Starting phenix.real_space_refine on Sun May 18 15:02:14 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9b6p_44273/05_2025/9b6p_44273.cif Found real_map, /net/cci-nas-00/data/ceres_data/9b6p_44273/05_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_44273/05_2025/9b6p_44273.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9b6p_44273/05_2025/9b6p_44273.map" model { file = "/net/cci-nas-00/data/ceres_data/9b6p_44273/05_2025/9b6p_44273.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9b6p_44273/05_2025/9b6p_44273.cif" } resolution = 3.13 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 1.000 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 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): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/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: 10.02, per 1000 atoms: 0.57 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: 4.11 Conformation dependent library (CDL) restraints added in 2.3 seconds 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: 2.25 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: 4.83 Time building geometry restraints manager: 4.85 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: 0.610 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: 0.020 Extract box with map and model: 0.700 Check model and map are aligned: 0.130 Set scattering table: 0.160 Process input model: 38.070 Find NCS groups from input model: 0.530 Set up NCS constraints: 0.080 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:2.710 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 43.010 ------------------------------------------------------------------------------- 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 : 22.24 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.99 (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 TRP 0.031 0.003 TRP H 140 HIS 0.009 0.002 HIS H 54 PHE 0.034 0.003 PHE L 122 TYR 0.037 0.003 TYR C 415 ARG 0.009 0.001 ARG F 734 Details of bonding type rmsd hydrogen bonds : bond 0.26190 ( 237) hydrogen bonds : angle 10.49700 ( 486) SS BOND : bond 0.00351 ( 3) SS BOND : angle 1.10948 ( 6) covalent geometry : bond 0.00587 (18182) covalent geometry : angle 0.95331 (24759) *********************** 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 : 1.803 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: 0.3039 time to fit residues: 223.6857 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 : 2.077 ------------------------------------------------------------------------------- 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 186 optimal weight: 1.9990 chunk 167 optimal weight: 8.9990 chunk 92 optimal weight: 9.9990 chunk 57 optimal weight: 5.9990 chunk 112 optimal weight: 20.0000 chunk 89 optimal weight: 5.9990 chunk 173 optimal weight: 10.0000 chunk 67 optimal weight: 6.9990 chunk 105 optimal weight: 0.8980 chunk 128 optimal weight: 5.9990 chunk 200 optimal weight: 6.9990 overall best weight: 4.1788 ------------------------------------------------------------------------------- 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 470 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 486 GLN 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 376 GLN ** 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 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 111 GLN Total number of N/Q/H flips: 41 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3597 r_free = 0.3597 target = 0.131207 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.119623 restraints weight = 32164.046| |-----------------------------------------------------------------------------| r_work (start): 0.3437 rms_B_bonded: 1.84 r_work: 0.3367 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.3269 rms_B_bonded: 4.11 restraints_weight: 0.2500 r_work (final): 0.3269 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7662 moved from start: 0.1932 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 18185 Z= 0.173 Angle : 0.643 9.006 24765 Z= 0.339 Chirality : 0.045 0.224 2550 Planarity : 0.005 0.066 3295 Dihedral : 6.829 58.416 2468 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 9.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 2.39 % Allowed : 7.58 % Favored : 90.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.90 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.33 (0.15), residues: 2195 helix: -3.78 (0.38), residues: 91 sheet: -0.78 (0.21), residues: 515 loop : -0.74 (0.13), residues: 1589 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP H 140 HIS 0.009 0.002 HIS H 54 PHE 0.028 0.002 PHE H 99 TYR 0.017 0.002 TYR H 72 ARG 0.010 0.001 ARG H 91 Details of bonding type rmsd hydrogen bonds : bond 0.03703 ( 237) hydrogen bonds : angle 7.27624 ( 486) SS BOND : bond 0.00708 ( 3) SS BOND : angle 0.59736 ( 6) covalent geometry : bond 0.00402 (18182) covalent geometry : angle 0.64351 (24759) *********************** 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 370 residues out of total 1927 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 324 time to evaluate : 1.814 Fit side-chains revert: symmetry clash REVERT: A 564 GLU cc_start: 0.6156 (pm20) cc_final: 0.5933 (pm20) REVERT: B 435 LEU cc_start: 0.8616 (OUTLIER) cc_final: 0.8342 (mt) REVERT: B 436 MET cc_start: 0.7933 (ptp) cc_final: 0.7328 (ptp) REVERT: B 456 GLN cc_start: 0.7709 (mt0) cc_final: 0.7460 (mm110) REVERT: B 529 GLU cc_start: 0.6644 (tt0) cc_final: 0.6280 (mt-10) REVERT: B 588 GLN cc_start: 0.6923 (OUTLIER) cc_final: 0.6297 (tp40) REVERT: C 306 TRP cc_start: 0.7548 (m-10) cc_final: 0.7225 (m-10) REVERT: C 391 ARG cc_start: 0.6769 (ttm110) cc_final: 0.5717 (tpt170) REVERT: C 501 PHE cc_start: 0.8061 (p90) cc_final: 0.7834 (p90) REVERT: C 579 GLN cc_start: 0.7057 (mt0) cc_final: 0.6816 (mm110) REVERT: D 533 ARG cc_start: 0.7193 (ptt-90) cc_final: 0.6827 (ptt-90) REVERT: D 613 TYR cc_start: 0.8301 (m-80) cc_final: 0.7402 (m-80) REVERT: D 640 MET cc_start: 0.7559 (mtp) cc_final: 0.7261 (mtp) REVERT: E 514 ARG cc_start: 0.7603 (mtm180) cc_final: 0.6653 (mtt-85) REVERT: E 534 PHE cc_start: 0.6683 (m-80) cc_final: 0.6435 (m-80) REVERT: E 609 ASP cc_start: 0.7479 (m-30) cc_final: 0.6716 (p0) REVERT: F 325 VAL cc_start: 0.7328 (OUTLIER) cc_final: 0.7067 (m) REVERT: F 391 ARG cc_start: 0.8149 (ttm110) cc_final: 0.7891 (ttm110) REVERT: F 415 TYR cc_start: 0.7640 (t80) cc_final: 0.7423 (t80) REVERT: F 550 ARG cc_start: 0.7383 (ttt-90) cc_final: 0.7157 (mtp-110) REVERT: F 562 ASN cc_start: 0.8083 (p0) cc_final: 0.7766 (p0) REVERT: F 679 VAL cc_start: 0.7785 (t) cc_final: 0.7524 (p) REVERT: H 72 TYR cc_start: 0.7593 (OUTLIER) cc_final: 0.7145 (p90) REVERT: L 91 THR cc_start: 0.7749 (p) cc_final: 0.7440 (p) outliers start: 46 outliers final: 32 residues processed: 353 average time/residue: 0.2860 time to fit residues: 152.1094 Evaluate side-chains 322 residues out of total 1927 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 286 time to evaluate : 1.794 ------------------------------------------------------------------------------- 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 479 ILE Chi-restraints excluded: chain B residue 588 GLN Chi-restraints excluded: chain C residue 239 VAL 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 494 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 264 THR 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 144 optimal weight: 9.9990 chunk 140 optimal weight: 5.9990 chunk 81 optimal weight: 8.9990 chunk 41 optimal weight: 6.9990 chunk 86 optimal weight: 5.9990 chunk 18 optimal weight: 5.9990 chunk 94 optimal weight: 1.9990 chunk 82 optimal weight: 6.9990 chunk 199 optimal weight: 20.0000 chunk 121 optimal weight: 1.9990 chunk 153 optimal weight: 8.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- 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** ** B 497 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 430 GLN C 487 GLN ** 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 376 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 430 GLN F 253 ASN F 305 ASN H 54 HIS L 60 GLN ** L 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3586 r_free = 0.3586 target = 0.130442 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.118890 restraints weight = 32145.268| |-----------------------------------------------------------------------------| r_work (start): 0.3428 rms_B_bonded: 1.84 r_work: 0.3359 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.3261 rms_B_bonded: 4.07 restraints_weight: 0.2500 r_work (final): 0.3261 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7682 moved from start: 0.2430 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 18185 Z= 0.169 Angle : 0.593 7.090 24765 Z= 0.313 Chirality : 0.043 0.238 2550 Planarity : 0.004 0.038 3295 Dihedral : 6.149 59.143 2444 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 8.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 2.44 % Allowed : 9.92 % Favored : 87.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.90 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.18 (0.16), residues: 2195 helix: -3.68 (0.40), residues: 91 sheet: -0.65 (0.21), residues: 512 loop : -0.65 (0.14), residues: 1592 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP H 140 HIS 0.005 0.001 HIS D 290 PHE 0.024 0.002 PHE H 99 TYR 0.020 0.002 TYR C 705 ARG 0.005 0.001 ARG H 91 Details of bonding type rmsd hydrogen bonds : bond 0.03340 ( 237) hydrogen bonds : angle 6.73797 ( 486) SS BOND : bond 0.00473 ( 3) SS BOND : angle 0.77394 ( 6) covalent geometry : bond 0.00395 (18182) covalent geometry : angle 0.59342 (24759) *********************** 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 333 residues out of total 1927 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 286 time to evaluate : 1.867 Fit side-chains revert: symmetry clash REVERT: A 347 ASP cc_start: 0.7275 (t70) cc_final: 0.6559 (t0) REVERT: A 564 GLU cc_start: 0.6202 (pm20) cc_final: 0.5966 (pm20) REVERT: B 456 GLN cc_start: 0.7840 (mt0) cc_final: 0.7555 (mm110) REVERT: C 306 TRP cc_start: 0.7580 (m-10) cc_final: 0.7315 (m-10) REVERT: C 391 ARG cc_start: 0.6727 (ttm110) cc_final: 0.5617 (tpt170) REVERT: C 579 GLN cc_start: 0.7060 (mt0) cc_final: 0.6808 (mm110) REVERT: D 533 ARG cc_start: 0.7261 (ptt-90) cc_final: 0.6939 (ptt-90) REVERT: D 613 TYR cc_start: 0.8297 (m-80) cc_final: 0.7321 (m-80) REVERT: D 640 MET cc_start: 0.7599 (mtp) cc_final: 0.7325 (mtp) REVERT: E 575 GLU cc_start: 0.7381 (mm-30) cc_final: 0.7163 (mm-30) REVERT: F 391 ARG cc_start: 0.8142 (ttm110) cc_final: 0.7882 (ttm110) REVERT: F 550 ARG cc_start: 0.7370 (ttt-90) cc_final: 0.7075 (mtp-110) REVERT: F 562 ASN cc_start: 0.8076 (p0) cc_final: 0.7718 (p0) REVERT: F 610 ARG cc_start: 0.8328 (ttm-80) cc_final: 0.8123 (ttm-80) REVERT: F 679 VAL cc_start: 0.7819 (t) cc_final: 0.7571 (p) REVERT: H 72 TYR cc_start: 0.7658 (OUTLIER) cc_final: 0.7055 (p90) outliers start: 47 outliers final: 37 residues processed: 315 average time/residue: 0.2826 time to fit residues: 135.9144 Evaluate side-chains 303 residues out of total 1927 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 265 time to evaluate : 1.919 ------------------------------------------------------------------------------- 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 479 ILE 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 699 ILE Chi-restraints excluded: chain C residue 729 THR Chi-restraints excluded: chain D residue 370 ASP Chi-restraints excluded: chain D residue 672 THR 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 405 LEU 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 H residue 32 GLN Chi-restraints excluded: chain H residue 46 PHE Chi-restraints excluded: chain H residue 72 TYR Chi-restraints excluded: chain H residue 90 SER 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 38 VAL 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 5 optimal weight: 20.0000 chunk 171 optimal weight: 10.0000 chunk 7 optimal weight: 0.7980 chunk 205 optimal weight: 5.9990 chunk 27 optimal weight: 10.0000 chunk 4 optimal weight: 3.9990 chunk 149 optimal weight: 20.0000 chunk 145 optimal weight: 10.0000 chunk 187 optimal weight: 7.9990 chunk 106 optimal weight: 0.0670 chunk 128 optimal weight: 0.2980 overall best weight: 2.2322 ------------------------------------------------------------------------------- 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 305 ASN 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 C 735 ASN D 253 ASN ** D 290 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 376 GLN F 253 ASN ** F 430 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 26 GLN ** L 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3597 r_free = 0.3597 target = 0.131394 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.119797 restraints weight = 32164.397| |-----------------------------------------------------------------------------| r_work (start): 0.3440 rms_B_bonded: 1.85 r_work: 0.3371 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.3274 rms_B_bonded: 4.10 restraints_weight: 0.2500 r_work (final): 0.3274 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7651 moved from start: 0.2758 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 18185 Z= 0.108 Angle : 0.518 6.120 24765 Z= 0.269 Chirality : 0.041 0.239 2550 Planarity : 0.004 0.035 3295 Dihedral : 5.473 57.992 2441 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 7.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 2.65 % Allowed : 11.11 % Favored : 86.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.90 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.91 (0.17), residues: 2195 helix: -3.61 (0.43), residues: 86 sheet: -0.35 (0.22), residues: 517 loop : -0.50 (0.15), residues: 1592 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP H 140 HIS 0.003 0.001 HIS C 255 PHE 0.014 0.001 PHE H 99 TYR 0.018 0.001 TYR C 705 ARG 0.005 0.000 ARG H 91 Details of bonding type rmsd hydrogen bonds : bond 0.02683 ( 237) hydrogen bonds : angle 6.20072 ( 486) SS BOND : bond 0.00220 ( 3) SS BOND : angle 0.64661 ( 6) covalent geometry : bond 0.00248 (18182) covalent geometry : angle 0.51841 (24759) *********************** 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 354 residues out of total 1927 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 303 time to evaluate : 1.858 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 347 ASP cc_start: 0.7288 (t70) cc_final: 0.6335 (t0) REVERT: A 565 GLU cc_start: 0.6621 (mp0) cc_final: 0.6330 (mp0) REVERT: B 456 GLN cc_start: 0.7772 (mt0) cc_final: 0.7483 (mm110) REVERT: C 306 TRP cc_start: 0.7520 (m-10) cc_final: 0.7298 (m-10) REVERT: C 391 ARG cc_start: 0.6682 (ttm110) cc_final: 0.5558 (tpt170) REVERT: D 533 ARG cc_start: 0.7293 (ptt-90) cc_final: 0.7022 (ptt-90) REVERT: D 613 TYR cc_start: 0.8294 (m-80) cc_final: 0.7325 (m-80) REVERT: D 640 MET cc_start: 0.7528 (mtp) cc_final: 0.7287 (mtp) REVERT: E 452 ASN cc_start: 0.8204 (OUTLIER) cc_final: 0.7608 (t0) REVERT: E 485 ARG cc_start: 0.7070 (OUTLIER) cc_final: 0.6852 (ttt-90) REVERT: E 575 GLU cc_start: 0.7373 (mm-30) cc_final: 0.7144 (mm-30) REVERT: F 391 ARG cc_start: 0.8134 (ttm110) cc_final: 0.7633 (ttm110) REVERT: F 562 ASN cc_start: 0.8092 (p0) cc_final: 0.7749 (p0) REVERT: F 679 VAL cc_start: 0.7790 (t) cc_final: 0.7585 (p) REVERT: H 72 TYR cc_start: 0.7648 (OUTLIER) cc_final: 0.7020 (p90) REVERT: H 101 GLN cc_start: 0.6965 (tm-30) cc_final: 0.6519 (tm-30) outliers start: 51 outliers final: 38 residues processed: 332 average time/residue: 0.2839 time to fit residues: 142.9654 Evaluate side-chains 305 residues out of total 1927 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 264 time to evaluate : 1.782 ------------------------------------------------------------------------------- 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 479 ILE Chi-restraints excluded: chain B residue 605 MET Chi-restraints excluded: chain B residue 625 THR 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 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 370 ASP Chi-restraints excluded: chain D residue 593 THR Chi-restraints excluded: chain D residue 612 VAL Chi-restraints excluded: chain D residue 672 THR Chi-restraints excluded: chain E residue 452 ASN 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 405 LEU 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 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 123 SER Chi-restraints excluded: chain H residue 128 LEU Chi-restraints excluded: chain L residue 38 VAL 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 108 optimal weight: 20.0000 chunk 70 optimal weight: 0.9980 chunk 207 optimal weight: 10.0000 chunk 185 optimal weight: 0.9990 chunk 119 optimal weight: 9.9990 chunk 41 optimal weight: 5.9990 chunk 169 optimal weight: 9.9990 chunk 3 optimal weight: 10.0000 chunk 165 optimal weight: 7.9990 chunk 217 optimal weight: 20.0000 chunk 68 optimal weight: 20.0000 overall best weight: 5.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 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 598 ASN ** B 497 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 597 GLN ** C 598 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 608 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 709 ASN D 272 ASN ** D 290 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 598 ASN E 519 ASN E 584 HIS ** F 253 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 262 ASN ** F 430 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 487 GLN L 60 GLN ** L 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.129871 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.118236 restraints weight = 32471.043| |-----------------------------------------------------------------------------| r_work (start): 0.3417 rms_B_bonded: 1.83 r_work: 0.3349 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.3252 rms_B_bonded: 4.05 restraints_weight: 0.2500 r_work (final): 0.3252 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7696 moved from start: 0.2889 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 18185 Z= 0.187 Angle : 0.585 7.479 24765 Z= 0.307 Chirality : 0.043 0.213 2550 Planarity : 0.004 0.038 3295 Dihedral : 5.754 57.757 2437 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 9.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.74 % Favored : 96.26 % Rotamer: Outliers : 3.22 % Allowed : 12.20 % Favored : 84.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.90 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.04 (0.17), residues: 2195 helix: -3.74 (0.42), residues: 86 sheet: -0.41 (0.22), residues: 516 loop : -0.61 (0.15), residues: 1593 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP A 619 HIS 0.006 0.001 HIS F 527 PHE 0.023 0.002 PHE H 99 TYR 0.015 0.002 TYR C 706 ARG 0.005 0.001 ARG H 117 Details of bonding type rmsd hydrogen bonds : bond 0.03037 ( 237) hydrogen bonds : angle 6.46123 ( 486) SS BOND : bond 0.00411 ( 3) SS BOND : angle 0.80575 ( 6) covalent geometry : bond 0.00439 (18182) covalent geometry : angle 0.58534 (24759) *********************** 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 325 residues out of total 1927 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 263 time to evaluate : 1.990 Fit side-chains revert: symmetry clash REVERT: A 347 ASP cc_start: 0.7343 (t70) cc_final: 0.6476 (t0) REVERT: A 565 GLU cc_start: 0.6673 (mp0) cc_final: 0.6388 (mp0) REVERT: B 436 MET cc_start: 0.7909 (ptp) cc_final: 0.7230 (ptp) REVERT: B 456 GLN cc_start: 0.7946 (mt0) cc_final: 0.7617 (mm110) REVERT: B 470 ASN cc_start: 0.7617 (OUTLIER) cc_final: 0.7378 (m-40) REVERT: C 306 TRP cc_start: 0.7625 (m-10) cc_final: 0.7402 (m-10) REVERT: C 391 ARG cc_start: 0.6646 (ttm110) cc_final: 0.5560 (tpt170) REVERT: D 613 TYR cc_start: 0.8348 (m-80) cc_final: 0.7377 (m-80) REVERT: D 640 MET cc_start: 0.7656 (mtp) cc_final: 0.7344 (mtp) REVERT: E 452 ASN cc_start: 0.8254 (OUTLIER) cc_final: 0.7789 (t0) REVERT: E 575 GLU cc_start: 0.7373 (mm-30) cc_final: 0.7169 (mm-30) REVERT: F 391 ARG cc_start: 0.8133 (ttm110) cc_final: 0.7851 (ttm110) REVERT: F 562 ASN cc_start: 0.8075 (p0) cc_final: 0.7725 (p0) REVERT: H 72 TYR cc_start: 0.7836 (OUTLIER) cc_final: 0.7012 (p90) outliers start: 62 outliers final: 48 residues processed: 298 average time/residue: 0.2715 time to fit residues: 125.1464 Evaluate side-chains 302 residues out of total 1927 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 251 time to evaluate : 1.815 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 239 VAL Chi-restraints excluded: chain C residue 243 SER 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 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 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 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 593 THR Chi-restraints excluded: chain F residue 702 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 123 SER Chi-restraints excluded: chain H residue 128 LEU 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 38 VAL Chi-restraints excluded: chain L residue 61 LEU Chi-restraints excluded: chain L residue 80 VAL 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 156 optimal weight: 10.0000 chunk 217 optimal weight: 6.9990 chunk 44 optimal weight: 10.0000 chunk 218 optimal weight: 5.9990 chunk 136 optimal weight: 10.0000 chunk 143 optimal weight: 20.0000 chunk 15 optimal weight: 20.0000 chunk 203 optimal weight: 0.8980 chunk 49 optimal weight: 0.5980 chunk 31 optimal weight: 0.0770 chunk 103 optimal weight: 20.0000 overall best weight: 2.9142 ------------------------------------------------------------------------------- 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 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** A 673 GLN ** B 497 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 598 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 608 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 272 ASN ** D 290 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 598 ASN ** F 253 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 430 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 = 0.3589 r_free = 0.3589 target = 0.130843 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.119309 restraints weight = 32337.642| |-----------------------------------------------------------------------------| r_work (start): 0.3432 rms_B_bonded: 1.84 r_work: 0.3364 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.3268 rms_B_bonded: 4.07 restraints_weight: 0.2500 r_work (final): 0.3268 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7672 moved from start: 0.3050 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 18185 Z= 0.126 Angle : 0.529 7.416 24765 Z= 0.274 Chirality : 0.041 0.206 2550 Planarity : 0.004 0.035 3295 Dihedral : 5.462 59.748 2437 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 8.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 3.22 % Allowed : 12.67 % Favored : 84.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.90 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.90 (0.17), residues: 2195 helix: -3.63 (0.45), residues: 80 sheet: -0.28 (0.23), residues: 497 loop : -0.53 (0.15), residues: 1618 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 619 HIS 0.003 0.001 HIS C 255 PHE 0.015 0.001 PHE H 99 TYR 0.013 0.001 TYR A 674 ARG 0.004 0.000 ARG B 533 Details of bonding type rmsd hydrogen bonds : bond 0.02667 ( 237) hydrogen bonds : angle 6.19419 ( 486) SS BOND : bond 0.00404 ( 3) SS BOND : angle 0.79133 ( 6) covalent geometry : bond 0.00293 (18182) covalent geometry : angle 0.52897 (24759) *********************** 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 332 residues out of total 1927 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 270 time to evaluate : 1.832 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 347 ASP cc_start: 0.7355 (t70) cc_final: 0.6500 (t0) REVERT: A 565 GLU cc_start: 0.6663 (mp0) cc_final: 0.6397 (mp0) REVERT: B 456 GLN cc_start: 0.7892 (mt0) cc_final: 0.7568 (mm110) REVERT: B 470 ASN cc_start: 0.7644 (OUTLIER) cc_final: 0.7403 (m-40) REVERT: B 529 GLU cc_start: 0.6287 (tt0) cc_final: 0.5958 (mt-10) REVERT: C 306 TRP cc_start: 0.7577 (m-10) cc_final: 0.7371 (m-10) REVERT: D 613 TYR cc_start: 0.8349 (m-80) cc_final: 0.7457 (m-80) REVERT: D 640 MET cc_start: 0.7631 (mtp) cc_final: 0.7394 (mtp) REVERT: D 657 ASP cc_start: 0.8025 (p0) cc_final: 0.7634 (t0) REVERT: E 452 ASN cc_start: 0.8216 (OUTLIER) cc_final: 0.7756 (t0) REVERT: E 575 GLU cc_start: 0.7365 (mm-30) cc_final: 0.7159 (mm-30) REVERT: F 228 TRP cc_start: 0.7489 (t-100) cc_final: 0.7244 (t-100) REVERT: F 391 ARG cc_start: 0.8129 (ttm110) cc_final: 0.7620 (ttm110) REVERT: F 562 ASN cc_start: 0.8057 (p0) cc_final: 0.7703 (p0) REVERT: F 706 TYR cc_start: 0.7861 (t80) cc_final: 0.7467 (t80) REVERT: H 72 TYR cc_start: 0.7796 (OUTLIER) cc_final: 0.7023 (p90) outliers start: 62 outliers final: 49 residues processed: 305 average time/residue: 0.2788 time to fit residues: 129.8856 Evaluate side-chains 308 residues out of total 1927 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 256 time to evaluate : 1.784 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 420 VAL 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 B residue 625 THR Chi-restraints excluded: chain C residue 239 VAL Chi-restraints excluded: chain C residue 243 SER 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 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 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 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 405 LEU 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 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 94 SER Chi-restraints excluded: chain H residue 123 SER Chi-restraints excluded: chain H residue 128 LEU 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 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 221 random chunks: chunk 209 optimal weight: 0.9990 chunk 150 optimal weight: 30.0000 chunk 148 optimal weight: 3.9990 chunk 164 optimal weight: 10.0000 chunk 127 optimal weight: 8.9990 chunk 170 optimal weight: 0.9980 chunk 75 optimal weight: 6.9990 chunk 118 optimal weight: 7.9990 chunk 15 optimal weight: 6.9990 chunk 95 optimal weight: 5.9990 chunk 162 optimal weight: 20.0000 overall best weight: 3.7988 ------------------------------------------------------------------------------- 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 608 GLN ** 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 253 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: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.130264 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.118685 restraints weight = 32237.530| |-----------------------------------------------------------------------------| r_work (start): 0.3423 rms_B_bonded: 1.84 r_work: 0.3354 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: 0.7683 moved from start: 0.3149 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= 0.146 Angle : 0.553 12.793 24765 Z= 0.286 Chirality : 0.042 0.195 2550 Planarity : 0.004 0.036 3295 Dihedral : 5.502 59.836 2437 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 8.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.87 % Favored : 96.13 % Rotamer: Outliers : 3.53 % Allowed : 12.82 % Favored : 83.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.90 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.92 (0.17), residues: 2195 helix: -3.59 (0.47), residues: 73 sheet: -0.32 (0.23), residues: 499 loop : -0.56 (0.15), residues: 1623 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP H 140 HIS 0.004 0.001 HIS C 290 PHE 0.017 0.002 PHE H 99 TYR 0.013 0.002 TYR C 706 ARG 0.004 0.001 ARG B 533 Details of bonding type rmsd hydrogen bonds : bond 0.02731 ( 237) hydrogen bonds : angle 6.19725 ( 486) SS BOND : bond 0.00353 ( 3) SS BOND : angle 0.78182 ( 6) covalent geometry : bond 0.00340 (18182) covalent geometry : angle 0.55342 (24759) *********************** 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 337 residues out of total 1927 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 269 time to evaluate : 1.864 Fit side-chains revert: symmetry clash REVERT: A 347 ASP cc_start: 0.7446 (t70) cc_final: 0.6582 (t0) REVERT: A 565 GLU cc_start: 0.6674 (mp0) cc_final: 0.6418 (mp0) REVERT: B 456 GLN cc_start: 0.7936 (mt0) cc_final: 0.7600 (mm110) REVERT: B 470 ASN cc_start: 0.7607 (OUTLIER) cc_final: 0.7365 (m-40) REVERT: C 306 TRP cc_start: 0.7616 (m-10) cc_final: 0.7399 (m-10) REVERT: D 340 SER cc_start: 0.7393 (OUTLIER) cc_final: 0.6947 (p) REVERT: D 533 ARG cc_start: 0.7077 (ptt-90) cc_final: 0.6480 (ptt-90) REVERT: D 613 TYR cc_start: 0.8366 (m-80) cc_final: 0.7474 (m-80) REVERT: D 657 ASP cc_start: 0.8015 (p0) cc_final: 0.7704 (t0) REVERT: E 452 ASN cc_start: 0.8277 (OUTLIER) cc_final: 0.7843 (t0) REVERT: F 228 TRP cc_start: 0.7541 (t-100) cc_final: 0.7255 (t-100) REVERT: F 391 ARG cc_start: 0.8122 (ttm110) cc_final: 0.7591 (ttm110) REVERT: F 562 ASN cc_start: 0.8069 (p0) cc_final: 0.7688 (p0) REVERT: F 706 TYR cc_start: 0.7878 (t80) cc_final: 0.7428 (t80) REVERT: H 72 TYR cc_start: 0.7894 (OUTLIER) cc_final: 0.6955 (p90) REVERT: L 69 LEU cc_start: 0.7709 (tp) cc_final: 0.7491 (tp) outliers start: 68 outliers final: 58 residues processed: 308 average time/residue: 0.2769 time to fit residues: 131.8367 Evaluate side-chains 323 residues out of total 1927 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 261 time to evaluate : 1.850 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 243 SER Chi-restraints excluded: chain A residue 420 VAL Chi-restraints excluded: chain A residue 668 ASN 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 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 243 SER 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 370 ASP Chi-restraints excluded: chain D residue 374 ILE 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 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 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 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 94 SER Chi-restraints excluded: chain H residue 123 SER Chi-restraints excluded: chain H residue 128 LEU 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 221 random chunks: chunk 180 optimal weight: 4.9990 chunk 122 optimal weight: 20.0000 chunk 201 optimal weight: 30.0000 chunk 30 optimal weight: 6.9990 chunk 79 optimal weight: 6.9990 chunk 77 optimal weight: 5.9990 chunk 20 optimal weight: 20.0000 chunk 7 optimal weight: 10.0000 chunk 76 optimal weight: 10.0000 chunk 135 optimal weight: 5.9990 chunk 210 optimal weight: 10.0000 overall best weight: 6.1990 ------------------------------------------------------------------------------- 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** ** B 497 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 608 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 630 HIS D 272 ASN ** D 290 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 598 ASN E 442 GLN ** F 253 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 430 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 630 HIS L 60 GLN ** L 73 ASN ** 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 = 0.3562 r_free = 0.3562 target = 0.128744 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.117197 restraints weight = 32283.039| |-----------------------------------------------------------------------------| r_work (start): 0.3398 rms_B_bonded: 1.84 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: 0.7713 moved from start: 0.3172 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 18185 Z= 0.213 Angle : 0.621 15.837 24765 Z= 0.322 Chirality : 0.044 0.187 2550 Planarity : 0.005 0.038 3295 Dihedral : 5.906 58.712 2437 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 9.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.01 % Favored : 94.99 % Rotamer: Outliers : 4.05 % Allowed : 12.46 % Favored : 83.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.90 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.16 (0.17), residues: 2195 helix: -3.66 (0.46), residues: 72 sheet: -0.48 (0.22), residues: 527 loop : -0.74 (0.15), residues: 1596 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 509 HIS 0.007 0.001 HIS C 290 PHE 0.023 0.002 PHE H 99 TYR 0.018 0.002 TYR E 443 ARG 0.008 0.001 ARG F 725 Details of bonding type rmsd hydrogen bonds : bond 0.03127 ( 237) hydrogen bonds : angle 6.54476 ( 486) SS BOND : bond 0.00474 ( 3) SS BOND : angle 0.96205 ( 6) covalent geometry : bond 0.00500 (18182) covalent geometry : angle 0.62042 (24759) *********************** 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 340 residues out of total 1927 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 262 time to evaluate : 2.072 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 347 ASP cc_start: 0.7504 (t70) cc_final: 0.6603 (t0) REVERT: A 565 GLU cc_start: 0.6691 (mp0) cc_final: 0.6412 (mp0) REVERT: B 456 GLN cc_start: 0.8009 (mt0) cc_final: 0.7653 (mm110) REVERT: B 470 ASN cc_start: 0.7675 (OUTLIER) cc_final: 0.7448 (m-40) REVERT: D 340 SER cc_start: 0.7299 (OUTLIER) cc_final: 0.6889 (p) REVERT: D 533 ARG cc_start: 0.7088 (ptt-90) cc_final: 0.6694 (ptt-90) REVERT: D 613 TYR cc_start: 0.8364 (m-80) cc_final: 0.7484 (m-80) REVERT: D 657 ASP cc_start: 0.8032 (p0) cc_final: 0.7716 (t0) REVERT: E 452 ASN cc_start: 0.8237 (OUTLIER) cc_final: 0.7851 (t0) REVERT: E 575 GLU cc_start: 0.7896 (mm-30) cc_final: 0.7531 (mm-30) REVERT: F 391 ARG cc_start: 0.8085 (ttm110) cc_final: 0.7537 (ttm110) REVERT: F 562 ASN cc_start: 0.8072 (p0) cc_final: 0.7767 (p0) REVERT: F 706 TYR cc_start: 0.7964 (t80) cc_final: 0.7473 (t80) REVERT: H 72 TYR cc_start: 0.7922 (OUTLIER) cc_final: 0.6783 (p90) REVERT: L 69 LEU cc_start: 0.7670 (tp) cc_final: 0.7411 (tp) REVERT: L 85 SER cc_start: 0.7606 (t) cc_final: 0.7220 (p) REVERT: L 91 THR cc_start: 0.7690 (p) cc_final: 0.7487 (p) outliers start: 78 outliers final: 61 residues processed: 314 average time/residue: 0.2747 time to fit residues: 134.9088 Evaluate side-chains 318 residues out of total 1927 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 253 time to evaluate : 1.864 ------------------------------------------------------------------------------- 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 235 LEU Chi-restraints excluded: chain C residue 239 VAL Chi-restraints excluded: chain C residue 243 SER 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 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 485 ARG 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 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 128 LEU Chi-restraints excluded: chain H residue 139 VAL 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 144 optimal weight: 7.9990 chunk 162 optimal weight: 6.9990 chunk 66 optimal weight: 9.9990 chunk 179 optimal weight: 20.0000 chunk 116 optimal weight: 10.0000 chunk 4 optimal weight: 7.9990 chunk 207 optimal weight: 7.9990 chunk 46 optimal weight: 6.9990 chunk 26 optimal weight: 10.0000 chunk 216 optimal weight: 0.0770 chunk 6 optimal weight: 9.9990 overall best weight: 6.0146 ------------------------------------------------------------------------------- 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 497 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 497 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 608 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 615 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 630 HIS D 272 ASN ** D 290 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 598 ASN E 442 GLN ** F 253 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.3566 r_free = 0.3566 target = 0.129083 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.117529 restraints weight = 32489.270| |-----------------------------------------------------------------------------| r_work (start): 0.3403 rms_B_bonded: 1.85 r_work: 0.3333 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.3235 rms_B_bonded: 4.09 restraints_weight: 0.2500 r_work (final): 0.3235 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7712 moved from start: 0.3229 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 18185 Z= 0.206 Angle : 0.615 13.099 24765 Z= 0.320 Chirality : 0.044 0.179 2550 Planarity : 0.005 0.039 3295 Dihedral : 5.958 59.484 2437 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 9.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.19 % Favored : 94.81 % Rotamer: Outliers : 3.69 % Allowed : 13.24 % Favored : 83.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.90 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.24 (0.17), residues: 2195 helix: -3.69 (0.46), residues: 72 sheet: -0.48 (0.22), residues: 514 loop : -0.82 (0.15), residues: 1609 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP A 619 HIS 0.006 0.001 HIS C 290 PHE 0.022 0.002 PHE H 99 TYR 0.018 0.002 TYR E 443 ARG 0.008 0.001 ARG F 725 Details of bonding type rmsd hydrogen bonds : bond 0.03094 ( 237) hydrogen bonds : angle 6.61397 ( 486) SS BOND : bond 0.00675 ( 3) SS BOND : angle 0.94030 ( 6) covalent geometry : bond 0.00484 (18182) covalent geometry : angle 0.61481 (24759) *********************** 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 332 residues out of total 1927 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 261 time to evaluate : 1.959 Fit side-chains revert: symmetry clash REVERT: A 347 ASP cc_start: 0.7499 (t70) cc_final: 0.6590 (t0) REVERT: A 565 GLU cc_start: 0.6708 (mp0) cc_final: 0.6438 (mp0) REVERT: B 456 GLN cc_start: 0.8004 (mt0) cc_final: 0.7658 (mm110) REVERT: B 470 ASN cc_start: 0.7698 (OUTLIER) cc_final: 0.7459 (m-40) REVERT: B 484 TYR cc_start: 0.7958 (t80) cc_final: 0.7696 (t80) REVERT: C 559 MET cc_start: 0.6550 (ttt) cc_final: 0.6033 (tpp) REVERT: D 340 SER cc_start: 0.7356 (OUTLIER) cc_final: 0.6955 (p) REVERT: D 533 ARG cc_start: 0.7094 (ptt-90) cc_final: 0.6691 (ptt-90) REVERT: D 657 ASP cc_start: 0.8037 (p0) cc_final: 0.7745 (t0) REVERT: E 452 ASN cc_start: 0.8217 (OUTLIER) cc_final: 0.7841 (t0) REVERT: E 575 GLU cc_start: 0.7887 (mm-30) cc_final: 0.7558 (mm-30) REVERT: F 391 ARG cc_start: 0.8088 (ttm110) cc_final: 0.7548 (ttm110) REVERT: F 562 ASN cc_start: 0.8075 (p0) cc_final: 0.7754 (p0) REVERT: F 706 TYR cc_start: 0.7949 (t80) cc_final: 0.7461 (t80) REVERT: F 718 GLU cc_start: 0.8215 (OUTLIER) cc_final: 0.7617 (mp0) REVERT: H 72 TYR cc_start: 0.7904 (OUTLIER) cc_final: 0.6845 (p90) REVERT: L 69 LEU cc_start: 0.7687 (tp) cc_final: 0.7423 (tp) REVERT: L 85 SER cc_start: 0.7639 (t) cc_final: 0.7285 (p) REVERT: L 91 THR cc_start: 0.7781 (p) cc_final: 0.7561 (p) outliers start: 71 outliers final: 60 residues processed: 306 average time/residue: 0.2723 time to fit residues: 129.3870 Evaluate side-chains 323 residues out of total 1927 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 258 time to evaluate : 1.934 ------------------------------------------------------------------------------- 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 239 VAL Chi-restraints excluded: chain C residue 243 SER 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 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 485 ARG 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 F residue 718 GLU 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 128 LEU Chi-restraints excluded: chain H residue 139 VAL Chi-restraints excluded: chain H residue 145 THR Chi-restraints excluded: chain L residue 25 THR 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 221 random chunks: chunk 116 optimal weight: 10.0000 chunk 183 optimal weight: 8.9990 chunk 11 optimal weight: 6.9990 chunk 128 optimal weight: 0.6980 chunk 16 optimal weight: 10.0000 chunk 161 optimal weight: 9.9990 chunk 82 optimal weight: 6.9990 chunk 60 optimal weight: 30.0000 chunk 125 optimal weight: 8.9990 chunk 112 optimal weight: 20.0000 chunk 154 optimal weight: 4.9990 overall best weight: 5.7388 ------------------------------------------------------------------------------- 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 497 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 497 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 608 GLN ** 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 253 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 319 ASN ** 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 = 0.3562 r_free = 0.3562 target = 0.128727 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.117253 restraints weight = 32397.895| |-----------------------------------------------------------------------------| r_work (start): 0.3408 rms_B_bonded: 1.82 r_work: 0.3340 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.3243 rms_B_bonded: 4.03 restraints_weight: 0.2500 r_work (final): 0.3243 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7710 moved from start: 0.3300 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 18185 Z= 0.200 Angle : 0.614 10.832 24765 Z= 0.320 Chirality : 0.044 0.174 2550 Planarity : 0.005 0.038 3295 Dihedral : 5.965 59.879 2437 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 9.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.56 % Favored : 94.44 % Rotamer: Outliers : 3.53 % Allowed : 13.71 % Favored : 82.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.90 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.24 (0.17), residues: 2195 helix: -3.68 (0.47), residues: 71 sheet: -0.49 (0.23), residues: 484 loop : -0.82 (0.14), residues: 1640 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP A 619 HIS 0.006 0.001 HIS C 290 PHE 0.021 0.002 PHE H 99 TYR 0.018 0.002 TYR E 443 ARG 0.007 0.001 ARG F 725 Details of bonding type rmsd hydrogen bonds : bond 0.03038 ( 237) hydrogen bonds : angle 6.59908 ( 486) SS BOND : bond 0.00468 ( 3) SS BOND : angle 0.95455 ( 6) covalent geometry : bond 0.00470 (18182) covalent geometry : angle 0.61401 (24759) ********************** 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 330 residues out of total 1927 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 262 time to evaluate : 2.018 Fit side-chains revert: symmetry clash REVERT: A 347 ASP cc_start: 0.7464 (t70) cc_final: 0.6526 (t0) REVERT: A 565 GLU cc_start: 0.6703 (mp0) cc_final: 0.6434 (mp0) REVERT: B 470 ASN cc_start: 0.7676 (OUTLIER) cc_final: 0.7420 (m-40) REVERT: B 484 TYR cc_start: 0.7911 (t80) cc_final: 0.7674 (t80) REVERT: C 559 MET cc_start: 0.6584 (ttt) cc_final: 0.6107 (tpp) REVERT: D 340 SER cc_start: 0.7353 (OUTLIER) cc_final: 0.6954 (p) REVERT: D 533 ARG cc_start: 0.7119 (ptt-90) cc_final: 0.6717 (ptt-90) REVERT: D 657 ASP cc_start: 0.8038 (p0) cc_final: 0.7753 (t0) REVERT: E 452 ASN cc_start: 0.8147 (OUTLIER) cc_final: 0.7785 (t0) REVERT: E 485 ARG cc_start: 0.7228 (OUTLIER) cc_final: 0.6604 (ttt180) REVERT: E 575 GLU cc_start: 0.7866 (mm-30) cc_final: 0.7530 (mm-30) REVERT: F 391 ARG cc_start: 0.8083 (ttm110) cc_final: 0.7553 (ttm110) REVERT: F 562 ASN cc_start: 0.8092 (p0) cc_final: 0.7662 (p0) REVERT: F 718 GLU cc_start: 0.8201 (OUTLIER) cc_final: 0.7603 (mp0) REVERT: H 72 TYR cc_start: 0.7895 (OUTLIER) cc_final: 0.6854 (p90) REVERT: L 69 LEU cc_start: 0.7656 (tp) cc_final: 0.7426 (tp) REVERT: L 85 SER cc_start: 0.7628 (t) cc_final: 0.7305 (p) REVERT: L 91 THR cc_start: 0.7810 (p) cc_final: 0.7600 (p) REVERT: L 101 GLN cc_start: 0.7060 (mm-40) cc_final: 0.6819 (mt0) outliers start: 68 outliers final: 60 residues processed: 308 average time/residue: 0.2614 time to fit residues: 125.2582 Evaluate side-chains 325 residues out of total 1927 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 259 time to evaluate : 1.781 ------------------------------------------------------------------------------- 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 239 VAL Chi-restraints excluded: chain C residue 243 SER 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 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 485 ARG 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 F residue 718 GLU 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 128 LEU Chi-restraints excluded: chain H residue 139 VAL Chi-restraints excluded: chain H residue 145 THR Chi-restraints excluded: chain L residue 25 THR 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 221 random chunks: chunk 201 optimal weight: 20.0000 chunk 128 optimal weight: 9.9990 chunk 178 optimal weight: 4.9990 chunk 163 optimal weight: 0.7980 chunk 80 optimal weight: 7.9990 chunk 79 optimal weight: 10.0000 chunk 169 optimal weight: 10.0000 chunk 34 optimal weight: 10.0000 chunk 156 optimal weight: 9.9990 chunk 162 optimal weight: 9.9990 chunk 89 optimal weight: 5.9990 overall best weight: 5.9588 ------------------------------------------------------------------------------- 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 497 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 497 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 608 GLN ** 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 253 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.3563 r_free = 0.3563 target = 0.128781 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.117264 restraints weight = 32434.968| |-----------------------------------------------------------------------------| 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: 0.3231 rms_B_bonded: 4.10 restraints_weight: 0.2500 r_work (final): 0.3231 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7716 moved from start: 0.3326 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 18185 Z= 0.206 Angle : 0.619 9.726 24765 Z= 0.323 Chirality : 0.044 0.171 2550 Planarity : 0.005 0.039 3295 Dihedral : 6.006 59.482 2437 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 9.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.33 % Favored : 94.67 % Rotamer: Outliers : 3.63 % Allowed : 13.66 % Favored : 82.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.90 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.34 (0.17), residues: 2195 helix: -3.69 (0.47), residues: 71 sheet: -0.55 (0.23), residues: 504 loop : -0.90 (0.15), residues: 1620 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP C 306 HIS 0.006 0.001 HIS C 290 PHE 0.022 0.002 PHE H 99 TYR 0.019 0.002 TYR E 443 ARG 0.007 0.001 ARG F 725 Details of bonding type rmsd hydrogen bonds : bond 0.03104 ( 237) hydrogen bonds : angle 6.63415 ( 486) SS BOND : bond 0.00518 ( 3) SS BOND : angle 0.94477 ( 6) covalent geometry : bond 0.00483 (18182) covalent geometry : angle 0.61925 (24759) =============================================================================== Job complete usr+sys time: 8200.98 seconds wall clock time: 143 minutes 2.08 seconds (8582.08 seconds total)