Starting phenix.real_space_refine on Wed Feb 4 00:31:25 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9ndq_49276/02_2026/9ndq_49276.cif Found real_map, /net/cci-nas-00/data/ceres_data/9ndq_49276/02_2026/9ndq_49276.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9ndq_49276/02_2026/9ndq_49276.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9ndq_49276/02_2026/9ndq_49276.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9ndq_49276/02_2026/9ndq_49276.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9ndq_49276/02_2026/9ndq_49276.map" } resolution = 3.0 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= 0.000 sd= 0.016 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 28 5.16 5 C 5086 2.51 5 N 1416 2.21 5 O 1372 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 8 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: 7902 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 2738 Number of conformers: 1 Conformer: "" Number of residues, atoms: 355, 2738 Classifications: {'peptide': 355} Link IDs: {'PCIS': 2, 'PTRANS': 26, 'TRANS': 326} Chain breaks: 6 Chain: "C" Number of atoms: 5164 Number of conformers: 1 Conformer: "" Number of residues, atoms: 683, 5164 Classifications: {'peptide': 683} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 3, 'PTRANS': 51, 'TRANS': 628} Chain breaks: 14 Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Time building chain proxies: 1.52, per 1000 atoms: 0.19 Number of scatterers: 7902 At special positions: 0 Unit cell: (93.312, 104.247, 131.22, 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 28 16.00 O 1372 8.00 N 1416 7.00 C 5086 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS C 466 " - pdb=" SG CYS C 469 " distance=2.05 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: 0.74 Conformation dependent library (CDL) restraints added in 278.0 milliseconds 1988 Ramachandran restraints generated. 994 Oldfield, 0 Emsley, 994 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1926 Finding SS restraints... Secondary structure from input PDB file: 39 helices and 11 sheets defined 43.4% alpha, 14.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.28 Creating SS restraints... Processing helix chain 'A' and resid 412 through 417 Processing helix chain 'A' and resid 426 through 438 removed outlier: 3.740A pdb=" N LYS A 431 " --> pdb=" O GLY A 427 " (cutoff:3.500A) Processing helix chain 'A' and resid 457 through 469 removed outlier: 3.961A pdb=" N LYS A 469 " --> pdb=" O ALA A 465 " (cutoff:3.500A) Processing helix chain 'A' and resid 504 through 510 removed outlier: 3.508A pdb=" N ALA A 508 " --> pdb=" O LEU A 504 " (cutoff:3.500A) Processing helix chain 'A' and resid 520 through 525 Processing helix chain 'A' and resid 554 through 560 removed outlier: 3.673A pdb=" N ILE A 558 " --> pdb=" O ASP A 554 " (cutoff:3.500A) Processing helix chain 'A' and resid 565 through 571 Processing helix chain 'A' and resid 578 through 590 Processing helix chain 'A' and resid 604 through 608 Processing helix chain 'A' and resid 638 through 661 removed outlier: 3.642A pdb=" N LEU A 642 " --> pdb=" O PRO A 638 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N ARG A 651 " --> pdb=" O GLY A 647 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N GLY A 652 " --> pdb=" O HIS A 648 " (cutoff:3.500A) Processing helix chain 'A' and resid 776 through 793 removed outlier: 3.503A pdb=" N MET A 780 " --> pdb=" O GLY A 776 " (cutoff:3.500A) Processing helix chain 'A' and resid 794 through 802 Processing helix chain 'A' and resid 852 through 859 Processing helix chain 'A' and resid 860 through 861 No H-bonds generated for 'chain 'A' and resid 860 through 861' Processing helix chain 'A' and resid 862 through 867 removed outlier: 4.004A pdb=" N HIS A 867 " --> pdb=" O ARG A 864 " (cutoff:3.500A) Processing helix chain 'C' and resid 56 through 65 Processing helix chain 'C' and resid 89 through 93 Processing helix chain 'C' and resid 94 through 113 removed outlier: 3.634A pdb=" N TRP C 98 " --> pdb=" O ASN C 94 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N GLU C 110 " --> pdb=" O LEU C 106 " (cutoff:3.500A) Processing helix chain 'C' and resid 163 through 172 removed outlier: 3.688A pdb=" N ARG C 168 " --> pdb=" O ALA C 164 " (cutoff:3.500A) removed outlier: 4.297A pdb=" N VAL C 169 " --> pdb=" O LEU C 165 " (cutoff:3.500A) Processing helix chain 'C' and resid 176 through 188 Processing helix chain 'C' and resid 189 through 193 Processing helix chain 'C' and resid 268 through 283 Processing helix chain 'C' and resid 297 through 301 Processing helix chain 'C' and resid 334 through 344 Processing helix chain 'C' and resid 352 through 356 removed outlier: 3.585A pdb=" N VAL C 355 " --> pdb=" O GLY C 352 " (cutoff:3.500A) Processing helix chain 'C' and resid 358 through 360 No H-bonds generated for 'chain 'C' and resid 358 through 360' Processing helix chain 'C' and resid 361 through 373 removed outlier: 3.741A pdb=" N VAL C 365 " --> pdb=" O ALA C 361 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N LEU C 373 " --> pdb=" O ALA C 369 " (cutoff:3.500A) Processing helix chain 'C' and resid 374 through 383 Processing helix chain 'C' and resid 412 through 425 Processing helix chain 'C' and resid 435 through 448 Processing helix chain 'C' and resid 451 through 466 removed outlier: 3.825A pdb=" N GLY C 455 " --> pdb=" O GLU C 451 " (cutoff:3.500A) Proline residue: C 463 - end of helix Processing helix chain 'C' and resid 471 through 492 removed outlier: 4.361A pdb=" N ILE C 487 " --> pdb=" O VAL C 483 " (cutoff:3.500A) removed outlier: 5.978A pdb=" N THR C 490 " --> pdb=" O GLN C 486 " (cutoff:3.500A) Processing helix chain 'C' and resid 520 through 542 Processing helix chain 'C' and resid 588 through 607 Processing helix chain 'C' and resid 618 through 638 Processing helix chain 'C' and resid 642 through 647 removed outlier: 3.585A pdb=" N TRP C 646 " --> pdb=" O ASP C 642 " (cutoff:3.500A) Processing helix chain 'C' and resid 660 through 673 removed outlier: 4.981A pdb=" N GLY C 667 " --> pdb=" O PHE C 664 " (cutoff:3.500A) removed outlier: 6.749A pdb=" N ALA C 668 " --> pdb=" O ARG C 665 " (cutoff:3.500A) removed outlier: 4.388A pdb=" N ASP C 671 " --> pdb=" O ALA C 668 " (cutoff:3.500A) Processing helix chain 'C' and resid 707 through 732 Processing helix chain 'C' and resid 746 through 750 Processing sheet with id=AA1, first strand: chain 'A' and resid 421 through 425 removed outlier: 6.616A pdb=" N ARG A 421 " --> pdb=" O HIS A 885 " (cutoff:3.500A) removed outlier: 6.817A pdb=" N VAL A 773 " --> pdb=" O LEU A 884 " (cutoff:3.500A) removed outlier: 7.833A pdb=" N SER A 886 " --> pdb=" O VAL A 773 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 451 through 456 removed outlier: 6.614A pdb=" N CYS A 451 " --> pdb=" O ALA A 551 " (cutoff:3.500A) removed outlier: 5.406A pdb=" N VAL A 535 " --> pdb=" O ILE A 615 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 624 through 627 Processing sheet with id=AA4, first strand: chain 'A' and resid 624 through 627 removed outlier: 5.372A pdb=" N GLY A 761 " --> pdb=" O SER A 678 " (cutoff:3.500A) removed outlier: 4.276A pdb=" N PHE A 675 " --> pdb=" O VAL A 843 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 48 through 55 removed outlier: 6.894A pdb=" N HIS C 32 " --> pdb=" O ALA C 20 " (cutoff:3.500A) removed outlier: 6.979A pdb=" N ALA C 20 " --> pdb=" O HIS C 32 " (cutoff:3.500A) removed outlier: 7.355A pdb=" N LEU C 34 " --> pdb=" O LEU C 18 " (cutoff:3.500A) removed outlier: 5.226A pdb=" N LEU C 18 " --> pdb=" O LEU C 34 " (cutoff:3.500A) removed outlier: 6.485A pdb=" N TYR C 36 " --> pdb=" O ILE C 16 " (cutoff:3.500A) removed outlier: 4.245A pdb=" N ILE C 16 " --> pdb=" O TYR C 36 " (cutoff:3.500A) removed outlier: 6.548A pdb=" N VAL C 38 " --> pdb=" O SER C 14 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 207 through 209 removed outlier: 6.683A pdb=" N PHE C 259 " --> pdb=" O PHE C 321 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 230 through 237 Processing sheet with id=AA8, first strand: chain 'C' and resid 295 through 296 Processing sheet with id=AA9, first strand: chain 'C' and resid 398 through 400 removed outlier: 3.595A pdb=" N THR C 578 " --> pdb=" O ASN C 573 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 497 through 501 removed outlier: 6.585A pdb=" N TRP C 507 " --> pdb=" O CYS C 499 " (cutoff:3.500A) removed outlier: 4.595A pdb=" N GLY C 501 " --> pdb=" O ALA C 505 " (cutoff:3.500A) removed outlier: 7.050A pdb=" N ALA C 505 " --> pdb=" O GLY C 501 " (cutoff:3.500A) removed outlier: 6.852A pdb=" N THR C 405 " --> pdb=" O VAL C 557 " (cutoff:3.500A) removed outlier: 4.880A pdb=" N VAL C 557 " --> pdb=" O THR C 405 " (cutoff:3.500A) removed outlier: 5.982A pdb=" N ARG C 407 " --> pdb=" O GLU C 555 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 648 through 650 379 hydrogen bonds defined for protein. 1029 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: 1.20 Time building geometry restraints manager: 0.93 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.15 - 1.28: 1269 1.28 - 1.41: 2100 1.41 - 1.55: 4693 1.55 - 1.68: 2 1.68 - 1.81: 37 Bond restraints: 8101 Sorted by residual: bond pdb=" C TRP C 384 " pdb=" N HIS C 385 " ideal model delta sigma weight residual 1.329 1.148 0.181 1.35e-02 5.49e+03 1.80e+02 bond pdb=" CA PRO C 396 " pdb=" C PRO C 396 " ideal model delta sigma weight residual 1.514 1.536 -0.022 5.50e-03 3.31e+04 1.54e+01 bond pdb=" CA PHE C 226 " pdb=" C PHE C 226 " ideal model delta sigma weight residual 1.523 1.454 0.069 1.80e-02 3.09e+03 1.48e+01 bond pdb=" C PRO C 396 " pdb=" O PRO C 396 " ideal model delta sigma weight residual 1.246 1.215 0.030 8.50e-03 1.38e+04 1.28e+01 bond pdb=" C ASN A 807 " pdb=" N PHE A 808 " ideal model delta sigma weight residual 1.334 1.276 0.058 1.79e-02 3.12e+03 1.05e+01 ... (remaining 8096 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.92: 10719 2.92 - 5.85: 308 5.85 - 8.77: 27 8.77 - 11.69: 8 11.69 - 14.61: 1 Bond angle restraints: 11063 Sorted by residual: angle pdb=" N ASN C 467 " pdb=" CA ASN C 467 " pdb=" C ASN C 467 " ideal model delta sigma weight residual 112.87 101.74 11.13 1.20e+00 6.94e-01 8.60e+01 angle pdb=" N VAL A 815 " pdb=" CA VAL A 815 " pdb=" C VAL A 815 " ideal model delta sigma weight residual 113.20 106.03 7.17 9.60e-01 1.09e+00 5.58e+01 angle pdb=" N LEU C 472 " pdb=" CA LEU C 472 " pdb=" C LEU C 472 " ideal model delta sigma weight residual 112.54 106.26 6.28 1.22e+00 6.72e-01 2.65e+01 angle pdb=" C ALA A 670 " pdb=" N TYR A 671 " pdb=" CA TYR A 671 " ideal model delta sigma weight residual 120.94 111.45 9.49 1.90e+00 2.77e-01 2.49e+01 angle pdb=" C GLN A 512 " pdb=" N GLN A 513 " pdb=" CA GLN A 513 " ideal model delta sigma weight residual 121.54 112.15 9.39 1.91e+00 2.74e-01 2.41e+01 ... (remaining 11058 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.45: 4332 16.45 - 32.89: 336 32.89 - 49.34: 78 49.34 - 65.78: 36 65.78 - 82.23: 8 Dihedral angle restraints: 4790 sinusoidal: 1820 harmonic: 2970 Sorted by residual: dihedral pdb=" CD ARG C 414 " pdb=" NE ARG C 414 " pdb=" CZ ARG C 414 " pdb=" NH1 ARG C 414 " ideal model delta sinusoidal sigma weight residual 0.00 -82.23 82.23 1 1.00e+01 1.00e-02 8.30e+01 dihedral pdb=" CD ARG C 168 " pdb=" NE ARG C 168 " pdb=" CZ ARG C 168 " pdb=" NH1 ARG C 168 " ideal model delta sinusoidal sigma weight residual 0.00 78.82 -78.82 1 1.00e+01 1.00e-02 7.74e+01 dihedral pdb=" CD ARG C 460 " pdb=" NE ARG C 460 " pdb=" CZ ARG C 460 " pdb=" NH1 ARG C 460 " ideal model delta sinusoidal sigma weight residual 0.00 -75.66 75.66 1 1.00e+01 1.00e-02 7.22e+01 ... (remaining 4787 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.067: 817 0.067 - 0.134: 360 0.134 - 0.201: 74 0.201 - 0.268: 7 0.268 - 0.335: 1 Chirality restraints: 1259 Sorted by residual: chirality pdb=" CB ILE A 760 " pdb=" CA ILE A 760 " pdb=" CG1 ILE A 760 " pdb=" CG2 ILE A 760 " both_signs ideal model delta sigma weight residual False 2.64 2.31 0.34 2.00e-01 2.50e+01 2.81e+00 chirality pdb=" CA GLN A 513 " pdb=" N GLN A 513 " pdb=" C GLN A 513 " pdb=" CB GLN A 513 " both_signs ideal model delta sigma weight residual False 2.51 2.25 0.26 2.00e-01 2.50e+01 1.65e+00 chirality pdb=" CB VAL C 494 " pdb=" CA VAL C 494 " pdb=" CG1 VAL C 494 " pdb=" CG2 VAL C 494 " both_signs ideal model delta sigma weight residual False -2.63 -2.38 -0.25 2.00e-01 2.50e+01 1.54e+00 ... (remaining 1256 not shown) Planarity restraints: 1434 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG C 414 " -1.084 9.50e-02 1.11e+02 4.86e-01 1.42e+02 pdb=" NE ARG C 414 " 0.066 2.00e-02 2.50e+03 pdb=" CZ ARG C 414 " 0.010 2.00e-02 2.50e+03 pdb=" NH1 ARG C 414 " -0.010 2.00e-02 2.50e+03 pdb=" NH2 ARG C 414 " -0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG C 168 " -1.076 9.50e-02 1.11e+02 4.82e-01 1.40e+02 pdb=" NE ARG C 168 " 0.065 2.00e-02 2.50e+03 pdb=" CZ ARG C 168 " 0.011 2.00e-02 2.50e+03 pdb=" NH1 ARG C 168 " -0.009 2.00e-02 2.50e+03 pdb=" NH2 ARG C 168 " -0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG C 460 " -1.064 9.50e-02 1.11e+02 4.77e-01 1.37e+02 pdb=" NE ARG C 460 " 0.064 2.00e-02 2.50e+03 pdb=" CZ ARG C 460 " 0.012 2.00e-02 2.50e+03 pdb=" NH1 ARG C 460 " -0.008 2.00e-02 2.50e+03 pdb=" NH2 ARG C 460 " -0.021 2.00e-02 2.50e+03 ... (remaining 1431 not shown) Histogram of nonbonded interaction distances: 2.04 - 2.61: 86 2.61 - 3.18: 6917 3.18 - 3.75: 12178 3.75 - 4.33: 17168 4.33 - 4.90: 28300 Nonbonded interactions: 64649 Sorted by model distance: nonbonded pdb=" OD1 ASP C 630 " pdb=" OH TYR C 739 " model vdw 2.035 3.040 nonbonded pdb=" OD1 ASP C 657 " pdb=" NH2 ARG C 681 " model vdw 2.154 3.120 nonbonded pdb=" O LEU C 109 " pdb=" OG1 THR C 113 " model vdw 2.199 3.040 nonbonded pdb=" OD2 ASP A 455 " pdb=" NH2 ARG A 463 " model vdw 2.201 3.120 nonbonded pdb=" O GLY A 802 " pdb=" OG SER A 803 " model vdw 2.222 3.040 ... (remaining 64644 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 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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: 6.610 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: 0.010 Extract box with map and model: 0.160 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 7.980 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.020 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:7.880 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.740 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6576 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 : 0.015 0.182 8102 Z= 0.711 Angle : 1.174 14.613 11065 Z= 0.695 Chirality : 0.073 0.335 1259 Planarity : 0.032 0.486 1434 Dihedral : 14.198 82.227 2861 Min Nonbonded Distance : 2.035 Molprobity Statistics. All-atom Clashscore : 14.23 Ramachandran Plot: Outliers : 0.20 % Allowed : 8.95 % Favored : 90.85 % Rotamer: Outliers : 3.81 % Allowed : 1.65 % Favored : 94.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.10 % 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: -2.82 (0.25), residues: 994 helix: -1.56 (0.23), residues: 405 sheet: -1.00 (0.44), residues: 158 loop : -2.45 (0.29), residues: 431 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG C 99 TYR 0.043 0.005 TYR C 558 PHE 0.029 0.004 PHE C 37 TRP 0.038 0.005 TRP A 555 HIS 0.015 0.003 HIS A 867 Details of bonding type rmsd covalent geometry : bond 0.01516 ( 8101) covalent geometry : angle 1.17244 (11063) SS BOND : bond 0.01724 ( 1) SS BOND : angle 4.48173 ( 2) hydrogen bonds : bond 0.18850 ( 375) hydrogen bonds : angle 8.40265 ( 1029) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1988 Ramachandran restraints generated. 994 Oldfield, 0 Emsley, 994 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1988 Ramachandran restraints generated. 994 Oldfield, 0 Emsley, 994 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 260 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 230 time to evaluate : 0.272 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 671 TYR cc_start: 0.7748 (t80) cc_final: 0.7444 (t80) REVERT: C 445 VAL cc_start: 0.7879 (t) cc_final: 0.7672 (m) REVERT: C 695 ASP cc_start: 0.7220 (m-30) cc_final: 0.6953 (m-30) outliers start: 30 outliers final: 12 residues processed: 250 average time/residue: 0.4710 time to fit residues: 124.4837 Evaluate side-chains 207 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 195 time to evaluate : 0.237 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 469 LYS Chi-restraints excluded: chain A residue 472 VAL Chi-restraints excluded: chain C residue 9 VAL Chi-restraints excluded: chain C residue 23 LEU Chi-restraints excluded: chain C residue 240 ARG Chi-restraints excluded: chain C residue 242 HIS Chi-restraints excluded: chain C residue 409 CYS Chi-restraints excluded: chain C residue 435 ARG Chi-restraints excluded: chain C residue 460 ARG Chi-restraints excluded: chain C residue 465 THR Chi-restraints excluded: chain C residue 480 MET Chi-restraints excluded: chain C residue 665 ARG Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 49 optimal weight: 0.9980 chunk 97 optimal weight: 0.9980 chunk 53 optimal weight: 0.3980 chunk 5 optimal weight: 0.8980 chunk 33 optimal weight: 0.5980 chunk 65 optimal weight: 0.6980 chunk 62 optimal weight: 0.5980 chunk 51 optimal weight: 0.5980 chunk 100 optimal weight: 0.9990 chunk 38 optimal weight: 0.3980 chunk 61 optimal weight: 0.6980 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 788 GLN A 885 HIS C 32 HIS C 385 HIS ** C 548 HIS ** 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 = 0.3950 r_free = 0.3950 target = 0.150260 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3762 r_free = 0.3762 target = 0.135870 restraints weight = 11651.075| |-----------------------------------------------------------------------------| r_work (start): 0.3742 rms_B_bonded: 2.11 r_work: 0.3629 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.3467 rms_B_bonded: 4.74 restraints_weight: 0.2500 r_work (final): 0.3467 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7446 moved from start: 0.2562 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.098 8102 Z= 0.198 Angle : 0.722 11.589 11065 Z= 0.369 Chirality : 0.049 0.334 1259 Planarity : 0.008 0.070 1434 Dihedral : 7.676 57.864 1161 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 10.75 Ramachandran Plot: Outliers : 0.20 % Allowed : 4.63 % Favored : 95.17 % Rotamer: Outliers : 3.18 % Allowed : 14.23 % Favored : 82.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.10 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % 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: -1.59 (0.26), residues: 994 helix: -0.19 (0.25), residues: 418 sheet: -0.82 (0.40), residues: 158 loop : -2.01 (0.30), residues: 418 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 540 TYR 0.024 0.002 TYR C 558 PHE 0.015 0.002 PHE C 293 TRP 0.020 0.002 TRP C 453 HIS 0.005 0.001 HIS A 860 Details of bonding type rmsd covalent geometry : bond 0.00443 ( 8101) covalent geometry : angle 0.71933 (11063) SS BOND : bond 0.00256 ( 1) SS BOND : angle 4.52526 ( 2) hydrogen bonds : bond 0.05040 ( 375) hydrogen bonds : angle 5.39649 ( 1029) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1988 Ramachandran restraints generated. 994 Oldfield, 0 Emsley, 994 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1988 Ramachandran restraints generated. 994 Oldfield, 0 Emsley, 994 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 232 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 207 time to evaluate : 0.174 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 468 GLU cc_start: 0.7224 (mt-10) cc_final: 0.6886 (mp0) REVERT: C 79 ARG cc_start: 0.7594 (OUTLIER) cc_final: 0.7369 (tpt170) REVERT: C 104 CYS cc_start: 0.7460 (p) cc_final: 0.7034 (t) REVERT: C 123 ARG cc_start: 0.6957 (ttt90) cc_final: 0.6653 (ttt90) REVERT: C 458 LEU cc_start: 0.8480 (mt) cc_final: 0.8101 (mp) REVERT: C 473 ARG cc_start: 0.7639 (mmt90) cc_final: 0.7423 (mtt90) REVERT: C 540 ARG cc_start: 0.8146 (ttm110) cc_final: 0.7890 (ttm-80) REVERT: C 586 LEU cc_start: 0.8074 (mt) cc_final: 0.7830 (mt) REVERT: C 695 ASP cc_start: 0.8021 (m-30) cc_final: 0.7671 (m-30) REVERT: C 714 GLU cc_start: 0.7913 (mm-30) cc_final: 0.7633 (mm-30) REVERT: C 717 ARG cc_start: 0.7881 (ttp-110) cc_final: 0.7423 (ttp-170) outliers start: 25 outliers final: 16 residues processed: 219 average time/residue: 0.3725 time to fit residues: 87.0980 Evaluate side-chains 211 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 194 time to evaluate : 0.172 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 472 VAL Chi-restraints excluded: chain A residue 476 TRP Chi-restraints excluded: chain A residue 779 THR Chi-restraints excluded: chain C residue 23 LEU Chi-restraints excluded: chain C residue 53 VAL Chi-restraints excluded: chain C residue 79 ARG Chi-restraints excluded: chain C residue 89 LEU Chi-restraints excluded: chain C residue 96 THR Chi-restraints excluded: chain C residue 240 ARG Chi-restraints excluded: chain C residue 242 HIS Chi-restraints excluded: chain C residue 367 SER Chi-restraints excluded: chain C residue 409 CYS Chi-restraints excluded: chain C residue 460 ARG Chi-restraints excluded: chain C residue 472 LEU Chi-restraints excluded: chain C residue 631 ARG Chi-restraints excluded: chain C residue 665 ARG Chi-restraints excluded: chain C residue 738 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 45 optimal weight: 3.9990 chunk 28 optimal weight: 1.9990 chunk 79 optimal weight: 2.9990 chunk 63 optimal weight: 0.9990 chunk 81 optimal weight: 2.9990 chunk 6 optimal weight: 0.9990 chunk 99 optimal weight: 1.9990 chunk 52 optimal weight: 2.9990 chunk 77 optimal weight: 0.7980 chunk 87 optimal weight: 2.9990 chunk 59 optimal weight: 0.9990 overall best weight: 1.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 860 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3902 r_free = 0.3902 target = 0.146349 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.3701 r_free = 0.3701 target = 0.131619 restraints weight = 11472.164| |-----------------------------------------------------------------------------| r_work (start): 0.3681 rms_B_bonded: 2.14 r_work: 0.3567 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.3402 rms_B_bonded: 4.69 restraints_weight: 0.2500 r_work (final): 0.3402 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7529 moved from start: 0.3286 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.154 8102 Z= 0.339 Angle : 0.788 11.843 11065 Z= 0.404 Chirality : 0.052 0.414 1259 Planarity : 0.008 0.066 1434 Dihedral : 6.861 53.775 1148 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 11.07 Ramachandran Plot: Outliers : 0.20 % Allowed : 5.94 % Favored : 93.86 % Rotamer: Outliers : 5.21 % Allowed : 15.37 % Favored : 79.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.10 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % 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: -1.50 (0.26), residues: 994 helix: -0.16 (0.24), residues: 433 sheet: -0.60 (0.40), residues: 160 loop : -2.04 (0.30), residues: 401 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C 603 TYR 0.024 0.003 TYR A 804 PHE 0.020 0.003 PHE C 408 TRP 0.023 0.003 TRP C 453 HIS 0.009 0.002 HIS A 885 Details of bonding type rmsd covalent geometry : bond 0.00785 ( 8101) covalent geometry : angle 0.78237 (11063) SS BOND : bond 0.00459 ( 1) SS BOND : angle 7.18857 ( 2) hydrogen bonds : bond 0.05945 ( 375) hydrogen bonds : angle 5.37892 ( 1029) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1988 Ramachandran restraints generated. 994 Oldfield, 0 Emsley, 994 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1988 Ramachandran restraints generated. 994 Oldfield, 0 Emsley, 994 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 239 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 198 time to evaluate : 0.193 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 468 GLU cc_start: 0.7208 (mt-10) cc_final: 0.6851 (mp0) REVERT: A 641 ARG cc_start: 0.7358 (mmm160) cc_final: 0.7000 (mmm-85) REVERT: C 49 ARG cc_start: 0.8181 (mtt-85) cc_final: 0.7945 (mtt-85) REVERT: C 79 ARG cc_start: 0.7674 (OUTLIER) cc_final: 0.7413 (tpt170) REVERT: C 116 VAL cc_start: 0.7841 (p) cc_final: 0.7626 (m) REVERT: C 123 ARG cc_start: 0.7018 (ttt90) cc_final: 0.6698 (ttt90) REVERT: C 313 LEU cc_start: 0.8111 (OUTLIER) cc_final: 0.7638 (pp) REVERT: C 345 LEU cc_start: 0.8718 (mp) cc_final: 0.8462 (mt) REVERT: C 458 LEU cc_start: 0.8531 (mt) cc_final: 0.8303 (mt) REVERT: C 460 ARG cc_start: 0.7760 (tpt90) cc_final: 0.7454 (tpt90) REVERT: C 473 ARG cc_start: 0.7874 (mtt90) cc_final: 0.7551 (mtt90) REVERT: C 480 MET cc_start: 0.7613 (mmm) cc_final: 0.7405 (mmm) REVERT: C 540 ARG cc_start: 0.8149 (ttm110) cc_final: 0.7819 (ttm-80) REVERT: C 695 ASP cc_start: 0.8071 (m-30) cc_final: 0.7814 (m-30) REVERT: C 714 GLU cc_start: 0.7907 (mm-30) cc_final: 0.6948 (mm-30) REVERT: C 718 GLU cc_start: 0.7919 (OUTLIER) cc_final: 0.6976 (mp0) outliers start: 41 outliers final: 18 residues processed: 222 average time/residue: 0.4064 time to fit residues: 96.1309 Evaluate side-chains 211 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 190 time to evaluate : 0.194 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 454 VAL Chi-restraints excluded: chain A residue 472 VAL Chi-restraints excluded: chain A residue 476 TRP Chi-restraints excluded: chain A residue 550 LEU Chi-restraints excluded: chain A residue 798 VAL Chi-restraints excluded: chain A residue 815 VAL Chi-restraints excluded: chain A residue 862 ASP Chi-restraints excluded: chain C residue 53 VAL Chi-restraints excluded: chain C residue 56 THR Chi-restraints excluded: chain C residue 79 ARG Chi-restraints excluded: chain C residue 89 LEU Chi-restraints excluded: chain C residue 191 CYS Chi-restraints excluded: chain C residue 271 LEU Chi-restraints excluded: chain C residue 313 LEU Chi-restraints excluded: chain C residue 367 SER Chi-restraints excluded: chain C residue 405 THR Chi-restraints excluded: chain C residue 409 CYS Chi-restraints excluded: chain C residue 509 VAL Chi-restraints excluded: chain C residue 633 ILE Chi-restraints excluded: chain C residue 665 ARG Chi-restraints excluded: chain C residue 718 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 39 optimal weight: 1.9990 chunk 101 optimal weight: 0.7980 chunk 79 optimal weight: 2.9990 chunk 12 optimal weight: 0.5980 chunk 32 optimal weight: 0.0870 chunk 5 optimal weight: 0.7980 chunk 85 optimal weight: 1.9990 chunk 87 optimal weight: 0.6980 chunk 14 optimal weight: 0.7980 chunk 68 optimal weight: 1.9990 chunk 86 optimal weight: 0.5980 overall best weight: 0.5558 ------------------------------------------------------------------------------- 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 = 0.3922 r_free = 0.3922 target = 0.148202 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3728 r_free = 0.3728 target = 0.133865 restraints weight = 11654.213| |-----------------------------------------------------------------------------| r_work (start): 0.3718 rms_B_bonded: 2.13 r_work: 0.3604 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.3442 rms_B_bonded: 4.75 restraints_weight: 0.2500 r_work (final): 0.3442 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7489 moved from start: 0.3589 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.117 8102 Z= 0.195 Angle : 0.676 14.940 11065 Z= 0.342 Chirality : 0.047 0.450 1259 Planarity : 0.006 0.047 1434 Dihedral : 5.640 53.848 1136 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 9.93 Ramachandran Plot: Outliers : 0.20 % Allowed : 4.53 % Favored : 95.27 % Rotamer: Outliers : 4.96 % Allowed : 17.28 % Favored : 77.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.10 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % 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: -1.15 (0.27), residues: 994 helix: 0.18 (0.26), residues: 434 sheet: -0.59 (0.38), residues: 180 loop : -1.90 (0.30), residues: 380 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 864 TYR 0.016 0.002 TYR A 804 PHE 0.012 0.002 PHE C 637 TRP 0.021 0.002 TRP C 453 HIS 0.005 0.001 HIS C 710 Details of bonding type rmsd covalent geometry : bond 0.00462 ( 8101) covalent geometry : angle 0.66328 (11063) SS BOND : bond 0.00789 ( 1) SS BOND : angle 9.67246 ( 2) hydrogen bonds : bond 0.04694 ( 375) hydrogen bonds : angle 4.96477 ( 1029) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1988 Ramachandran restraints generated. 994 Oldfield, 0 Emsley, 994 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1988 Ramachandran restraints generated. 994 Oldfield, 0 Emsley, 994 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 235 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 196 time to evaluate : 0.183 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 414 VAL cc_start: 0.7859 (m) cc_final: 0.7567 (t) REVERT: A 455 ASP cc_start: 0.7922 (OUTLIER) cc_final: 0.7599 (m-30) REVERT: A 468 GLU cc_start: 0.7237 (mt-10) cc_final: 0.6877 (mp0) REVERT: A 641 ARG cc_start: 0.7331 (mmm160) cc_final: 0.6959 (mmm-85) REVERT: C 49 ARG cc_start: 0.8145 (mtt-85) cc_final: 0.7889 (mtt-85) REVERT: C 79 ARG cc_start: 0.7709 (OUTLIER) cc_final: 0.7448 (tpt170) REVERT: C 116 VAL cc_start: 0.7759 (p) cc_final: 0.7552 (m) REVERT: C 123 ARG cc_start: 0.6986 (ttt90) cc_final: 0.6610 (ttt90) REVERT: C 345 LEU cc_start: 0.8704 (mp) cc_final: 0.8469 (mt) REVERT: C 458 LEU cc_start: 0.8506 (mt) cc_final: 0.8145 (mp) REVERT: C 460 ARG cc_start: 0.7788 (OUTLIER) cc_final: 0.7470 (tpt90) REVERT: C 473 ARG cc_start: 0.7701 (mtt90) cc_final: 0.7351 (mtt90) REVERT: C 525 GLU cc_start: 0.7639 (tp30) cc_final: 0.7357 (tp30) REVERT: C 540 ARG cc_start: 0.8087 (ttm110) cc_final: 0.7749 (ttm-80) REVERT: C 695 ASP cc_start: 0.7979 (m-30) cc_final: 0.7717 (m-30) REVERT: C 714 GLU cc_start: 0.7837 (mm-30) cc_final: 0.6813 (mm-30) REVERT: C 717 ARG cc_start: 0.7789 (OUTLIER) cc_final: 0.7310 (ttp-110) REVERT: C 718 GLU cc_start: 0.7902 (OUTLIER) cc_final: 0.7063 (mp0) outliers start: 39 outliers final: 17 residues processed: 217 average time/residue: 0.3824 time to fit residues: 88.5467 Evaluate side-chains 216 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 194 time to evaluate : 0.175 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 455 ASP Chi-restraints excluded: chain A residue 476 TRP Chi-restraints excluded: chain A residue 550 LEU Chi-restraints excluded: chain A residue 779 THR Chi-restraints excluded: chain A residue 801 ILE Chi-restraints excluded: chain A residue 815 VAL Chi-restraints excluded: chain A residue 841 LEU Chi-restraints excluded: chain A residue 862 ASP Chi-restraints excluded: chain C residue 53 VAL Chi-restraints excluded: chain C residue 79 ARG Chi-restraints excluded: chain C residue 96 THR Chi-restraints excluded: chain C residue 191 CYS Chi-restraints excluded: chain C residue 393 LEU Chi-restraints excluded: chain C residue 405 THR Chi-restraints excluded: chain C residue 460 ARG Chi-restraints excluded: chain C residue 472 LEU Chi-restraints excluded: chain C residue 509 VAL Chi-restraints excluded: chain C residue 546 LEU Chi-restraints excluded: chain C residue 627 ASP Chi-restraints excluded: chain C residue 631 ARG Chi-restraints excluded: chain C residue 717 ARG Chi-restraints excluded: chain C residue 718 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 99 optimal weight: 0.6980 chunk 17 optimal weight: 1.9990 chunk 61 optimal weight: 0.9990 chunk 18 optimal weight: 3.9990 chunk 65 optimal weight: 0.1980 chunk 12 optimal weight: 0.0980 chunk 22 optimal weight: 0.9980 chunk 66 optimal weight: 0.2980 chunk 21 optimal weight: 0.9990 chunk 70 optimal weight: 0.5980 chunk 75 optimal weight: 0.9980 overall best weight: 0.3780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 710 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3930 r_free = 0.3930 target = 0.148768 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 22)----------------| | r_work = 0.3738 r_free = 0.3738 target = 0.134472 restraints weight = 11671.512| |-----------------------------------------------------------------------------| r_work (start): 0.3731 rms_B_bonded: 2.14 r_work: 0.3618 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.3456 rms_B_bonded: 4.76 restraints_weight: 0.2500 r_work (final): 0.3456 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7471 moved from start: 0.3878 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.120 8102 Z= 0.161 Angle : 0.654 16.384 11065 Z= 0.325 Chirality : 0.046 0.443 1259 Planarity : 0.006 0.044 1434 Dihedral : 5.073 58.285 1130 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 9.61 Ramachandran Plot: Outliers : 0.20 % Allowed : 4.83 % Favored : 94.97 % Rotamer: Outliers : 4.32 % Allowed : 18.68 % Favored : 77.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.10 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % 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: -0.89 (0.27), residues: 994 helix: 0.44 (0.26), residues: 434 sheet: -0.57 (0.39), residues: 179 loop : -1.75 (0.31), residues: 381 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 537 TYR 0.015 0.001 TYR A 804 PHE 0.013 0.002 PHE C 259 TRP 0.028 0.002 TRP C 453 HIS 0.004 0.001 HIS C 548 Details of bonding type rmsd covalent geometry : bond 0.00384 ( 8101) covalent geometry : angle 0.63552 (11063) SS BOND : bond 0.01225 ( 1) SS BOND : angle 11.50684 ( 2) hydrogen bonds : bond 0.04349 ( 375) hydrogen bonds : angle 4.73601 ( 1029) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1988 Ramachandran restraints generated. 994 Oldfield, 0 Emsley, 994 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1988 Ramachandran restraints generated. 994 Oldfield, 0 Emsley, 994 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 228 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 194 time to evaluate : 0.190 Fit side-chains revert: symmetry clash REVERT: A 472 VAL cc_start: 0.4320 (OUTLIER) cc_final: 0.3841 (p) REVERT: A 641 ARG cc_start: 0.7287 (mmm160) cc_final: 0.6854 (mmm-85) REVERT: C 10 GLU cc_start: 0.6953 (tm-30) cc_final: 0.6713 (tm-30) REVERT: C 49 ARG cc_start: 0.8147 (mtt-85) cc_final: 0.7900 (mtt-85) REVERT: C 79 ARG cc_start: 0.7648 (OUTLIER) cc_final: 0.7402 (tpt170) REVERT: C 123 ARG cc_start: 0.6943 (ttt90) cc_final: 0.6562 (ttt90) REVERT: C 280 THR cc_start: 0.8097 (m) cc_final: 0.7890 (p) REVERT: C 303 ARG cc_start: 0.8082 (OUTLIER) cc_final: 0.7570 (mmm-85) REVERT: C 458 LEU cc_start: 0.8477 (mt) cc_final: 0.8205 (mt) REVERT: C 460 ARG cc_start: 0.7756 (OUTLIER) cc_final: 0.7442 (tpt90) REVERT: C 473 ARG cc_start: 0.7626 (mtt90) cc_final: 0.7264 (mtt90) REVERT: C 525 GLU cc_start: 0.7581 (tp30) cc_final: 0.7257 (tp30) REVERT: C 540 ARG cc_start: 0.8066 (ttm110) cc_final: 0.7743 (ttm-80) REVERT: C 695 ASP cc_start: 0.7964 (m-30) cc_final: 0.7678 (m-30) REVERT: C 718 GLU cc_start: 0.7906 (OUTLIER) cc_final: 0.7060 (mp0) REVERT: C 738 VAL cc_start: 0.8058 (t) cc_final: 0.7764 (m) REVERT: C 745 MET cc_start: 0.8000 (mmm) cc_final: 0.7775 (mtp) outliers start: 34 outliers final: 16 residues processed: 212 average time/residue: 0.4454 time to fit residues: 99.9333 Evaluate side-chains 212 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 191 time to evaluate : 0.260 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 472 VAL Chi-restraints excluded: chain A residue 476 TRP Chi-restraints excluded: chain A residue 550 LEU Chi-restraints excluded: chain A residue 779 THR Chi-restraints excluded: chain A residue 801 ILE Chi-restraints excluded: chain A residue 815 VAL Chi-restraints excluded: chain A residue 862 ASP Chi-restraints excluded: chain C residue 53 VAL Chi-restraints excluded: chain C residue 79 ARG Chi-restraints excluded: chain C residue 89 LEU Chi-restraints excluded: chain C residue 96 THR Chi-restraints excluded: chain C residue 303 ARG Chi-restraints excluded: chain C residue 367 SER Chi-restraints excluded: chain C residue 393 LEU Chi-restraints excluded: chain C residue 405 THR Chi-restraints excluded: chain C residue 460 ARG Chi-restraints excluded: chain C residue 472 LEU Chi-restraints excluded: chain C residue 509 VAL Chi-restraints excluded: chain C residue 627 ASP Chi-restraints excluded: chain C residue 631 ARG Chi-restraints excluded: chain C residue 718 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 26 optimal weight: 1.9990 chunk 18 optimal weight: 8.9990 chunk 82 optimal weight: 0.9980 chunk 98 optimal weight: 0.0040 chunk 78 optimal weight: 1.9990 chunk 5 optimal weight: 1.9990 chunk 77 optimal weight: 0.6980 chunk 73 optimal weight: 1.9990 chunk 90 optimal weight: 0.9980 chunk 32 optimal weight: 0.0870 chunk 83 optimal weight: 0.8980 overall best weight: 0.5370 ------------------------------------------------------------------------------- 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 = 0.3917 r_free = 0.3917 target = 0.147696 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3721 r_free = 0.3721 target = 0.133182 restraints weight = 11505.908| |-----------------------------------------------------------------------------| r_work (start): 0.3720 rms_B_bonded: 2.14 r_work: 0.3605 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.3443 rms_B_bonded: 4.76 restraints_weight: 0.2500 r_work (final): 0.3443 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7490 moved from start: 0.4004 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.146 8102 Z= 0.194 Angle : 0.688 17.953 11065 Z= 0.339 Chirality : 0.047 0.487 1259 Planarity : 0.006 0.045 1434 Dihedral : 5.050 58.528 1130 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 9.93 Ramachandran Plot: Outliers : 0.20 % Allowed : 4.83 % Favored : 94.97 % Rotamer: Outliers : 3.94 % Allowed : 20.84 % Favored : 75.22 % Cbeta Deviations : 0.10 % Peptide Plane: Cis-proline : 6.10 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % 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: -0.81 (0.27), residues: 994 helix: 0.49 (0.26), residues: 431 sheet: -0.43 (0.40), residues: 165 loop : -1.70 (0.30), residues: 398 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 864 TYR 0.014 0.002 TYR A 804 PHE 0.014 0.002 PHE C 259 TRP 0.033 0.002 TRP C 453 HIS 0.005 0.001 HIS C 710 Details of bonding type rmsd covalent geometry : bond 0.00475 ( 8101) covalent geometry : angle 0.66660 (11063) SS BOND : bond 0.01482 ( 1) SS BOND : angle 12.80458 ( 2) hydrogen bonds : bond 0.04492 ( 375) hydrogen bonds : angle 4.71866 ( 1029) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1988 Ramachandran restraints generated. 994 Oldfield, 0 Emsley, 994 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1988 Ramachandran restraints generated. 994 Oldfield, 0 Emsley, 994 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 236 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 205 time to evaluate : 0.193 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 455 ASP cc_start: 0.7913 (OUTLIER) cc_final: 0.7599 (m-30) REVERT: A 468 GLU cc_start: 0.7237 (mt-10) cc_final: 0.6871 (mp0) REVERT: A 640 ARG cc_start: 0.7847 (pmt170) cc_final: 0.7355 (pmt170) REVERT: A 641 ARG cc_start: 0.7284 (mmm160) cc_final: 0.6847 (mmm-85) REVERT: C 49 ARG cc_start: 0.8149 (mtt-85) cc_final: 0.7930 (mtt-85) REVERT: C 79 ARG cc_start: 0.7701 (OUTLIER) cc_final: 0.7461 (tpt170) REVERT: C 113 THR cc_start: 0.7873 (p) cc_final: 0.7652 (p) REVERT: C 123 ARG cc_start: 0.6998 (ttt90) cc_final: 0.6573 (ttt90) REVERT: C 137 GLU cc_start: 0.7187 (OUTLIER) cc_final: 0.6975 (mt-10) REVERT: C 280 THR cc_start: 0.8096 (m) cc_final: 0.7887 (p) REVERT: C 303 ARG cc_start: 0.8071 (OUTLIER) cc_final: 0.7561 (mmm-85) REVERT: C 458 LEU cc_start: 0.8484 (mt) cc_final: 0.8109 (mp) REVERT: C 460 ARG cc_start: 0.7775 (tpt90) cc_final: 0.7473 (tpt90) REVERT: C 473 ARG cc_start: 0.7648 (mtt90) cc_final: 0.7312 (mtt90) REVERT: C 525 GLU cc_start: 0.7636 (tp30) cc_final: 0.7290 (tp30) REVERT: C 540 ARG cc_start: 0.8090 (ttm110) cc_final: 0.7756 (ttm-80) REVERT: C 695 ASP cc_start: 0.8021 (m-30) cc_final: 0.7737 (m-30) REVERT: C 718 GLU cc_start: 0.7901 (OUTLIER) cc_final: 0.7050 (mp0) REVERT: C 745 MET cc_start: 0.8054 (mmm) cc_final: 0.7507 (mtm) outliers start: 31 outliers final: 17 residues processed: 224 average time/residue: 0.4357 time to fit residues: 103.5564 Evaluate side-chains 220 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 198 time to evaluate : 0.167 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 455 ASP Chi-restraints excluded: chain A residue 476 TRP Chi-restraints excluded: chain A residue 550 LEU Chi-restraints excluded: chain A residue 801 ILE Chi-restraints excluded: chain A residue 809 LEU Chi-restraints excluded: chain A residue 815 VAL Chi-restraints excluded: chain A residue 884 LEU Chi-restraints excluded: chain C residue 53 VAL Chi-restraints excluded: chain C residue 79 ARG Chi-restraints excluded: chain C residue 137 GLU Chi-restraints excluded: chain C residue 171 GLU Chi-restraints excluded: chain C residue 271 LEU Chi-restraints excluded: chain C residue 303 ARG Chi-restraints excluded: chain C residue 367 SER Chi-restraints excluded: chain C residue 393 LEU Chi-restraints excluded: chain C residue 409 CYS Chi-restraints excluded: chain C residue 472 LEU Chi-restraints excluded: chain C residue 509 VAL Chi-restraints excluded: chain C residue 627 ASP Chi-restraints excluded: chain C residue 631 ARG Chi-restraints excluded: chain C residue 718 GLU Chi-restraints excluded: chain C residue 719 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 40 optimal weight: 1.9990 chunk 81 optimal weight: 1.9990 chunk 38 optimal weight: 1.9990 chunk 14 optimal weight: 0.5980 chunk 78 optimal weight: 0.7980 chunk 102 optimal weight: 0.1980 chunk 15 optimal weight: 0.9980 chunk 43 optimal weight: 0.5980 chunk 54 optimal weight: 0.5980 chunk 67 optimal weight: 0.8980 chunk 89 optimal weight: 0.5980 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 576 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3915 r_free = 0.3915 target = 0.147599 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3720 r_free = 0.3720 target = 0.133086 restraints weight = 11625.810| |-----------------------------------------------------------------------------| r_work (start): 0.3704 rms_B_bonded: 2.16 r_work: 0.3583 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.3417 rms_B_bonded: 4.84 restraints_weight: 0.2500 r_work (final): 0.3417 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7498 moved from start: 0.4148 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.159 8102 Z= 0.191 Angle : 0.694 19.004 11065 Z= 0.340 Chirality : 0.047 0.527 1259 Planarity : 0.006 0.044 1434 Dihedral : 5.010 60.714 1130 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 9.55 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.13 % Favored : 94.77 % Rotamer: Outliers : 3.30 % Allowed : 21.98 % Favored : 74.71 % Cbeta Deviations : 0.10 % Peptide Plane: Cis-proline : 6.10 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % 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: -0.80 (0.27), residues: 994 helix: 0.50 (0.26), residues: 437 sheet: -0.60 (0.38), residues: 176 loop : -1.67 (0.31), residues: 381 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 882 TYR 0.013 0.002 TYR A 674 PHE 0.014 0.002 PHE C 31 TRP 0.041 0.002 TRP C 453 HIS 0.005 0.001 HIS C 710 Details of bonding type rmsd covalent geometry : bond 0.00470 ( 8101) covalent geometry : angle 0.66964 (11063) SS BOND : bond 0.01044 ( 1) SS BOND : angle 13.63618 ( 2) hydrogen bonds : bond 0.04419 ( 375) hydrogen bonds : angle 4.67021 ( 1029) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1988 Ramachandran restraints generated. 994 Oldfield, 0 Emsley, 994 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1988 Ramachandran restraints generated. 994 Oldfield, 0 Emsley, 994 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 228 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 202 time to evaluate : 0.178 Fit side-chains revert: symmetry clash REVERT: A 455 ASP cc_start: 0.7925 (OUTLIER) cc_final: 0.7606 (m-30) REVERT: A 468 GLU cc_start: 0.7222 (mt-10) cc_final: 0.6879 (mp0) REVERT: A 640 ARG cc_start: 0.7907 (pmt170) cc_final: 0.7400 (pmt170) REVERT: A 641 ARG cc_start: 0.7297 (mmm160) cc_final: 0.6822 (mmm-85) REVERT: A 808 PHE cc_start: 0.6776 (OUTLIER) cc_final: 0.6267 (t80) REVERT: C 35 VAL cc_start: 0.7978 (m) cc_final: 0.7761 (t) REVERT: C 49 ARG cc_start: 0.8150 (mtt-85) cc_final: 0.7920 (mtt-85) REVERT: C 79 ARG cc_start: 0.7736 (OUTLIER) cc_final: 0.7487 (tpt170) REVERT: C 113 THR cc_start: 0.7868 (p) cc_final: 0.7650 (p) REVERT: C 123 ARG cc_start: 0.7007 (ttt90) cc_final: 0.6574 (ttt90) REVERT: C 137 GLU cc_start: 0.7178 (OUTLIER) cc_final: 0.6973 (mt-10) REVERT: C 303 ARG cc_start: 0.8063 (OUTLIER) cc_final: 0.7548 (mmm-85) REVERT: C 458 LEU cc_start: 0.8488 (mt) cc_final: 0.8240 (mt) REVERT: C 460 ARG cc_start: 0.7799 (tpt90) cc_final: 0.7487 (tpt90) REVERT: C 473 ARG cc_start: 0.7669 (mtt90) cc_final: 0.7366 (mtt90) REVERT: C 525 GLU cc_start: 0.7644 (tp30) cc_final: 0.7228 (tp30) REVERT: C 540 ARG cc_start: 0.8104 (ttm110) cc_final: 0.7765 (ttm-80) REVERT: C 695 ASP cc_start: 0.8069 (m-30) cc_final: 0.7776 (m-30) REVERT: C 718 GLU cc_start: 0.7923 (OUTLIER) cc_final: 0.7086 (mp0) REVERT: C 745 MET cc_start: 0.8065 (mmm) cc_final: 0.7476 (mtm) outliers start: 26 outliers final: 16 residues processed: 218 average time/residue: 0.4262 time to fit residues: 98.5994 Evaluate side-chains 224 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 202 time to evaluate : 0.177 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 455 ASP Chi-restraints excluded: chain A residue 472 VAL Chi-restraints excluded: chain A residue 476 TRP Chi-restraints excluded: chain A residue 550 LEU Chi-restraints excluded: chain A residue 801 ILE Chi-restraints excluded: chain A residue 808 PHE Chi-restraints excluded: chain A residue 809 LEU Chi-restraints excluded: chain A residue 815 VAL Chi-restraints excluded: chain C residue 79 ARG Chi-restraints excluded: chain C residue 137 GLU Chi-restraints excluded: chain C residue 171 GLU Chi-restraints excluded: chain C residue 271 LEU Chi-restraints excluded: chain C residue 303 ARG Chi-restraints excluded: chain C residue 405 THR Chi-restraints excluded: chain C residue 409 CYS Chi-restraints excluded: chain C residue 472 LEU Chi-restraints excluded: chain C residue 509 VAL Chi-restraints excluded: chain C residue 627 ASP Chi-restraints excluded: chain C residue 631 ARG Chi-restraints excluded: chain C residue 680 VAL Chi-restraints excluded: chain C residue 718 GLU Chi-restraints excluded: chain C residue 719 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 47 optimal weight: 0.8980 chunk 20 optimal weight: 0.9990 chunk 14 optimal weight: 0.9990 chunk 61 optimal weight: 0.0370 chunk 84 optimal weight: 0.7980 chunk 89 optimal weight: 0.5980 chunk 56 optimal weight: 0.9980 chunk 68 optimal weight: 1.9990 chunk 41 optimal weight: 0.0870 chunk 51 optimal weight: 2.9990 chunk 28 optimal weight: 2.9990 overall best weight: 0.4836 ------------------------------------------------------------------------------- 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 = 0.3917 r_free = 0.3917 target = 0.147724 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3723 r_free = 0.3723 target = 0.133291 restraints weight = 11548.413| |-----------------------------------------------------------------------------| r_work (start): 0.3718 rms_B_bonded: 2.16 r_work: 0.3602 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.3439 rms_B_bonded: 4.78 restraints_weight: 0.2500 r_work (final): 0.3439 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7487 moved from start: 0.4255 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.178 8102 Z= 0.189 Angle : 0.708 19.634 11065 Z= 0.344 Chirality : 0.048 0.561 1259 Planarity : 0.006 0.044 1434 Dihedral : 4.985 62.064 1130 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 9.80 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.13 % Favored : 94.77 % Rotamer: Outliers : 3.81 % Allowed : 22.11 % Favored : 74.08 % Cbeta Deviations : 0.10 % Peptide Plane: Cis-proline : 6.10 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % 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: -0.76 (0.27), residues: 994 helix: 0.56 (0.26), residues: 437 sheet: -0.62 (0.38), residues: 176 loop : -1.65 (0.31), residues: 381 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG C 603 TYR 0.014 0.001 TYR A 674 PHE 0.015 0.002 PHE C 259 TRP 0.031 0.002 TRP C 453 HIS 0.005 0.001 HIS C 710 Details of bonding type rmsd covalent geometry : bond 0.00471 ( 8101) covalent geometry : angle 0.67946 (11063) SS BOND : bond 0.01348 ( 1) SS BOND : angle 14.84803 ( 2) hydrogen bonds : bond 0.04334 ( 375) hydrogen bonds : angle 4.61935 ( 1029) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1988 Ramachandran restraints generated. 994 Oldfield, 0 Emsley, 994 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1988 Ramachandran restraints generated. 994 Oldfield, 0 Emsley, 994 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 231 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 201 time to evaluate : 0.319 Fit side-chains revert: symmetry clash REVERT: A 455 ASP cc_start: 0.7890 (OUTLIER) cc_final: 0.7577 (m-30) REVERT: A 468 GLU cc_start: 0.7204 (mt-10) cc_final: 0.6869 (mp0) REVERT: A 472 VAL cc_start: 0.4519 (OUTLIER) cc_final: 0.3853 (p) REVERT: A 640 ARG cc_start: 0.7882 (pmt170) cc_final: 0.7365 (pmt170) REVERT: A 641 ARG cc_start: 0.7256 (mmm160) cc_final: 0.6793 (mmm-85) REVERT: A 808 PHE cc_start: 0.6790 (OUTLIER) cc_final: 0.6278 (t80) REVERT: C 35 VAL cc_start: 0.8006 (m) cc_final: 0.7786 (t) REVERT: C 49 ARG cc_start: 0.8156 (mtt-85) cc_final: 0.7927 (mtt-85) REVERT: C 79 ARG cc_start: 0.7605 (OUTLIER) cc_final: 0.7383 (tpt170) REVERT: C 113 THR cc_start: 0.7878 (p) cc_final: 0.7659 (p) REVERT: C 123 ARG cc_start: 0.7002 (ttt90) cc_final: 0.6572 (ttt90) REVERT: C 303 ARG cc_start: 0.8027 (OUTLIER) cc_final: 0.7517 (mmm-85) REVERT: C 458 LEU cc_start: 0.8496 (mt) cc_final: 0.8251 (mt) REVERT: C 460 ARG cc_start: 0.7760 (tpt90) cc_final: 0.7464 (tpt90) REVERT: C 509 VAL cc_start: 0.8452 (OUTLIER) cc_final: 0.8105 (m) REVERT: C 525 GLU cc_start: 0.7566 (tp30) cc_final: 0.7176 (tp30) REVERT: C 695 ASP cc_start: 0.8065 (m-30) cc_final: 0.7745 (m-30) REVERT: C 718 GLU cc_start: 0.7902 (OUTLIER) cc_final: 0.7074 (mp0) REVERT: C 745 MET cc_start: 0.8049 (mmm) cc_final: 0.7435 (mtm) outliers start: 30 outliers final: 18 residues processed: 215 average time/residue: 0.4601 time to fit residues: 104.7513 Evaluate side-chains 226 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 201 time to evaluate : 0.215 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 455 ASP Chi-restraints excluded: chain A residue 472 VAL Chi-restraints excluded: chain A residue 476 TRP Chi-restraints excluded: chain A residue 550 LEU Chi-restraints excluded: chain A residue 779 THR Chi-restraints excluded: chain A residue 801 ILE Chi-restraints excluded: chain A residue 808 PHE Chi-restraints excluded: chain A residue 809 LEU Chi-restraints excluded: chain A residue 815 VAL Chi-restraints excluded: chain A residue 862 ASP Chi-restraints excluded: chain C residue 79 ARG Chi-restraints excluded: chain C residue 171 GLU Chi-restraints excluded: chain C residue 191 CYS Chi-restraints excluded: chain C residue 271 LEU Chi-restraints excluded: chain C residue 303 ARG Chi-restraints excluded: chain C residue 367 SER Chi-restraints excluded: chain C residue 409 CYS Chi-restraints excluded: chain C residue 472 LEU Chi-restraints excluded: chain C residue 509 VAL Chi-restraints excluded: chain C residue 529 ARG Chi-restraints excluded: chain C residue 627 ASP Chi-restraints excluded: chain C residue 631 ARG Chi-restraints excluded: chain C residue 680 VAL Chi-restraints excluded: chain C residue 718 GLU Chi-restraints excluded: chain C residue 719 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 61 optimal weight: 0.9990 chunk 41 optimal weight: 0.0000 chunk 5 optimal weight: 0.9980 chunk 71 optimal weight: 0.9990 chunk 35 optimal weight: 2.9990 chunk 74 optimal weight: 0.8980 chunk 69 optimal weight: 0.9990 chunk 97 optimal weight: 0.8980 chunk 24 optimal weight: 0.6980 chunk 45 optimal weight: 0.0060 chunk 77 optimal weight: 0.7980 overall best weight: 0.4800 ------------------------------------------------------------------------------- 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 = 0.3918 r_free = 0.3918 target = 0.147874 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 23)----------------| | r_work = 0.3724 r_free = 0.3724 target = 0.133398 restraints weight = 11581.387| |-----------------------------------------------------------------------------| r_work (start): 0.3709 rms_B_bonded: 2.15 r_work: 0.3594 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.3431 rms_B_bonded: 4.77 restraints_weight: 0.2500 r_work (final): 0.3431 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7486 moved from start: 0.4335 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.172 8102 Z= 0.184 Angle : 0.703 18.905 11065 Z= 0.342 Chirality : 0.047 0.532 1259 Planarity : 0.006 0.044 1434 Dihedral : 4.927 61.084 1130 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 9.61 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.23 % Favored : 94.67 % Rotamer: Outliers : 3.56 % Allowed : 22.11 % Favored : 74.33 % Cbeta Deviations : 0.10 % Peptide Plane: Cis-proline : 6.10 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % 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: -0.63 (0.27), residues: 994 helix: 0.71 (0.26), residues: 431 sheet: -0.68 (0.38), residues: 180 loop : -1.54 (0.32), residues: 383 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C 603 TYR 0.014 0.001 TYR A 674 PHE 0.016 0.002 PHE C 259 TRP 0.054 0.002 TRP C 453 HIS 0.005 0.001 HIS C 710 Details of bonding type rmsd covalent geometry : bond 0.00459 ( 8101) covalent geometry : angle 0.67839 (11063) SS BOND : bond 0.01615 ( 1) SS BOND : angle 13.64370 ( 2) hydrogen bonds : bond 0.04369 ( 375) hydrogen bonds : angle 4.62456 ( 1029) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1988 Ramachandran restraints generated. 994 Oldfield, 0 Emsley, 994 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1988 Ramachandran restraints generated. 994 Oldfield, 0 Emsley, 994 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 226 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 198 time to evaluate : 0.273 Fit side-chains revert: symmetry clash REVERT: A 455 ASP cc_start: 0.7900 (OUTLIER) cc_final: 0.7583 (m-30) REVERT: A 468 GLU cc_start: 0.7204 (mt-10) cc_final: 0.6888 (mp0) REVERT: A 640 ARG cc_start: 0.7871 (pmt170) cc_final: 0.7367 (pmt170) REVERT: A 641 ARG cc_start: 0.7235 (mmm160) cc_final: 0.6775 (mmm-85) REVERT: A 808 PHE cc_start: 0.6797 (OUTLIER) cc_final: 0.6310 (t80) REVERT: C 35 VAL cc_start: 0.7982 (m) cc_final: 0.7772 (t) REVERT: C 49 ARG cc_start: 0.8166 (mtt-85) cc_final: 0.7939 (mtt-85) REVERT: C 79 ARG cc_start: 0.7628 (OUTLIER) cc_final: 0.7397 (tpt170) REVERT: C 113 THR cc_start: 0.7884 (p) cc_final: 0.7668 (p) REVERT: C 123 ARG cc_start: 0.7013 (ttt90) cc_final: 0.6580 (ttt90) REVERT: C 303 ARG cc_start: 0.8020 (OUTLIER) cc_final: 0.7438 (mmm-85) REVERT: C 458 LEU cc_start: 0.8483 (mt) cc_final: 0.8165 (mt) REVERT: C 460 ARG cc_start: 0.7770 (tpt90) cc_final: 0.7458 (tpt90) REVERT: C 473 ARG cc_start: 0.7397 (mtt90) cc_final: 0.6726 (mtt90) REVERT: C 509 VAL cc_start: 0.8442 (OUTLIER) cc_final: 0.8095 (m) REVERT: C 525 GLU cc_start: 0.7585 (tp30) cc_final: 0.7189 (tp30) REVERT: C 540 ARG cc_start: 0.8075 (ttm-80) cc_final: 0.7781 (ttm-80) REVERT: C 695 ASP cc_start: 0.8085 (m-30) cc_final: 0.7757 (m-30) REVERT: C 718 GLU cc_start: 0.7899 (OUTLIER) cc_final: 0.7071 (mp0) REVERT: C 745 MET cc_start: 0.8046 (mmm) cc_final: 0.7456 (mtm) outliers start: 28 outliers final: 18 residues processed: 211 average time/residue: 0.4527 time to fit residues: 101.3847 Evaluate side-chains 220 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 196 time to evaluate : 0.202 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 455 ASP Chi-restraints excluded: chain A residue 472 VAL Chi-restraints excluded: chain A residue 476 TRP Chi-restraints excluded: chain A residue 550 LEU Chi-restraints excluded: chain A residue 779 THR Chi-restraints excluded: chain A residue 801 ILE Chi-restraints excluded: chain A residue 808 PHE Chi-restraints excluded: chain A residue 809 LEU Chi-restraints excluded: chain A residue 815 VAL Chi-restraints excluded: chain A residue 862 ASP Chi-restraints excluded: chain C residue 79 ARG Chi-restraints excluded: chain C residue 171 GLU Chi-restraints excluded: chain C residue 191 CYS Chi-restraints excluded: chain C residue 271 LEU Chi-restraints excluded: chain C residue 303 ARG Chi-restraints excluded: chain C residue 367 SER Chi-restraints excluded: chain C residue 409 CYS Chi-restraints excluded: chain C residue 509 VAL Chi-restraints excluded: chain C residue 529 ARG Chi-restraints excluded: chain C residue 627 ASP Chi-restraints excluded: chain C residue 631 ARG Chi-restraints excluded: chain C residue 680 VAL Chi-restraints excluded: chain C residue 718 GLU Chi-restraints excluded: chain C residue 719 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 17 optimal weight: 0.5980 chunk 91 optimal weight: 1.9990 chunk 87 optimal weight: 0.1980 chunk 88 optimal weight: 0.9990 chunk 92 optimal weight: 0.6980 chunk 83 optimal weight: 0.9990 chunk 99 optimal weight: 0.9980 chunk 28 optimal weight: 1.9990 chunk 42 optimal weight: 0.0270 chunk 71 optimal weight: 0.9980 chunk 24 optimal weight: 0.0980 overall best weight: 0.3238 ------------------------------------------------------------------------------- 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 = 0.3933 r_free = 0.3933 target = 0.149096 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3742 r_free = 0.3742 target = 0.134759 restraints weight = 11535.570| |-----------------------------------------------------------------------------| r_work (start): 0.3722 rms_B_bonded: 2.13 r_work: 0.3605 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.3441 rms_B_bonded: 4.78 restraints_weight: 0.2500 r_work (final): 0.3441 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7470 moved from start: 0.4425 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.184 8102 Z= 0.166 Angle : 0.728 20.803 11065 Z= 0.350 Chirality : 0.047 0.603 1259 Planarity : 0.006 0.055 1434 Dihedral : 4.848 62.708 1130 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 9.80 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.93 % Favored : 94.97 % Rotamer: Outliers : 2.92 % Allowed : 23.00 % Favored : 74.08 % Cbeta Deviations : 0.10 % Peptide Plane: Cis-proline : 6.10 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % 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: -0.48 (0.27), residues: 994 helix: 0.80 (0.26), residues: 431 sheet: -0.48 (0.39), residues: 170 loop : -1.48 (0.32), residues: 393 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG C 603 TYR 0.011 0.001 TYR A 804 PHE 0.016 0.002 PHE C 259 TRP 0.049 0.002 TRP C 453 HIS 0.004 0.001 HIS C 710 Details of bonding type rmsd covalent geometry : bond 0.00421 ( 8101) covalent geometry : angle 0.69522 (11063) SS BOND : bond 0.01325 ( 1) SS BOND : angle 16.01814 ( 2) hydrogen bonds : bond 0.04097 ( 375) hydrogen bonds : angle 4.53401 ( 1029) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1988 Ramachandran restraints generated. 994 Oldfield, 0 Emsley, 994 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1988 Ramachandran restraints generated. 994 Oldfield, 0 Emsley, 994 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 219 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 196 time to evaluate : 0.283 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 455 ASP cc_start: 0.7878 (OUTLIER) cc_final: 0.7565 (m-30) REVERT: A 640 ARG cc_start: 0.7863 (pmt170) cc_final: 0.7348 (pmt170) REVERT: A 641 ARG cc_start: 0.7236 (mmm160) cc_final: 0.6765 (mmm-85) REVERT: A 808 PHE cc_start: 0.6761 (OUTLIER) cc_final: 0.6249 (t80) REVERT: C 35 VAL cc_start: 0.7966 (m) cc_final: 0.7748 (t) REVERT: C 40 ARG cc_start: 0.7574 (ttp-170) cc_final: 0.7364 (ttp-170) REVERT: C 49 ARG cc_start: 0.8154 (mtt-85) cc_final: 0.7929 (mtt-85) REVERT: C 79 ARG cc_start: 0.7545 (OUTLIER) cc_final: 0.7316 (tpt170) REVERT: C 113 THR cc_start: 0.7900 (p) cc_final: 0.7681 (p) REVERT: C 123 ARG cc_start: 0.7016 (ttt90) cc_final: 0.6563 (ttt90) REVERT: C 280 THR cc_start: 0.8093 (m) cc_final: 0.7888 (p) REVERT: C 458 LEU cc_start: 0.8462 (mt) cc_final: 0.8186 (mt) REVERT: C 460 ARG cc_start: 0.7732 (tpt90) cc_final: 0.7428 (tpt90) REVERT: C 509 VAL cc_start: 0.8456 (OUTLIER) cc_final: 0.8103 (m) REVERT: C 525 GLU cc_start: 0.7575 (tp30) cc_final: 0.7166 (tp30) REVERT: C 540 ARG cc_start: 0.8087 (ttm-80) cc_final: 0.7811 (ttm-80) REVERT: C 695 ASP cc_start: 0.8071 (m-30) cc_final: 0.7708 (m-30) REVERT: C 718 GLU cc_start: 0.7894 (OUTLIER) cc_final: 0.7066 (mp0) REVERT: C 745 MET cc_start: 0.8024 (mmm) cc_final: 0.7426 (mtm) outliers start: 23 outliers final: 16 residues processed: 206 average time/residue: 0.4701 time to fit residues: 102.5648 Evaluate side-chains 216 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 195 time to evaluate : 0.226 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 455 ASP Chi-restraints excluded: chain A residue 472 VAL Chi-restraints excluded: chain A residue 476 TRP Chi-restraints excluded: chain A residue 550 LEU Chi-restraints excluded: chain A residue 557 ARG Chi-restraints excluded: chain A residue 779 THR Chi-restraints excluded: chain A residue 808 PHE Chi-restraints excluded: chain A residue 809 LEU Chi-restraints excluded: chain A residue 815 VAL Chi-restraints excluded: chain C residue 79 ARG Chi-restraints excluded: chain C residue 171 GLU Chi-restraints excluded: chain C residue 191 CYS Chi-restraints excluded: chain C residue 271 LEU Chi-restraints excluded: chain C residue 367 SER Chi-restraints excluded: chain C residue 409 CYS Chi-restraints excluded: chain C residue 509 VAL Chi-restraints excluded: chain C residue 627 ASP Chi-restraints excluded: chain C residue 631 ARG Chi-restraints excluded: chain C residue 680 VAL Chi-restraints excluded: chain C residue 718 GLU Chi-restraints excluded: chain C residue 719 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 30 optimal weight: 0.4980 chunk 7 optimal weight: 0.9980 chunk 65 optimal weight: 0.9980 chunk 1 optimal weight: 2.9990 chunk 52 optimal weight: 3.9990 chunk 61 optimal weight: 0.9990 chunk 83 optimal weight: 0.9990 chunk 86 optimal weight: 0.7980 chunk 97 optimal weight: 0.9990 chunk 41 optimal weight: 0.0770 chunk 47 optimal weight: 0.4980 overall best weight: 0.5738 ------------------------------------------------------------------------------- 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 = 0.3915 r_free = 0.3915 target = 0.147522 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3718 r_free = 0.3718 target = 0.132944 restraints weight = 11484.783| |-----------------------------------------------------------------------------| r_work (start): 0.3701 rms_B_bonded: 2.15 r_work: 0.3586 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.3423 rms_B_bonded: 4.76 restraints_weight: 0.2500 r_work (final): 0.3423 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7491 moved from start: 0.4455 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.196 8102 Z= 0.207 Angle : 0.746 20.821 11065 Z= 0.361 Chirality : 0.048 0.595 1259 Planarity : 0.006 0.043 1434 Dihedral : 4.945 62.014 1130 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 9.80 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.03 % Favored : 94.87 % Rotamer: Outliers : 2.67 % Allowed : 23.38 % Favored : 73.95 % Cbeta Deviations : 0.10 % Peptide Plane: Cis-proline : 6.10 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % 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: -0.64 (0.27), residues: 994 helix: 0.69 (0.26), residues: 431 sheet: -0.71 (0.38), residues: 180 loop : -1.51 (0.32), residues: 383 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 540 TYR 0.017 0.002 TYR C 19 PHE 0.017 0.002 PHE C 259 TRP 0.046 0.002 TRP C 453 HIS 0.005 0.001 HIS C 710 Details of bonding type rmsd covalent geometry : bond 0.00515 ( 8101) covalent geometry : angle 0.71370 (11063) SS BOND : bond 0.01005 ( 1) SS BOND : angle 16.17423 ( 2) hydrogen bonds : bond 0.04487 ( 375) hydrogen bonds : angle 4.64969 ( 1029) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2642.22 seconds wall clock time: 45 minutes 34.29 seconds (2734.29 seconds total)