Starting phenix.real_space_refine on Wed Feb 4 15:35:47 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8yr9_39538/02_2026/8yr9_39538.cif Found real_map, /net/cci-nas-00/data/ceres_data/8yr9_39538/02_2026/8yr9_39538.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.18 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8yr9_39538/02_2026/8yr9_39538.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8yr9_39538/02_2026/8yr9_39538.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8yr9_39538/02_2026/8yr9_39538.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8yr9_39538/02_2026/8yr9_39538.map" } resolution = 3.18 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.032 sd= 0.117 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 40 5.16 5 C 7489 2.51 5 N 1792 2.21 5 O 1959 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 11 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 11280 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 5480 Number of conformers: 1 Conformer: "" Number of residues, atoms: 702, 5480 Classifications: {'peptide': 702} Link IDs: {'PTRANS': 31, 'TRANS': 670} Chain breaks: 1 Chain: "B" Number of atoms: 5478 Number of conformers: 1 Conformer: "" Number of residues, atoms: 702, 5478 Classifications: {'peptide': 702} Link IDs: {'PTRANS': 31, 'TRANS': 670} Chain breaks: 1 Chain: "A" Number of atoms: 161 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 161 Unusual residues: {'CLR': 2, 'Y01': 3} Classifications: {'undetermined': 5} Link IDs: {None: 4} Chain: "B" Number of atoms: 161 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 161 Unusual residues: {'CLR': 2, 'Y01': 3} Classifications: {'undetermined': 5} Link IDs: {None: 4} Time building chain proxies: 2.86, per 1000 atoms: 0.25 Number of scatterers: 11280 At special positions: 0 Unit cell: (98.58, 121.9, 104.94, 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 40 16.00 O 1959 8.00 N 1792 7.00 C 7489 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.10 Conformation dependent library (CDL) restraints added in 560.4 milliseconds 2792 Ramachandran restraints generated. 1396 Oldfield, 0 Emsley, 1396 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2628 Finding SS restraints... Secondary structure from input PDB file: 64 helices and 5 sheets defined 65.1% alpha, 3.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.38 Creating SS restraints... Processing helix chain 'A' and resid 19 through 25 Processing helix chain 'A' and resid 35 through 44 removed outlier: 3.512A pdb=" N CYS A 42 " --> pdb=" O HIS A 38 " (cutoff:3.500A) Processing helix chain 'A' and resid 46 through 58 Processing helix chain 'A' and resid 59 through 64 Processing helix chain 'A' and resid 72 through 98 removed outlier: 3.935A pdb=" N LEU A 96 " --> pdb=" O LEU A 92 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N LEU A 97 " --> pdb=" O ALA A 93 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N VAL A 98 " --> pdb=" O PHE A 94 " (cutoff:3.500A) Processing helix chain 'A' and resid 102 through 120 removed outlier: 3.569A pdb=" N LEU A 106 " --> pdb=" O PRO A 102 " (cutoff:3.500A) Proline residue: A 112 - end of helix removed outlier: 3.735A pdb=" N PHE A 118 " --> pdb=" O ILE A 114 " (cutoff:3.500A) Processing helix chain 'A' and resid 130 through 146 Processing helix chain 'A' and resid 169 through 196 removed outlier: 3.674A pdb=" N ARG A 173 " --> pdb=" O LEU A 169 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N VAL A 174 " --> pdb=" O ASP A 170 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N ARG A 175 " --> pdb=" O ASP A 171 " (cutoff:3.500A) Processing helix chain 'A' and resid 200 through 205 removed outlier: 3.701A pdb=" N LEU A 205 " --> pdb=" O VAL A 202 " (cutoff:3.500A) Processing helix chain 'A' and resid 206 through 225 Processing helix chain 'A' and resid 225 through 230 Processing helix chain 'A' and resid 242 through 252 Processing helix chain 'A' and resid 253 through 257 Processing helix chain 'A' and resid 258 through 282 Processing helix chain 'A' and resid 291 through 308 Processing helix chain 'A' and resid 332 through 339 Processing helix chain 'A' and resid 339 through 366 removed outlier: 3.845A pdb=" N VAL A 360 " --> pdb=" O SER A 356 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N TYR A 361 " --> pdb=" O VAL A 357 " (cutoff:3.500A) Processing helix chain 'A' and resid 370 through 388 Processing helix chain 'A' and resid 396 through 407 removed outlier: 3.516A pdb=" N GLY A 407 " --> pdb=" O GLN A 403 " (cutoff:3.500A) Processing helix chain 'A' and resid 411 through 427 Processing helix chain 'A' and resid 438 through 447 removed outlier: 3.619A pdb=" N ASN A 447 " --> pdb=" O LEU A 443 " (cutoff:3.500A) Processing helix chain 'A' and resid 447 through 453 removed outlier: 4.440A pdb=" N MET A 451 " --> pdb=" O ASN A 447 " (cutoff:3.500A) Processing helix chain 'A' and resid 454 through 456 No H-bonds generated for 'chain 'A' and resid 454 through 456' Processing helix chain 'A' and resid 457 through 465 Processing helix chain 'A' and resid 467 through 503 removed outlier: 6.954A pdb=" N LEU A 484 " --> pdb=" O ILE A 480 " (cutoff:3.500A) removed outlier: 9.743A pdb=" N GLY A 485 " --> pdb=" O VAL A 481 " (cutoff:3.500A) removed outlier: 4.214A pdb=" N LEU A 486 " --> pdb=" O LEU A 482 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N LEU A 488 " --> pdb=" O LEU A 484 " (cutoff:3.500A) removed outlier: 4.287A pdb=" N ALA A 489 " --> pdb=" O GLY A 485 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N ILE A 499 " --> pdb=" O GLN A 495 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N VAL A 500 " --> pdb=" O LEU A 496 " (cutoff:3.500A) Processing helix chain 'A' and resid 548 through 561 Processing helix chain 'A' and resid 563 through 584 Processing helix chain 'A' and resid 612 through 618 Processing helix chain 'A' and resid 661 through 677 removed outlier: 3.609A pdb=" N ILE A 677 " --> pdb=" O GLU A 673 " (cutoff:3.500A) Processing helix chain 'A' and resid 687 through 697 removed outlier: 3.551A pdb=" N ILE A 691 " --> pdb=" O ASP A 687 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N ARG A 696 " --> pdb=" O GLU A 692 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N TYR A 697 " --> pdb=" O LYS A 693 " (cutoff:3.500A) Processing helix chain 'A' and resid 705 through 707 No H-bonds generated for 'chain 'A' and resid 705 through 707' Processing helix chain 'A' and resid 712 through 725 Processing helix chain 'B' and resid 19 through 25 Processing helix chain 'B' and resid 35 through 44 removed outlier: 3.508A pdb=" N CYS B 42 " --> pdb=" O HIS B 38 " (cutoff:3.500A) Processing helix chain 'B' and resid 46 through 58 Processing helix chain 'B' and resid 59 through 64 Processing helix chain 'B' and resid 72 through 98 removed outlier: 3.941A pdb=" N LEU B 96 " --> pdb=" O LEU B 92 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N LEU B 97 " --> pdb=" O ALA B 93 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N VAL B 98 " --> pdb=" O PHE B 94 " (cutoff:3.500A) Processing helix chain 'B' and resid 102 through 120 removed outlier: 3.555A pdb=" N LEU B 106 " --> pdb=" O PRO B 102 " (cutoff:3.500A) Proline residue: B 112 - end of helix removed outlier: 3.733A pdb=" N PHE B 118 " --> pdb=" O ILE B 114 " (cutoff:3.500A) Processing helix chain 'B' and resid 130 through 146 Processing helix chain 'B' and resid 168 through 196 Processing helix chain 'B' and resid 200 through 205 removed outlier: 3.688A pdb=" N LEU B 205 " --> pdb=" O VAL B 202 " (cutoff:3.500A) Processing helix chain 'B' and resid 206 through 225 Processing helix chain 'B' and resid 225 through 230 Processing helix chain 'B' and resid 242 through 252 Processing helix chain 'B' and resid 253 through 257 Processing helix chain 'B' and resid 258 through 282 Processing helix chain 'B' and resid 291 through 308 removed outlier: 4.699A pdb=" N GLY B 306 " --> pdb=" O GLY B 302 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N CYS B 307 " --> pdb=" O VAL B 303 " (cutoff:3.500A) Processing helix chain 'B' and resid 332 through 339 Processing helix chain 'B' and resid 339 through 366 removed outlier: 3.851A pdb=" N VAL B 360 " --> pdb=" O SER B 356 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N TYR B 361 " --> pdb=" O VAL B 357 " (cutoff:3.500A) Processing helix chain 'B' and resid 370 through 388 Processing helix chain 'B' and resid 396 through 407 Processing helix chain 'B' and resid 411 through 427 Processing helix chain 'B' and resid 438 through 447 removed outlier: 3.585A pdb=" N ASN B 447 " --> pdb=" O LEU B 443 " (cutoff:3.500A) Processing helix chain 'B' and resid 448 through 453 Processing helix chain 'B' and resid 454 through 456 No H-bonds generated for 'chain 'B' and resid 454 through 456' Processing helix chain 'B' and resid 457 through 465 Processing helix chain 'B' and resid 467 through 503 removed outlier: 6.938A pdb=" N LEU B 484 " --> pdb=" O ILE B 480 " (cutoff:3.500A) removed outlier: 9.717A pdb=" N GLY B 485 " --> pdb=" O VAL B 481 " (cutoff:3.500A) removed outlier: 4.214A pdb=" N LEU B 486 " --> pdb=" O LEU B 482 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N LEU B 488 " --> pdb=" O LEU B 484 " (cutoff:3.500A) removed outlier: 4.284A pdb=" N ALA B 489 " --> pdb=" O GLY B 485 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N ILE B 499 " --> pdb=" O GLN B 495 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N VAL B 500 " --> pdb=" O LEU B 496 " (cutoff:3.500A) Processing helix chain 'B' and resid 548 through 561 Processing helix chain 'B' and resid 563 through 584 Processing helix chain 'B' and resid 609 through 618 removed outlier: 3.501A pdb=" N GLN B 612 " --> pdb=" O ASP B 609 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N ILE B 613 " --> pdb=" O ASN B 610 " (cutoff:3.500A) removed outlier: 5.196A pdb=" N GLU B 614 " --> pdb=" O ASN B 611 " (cutoff:3.500A) Processing helix chain 'B' and resid 661 through 676 Processing helix chain 'B' and resid 687 through 697 removed outlier: 3.546A pdb=" N ILE B 691 " --> pdb=" O ASP B 687 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N ARG B 696 " --> pdb=" O GLU B 692 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N TYR B 697 " --> pdb=" O LYS B 693 " (cutoff:3.500A) Processing helix chain 'B' and resid 705 through 707 No H-bonds generated for 'chain 'B' and resid 705 through 707' Processing helix chain 'B' and resid 712 through 725 Processing sheet with id=AA1, first strand: chain 'A' and resid 9 through 13 Processing sheet with id=AA2, first strand: chain 'A' and resid 127 through 128 Processing sheet with id=AA3, first strand: chain 'A' and resid 520 through 522 removed outlier: 4.503A pdb=" N ILE A 537 " --> pdb=" O LEU A 511 " (cutoff:3.500A) removed outlier: 8.615A pdb=" N ASN A 513 " --> pdb=" O VAL A 535 " (cutoff:3.500A) removed outlier: 12.709A pdb=" N VAL A 535 " --> pdb=" O ASN A 513 " (cutoff:3.500A) removed outlier: 6.473A pdb=" N LYS A 536 " --> pdb=" O ILE A 650 " (cutoff:3.500A) removed outlier: 7.544A pdb=" N ASP A 652 " --> pdb=" O LYS A 536 " (cutoff:3.500A) removed outlier: 7.130A pdb=" N PHE A 538 " --> pdb=" O ASP A 652 " (cutoff:3.500A) removed outlier: 7.652A pdb=" N PHE A 710 " --> pdb=" O VAL A 681 " (cutoff:3.500A) removed outlier: 6.120A pdb=" N ILE A 683 " --> pdb=" O PHE A 710 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 127 through 128 Processing sheet with id=AA5, first strand: chain 'B' and resid 520 through 522 removed outlier: 4.499A pdb=" N ILE B 537 " --> pdb=" O LEU B 511 " (cutoff:3.500A) removed outlier: 8.615A pdb=" N ASN B 513 " --> pdb=" O VAL B 535 " (cutoff:3.500A) removed outlier: 12.716A pdb=" N VAL B 535 " --> pdb=" O ASN B 513 " (cutoff:3.500A) removed outlier: 6.481A pdb=" N LYS B 536 " --> pdb=" O ILE B 650 " (cutoff:3.500A) removed outlier: 7.543A pdb=" N ASP B 652 " --> pdb=" O LYS B 536 " (cutoff:3.500A) removed outlier: 7.128A pdb=" N PHE B 538 " --> pdb=" O ASP B 652 " (cutoff:3.500A) removed outlier: 7.667A pdb=" N PHE B 710 " --> pdb=" O VAL B 681 " (cutoff:3.500A) removed outlier: 6.129A pdb=" N ILE B 683 " --> pdb=" O PHE B 710 " (cutoff:3.500A) 639 hydrogen bonds defined for protein. 1851 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.02 Time building geometry restraints manager: 1.48 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2048 1.33 - 1.45: 2656 1.45 - 1.57: 6783 1.57 - 1.70: 1 1.70 - 1.82: 60 Bond restraints: 11548 Sorted by residual: bond pdb=" CA ASN B 621 " pdb=" CB ASN B 621 " ideal model delta sigma weight residual 1.530 1.582 -0.052 1.57e-02 4.06e+03 1.11e+01 bond pdb=" C ASP B 239 " pdb=" N PRO B 240 " ideal model delta sigma weight residual 1.334 1.370 -0.036 2.34e-02 1.83e+03 2.36e+00 bond pdb=" C ASP A 239 " pdb=" N PRO A 240 " ideal model delta sigma weight residual 1.334 1.369 -0.036 2.34e-02 1.83e+03 2.31e+00 bond pdb=" CB ASN B 621 " pdb=" CG ASN B 621 " ideal model delta sigma weight residual 1.516 1.551 -0.035 2.50e-02 1.60e+03 1.98e+00 bond pdb=" CB GLU A 614 " pdb=" CG GLU A 614 " ideal model delta sigma weight residual 1.520 1.554 -0.034 3.00e-02 1.11e+03 1.26e+00 ... (remaining 11543 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.16: 15667 3.16 - 6.32: 59 6.32 - 9.47: 3 9.47 - 12.63: 0 12.63 - 15.79: 2 Bond angle restraints: 15731 Sorted by residual: angle pdb=" CA LEU A 69 " pdb=" CB LEU A 69 " pdb=" CG LEU A 69 " ideal model delta sigma weight residual 116.30 132.09 -15.79 3.50e+00 8.16e-02 2.04e+01 angle pdb=" CA LEU B 69 " pdb=" CB LEU B 69 " pdb=" CG LEU B 69 " ideal model delta sigma weight residual 116.30 131.86 -15.56 3.50e+00 8.16e-02 1.98e+01 angle pdb=" CA ASN B 621 " pdb=" CB ASN B 621 " pdb=" CG ASN B 621 " ideal model delta sigma weight residual 112.60 116.91 -4.31 1.00e+00 1.00e+00 1.86e+01 angle pdb=" C ASN B 621 " pdb=" CA ASN B 621 " pdb=" CB ASN B 621 " ideal model delta sigma weight residual 110.62 116.86 -6.24 1.51e+00 4.39e-01 1.71e+01 angle pdb=" N LYS B 70 " pdb=" CA LYS B 70 " pdb=" C LYS B 70 " ideal model delta sigma weight residual 114.62 110.43 4.19 1.14e+00 7.69e-01 1.35e+01 ... (remaining 15726 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.47: 6677 23.47 - 46.93: 601 46.93 - 70.40: 70 70.40 - 93.87: 6 93.87 - 117.34: 5 Dihedral angle restraints: 7359 sinusoidal: 3291 harmonic: 4068 Sorted by residual: dihedral pdb=" CBC Y01 A 802 " pdb=" CAR Y01 A 802 " pdb=" CAT Y01 A 802 " pdb=" CBH Y01 A 802 " ideal model delta sinusoidal sigma weight residual -57.13 60.21 -117.34 1 3.00e+01 1.11e-03 1.56e+01 dihedral pdb=" CAT Y01 B 803 " pdb=" CAR Y01 B 803 " pdb=" CBC Y01 B 803 " pdb=" CAV Y01 B 803 " ideal model delta sinusoidal sigma weight residual 58.10 -48.42 106.52 1 3.00e+01 1.11e-03 1.37e+01 dihedral pdb=" CBC Y01 B 803 " pdb=" CAR Y01 B 803 " pdb=" CAT Y01 B 803 " pdb=" CBH Y01 B 803 " ideal model delta sinusoidal sigma weight residual -57.13 49.19 -106.32 1 3.00e+01 1.11e-03 1.37e+01 ... (remaining 7356 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.034: 1306 0.034 - 0.068: 391 0.068 - 0.103: 141 0.103 - 0.137: 51 0.137 - 0.171: 1 Chirality restraints: 1890 Sorted by residual: chirality pdb=" CG LEU A 637 " pdb=" CB LEU A 637 " pdb=" CD1 LEU A 637 " pdb=" CD2 LEU A 637 " both_signs ideal model delta sigma weight residual False -2.59 -2.42 -0.17 2.00e-01 2.50e+01 7.31e-01 chirality pdb=" CA ASN B 621 " pdb=" N ASN B 621 " pdb=" C ASN B 621 " pdb=" CB ASN B 621 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.14 2.00e-01 2.50e+01 4.62e-01 chirality pdb=" CA ILE B 620 " pdb=" N ILE B 620 " pdb=" C ILE B 620 " pdb=" CB ILE B 620 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.56e-01 ... (remaining 1887 not shown) Planarity restraints: 1905 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASN B 621 " 0.012 2.00e-02 2.50e+03 2.35e-02 5.51e+00 pdb=" C ASN B 621 " -0.041 2.00e-02 2.50e+03 pdb=" O ASN B 621 " 0.016 2.00e-02 2.50e+03 pdb=" N THR B 622 " 0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLU B 614 " -0.009 2.00e-02 2.50e+03 1.91e-02 3.65e+00 pdb=" CD GLU B 614 " 0.033 2.00e-02 2.50e+03 pdb=" OE1 GLU B 614 " -0.012 2.00e-02 2.50e+03 pdb=" OE2 GLU B 614 " -0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C THR A 590 " 0.028 5.00e-02 4.00e+02 4.34e-02 3.01e+00 pdb=" N PRO A 591 " -0.075 5.00e-02 4.00e+02 pdb=" CA PRO A 591 " 0.022 5.00e-02 4.00e+02 pdb=" CD PRO A 591 " 0.024 5.00e-02 4.00e+02 ... (remaining 1902 not shown) Histogram of nonbonded interaction distances: 2.06 - 2.63: 102 2.63 - 3.19: 10146 3.19 - 3.76: 17332 3.76 - 4.33: 22540 4.33 - 4.90: 38879 Nonbonded interactions: 88999 Sorted by model distance: nonbonded pdb=" O ASN B 621 " pdb=" ND2 ASN B 621 " model vdw 2.058 3.120 nonbonded pdb=" OD1 ASP B 261 " pdb=" OG SER B 438 " model vdw 2.203 3.040 nonbonded pdb=" OG1 THR A 503 " pdb=" OH TYR A 545 " model vdw 2.204 3.040 nonbonded pdb=" OG1 THR A 475 " pdb=" OG SER A 491 " model vdw 2.205 3.040 nonbonded pdb=" OG1 THR B 503 " pdb=" OH TYR B 545 " model vdw 2.210 3.040 ... (remaining 88994 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 8 through 150 or resid 168 through 805)) selection = (chain 'B' and (resid 8 through 150 or resid 168 through 805)) } 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: 0.920 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.180 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 12.810 Find NCS groups from input model: 0.230 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.310 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.570 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7393 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 : 0.002 0.052 11548 Z= 0.111 Angle : 0.533 15.790 15731 Z= 0.277 Chirality : 0.040 0.171 1890 Planarity : 0.003 0.043 1905 Dihedral : 16.131 117.336 4731 Min Nonbonded Distance : 2.058 Molprobity Statistics. All-atom Clashscore : 8.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.23 % Favored : 94.77 % Rotamer: Outliers : 0.17 % Allowed : 25.62 % Favored : 74.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.48 (0.23), residues: 1396 helix: 2.25 (0.18), residues: 848 sheet: 3.07 (0.92), residues: 36 loop : -1.49 (0.26), residues: 512 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 68 TYR 0.008 0.001 TYR A 365 PHE 0.018 0.001 PHE A 627 TRP 0.019 0.002 TRP B 63 HIS 0.002 0.000 HIS B 714 Details of bonding type rmsd covalent geometry : bond 0.00219 (11548) covalent geometry : angle 0.53315 (15731) hydrogen bonds : bond 0.11644 ( 639) hydrogen bonds : angle 4.00329 ( 1851) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2792 Ramachandran restraints generated. 1396 Oldfield, 0 Emsley, 1396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2792 Ramachandran restraints generated. 1396 Oldfield, 0 Emsley, 1396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 1210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 101 time to evaluate : 0.436 Fit side-chains outliers start: 2 outliers final: 1 residues processed: 103 average time/residue: 0.0827 time to fit residues: 13.6952 Evaluate side-chains 96 residues out of total 1210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 95 time to evaluate : 0.418 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 621 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 98 optimal weight: 9.9990 chunk 107 optimal weight: 1.9990 chunk 10 optimal weight: 1.9990 chunk 66 optimal weight: 3.9990 chunk 130 optimal weight: 6.9990 chunk 124 optimal weight: 0.7980 chunk 103 optimal weight: 0.7980 chunk 77 optimal weight: 0.9980 chunk 122 optimal weight: 2.9990 chunk 91 optimal weight: 0.0970 chunk 55 optimal weight: 5.9990 overall best weight: 0.9380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 326 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 447 ASN B 621 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.119883 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3029 r_free = 0.3029 target = 0.085317 restraints weight = 16472.859| |-----------------------------------------------------------------------------| r_work (start): 0.3018 rms_B_bonded: 3.16 r_work: 0.2885 rms_B_bonded: 3.66 restraints_weight: 0.5000 r_work (final): 0.2885 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7426 moved from start: 0.0481 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 11548 Z= 0.121 Angle : 0.520 10.598 15731 Z= 0.267 Chirality : 0.040 0.133 1890 Planarity : 0.004 0.043 1905 Dihedral : 8.533 94.435 2182 Min Nonbonded Distance : 2.561 Molprobity Statistics. All-atom Clashscore : 6.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.52 % Favored : 93.48 % Rotamer: Outliers : 1.57 % Allowed : 23.31 % Favored : 75.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.53 (0.24), residues: 1396 helix: 2.22 (0.18), residues: 856 sheet: 2.99 (0.93), residues: 34 loop : -1.35 (0.28), residues: 506 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 539 TYR 0.008 0.001 TYR B 367 PHE 0.013 0.001 PHE B 130 TRP 0.014 0.001 TRP B 63 HIS 0.002 0.001 HIS B 714 Details of bonding type rmsd covalent geometry : bond 0.00275 (11548) covalent geometry : angle 0.52010 (15731) hydrogen bonds : bond 0.03199 ( 639) hydrogen bonds : angle 3.70657 ( 1851) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2792 Ramachandran restraints generated. 1396 Oldfield, 0 Emsley, 1396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2792 Ramachandran restraints generated. 1396 Oldfield, 0 Emsley, 1396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 1210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 109 time to evaluate : 0.426 Fit side-chains REVERT: B 610 ASN cc_start: 0.7806 (m-40) cc_final: 0.7581 (m-40) REVERT: B 614 GLU cc_start: 0.7412 (tm-30) cc_final: 0.7145 (tm-30) outliers start: 19 outliers final: 7 residues processed: 127 average time/residue: 0.0781 time to fit residues: 16.0251 Evaluate side-chains 100 residues out of total 1210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 93 time to evaluate : 0.336 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 CYS Chi-restraints excluded: chain A residue 572 ASN Chi-restraints excluded: chain A residue 598 VAL Chi-restraints excluded: chain A residue 646 LEU Chi-restraints excluded: chain B residue 448 LEU Chi-restraints excluded: chain B residue 572 ASN Chi-restraints excluded: chain B residue 598 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 113 optimal weight: 3.9990 chunk 46 optimal weight: 3.9990 chunk 89 optimal weight: 0.8980 chunk 21 optimal weight: 9.9990 chunk 63 optimal weight: 0.9990 chunk 93 optimal weight: 0.9990 chunk 92 optimal weight: 3.9990 chunk 51 optimal weight: 2.9990 chunk 9 optimal weight: 4.9990 chunk 83 optimal weight: 3.9990 chunk 131 optimal weight: 3.9990 overall best weight: 1.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.116028 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2966 r_free = 0.2966 target = 0.081214 restraints weight = 16839.333| |-----------------------------------------------------------------------------| r_work (start): 0.2964 rms_B_bonded: 3.16 r_work: 0.2829 rms_B_bonded: 3.63 restraints_weight: 0.5000 r_work (final): 0.2829 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7487 moved from start: 0.0838 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 11548 Z= 0.178 Angle : 0.554 11.912 15731 Z= 0.282 Chirality : 0.041 0.132 1890 Planarity : 0.004 0.043 1905 Dihedral : 7.233 58.378 2180 Min Nonbonded Distance : 2.572 Molprobity Statistics. All-atom Clashscore : 6.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.30 % Favored : 93.70 % Rotamer: Outliers : 3.06 % Allowed : 22.89 % Favored : 74.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.51 (0.24), residues: 1396 helix: 2.12 (0.18), residues: 856 sheet: 3.07 (0.89), residues: 36 loop : -1.20 (0.28), residues: 504 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 13 TYR 0.013 0.001 TYR A 9 PHE 0.016 0.001 PHE B 130 TRP 0.011 0.001 TRP B 63 HIS 0.004 0.001 HIS A 714 Details of bonding type rmsd covalent geometry : bond 0.00431 (11548) covalent geometry : angle 0.55395 (15731) hydrogen bonds : bond 0.03583 ( 639) hydrogen bonds : angle 3.74858 ( 1851) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2792 Ramachandran restraints generated. 1396 Oldfield, 0 Emsley, 1396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2792 Ramachandran restraints generated. 1396 Oldfield, 0 Emsley, 1396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 1210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 101 time to evaluate : 0.427 Fit side-chains REVERT: A 266 LEU cc_start: 0.7390 (OUTLIER) cc_final: 0.7148 (mp) REVERT: A 395 THR cc_start: 0.9301 (t) cc_final: 0.9085 (t) REVERT: B 395 THR cc_start: 0.9284 (t) cc_final: 0.9064 (t) REVERT: B 610 ASN cc_start: 0.8086 (m-40) cc_final: 0.7816 (m-40) REVERT: B 614 GLU cc_start: 0.7407 (tm-30) cc_final: 0.7115 (tm-30) outliers start: 37 outliers final: 26 residues processed: 130 average time/residue: 0.0825 time to fit residues: 17.2086 Evaluate side-chains 119 residues out of total 1210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 92 time to evaluate : 0.440 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 ILE Chi-restraints excluded: chain A residue 45 CYS Chi-restraints excluded: chain A residue 54 VAL Chi-restraints excluded: chain A residue 58 PHE Chi-restraints excluded: chain A residue 125 ILE Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 290 ILE Chi-restraints excluded: chain A residue 303 VAL Chi-restraints excluded: chain A residue 370 ASP Chi-restraints excluded: chain A residue 423 ILE Chi-restraints excluded: chain A residue 448 LEU Chi-restraints excluded: chain A residue 572 ASN Chi-restraints excluded: chain A residue 598 VAL Chi-restraints excluded: chain A residue 646 LEU Chi-restraints excluded: chain B residue 54 VAL Chi-restraints excluded: chain B residue 58 PHE Chi-restraints excluded: chain B residue 125 ILE Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 266 LEU Chi-restraints excluded: chain B residue 303 VAL Chi-restraints excluded: chain B residue 315 VAL Chi-restraints excluded: chain B residue 423 ILE Chi-restraints excluded: chain B residue 448 LEU Chi-restraints excluded: chain B residue 572 ASN Chi-restraints excluded: chain B residue 598 VAL Chi-restraints excluded: chain B residue 646 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 81 optimal weight: 5.9990 chunk 45 optimal weight: 0.9990 chunk 84 optimal weight: 10.0000 chunk 122 optimal weight: 0.0770 chunk 116 optimal weight: 0.5980 chunk 71 optimal weight: 2.9990 chunk 130 optimal weight: 6.9990 chunk 21 optimal weight: 4.9990 chunk 22 optimal weight: 0.8980 chunk 41 optimal weight: 0.7980 chunk 30 optimal weight: 0.1980 overall best weight: 0.5138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.119917 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3033 r_free = 0.3033 target = 0.085495 restraints weight = 16540.508| |-----------------------------------------------------------------------------| r_work (start): 0.3023 rms_B_bonded: 3.16 r_work: 0.2888 rms_B_bonded: 3.67 restraints_weight: 0.5000 r_work (final): 0.2888 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7427 moved from start: 0.0758 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 11548 Z= 0.101 Angle : 0.494 12.114 15731 Z= 0.254 Chirality : 0.040 0.132 1890 Planarity : 0.004 0.043 1905 Dihedral : 6.870 59.714 2180 Min Nonbonded Distance : 2.585 Molprobity Statistics. All-atom Clashscore : 5.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.66 % Favored : 94.34 % Rotamer: Outliers : 1.90 % Allowed : 23.31 % Favored : 74.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.61 (0.24), residues: 1396 helix: 2.28 (0.18), residues: 844 sheet: 3.11 (0.91), residues: 36 loop : -1.23 (0.28), residues: 516 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 13 TYR 0.007 0.001 TYR B 104 PHE 0.018 0.001 PHE A 94 TRP 0.013 0.001 TRP A 63 HIS 0.003 0.001 HIS B 714 Details of bonding type rmsd covalent geometry : bond 0.00217 (11548) covalent geometry : angle 0.49436 (15731) hydrogen bonds : bond 0.03131 ( 639) hydrogen bonds : angle 3.65650 ( 1851) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2792 Ramachandran restraints generated. 1396 Oldfield, 0 Emsley, 1396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2792 Ramachandran restraints generated. 1396 Oldfield, 0 Emsley, 1396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 1210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 105 time to evaluate : 0.347 Fit side-chains REVERT: A 395 THR cc_start: 0.9220 (t) cc_final: 0.9017 (t) REVERT: B 395 THR cc_start: 0.9182 (t) cc_final: 0.8979 (t) REVERT: B 610 ASN cc_start: 0.8048 (m-40) cc_final: 0.7793 (m-40) REVERT: B 614 GLU cc_start: 0.7364 (tm-30) cc_final: 0.7034 (tm-30) outliers start: 23 outliers final: 13 residues processed: 127 average time/residue: 0.0686 time to fit residues: 14.2608 Evaluate side-chains 109 residues out of total 1210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 96 time to evaluate : 0.417 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 149 VAL Chi-restraints excluded: chain A residue 370 ASP Chi-restraints excluded: chain A residue 448 LEU Chi-restraints excluded: chain A residue 572 ASN Chi-restraints excluded: chain A residue 590 THR Chi-restraints excluded: chain A residue 598 VAL Chi-restraints excluded: chain A residue 643 LYS Chi-restraints excluded: chain A residue 646 LEU Chi-restraints excluded: chain B residue 58 PHE Chi-restraints excluded: chain B residue 266 LEU Chi-restraints excluded: chain B residue 448 LEU Chi-restraints excluded: chain B residue 598 VAL Chi-restraints excluded: chain B residue 646 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 96 optimal weight: 5.9990 chunk 120 optimal weight: 6.9990 chunk 49 optimal weight: 4.9990 chunk 90 optimal weight: 3.9990 chunk 40 optimal weight: 0.4980 chunk 35 optimal weight: 2.9990 chunk 8 optimal weight: 2.9990 chunk 50 optimal weight: 10.0000 chunk 3 optimal weight: 20.0000 chunk 126 optimal weight: 9.9990 chunk 66 optimal weight: 3.9990 overall best weight: 2.8988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.114201 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2939 r_free = 0.2939 target = 0.079397 restraints weight = 16798.949| |-----------------------------------------------------------------------------| r_work (start): 0.2936 rms_B_bonded: 3.14 r_work: 0.2801 rms_B_bonded: 3.60 restraints_weight: 0.5000 r_work (final): 0.2801 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7522 moved from start: 0.1093 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.049 11548 Z= 0.243 Angle : 0.590 12.850 15731 Z= 0.302 Chirality : 0.043 0.162 1890 Planarity : 0.004 0.042 1905 Dihedral : 6.999 58.347 2180 Min Nonbonded Distance : 2.585 Molprobity Statistics. All-atom Clashscore : 5.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.88 % Favored : 93.12 % Rotamer: Outliers : 3.47 % Allowed : 23.97 % Favored : 72.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.41 (0.24), residues: 1396 helix: 2.05 (0.18), residues: 852 sheet: 2.93 (0.91), residues: 36 loop : -1.24 (0.28), residues: 508 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 13 TYR 0.016 0.002 TYR A 9 PHE 0.017 0.001 PHE A 130 TRP 0.009 0.001 TRP B 63 HIS 0.004 0.001 HIS A 714 Details of bonding type rmsd covalent geometry : bond 0.00593 (11548) covalent geometry : angle 0.58969 (15731) hydrogen bonds : bond 0.03796 ( 639) hydrogen bonds : angle 3.80643 ( 1851) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2792 Ramachandran restraints generated. 1396 Oldfield, 0 Emsley, 1396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2792 Ramachandran restraints generated. 1396 Oldfield, 0 Emsley, 1396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 1210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 96 time to evaluate : 0.429 Fit side-chains REVERT: A 266 LEU cc_start: 0.7262 (OUTLIER) cc_final: 0.7003 (mp) REVERT: A 310 LYS cc_start: 0.8241 (OUTLIER) cc_final: 0.7575 (tptt) REVERT: A 395 THR cc_start: 0.9345 (t) cc_final: 0.9124 (t) REVERT: A 614 GLU cc_start: 0.7386 (tm-30) cc_final: 0.7162 (tm-30) REVERT: B 395 THR cc_start: 0.9325 (t) cc_final: 0.9109 (t) REVERT: B 610 ASN cc_start: 0.8208 (m-40) cc_final: 0.7942 (m-40) REVERT: B 614 GLU cc_start: 0.7468 (tm-30) cc_final: 0.7118 (tm-30) outliers start: 42 outliers final: 31 residues processed: 132 average time/residue: 0.0843 time to fit residues: 17.7437 Evaluate side-chains 127 residues out of total 1210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 94 time to evaluate : 0.428 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 ILE Chi-restraints excluded: chain A residue 45 CYS Chi-restraints excluded: chain A residue 54 VAL Chi-restraints excluded: chain A residue 57 LEU Chi-restraints excluded: chain A residue 58 PHE Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 149 VAL Chi-restraints excluded: chain A residue 253 GLN Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 303 VAL Chi-restraints excluded: chain A residue 310 LYS Chi-restraints excluded: chain A residue 315 VAL Chi-restraints excluded: chain A residue 448 LEU Chi-restraints excluded: chain A residue 572 ASN Chi-restraints excluded: chain A residue 590 THR Chi-restraints excluded: chain A residue 598 VAL Chi-restraints excluded: chain A residue 646 LEU Chi-restraints excluded: chain A residue 691 ILE Chi-restraints excluded: chain B residue 45 CYS Chi-restraints excluded: chain B residue 54 VAL Chi-restraints excluded: chain B residue 58 PHE Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 149 VAL Chi-restraints excluded: chain B residue 182 VAL Chi-restraints excluded: chain B residue 253 GLN Chi-restraints excluded: chain B residue 266 LEU Chi-restraints excluded: chain B residue 315 VAL Chi-restraints excluded: chain B residue 448 LEU Chi-restraints excluded: chain B residue 498 THR Chi-restraints excluded: chain B residue 572 ASN Chi-restraints excluded: chain B residue 590 THR Chi-restraints excluded: chain B residue 598 VAL Chi-restraints excluded: chain B residue 646 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 87 optimal weight: 0.0870 chunk 25 optimal weight: 0.7980 chunk 122 optimal weight: 0.8980 chunk 44 optimal weight: 4.9990 chunk 55 optimal weight: 2.9990 chunk 117 optimal weight: 0.5980 chunk 70 optimal weight: 3.9990 chunk 75 optimal weight: 3.9990 chunk 68 optimal weight: 3.9990 chunk 60 optimal weight: 0.0270 chunk 45 optimal weight: 0.7980 overall best weight: 0.4616 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.118926 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3016 r_free = 0.3016 target = 0.084413 restraints weight = 16605.494| |-----------------------------------------------------------------------------| r_work (start): 0.3016 rms_B_bonded: 3.16 r_work: 0.2882 rms_B_bonded: 3.66 restraints_weight: 0.5000 r_work (final): 0.2882 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7448 moved from start: 0.0937 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 11548 Z= 0.107 Angle : 0.509 13.747 15731 Z= 0.259 Chirality : 0.040 0.152 1890 Planarity : 0.003 0.042 1905 Dihedral : 6.794 59.903 2180 Min Nonbonded Distance : 2.584 Molprobity Statistics. All-atom Clashscore : 5.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.59 % Favored : 94.41 % Rotamer: Outliers : 2.81 % Allowed : 24.13 % Favored : 73.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.60 (0.24), residues: 1396 helix: 2.26 (0.18), residues: 847 sheet: 3.09 (0.92), residues: 36 loop : -1.24 (0.28), residues: 513 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 13 TYR 0.007 0.001 TYR A 365 PHE 0.014 0.001 PHE A 627 TRP 0.015 0.001 TRP A 63 HIS 0.003 0.001 HIS B 714 Details of bonding type rmsd covalent geometry : bond 0.00232 (11548) covalent geometry : angle 0.50899 (15731) hydrogen bonds : bond 0.03196 ( 639) hydrogen bonds : angle 3.67276 ( 1851) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2792 Ramachandran restraints generated. 1396 Oldfield, 0 Emsley, 1396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2792 Ramachandran restraints generated. 1396 Oldfield, 0 Emsley, 1396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 1210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 100 time to evaluate : 0.376 Fit side-chains REVERT: A 238 THR cc_start: 0.7737 (OUTLIER) cc_final: 0.7395 (p) REVERT: A 395 THR cc_start: 0.9219 (t) cc_final: 0.9005 (t) REVERT: B 238 THR cc_start: 0.7733 (OUTLIER) cc_final: 0.7391 (p) REVERT: B 395 THR cc_start: 0.9185 (t) cc_final: 0.8975 (t) REVERT: B 610 ASN cc_start: 0.8129 (m-40) cc_final: 0.7862 (m-40) REVERT: B 614 GLU cc_start: 0.7367 (tm-30) cc_final: 0.7018 (tm-30) outliers start: 34 outliers final: 16 residues processed: 131 average time/residue: 0.0723 time to fit residues: 15.3891 Evaluate side-chains 111 residues out of total 1210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 93 time to evaluate : 0.427 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 CYS Chi-restraints excluded: chain A residue 58 PHE Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 149 VAL Chi-restraints excluded: chain A residue 238 THR Chi-restraints excluded: chain A residue 448 LEU Chi-restraints excluded: chain A residue 590 THR Chi-restraints excluded: chain A residue 598 VAL Chi-restraints excluded: chain A residue 646 LEU Chi-restraints excluded: chain A residue 679 VAL Chi-restraints excluded: chain B residue 58 PHE Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 149 VAL Chi-restraints excluded: chain B residue 238 THR Chi-restraints excluded: chain B residue 448 LEU Chi-restraints excluded: chain B residue 590 THR Chi-restraints excluded: chain B residue 598 VAL Chi-restraints excluded: chain B residue 646 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 125 optimal weight: 1.9990 chunk 16 optimal weight: 5.9990 chunk 97 optimal weight: 0.8980 chunk 98 optimal weight: 2.9990 chunk 30 optimal weight: 0.0670 chunk 25 optimal weight: 0.9990 chunk 21 optimal weight: 8.9990 chunk 11 optimal weight: 6.9990 chunk 68 optimal weight: 5.9990 chunk 29 optimal weight: 0.9990 chunk 60 optimal weight: 10.0000 overall best weight: 0.9924 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.118317 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3008 r_free = 0.3008 target = 0.083868 restraints weight = 16650.920| |-----------------------------------------------------------------------------| r_work (start): 0.3015 rms_B_bonded: 3.15 r_work: 0.2864 rms_B_bonded: 3.71 restraints_weight: 0.5000 r_work (final): 0.2864 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7467 moved from start: 0.0977 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 11548 Z= 0.120 Angle : 0.512 14.362 15731 Z= 0.259 Chirality : 0.040 0.178 1890 Planarity : 0.003 0.042 1905 Dihedral : 6.705 59.628 2180 Min Nonbonded Distance : 2.593 Molprobity Statistics. All-atom Clashscore : 5.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.73 % Favored : 93.27 % Rotamer: Outliers : 2.23 % Allowed : 24.96 % Favored : 72.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.62 (0.24), residues: 1396 helix: 2.24 (0.18), residues: 852 sheet: 3.08 (0.92), residues: 36 loop : -1.20 (0.28), residues: 508 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 13 TYR 0.008 0.001 TYR B 104 PHE 0.018 0.001 PHE B 94 TRP 0.012 0.001 TRP B 63 HIS 0.003 0.001 HIS B 714 Details of bonding type rmsd covalent geometry : bond 0.00276 (11548) covalent geometry : angle 0.51202 (15731) hydrogen bonds : bond 0.03224 ( 639) hydrogen bonds : angle 3.64389 ( 1851) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2792 Ramachandran restraints generated. 1396 Oldfield, 0 Emsley, 1396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2792 Ramachandran restraints generated. 1396 Oldfield, 0 Emsley, 1396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 1210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 96 time to evaluate : 0.448 Fit side-chains REVERT: A 238 THR cc_start: 0.7733 (OUTLIER) cc_final: 0.7396 (p) REVERT: A 310 LYS cc_start: 0.8261 (OUTLIER) cc_final: 0.7674 (tptt) REVERT: A 395 THR cc_start: 0.9238 (t) cc_final: 0.9025 (t) REVERT: B 238 THR cc_start: 0.7727 (OUTLIER) cc_final: 0.7391 (p) REVERT: B 410 THR cc_start: 0.9376 (p) cc_final: 0.9071 (t) REVERT: B 610 ASN cc_start: 0.8164 (m-40) cc_final: 0.7940 (m-40) REVERT: B 614 GLU cc_start: 0.7381 (tm-30) cc_final: 0.7027 (tm-30) outliers start: 27 outliers final: 20 residues processed: 123 average time/residue: 0.0827 time to fit residues: 16.3589 Evaluate side-chains 114 residues out of total 1210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 91 time to evaluate : 0.405 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 PHE Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 149 VAL Chi-restraints excluded: chain A residue 238 THR Chi-restraints excluded: chain A residue 253 GLN Chi-restraints excluded: chain A residue 310 LYS Chi-restraints excluded: chain A residue 448 LEU Chi-restraints excluded: chain A residue 455 PHE Chi-restraints excluded: chain A residue 590 THR Chi-restraints excluded: chain A residue 598 VAL Chi-restraints excluded: chain A residue 646 LEU Chi-restraints excluded: chain A residue 679 VAL Chi-restraints excluded: chain B residue 58 PHE Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 137 VAL Chi-restraints excluded: chain B residue 149 VAL Chi-restraints excluded: chain B residue 238 THR Chi-restraints excluded: chain B residue 448 LEU Chi-restraints excluded: chain B residue 455 PHE Chi-restraints excluded: chain B residue 590 THR Chi-restraints excluded: chain B residue 598 VAL Chi-restraints excluded: chain B residue 646 LEU Chi-restraints excluded: chain B residue 649 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 99 optimal weight: 0.0060 chunk 128 optimal weight: 6.9990 chunk 21 optimal weight: 8.9990 chunk 108 optimal weight: 6.9990 chunk 98 optimal weight: 8.9990 chunk 124 optimal weight: 0.6980 chunk 77 optimal weight: 5.9990 chunk 80 optimal weight: 0.0970 chunk 126 optimal weight: 20.0000 chunk 57 optimal weight: 7.9990 chunk 74 optimal weight: 0.9990 overall best weight: 1.5598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.116799 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2985 r_free = 0.2985 target = 0.082291 restraints weight = 16549.893| |-----------------------------------------------------------------------------| r_work (start): 0.2980 rms_B_bonded: 3.13 r_work: 0.2846 rms_B_bonded: 3.62 restraints_weight: 0.5000 r_work (final): 0.2846 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7475 moved from start: 0.1075 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 11548 Z= 0.150 Angle : 0.536 14.980 15731 Z= 0.271 Chirality : 0.041 0.189 1890 Planarity : 0.004 0.042 1905 Dihedral : 6.691 58.723 2180 Min Nonbonded Distance : 2.590 Molprobity Statistics. All-atom Clashscore : 5.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.73 % Favored : 93.27 % Rotamer: Outliers : 2.56 % Allowed : 24.63 % Favored : 72.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.60 (0.23), residues: 1396 helix: 2.22 (0.18), residues: 850 sheet: 2.87 (0.91), residues: 36 loop : -1.17 (0.28), residues: 510 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 13 TYR 0.009 0.001 TYR B 104 PHE 0.020 0.001 PHE A 94 TRP 0.011 0.001 TRP B 63 HIS 0.004 0.001 HIS B 714 Details of bonding type rmsd covalent geometry : bond 0.00356 (11548) covalent geometry : angle 0.53609 (15731) hydrogen bonds : bond 0.03392 ( 639) hydrogen bonds : angle 3.68871 ( 1851) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2792 Ramachandran restraints generated. 1396 Oldfield, 0 Emsley, 1396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2792 Ramachandran restraints generated. 1396 Oldfield, 0 Emsley, 1396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 1210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 94 time to evaluate : 0.478 Fit side-chains REVERT: A 238 THR cc_start: 0.7789 (OUTLIER) cc_final: 0.7448 (p) REVERT: A 310 LYS cc_start: 0.8207 (OUTLIER) cc_final: 0.7561 (tptt) REVERT: A 395 THR cc_start: 0.9274 (t) cc_final: 0.9059 (t) REVERT: B 238 THR cc_start: 0.7788 (OUTLIER) cc_final: 0.7449 (p) REVERT: B 610 ASN cc_start: 0.8190 (m-40) cc_final: 0.7957 (m-40) REVERT: B 614 GLU cc_start: 0.7489 (tm-30) cc_final: 0.7131 (tm-30) outliers start: 31 outliers final: 24 residues processed: 124 average time/residue: 0.0816 time to fit residues: 16.3860 Evaluate side-chains 116 residues out of total 1210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 89 time to evaluate : 0.426 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 CYS Chi-restraints excluded: chain A residue 58 PHE Chi-restraints excluded: chain A residue 125 ILE Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 149 VAL Chi-restraints excluded: chain A residue 182 VAL Chi-restraints excluded: chain A residue 238 THR Chi-restraints excluded: chain A residue 310 LYS Chi-restraints excluded: chain A residue 448 LEU Chi-restraints excluded: chain A residue 572 ASN Chi-restraints excluded: chain A residue 590 THR Chi-restraints excluded: chain A residue 598 VAL Chi-restraints excluded: chain A residue 646 LEU Chi-restraints excluded: chain A residue 679 VAL Chi-restraints excluded: chain B residue 58 PHE Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 137 VAL Chi-restraints excluded: chain B residue 149 VAL Chi-restraints excluded: chain B residue 238 THR Chi-restraints excluded: chain B residue 423 ILE Chi-restraints excluded: chain B residue 448 LEU Chi-restraints excluded: chain B residue 455 PHE Chi-restraints excluded: chain B residue 572 ASN Chi-restraints excluded: chain B residue 590 THR Chi-restraints excluded: chain B residue 598 VAL Chi-restraints excluded: chain B residue 646 LEU Chi-restraints excluded: chain B residue 649 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 100 optimal weight: 0.8980 chunk 80 optimal weight: 3.9990 chunk 1 optimal weight: 4.9990 chunk 93 optimal weight: 5.9990 chunk 47 optimal weight: 0.7980 chunk 87 optimal weight: 3.9990 chunk 24 optimal weight: 0.7980 chunk 3 optimal weight: 7.9990 chunk 85 optimal weight: 0.9980 chunk 130 optimal weight: 6.9990 chunk 128 optimal weight: 2.9990 overall best weight: 1.2982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.117590 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2993 r_free = 0.2993 target = 0.082956 restraints weight = 16550.010| |-----------------------------------------------------------------------------| r_work (start): 0.2989 rms_B_bonded: 3.15 r_work: 0.2856 rms_B_bonded: 3.63 restraints_weight: 0.5000 r_work (final): 0.2856 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7468 moved from start: 0.1106 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 11548 Z= 0.134 Angle : 0.529 15.547 15731 Z= 0.267 Chirality : 0.041 0.196 1890 Planarity : 0.004 0.041 1905 Dihedral : 6.614 58.305 2180 Min Nonbonded Distance : 2.590 Molprobity Statistics. All-atom Clashscore : 5.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.81 % Favored : 93.19 % Rotamer: Outliers : 3.06 % Allowed : 24.13 % Favored : 72.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.58 (0.24), residues: 1396 helix: 2.19 (0.18), residues: 853 sheet: 2.84 (0.92), residues: 36 loop : -1.16 (0.28), residues: 507 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 13 TYR 0.008 0.001 TYR A 104 PHE 0.026 0.001 PHE B 94 TRP 0.012 0.001 TRP B 63 HIS 0.004 0.001 HIS B 714 Details of bonding type rmsd covalent geometry : bond 0.00315 (11548) covalent geometry : angle 0.52933 (15731) hydrogen bonds : bond 0.03317 ( 639) hydrogen bonds : angle 3.67763 ( 1851) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2792 Ramachandran restraints generated. 1396 Oldfield, 0 Emsley, 1396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2792 Ramachandran restraints generated. 1396 Oldfield, 0 Emsley, 1396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 1210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 94 time to evaluate : 0.311 Fit side-chains REVERT: A 94 PHE cc_start: 0.8381 (m-80) cc_final: 0.8177 (m-80) REVERT: A 238 THR cc_start: 0.7782 (OUTLIER) cc_final: 0.7443 (p) REVERT: A 310 LYS cc_start: 0.8242 (OUTLIER) cc_final: 0.7600 (tptt) REVERT: A 395 THR cc_start: 0.9273 (t) cc_final: 0.9058 (t) REVERT: B 238 THR cc_start: 0.7745 (OUTLIER) cc_final: 0.7404 (p) REVERT: B 395 THR cc_start: 0.9207 (t) cc_final: 0.8988 (t) REVERT: B 610 ASN cc_start: 0.8177 (m-40) cc_final: 0.7940 (m-40) REVERT: B 614 GLU cc_start: 0.7488 (tm-30) cc_final: 0.7147 (tm-30) outliers start: 37 outliers final: 26 residues processed: 130 average time/residue: 0.0816 time to fit residues: 17.0946 Evaluate side-chains 120 residues out of total 1210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 91 time to evaluate : 0.439 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 CYS Chi-restraints excluded: chain A residue 58 PHE Chi-restraints excluded: chain A residue 125 ILE Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 149 VAL Chi-restraints excluded: chain A residue 182 VAL Chi-restraints excluded: chain A residue 238 THR Chi-restraints excluded: chain A residue 310 LYS Chi-restraints excluded: chain A residue 423 ILE Chi-restraints excluded: chain A residue 448 LEU Chi-restraints excluded: chain A residue 455 PHE Chi-restraints excluded: chain A residue 590 THR Chi-restraints excluded: chain A residue 598 VAL Chi-restraints excluded: chain A residue 646 LEU Chi-restraints excluded: chain A residue 679 VAL Chi-restraints excluded: chain B residue 58 PHE Chi-restraints excluded: chain B residue 125 ILE Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 137 VAL Chi-restraints excluded: chain B residue 149 VAL Chi-restraints excluded: chain B residue 238 THR Chi-restraints excluded: chain B residue 253 GLN Chi-restraints excluded: chain B residue 266 LEU Chi-restraints excluded: chain B residue 448 LEU Chi-restraints excluded: chain B residue 455 PHE Chi-restraints excluded: chain B residue 590 THR Chi-restraints excluded: chain B residue 598 VAL Chi-restraints excluded: chain B residue 646 LEU Chi-restraints excluded: chain B residue 649 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 77 optimal weight: 7.9990 chunk 116 optimal weight: 3.9990 chunk 109 optimal weight: 4.9990 chunk 139 optimal weight: 0.6980 chunk 94 optimal weight: 0.9990 chunk 51 optimal weight: 0.9990 chunk 8 optimal weight: 0.7980 chunk 104 optimal weight: 0.9980 chunk 21 optimal weight: 5.9990 chunk 11 optimal weight: 5.9990 chunk 22 optimal weight: 1.9990 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.118974 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3019 r_free = 0.3019 target = 0.084478 restraints weight = 16537.239| |-----------------------------------------------------------------------------| r_work (start): 0.2994 rms_B_bonded: 3.16 r_work: 0.2860 rms_B_bonded: 3.65 restraints_weight: 0.5000 r_work (final): 0.2860 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7396 moved from start: 0.1102 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 11548 Z= 0.114 Angle : 0.523 15.945 15731 Z= 0.262 Chirality : 0.040 0.197 1890 Planarity : 0.003 0.041 1905 Dihedral : 6.498 58.630 2180 Min Nonbonded Distance : 2.592 Molprobity Statistics. All-atom Clashscore : 5.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.30 % Favored : 93.70 % Rotamer: Outliers : 2.31 % Allowed : 24.71 % Favored : 72.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.63 (0.23), residues: 1396 helix: 2.29 (0.18), residues: 845 sheet: 2.80 (0.92), residues: 36 loop : -1.21 (0.28), residues: 515 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 13 TYR 0.007 0.001 TYR A 104 PHE 0.023 0.001 PHE B 94 TRP 0.014 0.001 TRP B 63 HIS 0.003 0.000 HIS B 714 Details of bonding type rmsd covalent geometry : bond 0.00260 (11548) covalent geometry : angle 0.52316 (15731) hydrogen bonds : bond 0.03168 ( 639) hydrogen bonds : angle 3.64262 ( 1851) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2792 Ramachandran restraints generated. 1396 Oldfield, 0 Emsley, 1396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2792 Ramachandran restraints generated. 1396 Oldfield, 0 Emsley, 1396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 1210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 102 time to evaluate : 0.413 Fit side-chains REVERT: A 310 LYS cc_start: 0.8177 (OUTLIER) cc_final: 0.7562 (tptt) REVERT: A 395 THR cc_start: 0.9247 (t) cc_final: 0.9026 (t) REVERT: B 238 THR cc_start: 0.7702 (OUTLIER) cc_final: 0.7377 (p) REVERT: B 395 THR cc_start: 0.9198 (t) cc_final: 0.8994 (t) REVERT: B 610 ASN cc_start: 0.8146 (m-40) cc_final: 0.7914 (m-40) REVERT: B 614 GLU cc_start: 0.7427 (tm-30) cc_final: 0.7092 (tm-30) outliers start: 28 outliers final: 23 residues processed: 129 average time/residue: 0.0706 time to fit residues: 14.7560 Evaluate side-chains 117 residues out of total 1210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 92 time to evaluate : 0.419 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 CYS Chi-restraints excluded: chain A residue 58 PHE Chi-restraints excluded: chain A residue 125 ILE Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 149 VAL Chi-restraints excluded: chain A residue 253 GLN Chi-restraints excluded: chain A residue 310 LYS Chi-restraints excluded: chain A residue 448 LEU Chi-restraints excluded: chain A residue 455 PHE Chi-restraints excluded: chain A residue 590 THR Chi-restraints excluded: chain A residue 598 VAL Chi-restraints excluded: chain A residue 646 LEU Chi-restraints excluded: chain A residue 679 VAL Chi-restraints excluded: chain B residue 58 PHE Chi-restraints excluded: chain B residue 125 ILE Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 137 VAL Chi-restraints excluded: chain B residue 149 VAL Chi-restraints excluded: chain B residue 238 THR Chi-restraints excluded: chain B residue 448 LEU Chi-restraints excluded: chain B residue 455 PHE Chi-restraints excluded: chain B residue 590 THR Chi-restraints excluded: chain B residue 598 VAL Chi-restraints excluded: chain B residue 646 LEU Chi-restraints excluded: chain B residue 649 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 0 optimal weight: 6.9990 chunk 84 optimal weight: 0.5980 chunk 104 optimal weight: 0.7980 chunk 4 optimal weight: 0.7980 chunk 34 optimal weight: 0.8980 chunk 68 optimal weight: 0.6980 chunk 79 optimal weight: 0.0040 chunk 26 optimal weight: 2.9990 chunk 126 optimal weight: 20.0000 chunk 135 optimal weight: 0.9980 chunk 37 optimal weight: 0.8980 overall best weight: 0.5792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 495 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.120085 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3039 r_free = 0.3039 target = 0.085714 restraints weight = 16563.061| |-----------------------------------------------------------------------------| r_work (start): 0.3014 rms_B_bonded: 3.17 r_work: 0.2881 rms_B_bonded: 3.67 restraints_weight: 0.5000 r_work (final): 0.2881 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7381 moved from start: 0.1115 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 11548 Z= 0.106 Angle : 0.521 15.658 15731 Z= 0.262 Chirality : 0.040 0.199 1890 Planarity : 0.004 0.041 1905 Dihedral : 6.410 58.302 2180 Min Nonbonded Distance : 2.594 Molprobity Statistics. All-atom Clashscore : 5.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.02 % Favored : 93.98 % Rotamer: Outliers : 1.98 % Allowed : 25.29 % Favored : 72.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.67 (0.23), residues: 1396 helix: 2.27 (0.18), residues: 856 sheet: 2.82 (0.91), residues: 36 loop : -1.15 (0.28), residues: 504 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 13 TYR 0.007 0.001 TYR A 104 PHE 0.025 0.001 PHE A 94 TRP 0.015 0.001 TRP B 63 HIS 0.003 0.000 HIS B 714 Details of bonding type rmsd covalent geometry : bond 0.00231 (11548) covalent geometry : angle 0.52117 (15731) hydrogen bonds : bond 0.03057 ( 639) hydrogen bonds : angle 3.60623 ( 1851) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2201.05 seconds wall clock time: 38 minutes 42.04 seconds (2322.04 seconds total)