Starting phenix.real_space_refine on Fri Dec 27 10:06:22 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8kgw_37234/12_2024/8kgw_37234.cif Found real_map, /net/cci-nas-00/data/ceres_data/8kgw_37234/12_2024/8kgw_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_37234/12_2024/8kgw_37234.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8kgw_37234/12_2024/8kgw_37234.map" model { file = "/net/cci-nas-00/data/ceres_data/8kgw_37234/12_2024/8kgw_37234.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8kgw_37234/12_2024/8kgw_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-5532/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: 3.20, per 1000 atoms: 0.79 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: 2.07 Conformation dependent library (CDL) restraints added in 510.8 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: 0.64 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: 1.39 Time building geometry restraints manager: 1.21 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: 0.570 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: 0.170 Check model and map are aligned: 0.020 Set scattering table: 0.040 Process input model: 14.770 Find NCS groups from input model: 0.030 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:2.970 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.590 ------------------------------------------------------------------------------- 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 4138 Z= 0.394 Angle : 0.863 13.434 5630 Z= 0.413 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 *********************** 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 : 0.359 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 69 average time/residue: 0.1494 time to fit residues: 13.3622 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 : 0.418 ------------------------------------------------------------------------------- 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: 1.9990 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: 0.3980 overall best weight: 1.2186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 177 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6858 moved from start: 0.1338 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 4138 Z= 0.269 Angle : 0.682 12.140 5630 Z= 0.328 Chirality : 0.042 0.137 661 Planarity : 0.005 0.057 699 Dihedral : 7.120 68.315 596 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 6.43 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: -0.44 (0.37), residues: 524 helix: 0.46 (0.30), residues: 335 sheet: None (None), residues: 0 loop : -1.61 (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 0.013 0.002 PHE A 557 TYR 0.013 0.002 TYR A 90 ARG 0.003 0.000 ARG A 97 *********************** 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 64 residues out of total 449 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 58 time to evaluate : 0.406 Fit side-chains outliers start: 6 outliers final: 5 residues processed: 63 average time/residue: 0.1462 time to fit residues: 12.1674 Evaluate side-chains 61 residues out of total 449 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 56 time to evaluate : 0.441 ------------------------------------------------------------------------------- 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 26 optimal weight: 0.9990 chunk 14 optimal weight: 0.4980 chunk 40 optimal weight: 30.0000 chunk 32 optimal weight: 1.9990 chunk 13 optimal weight: 1.9990 chunk 48 optimal weight: 0.7980 chunk 52 optimal weight: 0.8980 chunk 42 optimal weight: 2.9990 chunk 47 optimal weight: 1.9990 chunk 16 optimal weight: 1.9990 chunk 38 optimal weight: 9.9990 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 534 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6868 moved from start: 0.1702 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 4138 Z= 0.242 Angle : 0.654 8.341 5630 Z= 0.312 Chirality : 0.041 0.131 661 Planarity : 0.005 0.055 699 Dihedral : 6.239 78.095 596 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 5.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.58 % Favored : 95.42 % Rotamer: Outliers : 1.87 % Allowed : 10.77 % Favored : 87.35 % 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: -0.26 (0.37), residues: 524 helix: 0.58 (0.30), residues: 339 sheet: None (None), residues: 0 loop : -1.54 (0.43), residues: 185 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 170 HIS 0.003 0.001 HIS A 96 PHE 0.013 0.001 PHE A 107 TYR 0.010 0.001 TYR A 194 ARG 0.001 0.000 ARG A 97 *********************** 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 66 residues out of total 449 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 58 time to evaluate : 0.439 Fit side-chains REVERT: A 547 GLU cc_start: 0.7508 (mp0) cc_final: 0.7267 (mp0) outliers start: 8 outliers final: 5 residues processed: 66 average time/residue: 0.1458 time to fit residues: 12.8645 Evaluate side-chains 61 residues out of total 449 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 56 time to evaluate : 0.458 ------------------------------------------------------------------------------- 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 47 optimal weight: 0.8980 chunk 36 optimal weight: 5.9990 chunk 25 optimal weight: 1.9990 chunk 5 optimal weight: 0.6980 chunk 23 optimal weight: 1.9990 chunk 32 optimal weight: 0.0980 chunk 48 optimal weight: 0.4980 chunk 51 optimal weight: 0.5980 chunk 45 optimal weight: 0.5980 chunk 13 optimal weight: 1.9990 chunk 42 optimal weight: 0.0020 overall best weight: 0.3588 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6806 moved from start: 0.1843 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 4138 Z= 0.171 Angle : 0.591 8.360 5630 Z= 0.277 Chirality : 0.039 0.127 661 Planarity : 0.005 0.053 699 Dihedral : 6.065 86.275 596 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 5.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.82 % Favored : 96.18 % Rotamer: Outliers : 1.17 % Allowed : 13.35 % Favored : 85.48 % 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: 0.16 (0.38), residues: 524 helix: 0.99 (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 *********************** 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 61 residues out of total 449 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 56 time to evaluate : 0.503 Fit side-chains REVERT: A 321 ARG cc_start: 0.7429 (ttp80) cc_final: 0.6968 (tmt170) REVERT: A 547 GLU cc_start: 0.7563 (mp0) cc_final: 0.7281 (mp0) outliers start: 5 outliers final: 5 residues processed: 61 average time/residue: 0.1393 time to fit residues: 11.2696 Evaluate side-chains 58 residues out of total 449 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 53 time to evaluate : 0.439 ------------------------------------------------------------------------------- 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 29 optimal weight: 1.9990 chunk 0 optimal weight: 6.9990 chunk 38 optimal weight: 30.0000 chunk 21 optimal weight: 0.0980 chunk 43 optimal weight: 0.7980 chunk 35 optimal weight: 20.0000 chunk 26 optimal weight: 0.9980 chunk 45 optimal weight: 0.5980 chunk 12 optimal weight: 0.0170 chunk 17 optimal weight: 6.9990 chunk 46 optimal weight: 0.7980 overall best weight: 0.4618 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6807 moved from start: 0.1960 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 4138 Z= 0.173 Angle : 0.585 8.463 5630 Z= 0.274 Chirality : 0.039 0.126 661 Planarity : 0.005 0.051 699 Dihedral : 5.991 87.989 596 Min Nonbonded Distance : 2.571 Molprobity Statistics. All-atom Clashscore : 5.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.01 % Favored : 95.99 % Rotamer: Outliers : 2.11 % Allowed : 13.82 % Favored : 84.07 % 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: 0.23 (0.38), residues: 524 helix: 0.99 (0.30), residues: 340 sheet: None (None), residues: 0 loop : -1.40 (0.44), residues: 184 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 626 HIS 0.002 0.001 HIS A 471 PHE 0.011 0.001 PHE A 557 TYR 0.008 0.001 TYR A 613 ARG 0.001 0.000 ARG A 603 *********************** 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 64 residues out of total 449 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 55 time to evaluate : 0.442 Fit side-chains REVERT: A 179 LEU cc_start: 0.7602 (mp) cc_final: 0.7361 (mp) REVERT: A 321 ARG cc_start: 0.7449 (ttp80) cc_final: 0.6979 (tmt170) REVERT: A 547 GLU cc_start: 0.7583 (mp0) cc_final: 0.7277 (mp0) outliers start: 9 outliers final: 7 residues processed: 64 average time/residue: 0.1371 time to fit residues: 11.4594 Evaluate side-chains 62 residues out of total 449 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 55 time to evaluate : 0.418 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 10 optimal weight: 7.9990 chunk 30 optimal weight: 3.9990 chunk 12 optimal weight: 1.9990 chunk 51 optimal weight: 0.9990 chunk 42 optimal weight: 0.9980 chunk 23 optimal weight: 2.9990 chunk 4 optimal weight: 5.9990 chunk 16 optimal weight: 0.0670 chunk 26 optimal weight: 0.9980 chunk 49 optimal weight: 20.0000 chunk 5 optimal weight: 3.9990 overall best weight: 1.0122 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6869 moved from start: 0.2118 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 4138 Z= 0.230 Angle : 0.625 9.584 5630 Z= 0.295 Chirality : 0.040 0.126 661 Planarity : 0.005 0.050 699 Dihedral : 6.071 85.139 596 Min Nonbonded Distance : 2.570 Molprobity Statistics. All-atom Clashscore : 6.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.39 % Favored : 95.61 % Rotamer: Outliers : 2.34 % Allowed : 14.52 % 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: 0.10 (0.37), residues: 524 helix: 0.85 (0.30), residues: 340 sheet: None (None), residues: 0 loop : -1.39 (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 96 PHE 0.013 0.001 PHE A 107 TYR 0.010 0.001 TYR A 194 ARG 0.002 0.000 ARG A 605 *********************** 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: 10 poor density : 54 time to evaluate : 0.467 Fit side-chains REVERT: A 173 MET cc_start: 0.7598 (tmm) cc_final: 0.7236 (ttt) REVERT: A 179 LEU cc_start: 0.7770 (OUTLIER) cc_final: 0.7529 (mp) REVERT: A 321 ARG cc_start: 0.7507 (ttp80) cc_final: 0.7014 (tmt170) REVERT: A 546 GLN cc_start: 0.7346 (mm-40) cc_final: 0.6617 (tm-30) REVERT: A 547 GLU cc_start: 0.7564 (mp0) cc_final: 0.7251 (mp0) outliers start: 10 outliers final: 8 residues processed: 62 average time/residue: 0.1351 time to fit residues: 11.0972 Evaluate side-chains 63 residues out of total 449 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 54 time to evaluate : 0.443 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 29 optimal weight: 0.9990 chunk 37 optimal weight: 1.9990 chunk 43 optimal weight: 0.9990 chunk 28 optimal weight: 0.8980 chunk 51 optimal weight: 0.8980 chunk 31 optimal weight: 0.6980 chunk 23 optimal weight: 0.8980 chunk 20 optimal weight: 1.9990 chunk 30 optimal weight: 1.9990 chunk 15 optimal weight: 3.9990 chunk 10 optimal weight: 9.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6862 moved from start: 0.2211 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 4138 Z= 0.211 Angle : 0.614 10.534 5630 Z= 0.288 Chirality : 0.040 0.127 661 Planarity : 0.005 0.051 699 Dihedral : 6.092 88.801 596 Min Nonbonded Distance : 2.584 Molprobity Statistics. All-atom Clashscore : 6.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.20 % Favored : 95.80 % Rotamer: Outliers : 3.04 % Allowed : 14.29 % Favored : 82.67 % 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: 0.10 (0.37), residues: 524 helix: 0.87 (0.29), residues: 340 sheet: None (None), residues: 0 loop : -1.42 (0.44), 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 0.009 0.001 TYR A 194 ARG 0.001 0.000 ARG A 605 *********************** 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 68 residues out of total 449 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 55 time to evaluate : 0.422 Fit side-chains REVERT: A 173 MET cc_start: 0.7694 (tmm) cc_final: 0.7014 (ttp) REVERT: A 179 LEU cc_start: 0.7746 (OUTLIER) cc_final: 0.7517 (mp) REVERT: A 321 ARG cc_start: 0.7532 (ttp80) cc_final: 0.7011 (tmt170) REVERT: A 479 MET cc_start: 0.4048 (ppp) cc_final: 0.3782 (ppp) REVERT: A 546 GLN cc_start: 0.7275 (mm-40) cc_final: 0.6565 (tm-30) REVERT: A 547 GLU cc_start: 0.7562 (mp0) cc_final: 0.7249 (mp0) outliers start: 13 outliers final: 10 residues processed: 65 average time/residue: 0.1308 time to fit residues: 11.3174 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 : 0.496 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 VAL 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 516 LEU 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 9 optimal weight: 3.9990 chunk 32 optimal weight: 0.7980 chunk 34 optimal weight: 9.9990 chunk 25 optimal weight: 0.9990 chunk 4 optimal weight: 5.9990 chunk 40 optimal weight: 30.0000 chunk 46 optimal weight: 0.9980 chunk 48 optimal weight: 0.9980 chunk 44 optimal weight: 0.6980 chunk 47 optimal weight: 0.0370 chunk 28 optimal weight: 0.6980 overall best weight: 0.6458 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6844 moved from start: 0.2275 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 4138 Z= 0.188 Angle : 0.620 11.600 5630 Z= 0.285 Chirality : 0.039 0.126 661 Planarity : 0.005 0.051 699 Dihedral : 6.038 89.155 596 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 5.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.01 % Favored : 95.99 % Rotamer: Outliers : 2.34 % Allowed : 16.16 % 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: 0.20 (0.38), residues: 524 helix: 0.95 (0.30), residues: 340 sheet: None (None), residues: 0 loop : -1.40 (0.44), residues: 184 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 170 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 *********************** 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 68 residues out of total 449 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 58 time to evaluate : 0.442 Fit side-chains REVERT: A 173 MET cc_start: 0.7691 (tmm) cc_final: 0.7008 (ttp) REVERT: A 179 LEU cc_start: 0.7716 (OUTLIER) cc_final: 0.7488 (mp) REVERT: A 321 ARG cc_start: 0.7531 (ttp80) cc_final: 0.7005 (tmt170) REVERT: A 547 GLU cc_start: 0.7573 (mp0) cc_final: 0.7213 (mp0) REVERT: A 626 TRP cc_start: 0.8435 (t60) cc_final: 0.8224 (t-100) outliers start: 10 outliers final: 9 residues processed: 66 average time/residue: 0.1360 time to fit residues: 11.8919 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 : 0.441 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 VAL 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 20 optimal weight: 1.9990 chunk 37 optimal weight: 3.9990 chunk 14 optimal weight: 1.9990 chunk 43 optimal weight: 2.9990 chunk 45 optimal weight: 0.5980 chunk 47 optimal weight: 0.7980 chunk 31 optimal weight: 0.4980 chunk 50 optimal weight: 0.8980 chunk 30 optimal weight: 2.9990 chunk 23 optimal weight: 1.9990 chunk 34 optimal weight: 10.0000 overall best weight: 0.9582 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6870 moved from start: 0.2338 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 4138 Z= 0.228 Angle : 0.634 12.042 5630 Z= 0.298 Chirality : 0.040 0.128 661 Planarity : 0.005 0.049 699 Dihedral : 6.122 89.183 596 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 6.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.20 % Favored : 95.80 % 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: 0.13 (0.38), residues: 524 helix: 0.87 (0.29), residues: 340 sheet: None (None), residues: 0 loop : -1.36 (0.44), 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 0.013 0.001 PHE A 557 TYR 0.007 0.001 TYR A 194 ARG 0.001 0.000 ARG A 605 *********************** 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: 12 poor density : 59 time to evaluate : 0.456 Fit side-chains REVERT: A 173 MET cc_start: 0.7711 (tmm) cc_final: 0.7054 (ttp) REVERT: A 179 LEU cc_start: 0.7704 (OUTLIER) cc_final: 0.7470 (mp) REVERT: A 321 ARG cc_start: 0.7519 (ttp80) cc_final: 0.6991 (tmt170) REVERT: A 479 MET cc_start: 0.3614 (ppp) cc_final: 0.3355 (ppp) REVERT: A 546 GLN cc_start: 0.7368 (mm-40) cc_final: 0.6641 (tm-30) REVERT: A 547 GLU cc_start: 0.7546 (mp0) cc_final: 0.7252 (mp0) REVERT: A 626 TRP cc_start: 0.8430 (t60) cc_final: 0.8227 (t-100) outliers start: 12 outliers final: 10 residues processed: 67 average time/residue: 0.1312 time to fit residues: 11.7147 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 : 0.438 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 VAL 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 516 LEU 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 52 optimal weight: 1.9990 chunk 48 optimal weight: 0.8980 chunk 42 optimal weight: 0.9990 chunk 4 optimal weight: 5.9990 chunk 32 optimal weight: 0.9980 chunk 25 optimal weight: 0.5980 chunk 33 optimal weight: 0.1980 chunk 44 optimal weight: 0.9980 chunk 12 optimal weight: 0.7980 chunk 38 optimal weight: 0.2980 chunk 6 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 335 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6826 moved from start: 0.2373 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 4138 Z= 0.182 Angle : 0.606 12.325 5630 Z= 0.282 Chirality : 0.039 0.125 661 Planarity : 0.005 0.050 699 Dihedral : 5.932 87.253 596 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 6.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.82 % Favored : 96.18 % Rotamer: Outliers : 2.58 % Allowed : 16.16 % Favored : 81.26 % 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: 0.96 (0.30), residues: 344 sheet: None (None), residues: 0 loop : -1.43 (0.44), residues: 180 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 51 ARG 0.001 0.000 ARG A 603 ********************** 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 70 residues out of total 449 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 59 time to evaluate : 0.400 Fit side-chains REVERT: A 173 MET cc_start: 0.7649 (tmm) cc_final: 0.7178 (ttm) REVERT: A 177 GLN cc_start: 0.7679 (mm-40) cc_final: 0.7382 (mm110) REVERT: A 179 LEU cc_start: 0.7675 (OUTLIER) cc_final: 0.7437 (mp) REVERT: A 321 ARG cc_start: 0.7530 (ttp80) cc_final: 0.7006 (tmt170) REVERT: A 479 MET cc_start: 0.3642 (ppp) cc_final: 0.3391 (ppp) REVERT: A 546 GLN cc_start: 0.7352 (mm-40) cc_final: 0.6827 (tm-30) REVERT: A 547 GLU cc_start: 0.7551 (mp0) cc_final: 0.7232 (mp0) outliers start: 11 outliers final: 10 residues processed: 67 average time/residue: 0.1309 time to fit residues: 11.6322 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 : 0.424 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 VAL 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 516 LEU 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: 0.5980 chunk 42 optimal weight: 0.6980 chunk 17 optimal weight: 0.5980 chunk 43 optimal weight: 3.9990 chunk 5 optimal weight: 1.9990 chunk 7 optimal weight: 0.5980 chunk 36 optimal weight: 0.2980 chunk 2 optimal weight: 0.7980 chunk 30 optimal weight: 0.9980 chunk 48 optimal weight: 0.5980 chunk 28 optimal weight: 0.6980 overall best weight: 0.5380 ------------------------------------------------------------------------------- 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 = 0.4434 r_free = 0.4434 target = 0.205268 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3952 r_free = 0.3952 target = 0.156415 restraints weight = 4116.098| |-----------------------------------------------------------------------------| r_work (start): 0.3928 rms_B_bonded: 2.01 r_work: 0.3790 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work (final): 0.3790 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7128 moved from start: 0.2486 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 4138 Z= 0.186 Angle : 0.631 12.274 5630 Z= 0.288 Chirality : 0.039 0.125 661 Planarity : 0.005 0.051 699 Dihedral : 5.930 87.315 596 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 6.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.20 % Favored : 95.80 % Rotamer: Outliers : 2.58 % Allowed : 17.10 % Favored : 80.33 % 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: 0.36 (0.38), residues: 524 helix: 1.06 (0.30), residues: 341 sheet: None (None), residues: 0 loop : -1.30 (0.44), residues: 183 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.001 TRP A 626 HIS 0.002 0.001 HIS A 471 PHE 0.012 0.001 PHE A 557 TYR 0.008 0.001 TYR A 613 ARG 0.001 0.000 ARG A 627 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1292.33 seconds wall clock time: 24 minutes 8.88 seconds (1448.88 seconds total)