Starting phenix.real_space_refine on Wed Feb 4 12:23:47 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9qiv_53195/02_2026/9qiv_53195_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/9qiv_53195/02_2026/9qiv_53195.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.44 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9qiv_53195/02_2026/9qiv_53195.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9qiv_53195/02_2026/9qiv_53195.map" model { file = "/net/cci-nas-00/data/ceres_data/9qiv_53195/02_2026/9qiv_53195_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9qiv_53195/02_2026/9qiv_53195_neut.cif" } resolution = 3.44 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= -0.001 sd= 0.027 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: 5 Type Number sf(0) Gaussians P 9 5.49 5 S 50 5.16 5 C 6515 2.51 5 N 1727 2.21 5 O 1955 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 8 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 10256 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 2346 Number of conformers: 1 Conformer: "" Number of residues, atoms: 293, 2346 Classifications: {'peptide': 293} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 275} Chain: "B" Number of atoms: 7843 Number of conformers: 1 Conformer: "" Number of residues, atoms: 989, 7843 Classifications: {'peptide': 989} Link IDs: {'CIS': 1, 'PCIS': 4, 'PTRANS': 47, 'TRANS': 936} Chain breaks: 1 Chain: "B" Number of atoms: 67 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 67 Unusual residues: {'ATP': 1, 'IHP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 1.87, per 1000 atoms: 0.18 Number of scatterers: 10256 At special positions: 0 Unit cell: (84.15, 99.825, 127.05, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 50 16.00 P 9 15.00 O 1955 8.00 N 1727 7.00 C 6515 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: 0.73 Conformation dependent library (CDL) restraints added in 333.6 milliseconds 2552 Ramachandran restraints generated. 1276 Oldfield, 0 Emsley, 1276 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2438 Finding SS restraints... Secondary structure from input PDB file: 53 helices and 9 sheets defined 50.0% alpha, 12.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.26 Creating SS restraints... Processing helix chain 'A' and resid 4523 through 4534 removed outlier: 4.207A pdb=" N LYS A4534 " --> pdb=" O ALA A4530 " (cutoff:3.500A) Processing helix chain 'A' and resid 4559 through 4565 Processing helix chain 'A' and resid 4571 through 4589 removed outlier: 3.541A pdb=" N LEU A4589 " --> pdb=" O LEU A4585 " (cutoff:3.500A) Processing helix chain 'A' and resid 4676 through 4680 Processing helix chain 'A' and resid 4687 through 4699 Processing helix chain 'A' and resid 4703 through 4708 removed outlier: 3.648A pdb=" N GLU A4708 " --> pdb=" O TYR A4705 " (cutoff:3.500A) Processing helix chain 'A' and resid 4710 through 4715 removed outlier: 4.047A pdb=" N ARG A4713 " --> pdb=" O GLY A4710 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ARG A4715 " --> pdb=" O GLU A4712 " (cutoff:3.500A) Processing helix chain 'A' and resid 4717 through 4739 Processing helix chain 'A' and resid 4740 through 4746 Processing helix chain 'A' and resid 4751 through 4780 removed outlier: 5.565A pdb=" N VAL A4764 " --> pdb=" O TYR A4760 " (cutoff:3.500A) removed outlier: 5.912A pdb=" N GLU A4765 " --> pdb=" O LEU A4761 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N TYR A4780 " --> pdb=" O ASP A4776 " (cutoff:3.500A) Processing helix chain 'A' and resid 4786 through 4810 Processing helix chain 'B' and resid 40 through 52 removed outlier: 7.093A pdb=" N ARG B 46 " --> pdb=" O ALA B 42 " (cutoff:3.500A) removed outlier: 5.949A pdb=" N GLN B 47 " --> pdb=" O LEU B 43 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N VAL B 50 " --> pdb=" O ARG B 46 " (cutoff:3.500A) Processing helix chain 'B' and resid 52 through 60 Processing helix chain 'B' and resid 70 through 84 Processing helix chain 'B' and resid 97 through 103 removed outlier: 3.533A pdb=" N LEU B 101 " --> pdb=" O ALA B 98 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N GLY B 102 " --> pdb=" O TRP B 99 " (cutoff:3.500A) Processing helix chain 'B' and resid 108 through 115 Processing helix chain 'B' and resid 117 through 130 removed outlier: 3.547A pdb=" N VAL B 122 " --> pdb=" O ARG B 118 " (cutoff:3.500A) removed outlier: 4.370A pdb=" N LYS B 124 " --> pdb=" O GLU B 120 " (cutoff:3.500A) removed outlier: 5.338A pdb=" N HIS B 125 " --> pdb=" O ALA B 121 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N GLU B 128 " --> pdb=" O LYS B 124 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N LEU B 129 " --> pdb=" O HIS B 125 " (cutoff:3.500A) removed outlier: 4.224A pdb=" N ASN B 130 " --> pdb=" O ILE B 126 " (cutoff:3.500A) Processing helix chain 'B' and resid 148 through 154 removed outlier: 3.660A pdb=" N LYS B 153 " --> pdb=" O PHE B 150 " (cutoff:3.500A) Processing helix chain 'B' and resid 163 through 176 removed outlier: 3.699A pdb=" N SER B 176 " --> pdb=" O ASP B 172 " (cutoff:3.500A) Processing helix chain 'B' and resid 301 through 306 Processing helix chain 'B' and resid 320 through 340 Processing helix chain 'B' and resid 347 through 365 removed outlier: 3.556A pdb=" N GLU B 363 " --> pdb=" O THR B 359 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N THR B 364 " --> pdb=" O SER B 360 " (cutoff:3.500A) Processing helix chain 'B' and resid 372 through 382 Processing helix chain 'B' and resid 387 through 408 Processing helix chain 'B' and resid 421 through 427 removed outlier: 4.284A pdb=" N VAL B 425 " --> pdb=" O ALA B 421 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N SER B 427 " --> pdb=" O ASP B 423 " (cutoff:3.500A) Processing helix chain 'B' and resid 432 through 437 removed outlier: 4.056A pdb=" N PHE B 436 " --> pdb=" O GLU B 432 " (cutoff:3.500A) Processing helix chain 'B' and resid 443 through 460 removed outlier: 8.120A pdb=" N ASP B 452 " --> pdb=" O ALA B 448 " (cutoff:3.500A) removed outlier: 9.492A pdb=" N THR B 453 " --> pdb=" O CYS B 449 " (cutoff:3.500A) removed outlier: 4.193A pdb=" N LEU B 454 " --> pdb=" O ILE B 450 " (cutoff:3.500A) Processing helix chain 'B' and resid 469 through 483 Processing helix chain 'B' and resid 502 through 508 removed outlier: 3.592A pdb=" N ASN B 507 " --> pdb=" O SER B 504 " (cutoff:3.500A) Processing helix chain 'B' and resid 513 through 517 removed outlier: 3.620A pdb=" N ILE B 517 " --> pdb=" O PRO B 514 " (cutoff:3.500A) Processing helix chain 'B' and resid 520 through 533 removed outlier: 3.654A pdb=" N LYS B 531 " --> pdb=" O ASP B 527 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ILE B 532 " --> pdb=" O ALA B 528 " (cutoff:3.500A) Processing helix chain 'B' and resid 546 through 550 Processing helix chain 'B' and resid 554 through 561 Processing helix chain 'B' and resid 570 through 583 removed outlier: 3.539A pdb=" N ARG B 574 " --> pdb=" O ASN B 570 " (cutoff:3.500A) Processing helix chain 'B' and resid 610 through 614 Processing helix chain 'B' and resid 623 through 629 Processing helix chain 'B' and resid 633 through 650 removed outlier: 3.614A pdb=" N THR B 637 " --> pdb=" O ALA B 633 " (cutoff:3.500A) Processing helix chain 'B' and resid 650 through 663 Processing helix chain 'B' and resid 665 through 675 Processing helix chain 'B' and resid 681 through 691 Processing helix chain 'B' and resid 695 through 712 Processing helix chain 'B' and resid 712 through 722 Processing helix chain 'B' and resid 751 through 769 Processing helix chain 'B' and resid 775 through 778 Processing helix chain 'B' and resid 779 through 788 Processing helix chain 'B' and resid 821 through 834 Processing helix chain 'B' and resid 857 through 873 Processing helix chain 'B' and resid 879 through 888 Processing helix chain 'B' and resid 894 through 915 removed outlier: 3.699A pdb=" N THR B 898 " --> pdb=" O ILE B 894 " (cutoff:3.500A) Processing helix chain 'B' and resid 917 through 920 Processing helix chain 'B' and resid 967 through 980 Processing helix chain 'B' and resid 1001 through 1007 removed outlier: 3.534A pdb=" N LEU B1005 " --> pdb=" O ALA B1002 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N LYS B1006 " --> pdb=" O LYS B1003 " (cutoff:3.500A) Processing helix chain 'B' and resid 1008 through 1014 Processing sheet with id=AA1, first strand: chain 'A' and resid 4537 through 4540 removed outlier: 6.623A pdb=" N ILE A4608 " --> pdb=" O ASP A4602 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 4543 through 4545 Processing sheet with id=AA3, first strand: chain 'B' and resid 134 through 138 removed outlier: 3.666A pdb=" N CYS B 156 " --> pdb=" O HIS B 63 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 202 through 205 Processing sheet with id=AA5, first strand: chain 'B' and resid 260 through 262 removed outlier: 4.513A pdb=" N PHE B 244 " --> pdb=" O VAL B 291 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N PHE B 271 " --> pdb=" O VAL B 229 " (cutoff:3.500A) removed outlier: 6.402A pdb=" N SER B 270 " --> pdb=" O ILE B 266 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 538 through 541 removed outlier: 6.251A pdb=" N ILE B 493 " --> pdb=" O ASP B 539 " (cutoff:3.500A) removed outlier: 7.511A pdb=" N HIS B 541 " --> pdb=" O ILE B 493 " (cutoff:3.500A) removed outlier: 6.351A pdb=" N VAL B 495 " --> pdb=" O HIS B 541 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N VAL B 563 " --> pdb=" O ASN B 462 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N SER B 591 " --> pdb=" O THR B 566 " (cutoff:3.500A) removed outlier: 5.714A pdb=" N VAL B 602 " --> pdb=" O LYS B 922 " (cutoff:3.500A) removed outlier: 7.250A pdb=" N LYS B 922 " --> pdb=" O VAL B 602 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 944 through 947 removed outlier: 6.691A pdb=" N ILE B 950 " --> pdb=" O ILE B 946 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 958 through 961 removed outlier: 6.360A pdb=" N TRP B 958 " --> pdb=" O ARG B1044 " (cutoff:3.500A) removed outlier: 8.017A pdb=" N TYR B1046 " --> pdb=" O TRP B 958 " (cutoff:3.500A) removed outlier: 6.934A pdb=" N VAL B 960 " --> pdb=" O TYR B1046 " (cutoff:3.500A) removed outlier: 8.245A pdb=" N ASP B1023 " --> pdb=" O GLN B 988 " (cutoff:3.500A) removed outlier: 4.883A pdb=" N GLN B 988 " --> pdb=" O ASP B1023 " (cutoff:3.500A) removed outlier: 6.506A pdb=" N THR B1025 " --> pdb=" O VAL B 986 " (cutoff:3.500A) removed outlier: 4.326A pdb=" N VAL B 986 " --> pdb=" O THR B1025 " (cutoff:3.500A) removed outlier: 6.663A pdb=" N SER B1027 " --> pdb=" O THR B 984 " (cutoff:3.500A) removed outlier: 6.241A pdb=" N VAL B 986 " --> pdb=" O LEU B 993 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 958 through 961 removed outlier: 6.360A pdb=" N TRP B 958 " --> pdb=" O ARG B1044 " (cutoff:3.500A) removed outlier: 8.017A pdb=" N TYR B1046 " --> pdb=" O TRP B 958 " (cutoff:3.500A) removed outlier: 6.934A pdb=" N VAL B 960 " --> pdb=" O TYR B1046 " (cutoff:3.500A) 513 hydrogen bonds defined for protein. 1431 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: 1.51 Time building geometry restraints manager: 0.91 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: 3331 1.34 - 1.46: 1772 1.46 - 1.57: 5306 1.57 - 1.69: 11 1.69 - 1.81: 73 Bond restraints: 10493 Sorted by residual: bond pdb=" C1' ATP B1102 " pdb=" O4' ATP B1102 " ideal model delta sigma weight residual 1.416 1.404 0.012 1.30e-02 5.92e+03 8.36e-01 bond pdb=" N GLY B 491 " pdb=" CA GLY B 491 " ideal model delta sigma weight residual 1.463 1.447 0.016 2.07e-02 2.33e+03 5.82e-01 bond pdb=" CA CYS B 546 " pdb=" CB CYS B 546 " ideal model delta sigma weight residual 1.538 1.529 0.010 1.38e-02 5.25e+03 5.14e-01 bond pdb=" CB ARG B 615 " pdb=" CG ARG B 615 " ideal model delta sigma weight residual 1.520 1.541 -0.021 3.00e-02 1.11e+03 4.98e-01 bond pdb=" C ILE B 930 " pdb=" N PRO B 931 " ideal model delta sigma weight residual 1.338 1.351 -0.013 1.90e-02 2.77e+03 4.74e-01 ... (remaining 10488 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.04: 13806 1.04 - 2.09: 320 2.09 - 3.13: 95 3.13 - 4.18: 13 4.18 - 5.22: 7 Bond angle restraints: 14241 Sorted by residual: angle pdb=" C ARG B 642 " pdb=" N ASP B 643 " pdb=" CA ASP B 643 " ideal model delta sigma weight residual 121.14 117.35 3.79 1.75e+00 3.27e-01 4.68e+00 angle pdb=" C2' ATP B1102 " pdb=" C3' ATP B1102 " pdb=" C4' ATP B1102 " ideal model delta sigma weight residual 102.49 104.45 -1.96 1.00e+00 1.00e+00 3.85e+00 angle pdb=" CA CYS B 546 " pdb=" C CYS B 546 " pdb=" N PRO B 547 " ideal model delta sigma weight residual 117.82 119.21 -1.39 7.80e-01 1.64e+00 3.16e+00 angle pdb=" C ILE B 930 " pdb=" N PRO B 931 " pdb=" CA PRO B 931 " ideal model delta sigma weight residual 127.00 130.90 -3.90 2.40e+00 1.74e-01 2.65e+00 angle pdb=" C LEU B 279 " pdb=" N GLU B 280 " pdb=" CA GLU B 280 " ideal model delta sigma weight residual 120.68 123.12 -2.44 1.52e+00 4.33e-01 2.58e+00 ... (remaining 14236 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.30: 6001 17.30 - 34.61: 307 34.61 - 51.91: 64 51.91 - 69.21: 15 69.21 - 86.51: 6 Dihedral angle restraints: 6393 sinusoidal: 2639 harmonic: 3754 Sorted by residual: dihedral pdb=" CA THR A4587 " pdb=" C THR A4587 " pdb=" N SER A4588 " pdb=" CA SER A4588 " ideal model delta harmonic sigma weight residual 180.00 -163.67 -16.33 0 5.00e+00 4.00e-02 1.07e+01 dihedral pdb=" CB GLU B 794 " pdb=" CG GLU B 794 " pdb=" CD GLU B 794 " pdb=" OE1 GLU B 794 " ideal model delta sinusoidal sigma weight residual 0.00 -84.39 84.39 1 3.00e+01 1.11e-03 9.62e+00 dihedral pdb=" CA ARG B 615 " pdb=" CB ARG B 615 " pdb=" CG ARG B 615 " pdb=" CD ARG B 615 " ideal model delta sinusoidal sigma weight residual -60.00 -3.98 -56.02 3 1.50e+01 4.44e-03 9.38e+00 ... (remaining 6390 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.028: 983 0.028 - 0.056: 385 0.056 - 0.083: 118 0.083 - 0.111: 84 0.111 - 0.139: 20 Chirality restraints: 1590 Sorted by residual: chirality pdb=" CA ASP B 643 " pdb=" N ASP B 643 " pdb=" C ASP B 643 " pdb=" CB ASP B 643 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.14 2.00e-01 2.50e+01 4.82e-01 chirality pdb=" CA VAL B1022 " pdb=" N VAL B1022 " pdb=" C VAL B1022 " pdb=" CB VAL B1022 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 4.09e-01 chirality pdb=" CA ILE B 221 " pdb=" N ILE B 221 " pdb=" C ILE B 221 " pdb=" CB ILE B 221 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.05e-01 ... (remaining 1587 not shown) Planarity restraints: 1824 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLU B 280 " 0.030 5.00e-02 4.00e+02 4.56e-02 3.33e+00 pdb=" N PRO B 281 " -0.079 5.00e-02 4.00e+02 pdb=" CA PRO B 281 " 0.024 5.00e-02 4.00e+02 pdb=" CD PRO B 281 " 0.025 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASN A4656 " 0.026 5.00e-02 4.00e+02 3.87e-02 2.40e+00 pdb=" N PRO A4657 " -0.067 5.00e-02 4.00e+02 pdb=" CA PRO A4657 " 0.020 5.00e-02 4.00e+02 pdb=" CD PRO A4657 " 0.022 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER B 267 " -0.025 5.00e-02 4.00e+02 3.79e-02 2.30e+00 pdb=" N PRO B 268 " 0.066 5.00e-02 4.00e+02 pdb=" CA PRO B 268 " -0.019 5.00e-02 4.00e+02 pdb=" CD PRO B 268 " -0.021 5.00e-02 4.00e+02 ... (remaining 1821 not shown) Histogram of nonbonded interaction distances: 2.55 - 3.02: 5985 3.02 - 3.49: 10572 3.49 - 3.96: 16617 3.96 - 4.43: 19421 4.43 - 4.90: 30349 Nonbonded interactions: 82944 Sorted by model distance: nonbonded pdb=" O TRP B 640 " pdb=" OD1 ASP B 643 " model vdw 2.548 3.040 nonbonded pdb=" O2' ATP B1102 " pdb=" O3' ATP B1102 " model vdw 2.593 2.432 nonbonded pdb=" N SER B 267 " pdb=" O SER B 267 " model vdw 2.616 2.496 nonbonded pdb=" N GLN B 415 " pdb=" N TRP B 416 " model vdw 2.631 2.560 nonbonded pdb=" N PHE B 271 " pdb=" O PHE B 271 " model vdw 2.634 2.496 ... (remaining 82939 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.760 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: 0.020 Set scattering table: 0.030 Process input model: 8.830 Find NCS groups from input model: 0.050 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:0.970 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 11.800 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8877 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 : 0.002 0.021 10493 Z= 0.116 Angle : 0.443 5.219 14241 Z= 0.231 Chirality : 0.039 0.139 1590 Planarity : 0.004 0.046 1824 Dihedral : 11.404 86.512 3955 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 4.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.49 % Favored : 98.51 % Rotamer: Outliers : 0.79 % Allowed : 3.88 % Favored : 95.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.35 % Cis-general : 0.08 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.99 (0.25), residues: 1276 helix: 2.13 (0.23), residues: 557 sheet: 1.15 (0.40), residues: 186 loop : 0.63 (0.29), residues: 533 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 642 TYR 0.010 0.001 TYR B 44 PHE 0.012 0.001 PHE B 656 TRP 0.012 0.001 TRP B 660 HIS 0.002 0.000 HIS B1001 Details of bonding type rmsd covalent geometry : bond 0.00246 (10493) covalent geometry : angle 0.44259 (14241) hydrogen bonds : bond 0.15584 ( 509) hydrogen bonds : angle 6.53911 ( 1431) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2552 Ramachandran restraints generated. 1276 Oldfield, 0 Emsley, 1276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2552 Ramachandran restraints generated. 1276 Oldfield, 0 Emsley, 1276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 54 residues out of total 1133 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 45 time to evaluate : 0.278 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 4542 MET cc_start: 0.8372 (mpp) cc_final: 0.7670 (mpp) REVERT: A 4767 MET cc_start: 0.9513 (mmt) cc_final: 0.9028 (mmm) REVERT: B 658 LYS cc_start: 0.9444 (tppt) cc_final: 0.9114 (tppt) REVERT: B 717 GLN cc_start: 0.9004 (OUTLIER) cc_final: 0.8631 (tm-30) outliers start: 9 outliers final: 5 residues processed: 54 average time/residue: 0.0939 time to fit residues: 7.3220 Evaluate side-chains 40 residues out of total 1133 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 34 time to evaluate : 0.413 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4804 LEU Chi-restraints excluded: chain B residue 142 PHE Chi-restraints excluded: chain B residue 495 VAL Chi-restraints excluded: chain B residue 615 ARG Chi-restraints excluded: chain B residue 717 GLN Chi-restraints excluded: chain B residue 946 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 108 optimal weight: 9.9990 chunk 49 optimal weight: 0.9990 chunk 97 optimal weight: 2.9990 chunk 113 optimal weight: 1.9990 chunk 53 optimal weight: 5.9990 chunk 5 optimal weight: 0.7980 chunk 33 optimal weight: 0.9990 chunk 123 optimal weight: 6.9990 chunk 65 optimal weight: 0.6980 chunk 62 optimal weight: 0.0870 chunk 51 optimal weight: 10.0000 overall best weight: 0.7162 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 262 GLN B 290 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3243 r_free = 0.3243 target = 0.052004 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2857 r_free = 0.2857 target = 0.039590 restraints weight = 47076.809| |-----------------------------------------------------------------------------| r_work (start): 0.2841 rms_B_bonded: 4.18 r_work: 0.2686 rms_B_bonded: 4.68 restraints_weight: 0.5000 r_work (final): 0.2686 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8859 moved from start: 0.0728 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 10493 Z= 0.099 Angle : 0.461 8.634 14241 Z= 0.242 Chirality : 0.039 0.137 1590 Planarity : 0.004 0.044 1824 Dihedral : 6.245 66.576 1458 Min Nonbonded Distance : 2.571 Molprobity Statistics. All-atom Clashscore : 5.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.72 % Favored : 98.28 % Rotamer: Outliers : 1.06 % Allowed : 5.03 % Favored : 93.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.35 % Cis-general : 0.08 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.00 (0.25), residues: 1276 helix: 2.13 (0.22), residues: 577 sheet: 1.31 (0.41), residues: 173 loop : 0.52 (0.29), residues: 526 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A4574 TYR 0.012 0.001 TYR B1046 PHE 0.014 0.001 PHE B1047 TRP 0.008 0.001 TRP B 660 HIS 0.002 0.000 HIS B1001 Details of bonding type rmsd covalent geometry : bond 0.00207 (10493) covalent geometry : angle 0.46112 (14241) hydrogen bonds : bond 0.03881 ( 509) hydrogen bonds : angle 4.95617 ( 1431) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2552 Ramachandran restraints generated. 1276 Oldfield, 0 Emsley, 1276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2552 Ramachandran restraints generated. 1276 Oldfield, 0 Emsley, 1276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 51 residues out of total 1133 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 39 time to evaluate : 0.342 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 4542 MET cc_start: 0.8315 (mpp) cc_final: 0.7655 (mpp) REVERT: B 658 LYS cc_start: 0.9429 (tppt) cc_final: 0.9089 (tppt) outliers start: 12 outliers final: 7 residues processed: 50 average time/residue: 0.1009 time to fit residues: 7.4229 Evaluate side-chains 41 residues out of total 1133 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 34 time to evaluate : 0.366 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4804 LEU Chi-restraints excluded: chain B residue 142 PHE Chi-restraints excluded: chain B residue 495 VAL Chi-restraints excluded: chain B residue 615 ARG Chi-restraints excluded: chain B residue 699 CYS Chi-restraints excluded: chain B residue 889 LYS Chi-restraints excluded: chain B residue 960 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 58 optimal weight: 0.7980 chunk 17 optimal weight: 0.9990 chunk 32 optimal weight: 5.9990 chunk 14 optimal weight: 6.9990 chunk 21 optimal weight: 6.9990 chunk 46 optimal weight: 0.0170 chunk 120 optimal weight: 0.9990 chunk 65 optimal weight: 0.9980 chunk 90 optimal weight: 1.9990 chunk 61 optimal weight: 5.9990 chunk 118 optimal weight: 7.9990 overall best weight: 0.7622 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B1010 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3253 r_free = 0.3253 target = 0.053046 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2847 r_free = 0.2847 target = 0.039899 restraints weight = 46427.585| |-----------------------------------------------------------------------------| r_work (start): 0.2839 rms_B_bonded: 4.29 r_work: 0.2677 rms_B_bonded: 4.82 restraints_weight: 0.5000 r_work (final): 0.2677 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8838 moved from start: 0.1021 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 10493 Z= 0.090 Angle : 0.449 7.589 14241 Z= 0.229 Chirality : 0.039 0.131 1590 Planarity : 0.003 0.045 1824 Dihedral : 5.802 63.480 1453 Min Nonbonded Distance : 2.569 Molprobity Statistics. All-atom Clashscore : 5.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.65 % Favored : 98.35 % Rotamer: Outliers : 1.24 % Allowed : 5.38 % Favored : 93.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.35 % Cis-general : 0.08 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.06 (0.25), residues: 1276 helix: 2.26 (0.22), residues: 577 sheet: 1.27 (0.40), residues: 174 loop : 0.47 (0.29), residues: 525 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A4576 TYR 0.009 0.001 TYR B 44 PHE 0.026 0.001 PHE B1047 TRP 0.006 0.001 TRP B 660 HIS 0.002 0.000 HIS B 63 Details of bonding type rmsd covalent geometry : bond 0.00193 (10493) covalent geometry : angle 0.44911 (14241) hydrogen bonds : bond 0.03316 ( 509) hydrogen bonds : angle 4.49975 ( 1431) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2552 Ramachandran restraints generated. 1276 Oldfield, 0 Emsley, 1276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2552 Ramachandran restraints generated. 1276 Oldfield, 0 Emsley, 1276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 51 residues out of total 1133 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 37 time to evaluate : 0.428 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 4767 MET cc_start: 0.9425 (mmt) cc_final: 0.9172 (mmm) REVERT: B 214 LYS cc_start: 0.8224 (pttt) cc_final: 0.7932 (pttt) REVERT: B 658 LYS cc_start: 0.9443 (tppt) cc_final: 0.9111 (tppt) REVERT: B 717 GLN cc_start: 0.9021 (OUTLIER) cc_final: 0.8657 (tm-30) outliers start: 14 outliers final: 6 residues processed: 50 average time/residue: 0.1088 time to fit residues: 7.7573 Evaluate side-chains 41 residues out of total 1133 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 34 time to evaluate : 0.312 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 142 PHE Chi-restraints excluded: chain B residue 495 VAL Chi-restraints excluded: chain B residue 615 ARG Chi-restraints excluded: chain B residue 705 LEU Chi-restraints excluded: chain B residue 717 GLN Chi-restraints excluded: chain B residue 889 LYS Chi-restraints excluded: chain B residue 960 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 26 optimal weight: 0.9980 chunk 6 optimal weight: 1.9990 chunk 25 optimal weight: 0.1980 chunk 96 optimal weight: 2.9990 chunk 53 optimal weight: 7.9990 chunk 63 optimal weight: 5.9990 chunk 10 optimal weight: 8.9990 chunk 88 optimal weight: 0.4980 chunk 1 optimal weight: 0.9980 chunk 38 optimal weight: 6.9990 chunk 18 optimal weight: 0.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- 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 = 0.3242 r_free = 0.3242 target = 0.052669 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2846 r_free = 0.2846 target = 0.039918 restraints weight = 47181.939| |-----------------------------------------------------------------------------| r_work (start): 0.2842 rms_B_bonded: 4.29 r_work: 0.2678 rms_B_bonded: 4.83 restraints_weight: 0.5000 r_work (final): 0.2678 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8840 moved from start: 0.1210 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.020 10493 Z= 0.087 Angle : 0.434 7.616 14241 Z= 0.222 Chirality : 0.039 0.132 1590 Planarity : 0.003 0.044 1824 Dihedral : 5.448 61.360 1451 Min Nonbonded Distance : 2.573 Molprobity Statistics. All-atom Clashscore : 5.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.49 % Favored : 98.51 % Rotamer: Outliers : 1.24 % Allowed : 6.09 % Favored : 92.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.35 % Cis-general : 0.08 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.14 (0.24), residues: 1276 helix: 2.35 (0.22), residues: 571 sheet: 1.34 (0.39), residues: 172 loop : 0.51 (0.29), residues: 533 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A4576 TYR 0.008 0.001 TYR A4621 PHE 0.020 0.001 PHE B1047 TRP 0.007 0.001 TRP B 660 HIS 0.002 0.000 HIS A4758 Details of bonding type rmsd covalent geometry : bond 0.00186 (10493) covalent geometry : angle 0.43436 (14241) hydrogen bonds : bond 0.03036 ( 509) hydrogen bonds : angle 4.31778 ( 1431) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2552 Ramachandran restraints generated. 1276 Oldfield, 0 Emsley, 1276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2552 Ramachandran restraints generated. 1276 Oldfield, 0 Emsley, 1276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 52 residues out of total 1133 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 38 time to evaluate : 0.337 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 4767 MET cc_start: 0.9432 (mmt) cc_final: 0.9185 (mmm) REVERT: B 594 MET cc_start: 0.8822 (tmm) cc_final: 0.8473 (tmm) REVERT: B 658 LYS cc_start: 0.9444 (tppt) cc_final: 0.9110 (tppt) outliers start: 14 outliers final: 10 residues processed: 50 average time/residue: 0.0892 time to fit residues: 6.8212 Evaluate side-chains 47 residues out of total 1133 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 37 time to evaluate : 0.389 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 142 PHE Chi-restraints excluded: chain B residue 205 VAL Chi-restraints excluded: chain B residue 495 VAL Chi-restraints excluded: chain B residue 705 LEU Chi-restraints excluded: chain B residue 889 LYS Chi-restraints excluded: chain B residue 946 ILE Chi-restraints excluded: chain B residue 960 VAL Chi-restraints excluded: chain B residue 998 MET Chi-restraints excluded: chain B residue 1009 MET Chi-restraints excluded: chain B residue 1047 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 67 optimal weight: 0.8980 chunk 119 optimal weight: 4.9990 chunk 83 optimal weight: 6.9990 chunk 35 optimal weight: 4.9990 chunk 77 optimal weight: 0.4980 chunk 34 optimal weight: 4.9990 chunk 59 optimal weight: 0.8980 chunk 4 optimal weight: 0.0970 chunk 97 optimal weight: 0.7980 chunk 20 optimal weight: 8.9990 chunk 47 optimal weight: 1.9990 overall best weight: 0.6378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 760 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3244 r_free = 0.3244 target = 0.052687 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2847 r_free = 0.2847 target = 0.039930 restraints weight = 47353.010| |-----------------------------------------------------------------------------| r_work (start): 0.2835 rms_B_bonded: 4.31 r_work: 0.2671 rms_B_bonded: 4.85 restraints_weight: 0.5000 r_work (final): 0.2671 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8840 moved from start: 0.1350 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 10493 Z= 0.083 Angle : 0.438 7.752 14241 Z= 0.222 Chirality : 0.039 0.172 1590 Planarity : 0.003 0.045 1824 Dihedral : 5.233 59.871 1447 Min Nonbonded Distance : 2.576 Molprobity Statistics. All-atom Clashscore : 5.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.49 % Favored : 98.51 % Rotamer: Outliers : 1.15 % Allowed : 6.18 % Favored : 92.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.35 % Cis-general : 0.08 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.18 (0.24), residues: 1276 helix: 2.38 (0.22), residues: 573 sheet: 1.34 (0.39), residues: 172 loop : 0.53 (0.29), residues: 531 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A4576 TYR 0.009 0.001 TYR B 44 PHE 0.019 0.001 PHE B1047 TRP 0.006 0.001 TRP B 660 HIS 0.002 0.000 HIS A4758 Details of bonding type rmsd covalent geometry : bond 0.00178 (10493) covalent geometry : angle 0.43821 (14241) hydrogen bonds : bond 0.02903 ( 509) hydrogen bonds : angle 4.21438 ( 1431) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2552 Ramachandran restraints generated. 1276 Oldfield, 0 Emsley, 1276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2552 Ramachandran restraints generated. 1276 Oldfield, 0 Emsley, 1276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 51 residues out of total 1133 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 38 time to evaluate : 0.381 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 4767 MET cc_start: 0.9442 (mmt) cc_final: 0.9189 (mmm) REVERT: B 475 MET cc_start: 0.9495 (tpp) cc_final: 0.9283 (mmm) REVERT: B 594 MET cc_start: 0.8822 (tmm) cc_final: 0.8435 (tmm) REVERT: B 658 LYS cc_start: 0.9450 (tppt) cc_final: 0.9132 (tppt) REVERT: B 717 GLN cc_start: 0.9016 (OUTLIER) cc_final: 0.8649 (tm-30) outliers start: 13 outliers final: 9 residues processed: 48 average time/residue: 0.0858 time to fit residues: 6.4690 Evaluate side-chains 45 residues out of total 1133 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 35 time to evaluate : 0.325 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 142 PHE Chi-restraints excluded: chain B residue 205 VAL Chi-restraints excluded: chain B residue 232 LEU Chi-restraints excluded: chain B residue 495 VAL Chi-restraints excluded: chain B residue 705 LEU Chi-restraints excluded: chain B residue 717 GLN Chi-restraints excluded: chain B residue 889 LYS Chi-restraints excluded: chain B residue 960 VAL Chi-restraints excluded: chain B residue 998 MET Chi-restraints excluded: chain B residue 1009 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 31 optimal weight: 5.9990 chunk 50 optimal weight: 6.9990 chunk 79 optimal weight: 2.9990 chunk 113 optimal weight: 2.9990 chunk 47 optimal weight: 0.0270 chunk 19 optimal weight: 1.9990 chunk 90 optimal weight: 4.9990 chunk 69 optimal weight: 5.9990 chunk 43 optimal weight: 5.9990 chunk 68 optimal weight: 0.9980 chunk 98 optimal weight: 0.0270 overall best weight: 1.2100 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 415 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3222 r_free = 0.3222 target = 0.051930 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2824 r_free = 0.2824 target = 0.039297 restraints weight = 47772.387| |-----------------------------------------------------------------------------| r_work (start): 0.2822 rms_B_bonded: 4.23 r_work: 0.2659 rms_B_bonded: 4.76 restraints_weight: 0.5000 r_work (final): 0.2659 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8888 moved from start: 0.1480 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 10493 Z= 0.109 Angle : 0.445 8.180 14241 Z= 0.226 Chirality : 0.039 0.157 1590 Planarity : 0.003 0.046 1824 Dihedral : 5.216 57.654 1447 Min Nonbonded Distance : 2.567 Molprobity Statistics. All-atom Clashscore : 5.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.65 % Favored : 98.35 % Rotamer: Outliers : 1.32 % Allowed : 6.62 % Favored : 92.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.35 % Cis-general : 0.08 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.23 (0.25), residues: 1276 helix: 2.45 (0.22), residues: 573 sheet: 1.35 (0.39), residues: 172 loop : 0.53 (0.29), residues: 531 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A4576 TYR 0.008 0.001 TYR B 44 PHE 0.012 0.001 PHE B1047 TRP 0.005 0.001 TRP B 660 HIS 0.003 0.000 HIS B 677 Details of bonding type rmsd covalent geometry : bond 0.00243 (10493) covalent geometry : angle 0.44462 (14241) hydrogen bonds : bond 0.03008 ( 509) hydrogen bonds : angle 4.17171 ( 1431) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2552 Ramachandran restraints generated. 1276 Oldfield, 0 Emsley, 1276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2552 Ramachandran restraints generated. 1276 Oldfield, 0 Emsley, 1276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 52 residues out of total 1133 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 37 time to evaluate : 0.462 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 4767 MET cc_start: 0.9418 (mmt) cc_final: 0.9159 (mmm) REVERT: B 214 LYS cc_start: 0.8270 (pttt) cc_final: 0.8005 (pttt) REVERT: B 594 MET cc_start: 0.8827 (tmm) cc_final: 0.8339 (tmm) REVERT: B 658 LYS cc_start: 0.9458 (tppt) cc_final: 0.9152 (tppt) REVERT: B 717 GLN cc_start: 0.9034 (OUTLIER) cc_final: 0.8655 (tm-30) outliers start: 15 outliers final: 10 residues processed: 49 average time/residue: 0.1172 time to fit residues: 8.4964 Evaluate side-chains 46 residues out of total 1133 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 35 time to evaluate : 0.422 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4804 LEU Chi-restraints excluded: chain B residue 142 PHE Chi-restraints excluded: chain B residue 205 VAL Chi-restraints excluded: chain B residue 495 VAL Chi-restraints excluded: chain B residue 705 LEU Chi-restraints excluded: chain B residue 717 GLN Chi-restraints excluded: chain B residue 872 MET Chi-restraints excluded: chain B residue 889 LYS Chi-restraints excluded: chain B residue 960 VAL Chi-restraints excluded: chain B residue 1009 MET Chi-restraints excluded: chain B residue 1047 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 69 optimal weight: 2.9990 chunk 39 optimal weight: 0.8980 chunk 7 optimal weight: 7.9990 chunk 97 optimal weight: 0.7980 chunk 17 optimal weight: 4.9990 chunk 22 optimal weight: 7.9990 chunk 18 optimal weight: 0.0010 chunk 54 optimal weight: 8.9990 chunk 124 optimal weight: 0.7980 chunk 99 optimal weight: 1.9990 chunk 96 optimal weight: 1.9990 overall best weight: 0.8988 ------------------------------------------------------------------------------- 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 = 0.3231 r_free = 0.3231 target = 0.052221 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2834 r_free = 0.2834 target = 0.039623 restraints weight = 47184.075| |-----------------------------------------------------------------------------| r_work (start): 0.2824 rms_B_bonded: 4.27 r_work: 0.2660 rms_B_bonded: 4.84 restraints_weight: 0.5000 r_work (final): 0.2660 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8862 moved from start: 0.1590 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 10493 Z= 0.091 Angle : 0.449 8.752 14241 Z= 0.225 Chirality : 0.039 0.157 1590 Planarity : 0.003 0.047 1824 Dihedral : 5.161 57.426 1447 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 6.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.57 % Favored : 98.43 % Rotamer: Outliers : 1.24 % Allowed : 6.71 % Favored : 92.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.35 % Cis-general : 0.08 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.24 (0.25), residues: 1276 helix: 2.44 (0.22), residues: 573 sheet: 1.39 (0.39), residues: 172 loop : 0.53 (0.29), residues: 531 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A4576 TYR 0.008 0.001 TYR B 44 PHE 0.015 0.001 PHE B1047 TRP 0.006 0.001 TRP B 660 HIS 0.002 0.000 HIS B1049 Details of bonding type rmsd covalent geometry : bond 0.00200 (10493) covalent geometry : angle 0.44943 (14241) hydrogen bonds : bond 0.02878 ( 509) hydrogen bonds : angle 4.11994 ( 1431) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2552 Ramachandran restraints generated. 1276 Oldfield, 0 Emsley, 1276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2552 Ramachandran restraints generated. 1276 Oldfield, 0 Emsley, 1276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 50 residues out of total 1133 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 36 time to evaluate : 0.407 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 4767 MET cc_start: 0.9452 (mmt) cc_final: 0.9202 (mmm) REVERT: B 475 MET cc_start: 0.9078 (mmm) cc_final: 0.8824 (tpt) REVERT: B 594 MET cc_start: 0.8890 (tmm) cc_final: 0.8230 (tmm) REVERT: B 658 LYS cc_start: 0.9464 (tppt) cc_final: 0.9151 (tppt) outliers start: 14 outliers final: 9 residues processed: 47 average time/residue: 0.0975 time to fit residues: 6.9247 Evaluate side-chains 44 residues out of total 1133 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 35 time to evaluate : 0.411 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4804 LEU Chi-restraints excluded: chain B residue 142 PHE Chi-restraints excluded: chain B residue 205 VAL Chi-restraints excluded: chain B residue 495 VAL Chi-restraints excluded: chain B residue 699 CYS Chi-restraints excluded: chain B residue 705 LEU Chi-restraints excluded: chain B residue 889 LYS Chi-restraints excluded: chain B residue 960 VAL Chi-restraints excluded: chain B residue 1009 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 82 optimal weight: 5.9990 chunk 56 optimal weight: 3.9990 chunk 115 optimal weight: 4.9990 chunk 112 optimal weight: 0.6980 chunk 111 optimal weight: 1.9990 chunk 68 optimal weight: 0.6980 chunk 37 optimal weight: 5.9990 chunk 44 optimal weight: 0.4980 chunk 29 optimal weight: 0.6980 chunk 101 optimal weight: 3.9990 chunk 35 optimal weight: 0.3980 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 = 0.3231 r_free = 0.3231 target = 0.051882 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2838 r_free = 0.2838 target = 0.039231 restraints weight = 47680.181| |-----------------------------------------------------------------------------| r_work (start): 0.2836 rms_B_bonded: 4.24 r_work: 0.2675 rms_B_bonded: 4.76 restraints_weight: 0.5000 r_work (final): 0.2675 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8873 moved from start: 0.1679 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 10493 Z= 0.081 Angle : 0.445 9.246 14241 Z= 0.223 Chirality : 0.039 0.155 1590 Planarity : 0.003 0.049 1824 Dihedral : 5.147 57.225 1447 Min Nonbonded Distance : 2.575 Molprobity Statistics. All-atom Clashscore : 6.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.65 % Favored : 98.35 % Rotamer: Outliers : 0.97 % Allowed : 6.80 % Favored : 92.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.35 % Cis-general : 0.08 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.25 (0.25), residues: 1276 helix: 2.51 (0.22), residues: 566 sheet: 1.44 (0.39), residues: 172 loop : 0.48 (0.29), residues: 538 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A4576 TYR 0.007 0.001 TYR B 44 PHE 0.011 0.001 PHE B1047 TRP 0.005 0.001 TRP B 660 HIS 0.011 0.000 HIS B1001 Details of bonding type rmsd covalent geometry : bond 0.00175 (10493) covalent geometry : angle 0.44497 (14241) hydrogen bonds : bond 0.02793 ( 509) hydrogen bonds : angle 4.07687 ( 1431) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2552 Ramachandran restraints generated. 1276 Oldfield, 0 Emsley, 1276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2552 Ramachandran restraints generated. 1276 Oldfield, 0 Emsley, 1276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 49 residues out of total 1133 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 38 time to evaluate : 0.506 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 4767 MET cc_start: 0.9425 (mmt) cc_final: 0.9170 (mmm) REVERT: B 594 MET cc_start: 0.8852 (tmm) cc_final: 0.8166 (tmm) REVERT: B 658 LYS cc_start: 0.9456 (tppt) cc_final: 0.9143 (tppt) outliers start: 11 outliers final: 8 residues processed: 48 average time/residue: 0.0998 time to fit residues: 7.4639 Evaluate side-chains 43 residues out of total 1133 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 35 time to evaluate : 0.516 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4804 LEU Chi-restraints excluded: chain B residue 142 PHE Chi-restraints excluded: chain B residue 205 VAL Chi-restraints excluded: chain B residue 495 VAL Chi-restraints excluded: chain B residue 699 CYS Chi-restraints excluded: chain B residue 705 LEU Chi-restraints excluded: chain B residue 889 LYS Chi-restraints excluded: chain B residue 960 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 60 optimal weight: 3.9990 chunk 64 optimal weight: 1.9990 chunk 40 optimal weight: 4.9990 chunk 56 optimal weight: 0.8980 chunk 122 optimal weight: 0.6980 chunk 55 optimal weight: 0.9990 chunk 10 optimal weight: 7.9990 chunk 37 optimal weight: 5.9990 chunk 35 optimal weight: 0.6980 chunk 59 optimal weight: 0.8980 chunk 108 optimal weight: 7.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- 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 = 0.3230 r_free = 0.3230 target = 0.052042 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2839 r_free = 0.2839 target = 0.039677 restraints weight = 47075.264| |-----------------------------------------------------------------------------| r_work (start): 0.2826 rms_B_bonded: 4.21 r_work: 0.2663 rms_B_bonded: 4.77 restraints_weight: 0.5000 r_work (final): 0.2663 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8861 moved from start: 0.1755 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 10493 Z= 0.090 Angle : 0.454 9.491 14241 Z= 0.227 Chirality : 0.039 0.154 1590 Planarity : 0.003 0.049 1824 Dihedral : 5.119 57.151 1447 Min Nonbonded Distance : 2.558 Molprobity Statistics. All-atom Clashscore : 5.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.72 % Favored : 98.28 % Rotamer: Outliers : 0.79 % Allowed : 7.50 % Favored : 91.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.35 % Cis-general : 0.08 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.26 (0.25), residues: 1276 helix: 2.53 (0.22), residues: 567 sheet: 1.32 (0.39), residues: 174 loop : 0.50 (0.29), residues: 535 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A4576 TYR 0.008 0.001 TYR B 44 PHE 0.012 0.001 PHE B 656 TRP 0.007 0.001 TRP B 660 HIS 0.007 0.000 HIS B1001 Details of bonding type rmsd covalent geometry : bond 0.00198 (10493) covalent geometry : angle 0.45389 (14241) hydrogen bonds : bond 0.02789 ( 509) hydrogen bonds : angle 4.06956 ( 1431) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2552 Ramachandran restraints generated. 1276 Oldfield, 0 Emsley, 1276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2552 Ramachandran restraints generated. 1276 Oldfield, 0 Emsley, 1276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 45 residues out of total 1133 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 36 time to evaluate : 0.517 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 4767 MET cc_start: 0.9444 (mmt) cc_final: 0.9190 (mmm) REVERT: B 475 MET cc_start: 0.8950 (mmm) cc_final: 0.8720 (tpt) REVERT: B 594 MET cc_start: 0.8918 (tmm) cc_final: 0.8157 (tmm) REVERT: B 658 LYS cc_start: 0.9461 (tppt) cc_final: 0.9149 (tppt) outliers start: 9 outliers final: 8 residues processed: 45 average time/residue: 0.1014 time to fit residues: 7.0506 Evaluate side-chains 43 residues out of total 1133 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 35 time to evaluate : 0.438 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4804 LEU Chi-restraints excluded: chain B residue 142 PHE Chi-restraints excluded: chain B residue 205 VAL Chi-restraints excluded: chain B residue 495 VAL Chi-restraints excluded: chain B residue 699 CYS Chi-restraints excluded: chain B residue 705 LEU Chi-restraints excluded: chain B residue 889 LYS Chi-restraints excluded: chain B residue 960 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 119 optimal weight: 0.8980 chunk 38 optimal weight: 4.9990 chunk 59 optimal weight: 0.8980 chunk 116 optimal weight: 0.6980 chunk 89 optimal weight: 0.7980 chunk 99 optimal weight: 4.9990 chunk 68 optimal weight: 0.9990 chunk 104 optimal weight: 0.0060 chunk 67 optimal weight: 0.9980 chunk 24 optimal weight: 6.9990 chunk 98 optimal weight: 5.9990 overall best weight: 0.6596 ------------------------------------------------------------------------------- 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 = 0.3232 r_free = 0.3232 target = 0.052173 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2839 r_free = 0.2839 target = 0.039715 restraints weight = 46751.708| |-----------------------------------------------------------------------------| r_work (start): 0.2834 rms_B_bonded: 4.23 r_work: 0.2673 rms_B_bonded: 4.79 restraints_weight: 0.5000 r_work (final): 0.2673 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8858 moved from start: 0.1855 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 10493 Z= 0.084 Angle : 0.464 9.506 14241 Z= 0.231 Chirality : 0.039 0.153 1590 Planarity : 0.003 0.048 1824 Dihedral : 5.076 57.284 1447 Min Nonbonded Distance : 2.567 Molprobity Statistics. All-atom Clashscore : 5.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.57 % Favored : 98.43 % Rotamer: Outliers : 0.71 % Allowed : 7.59 % Favored : 91.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.35 % Cis-general : 0.08 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.22 (0.25), residues: 1276 helix: 2.52 (0.22), residues: 569 sheet: 1.25 (0.39), residues: 177 loop : 0.47 (0.29), residues: 530 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A4576 TYR 0.007 0.001 TYR B 44 PHE 0.014 0.001 PHE B1047 TRP 0.005 0.001 TRP B 378 HIS 0.007 0.000 HIS B1001 Details of bonding type rmsd covalent geometry : bond 0.00186 (10493) covalent geometry : angle 0.46412 (14241) hydrogen bonds : bond 0.02724 ( 509) hydrogen bonds : angle 4.03337 ( 1431) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2552 Ramachandran restraints generated. 1276 Oldfield, 0 Emsley, 1276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2552 Ramachandran restraints generated. 1276 Oldfield, 0 Emsley, 1276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 48 residues out of total 1133 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 40 time to evaluate : 0.431 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 4767 MET cc_start: 0.9451 (mmt) cc_final: 0.9132 (mmm) REVERT: B 594 MET cc_start: 0.8958 (tmm) cc_final: 0.8079 (tmm) REVERT: B 658 LYS cc_start: 0.9466 (tppt) cc_final: 0.9155 (tppt) outliers start: 8 outliers final: 8 residues processed: 48 average time/residue: 0.1113 time to fit residues: 7.9595 Evaluate side-chains 43 residues out of total 1133 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 35 time to evaluate : 0.459 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4804 LEU Chi-restraints excluded: chain B residue 142 PHE Chi-restraints excluded: chain B residue 205 VAL Chi-restraints excluded: chain B residue 495 VAL Chi-restraints excluded: chain B residue 699 CYS Chi-restraints excluded: chain B residue 705 LEU Chi-restraints excluded: chain B residue 889 LYS Chi-restraints excluded: chain B residue 960 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 36 optimal weight: 0.9990 chunk 43 optimal weight: 4.9990 chunk 11 optimal weight: 0.0570 chunk 115 optimal weight: 5.9990 chunk 47 optimal weight: 5.9990 chunk 116 optimal weight: 1.9990 chunk 55 optimal weight: 0.6980 chunk 105 optimal weight: 6.9990 chunk 107 optimal weight: 2.9990 chunk 67 optimal weight: 0.9980 chunk 60 optimal weight: 4.9990 overall best weight: 0.9502 ------------------------------------------------------------------------------- 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 = 0.3195 r_free = 0.3195 target = 0.051124 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2793 r_free = 0.2793 target = 0.038390 restraints weight = 47383.222| |-----------------------------------------------------------------------------| r_work (start): 0.2820 rms_B_bonded: 4.28 r_work: 0.2657 rms_B_bonded: 4.83 restraints_weight: 0.5000 r_work (final): 0.2657 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8872 moved from start: 0.1925 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 10493 Z= 0.099 Angle : 0.486 9.898 14241 Z= 0.242 Chirality : 0.039 0.153 1590 Planarity : 0.003 0.049 1824 Dihedral : 5.078 57.040 1447 Min Nonbonded Distance : 2.585 Molprobity Statistics. All-atom Clashscore : 5.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.72 % Favored : 98.28 % Rotamer: Outliers : 0.88 % Allowed : 7.86 % Favored : 91.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.35 % Cis-general : 0.08 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.22 (0.25), residues: 1276 helix: 2.52 (0.22), residues: 569 sheet: 1.24 (0.39), residues: 177 loop : 0.47 (0.29), residues: 530 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A4576 TYR 0.007 0.001 TYR B 44 PHE 0.013 0.001 PHE B 656 TRP 0.006 0.001 TRP B 660 HIS 0.009 0.001 HIS B1001 Details of bonding type rmsd covalent geometry : bond 0.00222 (10493) covalent geometry : angle 0.48585 (14241) hydrogen bonds : bond 0.02797 ( 509) hydrogen bonds : angle 3.99986 ( 1431) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1963.19 seconds wall clock time: 34 minutes 35.61 seconds (2075.61 seconds total)