) cc_final: 0.8271 (t70) REVERT: H 136 MET cc_start: 0.8866 (OUTLIER) cc_final: 0.8647 (ptp) REVERT: L 100 GLN cc_start: 0.7985 (OUTLIER) cc_final: 0.7576 (mt0) outliers start: 56 outliers final: 28 residues processed: 218 average time/residue: 0.8120 time to fit residues: 195.4253 Evaluate side-chains 212 residues out of total 2052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 172 time to evaluate : 0.787 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 239 VAL Chi-restraints excluded: chain A residue 430 GLN Chi-restraints excluded: chain A residue 485 ARG Chi-restraints excluded: chain A residue 641 LYS Chi-restraints excluded: chain A residue 681 VAL Chi-restraints excluded: chain B residue 449 LYS Chi-restraints excluded: chain B residue 469 SER Chi-restraints excluded: chain B residue 485 ARG Chi-restraints excluded: chain B residue 491 THR Chi-restraints excluded: chain B residue 500 GLU Chi-restraints excluded: chain C residue 238 ARG Chi-restraints excluded: chain C residue 314 ASN Chi-restraints excluded: chain C residue 348 SER Chi-restraints excluded: chain C residue 399 TYR Chi-restraints excluded: chain D residue 239 VAL Chi-restraints excluded: chain D residue 314 ASN Chi-restraints excluded: chain D residue 531 GLU Chi-restraints excluded: chain D residue 532 ASP Chi-restraints excluded: chain D residue 551 ASP Chi-restraints excluded: chain D residue 660 THR Chi-restraints excluded: chain E residue 449 LYS Chi-restraints excluded: chain E residue 491 THR Chi-restraints excluded: chain E residue 540 SER Chi-restraints excluded: chain E residue 580 VAL Chi-restraints excluded: chain F residue 239 VAL Chi-restraints excluded: chain F residue 529 GLU Chi-restraints excluded: chain F residue 550 ARG Chi-restraints excluded: chain F residue 725 ARG Chi-restraints excluded: chain H residue 23 VAL Chi-restraints excluded: chain H residue 56 VAL Chi-restraints excluded: chain H residue 57 ARG Chi-restraints excluded: chain H residue 75 ASP Chi-restraints excluded: chain H residue 82 ARG Chi-restraints excluded: chain H residue 101 GLU Chi-restraints excluded: chain H residue 102 LEU Chi-restraints excluded: chain H residue 136 MET Chi-restraints excluded: chain L residue 23 VAL Chi-restraints excluded: chain L residue 39 THR Chi-restraints excluded: chain L residue 100 GLN Chi-restraints excluded: chain L residue 115 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 0 optimal weight: 30.0000 chunk 151 optimal weight: 4.9990 chunk 70 optimal weight: 3.9990 chunk 148 optimal weight: 8.9990 chunk 152 optimal weight: 1.9990 chunk 226 optimal weight: 10.0000 chunk 63 optimal weight: 3.9990 chunk 40 optimal weight: 2.9990 chunk 37 optimal weight: 10.0000 chunk 61 optimal weight: 7.9990 chunk 230 optimal weight: 20.0000 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 290 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 290 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 262 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 290 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 430 GLN D 588 GLN F 254 ASN ** F 262 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 336 ASN F 673 GLN L 117 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3020 r_free = 0.3020 target = 0.090550 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2817 r_free = 0.2817 target = 0.078451 restraints weight = 29926.013| |-----------------------------------------------------------------------------| r_work (start): 0.2820 rms_B_bonded: 1.37 r_work: 0.2742 rms_B_bonded: 1.76 restraints_weight: 0.5000 r_work: 0.2646 rms_B_bonded: 3.01 restraints_weight: 0.2500 r_work (final): 0.2646 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8667 moved from start: 0.2260 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 19306 Z= 0.138 Angle : 0.526 7.780 26290 Z= 0.275 Chirality : 0.042 0.135 2720 Planarity : 0.004 0.037 3496 Dihedral : 5.742 72.616 2580 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 4.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 2.63 % Allowed : 8.72 % Favored : 88.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.75 % 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 aren not related in a simple way. whole: -0.61 (0.16), residues: 2339 helix: -3.44 (0.44), residues: 92 sheet: -0.36 (0.19), residues: 621 loop : -0.17 (0.15), residues: 1626 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 485 TYR 0.015 0.002 TYR C 701 PHE 0.013 0.001 PHE H 83 TRP 0.012 0.001 TRP E 509 HIS 0.008 0.001 HIS F 290 Details of bonding type rmsd covalent geometry : bond 0.00317 (19304) covalent geometry : angle 0.52608 (26286) SS BOND : bond 0.00337 ( 2) SS BOND : angle 0.97741 ( 4) hydrogen bonds : bond 0.02967 ( 240) hydrogen bonds : angle 5.79336 ( 462) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4678 Ramachandran restraints generated. 2339 Oldfield, 0 Emsley, 2339 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4678 Ramachandran restraints generated. 2339 Oldfield, 0 Emsley, 2339 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 227 residues out of total 2052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 173 time to evaluate : 0.806 Fit side-chains REVERT: A 485 ARG cc_start: 0.8539 (OUTLIER) cc_final: 0.7853 (ttm170) REVERT: A 564 GLU cc_start: 0.7127 (pp20) cc_final: 0.6832 (pp20) REVERT: A 588 GLN cc_start: 0.7837 (mp10) cc_final: 0.7403 (mm110) REVERT: A 590 GLN cc_start: 0.7775 (mt0) cc_final: 0.7455 (mt0) REVERT: A 641 LYS cc_start: 0.8639 (OUTLIER) cc_final: 0.8336 (mttt) REVERT: B 449 LYS cc_start: 0.8804 (OUTLIER) cc_final: 0.8416 (ttpp) REVERT: B 485 ARG cc_start: 0.8383 (OUTLIER) cc_final: 0.7943 (ttm170) REVERT: B 500 GLU cc_start: 0.7707 (OUTLIER) cc_final: 0.7003 (tm-30) REVERT: B 533 ARG cc_start: 0.7761 (ptt-90) cc_final: 0.7446 (ptt-90) REVERT: C 271 ASP cc_start: 0.8107 (m-30) cc_final: 0.7881 (m-30) REVERT: C 550 ARG cc_start: 0.8441 (OUTLIER) cc_final: 0.8062 (mtp85) REVERT: C 641 LYS cc_start: 0.8662 (ttmm) cc_final: 0.8347 (mmmm) REVERT: D 285 ASP cc_start: 0.8133 (t0) cc_final: 0.7697 (t0) REVERT: D 314 ASN cc_start: 0.8246 (OUTLIER) cc_final: 0.7695 (m-40) REVERT: D 474 GLN cc_start: 0.8279 (mt0) cc_final: 0.7540 (tp40) REVERT: D 485 ARG cc_start: 0.8888 (OUTLIER) cc_final: 0.8344 (ttt180) REVERT: D 532 ASP cc_start: 0.7736 (OUTLIER) cc_final: 0.7527 (p0) REVERT: E 514 ARG cc_start: 0.8019 (mtm180) cc_final: 0.5802 (tpt170) REVERT: F 258 LYS cc_start: 0.8322 (mtmt) cc_final: 0.7411 (mmpt) REVERT: F 529 GLU cc_start: 0.7871 (OUTLIER) cc_final: 0.7469 (tt0) REVERT: F 550 ARG cc_start: 0.8532 (OUTLIER) cc_final: 0.7438 (mtm180) REVERT: F 654 VAL cc_start: 0.7859 (t) cc_final: 0.7631 (m) REVERT: F 725 ARG cc_start: 0.8421 (OUTLIER) cc_final: 0.8140 (pmm-80) REVERT: H 57 ARG cc_start: 0.8847 (OUTLIER) cc_final: 0.7603 (ptm160) REVERT: H 118 ASP cc_start: 0.8490 (t0) cc_final: 0.8284 (t70) REVERT: L 100 GLN cc_start: 0.7969 (OUTLIER) cc_final: 0.7598 (mt0) outliers start: 54 outliers final: 28 residues processed: 213 average time/residue: 0.7083 time to fit residues: 166.8636 Evaluate side-chains 214 residues out of total 2052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 172 time to evaluate : 0.511 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 239 VAL Chi-restraints excluded: chain A residue 430 GLN Chi-restraints excluded: chain A residue 474 GLN Chi-restraints excluded: chain A residue 485 ARG Chi-restraints excluded: chain A residue 641 LYS Chi-restraints excluded: chain A residue 681 VAL Chi-restraints excluded: chain B residue 449 LYS Chi-restraints excluded: chain B residue 469 SER Chi-restraints excluded: chain B residue 485 ARG Chi-restraints excluded: chain B residue 491 THR Chi-restraints excluded: chain B residue 500 GLU Chi-restraints excluded: chain C residue 238 ARG Chi-restraints excluded: chain C residue 314 ASN Chi-restraints excluded: chain C residue 348 SER Chi-restraints excluded: chain C residue 399 TYR Chi-restraints excluded: chain C residue 499 SER Chi-restraints excluded: chain C residue 550 ARG Chi-restraints excluded: chain D residue 314 ASN Chi-restraints excluded: chain D residue 485 ARG Chi-restraints excluded: chain D residue 531 GLU Chi-restraints excluded: chain D residue 532 ASP Chi-restraints excluded: chain D residue 551 ASP Chi-restraints excluded: chain D residue 660 THR Chi-restraints excluded: chain E residue 449 LYS Chi-restraints excluded: chain E residue 491 THR Chi-restraints excluded: chain E residue 580 VAL Chi-restraints excluded: chain F residue 239 VAL Chi-restraints excluded: chain F residue 425 SER Chi-restraints excluded: chain F residue 529 GLU Chi-restraints excluded: chain F residue 550 ARG Chi-restraints excluded: chain F residue 725 ARG Chi-restraints excluded: chain H residue 23 VAL Chi-restraints excluded: chain H residue 56 VAL Chi-restraints excluded: chain H residue 57 ARG Chi-restraints excluded: chain H residue 75 ASP Chi-restraints excluded: chain H residue 82 ARG Chi-restraints excluded: chain H residue 101 GLU Chi-restraints excluded: chain H residue 102 LEU Chi-restraints excluded: chain L residue 23 VAL Chi-restraints excluded: chain L residue 39 THR Chi-restraints excluded: chain L residue 100 GLN Chi-restraints excluded: chain L residue 115 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 172 optimal weight: 20.0000 chunk 129 optimal weight: 10.0000 chunk 152 optimal weight: 20.0000 chunk 186 optimal weight: 9.9990 chunk 98 optimal weight: 8.9990 chunk 142 optimal weight: 5.9990 chunk 229 optimal weight: 10.0000 chunk 99 optimal weight: 0.9980 chunk 139 optimal weight: 8.9990 chunk 117 optimal weight: 10.0000 chunk 64 optimal weight: 9.9990 overall best weight: 6.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 290 HIS ** C 290 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 412 GLN ** D 290 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 430 GLN ** D 588 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 254 ASN ** F 262 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 428 HIS F 673 GLN L 117 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2997 r_free = 0.2997 target = 0.089244 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2794 r_free = 0.2794 target = 0.077130 restraints weight = 30090.322| |-----------------------------------------------------------------------------| r_work (start): 0.2794 rms_B_bonded: 1.37 r_work: 0.2715 rms_B_bonded: 1.75 restraints_weight: 0.5000 r_work: 0.2619 rms_B_bonded: 3.00 restraints_weight: 0.2500 r_work (final): 0.2619 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8690 moved from start: 0.2276 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 19306 Z= 0.233 Angle : 0.607 8.738 26290 Z= 0.319 Chirality : 0.046 0.137 2720 Planarity : 0.005 0.047 3496 Dihedral : 6.093 73.692 2577 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 4.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 2.97 % Allowed : 8.38 % Favored : 88.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.75 % 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 aren not related in a simple way. whole: -0.82 (0.16), residues: 2339 helix: -3.52 (0.43), residues: 92 sheet: -0.51 (0.19), residues: 575 loop : -0.34 (0.14), residues: 1672 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG C 485 TYR 0.020 0.002 TYR C 701 PHE 0.017 0.002 PHE H 83 TRP 0.015 0.002 TRP E 509 HIS 0.013 0.002 HIS F 290 Details of bonding type rmsd covalent geometry : bond 0.00541 (19304) covalent geometry : angle 0.60640 (26286) SS BOND : bond 0.00277 ( 2) SS BOND : angle 1.45252 ( 4) hydrogen bonds : bond 0.03539 ( 240) hydrogen bonds : angle 6.18604 ( 462) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4678 Ramachandran restraints generated. 2339 Oldfield, 0 Emsley, 2339 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4678 Ramachandran restraints generated. 2339 Oldfield, 0 Emsley, 2339 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 234 residues out of total 2052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 173 time to evaluate : 0.754 Fit side-chains REVERT: A 485 ARG cc_start: 0.8665 (OUTLIER) cc_final: 0.7616 (ttm170) REVERT: A 564 GLU cc_start: 0.7121 (pp20) cc_final: 0.6907 (pp20) REVERT: A 588 GLN cc_start: 0.7828 (mp10) cc_final: 0.7413 (mm110) REVERT: A 590 GLN cc_start: 0.7762 (mt0) cc_final: 0.7422 (mt0) REVERT: A 641 LYS cc_start: 0.8659 (OUTLIER) cc_final: 0.8348 (mttt) REVERT: B 449 LYS cc_start: 0.8800 (OUTLIER) cc_final: 0.8463 (ttpp) REVERT: B 485 ARG cc_start: 0.8496 (OUTLIER) cc_final: 0.7661 (ttm170) REVERT: C 550 ARG cc_start: 0.8475 (OUTLIER) cc_final: 0.7616 (mtp85) REVERT: C 641 LYS cc_start: 0.8707 (ttmm) cc_final: 0.8420 (mmmm) REVERT: D 285 ASP cc_start: 0.8187 (t0) cc_final: 0.7764 (t0) REVERT: D 314 ASN cc_start: 0.8328 (OUTLIER) cc_final: 0.7780 (m-40) REVERT: D 370 ASP cc_start: 0.7530 (m-30) cc_final: 0.7193 (m-30) REVERT: D 474 GLN cc_start: 0.8295 (mt0) cc_final: 0.7528 (tp40) REVERT: D 485 ARG cc_start: 0.8952 (OUTLIER) cc_final: 0.8135 (ttm170) REVERT: D 532 ASP cc_start: 0.7789 (OUTLIER) cc_final: 0.7538 (p0) REVERT: E 514 ARG cc_start: 0.8042 (mtm180) cc_final: 0.5809 (tpt170) REVERT: F 258 LYS cc_start: 0.8328 (mtmt) cc_final: 0.7365 (mmpt) REVERT: F 529 GLU cc_start: 0.7897 (OUTLIER) cc_final: 0.7484 (tt0) REVERT: F 550 ARG cc_start: 0.8546 (OUTLIER) cc_final: 0.7461 (mtm180) REVERT: F 654 VAL cc_start: 0.7855 (t) cc_final: 0.7616 (m) REVERT: F 725 ARG cc_start: 0.8458 (OUTLIER) cc_final: 0.8174 (pmm-80) REVERT: H 57 ARG cc_start: 0.8906 (OUTLIER) cc_final: 0.7622 (ptm160) REVERT: H 118 ASP cc_start: 0.8533 (t0) cc_final: 0.8315 (t70) outliers start: 61 outliers final: 36 residues processed: 217 average time/residue: 0.7307 time to fit residues: 175.0579 Evaluate side-chains 219 residues out of total 2052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 171 time to evaluate : 0.753 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 239 VAL Chi-restraints excluded: chain A residue 430 GLN Chi-restraints excluded: chain A residue 431 SER Chi-restraints excluded: chain A residue 485 ARG Chi-restraints excluded: chain A residue 641 LYS Chi-restraints excluded: chain A residue 681 VAL Chi-restraints excluded: chain B residue 449 LYS Chi-restraints excluded: chain B residue 469 SER Chi-restraints excluded: chain B residue 485 ARG Chi-restraints excluded: chain B residue 491 THR Chi-restraints excluded: chain B residue 500 GLU Chi-restraints excluded: chain C residue 238 ARG Chi-restraints excluded: chain C residue 314 ASN Chi-restraints excluded: chain C residue 339 THR Chi-restraints excluded: chain C residue 348 SER Chi-restraints excluded: chain C residue 399 TYR Chi-restraints excluded: chain C residue 499 SER Chi-restraints excluded: chain C residue 550 ARG Chi-restraints excluded: chain D residue 239 VAL Chi-restraints excluded: chain D residue 314 ASN Chi-restraints excluded: chain D residue 485 ARG Chi-restraints excluded: chain D residue 531 GLU Chi-restraints excluded: chain D residue 532 ASP Chi-restraints excluded: chain D residue 551 ASP Chi-restraints excluded: chain D residue 660 THR Chi-restraints excluded: chain E residue 449 LYS Chi-restraints excluded: chain E residue 491 THR Chi-restraints excluded: chain E residue 580 VAL Chi-restraints excluded: chain F residue 235 LEU Chi-restraints excluded: chain F residue 239 VAL Chi-restraints excluded: chain F residue 263 SER Chi-restraints excluded: chain F residue 334 ILE Chi-restraints excluded: chain F residue 425 SER Chi-restraints excluded: chain F residue 529 GLU Chi-restraints excluded: chain F residue 550 ARG Chi-restraints excluded: chain F residue 725 ARG Chi-restraints excluded: chain H residue 23 VAL Chi-restraints excluded: chain H residue 56 VAL Chi-restraints excluded: chain H residue 57 ARG Chi-restraints excluded: chain H residue 75 ASP Chi-restraints excluded: chain H residue 82 ARG Chi-restraints excluded: chain H residue 101 GLU Chi-restraints excluded: chain H residue 102 LEU Chi-restraints excluded: chain L residue 23 VAL Chi-restraints excluded: chain L residue 38 VAL Chi-restraints excluded: chain L residue 39 THR Chi-restraints excluded: chain L residue 100 GLN Chi-restraints excluded: chain L residue 115 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 206 optimal weight: 2.9990 chunk 156 optimal weight: 9.9990 chunk 135 optimal weight: 20.0000 chunk 62 optimal weight: 8.9990 chunk 148 optimal weight: 1.9990 chunk 63 optimal weight: 0.9980 chunk 106 optimal weight: 10.0000 chunk 20 optimal weight: 6.9990 chunk 65 optimal weight: 6.9990 chunk 131 optimal weight: 10.0000 chunk 27 optimal weight: 10.0000 overall best weight: 3.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 290 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 290 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 430 GLN ** D 588 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 254 ASN ** F 262 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 673 GLN L 117 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3014 r_free = 0.3014 target = 0.090175 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2810 r_free = 0.2810 target = 0.078061 restraints weight = 29955.946| |-----------------------------------------------------------------------------| r_work (start): 0.2812 rms_B_bonded: 1.37 r_work: 0.2734 rms_B_bonded: 1.75 restraints_weight: 0.5000 r_work: 0.2638 rms_B_bonded: 3.01 restraints_weight: 0.2500 r_work (final): 0.2638 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8673 moved from start: 0.2325 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 19306 Z= 0.150 Angle : 0.542 7.811 26290 Z= 0.284 Chirality : 0.043 0.135 2720 Planarity : 0.004 0.040 3496 Dihedral : 5.788 71.196 2577 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 4.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 2.29 % Allowed : 9.16 % Favored : 88.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.75 % 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 aren not related in a simple way. whole: -0.75 (0.16), residues: 2339 helix: -3.49 (0.43), residues: 92 sheet: -0.45 (0.19), residues: 601 loop : -0.28 (0.14), residues: 1646 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 485 TYR 0.016 0.002 TYR C 701 PHE 0.013 0.001 PHE H 83 TRP 0.012 0.001 TRP E 509 HIS 0.008 0.001 HIS F 290 Details of bonding type rmsd covalent geometry : bond 0.00348 (19304) covalent geometry : angle 0.54221 (26286) SS BOND : bond 0.00306 ( 2) SS BOND : angle 1.26551 ( 4) hydrogen bonds : bond 0.03061 ( 240) hydrogen bonds : angle 5.93054 ( 462) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4678 Ramachandran restraints generated. 2339 Oldfield, 0 Emsley, 2339 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4678 Ramachandran restraints generated. 2339 Oldfield, 0 Emsley, 2339 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 218 residues out of total 2052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 171 time to evaluate : 0.653 Fit side-chains REVERT: A 474 GLN cc_start: 0.6738 (mp10) cc_final: 0.6416 (tp40) REVERT: A 485 ARG cc_start: 0.8581 (OUTLIER) cc_final: 0.7851 (ttm170) REVERT: A 564 GLU cc_start: 0.7126 (pp20) cc_final: 0.6920 (pp20) REVERT: A 588 GLN cc_start: 0.7849 (mp10) cc_final: 0.7414 (mm110) REVERT: A 590 GLN cc_start: 0.7776 (mt0) cc_final: 0.7453 (mt0) REVERT: A 641 LYS cc_start: 0.8616 (OUTLIER) cc_final: 0.8326 (mttt) REVERT: B 449 LYS cc_start: 0.8791 (OUTLIER) cc_final: 0.8426 (ttpp) REVERT: B 485 ARG cc_start: 0.8397 (OUTLIER) cc_final: 0.7912 (ttm170) REVERT: C 641 LYS cc_start: 0.8679 (ttmm) cc_final: 0.8320 (mmmm) REVERT: D 285 ASP cc_start: 0.8162 (t0) cc_final: 0.7738 (t0) REVERT: D 314 ASN cc_start: 0.8330 (OUTLIER) cc_final: 0.7774 (m-40) REVERT: D 474 GLN cc_start: 0.8310 (mt0) cc_final: 0.7548 (tp40) REVERT: D 485 ARG cc_start: 0.8892 (OUTLIER) cc_final: 0.7706 (ttm170) REVERT: D 532 ASP cc_start: 0.7733 (OUTLIER) cc_final: 0.7528 (p0) REVERT: E 514 ARG cc_start: 0.7942 (mtm180) cc_final: 0.5761 (tpt170) REVERT: F 258 LYS cc_start: 0.8331 (mtmt) cc_final: 0.7385 (mmpt) REVERT: F 529 GLU cc_start: 0.7901 (OUTLIER) cc_final: 0.7475 (tt0) REVERT: F 550 ARG cc_start: 0.8561 (OUTLIER) cc_final: 0.7465 (mtm180) REVERT: F 654 VAL cc_start: 0.7827 (t) cc_final: 0.7590 (m) REVERT: F 725 ARG cc_start: 0.8432 (OUTLIER) cc_final: 0.8131 (pmm-80) REVERT: H 57 ARG cc_start: 0.8858 (OUTLIER) cc_final: 0.8367 (ptm160) REVERT: H 108 GLU cc_start: 0.7279 (pm20) cc_final: 0.7052 (pm20) REVERT: H 118 ASP cc_start: 0.8495 (t0) cc_final: 0.8291 (t70) outliers start: 47 outliers final: 31 residues processed: 207 average time/residue: 0.7309 time to fit residues: 166.5545 Evaluate side-chains 212 residues out of total 2052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 170 time to evaluate : 0.562 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 239 VAL Chi-restraints excluded: chain A residue 430 GLN Chi-restraints excluded: chain A residue 485 ARG Chi-restraints excluded: chain A residue 641 LYS Chi-restraints excluded: chain A residue 681 VAL Chi-restraints excluded: chain B residue 449 LYS Chi-restraints excluded: chain B residue 469 SER Chi-restraints excluded: chain B residue 485 ARG Chi-restraints excluded: chain B residue 491 THR Chi-restraints excluded: chain C residue 238 ARG Chi-restraints excluded: chain C residue 314 ASN Chi-restraints excluded: chain C residue 339 THR Chi-restraints excluded: chain C residue 348 SER Chi-restraints excluded: chain C residue 399 TYR Chi-restraints excluded: chain C residue 499 SER Chi-restraints excluded: chain D residue 239 VAL Chi-restraints excluded: chain D residue 314 ASN Chi-restraints excluded: chain D residue 485 ARG Chi-restraints excluded: chain D residue 531 GLU Chi-restraints excluded: chain D residue 532 ASP Chi-restraints excluded: chain D residue 551 ASP Chi-restraints excluded: chain D residue 660 THR Chi-restraints excluded: chain E residue 449 LYS Chi-restraints excluded: chain E residue 491 THR Chi-restraints excluded: chain E residue 580 VAL Chi-restraints excluded: chain F residue 235 LEU Chi-restraints excluded: chain F residue 239 VAL Chi-restraints excluded: chain F residue 425 SER Chi-restraints excluded: chain F residue 529 GLU Chi-restraints excluded: chain F residue 550 ARG Chi-restraints excluded: chain F residue 725 ARG Chi-restraints excluded: chain H residue 23 VAL Chi-restraints excluded: chain H residue 56 VAL Chi-restraints excluded: chain H residue 57 ARG Chi-restraints excluded: chain H residue 75 ASP Chi-restraints excluded: chain H residue 82 ARG Chi-restraints excluded: chain H residue 101 GLU Chi-restraints excluded: chain H residue 102 LEU Chi-restraints excluded: chain L residue 23 VAL Chi-restraints excluded: chain L residue 39 THR Chi-restraints excluded: chain L residue 100 GLN Chi-restraints excluded: chain L residue 115 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 116 optimal weight: 0.6980 chunk 15 optimal weight: 6.9990 chunk 159 optimal weight: 3.9990 chunk 223 optimal weight: 3.9990 chunk 158 optimal weight: 5.9990 chunk 103 optimal weight: 8.9990 chunk 170 optimal weight: 8.9990 chunk 133 optimal weight: 0.9980 chunk 144 optimal weight: 10.0000 chunk 212 optimal weight: 9.9990 chunk 188 optimal weight: 8.9990 overall best weight: 3.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 290 HIS ** D 290 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 430 GLN ** D 588 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 254 ASN ** F 262 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 290 HIS F 673 GLN H 129 ASN L 117 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3019 r_free = 0.3019 target = 0.090446 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2819 r_free = 0.2819 target = 0.078515 restraints weight = 29877.650| |-----------------------------------------------------------------------------| r_work (start): 0.2819 rms_B_bonded: 1.36 r_work: 0.2740 rms_B_bonded: 1.75 restraints_weight: 0.5000 r_work: 0.2644 rms_B_bonded: 3.00 restraints_weight: 0.2500 r_work (final): 0.2644 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8664 moved from start: 0.2374 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 19306 Z= 0.127 Angle : 0.520 7.352 26290 Z= 0.271 Chirality : 0.042 0.135 2720 Planarity : 0.004 0.036 3496 Dihedral : 5.541 68.492 2577 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 4.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Rotamer: Outliers : 2.44 % Allowed : 9.21 % Favored : 88.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.75 % 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 aren not related in a simple way. whole: -0.64 (0.16), residues: 2339 helix: -3.44 (0.44), residues: 92 sheet: -0.35 (0.19), residues: 601 loop : -0.22 (0.15), residues: 1646 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 485 TYR 0.014 0.001 TYR C 701 PHE 0.012 0.001 PHE C 535 TRP 0.013 0.001 TRP E 509 HIS 0.005 0.001 HIS D 290 Details of bonding type rmsd covalent geometry : bond 0.00291 (19304) covalent geometry : angle 0.51980 (26286) SS BOND : bond 0.00271 ( 2) SS BOND : angle 1.09090 ( 4) hydrogen bonds : bond 0.02877 ( 240) hydrogen bonds : angle 5.74042 ( 462) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4678 Ramachandran restraints generated. 2339 Oldfield, 0 Emsley, 2339 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4678 Ramachandran restraints generated. 2339 Oldfield, 0 Emsley, 2339 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 223 residues out of total 2052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 173 time to evaluate : 0.725 Fit side-chains REVERT: A 474 GLN cc_start: 0.6799 (mp10) cc_final: 0.6486 (tp-100) REVERT: A 564 GLU cc_start: 0.7103 (pp20) cc_final: 0.6901 (pp20) REVERT: A 588 GLN cc_start: 0.7835 (mp10) cc_final: 0.7401 (mm110) REVERT: A 590 GLN cc_start: 0.7777 (mt0) cc_final: 0.7403 (mt0) REVERT: A 641 LYS cc_start: 0.8617 (OUTLIER) cc_final: 0.8331 (mttt) REVERT: B 449 LYS cc_start: 0.8797 (OUTLIER) cc_final: 0.8438 (ttpp) REVERT: B 485 ARG cc_start: 0.8362 (OUTLIER) cc_final: 0.7964 (ttm170) REVERT: C 550 ARG cc_start: 0.8507 (mtp85) cc_final: 0.8155 (mtp85) REVERT: C 641 LYS cc_start: 0.8688 (ttmm) cc_final: 0.8364 (mmmm) REVERT: C 690 GLU cc_start: 0.7539 (pp20) cc_final: 0.7218 (pp20) REVERT: D 285 ASP cc_start: 0.8155 (t0) cc_final: 0.7730 (t0) REVERT: D 314 ASN cc_start: 0.8314 (OUTLIER) cc_final: 0.7762 (m-40) REVERT: D 398 GLU cc_start: 0.8396 (OUTLIER) cc_final: 0.7919 (mp0) REVERT: D 474 GLN cc_start: 0.8303 (mt0) cc_final: 0.7551 (tp40) REVERT: D 485 ARG cc_start: 0.8878 (OUTLIER) cc_final: 0.8348 (ttt180) REVERT: E 514 ARG cc_start: 0.7970 (mtm180) cc_final: 0.5803 (tpt170) REVERT: F 258 LYS cc_start: 0.8314 (mtmt) cc_final: 0.7408 (mmpt) REVERT: F 529 GLU cc_start: 0.7905 (OUTLIER) cc_final: 0.7473 (tt0) REVERT: F 550 ARG cc_start: 0.8550 (OUTLIER) cc_final: 0.7415 (mtm180) REVERT: F 654 VAL cc_start: 0.7818 (t) cc_final: 0.7588 (m) REVERT: H 57 ARG cc_start: 0.8856 (OUTLIER) cc_final: 0.8286 (ptm160) REVERT: H 118 ASP cc_start: 0.8439 (t0) cc_final: 0.8212 (t70) REVERT: L 100 GLN cc_start: 0.8021 (OUTLIER) cc_final: 0.7646 (mt0) outliers start: 50 outliers final: 27 residues processed: 213 average time/residue: 0.6979 time to fit residues: 164.9028 Evaluate side-chains 210 residues out of total 2052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 173 time to evaluate : 0.727 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 239 VAL Chi-restraints excluded: chain A residue 251 THR Chi-restraints excluded: chain A residue 430 GLN Chi-restraints excluded: chain A residue 641 LYS Chi-restraints excluded: chain A residue 681 VAL Chi-restraints excluded: chain B residue 449 LYS Chi-restraints excluded: chain B residue 469 SER Chi-restraints excluded: chain B residue 485 ARG Chi-restraints excluded: chain B residue 491 THR Chi-restraints excluded: chain C residue 238 ARG Chi-restraints excluded: chain C residue 314 ASN Chi-restraints excluded: chain C residue 339 THR Chi-restraints excluded: chain C residue 399 TYR Chi-restraints excluded: chain C residue 499 SER Chi-restraints excluded: chain C residue 580 VAL Chi-restraints excluded: chain D residue 239 VAL Chi-restraints excluded: chain D residue 314 ASN Chi-restraints excluded: chain D residue 398 GLU Chi-restraints excluded: chain D residue 485 ARG Chi-restraints excluded: chain D residue 531 GLU Chi-restraints excluded: chain E residue 449 LYS Chi-restraints excluded: chain E residue 491 THR Chi-restraints excluded: chain E residue 580 VAL Chi-restraints excluded: chain F residue 239 VAL Chi-restraints excluded: chain F residue 425 SER Chi-restraints excluded: chain F residue 529 GLU Chi-restraints excluded: chain F residue 550 ARG Chi-restraints excluded: chain F residue 673 GLN Chi-restraints excluded: chain H residue 23 VAL Chi-restraints excluded: chain H residue 56 VAL Chi-restraints excluded: chain H residue 57 ARG Chi-restraints excluded: chain H residue 75 ASP Chi-restraints excluded: chain H residue 102 LEU Chi-restraints excluded: chain L residue 23 VAL Chi-restraints excluded: chain L residue 39 THR Chi-restraints excluded: chain L residue 100 GLN Chi-restraints excluded: chain L residue 115 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 97 optimal weight: 6.9990 chunk 204 optimal weight: 9.9990 chunk 23 optimal weight: 20.0000 chunk 31 optimal weight: 6.9990 chunk 210 optimal weight: 20.0000 chunk 165 optimal weight: 10.0000 chunk 137 optimal weight: 0.4980 chunk 0 optimal weight: 30.0000 chunk 16 optimal weight: 8.9990 chunk 65 optimal weight: 5.9990 chunk 26 optimal weight: 10.0000 overall best weight: 5.8988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 290 HIS C 412 GLN C 668 ASN ** D 290 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 430 GLN ** D 588 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 254 ASN ** F 262 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 673 GLN ** H 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 73 ASN L 117 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3002 r_free = 0.3002 target = 0.089641 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2797 r_free = 0.2797 target = 0.077472 restraints weight = 29991.207| |-----------------------------------------------------------------------------| r_work (start): 0.2795 rms_B_bonded: 1.36 r_work: 0.2716 rms_B_bonded: 1.75 restraints_weight: 0.5000 r_work: 0.2620 rms_B_bonded: 2.99 restraints_weight: 0.2500 r_work (final): 0.2620 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8683 moved from start: 0.2356 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 19306 Z= 0.202 Angle : 0.585 9.283 26290 Z= 0.306 Chirality : 0.045 0.150 2720 Planarity : 0.004 0.053 3496 Dihedral : 5.817 68.664 2577 Min Nonbonded Distance : 2.265 Molprobity Statistics. All-atom Clashscore : 4.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 2.24 % Allowed : 9.31 % Favored : 88.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.75 % 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 aren not related in a simple way. whole: -0.76 (0.16), residues: 2339 helix: -3.48 (0.43), residues: 92 sheet: -0.42 (0.20), residues: 575 loop : -0.31 (0.14), residues: 1672 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 485 TYR 0.019 0.002 TYR C 701 PHE 0.013 0.002 PHE C 286 TRP 0.014 0.002 TRP E 509 HIS 0.007 0.002 HIS B 423 Details of bonding type rmsd covalent geometry : bond 0.00470 (19304) covalent geometry : angle 0.58533 (26286) SS BOND : bond 0.00391 ( 2) SS BOND : angle 1.25268 ( 4) hydrogen bonds : bond 0.03286 ( 240) hydrogen bonds : angle 5.98447 ( 462) =============================================================================== Job complete usr+sys time: 5829.63 seconds wall clock time: 100 minutes 42.18 seconds (6042.18 seconds total)