Starting phenix.real_space_refine on Fri Aug 22 16:22:38 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8gaq_29904/08_2025/8gaq_29904.cif Found real_map, /net/cci-nas-00/data/ceres_data/8gaq_29904/08_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 { model { file = "/net/cci-nas-00/data/ceres_data/8gaq_29904/08_2025/8gaq_29904.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8gaq_29904/08_2025/8gaq_29904.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8gaq_29904/08_2025/8gaq_29904.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8gaq_29904/08_2025/8gaq_29904.map" } resolution = 3.73 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.022 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/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: 1.65, per 1000 atoms: 0.28 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: 0.52 Conformation dependent library (CDL) restraints added in 250.3 milliseconds Enol-peptide restraints added in 238.4 nanoseconds 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: 0.20 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: 0.81 Time building geometry restraints manager: 0.69 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: 3.480 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: 0.000 Extract box with map and model: 0.120 Check model and map are aligned: 0.010 Set scattering table: 0.020 Process input model: 7.570 Find NCS groups from input model: 0.080 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.540 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 12.840 ------------------------------------------------------------------------------- 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= 0.191 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. 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 ARG 0.007 0.001 ARG C 218 TYR 0.016 0.003 TYR G 498 Details of bonding type rmsd covalent geometry : bond 0.00456 ( 5845) covalent geometry : angle 0.70076 ( 7855) hydrogen bonds : bond 0.14399 ( 420) hydrogen bonds : angle 6.68539 ( 1251) *********************** 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 : 0.258 Fit side-chains revert: symmetry clash REVERT: C 173 ASN cc_start: 0.6646 (m-40) cc_final: 0.6298 (m110) REVERT: E 332 ARG cc_start: 0.7860 (ptm-80) cc_final: 0.7510 (ptp90) REVERT: I 622 LEU cc_start: 0.8737 (tp) cc_final: 0.8528 (tp) REVERT: I 628 ARG cc_start: 0.7887 (ptt90) cc_final: 0.7598 (ptp90) outliers start: 1 outliers final: 0 residues processed: 160 average time/residue: 0.1348 time to fit residues: 25.7024 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 : 0.307 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 49 optimal weight: 0.5980 chunk 53 optimal weight: 0.4980 chunk 5 optimal weight: 0.6980 chunk 33 optimal weight: 0.7980 chunk 65 optimal weight: 0.1980 chunk 62 optimal weight: 0.9990 chunk 51 optimal weight: 0.5980 chunk 38 optimal weight: 0.0980 chunk 61 optimal weight: 1.9990 chunk 45 optimal weight: 1.9990 chunk 27 optimal weight: 2.9990 overall best weight: 0.3980 ------------------------------------------------------------------------------- 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 G 469 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4079 r_free = 0.4079 target = 0.182715 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3631 r_free = 0.3631 target = 0.139332 restraints weight = 7032.103| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3684 r_free = 0.3684 target = 0.144050 restraints weight = 4684.474| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3720 r_free = 0.3720 target = 0.147334 restraints weight = 3530.532| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.3746 r_free = 0.3746 target = 0.149710 restraints weight = 2891.197| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3761 r_free = 0.3761 target = 0.151164 restraints weight = 2505.483| |-----------------------------------------------------------------------------| r_work (final): 0.3746 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7349 moved from start: 0.2293 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= 0.129 Angle : 0.575 7.311 7855 Z= 0.295 Chirality : 0.038 0.183 990 Planarity : 0.005 0.041 995 Dihedral : 4.388 17.227 775 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 8.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.66 % Favored : 98.34 % Rotamer: Outliers : 1.07 % Allowed : 9.16 % Favored : 89.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.21 (0.30), residues: 725 helix: -0.55 (0.19), residues: 639 sheet: None (None), residues: 0 loop : -1.32 (0.76), residues: 86 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG E 366 TYR 0.013 0.002 TYR A 54 Details of bonding type rmsd covalent geometry : bond 0.00300 ( 5845) covalent geometry : angle 0.57518 ( 7855) hydrogen bonds : bond 0.03541 ( 420) hydrogen bonds : angle 4.13149 ( 1251) *********************** 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 132 residues out of total 655 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 125 time to evaluate : 0.254 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 240 LYS cc_start: 0.8022 (mttt) cc_final: 0.7756 (tmtt) REVERT: C 270 LYS cc_start: 0.7513 (tptm) cc_final: 0.7183 (tptm) REVERT: E 417 MET cc_start: 0.6271 (tpp) cc_final: 0.4906 (ttm) REVERT: G 487 ASN cc_start: 0.7670 (p0) cc_final: 0.7393 (p0) outliers start: 7 outliers final: 3 residues processed: 130 average time/residue: 0.1325 time to fit residues: 20.6239 Evaluate side-chains 118 residues out of total 655 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 115 time to evaluate : 0.223 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 129 LEU Chi-restraints excluded: chain C residue 295 LYS 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 17 optimal weight: 2.9990 chunk 42 optimal weight: 5.9990 chunk 21 optimal weight: 0.5980 chunk 2 optimal weight: 0.5980 chunk 5 optimal weight: 0.6980 chunk 68 optimal weight: 0.0980 chunk 20 optimal weight: 0.4980 chunk 19 optimal weight: 0.6980 chunk 10 optimal weight: 0.9980 chunk 23 optimal weight: 0.0970 chunk 52 optimal weight: 0.9980 overall best weight: 0.3778 ------------------------------------------------------------------------------- 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 = 0.4065 r_free = 0.4065 target = 0.181061 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3626 r_free = 0.3626 target = 0.139009 restraints weight = 7034.796| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3679 r_free = 0.3679 target = 0.143617 restraints weight = 4681.000| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3718 r_free = 0.3718 target = 0.147019 restraints weight = 3535.380| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3743 r_free = 0.3743 target = 0.149347 restraints weight = 2895.261| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3758 r_free = 0.3758 target = 0.150777 restraints weight = 2507.869| |-----------------------------------------------------------------------------| r_work (final): 0.3751 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7355 moved from start: 0.2833 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 5845 Z= 0.113 Angle : 0.550 10.767 7855 Z= 0.272 Chirality : 0.037 0.211 990 Planarity : 0.003 0.033 995 Dihedral : 3.939 17.156 775 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 6.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.52 % Favored : 98.48 % Rotamer: Outliers : 1.83 % Allowed : 11.15 % Favored : 87.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.59 (0.31), residues: 725 helix: -0.07 (0.20), residues: 645 sheet: None (None), residues: 0 loop : -1.88 (0.66), residues: 80 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 366 TYR 0.012 0.002 TYR A 54 Details of bonding type rmsd covalent geometry : bond 0.00263 ( 5845) covalent geometry : angle 0.55029 ( 7855) hydrogen bonds : bond 0.03051 ( 420) hydrogen bonds : angle 3.67107 ( 1251) *********************** 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 135 residues out of total 655 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 123 time to evaluate : 0.248 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 270 LYS cc_start: 0.7497 (tptm) cc_final: 0.7229 (tptm) REVERT: E 392 LEU cc_start: 0.8336 (mp) cc_final: 0.7698 (tt) REVERT: G 487 ASN cc_start: 0.7702 (p0) cc_final: 0.7431 (p0) outliers start: 12 outliers final: 6 residues processed: 127 average time/residue: 0.1258 time to fit residues: 19.3446 Evaluate side-chains 125 residues out of total 655 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 119 time to evaluate : 0.240 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 MET Chi-restraints excluded: chain C residue 178 LEU Chi-restraints excluded: chain C residue 295 LYS Chi-restraints excluded: chain E residue 351 LYS Chi-restraints excluded: chain G residue 452 LEU Chi-restraints excluded: chain G residue 504 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 17 optimal weight: 0.6980 chunk 35 optimal weight: 0.6980 chunk 34 optimal weight: 1.9990 chunk 52 optimal weight: 0.8980 chunk 25 optimal weight: 0.7980 chunk 9 optimal weight: 0.5980 chunk 10 optimal weight: 0.5980 chunk 2 optimal weight: 0.6980 chunk 38 optimal weight: 0.5980 chunk 27 optimal weight: 1.9990 chunk 68 optimal weight: 0.0980 overall best weight: 0.5180 ------------------------------------------------------------------------------- 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 = 0.4042 r_free = 0.4042 target = 0.178875 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3601 r_free = 0.3601 target = 0.137069 restraints weight = 7160.985| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3656 r_free = 0.3656 target = 0.141786 restraints weight = 4800.252| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3694 r_free = 0.3694 target = 0.145106 restraints weight = 3607.250| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3716 r_free = 0.3716 target = 0.147179 restraints weight = 2940.330| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3736 r_free = 0.3736 target = 0.148954 restraints weight = 2551.425| |-----------------------------------------------------------------------------| r_work (final): 0.3730 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7383 moved from start: 0.3082 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 5845 Z= 0.125 Angle : 0.549 6.144 7855 Z= 0.275 Chirality : 0.038 0.213 990 Planarity : 0.003 0.031 995 Dihedral : 3.875 16.117 775 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 7.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.52 % Favored : 98.48 % Rotamer: Outliers : 2.14 % Allowed : 12.67 % Favored : 85.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.42 (0.31), residues: 725 helix: 0.07 (0.20), residues: 643 sheet: None (None), residues: 0 loop : -2.03 (0.63), residues: 82 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG I 601 TYR 0.011 0.002 TYR A 54 Details of bonding type rmsd covalent geometry : bond 0.00303 ( 5845) covalent geometry : angle 0.54897 ( 7855) hydrogen bonds : bond 0.03030 ( 420) hydrogen bonds : angle 3.62608 ( 1251) *********************** 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 138 residues out of total 655 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 124 time to evaluate : 0.271 Fit side-chains revert: symmetry clash REVERT: C 270 LYS cc_start: 0.7509 (tptm) cc_final: 0.7240 (tptm) REVERT: G 487 ASN cc_start: 0.7749 (p0) cc_final: 0.7451 (p0) REVERT: I 688 LEU cc_start: 0.8390 (mp) cc_final: 0.8170 (tt) outliers start: 14 outliers final: 7 residues processed: 130 average time/residue: 0.1353 time to fit residues: 21.1556 Evaluate side-chains 122 residues out of total 655 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 115 time to evaluate : 0.261 ------------------------------------------------------------------------------- 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 E residue 357 MET Chi-restraints excluded: chain G residue 452 LEU Chi-restraints excluded: chain G residue 504 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 47 optimal weight: 1.9990 chunk 66 optimal weight: 0.2980 chunk 6 optimal weight: 0.6980 chunk 30 optimal weight: 2.9990 chunk 69 optimal weight: 0.5980 chunk 55 optimal weight: 0.7980 chunk 63 optimal weight: 0.5980 chunk 3 optimal weight: 4.9990 chunk 1 optimal weight: 6.9990 chunk 13 optimal weight: 1.9990 chunk 28 optimal weight: 3.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- 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 = 0.4019 r_free = 0.4019 target = 0.176451 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3569 r_free = 0.3569 target = 0.134561 restraints weight = 7211.190| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3625 r_free = 0.3625 target = 0.139281 restraints weight = 4835.063| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3663 r_free = 0.3663 target = 0.142598 restraints weight = 3628.513| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3684 r_free = 0.3684 target = 0.144598 restraints weight = 2951.898| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3706 r_free = 0.3706 target = 0.146448 restraints weight = 2559.138| |-----------------------------------------------------------------------------| r_work (final): 0.3708 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7416 moved from start: 0.3364 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 5845 Z= 0.135 Angle : 0.556 6.830 7855 Z= 0.279 Chirality : 0.039 0.179 990 Planarity : 0.003 0.032 995 Dihedral : 3.888 15.044 775 Min Nonbonded Distance : 2.417 Molprobity Statistics. All-atom Clashscore : 7.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.38 (0.31), residues: 725 helix: 0.09 (0.21), residues: 642 sheet: None (None), residues: 0 loop : -1.98 (0.63), residues: 83 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG I 601 TYR 0.011 0.002 TYR A 54 Details of bonding type rmsd covalent geometry : bond 0.00332 ( 5845) covalent geometry : angle 0.55591 ( 7855) hydrogen bonds : bond 0.03081 ( 420) hydrogen bonds : angle 3.61316 ( 1251) *********************** 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 135 residues out of total 655 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 118 time to evaluate : 0.285 Fit side-chains revert: symmetry clash REVERT: A 62 LEU cc_start: 0.8338 (OUTLIER) cc_final: 0.8039 (tt) REVERT: C 269 MET cc_start: 0.7349 (tpp) cc_final: 0.7148 (tpp) REVERT: C 270 LYS cc_start: 0.7606 (tptm) cc_final: 0.7355 (tptm) REVERT: G 487 ASN cc_start: 0.7832 (p0) cc_final: 0.7553 (p0) REVERT: I 654 LEU cc_start: 0.8472 (OUTLIER) cc_final: 0.8135 (tt) REVERT: I 688 LEU cc_start: 0.8400 (mp) cc_final: 0.7782 (tt) REVERT: I 713 MET cc_start: 0.6805 (tpt) cc_final: 0.6498 (tpp) outliers start: 17 outliers final: 10 residues processed: 128 average time/residue: 0.1214 time to fit residues: 18.9959 Evaluate side-chains 127 residues out of total 655 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 115 time to evaluate : 0.244 ------------------------------------------------------------------------------- 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 178 LEU Chi-restraints excluded: chain E residue 351 LYS Chi-restraints excluded: chain E residue 357 MET Chi-restraints excluded: chain G residue 469 ASN 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 63 optimal weight: 0.5980 chunk 65 optimal weight: 0.6980 chunk 44 optimal weight: 0.9980 chunk 24 optimal weight: 0.9990 chunk 55 optimal weight: 0.9990 chunk 45 optimal weight: 1.9990 chunk 35 optimal weight: 0.0970 chunk 10 optimal weight: 0.5980 chunk 40 optimal weight: 0.9990 chunk 26 optimal weight: 0.7980 chunk 18 optimal weight: 1.9990 overall best weight: 0.5578 ------------------------------------------------------------------------------- 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 = 0.4015 r_free = 0.4015 target = 0.176374 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.134627 restraints weight = 7178.175| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3618 r_free = 0.3618 target = 0.139123 restraints weight = 4804.484| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3650 r_free = 0.3650 target = 0.142081 restraints weight = 3621.858| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.3681 r_free = 0.3681 target = 0.144690 restraints weight = 2960.569| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3698 r_free = 0.3698 target = 0.146260 restraints weight = 2545.867| |-----------------------------------------------------------------------------| r_work (final): 0.3702 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7411 moved from start: 0.3555 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= 0.128 Angle : 0.545 6.935 7855 Z= 0.276 Chirality : 0.038 0.172 990 Planarity : 0.004 0.044 995 Dihedral : 3.787 16.777 775 Min Nonbonded Distance : 2.384 Molprobity Statistics. All-atom Clashscore : 7.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Rotamer: Outliers : 2.90 % Allowed : 13.28 % Favored : 83.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.26 (0.31), residues: 725 helix: 0.15 (0.21), residues: 643 sheet: None (None), residues: 0 loop : -1.76 (0.64), residues: 82 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG I 601 TYR 0.010 0.002 TYR A 54 Details of bonding type rmsd covalent geometry : bond 0.00313 ( 5845) covalent geometry : angle 0.54534 ( 7855) hydrogen bonds : bond 0.03072 ( 420) hydrogen bonds : angle 3.54456 ( 1251) *********************** 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 135 residues out of total 655 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 116 time to evaluate : 0.251 Fit side-chains REVERT: A 62 LEU cc_start: 0.8336 (OUTLIER) cc_final: 0.8037 (tt) REVERT: C 270 LYS cc_start: 0.7575 (tptm) cc_final: 0.7319 (tptm) REVERT: E 417 MET cc_start: 0.5005 (tpp) cc_final: 0.3956 (ttm) REVERT: G 487 ASN cc_start: 0.7909 (p0) cc_final: 0.7574 (p0) REVERT: I 654 LEU cc_start: 0.8469 (OUTLIER) cc_final: 0.8131 (tt) REVERT: I 713 MET cc_start: 0.6875 (tpt) cc_final: 0.6671 (tpp) outliers start: 19 outliers final: 12 residues processed: 126 average time/residue: 0.1271 time to fit residues: 19.3824 Evaluate side-chains 125 residues out of total 655 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 111 time to evaluate : 0.246 ------------------------------------------------------------------------------- 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 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 469 ASN 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 67 optimal weight: 0.5980 chunk 38 optimal weight: 0.9980 chunk 54 optimal weight: 0.4980 chunk 53 optimal weight: 0.6980 chunk 39 optimal weight: 0.9990 chunk 24 optimal weight: 0.5980 chunk 9 optimal weight: 0.2980 chunk 26 optimal weight: 0.9980 chunk 32 optimal weight: 0.5980 chunk 63 optimal weight: 0.0970 chunk 2 optimal weight: 0.9980 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 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 = 0.4068 r_free = 0.4068 target = 0.180862 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3629 r_free = 0.3629 target = 0.139236 restraints weight = 7101.964| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3681 r_free = 0.3681 target = 0.143822 restraints weight = 4699.794| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3716 r_free = 0.3716 target = 0.146966 restraints weight = 3530.779| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3737 r_free = 0.3737 target = 0.148946 restraints weight = 2886.210| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3757 r_free = 0.3757 target = 0.150675 restraints weight = 2508.798| |-----------------------------------------------------------------------------| r_work (final): 0.3761 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7394 moved from start: 0.3791 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 5845 Z= 0.115 Angle : 0.566 8.972 7855 Z= 0.279 Chirality : 0.037 0.181 990 Planarity : 0.004 0.034 995 Dihedral : 3.640 16.546 775 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 7.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.52 % Favored : 98.48 % Rotamer: Outliers : 2.60 % Allowed : 13.74 % Favored : 83.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.06 (0.31), residues: 725 helix: 0.28 (0.21), residues: 642 sheet: None (None), residues: 0 loop : -1.67 (0.61), residues: 83 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG I 601 TYR 0.009 0.002 TYR G 498 Details of bonding type rmsd covalent geometry : bond 0.00272 ( 5845) covalent geometry : angle 0.56638 ( 7855) hydrogen bonds : bond 0.02933 ( 420) hydrogen bonds : angle 3.43784 ( 1251) *********************** 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 133 residues out of total 655 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 116 time to evaluate : 0.291 Fit side-chains revert: symmetry clash REVERT: A 62 LEU cc_start: 0.8320 (OUTLIER) cc_final: 0.8036 (tt) REVERT: C 235 MET cc_start: 0.7359 (mmm) cc_final: 0.6966 (tpp) REVERT: C 270 LYS cc_start: 0.7506 (tptm) cc_final: 0.7027 (tppt) REVERT: E 358 LEU cc_start: 0.8497 (OUTLIER) cc_final: 0.8284 (tt) REVERT: G 487 ASN cc_start: 0.7914 (p0) cc_final: 0.7574 (p0) REVERT: I 654 LEU cc_start: 0.8419 (OUTLIER) cc_final: 0.8097 (tt) REVERT: I 713 MET cc_start: 0.6864 (tpt) cc_final: 0.6620 (tpp) outliers start: 17 outliers final: 11 residues processed: 126 average time/residue: 0.1254 time to fit residues: 19.1965 Evaluate side-chains 123 residues out of total 655 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 109 time to evaluate : 0.240 ------------------------------------------------------------------------------- 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 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 469 ASN Chi-restraints excluded: chain G residue 506 LEU 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 7 optimal weight: 0.5980 chunk 11 optimal weight: 0.4980 chunk 15 optimal weight: 0.9990 chunk 0 optimal weight: 4.9990 chunk 63 optimal weight: 0.7980 chunk 41 optimal weight: 1.9990 chunk 17 optimal weight: 0.3980 chunk 24 optimal weight: 0.5980 chunk 18 optimal weight: 0.8980 chunk 61 optimal weight: 0.9990 chunk 32 optimal weight: 0.7980 overall best weight: 0.5780 ------------------------------------------------------------------------------- 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 = 0.4051 r_free = 0.4051 target = 0.178991 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3609 r_free = 0.3609 target = 0.137594 restraints weight = 7094.215| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3661 r_free = 0.3661 target = 0.141969 restraints weight = 4783.737| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3694 r_free = 0.3694 target = 0.144910 restraints weight = 3631.130| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3714 r_free = 0.3714 target = 0.146797 restraints weight = 3002.048| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 45)----------------| | r_work = 0.3735 r_free = 0.3735 target = 0.148498 restraints weight = 2629.168| |-----------------------------------------------------------------------------| r_work (final): 0.3735 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7443 moved from start: 0.3943 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= 0.137 Angle : 0.599 9.144 7855 Z= 0.294 Chirality : 0.038 0.235 990 Planarity : 0.004 0.032 995 Dihedral : 3.710 16.025 775 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 8.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.93 % Favored : 98.07 % Rotamer: Outliers : 2.60 % Allowed : 14.20 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.21 (0.31), residues: 725 helix: 0.17 (0.21), residues: 644 sheet: None (None), residues: 0 loop : -1.67 (0.62), residues: 81 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG I 601 TYR 0.010 0.002 TYR A 54 Details of bonding type rmsd covalent geometry : bond 0.00335 ( 5845) covalent geometry : angle 0.59889 ( 7855) hydrogen bonds : bond 0.03212 ( 420) hydrogen bonds : angle 3.54266 ( 1251) *********************** 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 123 residues out of total 655 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 106 time to evaluate : 0.246 Fit side-chains REVERT: A 62 LEU cc_start: 0.8397 (OUTLIER) cc_final: 0.8125 (tt) REVERT: C 235 MET cc_start: 0.7499 (mmm) cc_final: 0.7099 (tpp) REVERT: C 270 LYS cc_start: 0.7484 (tptm) cc_final: 0.7005 (tppt) REVERT: E 358 LEU cc_start: 0.8527 (OUTLIER) cc_final: 0.8317 (tt) REVERT: G 487 ASN cc_start: 0.7962 (p0) cc_final: 0.7625 (p0) REVERT: I 593 VAL cc_start: 0.6007 (m) cc_final: 0.5803 (m) REVERT: I 654 LEU cc_start: 0.8518 (OUTLIER) cc_final: 0.8208 (tt) REVERT: I 713 MET cc_start: 0.6805 (tpt) cc_final: 0.6569 (tpp) outliers start: 17 outliers final: 12 residues processed: 117 average time/residue: 0.1132 time to fit residues: 16.3460 Evaluate side-chains 122 residues out of total 655 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 107 time to evaluate : 0.234 ------------------------------------------------------------------------------- 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 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 469 ASN 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 42 optimal weight: 5.9990 chunk 33 optimal weight: 0.0980 chunk 48 optimal weight: 0.9990 chunk 41 optimal weight: 1.9990 chunk 44 optimal weight: 1.9990 chunk 39 optimal weight: 1.9990 chunk 4 optimal weight: 1.9990 chunk 58 optimal weight: 2.9990 chunk 43 optimal weight: 3.9990 chunk 67 optimal weight: 1.9990 chunk 17 optimal weight: 0.9980 overall best weight: 1.2186 ------------------------------------------------------------------------------- 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 = 0.3998 r_free = 0.3998 target = 0.173382 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.132911 restraints weight = 7290.893| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3592 r_free = 0.3592 target = 0.136619 restraints weight = 5122.467| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3618 r_free = 0.3618 target = 0.138999 restraints weight = 4006.910| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3646 r_free = 0.3646 target = 0.141209 restraints weight = 3375.197| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3657 r_free = 0.3657 target = 0.142183 restraints weight = 2963.890| |-----------------------------------------------------------------------------| r_work (final): 0.3661 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7593 moved from start: 0.3978 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.046 5845 Z= 0.235 Angle : 0.744 8.652 7855 Z= 0.364 Chirality : 0.043 0.203 990 Planarity : 0.004 0.036 995 Dihedral : 4.288 18.145 775 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 8.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 3.05 % Allowed : 14.50 % Favored : 82.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.59 (0.31), residues: 725 helix: -0.16 (0.20), residues: 639 sheet: None (None), residues: 0 loop : -1.04 (0.70), residues: 86 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG I 601 TYR 0.016 0.003 TYR A 54 Details of bonding type rmsd covalent geometry : bond 0.00603 ( 5845) covalent geometry : angle 0.74397 ( 7855) hydrogen bonds : bond 0.04050 ( 420) hydrogen bonds : angle 4.05921 ( 1251) *********************** 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 133 residues out of total 655 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 113 time to evaluate : 0.253 Fit side-chains revert: symmetry clash REVERT: A 62 LEU cc_start: 0.8540 (OUTLIER) cc_final: 0.8318 (tt) REVERT: C 270 LYS cc_start: 0.7573 (tptm) cc_final: 0.7362 (tptm) REVERT: G 474 LEU cc_start: 0.8690 (OUTLIER) cc_final: 0.8427 (tt) REVERT: G 487 ASN cc_start: 0.7880 (p0) cc_final: 0.7550 (p0) REVERT: I 654 LEU cc_start: 0.8682 (OUTLIER) cc_final: 0.8476 (tt) outliers start: 20 outliers final: 8 residues processed: 124 average time/residue: 0.1374 time to fit residues: 20.4053 Evaluate side-chains 122 residues out of total 655 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 111 time to evaluate : 0.242 ------------------------------------------------------------------------------- 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 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 474 LEU 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 13 optimal weight: 0.3980 chunk 43 optimal weight: 0.8980 chunk 61 optimal weight: 0.0980 chunk 14 optimal weight: 4.9990 chunk 22 optimal weight: 0.0970 chunk 46 optimal weight: 0.8980 chunk 30 optimal weight: 0.8980 chunk 42 optimal weight: 3.9990 chunk 0 optimal weight: 4.9990 chunk 58 optimal weight: 1.9990 chunk 5 optimal weight: 0.6980 overall best weight: 0.4378 ------------------------------------------------------------------------------- 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 = 0.4052 r_free = 0.4052 target = 0.179262 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3606 r_free = 0.3606 target = 0.137310 restraints weight = 7135.908| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3656 r_free = 0.3656 target = 0.141616 restraints weight = 4766.547| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3691 r_free = 0.3691 target = 0.144694 restraints weight = 3611.035| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 46)----------------| | r_work = 0.3714 r_free = 0.3714 target = 0.146784 restraints weight = 2976.860| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 21)----------------| | r_work = 0.3726 r_free = 0.3726 target = 0.147862 restraints weight = 2600.242| |-----------------------------------------------------------------------------| r_work (final): 0.3732 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7424 moved from start: 0.4177 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 5845 Z= 0.128 Angle : 0.634 11.343 7855 Z= 0.309 Chirality : 0.039 0.223 990 Planarity : 0.004 0.031 995 Dihedral : 3.767 16.338 775 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 7.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.24 % Favored : 98.76 % Rotamer: Outliers : 1.68 % Allowed : 15.57 % Favored : 82.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.32 (0.31), residues: 725 helix: 0.10 (0.21), residues: 641 sheet: None (None), residues: 0 loop : -1.66 (0.63), residues: 84 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG I 601 TYR 0.008 0.002 TYR I 646 Details of bonding type rmsd covalent geometry : bond 0.00307 ( 5845) covalent geometry : angle 0.63395 ( 7855) hydrogen bonds : bond 0.03219 ( 420) hydrogen bonds : angle 3.55498 ( 1251) ********************** 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: 11 poor density : 112 time to evaluate : 0.284 Fit side-chains REVERT: A 62 LEU cc_start: 0.8323 (OUTLIER) cc_final: 0.8035 (tt) REVERT: G 487 ASN cc_start: 0.7751 (p0) cc_final: 0.7412 (p0) REVERT: I 601 ARG cc_start: 0.8123 (mtm-85) cc_final: 0.7815 (mtm-85) REVERT: I 654 LEU cc_start: 0.8559 (OUTLIER) cc_final: 0.8313 (tt) REVERT: I 662 ARG cc_start: 0.7846 (ttm-80) cc_final: 0.7596 (ttm-80) REVERT: I 713 MET cc_start: 0.6534 (tpp) cc_final: 0.4936 (ttm) outliers start: 11 outliers final: 7 residues processed: 119 average time/residue: 0.1198 time to fit residues: 17.4679 Evaluate side-chains 115 residues out of total 655 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 106 time to evaluate : 0.283 ------------------------------------------------------------------------------- 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 C residue 178 LEU 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 542 LEU 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 22 optimal weight: 0.6980 chunk 47 optimal weight: 0.6980 chunk 15 optimal weight: 4.9990 chunk 19 optimal weight: 0.7980 chunk 4 optimal weight: 0.9990 chunk 34 optimal weight: 0.8980 chunk 55 optimal weight: 0.1980 chunk 56 optimal weight: 5.9990 chunk 14 optimal weight: 0.6980 chunk 16 optimal weight: 0.6980 chunk 59 optimal weight: 0.3980 overall best weight: 0.5380 ------------------------------------------------------------------------------- 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 = 0.4044 r_free = 0.4044 target = 0.178564 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3598 r_free = 0.3598 target = 0.136563 restraints weight = 7052.112| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3647 r_free = 0.3647 target = 0.140794 restraints weight = 4767.566| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3681 r_free = 0.3681 target = 0.143799 restraints weight = 3630.936| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3702 r_free = 0.3702 target = 0.145674 restraints weight = 3014.409| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 51)----------------| | r_work = 0.3719 r_free = 0.3719 target = 0.147236 restraints weight = 2651.785| |-----------------------------------------------------------------------------| r_work (final): 0.3729 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7441 moved from start: 0.4237 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= 0.138 Angle : 0.649 11.060 7855 Z= 0.315 Chirality : 0.039 0.212 990 Planarity : 0.004 0.030 995 Dihedral : 3.754 15.999 775 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 8.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Rotamer: Outliers : 1.37 % Allowed : 16.64 % Favored : 81.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.32 (0.31), residues: 725 helix: 0.11 (0.21), residues: 644 sheet: None (None), residues: 0 loop : -1.75 (0.64), residues: 81 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG I 601 TYR 0.009 0.002 TYR G 498 Details of bonding type rmsd covalent geometry : bond 0.00339 ( 5845) covalent geometry : angle 0.64939 ( 7855) hydrogen bonds : bond 0.03251 ( 420) hydrogen bonds : angle 3.58505 ( 1251) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1162.01 seconds wall clock time: 20 minutes 46.81 seconds (1246.81 seconds total)