Starting phenix.real_space_refine on Mon May 19 07:46:44 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9b6q_44274/05_2025/9b6q_44274.cif Found real_map, /net/cci-nas-00/data/ceres_data/9b6q_44274/05_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_44274/05_2025/9b6q_44274.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9b6q_44274/05_2025/9b6q_44274.map" model { file = "/net/cci-nas-00/data/ceres_data/9b6q_44274/05_2025/9b6q_44274.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9b6q_44274/05_2025/9b6q_44274.cif" } resolution = 2.77 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/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: 10.72, per 1000 atoms: 0.57 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: 4.57 Conformation dependent library (CDL) restraints added in 2.7 seconds 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: 2.17 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: 5.36 Time building geometry restraints manager: 5.37 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: 0.390 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: 0.840 Check model and map are aligned: 0.160 Set scattering table: 0.190 Process input model: 41.310 Find NCS groups from input model: 0.450 Set up NCS constraints: 0.090 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:11.760 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 55.200 ------------------------------------------------------------------------------- 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 : 11.66 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.026 0.003 TRP F 281 HIS 0.017 0.003 HIS D 290 PHE 0.026 0.003 PHE C 534 TYR 0.026 0.003 TYR A 252 ARG 0.014 0.002 ARG C 734 Details of bonding type rmsd hydrogen bonds : bond 0.22422 ( 240) hydrogen bonds : angle 8.92975 ( 462) SS BOND : bond 0.00272 ( 2) SS BOND : angle 1.44600 ( 4) covalent geometry : bond 0.00594 (19304) covalent geometry : angle 0.91568 (26286) *********************** 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 : 2.075 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: 1.6090 time to fit residues: 585.1107 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 : 2.117 ------------------------------------------------------------------------------- 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 197 optimal weight: 5.9990 chunk 177 optimal weight: 4.9990 chunk 98 optimal weight: 9.9990 chunk 60 optimal weight: 20.0000 chunk 119 optimal weight: 9.9990 chunk 94 optimal weight: 6.9990 chunk 183 optimal weight: 8.9990 chunk 70 optimal weight: 0.6980 chunk 111 optimal weight: 9.9990 chunk 136 optimal weight: 9.9990 chunk 212 optimal weight: 6.9990 overall best weight: 5.1388 ------------------------------------------------------------------------------- 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 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: 50 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3032 r_free = 0.3032 target = 0.091473 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2829 r_free = 0.2829 target = 0.079290 restraints weight = 29734.406| |-----------------------------------------------------------------------------| r_work (start): 0.2831 rms_B_bonded: 1.37 r_work: 0.2754 rms_B_bonded: 1.75 restraints_weight: 0.5000 r_work: 0.2660 rms_B_bonded: 3.00 restraints_weight: 0.2500 r_work (final): 0.2660 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8651 moved from start: 0.1466 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= 0.192 Angle : 0.634 9.859 26290 Z= 0.334 Chirality : 0.046 0.145 2720 Planarity : 0.005 0.054 3496 Dihedral : 6.653 86.896 2586 Min Nonbonded Distance : 2.561 Molprobity Statistics. All-atom Clashscore : 5.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.62 % Favored : 98.38 % Rotamer: Outliers : 2.34 % Allowed : 6.92 % Favored : 90.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.75 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.94 (0.15), residues: 2339 helix: -3.45 (0.40), residues: 92 sheet: -0.61 (0.17), residues: 646 loop : -0.41 (0.14), residues: 1601 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP F 281 HIS 0.013 0.002 HIS C 290 PHE 0.023 0.002 PHE H 83 TYR 0.018 0.002 TYR F 701 ARG 0.007 0.001 ARG C 514 Details of bonding type rmsd hydrogen bonds : bond 0.04016 ( 240) hydrogen bonds : angle 6.73931 ( 462) SS BOND : bond 0.00410 ( 2) SS BOND : angle 1.28060 ( 4) covalent geometry : bond 0.00442 (19304) covalent geometry : angle 0.63349 (26286) *********************** 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 240 residues out of total 2052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 192 time to evaluate : 2.185 Fit side-chains REVERT: A 485 ARG cc_start: 0.8604 (OUTLIER) cc_final: 0.7181 (ttm170) REVERT: A 588 GLN cc_start: 0.7798 (mp10) cc_final: 0.7383 (mm-40) REVERT: A 590 GLN cc_start: 0.7766 (mt0) cc_final: 0.7473 (mt0) REVERT: B 500 GLU cc_start: 0.7721 (OUTLIER) cc_final: 0.6686 (tm-30) REVERT: B 533 ARG cc_start: 0.7807 (ptt-90) cc_final: 0.7553 (ptt180) REVERT: C 416 GLU cc_start: 0.8170 (OUTLIER) cc_final: 0.7839 (tp30) REVERT: C 641 LYS cc_start: 0.8741 (ttmm) cc_final: 0.8442 (mmmm) REVERT: D 370 ASP cc_start: 0.7262 (m-30) cc_final: 0.6785 (m-30) REVERT: D 373 MET cc_start: 0.8789 (ttt) cc_final: 0.8521 (ttt) REVERT: D 474 GLN cc_start: 0.8236 (mt0) cc_final: 0.7490 (tp40) REVERT: D 532 ASP cc_start: 0.7569 (OUTLIER) cc_final: 0.7336 (p0) REVERT: E 485 ARG cc_start: 0.8558 (OUTLIER) cc_final: 0.7032 (ttm170) REVERT: E 514 ARG cc_start: 0.7985 (mtm180) cc_final: 0.5813 (tpt170) REVERT: F 235 LEU cc_start: 0.8391 (OUTLIER) cc_final: 0.8100 (mp) REVERT: F 399 TYR cc_start: 0.7312 (t80) cc_final: 0.7092 (t80) REVERT: F 529 GLU cc_start: 0.7759 (OUTLIER) cc_final: 0.7333 (tt0) REVERT: F 550 ARG cc_start: 0.8493 (OUTLIER) cc_final: 0.7363 (mtm180) REVERT: F 654 VAL cc_start: 0.7967 (t) cc_final: 0.7729 (m) REVERT: F 725 ARG cc_start: 0.8444 (OUTLIER) cc_final: 0.8103 (pmm-80) REVERT: H 57 ARG cc_start: 0.8792 (OUTLIER) cc_final: 0.7534 (ptm160) REVERT: H 118 ASP cc_start: 0.8442 (t0) cc_final: 0.8199 (t70) REVERT: L 100 GLN cc_start: 0.8047 (OUTLIER) cc_final: 0.7548 (mp10) outliers start: 48 outliers final: 15 residues processed: 223 average time/residue: 1.5499 time to fit residues: 381.9255 Evaluate side-chains 195 residues out of total 2052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 169 time to evaluate : 2.046 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 348 SER 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 540 SER 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 68 optimal weight: 0.9990 chunk 167 optimal weight: 0.5980 chunk 47 optimal weight: 9.9990 chunk 106 optimal weight: 10.0000 chunk 6 optimal weight: 20.0000 chunk 186 optimal weight: 6.9990 chunk 14 optimal weight: 9.9990 chunk 107 optimal weight: 9.9990 chunk 228 optimal weight: 9.9990 chunk 225 optimal weight: 8.9990 chunk 233 optimal weight: 10.0000 overall best weight: 5.5188 ------------------------------------------------------------------------------- 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 C 608 GLN ** 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 F 624 HIS H 129 ASN L 73 ASN L 117 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3016 r_free = 0.3016 target = 0.090379 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2813 r_free = 0.2813 target = 0.078299 restraints weight = 30058.880| |-----------------------------------------------------------------------------| r_work (start): 0.2813 rms_B_bonded: 1.38 r_work: 0.2735 rms_B_bonded: 1.76 restraints_weight: 0.5000 r_work: 0.2639 rms_B_bonded: 3.02 restraints_weight: 0.2500 r_work (final): 0.2639 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8671 moved from start: 0.1823 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 19306 Z= 0.194 Angle : 0.601 9.610 26290 Z= 0.315 Chirality : 0.045 0.140 2720 Planarity : 0.005 0.071 3496 Dihedral : 6.206 79.354 2580 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 4.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 2.53 % Allowed : 7.70 % Favored : 89.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.75 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.86 (0.15), residues: 2339 helix: -3.44 (0.41), residues: 92 sheet: -0.59 (0.18), residues: 621 loop : -0.33 (0.14), residues: 1626 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP E 509 HIS 0.014 0.002 HIS F 290 PHE 0.018 0.002 PHE H 83 TYR 0.018 0.002 TYR C 701 ARG 0.006 0.001 ARG C 514 Details of bonding type rmsd hydrogen bonds : bond 0.03674 ( 240) hydrogen bonds : angle 6.36868 ( 462) SS BOND : bond 0.00419 ( 2) SS BOND : angle 1.24371 ( 4) covalent geometry : bond 0.00451 (19304) covalent geometry : angle 0.60116 (26286) *********************** 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 235 residues out of total 2052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 183 time to evaluate : 2.090 Fit side-chains REVERT: A 485 ARG cc_start: 0.8647 (OUTLIER) cc_final: 0.7332 (ttm170) REVERT: A 588 GLN cc_start: 0.7846 (mp10) cc_final: 0.7417 (mm110) REVERT: A 590 GLN cc_start: 0.7757 (mt0) cc_final: 0.7437 (mt0) REVERT: B 485 ARG cc_start: 0.8420 (OUTLIER) cc_final: 0.7778 (ttm170) REVERT: B 533 ARG cc_start: 0.7834 (ptt-90) cc_final: 0.7571 (ptt180) REVERT: C 399 TYR cc_start: 0.7383 (t80) cc_final: 0.7135 (t80) REVERT: D 370 ASP cc_start: 0.7392 (m-30) cc_final: 0.6888 (m-30) REVERT: D 384 ASP cc_start: 0.8119 (t0) cc_final: 0.7791 (t0) REVERT: D 474 GLN cc_start: 0.8246 (mt0) cc_final: 0.7502 (tp40) REVERT: D 532 ASP cc_start: 0.7653 (OUTLIER) cc_final: 0.7414 (p0) REVERT: E 485 ARG cc_start: 0.8580 (OUTLIER) cc_final: 0.7012 (ttm170) REVERT: E 514 ARG cc_start: 0.8034 (mtm180) cc_final: 0.6169 (mmt180) REVERT: F 235 LEU cc_start: 0.8417 (OUTLIER) cc_final: 0.8039 (mp) REVERT: F 259 GLN cc_start: 0.8823 (OUTLIER) cc_final: 0.7898 (tt0) REVERT: F 529 GLU cc_start: 0.7801 (OUTLIER) cc_final: 0.7427 (tt0) REVERT: F 550 ARG cc_start: 0.8497 (OUTLIER) cc_final: 0.7401 (mtm180) REVERT: F 588 GLN cc_start: 0.8046 (mp10) cc_final: 0.7769 (mp10) REVERT: F 654 VAL cc_start: 0.7901 (t) cc_final: 0.7689 (m) REVERT: F 725 ARG cc_start: 0.8419 (OUTLIER) cc_final: 0.8078 (pmm-80) REVERT: H 57 ARG cc_start: 0.8829 (OUTLIER) cc_final: 0.7560 (ptm160) REVERT: H 118 ASP cc_start: 0.8460 (t0) cc_final: 0.8226 (t70) REVERT: L 100 GLN cc_start: 0.7984 (OUTLIER) cc_final: 0.7501 (mt0) outliers start: 52 outliers final: 24 residues processed: 219 average time/residue: 1.4999 time to fit residues: 363.7295 Evaluate side-chains 205 residues out of total 2052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 170 time to evaluate : 2.044 ------------------------------------------------------------------------------- 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 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 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 725 ARG Chi-restraints excluded: chain H residue 23 VAL Chi-restraints excluded: chain H residue 25 GLU 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 22 optimal weight: 9.9990 chunk 175 optimal weight: 5.9990 chunk 93 optimal weight: 5.9990 chunk 121 optimal weight: 9.9990 chunk 68 optimal weight: 8.9990 chunk 65 optimal weight: 6.9990 chunk 172 optimal weight: 20.0000 chunk 56 optimal weight: 5.9990 chunk 18 optimal weight: 10.0000 chunk 67 optimal weight: 10.0000 chunk 2 optimal weight: 0.9980 overall best weight: 5.1988 ------------------------------------------------------------------------------- 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 262 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 290 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 588 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3011 r_free = 0.3011 target = 0.090159 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2809 r_free = 0.2809 target = 0.078043 restraints weight = 30194.073| |-----------------------------------------------------------------------------| r_work (start): 0.2806 rms_B_bonded: 1.38 r_work: 0.2727 rms_B_bonded: 1.76 restraints_weight: 0.5000 r_work: 0.2631 rms_B_bonded: 3.01 restraints_weight: 0.2500 r_work (final): 0.2631 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8675 moved from start: 0.1999 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= 0.182 Angle : 0.580 9.859 26290 Z= 0.302 Chirality : 0.044 0.138 2720 Planarity : 0.004 0.050 3496 Dihedral : 6.089 78.898 2580 Min Nonbonded Distance : 2.592 Molprobity Statistics. All-atom Clashscore : 4.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 2.68 % Allowed : 7.89 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.79 (0.16), residues: 2339 helix: -3.51 (0.41), residues: 92 sheet: -0.55 (0.18), residues: 621 loop : -0.27 (0.14), residues: 1626 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP E 509 HIS 0.012 0.002 HIS F 290 PHE 0.017 0.002 PHE H 83 TYR 0.018 0.002 TYR C 701 ARG 0.005 0.001 ARG C 514 Details of bonding type rmsd hydrogen bonds : bond 0.03338 ( 240) hydrogen bonds : angle 6.15752 ( 462) SS BOND : bond 0.00436 ( 2) SS BOND : angle 1.16181 ( 4) covalent geometry : bond 0.00423 (19304) covalent geometry : angle 0.57942 (26286) *********************** 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 230 residues out of total 2052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 175 time to evaluate : 2.208 Fit side-chains REVERT: A 485 ARG cc_start: 0.8643 (OUTLIER) cc_final: 0.8024 (ttm170) REVERT: A 588 GLN cc_start: 0.7802 (mp10) cc_final: 0.7438 (mm-40) REVERT: A 590 GLN cc_start: 0.7764 (mt0) cc_final: 0.7412 (mt0) REVERT: B 449 LYS cc_start: 0.8796 (OUTLIER) cc_final: 0.8411 (ttpp) REVERT: B 485 ARG cc_start: 0.8403 (OUTLIER) cc_final: 0.7819 (ttm170) REVERT: B 533 ARG cc_start: 0.7827 (ptt-90) cc_final: 0.7484 (ptt-90) REVERT: C 550 ARG cc_start: 0.8428 (mtp85) cc_final: 0.8141 (mtp85) REVERT: D 370 ASP cc_start: 0.7427 (m-30) cc_final: 0.6950 (m-30) REVERT: D 384 ASP cc_start: 0.8132 (t0) cc_final: 0.7832 (t0) REVERT: D 474 GLN cc_start: 0.8270 (mt0) cc_final: 0.7531 (tp40) REVERT: D 532 ASP cc_start: 0.7698 (OUTLIER) cc_final: 0.7454 (p0) REVERT: E 485 ARG cc_start: 0.8561 (OUTLIER) cc_final: 0.6973 (ttm170) REVERT: E 514 ARG cc_start: 0.8051 (mtm180) cc_final: 0.6167 (mmt180) REVERT: F 259 GLN cc_start: 0.8814 (OUTLIER) cc_final: 0.7917 (tt0) REVERT: F 529 GLU cc_start: 0.7793 (OUTLIER) cc_final: 0.7220 (tt0) REVERT: F 550 ARG cc_start: 0.8543 (OUTLIER) cc_final: 0.7440 (mtm180) REVERT: F 654 VAL cc_start: 0.7889 (t) cc_final: 0.7666 (m) REVERT: F 725 ARG cc_start: 0.8424 (OUTLIER) cc_final: 0.8104 (pmm-80) REVERT: H 57 ARG cc_start: 0.8839 (OUTLIER) cc_final: 0.7570 (ptm160) REVERT: H 118 ASP cc_start: 0.8506 (t0) cc_final: 0.8282 (t70) REVERT: L 100 GLN cc_start: 0.8022 (OUTLIER) cc_final: 0.7517 (mt0) outliers start: 55 outliers final: 29 residues processed: 214 average time/residue: 1.6174 time to fit residues: 381.6909 Evaluate side-chains 210 residues out of total 2052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 170 time to evaluate : 2.235 ------------------------------------------------------------------------------- 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 314 ASN Chi-restraints excluded: chain C residue 348 SER Chi-restraints excluded: chain C residue 499 SER 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 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 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 25 GLU 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 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 6 optimal weight: 6.9990 chunk 85 optimal weight: 9.9990 chunk 70 optimal weight: 6.9990 chunk 74 optimal weight: 5.9990 chunk 73 optimal weight: 4.9990 chunk 17 optimal weight: 20.0000 chunk 136 optimal weight: 9.9990 chunk 172 optimal weight: 20.0000 chunk 216 optimal weight: 7.9990 chunk 185 optimal weight: 9.9990 chunk 212 optimal weight: 9.9990 overall best weight: 6.5990 ------------------------------------------------------------------------------- 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** A 474 GLN C 290 HIS ** D 290 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 588 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 254 ASN ** F 262 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 129 ASN L 117 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2997 r_free = 0.2997 target = 0.089236 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2794 r_free = 0.2794 target = 0.077211 restraints weight = 30253.954| |-----------------------------------------------------------------------------| r_work (start): 0.2794 rms_B_bonded: 1.36 r_work: 0.2716 rms_B_bonded: 1.73 restraints_weight: 0.5000 r_work: 0.2620 rms_B_bonded: 2.97 restraints_weight: 0.2500 r_work (final): 0.2620 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8686 moved from start: 0.2113 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 19306 Z= 0.222 Angle : 0.603 9.202 26290 Z= 0.317 Chirality : 0.046 0.137 2720 Planarity : 0.005 0.052 3496 Dihedral : 6.221 76.401 2580 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 4.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 2.97 % Allowed : 7.94 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.88 (0.16), residues: 2339 helix: -3.55 (0.41), residues: 92 sheet: -0.61 (0.19), residues: 607 loop : -0.35 (0.14), residues: 1640 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP E 509 HIS 0.013 0.002 HIS F 290 PHE 0.016 0.002 PHE H 83 TYR 0.020 0.002 TYR C 701 ARG 0.009 0.001 ARG C 485 Details of bonding type rmsd hydrogen bonds : bond 0.03541 ( 240) hydrogen bonds : angle 6.24580 ( 462) SS BOND : bond 0.00535 ( 2) SS BOND : angle 1.17731 ( 4) covalent geometry : bond 0.00517 (19304) covalent geometry : angle 0.60315 (26286) *********************** 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 234 residues out of total 2052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 173 time to evaluate : 2.092 Fit side-chains REVERT: A 474 GLN cc_start: 0.7219 (mp-120) cc_final: 0.7018 (mp10) REVERT: A 485 ARG cc_start: 0.8669 (OUTLIER) cc_final: 0.7537 (ttm170) REVERT: A 588 GLN cc_start: 0.7819 (mp10) cc_final: 0.7409 (mm110) REVERT: A 590 GLN cc_start: 0.7763 (mt0) cc_final: 0.7417 (mt0) REVERT: A 641 LYS cc_start: 0.8654 (OUTLIER) cc_final: 0.8358 (mttt) REVERT: B 449 LYS cc_start: 0.8786 (OUTLIER) cc_final: 0.8438 (ttpp) REVERT: B 485 ARG cc_start: 0.8470 (OUTLIER) cc_final: 0.7650 (ttm170) REVERT: B 533 ARG cc_start: 0.7832 (ptt-90) cc_final: 0.7491 (ptt-90) REVERT: C 550 ARG cc_start: 0.8422 (mtp85) cc_final: 0.8153 (mtp85) REVERT: D 314 ASN cc_start: 0.8338 (OUTLIER) cc_final: 0.7795 (m-40) REVERT: D 370 ASP cc_start: 0.7342 (m-30) cc_final: 0.6871 (m-30) REVERT: D 474 GLN cc_start: 0.8286 (mt0) cc_final: 0.7531 (tp40) REVERT: D 532 ASP cc_start: 0.7811 (OUTLIER) cc_final: 0.7538 (p0) REVERT: E 485 ARG cc_start: 0.8625 (OUTLIER) cc_final: 0.7132 (ttm170) REVERT: E 514 ARG cc_start: 0.8060 (mtm180) cc_final: 0.6125 (mmt180) REVERT: F 259 GLN cc_start: 0.8825 (OUTLIER) cc_final: 0.7875 (tt0) REVERT: F 529 GLU cc_start: 0.7843 (OUTLIER) cc_final: 0.7451 (tt0) REVERT: F 550 ARG cc_start: 0.8559 (OUTLIER) cc_final: 0.7479 (mtm180) REVERT: F 654 VAL cc_start: 0.7903 (t) cc_final: 0.7650 (m) REVERT: F 725 ARG cc_start: 0.8465 (OUTLIER) cc_final: 0.8227 (pmm-80) REVERT: H 57 ARG cc_start: 0.8878 (OUTLIER) cc_final: 0.7575 (ptm160) REVERT: H 118 ASP cc_start: 0.8526 (t0) cc_final: 0.8300 (t70) REVERT: L 100 GLN cc_start: 0.7931 (OUTLIER) cc_final: 0.7439 (mt0) outliers start: 61 outliers final: 32 residues processed: 218 average time/residue: 1.5474 time to fit residues: 374.2282 Evaluate side-chains 215 residues out of total 2052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 170 time to evaluate : 2.327 ------------------------------------------------------------------------------- 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 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 C residue 348 SER 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 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 25 GLU 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 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 155 optimal weight: 5.9990 chunk 231 optimal weight: 9.9990 chunk 158 optimal weight: 9.9990 chunk 106 optimal weight: 0.9980 chunk 212 optimal weight: 7.9990 chunk 4 optimal weight: 8.9990 chunk 201 optimal weight: 1.9990 chunk 189 optimal weight: 9.9990 chunk 83 optimal weight: 0.9990 chunk 35 optimal weight: 6.9990 chunk 6 optimal weight: 10.0000 overall best weight: 3.3988 ------------------------------------------------------------------------------- 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 290 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 430 GLN D 588 GLN F 229 HIS 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: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3019 r_free = 0.3019 target = 0.090517 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.2815 r_free = 0.2815 target = 0.078375 restraints weight = 29825.185| |-----------------------------------------------------------------------------| r_work (start): 0.2819 rms_B_bonded: 1.38 r_work: 0.2742 rms_B_bonded: 1.75 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: 0.2220 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 19306 Z= 0.133 Angle : 0.530 8.890 26290 Z= 0.276 Chirality : 0.042 0.135 2720 Planarity : 0.004 0.039 3496 Dihedral : 5.812 75.558 2580 Min Nonbonded Distance : 2.562 Molprobity Statistics. All-atom Clashscore : 4.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.09 % Favored : 97.91 % Rotamer: Outliers : 2.63 % Allowed : 8.63 % Favored : 88.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.75 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.78 (0.16), residues: 2339 helix: -3.70 (0.38), residues: 104 sheet: -0.48 (0.19), residues: 621 loop : -0.25 (0.14), residues: 1614 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP E 509 HIS 0.008 0.001 HIS F 290 PHE 0.012 0.001 PHE C 535 TYR 0.015 0.002 TYR C 701 ARG 0.005 0.000 ARG C 485 Details of bonding type rmsd hydrogen bonds : bond 0.02974 ( 240) hydrogen bonds : angle 5.87554 ( 462) SS BOND : bond 0.00375 ( 2) SS BOND : angle 0.97876 ( 4) covalent geometry : bond 0.00307 (19304) covalent geometry : angle 0.52992 (26286) *********************** 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 229 residues out of total 2052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 175 time to evaluate : 2.184 Fit side-chains REVERT: A 485 ARG cc_start: 0.8544 (OUTLIER) cc_final: 0.7865 (ttm170) REVERT: A 564 GLU cc_start: 0.7163 (pp20) cc_final: 0.6899 (pp20) REVERT: A 565 GLU cc_start: 0.7519 (mp0) cc_final: 0.7160 (mp0) REVERT: A 588 GLN cc_start: 0.7836 (mp10) cc_final: 0.7408 (mm110) REVERT: A 590 GLN cc_start: 0.7795 (mt0) cc_final: 0.7460 (mt0) REVERT: A 641 LYS cc_start: 0.8637 (OUTLIER) cc_final: 0.8335 (mttt) REVERT: B 449 LYS cc_start: 0.8792 (OUTLIER) cc_final: 0.8421 (ttpp) REVERT: B 485 ARG cc_start: 0.8372 (OUTLIER) cc_final: 0.7947 (ttm170) REVERT: B 500 GLU cc_start: 0.7709 (OUTLIER) cc_final: 0.7003 (tm-30) REVERT: B 533 ARG cc_start: 0.7758 (ptt-90) cc_final: 0.7451 (ptt-90) REVERT: C 271 ASP cc_start: 0.8123 (m-30) cc_final: 0.7889 (m-30) REVERT: C 550 ARG cc_start: 0.8403 (mtp85) cc_final: 0.8050 (mtp85) REVERT: D 370 ASP cc_start: 0.7352 (m-30) cc_final: 0.6906 (m-30) REVERT: D 474 GLN cc_start: 0.8293 (mt0) cc_final: 0.7550 (tp40) REVERT: D 485 ARG cc_start: 0.8902 (OUTLIER) cc_final: 0.8076 (ttm170) REVERT: D 532 ASP cc_start: 0.7731 (OUTLIER) cc_final: 0.7493 (p0) REVERT: E 485 ARG cc_start: 0.8502 (OUTLIER) cc_final: 0.6906 (ttm170) REVERT: E 514 ARG cc_start: 0.8020 (mtm180) cc_final: 0.5799 (tpt170) REVERT: F 550 ARG cc_start: 0.8554 (OUTLIER) cc_final: 0.7431 (mtm180) REVERT: F 654 VAL cc_start: 0.7861 (t) cc_final: 0.7628 (m) REVERT: H 57 ARG cc_start: 0.8837 (OUTLIER) cc_final: 0.8311 (ptm160) REVERT: H 118 ASP cc_start: 0.8466 (t0) cc_final: 0.8255 (t70) REVERT: H 136 MET cc_start: 0.8865 (OUTLIER) cc_final: 0.8640 (ptp) REVERT: L 100 GLN cc_start: 0.8016 (OUTLIER) cc_final: 0.7649 (mt0) outliers start: 54 outliers final: 28 residues processed: 213 average time/residue: 1.5586 time to fit residues: 367.3018 Evaluate side-chains 208 residues out of total 2052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 168 time to evaluate : 2.151 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 B residue 531 GLU Chi-restraints excluded: chain C residue 238 ARG Chi-restraints excluded: chain C residue 314 ASN Chi-restraints excluded: chain C residue 399 TYR 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 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 580 VAL Chi-restraints excluded: chain F residue 239 VAL Chi-restraints excluded: chain F residue 263 SER Chi-restraints excluded: chain F residue 425 SER Chi-restraints excluded: chain F residue 550 ARG Chi-restraints excluded: chain H residue 23 VAL Chi-restraints excluded: chain H residue 25 GLU 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 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 134 optimal weight: 20.0000 chunk 68 optimal weight: 1.9990 chunk 140 optimal weight: 0.5980 chunk 154 optimal weight: 10.0000 chunk 150 optimal weight: 20.0000 chunk 66 optimal weight: 8.9990 chunk 171 optimal weight: 10.0000 chunk 227 optimal weight: 9.9990 chunk 166 optimal weight: 20.0000 chunk 23 optimal weight: 20.0000 chunk 159 optimal weight: 5.9990 overall best weight: 5.5188 ------------------------------------------------------------------------------- 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 290 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 430 GLN ** D 552 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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** H 141 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 = 0.3005 r_free = 0.3005 target = 0.089680 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2802 r_free = 0.2802 target = 0.077604 restraints weight = 29951.848| |-----------------------------------------------------------------------------| r_work (start): 0.2801 rms_B_bonded: 1.37 r_work: 0.2723 rms_B_bonded: 1.75 restraints_weight: 0.5000 r_work: 0.2627 rms_B_bonded: 3.00 restraints_weight: 0.2500 r_work (final): 0.2627 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8683 moved from start: 0.2249 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 19306 Z= 0.191 Angle : 0.573 8.583 26290 Z= 0.300 Chirality : 0.044 0.136 2720 Planarity : 0.004 0.045 3496 Dihedral : 6.003 74.154 2580 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 4.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 2.92 % Allowed : 8.28 % Favored : 88.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.75 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.80 (0.16), residues: 2339 helix: -3.51 (0.43), residues: 92 sheet: -0.54 (0.19), residues: 601 loop : -0.29 (0.14), residues: 1646 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP E 509 HIS 0.010 0.002 HIS F 290 PHE 0.013 0.002 PHE C 535 TYR 0.019 0.002 TYR C 701 ARG 0.006 0.001 ARG C 485 Details of bonding type rmsd hydrogen bonds : bond 0.03299 ( 240) hydrogen bonds : angle 6.04768 ( 462) SS BOND : bond 0.00449 ( 2) SS BOND : angle 1.03270 ( 4) covalent geometry : bond 0.00444 (19304) covalent geometry : angle 0.57275 (26286) *********************** 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 233 residues out of total 2052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 173 time to evaluate : 2.139 Fit side-chains REVERT: A 485 ARG cc_start: 0.8645 (OUTLIER) cc_final: 0.7482 (ttm170) REVERT: A 564 GLU cc_start: 0.7126 (pp20) cc_final: 0.6918 (pp20) REVERT: A 588 GLN cc_start: 0.7832 (mp10) cc_final: 0.7416 (mm110) REVERT: A 590 GLN cc_start: 0.7773 (mt0) cc_final: 0.7444 (mt0) REVERT: A 641 LYS cc_start: 0.8649 (OUTLIER) cc_final: 0.8345 (mttt) REVERT: B 449 LYS cc_start: 0.8805 (OUTLIER) cc_final: 0.8460 (ttpp) REVERT: B 485 ARG cc_start: 0.8450 (OUTLIER) cc_final: 0.7815 (ttm170) REVERT: B 533 ARG cc_start: 0.7733 (ptt-90) cc_final: 0.7406 (ptt-90) REVERT: C 271 ASP cc_start: 0.8138 (m-30) cc_final: 0.7914 (m-30) REVERT: C 550 ARG cc_start: 0.8426 (OUTLIER) cc_final: 0.8151 (mtp85) REVERT: D 285 ASP cc_start: 0.8170 (t0) cc_final: 0.7735 (t0) REVERT: D 314 ASN cc_start: 0.8312 (OUTLIER) cc_final: 0.7776 (m-40) REVERT: D 370 ASP cc_start: 0.7406 (m-30) cc_final: 0.6970 (m-30) REVERT: D 474 GLN cc_start: 0.8296 (mt0) cc_final: 0.7535 (tp40) REVERT: D 485 ARG cc_start: 0.8925 (OUTLIER) cc_final: 0.8111 (ttm170) REVERT: D 532 ASP cc_start: 0.7799 (OUTLIER) cc_final: 0.7569 (p0) REVERT: E 485 ARG cc_start: 0.8583 (OUTLIER) cc_final: 0.6992 (ttm170) REVERT: E 514 ARG cc_start: 0.8046 (mtm180) cc_final: 0.5814 (tpt170) REVERT: F 529 GLU cc_start: 0.7919 (OUTLIER) cc_final: 0.7527 (tt0) REVERT: F 550 ARG cc_start: 0.8530 (OUTLIER) cc_final: 0.7430 (mtm180) REVERT: F 654 VAL cc_start: 0.7839 (t) cc_final: 0.7602 (m) REVERT: F 725 ARG cc_start: 0.8439 (OUTLIER) cc_final: 0.8131 (pmm-80) REVERT: H 57 ARG cc_start: 0.8898 (OUTLIER) cc_final: 0.7642 (ptm160) REVERT: H 118 ASP cc_start: 0.8507 (t0) cc_final: 0.8299 (t70) REVERT: H 136 MET cc_start: 0.8855 (OUTLIER) cc_final: 0.8645 (ptp) REVERT: L 100 GLN cc_start: 0.7950 (OUTLIER) cc_final: 0.7533 (mt0) outliers start: 60 outliers final: 34 residues processed: 216 average time/residue: 1.5300 time to fit residues: 365.6834 Evaluate side-chains 219 residues out of total 2052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 170 time to evaluate : 2.077 ------------------------------------------------------------------------------- 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 348 SER Chi-restraints excluded: chain C residue 399 TYR Chi-restraints excluded: chain C residue 550 ARG 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 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 485 ARG 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 263 SER 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 25 GLU 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 H residue 141 GLN 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 209 optimal weight: 0.9990 chunk 104 optimal weight: 8.9990 chunk 145 optimal weight: 9.9990 chunk 223 optimal weight: 6.9990 chunk 87 optimal weight: 0.8980 chunk 26 optimal weight: 20.0000 chunk 95 optimal weight: 5.9990 chunk 63 optimal weight: 0.9990 chunk 132 optimal weight: 8.9990 chunk 39 optimal weight: 10.0000 chunk 189 optimal weight: 5.9990 overall best weight: 2.9788 ------------------------------------------------------------------------------- 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 290 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 430 GLN D 552 ASN ** D 588 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 254 ASN ** F 262 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 290 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 673 GLN H 141 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 = 0.3016 r_free = 0.3016 target = 0.090352 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2816 r_free = 0.2816 target = 0.078379 restraints weight = 30121.775| |-----------------------------------------------------------------------------| r_work (start): 0.2822 rms_B_bonded: 1.37 r_work: 0.2744 rms_B_bonded: 1.75 restraints_weight: 0.5000 r_work: 0.2648 rms_B_bonded: 3.00 restraints_weight: 0.2500 r_work (final): 0.2648 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8665 moved from start: 0.2311 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 19306 Z= 0.124 Angle : 0.524 9.364 26290 Z= 0.272 Chirality : 0.042 0.135 2720 Planarity : 0.004 0.038 3496 Dihedral : 5.720 74.278 2580 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 4.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 2.92 % Allowed : 8.67 % Favored : 88.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.75 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.65 (0.16), residues: 2339 helix: -3.45 (0.44), residues: 92 sheet: -0.39 (0.19), residues: 621 loop : -0.20 (0.15), residues: 1626 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP E 509 HIS 0.005 0.001 HIS D 290 PHE 0.012 0.001 PHE C 535 TYR 0.014 0.001 TYR C 701 ARG 0.005 0.000 ARG H 106 Details of bonding type rmsd hydrogen bonds : bond 0.02884 ( 240) hydrogen bonds : angle 5.76280 ( 462) SS BOND : bond 0.00332 ( 2) SS BOND : angle 0.84968 ( 4) covalent geometry : bond 0.00283 (19304) covalent geometry : angle 0.52414 (26286) *********************** 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 231 residues out of total 2052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 171 time to evaluate : 2.103 Fit side-chains REVERT: A 474 GLN cc_start: 0.6691 (mp10) cc_final: 0.6385 (tp-100) REVERT: A 485 ARG cc_start: 0.8526 (OUTLIER) cc_final: 0.7836 (ttm170) REVERT: A 531 GLU cc_start: 0.7331 (OUTLIER) cc_final: 0.7112 (mt-10) REVERT: A 588 GLN cc_start: 0.7829 (mp10) cc_final: 0.7395 (mm110) REVERT: A 590 GLN cc_start: 0.7779 (mt0) cc_final: 0.7458 (mt0) REVERT: A 641 LYS cc_start: 0.8620 (OUTLIER) cc_final: 0.8329 (mttt) REVERT: B 449 LYS cc_start: 0.8788 (OUTLIER) cc_final: 0.8424 (ttpp) REVERT: B 485 ARG cc_start: 0.8369 (OUTLIER) cc_final: 0.7990 (ttm170) REVERT: B 500 GLU cc_start: 0.7706 (OUTLIER) cc_final: 0.6925 (tm-30) REVERT: B 533 ARG cc_start: 0.7732 (ptt-90) cc_final: 0.7432 (ptt-90) REVERT: C 271 ASP cc_start: 0.8079 (m-30) cc_final: 0.7845 (m-30) REVERT: C 550 ARG cc_start: 0.8411 (OUTLIER) cc_final: 0.8076 (mtp85) REVERT: D 285 ASP cc_start: 0.8147 (t0) cc_final: 0.7712 (t0) REVERT: D 314 ASN cc_start: 0.8260 (OUTLIER) cc_final: 0.7697 (m-40) REVERT: D 474 GLN cc_start: 0.8279 (mt0) cc_final: 0.7538 (tp40) REVERT: D 485 ARG cc_start: 0.8873 (OUTLIER) cc_final: 0.8052 (ttm170) REVERT: D 532 ASP cc_start: 0.7725 (OUTLIER) cc_final: 0.7514 (p0) REVERT: E 514 ARG cc_start: 0.7959 (mtm180) cc_final: 0.5793 (tpt170) REVERT: F 258 LYS cc_start: 0.8327 (mtmt) cc_final: 0.7391 (mmpt) REVERT: F 529 GLU cc_start: 0.7918 (OUTLIER) cc_final: 0.7491 (tt0) REVERT: F 550 ARG cc_start: 0.8533 (OUTLIER) cc_final: 0.7426 (mtm180) REVERT: F 654 VAL cc_start: 0.7860 (t) cc_final: 0.7630 (m) REVERT: H 57 ARG cc_start: 0.8857 (OUTLIER) cc_final: 0.8291 (ptm160) REVERT: H 118 ASP cc_start: 0.8477 (t0) cc_final: 0.8257 (t70) REVERT: L 100 GLN cc_start: 0.7998 (OUTLIER) cc_final: 0.7559 (mt0) outliers start: 60 outliers final: 30 residues processed: 216 average time/residue: 1.5891 time to fit residues: 380.6998 Evaluate side-chains 212 residues out of total 2052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 168 time to evaluate : 2.247 ------------------------------------------------------------------------------- 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 485 ARG Chi-restraints excluded: chain A residue 531 GLU 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 B residue 531 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 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 673 GLN Chi-restraints excluded: chain H residue 23 VAL Chi-restraints excluded: chain H residue 25 GLU 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 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 72 optimal weight: 0.6980 chunk 104 optimal weight: 7.9990 chunk 138 optimal weight: 5.9990 chunk 59 optimal weight: 1.9990 chunk 148 optimal weight: 20.0000 chunk 26 optimal weight: 20.0000 chunk 196 optimal weight: 20.0000 chunk 199 optimal weight: 0.9990 chunk 97 optimal weight: 5.9990 chunk 86 optimal weight: 10.0000 chunk 31 optimal weight: 5.9990 overall best weight: 3.1388 ------------------------------------------------------------------------------- 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 290 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 430 GLN D 552 ASN ** D 588 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 254 ASN ** F 262 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 290 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 673 GLN H 141 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 = 0.3024 r_free = 0.3024 target = 0.090776 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2823 r_free = 0.2823 target = 0.078717 restraints weight = 29868.487| |-----------------------------------------------------------------------------| r_work (start): 0.2825 rms_B_bonded: 1.36 r_work: 0.2747 rms_B_bonded: 1.74 restraints_weight: 0.5000 r_work: 0.2651 rms_B_bonded: 3.00 restraints_weight: 0.2500 r_work (final): 0.2651 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8663 moved from start: 0.2343 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= 0.126 Angle : 0.521 7.539 26290 Z= 0.271 Chirality : 0.042 0.134 2720 Planarity : 0.004 0.036 3496 Dihedral : 5.562 71.832 2577 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 4.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.18 % Favored : 97.82 % Rotamer: Outliers : 2.49 % Allowed : 8.87 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.60 (0.16), residues: 2339 helix: -3.44 (0.44), residues: 92 sheet: -0.35 (0.19), residues: 621 loop : -0.17 (0.15), residues: 1626 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP E 509 HIS 0.005 0.001 HIS D 290 PHE 0.012 0.001 PHE C 535 TYR 0.014 0.001 TYR C 701 ARG 0.005 0.000 ARG H 106 Details of bonding type rmsd hydrogen bonds : bond 0.02873 ( 240) hydrogen bonds : angle 5.70988 ( 462) SS BOND : bond 0.00346 ( 2) SS BOND : angle 0.86079 ( 4) covalent geometry : bond 0.00290 (19304) covalent geometry : angle 0.52050 (26286) *********************** 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 223 residues out of total 2052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 172 time to evaluate : 2.143 Fit side-chains REVERT: A 474 GLN cc_start: 0.6690 (mp10) cc_final: 0.6378 (tp-100) REVERT: A 588 GLN cc_start: 0.7834 (mp10) cc_final: 0.7437 (mm-40) REVERT: A 590 GLN cc_start: 0.7771 (mt0) cc_final: 0.7445 (mt0) REVERT: A 641 LYS cc_start: 0.8620 (OUTLIER) cc_final: 0.8331 (mttt) REVERT: B 449 LYS cc_start: 0.8808 (OUTLIER) cc_final: 0.8451 (ttpp) REVERT: B 485 ARG cc_start: 0.8378 (OUTLIER) cc_final: 0.7950 (ttm170) REVERT: B 500 GLU cc_start: 0.7727 (OUTLIER) cc_final: 0.6709 (tm-30) REVERT: B 533 ARG cc_start: 0.7701 (ptt-90) cc_final: 0.7410 (ptt-90) REVERT: C 271 ASP cc_start: 0.8063 (m-30) cc_final: 0.7833 (m-30) REVERT: C 550 ARG cc_start: 0.8389 (OUTLIER) cc_final: 0.8043 (mtp85) REVERT: D 285 ASP cc_start: 0.8139 (t0) cc_final: 0.7702 (t0) REVERT: D 314 ASN cc_start: 0.8260 (OUTLIER) cc_final: 0.7695 (m-40) REVERT: D 474 GLN cc_start: 0.8291 (mt0) cc_final: 0.7555 (tp40) REVERT: D 485 ARG cc_start: 0.8881 (OUTLIER) cc_final: 0.8045 (ttm170) REVERT: D 532 ASP cc_start: 0.7708 (OUTLIER) cc_final: 0.7503 (p0) REVERT: E 514 ARG cc_start: 0.7952 (mtm180) cc_final: 0.5800 (tpt170) REVERT: F 258 LYS cc_start: 0.8319 (mtmt) cc_final: 0.7403 (mmpt) REVERT: F 529 GLU cc_start: 0.7904 (OUTLIER) cc_final: 0.7470 (tt0) REVERT: F 550 ARG cc_start: 0.8547 (OUTLIER) cc_final: 0.7398 (mtm180) REVERT: F 654 VAL cc_start: 0.7845 (t) cc_final: 0.7635 (m) REVERT: F 725 ARG cc_start: 0.8409 (OUTLIER) cc_final: 0.8149 (pmm-80) REVERT: H 57 ARG cc_start: 0.8862 (OUTLIER) cc_final: 0.8296 (ptm160) REVERT: H 118 ASP cc_start: 0.8495 (t0) cc_final: 0.8275 (t70) REVERT: L 100 GLN cc_start: 0.7926 (OUTLIER) cc_final: 0.7550 (mt0) outliers start: 51 outliers final: 29 residues processed: 210 average time/residue: 1.4931 time to fit residues: 347.9053 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 : 2.285 ------------------------------------------------------------------------------- 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 B residue 500 GLU Chi-restraints excluded: chain B residue 531 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 C residue 580 VAL Chi-restraints excluded: chain D residue 314 ASN Chi-restraints excluded: chain D residue 485 ARG Chi-restraints excluded: chain D residue 532 ASP 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 263 SER 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 25 GLU 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 H residue 141 GLN 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 156 optimal weight: 10.0000 chunk 174 optimal weight: 9.9990 chunk 145 optimal weight: 10.0000 chunk 168 optimal weight: 0.9990 chunk 187 optimal weight: 9.9990 chunk 132 optimal weight: 0.9990 chunk 30 optimal weight: 8.9990 chunk 108 optimal weight: 20.0000 chunk 90 optimal weight: 10.0000 chunk 164 optimal weight: 3.9990 chunk 212 optimal weight: 20.0000 overall best weight: 4.9990 ------------------------------------------------------------------------------- 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 290 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 430 GLN D 552 ASN ** D 588 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 254 ASN ** F 262 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 290 HIS H 141 GLN L 73 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 = 0.3004 r_free = 0.3004 target = 0.089550 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2802 r_free = 0.2802 target = 0.077575 restraints weight = 30097.674| |-----------------------------------------------------------------------------| r_work (start): 0.2808 rms_B_bonded: 1.36 r_work: 0.2730 rms_B_bonded: 1.74 restraints_weight: 0.5000 r_work: 0.2634 rms_B_bonded: 2.99 restraints_weight: 0.2500 r_work (final): 0.2634 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8677 moved from start: 0.2338 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 19306 Z= 0.176 Angle : 0.562 10.005 26290 Z= 0.293 Chirality : 0.044 0.135 2720 Planarity : 0.004 0.045 3496 Dihedral : 5.758 74.065 2577 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 4.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 2.24 % Allowed : 9.26 % Favored : 88.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.75 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.71 (0.16), residues: 2339 helix: -3.47 (0.43), residues: 92 sheet: -0.42 (0.19), residues: 601 loop : -0.25 (0.14), residues: 1646 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP E 509 HIS 0.006 0.001 HIS D 290 PHE 0.013 0.002 PHE H 83 TYR 0.018 0.002 TYR C 701 ARG 0.005 0.001 ARG E 485 Details of bonding type rmsd hydrogen bonds : bond 0.03147 ( 240) hydrogen bonds : angle 5.89033 ( 462) SS BOND : bond 0.00338 ( 2) SS BOND : angle 1.15759 ( 4) covalent geometry : bond 0.00409 (19304) covalent geometry : angle 0.56196 (26286) ********************** 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 214 residues out of total 2052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 168 time to evaluate : 2.336 Fit side-chains REVERT: A 474 GLN cc_start: 0.6656 (mp10) cc_final: 0.6357 (tp-100) REVERT: A 588 GLN cc_start: 0.7839 (mp10) cc_final: 0.7406 (mm110) REVERT: A 590 GLN cc_start: 0.7789 (mt0) cc_final: 0.7461 (mt0) REVERT: A 641 LYS cc_start: 0.8626 (OUTLIER) cc_final: 0.8337 (mttt) REVERT: B 449 LYS cc_start: 0.8813 (OUTLIER) cc_final: 0.8453 (ttpp) REVERT: B 485 ARG cc_start: 0.8452 (OUTLIER) cc_final: 0.7881 (ttm170) REVERT: B 500 GLU cc_start: 0.7740 (OUTLIER) cc_final: 0.6951 (tm-30) REVERT: B 533 ARG cc_start: 0.7698 (ptt-90) cc_final: 0.7385 (ptt-90) REVERT: C 271 ASP cc_start: 0.8106 (m-30) cc_final: 0.7876 (m-30) REVERT: C 550 ARG cc_start: 0.8434 (OUTLIER) cc_final: 0.8124 (mtp85) REVERT: D 285 ASP cc_start: 0.8156 (t0) cc_final: 0.7724 (t0) REVERT: D 314 ASN cc_start: 0.8317 (OUTLIER) cc_final: 0.7772 (m-40) REVERT: D 474 GLN cc_start: 0.8292 (mt0) cc_final: 0.7541 (tp40) REVERT: D 485 ARG cc_start: 0.8905 (OUTLIER) cc_final: 0.8086 (ttm170) REVERT: D 532 ASP cc_start: 0.7740 (OUTLIER) cc_final: 0.7536 (p0) REVERT: E 514 ARG cc_start: 0.7961 (mtm180) cc_final: 0.5774 (tpt170) REVERT: F 258 LYS cc_start: 0.8323 (mtmt) cc_final: 0.7382 (mmpt) REVERT: F 529 GLU cc_start: 0.7911 (OUTLIER) cc_final: 0.7483 (tt0) REVERT: F 550 ARG cc_start: 0.8537 (OUTLIER) cc_final: 0.7407 (mtm180) REVERT: F 654 VAL cc_start: 0.7823 (t) cc_final: 0.7595 (m) REVERT: F 725 ARG cc_start: 0.8426 (OUTLIER) cc_final: 0.8150 (pmm-80) REVERT: H 57 ARG cc_start: 0.8872 (OUTLIER) cc_final: 0.7609 (ptm160) REVERT: H 118 ASP cc_start: 0.8494 (t0) cc_final: 0.8280 (t70) REVERT: L 100 GLN cc_start: 0.7968 (OUTLIER) cc_final: 0.7543 (mt0) outliers start: 46 outliers final: 29 residues processed: 203 average time/residue: 1.5823 time to fit residues: 355.5179 Evaluate side-chains 210 residues out of total 2052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 168 time to evaluate : 2.374 ------------------------------------------------------------------------------- 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 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 C residue 580 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 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 F residue 725 ARG Chi-restraints excluded: chain H residue 23 VAL Chi-restraints excluded: chain H residue 25 GLU 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 H residue 141 GLN 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 166 optimal weight: 20.0000 chunk 138 optimal weight: 7.9990 chunk 69 optimal weight: 20.0000 chunk 91 optimal weight: 9.9990 chunk 129 optimal weight: 10.0000 chunk 82 optimal weight: 8.9990 chunk 112 optimal weight: 20.0000 chunk 183 optimal weight: 0.9980 chunk 151 optimal weight: 5.9990 chunk 2 optimal weight: 10.0000 chunk 15 optimal weight: 6.9990 overall best weight: 6.1988 ------------------------------------------------------------------------------- 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 290 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 430 GLN D 552 ASN ** D 588 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 254 ASN ** F 262 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 129 ASN L 117 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3007 r_free = 0.3007 target = 0.089787 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2804 r_free = 0.2804 target = 0.077688 restraints weight = 30066.560| |-----------------------------------------------------------------------------| r_work (start): 0.2803 rms_B_bonded: 1.37 r_work: 0.2725 rms_B_bonded: 1.75 restraints_weight: 0.5000 r_work: 0.2629 rms_B_bonded: 3.00 restraints_weight: 0.2500 r_work (final): 0.2629 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8678 moved from start: 0.2335 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 19306 Z= 0.199 Angle : 0.743 59.199 26290 Z= 0.416 Chirality : 0.044 0.135 2720 Planarity : 0.004 0.045 3496 Dihedral : 5.769 74.095 2577 Min Nonbonded Distance : 2.407 Molprobity Statistics. All-atom Clashscore : 4.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Rotamer: Outliers : 2.34 % Allowed : 9.11 % Favored : 88.55 % Cbeta Deviations : 0.05 % Peptide Plane: Cis-proline : 3.75 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.72 (0.16), residues: 2339 helix: -3.47 (0.43), residues: 92 sheet: -0.42 (0.19), residues: 601 loop : -0.26 (0.14), residues: 1646 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP E 509 HIS 0.006 0.001 HIS D 290 PHE 0.013 0.002 PHE H 83 TYR 0.018 0.002 TYR C 701 ARG 0.004 0.001 ARG H 106 Details of bonding type rmsd hydrogen bonds : bond 0.03176 ( 240) hydrogen bonds : angle 5.89278 ( 462) SS BOND : bond 0.00400 ( 2) SS BOND : angle 1.13604 ( 4) covalent geometry : bond 0.00457 (19304) covalent geometry : angle 0.74250 (26286) =============================================================================== Job complete usr+sys time: 11584.61 seconds wall clock time: 200 minutes 39.24 seconds (12039.24 seconds total)