Starting phenix.real_space_refine on Sun Apr 27 01:13:33 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8kgw_37234/04_2025/8kgw_37234.cif Found real_map, /net/cci-nas-00/data/ceres_data/8kgw_37234/04_2025/8kgw_37234.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8kgw_37234/04_2025/8kgw_37234.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8kgw_37234/04_2025/8kgw_37234.map" model { file = "/net/cci-nas-00/data/ceres_data/8kgw_37234/04_2025/8kgw_37234.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8kgw_37234/04_2025/8kgw_37234.cif" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs 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= -0.001 sd= 0.061 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 35 5.16 5 C 2664 2.51 5 N 645 2.21 5 O 692 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 9 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/chem_data/mon_lib" Total number of atoms: 4036 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 4011 Number of conformers: 1 Conformer: "" Number of residues, atoms: 532, 4011 Classifications: {'peptide': 532} Incomplete info: {'truncation_to_alanine': 22} Link IDs: {'PTRANS': 28, 'TRANS': 503} Chain breaks: 3 Unresolved non-hydrogen bonds: 79 Unresolved non-hydrogen angles: 96 Unresolved non-hydrogen dihedrals: 67 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLN:plan1': 2, 'ASP:plan': 1, 'TYR:plan': 1, 'ASN:plan1': 1, 'HIS:plan': 1, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 41 Chain: "A" Number of atoms: 25 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 25 Unusual residues: {'P2E': 1} Classifications: {'undetermined': 1} Time building chain proxies: 2.99, per 1000 atoms: 0.74 Number of scatterers: 4036 At special positions: 0 Unit cell: (71.764, 94.132, 75.492, 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 35 16.00 O 692 8.00 N 645 7.00 C 2664 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS A 420 " - pdb=" SG CYS A 511 " distance=2.03 Simple disulfide: pdb=" SG CYS A 444 " - pdb=" SG CYS A 494 " distance=2.03 Simple disulfide: pdb=" SG CYS A 450 " - pdb=" SG CYS A 470 " distance=2.03 Simple disulfide: pdb=" SG CYS A 459 " - pdb=" SG CYS A 507 " distance=2.03 Simple disulfide: pdb=" SG CYS A 474 " - pdb=" SG CYS A 492 " distance=2.02 Simple disulfide: pdb=" SG CYS A 580 " - pdb=" SG CYS A 594 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.98 Conformation dependent library (CDL) restraints added in 460.0 milliseconds 1048 Ramachandran restraints generated. 524 Oldfield, 0 Emsley, 524 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 982 Finding SS restraints... Secondary structure from input PDB file: 26 helices and 3 sheets defined 68.4% alpha, 2.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.44 Creating SS restraints... Processing helix chain 'A' and resid 30 through 64 removed outlier: 4.184A pdb=" N PHE A 34 " --> pdb=" O ASN A 30 " (cutoff:3.500A) removed outlier: 5.426A pdb=" N THR A 57 " --> pdb=" O LYS A 53 " (cutoff:3.500A) removed outlier: 5.480A pdb=" N THR A 58 " --> pdb=" O SER A 54 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N ILE A 59 " --> pdb=" O SER A 55 " (cutoff:3.500A) Processing helix chain 'A' and resid 66 through 91 removed outlier: 4.109A pdb=" N ASN A 77 " --> pdb=" O ILE A 73 " (cutoff:3.500A) removed outlier: 4.103A pdb=" N GLU A 78 " --> pdb=" O SER A 74 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N ASN A 81 " --> pdb=" O ASN A 77 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N ALA A 82 " --> pdb=" O GLU A 78 " (cutoff:3.500A) removed outlier: 4.695A pdb=" N ILE A 86 " --> pdb=" O ALA A 82 " (cutoff:3.500A) removed outlier: 5.166A pdb=" N PHE A 87 " --> pdb=" O ILE A 83 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N VAL A 88 " --> pdb=" O LEU A 84 " (cutoff:3.500A) Processing helix chain 'A' and resid 96 through 117 removed outlier: 3.625A pdb=" N LEU A 115 " --> pdb=" O GLY A 111 " (cutoff:3.500A) Processing helix chain 'A' and resid 117 through 122 removed outlier: 3.888A pdb=" N LEU A 121 " --> pdb=" O LEU A 117 " (cutoff:3.500A) removed outlier: 4.166A pdb=" N SER A 122 " --> pdb=" O PRO A 118 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 117 through 122' Processing helix chain 'A' and resid 169 through 184 Processing helix chain 'A' and resid 186 through 198 removed outlier: 3.720A pdb=" N PHE A 190 " --> pdb=" O PRO A 186 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N PHE A 198 " --> pdb=" O TYR A 194 " (cutoff:3.500A) Processing helix chain 'A' and resid 203 through 215 Processing helix chain 'A' and resid 217 through 230 removed outlier: 3.580A pdb=" N GLY A 222 " --> pdb=" O GLY A 218 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N TYR A 223 " --> pdb=" O PRO A 219 " (cutoff:3.500A) Processing helix chain 'A' and resid 256 through 273 removed outlier: 4.407A pdb=" N GLY A 260 " --> pdb=" O ALA A 256 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N LEU A 261 " --> pdb=" O TRP A 257 " (cutoff:3.500A) Processing helix chain 'A' and resid 274 through 278 Processing helix chain 'A' and resid 307 through 312 removed outlier: 3.690A pdb=" N PHE A 311 " --> pdb=" O SER A 307 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N ILE A 312 " --> pdb=" O LEU A 308 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 307 through 312' Processing helix chain 'A' and resid 314 through 324 removed outlier: 3.639A pdb=" N ILE A 318 " --> pdb=" O ARG A 314 " (cutoff:3.500A) Processing helix chain 'A' and resid 325 through 333 Processing helix chain 'A' and resid 338 through 346 removed outlier: 4.259A pdb=" N ILE A 342 " --> pdb=" O PHE A 338 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N GLY A 344 " --> pdb=" O SER A 340 " (cutoff:3.500A) Processing helix chain 'A' and resid 348 through 357 removed outlier: 3.642A pdb=" N PHE A 352 " --> pdb=" O PHE A 348 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N TYR A 357 " --> pdb=" O LEU A 353 " (cutoff:3.500A) Processing helix chain 'A' and resid 360 through 390 removed outlier: 4.359A pdb=" N LEU A 373 " --> pdb=" O GLY A 369 " (cutoff:3.500A) Proline residue: A 374 - end of helix removed outlier: 3.556A pdb=" N MET A 380 " --> pdb=" O ALA A 376 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N LEU A 381 " --> pdb=" O ALA A 377 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N PHE A 390 " --> pdb=" O LEU A 386 " (cutoff:3.500A) Processing helix chain 'A' and resid 396 through 411 removed outlier: 3.607A pdb=" N THR A 402 " --> pdb=" O PRO A 398 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N ILE A 405 " --> pdb=" O ALA A 401 " (cutoff:3.500A) Processing helix chain 'A' and resid 414 through 419 removed outlier: 4.006A pdb=" N GLY A 419 " --> pdb=" O LEU A 415 " (cutoff:3.500A) Processing helix chain 'A' and resid 468 through 473 Processing helix chain 'A' and resid 511 through 515 Processing helix chain 'A' and resid 521 through 530 Processing helix chain 'A' and resid 533 through 544 removed outlier: 3.700A pdb=" N MET A 539 " --> pdb=" O PRO A 535 " (cutoff:3.500A) removed outlier: 4.472A pdb=" N VAL A 540 " --> pdb=" O LEU A 536 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N LEU A 541 " --> pdb=" O TYR A 537 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N VAL A 543 " --> pdb=" O MET A 539 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N VAL A 544 " --> pdb=" O VAL A 540 " (cutoff:3.500A) Processing helix chain 'A' and resid 545 through 547 No H-bonds generated for 'chain 'A' and resid 545 through 547' Processing helix chain 'A' and resid 548 through 564 Processing helix chain 'A' and resid 567 through 579 removed outlier: 4.020A pdb=" N SER A 579 " --> pdb=" O THR A 575 " (cutoff:3.500A) Processing helix chain 'A' and resid 598 through 629 removed outlier: 3.777A pdb=" N ASP A 604 " --> pdb=" O ASP A 600 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N LEU A 609 " --> pdb=" O ARG A 605 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N GLN A 610 " --> pdb=" O TYR A 606 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N LYS A 614 " --> pdb=" O GLN A 610 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N GLY A 617 " --> pdb=" O TYR A 613 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N LEU A 620 " --> pdb=" O LEU A 616 " (cutoff:3.500A) removed outlier: 4.270A pdb=" N LEU A 621 " --> pdb=" O GLY A 617 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N CYS A 622 " --> pdb=" O MET A 618 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 458 through 459 removed outlier: 3.720A pdb=" N VAL A 458 " --> pdb=" O TYR A 466 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N TYR A 466 " --> pdb=" O VAL A 458 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 489 through 490 Processing sheet with id=AA3, first strand: chain 'A' and resid 582 through 585 removed outlier: 6.947A pdb=" N ARG A 582 " --> pdb=" O CYS A 594 " (cutoff:3.500A) removed outlier: 4.698A pdb=" N CYS A 594 " --> pdb=" O ARG A 582 " (cutoff:3.500A) removed outlier: 5.683A pdb=" N ASN A 584 " --> pdb=" O GLY A 592 " (cutoff:3.500A) 215 hydrogen bonds defined for protein. 630 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: 1.02 Time building geometry restraints manager: 1.12 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.31: 605 1.31 - 1.44: 1153 1.44 - 1.56: 2327 1.56 - 1.69: 3 1.69 - 1.81: 50 Bond restraints: 4138 Sorted by residual: bond pdb=" C12 P2E A 701 " pdb=" C8 P2E A 701 " ideal model delta sigma weight residual 1.538 1.396 0.142 2.00e-02 2.50e+03 5.07e+01 bond pdb=" C10 P2E A 701 " pdb=" C9 P2E A 701 " ideal model delta sigma weight residual 1.512 1.373 0.139 2.00e-02 2.50e+03 4.81e+01 bond pdb=" C11 P2E A 701 " pdb=" O4 P2E A 701 " ideal model delta sigma weight residual 1.402 1.288 0.114 2.00e-02 2.50e+03 3.25e+01 bond pdb=" C11 P2E A 701 " pdb=" C12 P2E A 701 " ideal model delta sigma weight residual 1.529 1.627 -0.098 2.00e-02 2.50e+03 2.41e+01 bond pdb=" C8 P2E A 701 " pdb=" C9 P2E A 701 " ideal model delta sigma weight residual 1.515 1.605 -0.090 2.00e-02 2.50e+03 2.04e+01 ... (remaining 4133 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.69: 5527 2.69 - 5.37: 77 5.37 - 8.06: 22 8.06 - 10.75: 1 10.75 - 13.43: 3 Bond angle restraints: 5630 Sorted by residual: angle pdb=" C13 P2E A 701 " pdb=" C14 P2E A 701 " pdb=" C15 P2E A 701 " ideal model delta sigma weight residual 125.85 112.42 13.43 3.00e+00 1.11e-01 2.01e+01 angle pdb=" C4 P2E A 701 " pdb=" C5 P2E A 701 " pdb=" C6 P2E A 701 " ideal model delta sigma weight residual 127.52 114.15 13.37 3.00e+00 1.11e-01 1.99e+01 angle pdb=" C12 P2E A 701 " pdb=" C13 P2E A 701 " pdb=" C14 P2E A 701 " ideal model delta sigma weight residual 124.37 112.72 11.65 3.00e+00 1.11e-01 1.51e+01 angle pdb=" N GLN A 556 " pdb=" CA GLN A 556 " pdb=" C GLN A 556 " ideal model delta sigma weight residual 111.07 107.45 3.62 1.07e+00 8.73e-01 1.15e+01 angle pdb=" C ILE A 187 " pdb=" N GLN A 188 " pdb=" CA GLN A 188 " ideal model delta sigma weight residual 119.83 123.15 -3.32 1.11e+00 8.12e-01 8.95e+00 ... (remaining 5625 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.42: 2214 17.42 - 34.83: 182 34.83 - 52.25: 39 52.25 - 69.67: 5 69.67 - 87.08: 6 Dihedral angle restraints: 2446 sinusoidal: 918 harmonic: 1528 Sorted by residual: dihedral pdb=" CB CYS A 474 " pdb=" SG CYS A 474 " pdb=" SG CYS A 492 " pdb=" CB CYS A 492 " ideal model delta sinusoidal sigma weight residual -86.00 -124.05 38.05 1 1.00e+01 1.00e-02 2.04e+01 dihedral pdb=" CB CYS A 580 " pdb=" SG CYS A 580 " pdb=" SG CYS A 594 " pdb=" CB CYS A 594 " ideal model delta sinusoidal sigma weight residual -86.00 -123.03 37.03 1 1.00e+01 1.00e-02 1.94e+01 dihedral pdb=" CB CYS A 420 " pdb=" SG CYS A 420 " pdb=" SG CYS A 511 " pdb=" CB CYS A 511 " ideal model delta sinusoidal sigma weight residual -86.00 -54.02 -31.98 1 1.00e+01 1.00e-02 1.46e+01 ... (remaining 2443 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.064: 556 0.064 - 0.128: 95 0.128 - 0.193: 8 0.193 - 0.257: 1 0.257 - 0.321: 1 Chirality restraints: 661 Sorted by residual: chirality pdb=" C15 P2E A 701 " pdb=" C14 P2E A 701 " pdb=" C16 P2E A 701 " pdb=" O5 P2E A 701 " both_signs ideal model delta sigma weight residual False 2.23 2.55 -0.32 2.00e-01 2.50e+01 2.57e+00 chirality pdb=" CA LEU A 76 " pdb=" N LEU A 76 " pdb=" C LEU A 76 " pdb=" CB LEU A 76 " both_signs ideal model delta sigma weight residual False 2.51 2.71 -0.20 2.00e-01 2.50e+01 9.98e-01 chirality pdb=" C12 P2E A 701 " pdb=" C11 P2E A 701 " pdb=" C13 P2E A 701 " pdb=" C8 P2E A 701 " both_signs ideal model delta sigma weight residual False 2.63 2.82 -0.19 2.00e-01 2.50e+01 8.66e-01 ... (remaining 658 not shown) Planarity restraints: 699 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASN A 534 " 0.043 5.00e-02 4.00e+02 6.43e-02 6.62e+00 pdb=" N PRO A 535 " -0.111 5.00e-02 4.00e+02 pdb=" CA PRO A 535 " 0.033 5.00e-02 4.00e+02 pdb=" CD PRO A 535 " 0.036 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE A 315 " 0.034 5.00e-02 4.00e+02 5.11e-02 4.17e+00 pdb=" N PRO A 316 " -0.088 5.00e-02 4.00e+02 pdb=" CA PRO A 316 " 0.026 5.00e-02 4.00e+02 pdb=" CD PRO A 316 " 0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL A 413 " 0.032 5.00e-02 4.00e+02 4.81e-02 3.71e+00 pdb=" N PRO A 414 " -0.083 5.00e-02 4.00e+02 pdb=" CA PRO A 414 " 0.024 5.00e-02 4.00e+02 pdb=" CD PRO A 414 " 0.027 5.00e-02 4.00e+02 ... (remaining 696 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 794 2.77 - 3.30: 3907 3.30 - 3.84: 6338 3.84 - 4.37: 7146 4.37 - 4.90: 12444 Nonbonded interactions: 30629 Sorted by model distance: nonbonded pdb=" O PHE A 113 " pdb=" OG1 THR A 116 " model vdw 2.241 3.040 nonbonded pdb=" O PHE A 416 " pdb=" NH1 ARG A 603 " model vdw 2.327 3.120 nonbonded pdb=" NZ LYS A 355 " pdb=" O ALA A 595 " model vdw 2.375 3.120 nonbonded pdb=" NZ LYS A 32 " pdb=" OH TYR A 207 " model vdw 2.386 3.120 nonbonded pdb=" O SER A 55 " pdb=" OG SER A 55 " model vdw 2.389 3.040 ... (remaining 30624 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== 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: 0.950 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 0.150 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 13.840 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.890 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.960 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6784 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.142 4144 Z= 0.300 Angle : 0.863 13.434 5642 Z= 0.412 Chirality : 0.048 0.321 661 Planarity : 0.006 0.064 699 Dihedral : 13.650 87.084 1446 Min Nonbonded Distance : 2.241 Molprobity Statistics. All-atom Clashscore : 4.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.63 % Favored : 96.37 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.70 (0.36), residues: 524 helix: 0.28 (0.30), residues: 325 sheet: None (None), residues: 0 loop : -1.66 (0.39), residues: 199 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 170 HIS 0.004 0.001 HIS A 96 PHE 0.020 0.001 PHE A 348 TYR 0.009 0.001 TYR A 363 ARG 0.002 0.000 ARG A 627 Details of bonding type rmsd hydrogen bonds : bond 0.18191 ( 215) hydrogen bonds : angle 6.34786 ( 630) SS BOND : bond 0.00389 ( 6) SS BOND : angle 0.70961 ( 12) covalent geometry : bond 0.00600 ( 4138) covalent geometry : angle 0.86285 ( 5630) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1048 Ramachandran restraints generated. 524 Oldfield, 0 Emsley, 524 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1048 Ramachandran restraints generated. 524 Oldfield, 0 Emsley, 524 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 69 residues out of total 449 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 69 time to evaluate : 0.453 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 69 average time/residue: 0.1485 time to fit residues: 13.2756 Evaluate side-chains 52 residues out of total 449 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 52 time to evaluate : 0.396 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 44 optimal weight: 3.9990 chunk 40 optimal weight: 30.0000 chunk 22 optimal weight: 3.9990 chunk 13 optimal weight: 0.9990 chunk 27 optimal weight: 0.6980 chunk 21 optimal weight: 2.9990 chunk 41 optimal weight: 1.9990 chunk 16 optimal weight: 1.9990 chunk 25 optimal weight: 1.9990 chunk 30 optimal weight: 5.9990 chunk 48 optimal weight: 0.5980 overall best weight: 1.2586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 177 GLN A 534 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4393 r_free = 0.4393 target = 0.202143 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3912 r_free = 0.3912 target = 0.152935 restraints weight = 4121.790| |-----------------------------------------------------------------------------| r_work (start): 0.3892 rms_B_bonded: 2.01 r_work: 0.3757 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work: 0.3619 rms_B_bonded: 4.82 restraints_weight: 0.2500 r_work (final): 0.3619 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7261 moved from start: 0.1421 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 4144 Z= 0.179 Angle : 0.688 12.234 5642 Z= 0.331 Chirality : 0.042 0.136 661 Planarity : 0.005 0.057 699 Dihedral : 6.987 68.310 596 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 7.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.58 % Favored : 95.42 % Rotamer: Outliers : 1.41 % Allowed : 7.49 % Favored : 91.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.46 (0.37), residues: 524 helix: 0.44 (0.30), residues: 335 sheet: None (None), residues: 0 loop : -1.62 (0.41), residues: 189 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 583 HIS 0.003 0.001 HIS A 513 PHE 0.014 0.002 PHE A 557 TYR 0.011 0.002 TYR A 90 ARG 0.003 0.001 ARG A 97 Details of bonding type rmsd hydrogen bonds : bond 0.04958 ( 215) hydrogen bonds : angle 4.80049 ( 630) SS BOND : bond 0.00302 ( 6) SS BOND : angle 0.77425 ( 12) covalent geometry : bond 0.00429 ( 4138) covalent geometry : angle 0.68762 ( 5630) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1048 Ramachandran restraints generated. 524 Oldfield, 0 Emsley, 524 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1048 Ramachandran restraints generated. 524 Oldfield, 0 Emsley, 524 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 449 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 60 time to evaluate : 0.458 Fit side-chains outliers start: 6 outliers final: 5 residues processed: 65 average time/residue: 0.1416 time to fit residues: 12.0981 Evaluate side-chains 62 residues out of total 449 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 57 time to evaluate : 0.389 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 308 LEU Chi-restraints excluded: chain A residue 378 LEU Chi-restraints excluded: chain A residue 406 THR Chi-restraints excluded: chain A residue 575 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 49 optimal weight: 0.7980 chunk 2 optimal weight: 0.8980 chunk 48 optimal weight: 3.9990 chunk 39 optimal weight: 7.9990 chunk 10 optimal weight: 8.9990 chunk 15 optimal weight: 2.9990 chunk 45 optimal weight: 0.6980 chunk 5 optimal weight: 0.8980 chunk 14 optimal weight: 0.6980 chunk 7 optimal weight: 0.9980 chunk 11 optimal weight: 0.8980 overall best weight: 0.7980 ------------------------------------------------------------------------------- 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 = 0.4396 r_free = 0.4396 target = 0.202255 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3898 r_free = 0.3898 target = 0.150792 restraints weight = 4195.158| |-----------------------------------------------------------------------------| r_work (start): 0.3923 rms_B_bonded: 2.27 r_work: 0.3797 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work (final): 0.3797 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7110 moved from start: 0.1630 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 4144 Z= 0.140 Angle : 0.634 8.320 5642 Z= 0.302 Chirality : 0.040 0.132 661 Planarity : 0.005 0.054 699 Dihedral : 6.293 77.039 596 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 5.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.01 % Favored : 95.99 % Rotamer: Outliers : 1.64 % Allowed : 10.77 % Favored : 87.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.17 (0.38), residues: 524 helix: 0.67 (0.30), residues: 339 sheet: None (None), residues: 0 loop : -1.52 (0.43), residues: 185 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 170 HIS 0.002 0.001 HIS A 471 PHE 0.012 0.001 PHE A 311 TYR 0.009 0.001 TYR A 90 ARG 0.002 0.000 ARG A 321 Details of bonding type rmsd hydrogen bonds : bond 0.04201 ( 215) hydrogen bonds : angle 4.46932 ( 630) SS BOND : bond 0.00153 ( 6) SS BOND : angle 0.48020 ( 12) covalent geometry : bond 0.00331 ( 4138) covalent geometry : angle 0.63450 ( 5630) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1048 Ramachandran restraints generated. 524 Oldfield, 0 Emsley, 524 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1048 Ramachandran restraints generated. 524 Oldfield, 0 Emsley, 524 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 63 residues out of total 449 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 56 time to evaluate : 0.378 Fit side-chains REVERT: A 547 GLU cc_start: 0.7693 (mp0) cc_final: 0.7466 (mp0) outliers start: 7 outliers final: 4 residues processed: 63 average time/residue: 0.1409 time to fit residues: 11.7365 Evaluate side-chains 59 residues out of total 449 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 55 time to evaluate : 0.492 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 308 LEU Chi-restraints excluded: chain A residue 378 LEU Chi-restraints excluded: chain A residue 406 THR Chi-restraints excluded: chain A residue 575 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 10 optimal weight: 0.9980 chunk 23 optimal weight: 2.9990 chunk 8 optimal weight: 0.1980 chunk 35 optimal weight: 8.9990 chunk 9 optimal weight: 0.9980 chunk 42 optimal weight: 0.7980 chunk 2 optimal weight: 0.8980 chunk 16 optimal weight: 0.0570 chunk 28 optimal weight: 0.9990 chunk 17 optimal weight: 0.0570 chunk 32 optimal weight: 1.9990 overall best weight: 0.4016 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 556 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4437 r_free = 0.4437 target = 0.206803 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3971 r_free = 0.3971 target = 0.158175 restraints weight = 4115.768| |-----------------------------------------------------------------------------| r_work (start): 0.3946 rms_B_bonded: 2.06 r_work: 0.3812 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work: 0.3672 rms_B_bonded: 4.99 restraints_weight: 0.2500 r_work (final): 0.3672 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7166 moved from start: 0.1822 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 4144 Z= 0.115 Angle : 0.585 7.502 5642 Z= 0.275 Chirality : 0.039 0.127 661 Planarity : 0.005 0.053 699 Dihedral : 6.048 86.088 596 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 5.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.01 % Favored : 95.99 % Rotamer: Outliers : 1.17 % Allowed : 12.88 % Favored : 85.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.21 (0.38), residues: 524 helix: 1.04 (0.30), residues: 333 sheet: None (None), residues: 0 loop : -1.47 (0.43), residues: 191 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 626 HIS 0.003 0.001 HIS A 471 PHE 0.011 0.001 PHE A 277 TYR 0.008 0.001 TYR A 613 ARG 0.002 0.000 ARG A 603 Details of bonding type rmsd hydrogen bonds : bond 0.03367 ( 215) hydrogen bonds : angle 4.03466 ( 630) SS BOND : bond 0.00122 ( 6) SS BOND : angle 0.38163 ( 12) covalent geometry : bond 0.00263 ( 4138) covalent geometry : angle 0.58523 ( 5630) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1048 Ramachandran restraints generated. 524 Oldfield, 0 Emsley, 524 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1048 Ramachandran restraints generated. 524 Oldfield, 0 Emsley, 524 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 60 residues out of total 449 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 55 time to evaluate : 0.385 Fit side-chains REVERT: A 547 GLU cc_start: 0.7845 (mp0) cc_final: 0.7605 (mp0) outliers start: 5 outliers final: 5 residues processed: 60 average time/residue: 0.1266 time to fit residues: 10.0844 Evaluate side-chains 59 residues out of total 449 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 54 time to evaluate : 0.385 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 116 THR Chi-restraints excluded: chain A residue 308 LEU Chi-restraints excluded: chain A residue 378 LEU Chi-restraints excluded: chain A residue 406 THR Chi-restraints excluded: chain A residue 575 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 31 optimal weight: 0.7980 chunk 41 optimal weight: 0.4980 chunk 29 optimal weight: 0.9990 chunk 43 optimal weight: 0.8980 chunk 30 optimal weight: 1.9990 chunk 2 optimal weight: 0.7980 chunk 17 optimal weight: 6.9990 chunk 27 optimal weight: 3.9990 chunk 9 optimal weight: 2.9990 chunk 3 optimal weight: 1.9990 chunk 52 optimal weight: 0.6980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 556 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4408 r_free = 0.4408 target = 0.203071 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3924 r_free = 0.3924 target = 0.153656 restraints weight = 4233.948| |-----------------------------------------------------------------------------| r_work (start): 0.3915 rms_B_bonded: 2.08 r_work: 0.3780 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work (final): 0.3780 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7120 moved from start: 0.1920 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 4144 Z= 0.131 Angle : 0.607 8.807 5642 Z= 0.285 Chirality : 0.040 0.127 661 Planarity : 0.005 0.051 699 Dihedral : 6.005 85.003 596 Min Nonbonded Distance : 2.558 Molprobity Statistics. All-atom Clashscore : 6.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.82 % Favored : 96.18 % Rotamer: Outliers : 2.34 % Allowed : 13.82 % Favored : 83.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.21 (0.38), residues: 524 helix: 0.95 (0.30), residues: 340 sheet: None (None), residues: 0 loop : -1.36 (0.44), residues: 184 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 583 HIS 0.002 0.001 HIS A 471 PHE 0.012 0.001 PHE A 557 TYR 0.009 0.001 TYR A 194 ARG 0.001 0.000 ARG A 603 Details of bonding type rmsd hydrogen bonds : bond 0.03686 ( 215) hydrogen bonds : angle 4.07919 ( 630) SS BOND : bond 0.00155 ( 6) SS BOND : angle 0.36253 ( 12) covalent geometry : bond 0.00309 ( 4138) covalent geometry : angle 0.60768 ( 5630) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1048 Ramachandran restraints generated. 524 Oldfield, 0 Emsley, 524 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1048 Ramachandran restraints generated. 524 Oldfield, 0 Emsley, 524 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 63 residues out of total 449 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 53 time to evaluate : 0.412 Fit side-chains REVERT: A 547 GLU cc_start: 0.7743 (mp0) cc_final: 0.7461 (mp0) outliers start: 10 outliers final: 8 residues processed: 63 average time/residue: 0.1390 time to fit residues: 11.5664 Evaluate side-chains 60 residues out of total 449 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 52 time to evaluate : 0.392 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 116 THR Chi-restraints excluded: chain A residue 204 SER Chi-restraints excluded: chain A residue 230 LEU Chi-restraints excluded: chain A residue 308 LEU Chi-restraints excluded: chain A residue 378 LEU Chi-restraints excluded: chain A residue 406 THR Chi-restraints excluded: chain A residue 575 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 43 optimal weight: 0.3980 chunk 11 optimal weight: 0.7980 chunk 36 optimal weight: 3.9990 chunk 30 optimal weight: 1.9990 chunk 23 optimal weight: 2.9990 chunk 45 optimal weight: 0.5980 chunk 7 optimal weight: 3.9990 chunk 28 optimal weight: 0.9980 chunk 8 optimal weight: 0.9990 chunk 52 optimal weight: 1.9990 chunk 48 optimal weight: 6.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- 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 = 0.4436 r_free = 0.4436 target = 0.206474 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3947 r_free = 0.3947 target = 0.155918 restraints weight = 4150.759| |-----------------------------------------------------------------------------| r_work (start): 0.3920 rms_B_bonded: 2.24 r_work: 0.3793 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work (final): 0.3793 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7117 moved from start: 0.2065 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 4144 Z= 0.129 Angle : 0.611 9.468 5642 Z= 0.285 Chirality : 0.040 0.126 661 Planarity : 0.005 0.051 699 Dihedral : 6.017 86.699 596 Min Nonbonded Distance : 2.572 Molprobity Statistics. All-atom Clashscore : 6.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.01 % Favored : 95.99 % Rotamer: Outliers : 2.58 % Allowed : 14.29 % Favored : 83.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.22 (0.38), residues: 524 helix: 0.96 (0.30), residues: 340 sheet: None (None), residues: 0 loop : -1.37 (0.44), residues: 184 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 170 HIS 0.002 0.001 HIS A 471 PHE 0.012 0.001 PHE A 557 TYR 0.008 0.001 TYR A 194 ARG 0.001 0.000 ARG A 605 Details of bonding type rmsd hydrogen bonds : bond 0.03613 ( 215) hydrogen bonds : angle 3.99889 ( 630) SS BOND : bond 0.00148 ( 6) SS BOND : angle 0.31846 ( 12) covalent geometry : bond 0.00306 ( 4138) covalent geometry : angle 0.61143 ( 5630) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1048 Ramachandran restraints generated. 524 Oldfield, 0 Emsley, 524 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1048 Ramachandran restraints generated. 524 Oldfield, 0 Emsley, 524 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 64 residues out of total 449 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 53 time to evaluate : 0.391 Fit side-chains REVERT: A 179 LEU cc_start: 0.8160 (OUTLIER) cc_final: 0.7918 (mp) REVERT: A 547 GLU cc_start: 0.7746 (mp0) cc_final: 0.7453 (mp0) outliers start: 11 outliers final: 9 residues processed: 63 average time/residue: 0.1238 time to fit residues: 10.4262 Evaluate side-chains 64 residues out of total 449 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 54 time to evaluate : 0.389 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 116 THR Chi-restraints excluded: chain A residue 179 LEU Chi-restraints excluded: chain A residue 204 SER Chi-restraints excluded: chain A residue 230 LEU Chi-restraints excluded: chain A residue 308 LEU Chi-restraints excluded: chain A residue 378 LEU Chi-restraints excluded: chain A residue 406 THR Chi-restraints excluded: chain A residue 516 LEU Chi-restraints excluded: chain A residue 575 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 23 optimal weight: 1.9990 chunk 30 optimal weight: 0.8980 chunk 9 optimal weight: 0.0010 chunk 37 optimal weight: 0.9980 chunk 47 optimal weight: 0.9990 chunk 36 optimal weight: 6.9990 chunk 14 optimal weight: 1.9990 chunk 48 optimal weight: 2.9990 chunk 12 optimal weight: 0.3980 chunk 5 optimal weight: 3.9990 chunk 35 optimal weight: 10.0000 overall best weight: 0.6588 ------------------------------------------------------------------------------- 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 = 0.4411 r_free = 0.4411 target = 0.203502 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3910 r_free = 0.3910 target = 0.152221 restraints weight = 4249.355| |-----------------------------------------------------------------------------| r_work (start): 0.3920 rms_B_bonded: 2.30 r_work: 0.3792 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work (final): 0.3792 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7098 moved from start: 0.2158 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 4144 Z= 0.123 Angle : 0.607 10.316 5642 Z= 0.283 Chirality : 0.039 0.126 661 Planarity : 0.005 0.051 699 Dihedral : 6.042 89.941 596 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 5.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.01 % Favored : 95.99 % Rotamer: Outliers : 2.58 % Allowed : 14.99 % Favored : 82.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.28 (0.38), residues: 524 helix: 1.02 (0.30), residues: 340 sheet: None (None), residues: 0 loop : -1.38 (0.44), residues: 184 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 170 HIS 0.002 0.001 HIS A 471 PHE 0.012 0.001 PHE A 557 TYR 0.008 0.001 TYR A 194 ARG 0.001 0.000 ARG A 603 Details of bonding type rmsd hydrogen bonds : bond 0.03459 ( 215) hydrogen bonds : angle 3.92704 ( 630) SS BOND : bond 0.00136 ( 6) SS BOND : angle 0.29988 ( 12) covalent geometry : bond 0.00289 ( 4138) covalent geometry : angle 0.60787 ( 5630) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1048 Ramachandran restraints generated. 524 Oldfield, 0 Emsley, 524 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1048 Ramachandran restraints generated. 524 Oldfield, 0 Emsley, 524 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 449 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 55 time to evaluate : 0.397 Fit side-chains REVERT: A 179 LEU cc_start: 0.8148 (OUTLIER) cc_final: 0.7924 (mp) REVERT: A 479 MET cc_start: 0.3992 (ppp) cc_final: 0.3731 (ppp) REVERT: A 547 GLU cc_start: 0.7736 (mp0) cc_final: 0.7433 (mp0) REVERT: A 626 TRP cc_start: 0.8784 (t60) cc_final: 0.8477 (t-100) outliers start: 11 outliers final: 8 residues processed: 65 average time/residue: 0.1278 time to fit residues: 11.0845 Evaluate side-chains 62 residues out of total 449 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 53 time to evaluate : 0.414 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 115 LEU Chi-restraints excluded: chain A residue 179 LEU Chi-restraints excluded: chain A residue 230 LEU Chi-restraints excluded: chain A residue 308 LEU Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 378 LEU Chi-restraints excluded: chain A residue 406 THR Chi-restraints excluded: chain A residue 575 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 47 optimal weight: 0.7980 chunk 18 optimal weight: 10.0000 chunk 22 optimal weight: 3.9990 chunk 28 optimal weight: 0.5980 chunk 5 optimal weight: 0.9980 chunk 50 optimal weight: 2.9990 chunk 13 optimal weight: 0.7980 chunk 40 optimal weight: 0.1980 chunk 21 optimal weight: 2.9990 chunk 48 optimal weight: 0.9990 chunk 3 optimal weight: 1.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- 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 = 0.4418 r_free = 0.4418 target = 0.204131 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3915 r_free = 0.3915 target = 0.152698 restraints weight = 4183.338| |-----------------------------------------------------------------------------| r_work (start): 0.3887 rms_B_bonded: 2.28 r_work: 0.3748 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.3748 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7103 moved from start: 0.2202 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 4144 Z= 0.125 Angle : 0.619 11.648 5642 Z= 0.286 Chirality : 0.039 0.126 661 Planarity : 0.005 0.051 699 Dihedral : 6.034 89.194 596 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 6.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.01 % Favored : 95.99 % Rotamer: Outliers : 2.81 % Allowed : 15.69 % Favored : 81.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.24 (0.38), residues: 524 helix: 1.02 (0.30), residues: 340 sheet: None (None), residues: 0 loop : -1.45 (0.44), residues: 184 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 170 HIS 0.002 0.001 HIS A 513 PHE 0.012 0.001 PHE A 557 TYR 0.009 0.001 TYR A 194 ARG 0.001 0.000 ARG A 603 Details of bonding type rmsd hydrogen bonds : bond 0.03466 ( 215) hydrogen bonds : angle 3.92385 ( 630) SS BOND : bond 0.00122 ( 6) SS BOND : angle 0.29655 ( 12) covalent geometry : bond 0.00296 ( 4138) covalent geometry : angle 0.61977 ( 5630) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1048 Ramachandran restraints generated. 524 Oldfield, 0 Emsley, 524 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1048 Ramachandran restraints generated. 524 Oldfield, 0 Emsley, 524 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 69 residues out of total 449 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 57 time to evaluate : 0.416 Fit side-chains REVERT: A 179 LEU cc_start: 0.8157 (OUTLIER) cc_final: 0.7929 (mp) REVERT: A 333 LEU cc_start: 0.7315 (mt) cc_final: 0.7100 (mp) REVERT: A 547 GLU cc_start: 0.7753 (mp0) cc_final: 0.7448 (mp0) REVERT: A 626 TRP cc_start: 0.8785 (t60) cc_final: 0.8476 (t-100) outliers start: 12 outliers final: 10 residues processed: 67 average time/residue: 0.1496 time to fit residues: 13.3203 Evaluate side-chains 67 residues out of total 449 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 56 time to evaluate : 0.443 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 VAL Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 115 LEU Chi-restraints excluded: chain A residue 179 LEU Chi-restraints excluded: chain A residue 204 SER Chi-restraints excluded: chain A residue 230 LEU Chi-restraints excluded: chain A residue 308 LEU Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 378 LEU Chi-restraints excluded: chain A residue 406 THR Chi-restraints excluded: chain A residue 575 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 50 optimal weight: 0.9990 chunk 18 optimal weight: 10.0000 chunk 44 optimal weight: 0.7980 chunk 22 optimal weight: 4.9990 chunk 1 optimal weight: 1.9990 chunk 10 optimal weight: 2.9990 chunk 17 optimal weight: 3.9990 chunk 26 optimal weight: 0.9980 chunk 51 optimal weight: 0.5980 chunk 35 optimal weight: 0.3980 chunk 29 optimal weight: 0.5980 overall best weight: 0.6780 ------------------------------------------------------------------------------- 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 = 0.4419 r_free = 0.4419 target = 0.204346 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3920 r_free = 0.3920 target = 0.152962 restraints weight = 4215.151| |-----------------------------------------------------------------------------| r_work (start): 0.3914 rms_B_bonded: 2.29 r_work: 0.3786 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work (final): 0.3786 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7091 moved from start: 0.2283 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 4144 Z= 0.127 Angle : 0.625 12.103 5642 Z= 0.290 Chirality : 0.040 0.126 661 Planarity : 0.005 0.052 699 Dihedral : 6.032 88.237 596 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 6.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.20 % Favored : 95.80 % Rotamer: Outliers : 3.04 % Allowed : 15.93 % Favored : 81.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.22 (0.38), residues: 524 helix: 1.04 (0.30), residues: 340 sheet: None (None), residues: 0 loop : -1.54 (0.43), residues: 184 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 170 HIS 0.002 0.001 HIS A 471 PHE 0.012 0.001 PHE A 557 TYR 0.006 0.001 TYR A 613 ARG 0.001 0.000 ARG A 603 Details of bonding type rmsd hydrogen bonds : bond 0.03505 ( 215) hydrogen bonds : angle 3.92549 ( 630) SS BOND : bond 0.00115 ( 6) SS BOND : angle 0.29894 ( 12) covalent geometry : bond 0.00301 ( 4138) covalent geometry : angle 0.62545 ( 5630) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1048 Ramachandran restraints generated. 524 Oldfield, 0 Emsley, 524 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1048 Ramachandran restraints generated. 524 Oldfield, 0 Emsley, 524 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 449 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 58 time to evaluate : 0.439 Fit side-chains REVERT: A 179 LEU cc_start: 0.8141 (OUTLIER) cc_final: 0.7909 (mp) REVERT: A 479 MET cc_start: 0.3543 (ppp) cc_final: 0.3290 (ppp) REVERT: A 547 GLU cc_start: 0.7751 (mp0) cc_final: 0.7438 (mp0) REVERT: A 626 TRP cc_start: 0.8775 (t60) cc_final: 0.8520 (t-100) outliers start: 13 outliers final: 10 residues processed: 67 average time/residue: 0.1392 time to fit residues: 12.4969 Evaluate side-chains 68 residues out of total 449 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 57 time to evaluate : 0.430 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 VAL Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 115 LEU Chi-restraints excluded: chain A residue 179 LEU Chi-restraints excluded: chain A residue 204 SER Chi-restraints excluded: chain A residue 230 LEU Chi-restraints excluded: chain A residue 308 LEU Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 378 LEU Chi-restraints excluded: chain A residue 406 THR Chi-restraints excluded: chain A residue 575 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 11 optimal weight: 1.9990 chunk 46 optimal weight: 0.9980 chunk 12 optimal weight: 0.8980 chunk 28 optimal weight: 0.9980 chunk 42 optimal weight: 0.6980 chunk 38 optimal weight: 3.9990 chunk 33 optimal weight: 0.6980 chunk 7 optimal weight: 0.7980 chunk 20 optimal weight: 0.9980 chunk 49 optimal weight: 10.0000 chunk 45 optimal weight: 0.7980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 335 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4413 r_free = 0.4413 target = 0.203662 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3916 r_free = 0.3916 target = 0.152514 restraints weight = 4226.569| |-----------------------------------------------------------------------------| r_work (start): 0.3919 rms_B_bonded: 2.28 r_work: 0.3791 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work (final): 0.3791 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7105 moved from start: 0.2313 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 4144 Z= 0.133 Angle : 0.632 12.251 5642 Z= 0.295 Chirality : 0.040 0.126 661 Planarity : 0.005 0.050 699 Dihedral : 6.049 88.516 596 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 7.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.20 % Favored : 95.80 % Rotamer: Outliers : 2.58 % Allowed : 16.39 % Favored : 81.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.20 (0.38), residues: 524 helix: 0.99 (0.30), residues: 340 sheet: None (None), residues: 0 loop : -1.48 (0.43), residues: 184 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 170 HIS 0.002 0.001 HIS A 96 PHE 0.012 0.001 PHE A 557 TYR 0.008 0.001 TYR A 194 ARG 0.001 0.000 ARG A 605 Details of bonding type rmsd hydrogen bonds : bond 0.03610 ( 215) hydrogen bonds : angle 4.00032 ( 630) SS BOND : bond 0.00132 ( 6) SS BOND : angle 0.29973 ( 12) covalent geometry : bond 0.00317 ( 4138) covalent geometry : angle 0.63219 ( 5630) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1048 Ramachandran restraints generated. 524 Oldfield, 0 Emsley, 524 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1048 Ramachandran restraints generated. 524 Oldfield, 0 Emsley, 524 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 69 residues out of total 449 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 58 time to evaluate : 0.429 Fit side-chains REVERT: A 179 LEU cc_start: 0.8170 (OUTLIER) cc_final: 0.7928 (mp) REVERT: A 479 MET cc_start: 0.3582 (ppp) cc_final: 0.3332 (ppp) REVERT: A 546 GLN cc_start: 0.7198 (mm-40) cc_final: 0.6759 (tm-30) REVERT: A 547 GLU cc_start: 0.7751 (mp0) cc_final: 0.7511 (mp0) REVERT: A 626 TRP cc_start: 0.8738 (t60) cc_final: 0.8492 (t-100) outliers start: 11 outliers final: 10 residues processed: 66 average time/residue: 0.1795 time to fit residues: 15.6349 Evaluate side-chains 68 residues out of total 449 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 57 time to evaluate : 0.485 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 VAL Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 115 LEU Chi-restraints excluded: chain A residue 179 LEU Chi-restraints excluded: chain A residue 204 SER Chi-restraints excluded: chain A residue 230 LEU Chi-restraints excluded: chain A residue 308 LEU Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 378 LEU Chi-restraints excluded: chain A residue 406 THR Chi-restraints excluded: chain A residue 575 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 18 optimal weight: 3.9990 chunk 9 optimal weight: 0.8980 chunk 35 optimal weight: 7.9990 chunk 12 optimal weight: 0.0470 chunk 26 optimal weight: 1.9990 chunk 44 optimal weight: 0.9980 chunk 49 optimal weight: 10.0000 chunk 22 optimal weight: 0.8980 chunk 39 optimal weight: 7.9990 chunk 5 optimal weight: 0.0970 chunk 32 optimal weight: 0.7980 overall best weight: 0.5476 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 335 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4428 r_free = 0.4428 target = 0.205153 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3929 r_free = 0.3929 target = 0.153890 restraints weight = 4170.455| |-----------------------------------------------------------------------------| r_work (start): 0.3898 rms_B_bonded: 2.29 r_work: 0.3761 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work (final): 0.3761 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7084 moved from start: 0.2358 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 4144 Z= 0.120 Angle : 0.634 12.254 5642 Z= 0.289 Chirality : 0.039 0.125 661 Planarity : 0.005 0.052 699 Dihedral : 5.943 86.587 596 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 6.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.20 % Favored : 95.80 % Rotamer: Outliers : 2.11 % Allowed : 16.86 % Favored : 81.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.29 (0.38), residues: 524 helix: 1.05 (0.30), residues: 341 sheet: None (None), residues: 0 loop : -1.42 (0.44), residues: 183 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 170 HIS 0.002 0.001 HIS A 471 PHE 0.012 0.001 PHE A 557 TYR 0.008 0.001 TYR A 51 ARG 0.001 0.000 ARG A 603 Details of bonding type rmsd hydrogen bonds : bond 0.03347 ( 215) hydrogen bonds : angle 3.87884 ( 630) SS BOND : bond 0.00109 ( 6) SS BOND : angle 0.27975 ( 12) covalent geometry : bond 0.00279 ( 4138) covalent geometry : angle 0.63465 ( 5630) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3049.44 seconds wall clock time: 53 minutes 8.71 seconds (3188.71 seconds total)