Starting phenix.real_space_refine on Tue Feb 11 13:26:37 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8gaq_29904/02_2025/8gaq_29904.cif Found real_map, /net/cci-nas-00/data/ceres_data/8gaq_29904/02_2025/8gaq_29904.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.73 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8gaq_29904/02_2025/8gaq_29904.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8gaq_29904/02_2025/8gaq_29904.map" model { file = "/net/cci-nas-00/data/ceres_data/8gaq_29904/02_2025/8gaq_29904.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8gaq_29904/02_2025/8gaq_29904.cif" } resolution = 3.73 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= 0.000 sd= 0.022 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 30 5.16 5 C 3715 2.51 5 N 955 2.21 5 O 1125 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 100 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib" Total number of atoms: 5825 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 1165 Number of conformers: 1 Conformer: "" Number of residues, atoms: 147, 1165 Classifications: {'peptide': 147} Link IDs: {'PTRANS': 4, 'TRANS': 142} Chain: "C" Number of atoms: 1165 Number of conformers: 1 Conformer: "" Number of residues, atoms: 147, 1165 Classifications: {'peptide': 147} Link IDs: {'PTRANS': 4, 'TRANS': 142} Chain: "E" Number of atoms: 1165 Number of conformers: 1 Conformer: "" Number of residues, atoms: 147, 1165 Classifications: {'peptide': 147} Link IDs: {'PTRANS': 4, 'TRANS': 142} Chain: "G" Number of atoms: 1165 Number of conformers: 1 Conformer: "" Number of residues, atoms: 147, 1165 Classifications: {'peptide': 147} Link IDs: {'PTRANS': 4, 'TRANS': 142} Chain: "I" Number of atoms: 1165 Number of conformers: 1 Conformer: "" Number of residues, atoms: 147, 1165 Classifications: {'peptide': 147} Link IDs: {'PTRANS': 4, 'TRANS': 142} Time building chain proxies: 4.57, per 1000 atoms: 0.78 Number of scatterers: 5825 At special positions: 0 Unit cell: (79.65, 76.995, 75.225, 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 30 16.00 O 1125 8.00 N 955 7.00 C 3715 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.33 Conformation dependent library (CDL) restraints added in 674.7 milliseconds 1450 Ramachandran restraints generated. 725 Oldfield, 0 Emsley, 725 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1420 Finding SS restraints... Secondary structure from input PDB file: 50 helices and 0 sheets defined 91.6% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.60 Creating SS restraints... Processing helix chain 'A' and resid 1 through 15 Processing helix chain 'A' and resid 16 through 34 removed outlier: 3.544A pdb=" N LEU A 20 " --> pdb=" O ASP A 16 " (cutoff:3.500A) removed outlier: 4.092A pdb=" N ARG A 22 " --> pdb=" O GLU A 18 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N VAL A 33 " --> pdb=" O LEU A 29 " (cutoff:3.500A) Processing helix chain 'A' and resid 34 through 48 removed outlier: 3.759A pdb=" N LEU A 38 " --> pdb=" O ASP A 34 " (cutoff:3.500A) removed outlier: 4.189A pdb=" N VAL A 39 " --> pdb=" O PRO A 35 " (cutoff:3.500A) removed outlier: 4.714A pdb=" N GLU A 40 " --> pdb=" O ARG A 36 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N ASN A 43 " --> pdb=" O VAL A 39 " (cutoff:3.500A) Processing helix chain 'A' and resid 50 through 66 removed outlier: 3.737A pdb=" N VAL A 66 " --> pdb=" O LEU A 62 " (cutoff:3.500A) Processing helix chain 'A' and resid 70 through 83 removed outlier: 3.590A pdb=" N LEU A 74 " --> pdb=" O ARG A 70 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N LEU A 76 " --> pdb=" O LEU A 72 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N GLU A 80 " --> pdb=" O LEU A 76 " (cutoff:3.500A) Processing helix chain 'A' and resid 86 through 99 removed outlier: 4.166A pdb=" N LYS A 92 " --> pdb=" O LYS A 88 " (cutoff:3.500A) Processing helix chain 'A' and resid 102 through 116 removed outlier: 4.008A pdb=" N GLU A 114 " --> pdb=" O LEU A 110 " (cutoff:3.500A) Processing helix chain 'A' and resid 118 through 134 removed outlier: 4.215A pdb=" N GLU A 127 " --> pdb=" O LYS A 123 " (cutoff:3.500A) Processing helix chain 'A' and resid 136 through 146 Processing helix chain 'C' and resid 150 through 163 Processing helix chain 'C' and resid 164 through 182 removed outlier: 3.890A pdb=" N VAL C 181 " --> pdb=" O LEU C 177 " (cutoff:3.500A) Processing helix chain 'C' and resid 185 through 197 removed outlier: 3.503A pdb=" N GLY C 197 " --> pdb=" O ALA C 193 " (cutoff:3.500A) Processing helix chain 'C' and resid 198 through 212 Processing helix chain 'C' and resid 213 through 215 No H-bonds generated for 'chain 'C' and resid 213 through 215' Processing helix chain 'C' and resid 216 through 231 removed outlier: 3.913A pdb=" N GLU C 228 " --> pdb=" O LEU C 224 " (cutoff:3.500A) Processing helix chain 'C' and resid 232 through 247 removed outlier: 3.867A pdb=" N LYS C 240 " --> pdb=" O LYS C 236 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N ASN C 241 " --> pdb=" O GLU C 237 " (cutoff:3.500A) removed outlier: 4.401A pdb=" N LEU C 244 " --> pdb=" O LYS C 240 " (cutoff:3.500A) Processing helix chain 'C' and resid 252 through 255 Processing helix chain 'C' and resid 256 through 264 removed outlier: 4.451A pdb=" N GLU C 262 " --> pdb=" O LEU C 258 " (cutoff:3.500A) Processing helix chain 'C' and resid 266 through 281 removed outlier: 4.294A pdb=" N GLU C 275 " --> pdb=" O LYS C 271 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N ILE C 276 " --> pdb=" O GLU C 272 " (cutoff:3.500A) Processing helix chain 'C' and resid 284 through 294 removed outlier: 3.539A pdb=" N ALA C 288 " --> pdb=" O ASP C 284 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N VAL C 289 " --> pdb=" O PRO C 285 " (cutoff:3.500A) Processing helix chain 'E' and resid 298 through 309 Processing helix chain 'E' and resid 312 through 330 removed outlier: 3.572A pdb=" N VAL E 329 " --> pdb=" O LEU E 325 " (cutoff:3.500A) Processing helix chain 'E' and resid 333 through 345 Processing helix chain 'E' and resid 346 through 362 removed outlier: 3.870A pdb=" N VAL E 362 " --> pdb=" O LEU E 358 " (cutoff:3.500A) Processing helix chain 'E' and resid 364 through 379 removed outlier: 3.630A pdb=" N LEU E 368 " --> pdb=" O ASP E 364 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N VAL E 369 " --> pdb=" O PRO E 365 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N LEU E 370 " --> pdb=" O ARG E 366 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N GLU E 376 " --> pdb=" O LEU E 372 " (cutoff:3.500A) Processing helix chain 'E' and resid 382 through 395 removed outlier: 4.112A pdb=" N LYS E 388 " --> pdb=" O LYS E 384 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N LEU E 392 " --> pdb=" O LYS E 388 " (cutoff:3.500A) Processing helix chain 'E' and resid 400 through 403 Processing helix chain 'E' and resid 404 through 412 removed outlier: 4.138A pdb=" N GLU E 410 " --> pdb=" O LEU E 406 " (cutoff:3.500A) Processing helix chain 'E' and resid 414 through 430 removed outlier: 4.149A pdb=" N GLU E 430 " --> pdb=" O ASP E 426 " (cutoff:3.500A) Processing helix chain 'E' and resid 432 through 442 removed outlier: 3.650A pdb=" N ALA E 436 " --> pdb=" O ASP E 432 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N VAL E 437 " --> pdb=" O PRO E 433 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N LEU E 438 " --> pdb=" O ARG E 434 " (cutoff:3.500A) Processing helix chain 'G' and resid 446 through 459 removed outlier: 3.790A pdb=" N GLU G 457 " --> pdb=" O ARG G 453 " (cutoff:3.500A) Processing helix chain 'G' and resid 460 through 477 removed outlier: 3.594A pdb=" N VAL G 477 " --> pdb=" O LEU G 473 " (cutoff:3.500A) Processing helix chain 'G' and resid 478 through 480 No H-bonds generated for 'chain 'G' and resid 478 through 480' Processing helix chain 'G' and resid 481 through 492 Processing helix chain 'G' and resid 494 through 510 removed outlier: 3.876A pdb=" N VAL G 510 " --> pdb=" O LEU G 506 " (cutoff:3.500A) Processing helix chain 'G' and resid 512 through 527 removed outlier: 4.307A pdb=" N GLU G 524 " --> pdb=" O LEU G 520 " (cutoff:3.500A) Processing helix chain 'G' and resid 530 through 543 removed outlier: 4.202A pdb=" N LYS G 536 " --> pdb=" O LYS G 532 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N ASN G 537 " --> pdb=" O GLU G 533 " (cutoff:3.500A) removed outlier: 4.479A pdb=" N LEU G 540 " --> pdb=" O LYS G 536 " (cutoff:3.500A) Processing helix chain 'G' and resid 548 through 551 Processing helix chain 'G' and resid 552 through 560 removed outlier: 4.386A pdb=" N GLU G 558 " --> pdb=" O LEU G 554 " (cutoff:3.500A) Processing helix chain 'G' and resid 562 through 578 removed outlier: 4.036A pdb=" N GLU G 578 " --> pdb=" O ASP G 574 " (cutoff:3.500A) Processing helix chain 'G' and resid 580 through 590 Processing helix chain 'I' and resid 594 through 607 Processing helix chain 'I' and resid 608 through 626 removed outlier: 4.113A pdb=" N ARG I 614 " --> pdb=" O GLU I 610 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N VAL I 625 " --> pdb=" O LEU I 621 " (cutoff:3.500A) Processing helix chain 'I' and resid 629 through 640 removed outlier: 3.595A pdb=" N ASN I 635 " --> pdb=" O VAL I 631 " (cutoff:3.500A) Processing helix chain 'I' and resid 642 through 658 removed outlier: 3.889A pdb=" N VAL I 658 " --> pdb=" O LEU I 654 " (cutoff:3.500A) Processing helix chain 'I' and resid 660 through 675 removed outlier: 3.992A pdb=" N GLU I 672 " --> pdb=" O LEU I 668 " (cutoff:3.500A) Processing helix chain 'I' and resid 678 through 691 removed outlier: 3.948A pdb=" N LYS I 684 " --> pdb=" O LYS I 680 " (cutoff:3.500A) removed outlier: 4.129A pdb=" N LEU I 688 " --> pdb=" O LYS I 684 " (cutoff:3.500A) Processing helix chain 'I' and resid 696 through 708 removed outlier: 4.055A pdb=" N LEU I 702 " --> pdb=" O LEU I 698 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N GLU I 706 " --> pdb=" O LEU I 702 " (cutoff:3.500A) Processing helix chain 'I' and resid 710 through 726 removed outlier: 3.743A pdb=" N GLU I 719 " --> pdb=" O LYS I 715 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N GLU I 726 " --> pdb=" O ASP I 722 " (cutoff:3.500A) Processing helix chain 'I' and resid 728 through 738 420 hydrogen bonds defined for protein. 1251 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: 1.68 Time building geometry restraints manager: 1.57 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 1984 1.34 - 1.46: 102 1.46 - 1.57: 3699 1.57 - 1.69: 0 1.69 - 1.80: 60 Bond restraints: 5845 Sorted by residual: bond pdb=" CB VAL G 553 " pdb=" CG1 VAL G 553 " ideal model delta sigma weight residual 1.521 1.484 0.037 3.30e-02 9.18e+02 1.28e+00 bond pdb=" CB VAL I 701 " pdb=" CG1 VAL I 701 " ideal model delta sigma weight residual 1.521 1.484 0.037 3.30e-02 9.18e+02 1.24e+00 bond pdb=" CA ASP I 608 " pdb=" CB ASP I 608 " ideal model delta sigma weight residual 1.527 1.545 -0.017 1.61e-02 3.86e+03 1.18e+00 bond pdb=" CA ASP E 312 " pdb=" C ASP E 312 " ideal model delta sigma weight residual 1.532 1.523 0.010 9.60e-03 1.09e+04 1.03e+00 bond pdb=" CB VAL C 257 " pdb=" CG1 VAL C 257 " ideal model delta sigma weight residual 1.521 1.488 0.033 3.30e-02 9.18e+02 1.02e+00 ... (remaining 5840 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.37: 7408 1.37 - 2.75: 375 2.75 - 4.12: 59 4.12 - 5.50: 11 5.50 - 6.87: 2 Bond angle restraints: 7855 Sorted by residual: angle pdb=" N VAL G 551 " pdb=" CA VAL G 551 " pdb=" C VAL G 551 " ideal model delta sigma weight residual 112.43 107.18 5.25 9.20e-01 1.18e+00 3.26e+01 angle pdb=" N LEU E 392 " pdb=" CA LEU E 392 " pdb=" C LEU E 392 " ideal model delta sigma weight residual 112.93 109.18 3.75 1.12e+00 7.97e-01 1.12e+01 angle pdb=" N LEU G 541 " pdb=" CA LEU G 541 " pdb=" C LEU G 541 " ideal model delta sigma weight residual 114.04 110.01 4.03 1.24e+00 6.50e-01 1.06e+01 angle pdb=" N LEU I 688 " pdb=" CA LEU I 688 " pdb=" C LEU I 688 " ideal model delta sigma weight residual 112.93 109.30 3.63 1.12e+00 7.97e-01 1.05e+01 angle pdb=" N LEU G 540 " pdb=" CA LEU G 540 " pdb=" C LEU G 540 " ideal model delta sigma weight residual 112.93 109.83 3.10 1.12e+00 7.97e-01 7.68e+00 ... (remaining 7850 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.82: 3409 17.82 - 35.63: 276 35.63 - 53.45: 66 53.45 - 71.27: 31 71.27 - 89.09: 23 Dihedral angle restraints: 3805 sinusoidal: 1650 harmonic: 2155 Sorted by residual: dihedral pdb=" CA ASP I 694 " pdb=" C ASP I 694 " pdb=" N PRO I 695 " pdb=" CA PRO I 695 " ideal model delta harmonic sigma weight residual -180.00 -160.97 -19.03 0 5.00e+00 4.00e-02 1.45e+01 dihedral pdb=" CA ASP G 478 " pdb=" C ASP G 478 " pdb=" N PRO G 479 " pdb=" CA PRO G 479 " ideal model delta harmonic sigma weight residual -180.00 -162.36 -17.64 0 5.00e+00 4.00e-02 1.24e+01 dihedral pdb=" CA VAL C 255 " pdb=" C VAL C 255 " pdb=" N LEU C 256 " pdb=" CA LEU C 256 " ideal model delta harmonic sigma weight residual 180.00 162.38 17.62 0 5.00e+00 4.00e-02 1.24e+01 ... (remaining 3802 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.034: 648 0.034 - 0.068: 264 0.068 - 0.101: 52 0.101 - 0.135: 22 0.135 - 0.169: 4 Chirality restraints: 990 Sorted by residual: chirality pdb=" CA ASP I 608 " pdb=" N ASP I 608 " pdb=" C ASP I 608 " pdb=" CB ASP I 608 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.17 2.00e-01 2.50e+01 7.12e-01 chirality pdb=" CB VAL A 101 " pdb=" CA VAL A 101 " pdb=" CG1 VAL A 101 " pdb=" CG2 VAL A 101 " both_signs ideal model delta sigma weight residual False -2.63 -2.47 -0.15 2.00e-01 2.50e+01 5.97e-01 chirality pdb=" CB VAL E 397 " pdb=" CA VAL E 397 " pdb=" CG1 VAL E 397 " pdb=" CG2 VAL E 397 " both_signs ideal model delta sigma weight residual False -2.63 -2.49 -0.14 2.00e-01 2.50e+01 4.97e-01 ... (remaining 987 not shown) Planarity restraints: 995 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP I 660 " -0.031 5.00e-02 4.00e+02 4.76e-02 3.62e+00 pdb=" N PRO I 661 " 0.082 5.00e-02 4.00e+02 pdb=" CA PRO I 661 " -0.024 5.00e-02 4.00e+02 pdb=" CD PRO I 661 " -0.026 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP I 728 " 0.031 5.00e-02 4.00e+02 4.69e-02 3.52e+00 pdb=" N PRO I 729 " -0.081 5.00e-02 4.00e+02 pdb=" CA PRO I 729 " 0.024 5.00e-02 4.00e+02 pdb=" CD PRO I 729 " 0.026 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP E 364 " -0.029 5.00e-02 4.00e+02 4.50e-02 3.24e+00 pdb=" N PRO E 365 " 0.078 5.00e-02 4.00e+02 pdb=" CA PRO E 365 " -0.023 5.00e-02 4.00e+02 pdb=" CD PRO E 365 " -0.025 5.00e-02 4.00e+02 ... (remaining 992 not shown) Histogram of nonbonded interaction distances: 2.28 - 2.80: 1286 2.80 - 3.33: 6254 3.33 - 3.85: 9017 3.85 - 4.38: 10624 4.38 - 4.90: 17742 Nonbonded interactions: 44923 Sorted by model distance: nonbonded pdb=" OE2 GLU G 465 " pdb=" ND2 ASN G 469 " model vdw 2.278 3.120 nonbonded pdb=" NH2 ARG G 582 " pdb=" OD2 ASP I 728 " model vdw 2.288 3.120 nonbonded pdb=" OD1 ASN A 43 " pdb=" N THR A 44 " model vdw 2.341 3.120 nonbonded pdb=" OD2 ASP A 136 " pdb=" NH2 ARG I 730 " model vdw 2.343 3.120 nonbonded pdb=" OD1 ASN G 487 " pdb=" N THR G 488 " model vdw 2.375 3.120 ... (remaining 44918 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.01 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'E' selection = chain 'G' selection = chain 'I' } 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=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue 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: 3.440 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: 0.210 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 17.520 Find NCS groups from input model: 0.230 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.690 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.210 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7463 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 : 0.005 0.037 5845 Z= 0.284 Angle : 0.701 6.872 7855 Z= 0.407 Chirality : 0.039 0.169 990 Planarity : 0.005 0.048 995 Dihedral : 16.745 89.085 2385 Min Nonbonded Distance : 2.278 Molprobity Statistics. All-atom Clashscore : 5.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.66 % Favored : 98.34 % Rotamer: Outliers : 0.15 % Allowed : 4.12 % Favored : 95.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -3.14 (0.27), residues: 725 helix: -1.78 (0.18), residues: 625 sheet: None (None), residues: 0 loop : -2.52 (0.68), residues: 100 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.016 0.003 TYR G 498 ARG 0.007 0.001 ARG C 218 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1450 Ramachandran restraints generated. 725 Oldfield, 0 Emsley, 725 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1450 Ramachandran restraints generated. 725 Oldfield, 0 Emsley, 725 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 655 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 159 time to evaluate : 0.672 Fit side-chains revert: symmetry clash REVERT: C 173 ASN cc_start: 0.6646 (m-40) cc_final: 0.6295 (m110) REVERT: E 332 ARG cc_start: 0.7860 (ptm-80) cc_final: 0.7509 (ptp90) REVERT: I 622 LEU cc_start: 0.8737 (tp) cc_final: 0.8527 (tp) REVERT: I 628 ARG cc_start: 0.7887 (ptt90) cc_final: 0.7599 (ptp90) outliers start: 1 outliers final: 0 residues processed: 160 average time/residue: 0.2792 time to fit residues: 53.4202 Evaluate side-chains 107 residues out of total 655 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 107 time to evaluate : 0.736 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 59 optimal weight: 0.3980 chunk 53 optimal weight: 0.9990 chunk 29 optimal weight: 3.9990 chunk 18 optimal weight: 0.5980 chunk 35 optimal weight: 0.5980 chunk 28 optimal weight: 3.9990 chunk 54 optimal weight: 0.5980 chunk 21 optimal weight: 0.7980 chunk 33 optimal weight: 0.7980 chunk 40 optimal weight: 0.7980 chunk 63 optimal weight: 0.5980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 93 ASN C 173 ASN E 306 GLN G 469 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4052 r_free = 0.4052 target = 0.180501 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3594 r_free = 0.3594 target = 0.136810 restraints weight = 6962.764| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3645 r_free = 0.3645 target = 0.141269 restraints weight = 4668.115| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3683 r_free = 0.3683 target = 0.144669 restraints weight = 3530.223| |-----------------------------------------------------------------------------| r_work (final): 0.3675 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7446 moved from start: 0.2273 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 5845 Z= 0.219 Angle : 0.598 7.277 7855 Z= 0.306 Chirality : 0.039 0.173 990 Planarity : 0.005 0.043 995 Dihedral : 4.510 16.560 775 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 8.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.93 % Favored : 98.07 % Rotamer: Outliers : 1.07 % Allowed : 9.77 % Favored : 89.16 % 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: -1.28 (0.30), residues: 725 helix: -0.61 (0.19), residues: 639 sheet: None (None), residues: 0 loop : -1.30 (0.77), residues: 86 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.014 0.002 TYR A 54 ARG 0.008 0.001 ARG E 366 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1450 Ramachandran restraints generated. 725 Oldfield, 0 Emsley, 725 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1450 Ramachandran restraints generated. 725 Oldfield, 0 Emsley, 725 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 655 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 122 time to evaluate : 0.694 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 270 LYS cc_start: 0.7515 (tptm) cc_final: 0.7188 (tptm) REVERT: E 332 ARG cc_start: 0.7952 (ptm-80) cc_final: 0.7421 (ptp90) REVERT: E 366 ARG cc_start: 0.7321 (ttm110) cc_final: 0.7119 (mtp-110) REVERT: E 417 MET cc_start: 0.6235 (tpp) cc_final: 0.4793 (ttm) REVERT: E 434 ARG cc_start: 0.7714 (ttm-80) cc_final: 0.7435 (ttm-80) REVERT: G 469 ASN cc_start: 0.7161 (t0) cc_final: 0.6955 (t0) REVERT: G 487 ASN cc_start: 0.7586 (p0) cc_final: 0.7323 (p0) outliers start: 7 outliers final: 2 residues processed: 126 average time/residue: 0.2821 time to fit residues: 42.8072 Evaluate side-chains 116 residues out of total 655 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 114 time to evaluate : 0.594 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 129 LEU Chi-restraints excluded: chain I residue 600 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 0 optimal weight: 6.9990 chunk 2 optimal weight: 0.3980 chunk 15 optimal weight: 4.9990 chunk 18 optimal weight: 0.5980 chunk 31 optimal weight: 0.9980 chunk 63 optimal weight: 0.1980 chunk 64 optimal weight: 1.9990 chunk 47 optimal weight: 0.9980 chunk 38 optimal weight: 0.3980 chunk 21 optimal weight: 0.8980 chunk 41 optimal weight: 2.9990 overall best weight: 0.4980 ------------------------------------------------------------------------------- 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 = 0.4027 r_free = 0.4027 target = 0.178075 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.135691 restraints weight = 6946.077| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3637 r_free = 0.3637 target = 0.140345 restraints weight = 4628.365| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3675 r_free = 0.3675 target = 0.143630 restraints weight = 3474.411| |-----------------------------------------------------------------------------| r_work (final): 0.3671 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7433 moved from start: 0.2775 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 5845 Z= 0.187 Angle : 0.565 10.699 7855 Z= 0.280 Chirality : 0.038 0.163 990 Planarity : 0.004 0.035 995 Dihedral : 4.071 16.891 775 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 7.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.66 % Favored : 98.34 % Rotamer: Outliers : 2.14 % Allowed : 10.99 % Favored : 86.87 % 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: -0.65 (0.31), residues: 725 helix: -0.14 (0.20), residues: 642 sheet: None (None), residues: 0 loop : -1.59 (0.72), residues: 83 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.012 0.002 TYR A 54 ARG 0.006 0.001 ARG E 366 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1450 Ramachandran restraints generated. 725 Oldfield, 0 Emsley, 725 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1450 Ramachandran restraints generated. 725 Oldfield, 0 Emsley, 725 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 655 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 126 time to evaluate : 0.702 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 270 LYS cc_start: 0.7457 (tptm) cc_final: 0.7188 (tptm) REVERT: E 417 MET cc_start: 0.6414 (tpp) cc_final: 0.4886 (ttm) REVERT: E 434 ARG cc_start: 0.7766 (ttm-80) cc_final: 0.7410 (ttm-80) REVERT: G 487 ASN cc_start: 0.7724 (p0) cc_final: 0.7423 (p0) outliers start: 14 outliers final: 7 residues processed: 132 average time/residue: 0.2731 time to fit residues: 43.7496 Evaluate side-chains 125 residues out of total 655 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 118 time to evaluate : 0.675 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 MET Chi-restraints excluded: chain A residue 109 VAL Chi-restraints excluded: chain C residue 178 LEU Chi-restraints excluded: chain E residue 351 LYS Chi-restraints excluded: chain G residue 452 LEU Chi-restraints excluded: chain G residue 504 ILE Chi-restraints excluded: chain I residue 600 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 1 optimal weight: 6.9990 chunk 15 optimal weight: 3.9990 chunk 58 optimal weight: 0.7980 chunk 3 optimal weight: 4.9990 chunk 48 optimal weight: 0.9980 chunk 39 optimal weight: 0.9980 chunk 63 optimal weight: 0.5980 chunk 59 optimal weight: 0.9990 chunk 18 optimal weight: 1.9990 chunk 23 optimal weight: 0.7980 chunk 0 optimal weight: 2.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- 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 = 0.3998 r_free = 0.3998 target = 0.174487 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.132524 restraints weight = 7233.352| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3596 r_free = 0.3596 target = 0.137000 restraints weight = 4913.245| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3634 r_free = 0.3634 target = 0.140254 restraints weight = 3734.598| |-----------------------------------------------------------------------------| r_work (final): 0.3630 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7530 moved from start: 0.3118 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 5845 Z= 0.266 Angle : 0.599 6.403 7855 Z= 0.301 Chirality : 0.040 0.218 990 Planarity : 0.004 0.041 995 Dihedral : 4.228 16.810 775 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 7.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.21 % Favored : 97.79 % Rotamer: Outliers : 3.21 % Allowed : 11.45 % Favored : 85.34 % 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: -0.53 (0.31), residues: 725 helix: -0.09 (0.20), residues: 640 sheet: None (None), residues: 0 loop : -1.28 (0.78), residues: 85 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.013 0.003 TYR A 54 ARG 0.006 0.001 ARG I 662 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1450 Ramachandran restraints generated. 725 Oldfield, 0 Emsley, 725 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1450 Ramachandran restraints generated. 725 Oldfield, 0 Emsley, 725 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 655 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 123 time to evaluate : 0.709 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 270 LYS cc_start: 0.7521 (tptm) cc_final: 0.7285 (tptm) REVERT: G 487 ASN cc_start: 0.7849 (p0) cc_final: 0.7524 (p0) REVERT: I 645 MET cc_start: 0.6100 (ttt) cc_final: 0.5876 (ttt) REVERT: I 654 LEU cc_start: 0.8547 (OUTLIER) cc_final: 0.8223 (tt) outliers start: 21 outliers final: 12 residues processed: 133 average time/residue: 0.2914 time to fit residues: 46.4010 Evaluate side-chains 128 residues out of total 655 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 115 time to evaluate : 0.721 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 MET Chi-restraints excluded: chain A residue 109 VAL Chi-restraints excluded: chain A residue 129 LEU Chi-restraints excluded: chain C residue 178 LEU Chi-restraints excluded: chain E residue 351 LYS Chi-restraints excluded: chain E residue 357 MET Chi-restraints excluded: chain G residue 452 LEU Chi-restraints excluded: chain G residue 504 ILE Chi-restraints excluded: chain G residue 505 MET Chi-restraints excluded: chain G residue 542 LEU Chi-restraints excluded: chain G residue 546 ASP Chi-restraints excluded: chain I residue 600 LEU Chi-restraints excluded: chain I residue 654 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 22 optimal weight: 0.7980 chunk 56 optimal weight: 5.9990 chunk 14 optimal weight: 5.9990 chunk 52 optimal weight: 0.9990 chunk 33 optimal weight: 0.6980 chunk 19 optimal weight: 2.9990 chunk 44 optimal weight: 0.9980 chunk 7 optimal weight: 0.7980 chunk 57 optimal weight: 0.8980 chunk 39 optimal weight: 0.9980 chunk 68 optimal weight: 2.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 191 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3988 r_free = 0.3988 target = 0.173964 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3545 r_free = 0.3545 target = 0.132779 restraints weight = 7075.759| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3597 r_free = 0.3597 target = 0.137174 restraints weight = 4849.021| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3634 r_free = 0.3634 target = 0.140339 restraints weight = 3694.792| |-----------------------------------------------------------------------------| r_work (final): 0.3631 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7534 moved from start: 0.3388 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 5845 Z= 0.264 Angle : 0.606 7.199 7855 Z= 0.301 Chirality : 0.040 0.176 990 Planarity : 0.004 0.042 995 Dihedral : 4.162 16.727 775 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 8.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.21 % Favored : 97.79 % Rotamer: Outliers : 2.60 % Allowed : 13.28 % Favored : 84.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.50 (0.31), residues: 725 helix: -0.06 (0.20), residues: 641 sheet: None (None), residues: 0 loop : -1.34 (0.76), residues: 84 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.012 0.002 TYR A 54 ARG 0.011 0.001 ARG I 662 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1450 Ramachandran restraints generated. 725 Oldfield, 0 Emsley, 725 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1450 Ramachandran restraints generated. 725 Oldfield, 0 Emsley, 725 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 655 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 121 time to evaluate : 0.719 Fit side-chains revert: symmetry clash REVERT: A 62 LEU cc_start: 0.8446 (OUTLIER) cc_final: 0.8192 (tt) REVERT: C 270 LYS cc_start: 0.7557 (tptm) cc_final: 0.7344 (tptm) REVERT: E 358 LEU cc_start: 0.8592 (OUTLIER) cc_final: 0.8391 (tt) REVERT: E 417 MET cc_start: 0.6571 (tpp) cc_final: 0.5102 (ttm) REVERT: G 487 ASN cc_start: 0.7921 (p0) cc_final: 0.7597 (p0) REVERT: I 593 VAL cc_start: 0.6417 (m) cc_final: 0.6204 (m) REVERT: I 645 MET cc_start: 0.5823 (ttt) cc_final: 0.5622 (ttt) REVERT: I 654 LEU cc_start: 0.8544 (OUTLIER) cc_final: 0.8244 (tt) outliers start: 17 outliers final: 10 residues processed: 131 average time/residue: 0.2856 time to fit residues: 45.2800 Evaluate side-chains 128 residues out of total 655 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 115 time to evaluate : 0.877 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 LEU Chi-restraints excluded: chain A residue 109 VAL Chi-restraints excluded: chain A residue 129 LEU Chi-restraints excluded: chain A residue 130 ASP Chi-restraints excluded: chain C residue 178 LEU Chi-restraints excluded: chain E residue 351 LYS Chi-restraints excluded: chain E residue 357 MET Chi-restraints excluded: chain E residue 358 LEU Chi-restraints excluded: chain G residue 505 MET Chi-restraints excluded: chain G residue 542 LEU Chi-restraints excluded: chain G residue 546 ASP Chi-restraints excluded: chain I residue 600 LEU Chi-restraints excluded: chain I residue 654 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 26 optimal weight: 0.5980 chunk 53 optimal weight: 1.9990 chunk 9 optimal weight: 0.9990 chunk 8 optimal weight: 0.5980 chunk 30 optimal weight: 0.6980 chunk 62 optimal weight: 0.5980 chunk 5 optimal weight: 0.8980 chunk 48 optimal weight: 0.9990 chunk 1 optimal weight: 1.9990 chunk 22 optimal weight: 0.6980 chunk 68 optimal weight: 0.9980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 191 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4048 r_free = 0.4048 target = 0.178695 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3612 r_free = 0.3612 target = 0.137940 restraints weight = 7046.726| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3657 r_free = 0.3657 target = 0.141896 restraints weight = 4919.028| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3691 r_free = 0.3691 target = 0.144823 restraints weight = 3812.034| |-----------------------------------------------------------------------------| r_work (final): 0.3691 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7549 moved from start: 0.3623 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 5845 Z= 0.218 Angle : 0.573 6.844 7855 Z= 0.288 Chirality : 0.039 0.192 990 Planarity : 0.004 0.039 995 Dihedral : 4.032 17.761 775 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 7.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Rotamer: Outliers : 2.29 % Allowed : 14.35 % Favored : 83.36 % 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: -0.42 (0.32), residues: 725 helix: -0.00 (0.21), residues: 641 sheet: None (None), residues: 0 loop : -1.31 (0.75), residues: 84 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.010 0.002 TYR G 498 ARG 0.012 0.001 ARG I 662 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1450 Ramachandran restraints generated. 725 Oldfield, 0 Emsley, 725 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1450 Ramachandran restraints generated. 725 Oldfield, 0 Emsley, 725 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 655 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 114 time to evaluate : 0.658 Fit side-chains REVERT: A 62 LEU cc_start: 0.8454 (OUTLIER) cc_final: 0.8195 (tt) REVERT: C 270 LYS cc_start: 0.7619 (tptm) cc_final: 0.7398 (tptm) REVERT: E 417 MET cc_start: 0.6612 (tpp) cc_final: 0.4908 (ttm) REVERT: G 487 ASN cc_start: 0.7772 (p0) cc_final: 0.7461 (p0) REVERT: I 593 VAL cc_start: 0.6507 (m) cc_final: 0.6277 (m) REVERT: I 654 LEU cc_start: 0.8577 (OUTLIER) cc_final: 0.8254 (tt) outliers start: 15 outliers final: 8 residues processed: 125 average time/residue: 0.2762 time to fit residues: 41.8210 Evaluate side-chains 119 residues out of total 655 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 109 time to evaluate : 0.739 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 LEU Chi-restraints excluded: chain A residue 109 VAL Chi-restraints excluded: chain A residue 129 LEU Chi-restraints excluded: chain E residue 351 LYS Chi-restraints excluded: chain E residue 357 MET Chi-restraints excluded: chain G residue 452 LEU Chi-restraints excluded: chain G residue 505 MET Chi-restraints excluded: chain G residue 542 LEU Chi-restraints excluded: chain G residue 546 ASP Chi-restraints excluded: chain I residue 654 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 14 optimal weight: 5.9990 chunk 19 optimal weight: 0.5980 chunk 24 optimal weight: 0.9990 chunk 20 optimal weight: 1.9990 chunk 5 optimal weight: 0.7980 chunk 36 optimal weight: 0.0170 chunk 50 optimal weight: 0.5980 chunk 33 optimal weight: 0.9980 chunk 10 optimal weight: 0.5980 chunk 0 optimal weight: 4.9990 chunk 53 optimal weight: 1.9990 overall best weight: 0.5218 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 191 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4054 r_free = 0.4054 target = 0.179296 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3612 r_free = 0.3612 target = 0.137750 restraints weight = 7068.227| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3663 r_free = 0.3663 target = 0.142163 restraints weight = 4781.732| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3696 r_free = 0.3696 target = 0.145208 restraints weight = 3632.267| |-----------------------------------------------------------------------------| r_work (final): 0.3700 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7502 moved from start: 0.3852 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 5845 Z= 0.195 Angle : 0.586 9.198 7855 Z= 0.289 Chirality : 0.038 0.176 990 Planarity : 0.004 0.041 995 Dihedral : 3.876 18.222 775 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 7.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.93 % Favored : 98.07 % Rotamer: Outliers : 2.29 % Allowed : 14.50 % Favored : 83.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.30 (0.31), residues: 725 helix: 0.11 (0.21), residues: 641 sheet: None (None), residues: 0 loop : -1.58 (0.69), residues: 84 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.009 0.002 TYR G 498 ARG 0.013 0.001 ARG I 662 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1450 Ramachandran restraints generated. 725 Oldfield, 0 Emsley, 725 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1450 Ramachandran restraints generated. 725 Oldfield, 0 Emsley, 725 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 655 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 114 time to evaluate : 0.745 Fit side-chains revert: symmetry clash REVERT: A 62 LEU cc_start: 0.8426 (OUTLIER) cc_final: 0.8155 (tt) REVERT: C 270 LYS cc_start: 0.7609 (tptm) cc_final: 0.7404 (tptm) REVERT: E 314 GLU cc_start: 0.7002 (tp30) cc_final: 0.6778 (tp30) REVERT: E 358 LEU cc_start: 0.8556 (OUTLIER) cc_final: 0.8346 (tt) REVERT: G 487 ASN cc_start: 0.7745 (p0) cc_final: 0.7427 (p0) REVERT: I 593 VAL cc_start: 0.6044 (m) cc_final: 0.5813 (m) REVERT: I 654 LEU cc_start: 0.8530 (OUTLIER) cc_final: 0.8203 (tt) REVERT: I 713 MET cc_start: 0.5988 (tmm) cc_final: 0.5645 (tpt) outliers start: 15 outliers final: 9 residues processed: 124 average time/residue: 0.2801 time to fit residues: 42.5835 Evaluate side-chains 122 residues out of total 655 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 110 time to evaluate : 0.670 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 MET Chi-restraints excluded: chain A residue 62 LEU Chi-restraints excluded: chain A residue 109 VAL Chi-restraints excluded: chain A residue 129 LEU Chi-restraints excluded: chain A residue 130 ASP Chi-restraints excluded: chain C residue 257 VAL Chi-restraints excluded: chain E residue 351 LYS Chi-restraints excluded: chain E residue 357 MET Chi-restraints excluded: chain E residue 358 LEU Chi-restraints excluded: chain G residue 452 LEU Chi-restraints excluded: chain G residue 542 LEU Chi-restraints excluded: chain I residue 654 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 66 optimal weight: 0.9980 chunk 35 optimal weight: 0.6980 chunk 47 optimal weight: 0.8980 chunk 3 optimal weight: 0.0970 chunk 41 optimal weight: 0.1980 chunk 19 optimal weight: 1.9990 chunk 43 optimal weight: 2.9990 chunk 4 optimal weight: 0.9990 chunk 33 optimal weight: 0.5980 chunk 60 optimal weight: 0.9990 chunk 42 optimal weight: 4.9990 overall best weight: 0.4978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 173 ASN C 191 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4050 r_free = 0.4050 target = 0.179016 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3615 r_free = 0.3615 target = 0.137962 restraints weight = 6984.223| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3665 r_free = 0.3665 target = 0.142334 restraints weight = 4723.626| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3701 r_free = 0.3701 target = 0.145462 restraints weight = 3593.738| |-----------------------------------------------------------------------------| r_work (final): 0.3709 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7486 moved from start: 0.4001 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 5845 Z= 0.200 Angle : 0.610 9.206 7855 Z= 0.300 Chirality : 0.039 0.229 990 Planarity : 0.004 0.035 995 Dihedral : 3.799 17.867 775 Min Nonbonded Distance : 2.313 Molprobity Statistics. All-atom Clashscore : 8.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.66 % Favored : 98.34 % Rotamer: Outliers : 2.44 % Allowed : 14.96 % Favored : 82.60 % 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: -0.30 (0.31), residues: 725 helix: 0.15 (0.21), residues: 640 sheet: None (None), residues: 0 loop : -1.97 (0.61), residues: 85 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.009 0.002 TYR G 498 ARG 0.008 0.001 ARG A 70 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1450 Ramachandran restraints generated. 725 Oldfield, 0 Emsley, 725 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1450 Ramachandran restraints generated. 725 Oldfield, 0 Emsley, 725 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 655 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 112 time to evaluate : 0.671 Fit side-chains REVERT: A 62 LEU cc_start: 0.8431 (OUTLIER) cc_final: 0.8161 (tt) REVERT: C 270 LYS cc_start: 0.7594 (tptm) cc_final: 0.7387 (tptm) REVERT: E 417 MET cc_start: 0.6398 (tpp) cc_final: 0.5028 (ttm) REVERT: G 487 ASN cc_start: 0.7753 (p0) cc_final: 0.7442 (p0) REVERT: I 593 VAL cc_start: 0.5996 (m) cc_final: 0.5727 (m) REVERT: I 654 LEU cc_start: 0.8515 (OUTLIER) cc_final: 0.8185 (tt) REVERT: I 662 ARG cc_start: 0.7614 (ttm110) cc_final: 0.7345 (ttm-80) REVERT: I 713 MET cc_start: 0.6043 (tmm) cc_final: 0.5588 (tpt) outliers start: 16 outliers final: 11 residues processed: 121 average time/residue: 0.2755 time to fit residues: 41.0281 Evaluate side-chains 121 residues out of total 655 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 108 time to evaluate : 0.667 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 MET Chi-restraints excluded: chain A residue 62 LEU Chi-restraints excluded: chain A residue 109 VAL Chi-restraints excluded: chain A residue 129 LEU Chi-restraints excluded: chain A residue 130 ASP Chi-restraints excluded: chain C residue 257 VAL Chi-restraints excluded: chain E residue 357 MET Chi-restraints excluded: chain G residue 452 LEU Chi-restraints excluded: chain G residue 505 MET Chi-restraints excluded: chain G residue 539 MET Chi-restraints excluded: chain G residue 542 LEU Chi-restraints excluded: chain G residue 546 ASP Chi-restraints excluded: chain I residue 654 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 49 optimal weight: 0.5980 chunk 21 optimal weight: 0.4980 chunk 5 optimal weight: 0.8980 chunk 7 optimal weight: 0.4980 chunk 42 optimal weight: 5.9990 chunk 51 optimal weight: 0.6980 chunk 45 optimal weight: 0.3980 chunk 12 optimal weight: 1.9990 chunk 35 optimal weight: 0.6980 chunk 11 optimal weight: 0.0970 chunk 10 optimal weight: 0.7980 overall best weight: 0.4178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 191 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3991 r_free = 0.3991 target = 0.175192 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3554 r_free = 0.3554 target = 0.134003 restraints weight = 7125.416| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3603 r_free = 0.3603 target = 0.138401 restraints weight = 4739.397| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3639 r_free = 0.3639 target = 0.141550 restraints weight = 3573.208| |-----------------------------------------------------------------------------| r_work (final): 0.3644 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7442 moved from start: 0.4166 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 5845 Z= 0.193 Angle : 0.617 9.353 7855 Z= 0.301 Chirality : 0.038 0.241 990 Planarity : 0.004 0.035 995 Dihedral : 3.682 17.265 775 Min Nonbonded Distance : 2.284 Molprobity Statistics. All-atom Clashscore : 8.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.66 % Favored : 98.34 % Rotamer: Outliers : 1.98 % Allowed : 15.11 % Favored : 82.90 % Cbeta Deviations : 0.14 % 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: -0.14 (0.31), residues: 725 helix: 0.25 (0.21), residues: 643 sheet: None (None), residues: 0 loop : -1.90 (0.61), residues: 82 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.008 0.002 TYR G 498 ARG 0.007 0.001 ARG E 366 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1450 Ramachandran restraints generated. 725 Oldfield, 0 Emsley, 725 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1450 Ramachandran restraints generated. 725 Oldfield, 0 Emsley, 725 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 655 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 114 time to evaluate : 0.704 Fit side-chains REVERT: A 62 LEU cc_start: 0.8381 (OUTLIER) cc_final: 0.8094 (tt) REVERT: E 312 ASP cc_start: 0.7284 (p0) cc_final: 0.6802 (p0) REVERT: E 314 GLU cc_start: 0.6807 (tm-30) cc_final: 0.6584 (tp30) REVERT: G 487 ASN cc_start: 0.7727 (p0) cc_final: 0.7380 (p0) REVERT: I 593 VAL cc_start: 0.5479 (m) cc_final: 0.5268 (m) REVERT: I 662 ARG cc_start: 0.7510 (ttm110) cc_final: 0.7304 (ttm-80) REVERT: I 713 MET cc_start: 0.6054 (tmm) cc_final: 0.5573 (tpt) outliers start: 13 outliers final: 10 residues processed: 122 average time/residue: 0.2731 time to fit residues: 41.4119 Evaluate side-chains 118 residues out of total 655 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 107 time to evaluate : 0.713 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 MET Chi-restraints excluded: chain A residue 62 LEU Chi-restraints excluded: chain A residue 109 VAL Chi-restraints excluded: chain A residue 129 LEU Chi-restraints excluded: chain A residue 130 ASP Chi-restraints excluded: chain C residue 257 VAL Chi-restraints excluded: chain E residue 351 LYS Chi-restraints excluded: chain E residue 357 MET Chi-restraints excluded: chain G residue 539 MET Chi-restraints excluded: chain G residue 542 LEU Chi-restraints excluded: chain G residue 546 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 62 optimal weight: 0.6980 chunk 61 optimal weight: 0.9990 chunk 33 optimal weight: 0.5980 chunk 4 optimal weight: 0.5980 chunk 68 optimal weight: 0.6980 chunk 3 optimal weight: 0.0870 chunk 25 optimal weight: 0.9980 chunk 12 optimal weight: 0.7980 chunk 22 optimal weight: 0.0470 chunk 53 optimal weight: 0.7980 chunk 17 optimal weight: 0.8980 overall best weight: 0.4056 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 191 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3986 r_free = 0.3986 target = 0.175150 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3545 r_free = 0.3545 target = 0.133585 restraints weight = 7313.769| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3598 r_free = 0.3598 target = 0.138206 restraints weight = 4836.753| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3636 r_free = 0.3636 target = 0.141526 restraints weight = 3624.423| |-----------------------------------------------------------------------------| r_work (final): 0.3635 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7431 moved from start: 0.4326 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 5845 Z= 0.192 Angle : 0.632 10.070 7855 Z= 0.309 Chirality : 0.039 0.228 990 Planarity : 0.004 0.033 995 Dihedral : 3.618 17.158 775 Min Nonbonded Distance : 2.284 Molprobity Statistics. All-atom Clashscore : 7.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.38 % Favored : 98.62 % Rotamer: Outliers : 1.98 % Allowed : 15.57 % Favored : 82.44 % Cbeta Deviations : 0.14 % 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 (0.31), residues: 725 helix: 0.26 (0.21), residues: 644 sheet: None (None), residues: 0 loop : -1.82 (0.62), residues: 81 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.008 0.002 TYR G 498 ARG 0.007 0.001 ARG E 366 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1450 Ramachandran restraints generated. 725 Oldfield, 0 Emsley, 725 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1450 Ramachandran restraints generated. 725 Oldfield, 0 Emsley, 725 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 655 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 110 time to evaluate : 0.696 Fit side-chains REVERT: A 62 LEU cc_start: 0.8372 (OUTLIER) cc_final: 0.8083 (tt) REVERT: E 312 ASP cc_start: 0.7404 (p0) cc_final: 0.6972 (p0) REVERT: E 314 GLU cc_start: 0.6750 (tm-30) cc_final: 0.6466 (tp30) REVERT: E 417 MET cc_start: 0.6354 (tpp) cc_final: 0.4850 (mtt) REVERT: G 487 ASN cc_start: 0.7717 (p0) cc_final: 0.7372 (p0) REVERT: G 514 ARG cc_start: 0.7578 (ttm-80) cc_final: 0.7287 (ttm110) REVERT: I 654 LEU cc_start: 0.8571 (OUTLIER) cc_final: 0.8264 (tt) REVERT: I 662 ARG cc_start: 0.7440 (ttm110) cc_final: 0.7173 (ttm-80) REVERT: I 713 MET cc_start: 0.5988 (tmm) cc_final: 0.5516 (tpt) outliers start: 13 outliers final: 9 residues processed: 118 average time/residue: 0.2522 time to fit residues: 36.7871 Evaluate side-chains 118 residues out of total 655 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 107 time to evaluate : 0.804 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 MET Chi-restraints excluded: chain A residue 62 LEU Chi-restraints excluded: chain A residue 109 VAL Chi-restraints excluded: chain A residue 129 LEU Chi-restraints excluded: chain A residue 130 ASP Chi-restraints excluded: chain E residue 351 LYS Chi-restraints excluded: chain E residue 357 MET Chi-restraints excluded: chain G residue 539 MET Chi-restraints excluded: chain G residue 542 LEU Chi-restraints excluded: chain G residue 546 ASP Chi-restraints excluded: chain I residue 654 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 48 optimal weight: 0.5980 chunk 66 optimal weight: 0.9990 chunk 5 optimal weight: 0.7980 chunk 24 optimal weight: 0.5980 chunk 29 optimal weight: 6.9990 chunk 9 optimal weight: 2.9990 chunk 1 optimal weight: 5.9990 chunk 13 optimal weight: 0.8980 chunk 57 optimal weight: 3.9990 chunk 28 optimal weight: 1.9990 chunk 23 optimal weight: 0.6980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 191 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3957 r_free = 0.3957 target = 0.172271 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.130711 restraints weight = 7232.833| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.135224 restraints weight = 4854.106| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3600 r_free = 0.3600 target = 0.138301 restraints weight = 3660.761| |-----------------------------------------------------------------------------| r_work (final): 0.3606 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7496 moved from start: 0.4359 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 5845 Z= 0.265 Angle : 0.701 9.551 7855 Z= 0.346 Chirality : 0.040 0.221 990 Planarity : 0.004 0.056 995 Dihedral : 3.890 16.985 775 Min Nonbonded Distance : 2.286 Molprobity Statistics. All-atom Clashscore : 8.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.93 % Favored : 98.07 % Rotamer: Outliers : 2.14 % Allowed : 16.34 % Favored : 81.53 % 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 (0.31), residues: 725 helix: 0.18 (0.21), residues: 639 sheet: None (None), residues: 0 loop : -1.57 (0.66), residues: 86 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.011 0.002 TYR A 54 ARG 0.014 0.001 ARG I 601 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1981.99 seconds wall clock time: 36 minutes 26.90 seconds (2186.90 seconds total)