Starting phenix.real_space_refine on Sun Aug 24 04:58:36 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9b6p_44273/08_2025/9b6p_44273.cif Found real_map, /net/cci-nas-00/data/ceres_data/9b6p_44273/08_2025/9b6p_44273.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.13 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9b6p_44273/08_2025/9b6p_44273.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9b6p_44273/08_2025/9b6p_44273.map" model { file = "/net/cci-nas-00/data/ceres_data/9b6p_44273/08_2025/9b6p_44273.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9b6p_44273/08_2025/9b6p_44273.cif" } resolution = 3.13 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 1.000 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 65 5.16 5 C 11128 2.51 5 N 3068 2.21 5 O 3407 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 84 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 17668 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 2629 Number of conformers: 1 Conformer: "" Number of residues, atoms: 334, 2629 Classifications: {'peptide': 334} Link IDs: {'PCIS': 1, 'PTRANS': 27, 'TRANS': 305} Chain breaks: 3 Chain: "B" Number of atoms: 1366 Number of conformers: 1 Conformer: "" Number of residues, atoms: 176, 1366 Classifications: {'peptide': 176} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 162} Chain breaks: 2 Chain: "C" Number of atoms: 3852 Number of conformers: 1 Conformer: "" Number of residues, atoms: 481, 3852 Classifications: {'peptide': 481} Link IDs: {'PCIS': 1, 'PTRANS': 31, 'TRANS': 448} Chain breaks: 5 Chain: "D" Number of atoms: 2772 Number of conformers: 1 Conformer: "" Number of residues, atoms: 353, 2772 Classifications: {'peptide': 353} Link IDs: {'PCIS': 1, 'PTRANS': 27, 'TRANS': 324} Chain breaks: 2 Chain: "E" Number of atoms: 1366 Number of conformers: 1 Conformer: "" Number of residues, atoms: 176, 1366 Classifications: {'peptide': 176} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 162} Chain breaks: 2 Chain: "F" Number of atoms: 3902 Number of conformers: 1 Conformer: "" Number of residues, atoms: 488, 3902 Classifications: {'peptide': 488} Link IDs: {'PCIS': 1, 'PTRANS': 31, 'TRANS': 455} Chain breaks: 4 Chain: "H" Number of atoms: 990 Number of conformers: 1 Conformer: "" Number of residues, atoms: 130, 990 Classifications: {'peptide': 130} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 127} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Chain: "L" Number of atoms: 791 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 791 Classifications: {'peptide': 109} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 101} Time building chain proxies: 4.91, per 1000 atoms: 0.28 Number of scatterers: 17668 At special positions: 0 Unit cell: (155.4, 120.12, 92.4, 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 65 16.00 O 3407 8.00 N 3068 7.00 C 11128 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS H 41 " - pdb=" SG CYS H 115 " distance=2.03 Simple disulfide: pdb=" SG CYS H 121 " - pdb=" SG CYS H 126 " distance=2.04 Simple disulfide: pdb=" SG CYS L 42 " - pdb=" SG CYS L 110 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.51 Conformation dependent library (CDL) restraints added in 929.5 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 4390 Ramachandran restraints generated. 2195 Oldfield, 0 Emsley, 2195 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4106 Finding SS restraints... Secondary structure from input PDB file: 32 helices and 51 sheets defined 7.6% alpha, 16.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.61 Creating SS restraints... Processing helix chain 'A' and resid 252 through 256 Processing helix chain 'A' and resid 262 through 266 Processing helix chain 'A' and resid 288 through 292 Processing helix chain 'A' and resid 355 through 359 removed outlier: 3.605A pdb=" N SER A 358 " --> pdb=" O VAL A 355 " (cutoff:3.500A) removed outlier: 4.234A pdb=" N ALA A 359 " --> pdb=" O LEU A 356 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 355 through 359' Processing helix chain 'A' and resid 396 through 400 Processing helix chain 'A' and resid 492 through 496 Processing helix chain 'A' and resid 563 through 567 Processing helix chain 'B' and resid 431 through 435 removed outlier: 3.950A pdb=" N LEU B 435 " --> pdb=" O LEU B 432 " (cutoff:3.500A) Processing helix chain 'C' and resid 252 through 256 Processing helix chain 'C' and resid 288 through 292 Processing helix chain 'C' and resid 294 through 303 Processing helix chain 'C' and resid 355 through 359 removed outlier: 3.831A pdb=" N SER C 358 " --> pdb=" O VAL C 355 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ALA C 359 " --> pdb=" O LEU C 356 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 355 through 359' Processing helix chain 'C' and resid 431 through 435 removed outlier: 3.788A 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 563 through 568 removed outlier: 3.579A pdb=" N ILE C 566 " --> pdb=" O GLU C 563 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N THR C 568 " --> pdb=" O GLU C 565 " (cutoff:3.500A) Processing helix chain 'D' and resid 251 through 255 removed outlier: 4.282A pdb=" N ASN D 254 " --> pdb=" O THR D 251 " (cutoff:3.500A) Processing helix chain 'D' and resid 263 through 265 No H-bonds generated for 'chain 'D' and resid 263 through 265' Processing helix chain 'D' and resid 396 through 400 Processing helix chain 'D' and resid 554 through 556 No H-bonds generated for 'chain 'D' and resid 554 through 556' Processing helix chain 'D' and resid 563 through 569 removed outlier: 4.308A pdb=" N THR D 568 " --> pdb=" O GLU D 565 " (cutoff:3.500A) Processing helix chain 'E' and resid 565 through 569 removed outlier: 3.993A pdb=" N THR E 568 " --> pdb=" O GLU E 565 " (cutoff:3.500A) Processing helix chain 'F' and resid 252 through 256 Processing helix chain 'F' and resid 262 through 266 Processing helix chain 'F' and resid 288 through 293 removed outlier: 4.256A pdb=" N HIS F 292 " --> pdb=" O ARG F 288 " (cutoff:3.500A) Processing helix chain 'F' and resid 294 through 303 Processing helix chain 'F' and resid 431 through 435 removed outlier: 3.697A pdb=" N LEU F 435 " --> pdb=" O LEU F 432 " (cutoff:3.500A) Processing helix chain 'F' and resid 470 through 474 Processing helix chain 'F' and resid 563 through 568 removed outlier: 4.040A pdb=" N THR F 568 " --> pdb=" O GLU F 565 " (cutoff:3.500A) Processing helix chain 'H' and resid 71 through 75 removed outlier: 4.164A pdb=" N SER H 75 " --> pdb=" O TYR H 72 " (cutoff:3.500A) Processing helix chain 'H' and resid 106 through 110 removed outlier: 3.875A pdb=" N THR H 110 " --> pdb=" O ALA H 107 " (cutoff:3.500A) Processing helix chain 'H' and resid 122 through 126 Processing helix chain 'L' and resid 101 through 105 Processing sheet with id=AA1, first strand: chain 'A' and resid 371 through 373 removed outlier: 9.373A pdb=" N PHE A 372 " --> pdb=" O THR A 244 " (cutoff:3.500A) removed outlier: 6.540A pdb=" N THR A 246 " --> pdb=" O PHE A 372 " (cutoff:3.500A) 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 483 through 484 removed outlier: 3.651A pdb=" N SER A 483 " --> pdb=" O GLN A 599 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 488 through 490 Processing sheet with id=AA5, first strand: chain 'A' and resid 514 through 517 removed outlier: 4.024A pdb=" N GLY C 578 " --> pdb=" O VAL C 596 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 578 through 581 removed outlier: 3.954A pdb=" N GLY A 578 " --> pdb=" O VAL A 596 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 606 through 607 Processing sheet with id=AA8, first strand: chain 'A' and resid 619 through 621 removed outlier: 5.673A pdb=" N ALA A 620 " --> pdb=" O MET A 640 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'A' and resid 627 through 628 removed outlier: 6.593A pdb=" N ILE C 479 " --> pdb=" O VAL C 606 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 445 through 449 removed outlier: 6.763A pdb=" N LYS B 462 " --> pdb=" O SER B 448 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 479 through 480 removed outlier: 6.398A pdb=" N ILE B 479 " --> pdb=" O VAL B 606 " (cutoff:3.500A) removed outlier: 4.236A pdb=" N MET B 605 " --> pdb=" O PHE C 629 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N GLY C 627 " --> pdb=" O TRP B 607 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 483 through 484 Processing sheet with id=AB4, first strand: chain 'B' and resid 488 through 490 Processing sheet with id=AB5, first strand: chain 'B' and resid 508 through 511 Processing sheet with id=AB6, first strand: chain 'B' and resid 593 through 596 removed outlier: 3.929A 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 426 through 428 Processing sheet with id=AC1, first strand: chain 'C' and resid 445 through 451 removed outlier: 6.629A pdb=" N LYS C 462 " --> pdb=" O SER C 448 " (cutoff:3.500A) removed outlier: 4.049A 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 removed outlier: 3.509A pdb=" N SER C 483 " --> pdb=" O GLN C 599 " (cutoff:3.500A) 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 619 through 621 Processing sheet with id=AC5, first strand: chain 'D' and resid 371 through 373 removed outlier: 3.578A pdb=" N PHE D 372 " --> pdb=" O THR D 246 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'D' and resid 258 through 261 Processing sheet with id=AC7, first strand: chain 'D' and resid 479 through 480 removed outlier: 6.239A pdb=" N ILE D 479 " --> pdb=" O VAL D 606 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N MET D 605 " --> pdb=" O PHE E 629 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'D' and resid 483 through 484 Processing sheet with id=AC9, first strand: chain 'D' and resid 488 through 490 Processing sheet with id=AD1, first strand: chain 'D' and resid 514 through 517 Processing sheet with id=AD2, first strand: chain 'D' and resid 542 through 544 Processing sheet with id=AD3, first strand: chain 'D' and resid 551 through 553 removed outlier: 7.288A pdb=" N ASP D 551 " --> pdb=" O VAL F 465 " (cutoff:3.500A) removed outlier: 7.412A pdb=" N VAL F 465 " --> pdb=" O ASP D 551 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N THR F 450 " --> pdb=" O THR F 460 " (cutoff:3.500A) removed outlier: 6.650A pdb=" N LYS F 462 " --> pdb=" O SER F 448 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'D' and resid 578 through 581 removed outlier: 3.916A pdb=" N GLY D 578 " --> pdb=" O VAL D 596 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'D' and resid 619 through 621 removed outlier: 6.133A pdb=" N ALA D 620 " --> pdb=" O MET D 640 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD5 Processing sheet with id=AD6, first strand: chain 'D' and resid 627 through 628 removed outlier: 6.386A pdb=" N ILE F 479 " --> pdb=" O VAL F 606 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'E' and resid 445 through 451 removed outlier: 5.782A pdb=" N LEU E 447 " --> pdb=" O SER E 464 " (cutoff:3.500A) removed outlier: 6.498A pdb=" N SER E 464 " --> pdb=" O LEU E 447 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N ILE E 451 " --> pdb=" O THR E 460 " (cutoff:3.500A) removed outlier: 6.381A pdb=" N THR E 460 " --> pdb=" O ILE E 451 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'E' and resid 479 through 480 removed outlier: 6.154A pdb=" N ILE E 479 " --> pdb=" O VAL E 606 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N MET E 605 " --> pdb=" O PHE F 629 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'E' and resid 483 through 484 removed outlier: 3.570A pdb=" N SER E 483 " --> pdb=" O GLN E 599 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'E' and resid 488 through 490 Processing sheet with id=AE2, first strand: chain 'E' and resid 508 through 511 Processing sheet with id=AE3, first strand: chain 'E' and resid 593 through 596 removed outlier: 4.160A pdb=" N GLY E 578 " --> pdb=" O VAL E 596 " (cutoff:3.500A) Processing sheet with id=AE4, 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=AE5, first strand: chain 'F' and resid 258 through 261 Processing sheet with id=AE6, first strand: chain 'F' and resid 383 through 384 Processing sheet with id=AE7, first strand: chain 'F' and resid 427 through 428 removed outlier: 6.067A 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 23 removed outlier: 3.672A pdb=" N SER H 44 " --> pdb=" O GLN H 22 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'H' and resid 52 through 58 removed outlier: 7.095A pdb=" N PHE H 53 " --> pdb=" O VAL H 69 " (cutoff:3.500A) removed outlier: 4.869A pdb=" N VAL H 69 " --> pdb=" O PHE H 53 " (cutoff:3.500A) removed outlier: 6.651A pdb=" N TRP H 55 " --> pdb=" O VAL H 67 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'H' and resid 64 through 70 current: chain 'H' and resid 137 through 140 Processing sheet with id=AF5, first strand: chain 'L' and resid 30 through 32 WARNING: can't find start of bonding for strands! previous: chain 'L' and resid 30 through 32 current: chain 'L' and resid 67 through 70 WARNING: can't find start of bonding for strands! previous: chain 'L' and resid 67 through 70 current: chain 'L' and resid 120 through 122 No H-bonds generated for sheet with id=AF5 Processing sheet with id=AF6, first strand: chain 'L' and resid 37 through 42 removed outlier: 3.566A pdb=" N SER L 89 " --> pdb=" O SER L 92 " (cutoff:3.500A) 237 hydrogen bonds defined for protein. 486 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.70 Time building geometry restraints manager: 1.89 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 3601 1.33 - 1.45: 4896 1.45 - 1.57: 9573 1.57 - 1.69: 0 1.69 - 1.82: 112 Bond restraints: 18182 Sorted by residual: bond pdb=" C VAL C 493 " pdb=" O VAL C 493 " ideal model delta sigma weight residual 1.237 1.203 0.034 1.17e-02 7.31e+03 8.69e+00 bond pdb=" C GLY H 129 " pdb=" O GLY H 129 " ideal model delta sigma weight residual 1.238 1.209 0.029 1.13e-02 7.83e+03 6.45e+00 bond pdb=" C PRO F 366 " pdb=" N PHE F 367 " ideal model delta sigma weight residual 1.332 1.299 0.034 1.44e-02 4.82e+03 5.43e+00 bond pdb=" N ASP H 73 " pdb=" CA ASP H 73 " ideal model delta sigma weight residual 1.456 1.484 -0.028 1.23e-02 6.61e+03 5.07e+00 bond pdb=" N TYR H 133 " pdb=" CA TYR H 133 " ideal model delta sigma weight residual 1.458 1.496 -0.038 1.77e-02 3.19e+03 4.54e+00 ... (remaining 18177 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.34: 23965 2.34 - 4.67: 695 4.67 - 7.01: 70 7.01 - 9.34: 19 9.34 - 11.68: 10 Bond angle restraints: 24759 Sorted by residual: angle pdb=" N VAL H 67 " pdb=" CA VAL H 67 " pdb=" C VAL H 67 " ideal model delta sigma weight residual 110.72 119.64 -8.92 1.01e+00 9.80e-01 7.80e+01 angle pdb=" N GLY B 453 " pdb=" CA GLY B 453 " pdb=" C GLY B 453 " ideal model delta sigma weight residual 111.72 122.98 -11.26 1.31e+00 5.83e-01 7.39e+01 angle pdb=" N THR C 729 " pdb=" CA THR C 729 " pdb=" C THR C 729 " ideal model delta sigma weight residual 111.36 120.29 -8.93 1.09e+00 8.42e-01 6.71e+01 angle pdb=" N ARG C 485 " pdb=" CA ARG C 485 " pdb=" C ARG C 485 " ideal model delta sigma weight residual 110.24 121.92 -11.68 1.47e+00 4.63e-01 6.31e+01 angle pdb=" N GLY F 539 " pdb=" CA GLY F 539 " pdb=" C GLY F 539 " ideal model delta sigma weight residual 112.73 121.89 -9.16 1.20e+00 6.94e-01 5.83e+01 ... (remaining 24754 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.52: 10064 16.52 - 33.04: 431 33.04 - 49.56: 78 49.56 - 66.08: 19 66.08 - 82.61: 12 Dihedral angle restraints: 10604 sinusoidal: 4163 harmonic: 6441 Sorted by residual: dihedral pdb=" CA TRP H 140 " pdb=" C TRP H 140 " pdb=" N GLY H 141 " pdb=" CA GLY H 141 " ideal model delta harmonic sigma weight residual -180.00 -152.47 -27.53 0 5.00e+00 4.00e-02 3.03e+01 dihedral pdb=" CA ASN A 519 " pdb=" C ASN A 519 " pdb=" N PRO A 520 " pdb=" CA PRO A 520 " ideal model delta harmonic sigma weight residual 0.00 -24.11 24.11 0 5.00e+00 4.00e-02 2.33e+01 dihedral pdb=" CA SER H 122 " pdb=" C SER H 122 " pdb=" N SER H 123 " pdb=" CA SER H 123 " ideal model delta harmonic sigma weight residual 180.00 -156.15 -23.85 0 5.00e+00 4.00e-02 2.28e+01 ... (remaining 10601 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.088: 2232 0.088 - 0.177: 275 0.177 - 0.265: 33 0.265 - 0.354: 7 0.354 - 0.442: 3 Chirality restraints: 2550 Sorted by residual: chirality pdb=" CA THR C 729 " pdb=" N THR C 729 " pdb=" C THR C 729 " pdb=" CB THR C 729 " both_signs ideal model delta sigma weight residual False 2.53 2.08 0.44 2.00e-01 2.50e+01 4.88e+00 chirality pdb=" CA ARG C 485 " pdb=" N ARG C 485 " pdb=" C ARG C 485 " pdb=" CB ARG C 485 " both_signs ideal model delta sigma weight residual False 2.51 2.09 0.42 2.00e-01 2.50e+01 4.40e+00 chirality pdb=" CA ALA B 587 " pdb=" N ALA B 587 " pdb=" C ALA B 587 " pdb=" CB ALA B 587 " both_signs ideal model delta sigma weight residual False 2.48 2.11 0.38 2.00e-01 2.50e+01 3.56e+00 ... (remaining 2547 not shown) Planarity restraints: 3295 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA PHE D 543 " 0.013 2.00e-02 2.50e+03 2.59e-02 6.72e+00 pdb=" C PHE D 543 " -0.045 2.00e-02 2.50e+03 pdb=" O PHE D 543 " 0.017 2.00e-02 2.50e+03 pdb=" N GLY D 544 " 0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA TYR C 484 " -0.011 2.00e-02 2.50e+03 2.20e-02 4.83e+00 pdb=" C TYR C 484 " 0.038 2.00e-02 2.50e+03 pdb=" O TYR C 484 " -0.014 2.00e-02 2.50e+03 pdb=" N ARG C 485 " -0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR C 415 " 0.022 2.00e-02 2.50e+03 1.53e-02 4.67e+00 pdb=" CG TYR C 415 " -0.037 2.00e-02 2.50e+03 pdb=" CD1 TYR C 415 " 0.002 2.00e-02 2.50e+03 pdb=" CD2 TYR C 415 " 0.003 2.00e-02 2.50e+03 pdb=" CE1 TYR C 415 " 0.004 2.00e-02 2.50e+03 pdb=" CE2 TYR C 415 " 0.003 2.00e-02 2.50e+03 pdb=" CZ TYR C 415 " 0.002 2.00e-02 2.50e+03 pdb=" OH TYR C 415 " 0.003 2.00e-02 2.50e+03 ... (remaining 3292 not shown) Histogram of nonbonded interaction distances: 2.08 - 2.64: 358 2.64 - 3.21: 16416 3.21 - 3.77: 28027 3.77 - 4.34: 40295 4.34 - 4.90: 65391 Nonbonded interactions: 150487 Sorted by model distance: nonbonded pdb=" O ASN F 498 " pdb=" ND2 ASN F 498 " model vdw 2.076 3.120 nonbonded pdb=" NE2 GLN B 585 " pdb=" CZ PHE C 501 " model vdw 2.136 3.420 nonbonded pdb=" NE2 GLN B 585 " pdb=" CE1 PHE C 501 " model vdw 2.164 3.420 nonbonded pdb=" OD1 ASP H 138 " pdb=" N VAL H 139 " model vdw 2.199 3.120 nonbonded pdb=" OH TYR D 395 " pdb=" OD1 ASN F 735 " model vdw 2.203 3.040 ... (remaining 150482 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' and (resid 241 through 541 or resid 561 through 681)) } ncs_group { reference = chain 'B' selection = chain 'E' } ncs_group { reference = chain 'C' selection = (chain 'F' and (resid 224 through 337 or resid 340 through 395 or resid 401 thro \ ugh 653 or resid 670 through 736)) } 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: 0.730 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.310 Check model and map are aligned: 0.060 Set scattering table: 0.050 Process input model: 17.000 Find NCS groups from input model: 0.240 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.320 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.750 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7371 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 0.058 18185 Z= 0.297 Angle : 0.953 11.676 24765 Z= 0.597 Chirality : 0.062 0.442 2550 Planarity : 0.005 0.045 3295 Dihedral : 10.469 82.606 6489 Min Nonbonded Distance : 2.076 Molprobity Statistics. All-atom Clashscore : 22.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 1.82 % Allowed : 3.17 % Favored : 95.02 % Cbeta Deviations : 0.15 % Peptide Plane: Cis-proline : 3.90 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.99 (0.14), residues: 2195 helix: -4.71 (0.21), residues: 95 sheet: -1.20 (0.20), residues: 498 loop : -1.19 (0.12), residues: 1602 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG F 734 TYR 0.037 0.003 TYR C 415 PHE 0.034 0.003 PHE L 122 TRP 0.031 0.003 TRP H 140 HIS 0.009 0.002 HIS H 54 Details of bonding type rmsd covalent geometry : bond 0.00587 (18182) covalent geometry : angle 0.95331 (24759) SS BOND : bond 0.00351 ( 3) SS BOND : angle 1.10948 ( 6) hydrogen bonds : bond 0.26190 ( 237) hydrogen bonds : angle 10.49700 ( 486) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4390 Ramachandran restraints generated. 2195 Oldfield, 0 Emsley, 2195 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4390 Ramachandran restraints generated. 2195 Oldfield, 0 Emsley, 2195 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 505 residues out of total 1927 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 470 time to evaluate : 0.637 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 306 TRP cc_start: 0.7085 (m-10) cc_final: 0.6796 (m-10) REVERT: C 382 LEU cc_start: 0.7487 (mt) cc_final: 0.7195 (mt) REVERT: C 391 ARG cc_start: 0.6800 (ttm110) cc_final: 0.6118 (tpt170) REVERT: C 579 GLN cc_start: 0.6743 (mt0) cc_final: 0.6505 (mm110) REVERT: D 347 ASP cc_start: 0.6159 (t0) cc_final: 0.5769 (p0) REVERT: D 613 TYR cc_start: 0.8044 (m-80) cc_final: 0.7277 (m-80) REVERT: D 640 MET cc_start: 0.7348 (mtp) cc_final: 0.7143 (mtp) REVERT: E 511 LEU cc_start: 0.7035 (tp) cc_final: 0.6714 (tt) REVERT: E 533 ARG cc_start: 0.6615 (ptt-90) cc_final: 0.6320 (ptt90) REVERT: E 534 PHE cc_start: 0.6819 (m-80) cc_final: 0.6513 (m-80) REVERT: F 391 ARG cc_start: 0.8047 (ttm110) cc_final: 0.7774 (ttm110) REVERT: F 562 ASN cc_start: 0.7556 (p0) cc_final: 0.7307 (p0) REVERT: F 610 ARG cc_start: 0.8319 (ttm-80) cc_final: 0.7786 (ttt90) REVERT: F 706 TYR cc_start: 0.7367 (t80) cc_final: 0.7077 (t80) REVERT: H 72 TYR cc_start: 0.7178 (OUTLIER) cc_final: 0.6745 (p90) REVERT: L 26 GLN cc_start: 0.6317 (mt0) cc_final: 0.6057 (mt0) outliers start: 35 outliers final: 23 residues processed: 498 average time/residue: 0.1442 time to fit residues: 106.9691 Evaluate side-chains 324 residues out of total 1927 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 300 time to evaluate : 0.745 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 535 PHE Chi-restraints excluded: chain B residue 450 THR Chi-restraints excluded: chain B residue 458 GLN Chi-restraints excluded: chain B residue 585 GLN Chi-restraints excluded: chain C residue 488 ARG Chi-restraints excluded: chain C residue 489 VAL Chi-restraints excluded: chain C residue 562 ASN Chi-restraints excluded: chain C residue 564 GLU Chi-restraints excluded: chain C residue 699 ILE Chi-restraints excluded: chain C residue 729 THR Chi-restraints excluded: chain D residue 389 VAL Chi-restraints excluded: chain D residue 392 SER Chi-restraints excluded: chain D residue 535 PHE Chi-restraints excluded: chain F residue 230 CYS Chi-restraints excluded: chain H residue 46 PHE Chi-restraints excluded: chain H residue 70 ILE Chi-restraints excluded: chain H residue 72 TYR Chi-restraints excluded: chain H residue 93 ASN Chi-restraints excluded: chain H residue 128 LEU Chi-restraints excluded: chain H residue 132 TYR Chi-restraints excluded: chain L residue 49 ILE Chi-restraints excluded: chain L residue 69 LEU Chi-restraints excluded: chain L residue 75 ASN Chi-restraints excluded: chain L residue 80 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 221 random chunks: chunk 216 optimal weight: 0.9980 chunk 98 optimal weight: 20.0000 chunk 194 optimal weight: 4.9990 chunk 107 optimal weight: 7.9990 chunk 10 optimal weight: 9.9990 chunk 66 optimal weight: 0.9990 chunk 130 optimal weight: 5.9990 chunk 124 optimal weight: 0.9990 chunk 103 optimal weight: 30.0000 chunk 200 optimal weight: 6.9990 chunk 212 optimal weight: 8.9990 overall best weight: 2.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 253 ASN ** A 387 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 497 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 570 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 608 GLN A 624 HIS A 646 GLN A 651 ASN B 430 GLN B 452 ASN ** B 497 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 515 ASN B 584 HIS C 304 ASN ** C 430 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 495 GLN C 562 ASN C 585 GLN ** C 608 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 624 HIS C 646 GLN C 673 GLN ** C 700 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 709 ASN D 272 ASN ** D 290 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 497 ASN D 608 GLN D 646 GLN D 651 ASN D 673 GLN ** E 430 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 458 GLN E 474 GLN E 497 ASN E 608 GLN E 624 HIS F 229 HIS ** F 253 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 598 ASN F 608 GLN F 624 HIS F 646 GLN F 651 ASN F 673 GLN H 22 GLN H 76 ASN H 93 ASN L 60 GLN ** L 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 111 GLN Total number of N/Q/H flips: 40 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3609 r_free = 0.3609 target = 0.132080 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.120423 restraints weight = 32198.638| |-----------------------------------------------------------------------------| r_work (start): 0.3452 rms_B_bonded: 1.85 r_work: 0.3381 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.3284 rms_B_bonded: 4.12 restraints_weight: 0.2500 r_work (final): 0.3284 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7641 moved from start: 0.1965 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 18185 Z= 0.142 Angle : 0.611 7.964 24765 Z= 0.321 Chirality : 0.044 0.226 2550 Planarity : 0.004 0.057 3295 Dihedral : 6.628 59.792 2468 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 9.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Rotamer: Outliers : 2.34 % Allowed : 7.58 % Favored : 90.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.90 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.20 (0.15), residues: 2195 helix: -3.80 (0.40), residues: 85 sheet: -0.72 (0.21), residues: 513 loop : -0.64 (0.13), residues: 1597 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG H 91 TYR 0.016 0.002 TYR A 674 PHE 0.024 0.002 PHE H 99 TRP 0.023 0.002 TRP H 140 HIS 0.009 0.001 HIS H 54 Details of bonding type rmsd covalent geometry : bond 0.00323 (18182) covalent geometry : angle 0.61051 (24759) SS BOND : bond 0.00359 ( 3) SS BOND : angle 0.73691 ( 6) hydrogen bonds : bond 0.03816 ( 237) hydrogen bonds : angle 7.17342 ( 486) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4390 Ramachandran restraints generated. 2195 Oldfield, 0 Emsley, 2195 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4390 Ramachandran restraints generated. 2195 Oldfield, 0 Emsley, 2195 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 382 residues out of total 1927 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 337 time to evaluate : 0.653 Fit side-chains revert: symmetry clash REVERT: B 435 LEU cc_start: 0.8584 (OUTLIER) cc_final: 0.8309 (mt) REVERT: B 436 MET cc_start: 0.7866 (ptp) cc_final: 0.7198 (ptp) REVERT: B 441 ASP cc_start: 0.6191 (m-30) cc_final: 0.5857 (m-30) REVERT: B 456 GLN cc_start: 0.7667 (mt0) cc_final: 0.7415 (mm110) REVERT: B 529 GLU cc_start: 0.6609 (tt0) cc_final: 0.6235 (mt-10) REVERT: B 588 GLN cc_start: 0.6958 (OUTLIER) cc_final: 0.6299 (tp40) REVERT: B 592 GLN cc_start: 0.7530 (mt0) cc_final: 0.7314 (mt0) REVERT: C 306 TRP cc_start: 0.7468 (m-10) cc_final: 0.7136 (m-10) REVERT: C 391 ARG cc_start: 0.6792 (ttm110) cc_final: 0.5738 (tpt170) REVERT: D 613 TYR cc_start: 0.8286 (m-80) cc_final: 0.7418 (m-80) REVERT: D 640 MET cc_start: 0.7524 (mtp) cc_final: 0.7200 (mtp) REVERT: E 514 ARG cc_start: 0.7588 (mtm180) cc_final: 0.6631 (mtt-85) REVERT: E 534 PHE cc_start: 0.6685 (m-80) cc_final: 0.6449 (m-80) REVERT: E 609 ASP cc_start: 0.7452 (m-30) cc_final: 0.6706 (p0) REVERT: F 325 VAL cc_start: 0.7336 (OUTLIER) cc_final: 0.7092 (m) REVERT: F 391 ARG cc_start: 0.8154 (ttm110) cc_final: 0.7897 (ttm110) REVERT: F 562 ASN cc_start: 0.8097 (p0) cc_final: 0.7787 (p0) REVERT: F 679 VAL cc_start: 0.7762 (t) cc_final: 0.7501 (p) REVERT: H 72 TYR cc_start: 0.7559 (OUTLIER) cc_final: 0.7131 (p90) REVERT: L 73 ASN cc_start: 0.7358 (t0) cc_final: 0.7142 (t0) REVERT: L 91 THR cc_start: 0.7759 (p) cc_final: 0.7437 (p) outliers start: 45 outliers final: 30 residues processed: 363 average time/residue: 0.1281 time to fit residues: 70.2948 Evaluate side-chains 319 residues out of total 1927 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 285 time to evaluate : 0.576 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 420 VAL Chi-restraints excluded: chain B residue 435 LEU Chi-restraints excluded: chain B residue 447 LEU Chi-restraints excluded: chain B residue 458 GLN Chi-restraints excluded: chain B residue 470 ASN Chi-restraints excluded: chain B residue 479 ILE Chi-restraints excluded: chain B residue 588 GLN Chi-restraints excluded: chain C residue 389 VAL Chi-restraints excluded: chain C residue 488 ARG Chi-restraints excluded: chain C residue 492 THR Chi-restraints excluded: chain C residue 564 GLU Chi-restraints excluded: chain C residue 592 GLN Chi-restraints excluded: chain C residue 699 ILE Chi-restraints excluded: chain C residue 729 THR Chi-restraints excluded: chain D residue 370 ASP Chi-restraints excluded: chain D residue 567 LYS Chi-restraints excluded: chain D residue 672 THR Chi-restraints excluded: chain E residue 479 ILE Chi-restraints excluded: chain E residue 485 ARG Chi-restraints excluded: chain E residue 493 VAL Chi-restraints excluded: chain F residue 325 VAL Chi-restraints excluded: chain F residue 414 SER Chi-restraints excluded: chain F residue 564 GLU Chi-restraints excluded: chain H residue 32 GLN Chi-restraints excluded: chain H residue 46 PHE Chi-restraints excluded: chain H residue 52 VAL Chi-restraints excluded: chain H residue 72 TYR Chi-restraints excluded: chain H residue 123 SER Chi-restraints excluded: chain H residue 128 LEU Chi-restraints excluded: chain H residue 132 TYR Chi-restraints excluded: chain L residue 30 VAL Chi-restraints excluded: chain L residue 61 LEU Chi-restraints excluded: chain L residue 80 VAL Chi-restraints excluded: chain L residue 111 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 221 random chunks: chunk 177 optimal weight: 0.9980 chunk 205 optimal weight: 10.0000 chunk 32 optimal weight: 9.9990 chunk 10 optimal weight: 20.0000 chunk 104 optimal weight: 8.9990 chunk 83 optimal weight: 9.9990 chunk 28 optimal weight: 7.9990 chunk 144 optimal weight: 20.0000 chunk 84 optimal weight: 20.0000 chunk 102 optimal weight: 20.0000 chunk 51 optimal weight: 10.0000 overall best weight: 7.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 259 GLN ** A 290 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 387 GLN ** A 497 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 570 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 598 ASN B 470 ASN ** B 497 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 430 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 486 GLN C 487 GLN C 597 GLN ** C 598 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 608 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 700 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 709 ASN D 272 ASN ** D 290 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 376 GLN D 624 HIS E 430 GLN E 584 HIS F 253 ASN F 305 ASN F 487 GLN H 54 HIS L 60 GLN ** L 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 111 GLN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.128871 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.117224 restraints weight = 32762.418| |-----------------------------------------------------------------------------| r_work (start): 0.3397 rms_B_bonded: 1.85 r_work: 0.3328 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.3230 rms_B_bonded: 4.08 restraints_weight: 0.2500 r_work (final): 0.3230 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7718 moved from start: 0.2472 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.059 18185 Z= 0.263 Angle : 0.692 8.702 24765 Z= 0.367 Chirality : 0.047 0.315 2550 Planarity : 0.005 0.047 3295 Dihedral : 6.615 57.710 2444 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 11.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.37 % Favored : 96.63 % Rotamer: Outliers : 3.17 % Allowed : 10.02 % Favored : 86.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.90 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.38 (0.16), residues: 2195 helix: -3.80 (0.39), residues: 92 sheet: -0.75 (0.22), residues: 481 loop : -0.81 (0.14), residues: 1622 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG H 117 TYR 0.020 0.003 TYR C 577 PHE 0.033 0.003 PHE H 99 TRP 0.029 0.003 TRP H 140 HIS 0.008 0.002 HIS D 290 Details of bonding type rmsd covalent geometry : bond 0.00617 (18182) covalent geometry : angle 0.69237 (24759) SS BOND : bond 0.00431 ( 3) SS BOND : angle 0.99490 ( 6) hydrogen bonds : bond 0.03872 ( 237) hydrogen bonds : angle 7.10704 ( 486) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4390 Ramachandran restraints generated. 2195 Oldfield, 0 Emsley, 2195 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4390 Ramachandran restraints generated. 2195 Oldfield, 0 Emsley, 2195 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 342 residues out of total 1927 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 281 time to evaluate : 0.728 Fit side-chains revert: symmetry clash REVERT: A 347 ASP cc_start: 0.7277 (t70) cc_final: 0.6291 (t0) REVERT: B 436 MET cc_start: 0.8023 (ptp) cc_final: 0.7601 (ptp) REVERT: B 456 GLN cc_start: 0.7996 (mt0) cc_final: 0.7683 (mm110) REVERT: B 470 ASN cc_start: 0.7564 (OUTLIER) cc_final: 0.7238 (m-40) REVERT: B 484 TYR cc_start: 0.7983 (t80) cc_final: 0.7665 (t80) REVERT: B 485 ARG cc_start: 0.7452 (ttp-170) cc_final: 0.7204 (ttm170) REVERT: C 306 TRP cc_start: 0.7630 (m-10) cc_final: 0.7376 (m-10) REVERT: C 391 ARG cc_start: 0.6739 (ttm110) cc_final: 0.5632 (tpt170) REVERT: C 550 ARG cc_start: 0.8002 (mmm-85) cc_final: 0.7787 (mmm160) REVERT: D 613 TYR cc_start: 0.8367 (m-80) cc_final: 0.7375 (m-80) REVERT: D 640 MET cc_start: 0.7638 (mtp) cc_final: 0.7376 (mtp) REVERT: E 452 ASN cc_start: 0.8188 (OUTLIER) cc_final: 0.7682 (t0) REVERT: E 575 GLU cc_start: 0.7455 (mm-30) cc_final: 0.7233 (mm-30) REVERT: F 391 ARG cc_start: 0.8130 (ttm110) cc_final: 0.7877 (ttm110) REVERT: F 562 ASN cc_start: 0.8069 (p0) cc_final: 0.7719 (p0) REVERT: F 679 VAL cc_start: 0.7765 (t) cc_final: 0.7551 (p) REVERT: H 72 TYR cc_start: 0.7758 (OUTLIER) cc_final: 0.6939 (p90) outliers start: 61 outliers final: 45 residues processed: 318 average time/residue: 0.1444 time to fit residues: 70.1997 Evaluate side-chains 304 residues out of total 1927 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 256 time to evaluate : 0.680 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 389 VAL Chi-restraints excluded: chain A residue 420 VAL Chi-restraints excluded: chain B residue 435 LEU Chi-restraints excluded: chain B residue 447 LEU Chi-restraints excluded: chain B residue 458 GLN Chi-restraints excluded: chain B residue 470 ASN Chi-restraints excluded: chain B residue 479 ILE Chi-restraints excluded: chain B residue 585 GLN Chi-restraints excluded: chain B residue 625 THR Chi-restraints excluded: chain C residue 235 LEU Chi-restraints excluded: chain C residue 239 VAL Chi-restraints excluded: chain C residue 389 VAL Chi-restraints excluded: chain C residue 392 SER Chi-restraints excluded: chain C residue 435 LEU Chi-restraints excluded: chain C residue 488 ARG Chi-restraints excluded: chain C residue 494 THR Chi-restraints excluded: chain C residue 568 THR Chi-restraints excluded: chain C residue 592 GLN Chi-restraints excluded: chain C residue 593 THR Chi-restraints excluded: chain C residue 680 SER Chi-restraints excluded: chain C residue 699 ILE Chi-restraints excluded: chain C residue 729 THR Chi-restraints excluded: chain D residue 489 VAL Chi-restraints excluded: chain D residue 672 THR Chi-restraints excluded: chain E residue 452 ASN Chi-restraints excluded: chain E residue 461 LEU Chi-restraints excluded: chain E residue 479 ILE Chi-restraints excluded: chain E residue 485 ARG Chi-restraints excluded: chain E residue 493 VAL Chi-restraints excluded: chain E residue 537 LEU Chi-restraints excluded: chain F residue 264 THR Chi-restraints excluded: chain F residue 278 SER Chi-restraints excluded: chain F residue 344 VAL Chi-restraints excluded: chain F residue 414 SER Chi-restraints excluded: chain F residue 564 GLU Chi-restraints excluded: chain F residue 702 THR Chi-restraints excluded: chain F residue 717 THR Chi-restraints excluded: chain H residue 32 GLN Chi-restraints excluded: chain H residue 46 PHE Chi-restraints excluded: chain H residue 52 VAL Chi-restraints excluded: chain H residue 72 TYR Chi-restraints excluded: chain H residue 123 SER Chi-restraints excluded: chain H residue 128 LEU Chi-restraints excluded: chain H residue 132 TYR Chi-restraints excluded: chain H residue 145 THR Chi-restraints excluded: chain L residue 30 VAL Chi-restraints excluded: chain L residue 61 LEU Chi-restraints excluded: chain L residue 80 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 221 random chunks: chunk 35 optimal weight: 2.9990 chunk 18 optimal weight: 9.9990 chunk 147 optimal weight: 0.9980 chunk 127 optimal weight: 0.0980 chunk 63 optimal weight: 10.0000 chunk 132 optimal weight: 8.9990 chunk 1 optimal weight: 0.9990 chunk 219 optimal weight: 9.9990 chunk 144 optimal weight: 7.9990 chunk 213 optimal weight: 7.9990 chunk 34 optimal weight: 0.5980 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 259 GLN ** A 290 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 292 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 497 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 570 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 497 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 430 GLN C 597 GLN C 608 GLN ** C 700 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 709 ASN ** D 253 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 496 ASN ** F 430 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3607 r_free = 0.3607 target = 0.132196 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.120681 restraints weight = 32193.356| |-----------------------------------------------------------------------------| r_work (start): 0.3452 rms_B_bonded: 1.84 r_work: 0.3383 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.3286 rms_B_bonded: 4.09 restraints_weight: 0.2500 r_work (final): 0.3286 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7641 moved from start: 0.2817 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 18185 Z= 0.095 Angle : 0.522 6.173 24765 Z= 0.271 Chirality : 0.041 0.252 2550 Planarity : 0.004 0.036 3295 Dihedral : 5.526 58.537 2441 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 7.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.69 % Favored : 97.31 % Rotamer: Outliers : 1.92 % Allowed : 12.10 % Favored : 85.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.90 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.97 (0.17), residues: 2195 helix: -3.63 (0.43), residues: 86 sheet: -0.40 (0.22), residues: 515 loop : -0.54 (0.14), residues: 1594 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG H 91 TYR 0.017 0.001 TYR A 674 PHE 0.012 0.001 PHE H 99 TRP 0.022 0.001 TRP H 140 HIS 0.003 0.001 HIS C 255 Details of bonding type rmsd covalent geometry : bond 0.00214 (18182) covalent geometry : angle 0.52219 (24759) SS BOND : bond 0.00187 ( 3) SS BOND : angle 0.80809 ( 6) hydrogen bonds : bond 0.02666 ( 237) hydrogen bonds : angle 6.23607 ( 486) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4390 Ramachandran restraints generated. 2195 Oldfield, 0 Emsley, 2195 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4390 Ramachandran restraints generated. 2195 Oldfield, 0 Emsley, 2195 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 335 residues out of total 1927 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 298 time to evaluate : 0.737 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 347 ASP cc_start: 0.7261 (t70) cc_final: 0.6320 (t0) REVERT: A 565 GLU cc_start: 0.6630 (mp0) cc_final: 0.6366 (mp0) REVERT: B 456 GLN cc_start: 0.7812 (mt0) cc_final: 0.7501 (mm110) REVERT: B 484 TYR cc_start: 0.7940 (t80) cc_final: 0.7609 (t80) REVERT: C 391 ARG cc_start: 0.6642 (ttm110) cc_final: 0.5568 (tpt170) REVERT: D 613 TYR cc_start: 0.8298 (m-80) cc_final: 0.7330 (m-80) REVERT: D 640 MET cc_start: 0.7529 (mtp) cc_final: 0.7289 (mtp) REVERT: E 575 GLU cc_start: 0.7304 (mm-30) cc_final: 0.7080 (mm-30) REVERT: F 391 ARG cc_start: 0.8151 (ttm110) cc_final: 0.7644 (ttm110) REVERT: F 562 ASN cc_start: 0.8085 (p0) cc_final: 0.7736 (p0) REVERT: F 679 VAL cc_start: 0.7735 (t) cc_final: 0.7498 (p) REVERT: H 72 TYR cc_start: 0.7618 (OUTLIER) cc_final: 0.7059 (p90) REVERT: H 101 GLN cc_start: 0.6971 (tm-30) cc_final: 0.6500 (tm-30) outliers start: 37 outliers final: 26 residues processed: 317 average time/residue: 0.1364 time to fit residues: 66.6462 Evaluate side-chains 293 residues out of total 1927 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 266 time to evaluate : 0.678 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 420 VAL Chi-restraints excluded: chain B residue 435 LEU Chi-restraints excluded: chain B residue 447 LEU Chi-restraints excluded: chain B residue 458 GLN Chi-restraints excluded: chain B residue 470 ASN Chi-restraints excluded: chain B residue 479 ILE Chi-restraints excluded: chain B residue 605 MET Chi-restraints excluded: chain C residue 235 LEU Chi-restraints excluded: chain C residue 389 VAL Chi-restraints excluded: chain C residue 435 LEU Chi-restraints excluded: chain C residue 488 ARG Chi-restraints excluded: chain C residue 592 GLN Chi-restraints excluded: chain C residue 593 THR Chi-restraints excluded: chain C residue 699 ILE Chi-restraints excluded: chain C residue 729 THR Chi-restraints excluded: chain E residue 473 VAL Chi-restraints excluded: chain E residue 479 ILE Chi-restraints excluded: chain E residue 537 LEU Chi-restraints excluded: chain F residue 564 GLU Chi-restraints excluded: chain F residue 593 THR Chi-restraints excluded: chain H residue 32 GLN Chi-restraints excluded: chain H residue 56 VAL Chi-restraints excluded: chain H residue 72 TYR Chi-restraints excluded: chain H residue 123 SER Chi-restraints excluded: chain L residue 25 THR Chi-restraints excluded: chain L residue 80 VAL Chi-restraints excluded: chain L residue 117 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 221 random chunks: chunk 165 optimal weight: 9.9990 chunk 96 optimal weight: 7.9990 chunk 129 optimal weight: 20.0000 chunk 44 optimal weight: 6.9990 chunk 195 optimal weight: 8.9990 chunk 216 optimal weight: 8.9990 chunk 119 optimal weight: 0.8980 chunk 11 optimal weight: 5.9990 chunk 15 optimal weight: 9.9990 chunk 97 optimal weight: 0.8980 chunk 121 optimal weight: 10.0000 overall best weight: 4.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 290 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 497 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 570 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 470 ASN ** B 497 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 305 ASN ** D 253 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 272 ASN ** D 290 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 519 ASN ** F 262 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 430 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 60 GLN ** L 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3581 r_free = 0.3581 target = 0.130133 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.118634 restraints weight = 32321.316| |-----------------------------------------------------------------------------| r_work (start): 0.3421 rms_B_bonded: 1.84 r_work: 0.3351 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.3253 rms_B_bonded: 4.07 restraints_weight: 0.2500 r_work (final): 0.3253 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7690 moved from start: 0.2903 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 18185 Z= 0.169 Angle : 0.575 7.905 24765 Z= 0.300 Chirality : 0.043 0.230 2550 Planarity : 0.004 0.037 3295 Dihedral : 5.687 58.686 2435 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 9.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.64 % Favored : 96.36 % Rotamer: Outliers : 3.17 % Allowed : 12.20 % Favored : 84.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.90 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.03 (0.17), residues: 2195 helix: -3.72 (0.42), residues: 86 sheet: -0.41 (0.22), residues: 497 loop : -0.59 (0.14), residues: 1612 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG H 117 TYR 0.016 0.002 TYR C 706 PHE 0.022 0.002 PHE H 99 TRP 0.021 0.002 TRP A 619 HIS 0.005 0.001 HIS F 527 Details of bonding type rmsd covalent geometry : bond 0.00395 (18182) covalent geometry : angle 0.57442 (24759) SS BOND : bond 0.00432 ( 3) SS BOND : angle 0.90206 ( 6) hydrogen bonds : bond 0.02933 ( 237) hydrogen bonds : angle 6.42482 ( 486) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4390 Ramachandran restraints generated. 2195 Oldfield, 0 Emsley, 2195 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4390 Ramachandran restraints generated. 2195 Oldfield, 0 Emsley, 2195 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 335 residues out of total 1927 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 274 time to evaluate : 0.706 Fit side-chains revert: symmetry clash REVERT: A 347 ASP cc_start: 0.7317 (t70) cc_final: 0.6458 (t0) REVERT: A 565 GLU cc_start: 0.6679 (mp0) cc_final: 0.6421 (mp0) REVERT: B 456 GLN cc_start: 0.7950 (mt0) cc_final: 0.7605 (mm110) REVERT: C 391 ARG cc_start: 0.6622 (ttm110) cc_final: 0.5550 (tpt170) REVERT: D 613 TYR cc_start: 0.8337 (m-80) cc_final: 0.7366 (m-80) REVERT: D 640 MET cc_start: 0.7628 (mtp) cc_final: 0.7324 (mtp) REVERT: E 452 ASN cc_start: 0.8277 (OUTLIER) cc_final: 0.7798 (t0) REVERT: F 391 ARG cc_start: 0.8120 (ttm110) cc_final: 0.7601 (ttm110) REVERT: F 562 ASN cc_start: 0.8068 (p0) cc_final: 0.7722 (p0) REVERT: F 679 VAL cc_start: 0.7746 (t) cc_final: 0.7527 (p) REVERT: H 72 TYR cc_start: 0.7846 (OUTLIER) cc_final: 0.7036 (p90) REVERT: H 101 GLN cc_start: 0.6990 (tm-30) cc_final: 0.6539 (tm-30) outliers start: 61 outliers final: 44 residues processed: 304 average time/residue: 0.1368 time to fit residues: 64.0008 Evaluate side-chains 313 residues out of total 1927 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 267 time to evaluate : 0.538 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 389 VAL Chi-restraints excluded: chain A residue 420 VAL Chi-restraints excluded: chain B residue 447 LEU Chi-restraints excluded: chain B residue 458 GLN Chi-restraints excluded: chain B residue 479 ILE Chi-restraints excluded: chain B residue 605 MET Chi-restraints excluded: chain C residue 239 VAL Chi-restraints excluded: chain C residue 389 VAL Chi-restraints excluded: chain C residue 392 SER Chi-restraints excluded: chain C residue 435 LEU Chi-restraints excluded: chain C residue 488 ARG Chi-restraints excluded: chain C residue 494 THR Chi-restraints excluded: chain C residue 592 GLN Chi-restraints excluded: chain C residue 593 THR Chi-restraints excluded: chain C residue 680 SER Chi-restraints excluded: chain C residue 681 VAL Chi-restraints excluded: chain C residue 699 ILE Chi-restraints excluded: chain C residue 729 THR Chi-restraints excluded: chain D residue 370 ASP Chi-restraints excluded: chain D residue 489 VAL Chi-restraints excluded: chain D residue 567 LYS Chi-restraints excluded: chain D residue 593 THR Chi-restraints excluded: chain D residue 672 THR Chi-restraints excluded: chain E residue 452 ASN Chi-restraints excluded: chain E residue 473 VAL Chi-restraints excluded: chain E residue 479 ILE Chi-restraints excluded: chain E residue 493 VAL Chi-restraints excluded: chain E residue 537 LEU Chi-restraints excluded: chain F residue 264 THR Chi-restraints excluded: chain F residue 414 SER Chi-restraints excluded: chain F residue 465 VAL Chi-restraints excluded: chain F residue 564 GLU Chi-restraints excluded: chain F residue 593 THR Chi-restraints excluded: chain F residue 702 THR Chi-restraints excluded: chain F residue 717 THR Chi-restraints excluded: chain H residue 32 GLN Chi-restraints excluded: chain H residue 52 VAL Chi-restraints excluded: chain H residue 72 TYR Chi-restraints excluded: chain H residue 115 CYS Chi-restraints excluded: chain H residue 123 SER Chi-restraints excluded: chain H residue 139 VAL Chi-restraints excluded: chain L residue 25 THR Chi-restraints excluded: chain L residue 30 VAL Chi-restraints excluded: chain L residue 80 VAL Chi-restraints excluded: chain L residue 111 GLN Chi-restraints excluded: chain L residue 117 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 221 random chunks: chunk 12 optimal weight: 10.0000 chunk 161 optimal weight: 9.9990 chunk 162 optimal weight: 7.9990 chunk 88 optimal weight: 6.9990 chunk 16 optimal weight: 7.9990 chunk 17 optimal weight: 0.0060 chunk 164 optimal weight: 5.9990 chunk 32 optimal weight: 9.9990 chunk 163 optimal weight: 0.9990 chunk 207 optimal weight: 10.0000 chunk 68 optimal weight: 8.9990 overall best weight: 4.4004 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 290 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 497 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 570 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 673 GLN ** B 497 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 253 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 272 ASN ** D 290 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 598 ASN F 262 ASN ** F 430 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 615 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 60 GLN ** L 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.130223 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.118695 restraints weight = 32131.184| |-----------------------------------------------------------------------------| r_work (start): 0.3423 rms_B_bonded: 1.83 r_work: 0.3354 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.3257 rms_B_bonded: 4.05 restraints_weight: 0.2500 r_work (final): 0.3257 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7688 moved from start: 0.3046 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 18185 Z= 0.161 Angle : 0.566 13.176 24765 Z= 0.293 Chirality : 0.042 0.219 2550 Planarity : 0.004 0.037 3295 Dihedral : 5.666 59.204 2435 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 9.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.78 % Favored : 96.22 % Rotamer: Outliers : 3.27 % Allowed : 12.82 % Favored : 83.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.90 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.02 (0.17), residues: 2195 helix: -3.65 (0.45), residues: 80 sheet: -0.39 (0.22), residues: 506 loop : -0.61 (0.15), residues: 1609 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 533 TYR 0.015 0.002 TYR C 705 PHE 0.019 0.002 PHE H 99 TRP 0.023 0.002 TRP A 619 HIS 0.004 0.001 HIS F 527 Details of bonding type rmsd covalent geometry : bond 0.00379 (18182) covalent geometry : angle 0.56619 (24759) SS BOND : bond 0.00387 ( 3) SS BOND : angle 0.82993 ( 6) hydrogen bonds : bond 0.02824 ( 237) hydrogen bonds : angle 6.40909 ( 486) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4390 Ramachandran restraints generated. 2195 Oldfield, 0 Emsley, 2195 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4390 Ramachandran restraints generated. 2195 Oldfield, 0 Emsley, 2195 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 327 residues out of total 1927 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 264 time to evaluate : 0.521 Fit side-chains revert: symmetry clash REVERT: A 347 ASP cc_start: 0.7414 (t70) cc_final: 0.6541 (t0) REVERT: A 565 GLU cc_start: 0.6655 (mp0) cc_final: 0.6407 (mp0) REVERT: B 456 GLN cc_start: 0.7968 (mt0) cc_final: 0.7629 (mm110) REVERT: B 484 TYR cc_start: 0.7932 (t80) cc_final: 0.7658 (t80) REVERT: D 533 ARG cc_start: 0.7099 (ptt-90) cc_final: 0.6632 (ptt-90) REVERT: D 613 TYR cc_start: 0.8362 (m-80) cc_final: 0.7392 (m-80) REVERT: D 640 MET cc_start: 0.7651 (mtp) cc_final: 0.7360 (mtp) REVERT: E 452 ASN cc_start: 0.8282 (OUTLIER) cc_final: 0.7853 (t0) REVERT: E 575 GLU cc_start: 0.7871 (mm-30) cc_final: 0.7526 (mm-30) REVERT: F 391 ARG cc_start: 0.8116 (ttm110) cc_final: 0.7588 (ttm110) REVERT: F 562 ASN cc_start: 0.8065 (p0) cc_final: 0.7726 (p0) REVERT: H 66 TRP cc_start: 0.7890 (t60) cc_final: 0.7602 (t60) REVERT: H 72 TYR cc_start: 0.7840 (OUTLIER) cc_final: 0.6915 (p90) REVERT: H 101 GLN cc_start: 0.6982 (tm-30) cc_final: 0.6559 (tm-30) outliers start: 63 outliers final: 53 residues processed: 302 average time/residue: 0.1250 time to fit residues: 58.3870 Evaluate side-chains 309 residues out of total 1927 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 254 time to evaluate : 0.695 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 389 VAL Chi-restraints excluded: chain A residue 420 VAL Chi-restraints excluded: chain A residue 640 MET Chi-restraints excluded: chain A residue 679 VAL Chi-restraints excluded: chain B residue 435 LEU Chi-restraints excluded: chain B residue 447 LEU Chi-restraints excluded: chain B residue 451 ILE Chi-restraints excluded: chain B residue 458 GLN Chi-restraints excluded: chain B residue 479 ILE Chi-restraints excluded: chain B residue 605 MET Chi-restraints excluded: chain C residue 235 LEU Chi-restraints excluded: chain C residue 373 MET Chi-restraints excluded: chain C residue 389 VAL Chi-restraints excluded: chain C residue 392 SER Chi-restraints excluded: chain C residue 435 LEU Chi-restraints excluded: chain C residue 465 VAL Chi-restraints excluded: chain C residue 488 ARG Chi-restraints excluded: chain C residue 494 THR Chi-restraints excluded: chain C residue 568 THR Chi-restraints excluded: chain C residue 592 GLN Chi-restraints excluded: chain C residue 593 THR Chi-restraints excluded: chain C residue 680 SER Chi-restraints excluded: chain C residue 681 VAL Chi-restraints excluded: chain C residue 699 ILE Chi-restraints excluded: chain C residue 729 THR Chi-restraints excluded: chain D residue 370 ASP Chi-restraints excluded: chain D residue 489 VAL Chi-restraints excluded: chain D residue 567 LYS Chi-restraints excluded: chain D residue 593 THR Chi-restraints excluded: chain D residue 672 THR Chi-restraints excluded: chain E residue 452 ASN Chi-restraints excluded: chain E residue 473 VAL Chi-restraints excluded: chain E residue 479 ILE Chi-restraints excluded: chain E residue 493 VAL Chi-restraints excluded: chain E residue 537 LEU Chi-restraints excluded: chain F residue 264 THR Chi-restraints excluded: chain F residue 278 SER Chi-restraints excluded: chain F residue 344 VAL Chi-restraints excluded: chain F residue 414 SER Chi-restraints excluded: chain F residue 564 GLU Chi-restraints excluded: chain F residue 593 THR Chi-restraints excluded: chain F residue 702 THR Chi-restraints excluded: chain F residue 717 THR Chi-restraints excluded: chain H residue 32 GLN Chi-restraints excluded: chain H residue 52 VAL Chi-restraints excluded: chain H residue 69 VAL Chi-restraints excluded: chain H residue 72 TYR Chi-restraints excluded: chain H residue 94 SER Chi-restraints excluded: chain H residue 123 SER Chi-restraints excluded: chain H residue 139 VAL Chi-restraints excluded: chain L residue 25 THR Chi-restraints excluded: chain L residue 30 VAL Chi-restraints excluded: chain L residue 80 VAL Chi-restraints excluded: chain L residue 111 GLN Chi-restraints excluded: chain L residue 117 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 221 random chunks: chunk 179 optimal weight: 20.0000 chunk 120 optimal weight: 20.0000 chunk 163 optimal weight: 0.9990 chunk 119 optimal weight: 9.9990 chunk 50 optimal weight: 40.0000 chunk 85 optimal weight: 9.9990 chunk 134 optimal weight: 2.9990 chunk 214 optimal weight: 9.9990 chunk 64 optimal weight: 10.0000 chunk 33 optimal weight: 10.0000 chunk 166 optimal weight: 9.9990 overall best weight: 6.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 290 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 497 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 570 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 497 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 628 ASN C 630 HIS ** D 253 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 272 ASN ** D 290 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 598 ASN ** F 430 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 615 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 630 HIS ** L 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3557 r_free = 0.3557 target = 0.128429 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.116915 restraints weight = 32566.078| |-----------------------------------------------------------------------------| r_work (start): 0.3393 rms_B_bonded: 1.83 r_work: 0.3324 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.3226 rms_B_bonded: 4.05 restraints_weight: 0.2500 r_work (final): 0.3226 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7719 moved from start: 0.3117 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 18185 Z= 0.231 Angle : 0.639 14.520 24765 Z= 0.333 Chirality : 0.045 0.237 2550 Planarity : 0.005 0.040 3295 Dihedral : 6.047 58.302 2435 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 10.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.97 % Favored : 95.03 % Rotamer: Outliers : 3.89 % Allowed : 13.19 % Favored : 82.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.90 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.25 (0.17), residues: 2195 helix: -3.67 (0.46), residues: 72 sheet: -0.52 (0.22), residues: 524 loop : -0.81 (0.15), residues: 1599 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG H 117 TYR 0.021 0.002 TYR E 443 PHE 0.026 0.002 PHE H 99 TRP 0.020 0.002 TRP C 306 HIS 0.007 0.002 HIS C 290 Details of bonding type rmsd covalent geometry : bond 0.00541 (18182) covalent geometry : angle 0.63925 (24759) SS BOND : bond 0.00801 ( 3) SS BOND : angle 1.10903 ( 6) hydrogen bonds : bond 0.03240 ( 237) hydrogen bonds : angle 6.76926 ( 486) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4390 Ramachandran restraints generated. 2195 Oldfield, 0 Emsley, 2195 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4390 Ramachandran restraints generated. 2195 Oldfield, 0 Emsley, 2195 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 333 residues out of total 1927 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 258 time to evaluate : 0.761 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 347 ASP cc_start: 0.7444 (t70) cc_final: 0.6513 (t0) REVERT: A 565 GLU cc_start: 0.6695 (mp0) cc_final: 0.6421 (mp0) REVERT: B 436 MET cc_start: 0.7909 (ptp) cc_final: 0.7258 (ptp) REVERT: B 456 GLN cc_start: 0.8067 (mt0) cc_final: 0.7709 (mm110) REVERT: B 470 ASN cc_start: 0.7684 (OUTLIER) cc_final: 0.7402 (m-40) REVERT: D 340 SER cc_start: 0.7374 (OUTLIER) cc_final: 0.6971 (p) REVERT: D 533 ARG cc_start: 0.7127 (ptt-90) cc_final: 0.6665 (ptt-90) REVERT: D 550 ARG cc_start: 0.6865 (OUTLIER) cc_final: 0.6262 (ttt-90) REVERT: D 613 TYR cc_start: 0.8376 (m-80) cc_final: 0.7484 (m-80) REVERT: D 640 MET cc_start: 0.7680 (mtp) cc_final: 0.7479 (mtp) REVERT: E 452 ASN cc_start: 0.8234 (OUTLIER) cc_final: 0.7843 (t0) REVERT: E 575 GLU cc_start: 0.7890 (mm-30) cc_final: 0.7586 (mm-30) REVERT: F 391 ARG cc_start: 0.8102 (ttm110) cc_final: 0.7573 (ttm110) REVERT: F 562 ASN cc_start: 0.8056 (p0) cc_final: 0.7714 (p0) REVERT: H 66 TRP cc_start: 0.7888 (t60) cc_final: 0.7606 (t60) REVERT: H 72 TYR cc_start: 0.7971 (OUTLIER) cc_final: 0.6742 (p90) REVERT: H 101 GLN cc_start: 0.6947 (tm-30) cc_final: 0.6516 (tm-30) REVERT: L 71 TYR cc_start: 0.7132 (p90) cc_final: 0.6900 (p90) outliers start: 75 outliers final: 53 residues processed: 303 average time/residue: 0.1338 time to fit residues: 62.9894 Evaluate side-chains 310 residues out of total 1927 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 252 time to evaluate : 0.698 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 389 VAL Chi-restraints excluded: chain A residue 420 VAL Chi-restraints excluded: chain A residue 640 MET Chi-restraints excluded: chain A residue 679 VAL Chi-restraints excluded: chain B residue 435 LEU Chi-restraints excluded: chain B residue 447 LEU Chi-restraints excluded: chain B residue 458 GLN Chi-restraints excluded: chain B residue 470 ASN Chi-restraints excluded: chain B residue 479 ILE Chi-restraints excluded: chain B residue 605 MET Chi-restraints excluded: chain B residue 625 THR Chi-restraints excluded: chain C residue 373 MET Chi-restraints excluded: chain C residue 389 VAL Chi-restraints excluded: chain C residue 392 SER Chi-restraints excluded: chain C residue 435 LEU Chi-restraints excluded: chain C residue 465 VAL Chi-restraints excluded: chain C residue 488 ARG Chi-restraints excluded: chain C residue 494 THR Chi-restraints excluded: chain C residue 568 THR Chi-restraints excluded: chain C residue 592 GLN Chi-restraints excluded: chain C residue 593 THR Chi-restraints excluded: chain C residue 680 SER Chi-restraints excluded: chain C residue 681 VAL Chi-restraints excluded: chain C residue 699 ILE Chi-restraints excluded: chain C residue 729 THR Chi-restraints excluded: chain D residue 340 SER Chi-restraints excluded: chain D residue 489 VAL Chi-restraints excluded: chain D residue 550 ARG Chi-restraints excluded: chain D residue 593 THR Chi-restraints excluded: chain D residue 672 THR Chi-restraints excluded: chain E residue 452 ASN Chi-restraints excluded: chain E residue 461 LEU Chi-restraints excluded: chain E residue 473 VAL Chi-restraints excluded: chain E residue 479 ILE Chi-restraints excluded: chain E residue 493 VAL Chi-restraints excluded: chain E residue 537 LEU Chi-restraints excluded: chain F residue 264 THR Chi-restraints excluded: chain F residue 278 SER Chi-restraints excluded: chain F residue 344 VAL Chi-restraints excluded: chain F residue 414 SER Chi-restraints excluded: chain F residue 465 VAL Chi-restraints excluded: chain F residue 564 GLU Chi-restraints excluded: chain F residue 702 THR Chi-restraints excluded: chain F residue 717 THR Chi-restraints excluded: chain H residue 32 GLN Chi-restraints excluded: chain H residue 52 VAL Chi-restraints excluded: chain H residue 69 VAL Chi-restraints excluded: chain H residue 72 TYR Chi-restraints excluded: chain H residue 94 SER Chi-restraints excluded: chain H residue 115 CYS Chi-restraints excluded: chain H residue 123 SER Chi-restraints excluded: chain H residue 145 THR Chi-restraints excluded: chain L residue 25 THR Chi-restraints excluded: chain L residue 30 VAL Chi-restraints excluded: chain L residue 38 VAL Chi-restraints excluded: chain L residue 80 VAL Chi-restraints excluded: chain L residue 111 GLN Chi-restraints excluded: chain L residue 117 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 221 random chunks: chunk 130 optimal weight: 6.9990 chunk 163 optimal weight: 0.7980 chunk 13 optimal weight: 6.9990 chunk 55 optimal weight: 10.0000 chunk 37 optimal weight: 7.9990 chunk 6 optimal weight: 10.0000 chunk 21 optimal weight: 5.9990 chunk 117 optimal weight: 20.0000 chunk 182 optimal weight: 7.9990 chunk 139 optimal weight: 20.0000 chunk 114 optimal weight: 8.9990 overall best weight: 5.7588 ------------------------------------------------------------------------------- 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 497 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 570 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 497 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 628 ASN C 630 HIS ** D 253 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 272 ASN ** D 290 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 598 ASN E 442 GLN ** F 430 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 615 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.128568 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.116969 restraints weight = 32450.118| |-----------------------------------------------------------------------------| r_work (start): 0.3400 rms_B_bonded: 1.84 r_work: 0.3330 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.3232 rms_B_bonded: 4.09 restraints_weight: 0.2500 r_work (final): 0.3232 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7713 moved from start: 0.3201 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 18185 Z= 0.200 Angle : 0.613 13.627 24765 Z= 0.319 Chirality : 0.044 0.226 2550 Planarity : 0.005 0.040 3295 Dihedral : 5.970 59.059 2435 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 9.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.10 % Favored : 94.90 % Rotamer: Outliers : 3.58 % Allowed : 13.91 % Favored : 82.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.90 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.31 (0.17), residues: 2195 helix: -3.65 (0.47), residues: 71 sheet: -0.58 (0.22), residues: 524 loop : -0.86 (0.15), residues: 1600 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG D 476 TYR 0.015 0.002 TYR C 706 PHE 0.022 0.002 PHE H 99 TRP 0.018 0.002 TRP C 306 HIS 0.005 0.001 HIS A 290 Details of bonding type rmsd covalent geometry : bond 0.00469 (18182) covalent geometry : angle 0.61323 (24759) SS BOND : bond 0.00477 ( 3) SS BOND : angle 1.00321 ( 6) hydrogen bonds : bond 0.03059 ( 237) hydrogen bonds : angle 6.71349 ( 486) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4390 Ramachandran restraints generated. 2195 Oldfield, 0 Emsley, 2195 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4390 Ramachandran restraints generated. 2195 Oldfield, 0 Emsley, 2195 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 325 residues out of total 1927 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 256 time to evaluate : 0.701 Fit side-chains revert: symmetry clash REVERT: A 347 ASP cc_start: 0.7438 (t70) cc_final: 0.6518 (t0) REVERT: A 565 GLU cc_start: 0.6711 (mp0) cc_final: 0.6450 (mp0) REVERT: B 436 MET cc_start: 0.7868 (ptp) cc_final: 0.7216 (ptp) REVERT: B 456 GLN cc_start: 0.8039 (mt0) cc_final: 0.7680 (mm110) REVERT: B 470 ASN cc_start: 0.7727 (OUTLIER) cc_final: 0.7428 (m-40) REVERT: B 484 TYR cc_start: 0.7929 (t80) cc_final: 0.7686 (t80) REVERT: D 340 SER cc_start: 0.7354 (OUTLIER) cc_final: 0.6956 (p) REVERT: D 533 ARG cc_start: 0.7099 (ptt-90) cc_final: 0.6619 (ptt-90) REVERT: D 640 MET cc_start: 0.7663 (mtp) cc_final: 0.7450 (mtp) REVERT: E 452 ASN cc_start: 0.8240 (OUTLIER) cc_final: 0.7853 (t0) REVERT: E 575 GLU cc_start: 0.7865 (mm-30) cc_final: 0.7575 (mm-30) REVERT: F 391 ARG cc_start: 0.8114 (ttm110) cc_final: 0.7588 (ttm110) REVERT: F 562 ASN cc_start: 0.8055 (p0) cc_final: 0.7706 (p0) REVERT: H 66 TRP cc_start: 0.7912 (t60) cc_final: 0.7639 (t60) REVERT: H 72 TYR cc_start: 0.7938 (OUTLIER) cc_final: 0.6820 (p90) REVERT: L 69 LEU cc_start: 0.7730 (tp) cc_final: 0.7480 (tp) outliers start: 69 outliers final: 56 residues processed: 296 average time/residue: 0.1291 time to fit residues: 59.9786 Evaluate side-chains 311 residues out of total 1927 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 251 time to evaluate : 0.697 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 243 SER Chi-restraints excluded: chain A residue 389 VAL Chi-restraints excluded: chain A residue 420 VAL Chi-restraints excluded: chain A residue 679 VAL Chi-restraints excluded: chain B residue 435 LEU Chi-restraints excluded: chain B residue 447 LEU Chi-restraints excluded: chain B residue 458 GLN Chi-restraints excluded: chain B residue 470 ASN Chi-restraints excluded: chain B residue 479 ILE Chi-restraints excluded: chain B residue 605 MET Chi-restraints excluded: chain B residue 609 ASP Chi-restraints excluded: chain B residue 625 THR Chi-restraints excluded: chain C residue 373 MET Chi-restraints excluded: chain C residue 389 VAL Chi-restraints excluded: chain C residue 392 SER Chi-restraints excluded: chain C residue 435 LEU Chi-restraints excluded: chain C residue 465 VAL Chi-restraints excluded: chain C residue 488 ARG Chi-restraints excluded: chain C residue 494 THR Chi-restraints excluded: chain C residue 568 THR Chi-restraints excluded: chain C residue 592 GLN Chi-restraints excluded: chain C residue 593 THR Chi-restraints excluded: chain C residue 630 HIS Chi-restraints excluded: chain C residue 680 SER Chi-restraints excluded: chain C residue 681 VAL Chi-restraints excluded: chain C residue 699 ILE Chi-restraints excluded: chain C residue 729 THR Chi-restraints excluded: chain D residue 340 SER Chi-restraints excluded: chain D residue 489 VAL Chi-restraints excluded: chain D residue 593 THR Chi-restraints excluded: chain D residue 672 THR Chi-restraints excluded: chain E residue 452 ASN Chi-restraints excluded: chain E residue 473 VAL Chi-restraints excluded: chain E residue 479 ILE Chi-restraints excluded: chain E residue 493 VAL Chi-restraints excluded: chain E residue 537 LEU Chi-restraints excluded: chain F residue 264 THR Chi-restraints excluded: chain F residue 278 SER Chi-restraints excluded: chain F residue 325 VAL Chi-restraints excluded: chain F residue 344 VAL Chi-restraints excluded: chain F residue 414 SER Chi-restraints excluded: chain F residue 465 VAL Chi-restraints excluded: chain F residue 564 GLU Chi-restraints excluded: chain F residue 702 THR Chi-restraints excluded: chain F residue 717 THR Chi-restraints excluded: chain H residue 32 GLN Chi-restraints excluded: chain H residue 52 VAL Chi-restraints excluded: chain H residue 56 VAL Chi-restraints excluded: chain H residue 72 TYR Chi-restraints excluded: chain H residue 94 SER Chi-restraints excluded: chain H residue 115 CYS Chi-restraints excluded: chain H residue 123 SER Chi-restraints excluded: chain H residue 145 THR Chi-restraints excluded: chain L residue 25 THR Chi-restraints excluded: chain L residue 30 VAL Chi-restraints excluded: chain L residue 38 VAL Chi-restraints excluded: chain L residue 61 LEU Chi-restraints excluded: chain L residue 80 VAL Chi-restraints excluded: chain L residue 111 GLN Chi-restraints excluded: chain L residue 117 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 221 random chunks: chunk 160 optimal weight: 10.0000 chunk 155 optimal weight: 20.0000 chunk 41 optimal weight: 5.9990 chunk 38 optimal weight: 6.9990 chunk 133 optimal weight: 0.2980 chunk 49 optimal weight: 3.9990 chunk 192 optimal weight: 2.9990 chunk 72 optimal weight: 8.9990 chunk 122 optimal weight: 20.0000 chunk 169 optimal weight: 10.0000 chunk 134 optimal weight: 3.9990 overall best weight: 3.4588 ------------------------------------------------------------------------------- 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 497 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 570 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 497 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 630 HIS ** D 253 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 272 ASN ** D 290 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 598 ASN E 442 GLN ** F 430 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 615 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.130298 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.118777 restraints weight = 32305.857| |-----------------------------------------------------------------------------| r_work (start): 0.3424 rms_B_bonded: 1.84 r_work: 0.3355 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.3257 rms_B_bonded: 4.07 restraints_weight: 0.2500 r_work (final): 0.3257 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7689 moved from start: 0.3253 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 18185 Z= 0.140 Angle : 0.561 10.428 24765 Z= 0.291 Chirality : 0.042 0.213 2550 Planarity : 0.004 0.039 3295 Dihedral : 5.725 59.536 2435 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 8.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.19 % Favored : 95.81 % Rotamer: Outliers : 3.12 % Allowed : 14.75 % Favored : 82.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.90 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.19 (0.17), residues: 2195 helix: -3.60 (0.48), residues: 71 sheet: -0.52 (0.22), residues: 522 loop : -0.76 (0.15), residues: 1602 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG D 476 TYR 0.012 0.002 TYR A 674 PHE 0.017 0.002 PHE H 99 TRP 0.027 0.002 TRP A 619 HIS 0.008 0.001 HIS C 630 Details of bonding type rmsd covalent geometry : bond 0.00326 (18182) covalent geometry : angle 0.56076 (24759) SS BOND : bond 0.00339 ( 3) SS BOND : angle 0.78868 ( 6) hydrogen bonds : bond 0.02741 ( 237) hydrogen bonds : angle 6.46753 ( 486) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4390 Ramachandran restraints generated. 2195 Oldfield, 0 Emsley, 2195 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4390 Ramachandran restraints generated. 2195 Oldfield, 0 Emsley, 2195 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 326 residues out of total 1927 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 266 time to evaluate : 0.859 Fit side-chains revert: symmetry clash REVERT: A 347 ASP cc_start: 0.7404 (t70) cc_final: 0.6451 (t0) REVERT: A 565 GLU cc_start: 0.6729 (mp0) cc_final: 0.6488 (mp0) REVERT: B 456 GLN cc_start: 0.7973 (mt0) cc_final: 0.7645 (mm110) REVERT: B 484 TYR cc_start: 0.7898 (t80) cc_final: 0.7668 (t80) REVERT: B 529 GLU cc_start: 0.6350 (mt-10) cc_final: 0.5989 (mt-10) REVERT: C 559 MET cc_start: 0.6454 (ttt) cc_final: 0.6083 (tpp) REVERT: D 340 SER cc_start: 0.7336 (OUTLIER) cc_final: 0.6921 (p) REVERT: D 640 MET cc_start: 0.7660 (mtp) cc_final: 0.7397 (mtp) REVERT: D 657 ASP cc_start: 0.8012 (p0) cc_final: 0.7718 (t0) REVERT: E 452 ASN cc_start: 0.8186 (OUTLIER) cc_final: 0.7793 (t0) REVERT: E 575 GLU cc_start: 0.7774 (mm-30) cc_final: 0.7510 (mm-30) REVERT: F 228 TRP cc_start: 0.7517 (t-100) cc_final: 0.7261 (t-100) REVERT: F 391 ARG cc_start: 0.8106 (ttm110) cc_final: 0.7595 (ttm110) REVERT: F 562 ASN cc_start: 0.8062 (p0) cc_final: 0.7699 (p0) REVERT: F 706 TYR cc_start: 0.7854 (t80) cc_final: 0.7398 (t80) REVERT: H 66 TRP cc_start: 0.7913 (t60) cc_final: 0.7647 (t60) REVERT: H 72 TYR cc_start: 0.7895 (OUTLIER) cc_final: 0.6891 (p90) REVERT: L 85 SER cc_start: 0.7579 (t) cc_final: 0.7237 (p) outliers start: 60 outliers final: 55 residues processed: 302 average time/residue: 0.1323 time to fit residues: 62.6746 Evaluate side-chains 315 residues out of total 1927 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 257 time to evaluate : 0.796 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 243 SER Chi-restraints excluded: chain A residue 389 VAL Chi-restraints excluded: chain A residue 420 VAL Chi-restraints excluded: chain A residue 679 VAL Chi-restraints excluded: chain B residue 435 LEU Chi-restraints excluded: chain B residue 447 LEU Chi-restraints excluded: chain B residue 451 ILE Chi-restraints excluded: chain B residue 458 GLN Chi-restraints excluded: chain B residue 470 ASN Chi-restraints excluded: chain B residue 479 ILE Chi-restraints excluded: chain B residue 605 MET Chi-restraints excluded: chain C residue 373 MET Chi-restraints excluded: chain C residue 389 VAL Chi-restraints excluded: chain C residue 392 SER Chi-restraints excluded: chain C residue 435 LEU Chi-restraints excluded: chain C residue 465 VAL Chi-restraints excluded: chain C residue 488 ARG Chi-restraints excluded: chain C residue 494 THR Chi-restraints excluded: chain C residue 568 THR Chi-restraints excluded: chain C residue 592 GLN Chi-restraints excluded: chain C residue 593 THR Chi-restraints excluded: chain C residue 680 SER Chi-restraints excluded: chain C residue 681 VAL Chi-restraints excluded: chain C residue 699 ILE Chi-restraints excluded: chain C residue 729 THR Chi-restraints excluded: chain D residue 340 SER Chi-restraints excluded: chain D residue 489 VAL Chi-restraints excluded: chain D residue 567 LYS Chi-restraints excluded: chain D residue 593 THR Chi-restraints excluded: chain D residue 672 THR Chi-restraints excluded: chain E residue 452 ASN Chi-restraints excluded: chain E residue 461 LEU Chi-restraints excluded: chain E residue 473 VAL Chi-restraints excluded: chain E residue 479 ILE Chi-restraints excluded: chain E residue 493 VAL Chi-restraints excluded: chain E residue 537 LEU Chi-restraints excluded: chain F residue 249 LEU Chi-restraints excluded: chain F residue 264 THR Chi-restraints excluded: chain F residue 278 SER Chi-restraints excluded: chain F residue 325 VAL Chi-restraints excluded: chain F residue 344 VAL Chi-restraints excluded: chain F residue 405 LEU Chi-restraints excluded: chain F residue 414 SER Chi-restraints excluded: chain F residue 465 VAL Chi-restraints excluded: chain F residue 564 GLU Chi-restraints excluded: chain F residue 702 THR Chi-restraints excluded: chain F residue 717 THR Chi-restraints excluded: chain H residue 32 GLN Chi-restraints excluded: chain H residue 52 VAL Chi-restraints excluded: chain H residue 56 VAL Chi-restraints excluded: chain H residue 72 TYR Chi-restraints excluded: chain H residue 94 SER Chi-restraints excluded: chain H residue 115 CYS Chi-restraints excluded: chain H residue 123 SER Chi-restraints excluded: chain L residue 25 THR Chi-restraints excluded: chain L residue 80 VAL Chi-restraints excluded: chain L residue 111 GLN Chi-restraints excluded: chain L residue 117 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 221 random chunks: chunk 164 optimal weight: 7.9990 chunk 95 optimal weight: 9.9990 chunk 47 optimal weight: 9.9990 chunk 219 optimal weight: 9.9990 chunk 36 optimal weight: 6.9990 chunk 114 optimal weight: 0.0050 chunk 210 optimal weight: 10.0000 chunk 174 optimal weight: 2.9990 chunk 207 optimal weight: 5.9990 chunk 196 optimal weight: 4.9990 chunk 130 optimal weight: 6.9990 overall best weight: 4.2002 ------------------------------------------------------------------------------- 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 360 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 497 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 570 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 497 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 253 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 272 ASN ** D 290 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 598 ASN E 442 GLN ** F 430 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 615 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3581 r_free = 0.3581 target = 0.130174 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.118602 restraints weight = 32159.570| |-----------------------------------------------------------------------------| r_work (start): 0.3424 rms_B_bonded: 1.83 r_work: 0.3355 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.3257 rms_B_bonded: 4.08 restraints_weight: 0.2500 r_work (final): 0.3257 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7695 moved from start: 0.3316 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 18185 Z= 0.157 Angle : 0.571 8.937 24765 Z= 0.296 Chirality : 0.042 0.212 2550 Planarity : 0.004 0.039 3295 Dihedral : 5.696 59.534 2435 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 9.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.69 % Favored : 95.31 % Rotamer: Outliers : 3.27 % Allowed : 14.49 % Favored : 82.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.90 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.22 (0.17), residues: 2195 helix: -3.64 (0.47), residues: 72 sheet: -0.55 (0.22), residues: 526 loop : -0.78 (0.15), residues: 1597 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG D 476 TYR 0.019 0.002 TYR L 71 PHE 0.019 0.002 PHE H 99 TRP 0.024 0.002 TRP A 619 HIS 0.004 0.001 HIS F 527 Details of bonding type rmsd covalent geometry : bond 0.00367 (18182) covalent geometry : angle 0.57139 (24759) SS BOND : bond 0.00352 ( 3) SS BOND : angle 0.79360 ( 6) hydrogen bonds : bond 0.02784 ( 237) hydrogen bonds : angle 6.41049 ( 486) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4390 Ramachandran restraints generated. 2195 Oldfield, 0 Emsley, 2195 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4390 Ramachandran restraints generated. 2195 Oldfield, 0 Emsley, 2195 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 324 residues out of total 1927 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 261 time to evaluate : 0.730 Fit side-chains revert: symmetry clash REVERT: A 347 ASP cc_start: 0.7419 (t70) cc_final: 0.6482 (t0) REVERT: A 565 GLU cc_start: 0.6724 (mp0) cc_final: 0.6475 (mp0) REVERT: B 456 GLN cc_start: 0.7988 (mt0) cc_final: 0.7655 (mm110) REVERT: B 484 TYR cc_start: 0.7893 (t80) cc_final: 0.7684 (t80) REVERT: C 559 MET cc_start: 0.6429 (ttt) cc_final: 0.6042 (tpp) REVERT: D 340 SER cc_start: 0.7309 (OUTLIER) cc_final: 0.6898 (p) REVERT: D 533 ARG cc_start: 0.7214 (ptt-90) cc_final: 0.6996 (ptt-90) REVERT: D 640 MET cc_start: 0.7671 (mtp) cc_final: 0.7440 (mtp) REVERT: D 657 ASP cc_start: 0.7998 (p0) cc_final: 0.7721 (t0) REVERT: E 452 ASN cc_start: 0.8164 (OUTLIER) cc_final: 0.7794 (t0) REVERT: E 575 GLU cc_start: 0.7753 (mm-30) cc_final: 0.7494 (mm-30) REVERT: F 228 TRP cc_start: 0.7534 (t-100) cc_final: 0.7281 (t-100) REVERT: F 391 ARG cc_start: 0.8120 (ttm110) cc_final: 0.7617 (ttm110) REVERT: F 562 ASN cc_start: 0.8055 (p0) cc_final: 0.7673 (p0) REVERT: F 706 TYR cc_start: 0.7886 (t80) cc_final: 0.7375 (t80) REVERT: H 66 TRP cc_start: 0.7929 (t60) cc_final: 0.7671 (t60) REVERT: H 72 TYR cc_start: 0.7884 (OUTLIER) cc_final: 0.6933 (p90) REVERT: L 69 LEU cc_start: 0.7675 (tp) cc_final: 0.7440 (tp) REVERT: L 85 SER cc_start: 0.7569 (t) cc_final: 0.7239 (p) outliers start: 63 outliers final: 58 residues processed: 298 average time/residue: 0.1326 time to fit residues: 62.1476 Evaluate side-chains 319 residues out of total 1927 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 258 time to evaluate : 0.695 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 243 SER Chi-restraints excluded: chain A residue 389 VAL Chi-restraints excluded: chain A residue 420 VAL Chi-restraints excluded: chain A residue 679 VAL Chi-restraints excluded: chain B residue 435 LEU Chi-restraints excluded: chain B residue 447 LEU Chi-restraints excluded: chain B residue 451 ILE Chi-restraints excluded: chain B residue 458 GLN Chi-restraints excluded: chain B residue 470 ASN Chi-restraints excluded: chain B residue 479 ILE Chi-restraints excluded: chain B residue 605 MET Chi-restraints excluded: chain B residue 609 ASP Chi-restraints excluded: chain C residue 373 MET Chi-restraints excluded: chain C residue 389 VAL Chi-restraints excluded: chain C residue 392 SER Chi-restraints excluded: chain C residue 435 LEU Chi-restraints excluded: chain C residue 465 VAL Chi-restraints excluded: chain C residue 488 ARG Chi-restraints excluded: chain C residue 494 THR Chi-restraints excluded: chain C residue 568 THR Chi-restraints excluded: chain C residue 585 GLN Chi-restraints excluded: chain C residue 592 GLN Chi-restraints excluded: chain C residue 593 THR Chi-restraints excluded: chain C residue 680 SER Chi-restraints excluded: chain C residue 681 VAL Chi-restraints excluded: chain C residue 699 ILE Chi-restraints excluded: chain C residue 729 THR Chi-restraints excluded: chain D residue 340 SER Chi-restraints excluded: chain D residue 489 VAL Chi-restraints excluded: chain D residue 567 LYS Chi-restraints excluded: chain D residue 593 THR Chi-restraints excluded: chain D residue 672 THR Chi-restraints excluded: chain E residue 452 ASN Chi-restraints excluded: chain E residue 461 LEU Chi-restraints excluded: chain E residue 473 VAL Chi-restraints excluded: chain E residue 479 ILE Chi-restraints excluded: chain E residue 493 VAL Chi-restraints excluded: chain E residue 537 LEU Chi-restraints excluded: chain F residue 249 LEU Chi-restraints excluded: chain F residue 264 THR Chi-restraints excluded: chain F residue 278 SER Chi-restraints excluded: chain F residue 325 VAL Chi-restraints excluded: chain F residue 344 VAL Chi-restraints excluded: chain F residue 405 LEU Chi-restraints excluded: chain F residue 414 SER Chi-restraints excluded: chain F residue 465 VAL Chi-restraints excluded: chain F residue 564 GLU Chi-restraints excluded: chain F residue 702 THR Chi-restraints excluded: chain F residue 717 THR Chi-restraints excluded: chain H residue 32 GLN Chi-restraints excluded: chain H residue 52 VAL Chi-restraints excluded: chain H residue 56 VAL Chi-restraints excluded: chain H residue 72 TYR Chi-restraints excluded: chain H residue 94 SER Chi-restraints excluded: chain H residue 115 CYS Chi-restraints excluded: chain H residue 123 SER Chi-restraints excluded: chain L residue 25 THR Chi-restraints excluded: chain L residue 38 VAL Chi-restraints excluded: chain L residue 80 VAL Chi-restraints excluded: chain L residue 111 GLN Chi-restraints excluded: chain L residue 117 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 221 random chunks: chunk 8 optimal weight: 0.3980 chunk 191 optimal weight: 9.9990 chunk 176 optimal weight: 20.0000 chunk 184 optimal weight: 20.0000 chunk 25 optimal weight: 6.9990 chunk 85 optimal weight: 0.7980 chunk 89 optimal weight: 5.9990 chunk 212 optimal weight: 2.9990 chunk 26 optimal weight: 6.9990 chunk 64 optimal weight: 10.0000 chunk 63 optimal weight: 9.9990 overall best weight: 3.4386 ------------------------------------------------------------------------------- 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 360 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 497 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 570 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 497 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 615 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 253 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 272 ASN ** D 290 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 584 HIS D 598 ASN ** F 430 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 615 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 60 GLN ** L 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3580 r_free = 0.3580 target = 0.130192 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.118617 restraints weight = 32347.929| |-----------------------------------------------------------------------------| r_work (start): 0.3430 rms_B_bonded: 1.85 r_work: 0.3360 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.3262 rms_B_bonded: 4.10 restraints_weight: 0.2500 r_work (final): 0.3262 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7684 moved from start: 0.3373 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 18185 Z= 0.136 Angle : 0.546 8.207 24765 Z= 0.282 Chirality : 0.042 0.203 2550 Planarity : 0.004 0.038 3295 Dihedral : 5.533 58.934 2435 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 8.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.05 % Favored : 95.95 % Rotamer: Outliers : 3.22 % Allowed : 14.54 % Favored : 82.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.90 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.19 (0.17), residues: 2195 helix: -3.63 (0.47), residues: 72 sheet: -0.57 (0.22), residues: 536 loop : -0.73 (0.15), residues: 1587 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG D 476 TYR 0.018 0.002 TYR L 71 PHE 0.017 0.002 PHE H 99 TRP 0.023 0.002 TRP A 619 HIS 0.004 0.001 HIS F 527 Details of bonding type rmsd covalent geometry : bond 0.00316 (18182) covalent geometry : angle 0.54622 (24759) SS BOND : bond 0.00324 ( 3) SS BOND : angle 0.70397 ( 6) hydrogen bonds : bond 0.02624 ( 237) hydrogen bonds : angle 6.24870 ( 486) =============================================================================== Job complete usr+sys time: 4105.89 seconds wall clock time: 71 minutes 23.92 seconds (4283.92 seconds total)