Starting phenix.real_space_refine on Sat Jan 18 13:02:52 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ygg_39249/01_2025/8ygg_39249.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ygg_39249/01_2025/8ygg_39249.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.98 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8ygg_39249/01_2025/8ygg_39249.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ygg_39249/01_2025/8ygg_39249.map" model { file = "/net/cci-nas-00/data/ceres_data/8ygg_39249/01_2025/8ygg_39249.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ygg_39249/01_2025/8ygg_39249.cif" } resolution = 2.98 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.041 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 52 5.16 5 C 7774 2.51 5 N 2082 2.21 5 O 2188 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 32 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/chem_data/mon_lib" Total number of atoms: 12096 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 6048 Number of conformers: 1 Conformer: "" Number of residues, atoms: 745, 6048 Classifications: {'peptide': 745} Link IDs: {'PTRANS': 30, 'TRANS': 714} Chain breaks: 2 Chain: "B" Number of atoms: 6048 Number of conformers: 1 Conformer: "" Number of residues, atoms: 745, 6048 Classifications: {'peptide': 745} Link IDs: {'PTRANS': 30, 'TRANS': 714} Chain breaks: 2 Time building chain proxies: 7.20, per 1000 atoms: 0.60 Number of scatterers: 12096 At special positions: 0 Unit cell: (113.4, 108, 114.48, 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 52 16.00 O 2188 8.00 N 2082 7.00 C 7774 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: 2.79 Conformation dependent library (CDL) restraints added in 1.5 seconds 2956 Ramachandran restraints generated. 1478 Oldfield, 0 Emsley, 1478 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2800 Finding SS restraints... Secondary structure from input PDB file: 70 helices and 16 sheets defined 53.4% alpha, 10.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.43 Creating SS restraints... Processing helix chain 'A' and resid 428 through 431 Processing helix chain 'A' and resid 439 through 451 Processing helix chain 'A' and resid 452 through 456 Processing helix chain 'A' and resid 503 through 513 Processing helix chain 'A' and resid 522 through 528 Processing helix chain 'A' and resid 542 through 547 Processing helix chain 'A' and resid 547 through 560 removed outlier: 3.535A pdb=" N LEU A 551 " --> pdb=" O LYS A 547 " (cutoff:3.500A) Processing helix chain 'A' and resid 560 through 566 removed outlier: 3.651A pdb=" N ILE A 564 " --> pdb=" O TRP A 560 " (cutoff:3.500A) Processing helix chain 'A' and resid 592 through 603 Processing helix chain 'A' and resid 616 through 620 Processing helix chain 'A' and resid 621 through 631 removed outlier: 3.716A pdb=" N HIS A 631 " --> pdb=" O SER A 627 " (cutoff:3.500A) Processing helix chain 'A' and resid 631 through 635 removed outlier: 3.643A pdb=" N MET A 635 " --> pdb=" O HIS A 631 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 631 through 635' Processing helix chain 'A' and resid 642 through 653 removed outlier: 4.123A pdb=" N GLU A 647 " --> pdb=" O ASP A 643 " (cutoff:3.500A) Processing helix chain 'A' and resid 672 through 683 Processing helix chain 'A' and resid 687 through 694 Processing helix chain 'A' and resid 694 through 705 Processing helix chain 'A' and resid 715 through 729 Processing helix chain 'A' and resid 738 through 749 Processing helix chain 'A' and resid 754 through 767 Processing helix chain 'A' and resid 788 through 793 removed outlier: 3.651A pdb=" N GLY A 791 " --> pdb=" O ARG A 788 " (cutoff:3.500A) Processing helix chain 'A' and resid 806 through 814 removed outlier: 4.649A pdb=" N THR A 812 " --> pdb=" O GLU A 808 " (cutoff:3.500A) Processing helix chain 'A' and resid 815 through 819 Processing helix chain 'A' and resid 864 through 878 removed outlier: 4.449A pdb=" N LYS A 878 " --> pdb=" O ALA A 874 " (cutoff:3.500A) Processing helix chain 'A' and resid 882 through 893 Processing helix chain 'A' and resid 942 through 952 Processing helix chain 'A' and resid 953 through 958 Processing helix chain 'A' and resid 982 through 990 Processing helix chain 'A' and resid 997 through 1004 Processing helix chain 'A' and resid 1027 through 1070 removed outlier: 3.704A pdb=" N ILE A1031 " --> pdb=" O SER A1027 " (cutoff:3.500A) Proline residue: A1037 - end of helix Processing helix chain 'A' and resid 1081 through 1092 Processing helix chain 'A' and resid 1098 through 1104 removed outlier: 3.520A pdb=" N SER A1104 " --> pdb=" O SER A1100 " (cutoff:3.500A) Processing helix chain 'A' and resid 1109 through 1117 Processing helix chain 'A' and resid 1122 through 1127 Processing helix chain 'A' and resid 1129 through 1133 Processing helix chain 'A' and resid 1134 through 1159 Processing helix chain 'A' and resid 1166 through 1187 Processing helix chain 'B' and resid 439 through 451 Processing helix chain 'B' and resid 452 through 456 Processing helix chain 'B' and resid 503 through 513 Processing helix chain 'B' and resid 522 through 528 removed outlier: 3.561A pdb=" N ARG B 526 " --> pdb=" O THR B 522 " (cutoff:3.500A) Processing helix chain 'B' and resid 543 through 560 removed outlier: 3.788A pdb=" N LEU B 549 " --> pdb=" O CYS B 545 " (cutoff:3.500A) Processing helix chain 'B' and resid 560 through 566 removed outlier: 3.876A pdb=" N ILE B 564 " --> pdb=" O TRP B 560 " (cutoff:3.500A) Processing helix chain 'B' and resid 592 through 603 Processing helix chain 'B' and resid 616 through 620 removed outlier: 3.713A pdb=" N HIS B 620 " --> pdb=" O LEU B 617 " (cutoff:3.500A) Processing helix chain 'B' and resid 621 through 631 removed outlier: 3.716A pdb=" N HIS B 631 " --> pdb=" O SER B 627 " (cutoff:3.500A) Processing helix chain 'B' and resid 632 through 634 No H-bonds generated for 'chain 'B' and resid 632 through 634' Processing helix chain 'B' and resid 642 through 654 removed outlier: 4.407A pdb=" N GLU B 647 " --> pdb=" O ASP B 643 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N HIS B 650 " --> pdb=" O LYS B 646 " (cutoff:3.500A) Processing helix chain 'B' and resid 659 through 664 Processing helix chain 'B' and resid 672 through 683 removed outlier: 3.511A pdb=" N VAL B 682 " --> pdb=" O SER B 678 " (cutoff:3.500A) Processing helix chain 'B' and resid 687 through 707 removed outlier: 3.749A pdb=" N THR B 695 " --> pdb=" O LEU B 691 " (cutoff:3.500A) removed outlier: 4.442A pdb=" N LYS B 696 " --> pdb=" O GLN B 692 " (cutoff:3.500A) Processing helix chain 'B' and resid 715 through 730 Processing helix chain 'B' and resid 738 through 750 Processing helix chain 'B' and resid 754 through 767 Processing helix chain 'B' and resid 788 through 793 removed outlier: 3.643A pdb=" N GLY B 792 " --> pdb=" O HIS B 789 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N LYS B 793 " --> pdb=" O LEU B 790 " (cutoff:3.500A) Processing helix chain 'B' and resid 806 through 814 Processing helix chain 'B' and resid 815 through 822 removed outlier: 4.035A pdb=" N TRP B 820 " --> pdb=" O GLU B 817 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N LEU B 822 " --> pdb=" O SER B 819 " (cutoff:3.500A) Processing helix chain 'B' and resid 864 through 878 removed outlier: 4.489A pdb=" N LYS B 878 " --> pdb=" O ALA B 874 " (cutoff:3.500A) Processing helix chain 'B' and resid 882 through 891 Processing helix chain 'B' and resid 942 through 953 removed outlier: 3.602A pdb=" N SER B 953 " --> pdb=" O SER B 949 " (cutoff:3.500A) Processing helix chain 'B' and resid 955 through 958 Processing helix chain 'B' and resid 981 through 990 removed outlier: 4.194A pdb=" N ARG B 985 " --> pdb=" O ASN B 981 " (cutoff:3.500A) Processing helix chain 'B' and resid 997 through 1003 Processing helix chain 'B' and resid 1027 through 1070 removed outlier: 3.553A pdb=" N ILE B1031 " --> pdb=" O SER B1027 " (cutoff:3.500A) Proline residue: B1037 - end of helix removed outlier: 3.605A pdb=" N GLN B1044 " --> pdb=" O ARG B1040 " (cutoff:3.500A) Processing helix chain 'B' and resid 1081 through 1092 Processing helix chain 'B' and resid 1098 through 1104 Processing helix chain 'B' and resid 1109 through 1117 Processing helix chain 'B' and resid 1122 through 1127 Processing helix chain 'B' and resid 1129 through 1133 Processing helix chain 'B' and resid 1134 through 1159 Processing helix chain 'B' and resid 1166 through 1187 Processing sheet with id=AA1, first strand: chain 'A' and resid 465 through 469 removed outlier: 5.997A pdb=" N LEU A 434 " --> pdb=" O VAL A 535 " (cutoff:3.500A) removed outlier: 6.691A pdb=" N CYS A 537 " --> pdb=" O LEU A 434 " (cutoff:3.500A) removed outlier: 6.005A pdb=" N ALA A 436 " --> pdb=" O CYS A 537 " (cutoff:3.500A) removed outlier: 6.011A pdb=" N ILE A 534 " --> pdb=" O LYS A 570 " (cutoff:3.500A) removed outlier: 7.156A pdb=" N LEU A 572 " --> pdb=" O ILE A 534 " (cutoff:3.500A) removed outlier: 6.840A pdb=" N ALA A 536 " --> pdb=" O LEU A 572 " (cutoff:3.500A) removed outlier: 5.626A pdb=" N VAL A 569 " --> pdb=" O PHE A 639 " (cutoff:3.500A) removed outlier: 8.197A pdb=" N ILE A 685 " --> pdb=" O VAL A 636 " (cutoff:3.500A) removed outlier: 6.390A pdb=" N THR A 638 " --> pdb=" O ILE A 685 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 588 through 590 Processing sheet with id=AA3, first strand: chain 'A' and resid 736 through 737 Processing sheet with id=AA4, first strand: chain 'A' and resid 824 through 827 removed outlier: 4.517A pdb=" N VAL A 825 " --> pdb=" O ALA A 832 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 849 through 852 removed outlier: 3.619A pdb=" N TYR A 858 " --> pdb=" O ASN A 851 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 909 through 913 Processing sheet with id=AA7, first strand: chain 'A' and resid 923 through 926 Processing sheet with id=AA8, first strand: chain 'A' and resid 1014 through 1016 Processing sheet with id=AA9, first strand: chain 'B' and resid 465 through 469 removed outlier: 6.086A pdb=" N LEU B 434 " --> pdb=" O VAL B 535 " (cutoff:3.500A) removed outlier: 6.780A pdb=" N CYS B 537 " --> pdb=" O LEU B 434 " (cutoff:3.500A) removed outlier: 6.218A pdb=" N ALA B 436 " --> pdb=" O CYS B 537 " (cutoff:3.500A) removed outlier: 6.046A pdb=" N ILE B 534 " --> pdb=" O LYS B 570 " (cutoff:3.500A) removed outlier: 7.440A pdb=" N LEU B 572 " --> pdb=" O ILE B 534 " (cutoff:3.500A) removed outlier: 7.085A pdb=" N ALA B 536 " --> pdb=" O LEU B 572 " (cutoff:3.500A) removed outlier: 5.707A pdb=" N VAL B 569 " --> pdb=" O PHE B 639 " (cutoff:3.500A) removed outlier: 7.811A pdb=" N ILE B 685 " --> pdb=" O VAL B 636 " (cutoff:3.500A) removed outlier: 6.142A pdb=" N THR B 638 " --> pdb=" O ILE B 685 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 588 through 590 Processing sheet with id=AB2, first strand: chain 'B' and resid 736 through 737 Processing sheet with id=AB3, first strand: chain 'B' and resid 824 through 827 removed outlier: 4.855A pdb=" N VAL B 825 " --> pdb=" O ALA B 832 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 849 through 852 Processing sheet with id=AB5, first strand: chain 'B' and resid 909 through 913 Processing sheet with id=AB6, first strand: chain 'B' and resid 923 through 926 Processing sheet with id=AB7, first strand: chain 'B' and resid 1014 through 1016 593 hydrogen bonds defined for protein. 1656 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: 4.16 Time building geometry restraints manager: 3.24 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2932 1.33 - 1.45: 2648 1.45 - 1.58: 6722 1.58 - 1.70: 0 1.70 - 1.82: 82 Bond restraints: 12384 Sorted by residual: bond pdb=" CA ASP B 543 " pdb=" C ASP B 543 " ideal model delta sigma weight residual 1.524 1.485 0.039 1.24e-02 6.50e+03 9.92e+00 bond pdb=" C PHE B1164 " pdb=" N PRO B1165 " ideal model delta sigma weight residual 1.332 1.372 -0.040 1.30e-02 5.92e+03 9.58e+00 bond pdb=" C PHE A1164 " pdb=" N PRO A1165 " ideal model delta sigma weight residual 1.332 1.370 -0.038 1.30e-02 5.92e+03 8.58e+00 bond pdb=" C CYS B 545 " pdb=" O CYS B 545 " ideal model delta sigma weight residual 1.237 1.208 0.029 1.17e-02 7.31e+03 5.96e+00 bond pdb=" CA PHE B1164 " pdb=" C PHE B1164 " ideal model delta sigma weight residual 1.524 1.550 -0.026 1.26e-02 6.30e+03 4.35e+00 ... (remaining 12379 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.65: 16559 2.65 - 5.29: 130 5.29 - 7.94: 22 7.94 - 10.58: 9 10.58 - 13.23: 6 Bond angle restraints: 16726 Sorted by residual: angle pdb=" N SER B1162 " pdb=" CA SER B1162 " pdb=" C SER B1162 " ideal model delta sigma weight residual 112.75 124.18 -11.43 1.36e+00 5.41e-01 7.07e+01 angle pdb=" N GLY A 544 " pdb=" CA GLY A 544 " pdb=" C GLY A 544 " ideal model delta sigma weight residual 111.54 100.64 10.90 1.36e+00 5.41e-01 6.42e+01 angle pdb=" N SER A1162 " pdb=" CA SER A1162 " pdb=" C SER A1162 " ideal model delta sigma weight residual 112.75 123.57 -10.82 1.36e+00 5.41e-01 6.33e+01 angle pdb=" N PHE A1164 " pdb=" CA PHE A1164 " pdb=" C PHE A1164 " ideal model delta sigma weight residual 108.13 101.81 6.32 9.00e-01 1.23e+00 4.93e+01 angle pdb=" CA GLY A 544 " pdb=" C GLY A 544 " pdb=" O GLY A 544 " ideal model delta sigma weight residual 121.58 115.34 6.24 9.00e-01 1.23e+00 4.80e+01 ... (remaining 16721 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.76: 6601 17.76 - 35.51: 627 35.51 - 53.27: 159 53.27 - 71.03: 29 71.03 - 88.79: 18 Dihedral angle restraints: 7434 sinusoidal: 3066 harmonic: 4368 Sorted by residual: dihedral pdb=" N CYS A 545 " pdb=" C CYS A 545 " pdb=" CA CYS A 545 " pdb=" CB CYS A 545 " ideal model delta harmonic sigma weight residual 122.80 134.52 -11.72 0 2.50e+00 1.60e-01 2.20e+01 dihedral pdb=" C CYS A 545 " pdb=" N CYS A 545 " pdb=" CA CYS A 545 " pdb=" CB CYS A 545 " ideal model delta harmonic sigma weight residual -122.60 -132.02 9.42 0 2.50e+00 1.60e-01 1.42e+01 dihedral pdb=" C SER B1162 " pdb=" N SER B1162 " pdb=" CA SER B1162 " pdb=" CB SER B1162 " ideal model delta harmonic sigma weight residual -122.60 -131.96 9.36 0 2.50e+00 1.60e-01 1.40e+01 ... (remaining 7431 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.104: 1769 0.104 - 0.207: 34 0.207 - 0.311: 0 0.311 - 0.414: 1 0.414 - 0.518: 2 Chirality restraints: 1806 Sorted by residual: chirality pdb=" CA SER B1162 " pdb=" N SER B1162 " pdb=" C SER B1162 " pdb=" CB SER B1162 " both_signs ideal model delta sigma weight residual False 2.51 1.99 0.52 2.00e-01 2.50e+01 6.70e+00 chirality pdb=" CA SER A1162 " pdb=" N SER A1162 " pdb=" C SER A1162 " pdb=" CB SER A1162 " both_signs ideal model delta sigma weight residual False 2.51 2.07 0.44 2.00e-01 2.50e+01 4.92e+00 chirality pdb=" CA CYS A 545 " pdb=" N CYS A 545 " pdb=" C CYS A 545 " pdb=" CB CYS A 545 " both_signs ideal model delta sigma weight residual False 2.51 2.12 0.39 2.00e-01 2.50e+01 3.77e+00 ... (remaining 1803 not shown) Planarity restraints: 2132 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LEU B 542 " 0.014 2.00e-02 2.50e+03 2.82e-02 7.95e+00 pdb=" C LEU B 542 " -0.049 2.00e-02 2.50e+03 pdb=" O LEU B 542 " 0.018 2.00e-02 2.50e+03 pdb=" N ASP B 543 " 0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASP B 543 " -0.014 2.00e-02 2.50e+03 2.79e-02 7.76e+00 pdb=" C ASP B 543 " 0.048 2.00e-02 2.50e+03 pdb=" O ASP B 543 " -0.018 2.00e-02 2.50e+03 pdb=" N GLY B 544 " -0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C SER B1162 " -0.028 5.00e-02 4.00e+02 4.29e-02 2.94e+00 pdb=" N PRO B1163 " 0.074 5.00e-02 4.00e+02 pdb=" CA PRO B1163 " -0.020 5.00e-02 4.00e+02 pdb=" CD PRO B1163 " -0.026 5.00e-02 4.00e+02 ... (remaining 2129 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.77: 2210 2.77 - 3.30: 11952 3.30 - 3.83: 21329 3.83 - 4.37: 25240 4.37 - 4.90: 42237 Nonbonded interactions: 102968 Sorted by model distance: nonbonded pdb=" N GLU B 593 " pdb=" OE1 GLU B 593 " model vdw 2.233 3.120 nonbonded pdb=" OH TYR B1043 " pdb=" OE1 GLU B1173 " model vdw 2.240 3.040 nonbonded pdb=" O GLN A1099 " pdb=" OG1 THR A1103 " model vdw 2.244 3.040 nonbonded pdb=" O SER A1100 " pdb=" OG SER A1104 " model vdw 2.246 3.040 nonbonded pdb=" OD2 ASP B 818 " pdb=" NH2 ARG B1039 " model vdw 2.262 3.120 ... (remaining 102963 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: 0.06 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.840 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.460 Check model and map are aligned: 0.090 Set scattering table: 0.100 Process input model: 28.220 Find NCS groups from input model: 0.380 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:13.220 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 43.380 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8768 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 : 0.003 0.042 12384 Z= 0.184 Angle : 0.650 13.227 16726 Z= 0.371 Chirality : 0.043 0.518 1806 Planarity : 0.003 0.045 2132 Dihedral : 15.453 88.785 4634 Min Nonbonded Distance : 2.233 Molprobity Statistics. All-atom Clashscore : 9.55 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.71 % Favored : 97.23 % Rotamer: Outliers : 2.07 % Allowed : 16.67 % Favored : 81.26 % Cbeta Deviations : 0.07 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.81 (0.23), residues: 1478 helix: 1.73 (0.21), residues: 702 sheet: -1.29 (0.35), residues: 224 loop : -0.09 (0.27), residues: 552 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 856 HIS 0.004 0.000 HIS B1192 PHE 0.016 0.001 PHE B1164 TYR 0.018 0.001 TYR B1033 ARG 0.008 0.000 ARG A 929 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2956 Ramachandran restraints generated. 1478 Oldfield, 0 Emsley, 1478 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2956 Ramachandran restraints generated. 1478 Oldfield, 0 Emsley, 1478 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 1302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 61 time to evaluate : 1.465 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 547 LYS cc_start: 0.8919 (OUTLIER) cc_final: 0.7593 (tttt) REVERT: A 701 ASP cc_start: 0.9182 (t70) cc_final: 0.8891 (OUTLIER) REVERT: B 957 MET cc_start: 0.9389 (mmt) cc_final: 0.8843 (mpt) outliers start: 27 outliers final: 20 residues processed: 86 average time/residue: 1.2582 time to fit residues: 118.8348 Evaluate side-chains 81 residues out of total 1302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 61 time to evaluate : 1.443 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 416 ASP Chi-restraints excluded: chain A residue 542 LEU Chi-restraints excluded: chain A residue 545 CYS Chi-restraints excluded: chain A residue 547 LYS Chi-restraints excluded: chain A residue 588 VAL Chi-restraints excluded: chain A residue 636 VAL Chi-restraints excluded: chain A residue 669 VAL Chi-restraints excluded: chain A residue 895 THR Chi-restraints excluded: chain A residue 925 VAL Chi-restraints excluded: chain B residue 416 ASP Chi-restraints excluded: chain B residue 443 LEU Chi-restraints excluded: chain B residue 534 ILE Chi-restraints excluded: chain B residue 569 VAL Chi-restraints excluded: chain B residue 669 VAL Chi-restraints excluded: chain B residue 816 THR Chi-restraints excluded: chain B residue 978 LEU Chi-restraints excluded: chain B residue 1022 ILE Chi-restraints excluded: chain B residue 1061 GLU Chi-restraints excluded: chain B residue 1162 SER Chi-restraints excluded: chain B residue 1182 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 124 optimal weight: 0.7980 chunk 112 optimal weight: 6.9990 chunk 62 optimal weight: 6.9990 chunk 38 optimal weight: 4.9990 chunk 75 optimal weight: 9.9990 chunk 59 optimal weight: 0.8980 chunk 116 optimal weight: 2.9990 chunk 44 optimal weight: 5.9990 chunk 70 optimal weight: 0.1980 chunk 86 optimal weight: 0.8980 chunk 134 optimal weight: 0.8980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 623 HIS A 690 HIS A 851 ASN B 690 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3129 r_free = 0.3129 target = 0.055035 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2750 r_free = 0.2750 target = 0.041889 restraints weight = 43979.009| |-----------------------------------------------------------------------------| r_work (start): 0.2735 rms_B_bonded: 3.53 r_work: 0.2588 rms_B_bonded: 3.97 restraints_weight: 0.5000 r_work (final): 0.2588 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8782 moved from start: 0.0901 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 12384 Z= 0.159 Angle : 0.494 8.818 16726 Z= 0.260 Chirality : 0.039 0.147 1806 Planarity : 0.003 0.030 2132 Dihedral : 5.032 55.051 1687 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 6.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 2.61 % Allowed : 15.28 % Favored : 82.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.85 (0.23), residues: 1478 helix: 1.71 (0.20), residues: 708 sheet: -1.21 (0.36), residues: 222 loop : -0.06 (0.28), residues: 548 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B1189 HIS 0.003 0.000 HIS A 650 PHE 0.011 0.001 PHE A1107 TYR 0.014 0.001 TYR B1079 ARG 0.006 0.000 ARG B 662 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2956 Ramachandran restraints generated. 1478 Oldfield, 0 Emsley, 1478 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2956 Ramachandran restraints generated. 1478 Oldfield, 0 Emsley, 1478 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 1302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 71 time to evaluate : 1.312 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 701 ASP cc_start: 0.9165 (t70) cc_final: 0.8878 (OUTLIER) REVERT: A 983 LEU cc_start: 0.9500 (OUTLIER) cc_final: 0.9296 (mm) REVERT: A 987 MET cc_start: 0.9662 (mmm) cc_final: 0.9421 (mmm) REVERT: B 1048 MET cc_start: 0.9261 (mpt) cc_final: 0.9058 (mpp) REVERT: B 1147 LYS cc_start: 0.9547 (tppt) cc_final: 0.9344 (mmmm) outliers start: 34 outliers final: 16 residues processed: 99 average time/residue: 1.2734 time to fit residues: 137.8245 Evaluate side-chains 75 residues out of total 1302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 59 time to evaluate : 1.518 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 579 VAL Chi-restraints excluded: chain A residue 588 VAL Chi-restraints excluded: chain A residue 636 VAL Chi-restraints excluded: chain A residue 669 VAL Chi-restraints excluded: chain A residue 895 THR Chi-restraints excluded: chain A residue 925 VAL Chi-restraints excluded: chain A residue 931 MET Chi-restraints excluded: chain A residue 983 LEU Chi-restraints excluded: chain A residue 1078 HIS Chi-restraints excluded: chain B residue 443 LEU Chi-restraints excluded: chain B residue 534 ILE Chi-restraints excluded: chain B residue 542 LEU Chi-restraints excluded: chain B residue 669 VAL Chi-restraints excluded: chain B residue 816 THR Chi-restraints excluded: chain B residue 978 LEU Chi-restraints excluded: chain B residue 1061 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 129 optimal weight: 0.6980 chunk 70 optimal weight: 1.9990 chunk 7 optimal weight: 0.8980 chunk 83 optimal weight: 0.7980 chunk 59 optimal weight: 3.9990 chunk 79 optimal weight: 8.9990 chunk 63 optimal weight: 3.9990 chunk 128 optimal weight: 3.9990 chunk 11 optimal weight: 0.9980 chunk 29 optimal weight: 3.9990 chunk 109 optimal weight: 1.9990 overall best weight: 1.0782 ------------------------------------------------------------------------------- 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 = 0.3109 r_free = 0.3109 target = 0.054305 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2725 r_free = 0.2725 target = 0.041082 restraints weight = 44918.835| |-----------------------------------------------------------------------------| r_work (start): 0.2711 rms_B_bonded: 3.57 r_work: 0.2562 rms_B_bonded: 4.00 restraints_weight: 0.5000 r_work (final): 0.2562 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8798 moved from start: 0.1131 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 12384 Z= 0.183 Angle : 0.484 7.674 16726 Z= 0.254 Chirality : 0.039 0.135 1806 Planarity : 0.003 0.032 2132 Dihedral : 4.678 55.013 1670 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 6.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % Rotamer: Outliers : 2.23 % Allowed : 16.13 % Favored : 81.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.94 (0.23), residues: 1478 helix: 1.78 (0.20), residues: 706 sheet: -1.15 (0.36), residues: 222 loop : 0.01 (0.28), residues: 550 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B1189 HIS 0.003 0.000 HIS B 748 PHE 0.008 0.001 PHE A1164 TYR 0.013 0.001 TYR B1079 ARG 0.008 0.000 ARG B1140 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2956 Ramachandran restraints generated. 1478 Oldfield, 0 Emsley, 1478 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2956 Ramachandran restraints generated. 1478 Oldfield, 0 Emsley, 1478 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 1302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 65 time to evaluate : 1.387 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 756 MET cc_start: 0.8942 (tmm) cc_final: 0.8619 (tmm) REVERT: A 856 TRP cc_start: 0.8088 (OUTLIER) cc_final: 0.6584 (m-90) REVERT: A 957 MET cc_start: 0.9399 (mmm) cc_final: 0.9057 (mmm) REVERT: A 983 LEU cc_start: 0.9503 (OUTLIER) cc_final: 0.9204 (mt) REVERT: A 987 MET cc_start: 0.9645 (mmm) cc_final: 0.9406 (mmm) REVERT: B 1118 LEU cc_start: 0.9279 (mm) cc_final: 0.8953 (pt) outliers start: 29 outliers final: 18 residues processed: 88 average time/residue: 1.2646 time to fit residues: 122.5659 Evaluate side-chains 77 residues out of total 1302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 57 time to evaluate : 1.482 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 542 LEU Chi-restraints excluded: chain A residue 579 VAL Chi-restraints excluded: chain A residue 588 VAL Chi-restraints excluded: chain A residue 636 VAL Chi-restraints excluded: chain A residue 669 VAL Chi-restraints excluded: chain A residue 856 TRP Chi-restraints excluded: chain A residue 895 THR Chi-restraints excluded: chain A residue 925 VAL Chi-restraints excluded: chain A residue 931 MET Chi-restraints excluded: chain A residue 983 LEU Chi-restraints excluded: chain A residue 1078 HIS Chi-restraints excluded: chain B residue 438 GLU Chi-restraints excluded: chain B residue 443 LEU Chi-restraints excluded: chain B residue 534 ILE Chi-restraints excluded: chain B residue 542 LEU Chi-restraints excluded: chain B residue 647 GLU Chi-restraints excluded: chain B residue 669 VAL Chi-restraints excluded: chain B residue 816 THR Chi-restraints excluded: chain B residue 978 LEU Chi-restraints excluded: chain B residue 1061 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 128 optimal weight: 4.9990 chunk 59 optimal weight: 0.7980 chunk 27 optimal weight: 3.9990 chunk 136 optimal weight: 0.2980 chunk 52 optimal weight: 2.9990 chunk 81 optimal weight: 9.9990 chunk 6 optimal weight: 0.9980 chunk 134 optimal weight: 0.9990 chunk 107 optimal weight: 5.9990 chunk 12 optimal weight: 2.9990 chunk 133 optimal weight: 3.9990 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 540 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3096 r_free = 0.3096 target = 0.053751 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2710 r_free = 0.2710 target = 0.040554 restraints weight = 44624.420| |-----------------------------------------------------------------------------| r_work (start): 0.2695 rms_B_bonded: 3.51 r_work: 0.2546 rms_B_bonded: 3.95 restraints_weight: 0.5000 r_work (final): 0.2546 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8808 moved from start: 0.1357 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.101 12384 Z= 0.209 Angle : 0.522 12.171 16726 Z= 0.274 Chirality : 0.039 0.148 1806 Planarity : 0.003 0.031 2132 Dihedral : 4.699 55.588 1670 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 6.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer: Outliers : 2.92 % Allowed : 15.67 % Favored : 81.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.94 (0.23), residues: 1478 helix: 1.75 (0.20), residues: 706 sheet: -1.10 (0.36), residues: 222 loop : 0.02 (0.28), residues: 550 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B1189 HIS 0.002 0.000 HIS B 650 PHE 0.009 0.001 PHE B 649 TYR 0.027 0.001 TYR B1029 ARG 0.006 0.000 ARG B1140 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2956 Ramachandran restraints generated. 1478 Oldfield, 0 Emsley, 1478 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2956 Ramachandran restraints generated. 1478 Oldfield, 0 Emsley, 1478 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 1302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 62 time to evaluate : 1.545 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 856 TRP cc_start: 0.8117 (OUTLIER) cc_final: 0.6647 (m-90) REVERT: A 957 MET cc_start: 0.9423 (mmm) cc_final: 0.9152 (mmm) REVERT: A 983 LEU cc_start: 0.9511 (OUTLIER) cc_final: 0.9230 (mt) REVERT: B 749 MET cc_start: 0.9107 (OUTLIER) cc_final: 0.8405 (mtp) REVERT: B 929 ARG cc_start: 0.9340 (mtm110) cc_final: 0.8583 (ttp80) REVERT: B 1118 LEU cc_start: 0.9287 (mm) cc_final: 0.8967 (pt) REVERT: B 1147 LYS cc_start: 0.9596 (OUTLIER) cc_final: 0.9350 (mmmm) outliers start: 38 outliers final: 19 residues processed: 93 average time/residue: 1.1471 time to fit residues: 117.9658 Evaluate side-chains 83 residues out of total 1302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 60 time to evaluate : 1.455 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 542 LEU Chi-restraints excluded: chain A residue 579 VAL Chi-restraints excluded: chain A residue 588 VAL Chi-restraints excluded: chain A residue 636 VAL Chi-restraints excluded: chain A residue 669 VAL Chi-restraints excluded: chain A residue 674 THR Chi-restraints excluded: chain A residue 856 TRP Chi-restraints excluded: chain A residue 895 THR Chi-restraints excluded: chain A residue 925 VAL Chi-restraints excluded: chain A residue 931 MET Chi-restraints excluded: chain A residue 983 LEU Chi-restraints excluded: chain A residue 1078 HIS Chi-restraints excluded: chain B residue 443 LEU Chi-restraints excluded: chain B residue 534 ILE Chi-restraints excluded: chain B residue 542 LEU Chi-restraints excluded: chain B residue 669 VAL Chi-restraints excluded: chain B residue 749 MET Chi-restraints excluded: chain B residue 816 THR Chi-restraints excluded: chain B residue 925 VAL Chi-restraints excluded: chain B residue 978 LEU Chi-restraints excluded: chain B residue 1061 GLU Chi-restraints excluded: chain B residue 1147 LYS Chi-restraints excluded: chain B residue 1182 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 45 optimal weight: 4.9990 chunk 85 optimal weight: 3.9990 chunk 123 optimal weight: 4.9990 chunk 71 optimal weight: 1.9990 chunk 83 optimal weight: 8.9990 chunk 13 optimal weight: 7.9990 chunk 132 optimal weight: 1.9990 chunk 0 optimal weight: 8.9990 chunk 92 optimal weight: 0.7980 chunk 34 optimal weight: 4.9990 chunk 87 optimal weight: 5.9990 overall best weight: 2.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1010 HIS B 523 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3035 r_free = 0.3035 target = 0.051515 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2636 r_free = 0.2636 target = 0.038242 restraints weight = 45417.119| |-----------------------------------------------------------------------------| r_work (start): 0.2621 rms_B_bonded: 3.50 r_work: 0.2469 rms_B_bonded: 3.94 restraints_weight: 0.5000 r_work (final): 0.2469 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8842 moved from start: 0.1702 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.069 12384 Z= 0.371 Angle : 0.575 10.372 16726 Z= 0.298 Chirality : 0.042 0.179 1806 Planarity : 0.004 0.048 2132 Dihedral : 4.974 52.576 1670 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 8.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer: Outliers : 2.76 % Allowed : 16.05 % Favored : 81.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.85 (0.23), residues: 1478 helix: 1.70 (0.20), residues: 704 sheet: -1.18 (0.35), residues: 222 loop : -0.04 (0.28), residues: 552 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B1189 HIS 0.003 0.001 HIS B 748 PHE 0.011 0.001 PHE B 990 TYR 0.020 0.001 TYR A 966 ARG 0.008 0.000 ARG A 929 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2956 Ramachandran restraints generated. 1478 Oldfield, 0 Emsley, 1478 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2956 Ramachandran restraints generated. 1478 Oldfield, 0 Emsley, 1478 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 1302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 59 time to evaluate : 1.434 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 438 GLU cc_start: 0.8052 (tp30) cc_final: 0.7704 (pm20) REVERT: A 856 TRP cc_start: 0.8200 (OUTLIER) cc_final: 0.6771 (m-90) REVERT: A 929 ARG cc_start: 0.9399 (mtp-110) cc_final: 0.9171 (ttp-110) REVERT: A 987 MET cc_start: 0.9588 (mmm) cc_final: 0.9332 (mmm) REVERT: B 749 MET cc_start: 0.9188 (OUTLIER) cc_final: 0.8464 (mtp) REVERT: B 929 ARG cc_start: 0.9394 (mtm110) cc_final: 0.8573 (ttp80) REVERT: B 931 MET cc_start: 0.8906 (OUTLIER) cc_final: 0.8691 (ptm) REVERT: B 1048 MET cc_start: 0.9500 (mtm) cc_final: 0.9014 (mpp) REVERT: B 1147 LYS cc_start: 0.9612 (OUTLIER) cc_final: 0.9378 (mmmm) outliers start: 36 outliers final: 23 residues processed: 88 average time/residue: 1.2556 time to fit residues: 121.4265 Evaluate side-chains 83 residues out of total 1302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 56 time to evaluate : 1.370 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 542 LEU Chi-restraints excluded: chain A residue 579 VAL Chi-restraints excluded: chain A residue 588 VAL Chi-restraints excluded: chain A residue 636 VAL Chi-restraints excluded: chain A residue 659 LEU Chi-restraints excluded: chain A residue 669 VAL Chi-restraints excluded: chain A residue 674 THR Chi-restraints excluded: chain A residue 856 TRP Chi-restraints excluded: chain A residue 895 THR Chi-restraints excluded: chain A residue 925 VAL Chi-restraints excluded: chain A residue 1078 HIS Chi-restraints excluded: chain A residue 1100 SER Chi-restraints excluded: chain B residue 443 LEU Chi-restraints excluded: chain B residue 534 ILE Chi-restraints excluded: chain B residue 542 LEU Chi-restraints excluded: chain B residue 669 VAL Chi-restraints excluded: chain B residue 749 MET Chi-restraints excluded: chain B residue 789 HIS Chi-restraints excluded: chain B residue 816 THR Chi-restraints excluded: chain B residue 925 VAL Chi-restraints excluded: chain B residue 931 MET Chi-restraints excluded: chain B residue 978 LEU Chi-restraints excluded: chain B residue 1022 ILE Chi-restraints excluded: chain B residue 1061 GLU Chi-restraints excluded: chain B residue 1110 ILE Chi-restraints excluded: chain B residue 1147 LYS Chi-restraints excluded: chain B residue 1182 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 115 optimal weight: 0.6980 chunk 129 optimal weight: 0.9990 chunk 120 optimal weight: 2.9990 chunk 135 optimal weight: 3.9990 chunk 25 optimal weight: 0.9990 chunk 23 optimal weight: 5.9990 chunk 37 optimal weight: 3.9990 chunk 67 optimal weight: 0.9990 chunk 111 optimal weight: 2.9990 chunk 21 optimal weight: 0.0470 chunk 94 optimal weight: 3.9990 overall best weight: 0.7484 ------------------------------------------------------------------------------- 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 = 0.3089 r_free = 0.3089 target = 0.053600 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2705 r_free = 0.2705 target = 0.040441 restraints weight = 45191.196| |-----------------------------------------------------------------------------| r_work (start): 0.2691 rms_B_bonded: 3.54 r_work: 0.2545 rms_B_bonded: 3.95 restraints_weight: 0.5000 r_work (final): 0.2545 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8804 moved from start: 0.1595 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 12384 Z= 0.159 Angle : 0.508 9.905 16726 Z= 0.260 Chirality : 0.039 0.146 1806 Planarity : 0.003 0.030 2132 Dihedral : 4.770 54.187 1670 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 6.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 3.00 % Allowed : 15.98 % Favored : 81.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.97 (0.23), residues: 1478 helix: 1.77 (0.20), residues: 708 sheet: -1.13 (0.35), residues: 222 loop : 0.06 (0.28), residues: 548 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B1189 HIS 0.002 0.000 HIS A1092 PHE 0.008 0.001 PHE B 710 TYR 0.012 0.001 TYR B1029 ARG 0.006 0.000 ARG A 929 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2956 Ramachandran restraints generated. 1478 Oldfield, 0 Emsley, 1478 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2956 Ramachandran restraints generated. 1478 Oldfield, 0 Emsley, 1478 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 1302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 64 time to evaluate : 1.459 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 438 GLU cc_start: 0.7929 (tp30) cc_final: 0.7588 (pm20) REVERT: A 503 LYS cc_start: 0.9678 (tppp) cc_final: 0.9423 (mmpt) REVERT: A 987 MET cc_start: 0.9624 (mmm) cc_final: 0.9346 (mmm) REVERT: B 916 TYR cc_start: 0.8511 (m-10) cc_final: 0.8174 (m-10) REVERT: B 929 ARG cc_start: 0.9363 (mtm110) cc_final: 0.8987 (ttp80) REVERT: B 1048 MET cc_start: 0.9453 (mtm) cc_final: 0.9157 (mtm) REVERT: B 1118 LEU cc_start: 0.9226 (mm) cc_final: 0.8917 (pt) REVERT: B 1147 LYS cc_start: 0.9596 (OUTLIER) cc_final: 0.9377 (mmmm) outliers start: 39 outliers final: 20 residues processed: 96 average time/residue: 1.2269 time to fit residues: 129.9458 Evaluate side-chains 80 residues out of total 1302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 59 time to evaluate : 1.269 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 542 LEU Chi-restraints excluded: chain A residue 579 VAL Chi-restraints excluded: chain A residue 588 VAL Chi-restraints excluded: chain A residue 636 VAL Chi-restraints excluded: chain A residue 659 LEU Chi-restraints excluded: chain A residue 669 VAL Chi-restraints excluded: chain A residue 674 THR Chi-restraints excluded: chain A residue 895 THR Chi-restraints excluded: chain A residue 925 VAL Chi-restraints excluded: chain A residue 1027 SER Chi-restraints excluded: chain A residue 1078 HIS Chi-restraints excluded: chain B residue 443 LEU Chi-restraints excluded: chain B residue 534 ILE Chi-restraints excluded: chain B residue 542 LEU Chi-restraints excluded: chain B residue 669 VAL Chi-restraints excluded: chain B residue 816 THR Chi-restraints excluded: chain B residue 925 VAL Chi-restraints excluded: chain B residue 978 LEU Chi-restraints excluded: chain B residue 1061 GLU Chi-restraints excluded: chain B residue 1147 LYS Chi-restraints excluded: chain B residue 1182 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 32 optimal weight: 0.9990 chunk 116 optimal weight: 0.7980 chunk 75 optimal weight: 0.1980 chunk 119 optimal weight: 5.9990 chunk 141 optimal weight: 9.9990 chunk 12 optimal weight: 3.9990 chunk 9 optimal weight: 0.6980 chunk 121 optimal weight: 7.9990 chunk 84 optimal weight: 0.9980 chunk 56 optimal weight: 3.9990 chunk 130 optimal weight: 0.6980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 506 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3098 r_free = 0.3098 target = 0.053917 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2716 r_free = 0.2716 target = 0.040800 restraints weight = 44644.450| |-----------------------------------------------------------------------------| r_work (start): 0.2702 rms_B_bonded: 3.54 r_work: 0.2555 rms_B_bonded: 3.96 restraints_weight: 0.5000 r_work (final): 0.2555 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8801 moved from start: 0.1624 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 12384 Z= 0.157 Angle : 0.519 9.266 16726 Z= 0.264 Chirality : 0.039 0.147 1806 Planarity : 0.003 0.034 2132 Dihedral : 4.700 55.381 1670 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 6.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 2.69 % Allowed : 16.82 % Favored : 80.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.01 (0.23), residues: 1478 helix: 1.82 (0.20), residues: 708 sheet: -1.12 (0.35), residues: 222 loop : 0.06 (0.28), residues: 548 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 856 HIS 0.002 0.000 HIS A1092 PHE 0.008 0.001 PHE B 710 TYR 0.014 0.001 TYR B1029 ARG 0.007 0.000 ARG A 929 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2956 Ramachandran restraints generated. 1478 Oldfield, 0 Emsley, 1478 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2956 Ramachandran restraints generated. 1478 Oldfield, 0 Emsley, 1478 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 1302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 63 time to evaluate : 1.381 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 438 GLU cc_start: 0.7890 (tp30) cc_final: 0.7572 (pm20) REVERT: A 503 LYS cc_start: 0.9689 (tppp) cc_final: 0.9417 (mmpt) REVERT: A 929 ARG cc_start: 0.9097 (ttp-110) cc_final: 0.8658 (tpm170) REVERT: A 957 MET cc_start: 0.9326 (mmm) cc_final: 0.8994 (mmm) REVERT: A 987 MET cc_start: 0.9668 (mmm) cc_final: 0.9383 (mmm) REVERT: B 749 MET cc_start: 0.9103 (OUTLIER) cc_final: 0.8450 (mtp) REVERT: B 929 ARG cc_start: 0.9374 (mtm110) cc_final: 0.9146 (ttp80) REVERT: B 931 MET cc_start: 0.9231 (ptm) cc_final: 0.9005 (ptm) REVERT: B 957 MET cc_start: 0.9416 (mmt) cc_final: 0.8875 (mpt) REVERT: B 1110 ILE cc_start: 0.9255 (OUTLIER) cc_final: 0.9027 (tp) REVERT: B 1118 LEU cc_start: 0.9221 (mm) cc_final: 0.8945 (pt) REVERT: B 1147 LYS cc_start: 0.9582 (OUTLIER) cc_final: 0.9346 (mmmm) outliers start: 35 outliers final: 21 residues processed: 93 average time/residue: 1.2349 time to fit residues: 126.3218 Evaluate side-chains 85 residues out of total 1302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 61 time to evaluate : 1.377 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 534 ILE Chi-restraints excluded: chain A residue 542 LEU Chi-restraints excluded: chain A residue 579 VAL Chi-restraints excluded: chain A residue 588 VAL Chi-restraints excluded: chain A residue 636 VAL Chi-restraints excluded: chain A residue 659 LEU Chi-restraints excluded: chain A residue 669 VAL Chi-restraints excluded: chain A residue 674 THR Chi-restraints excluded: chain A residue 895 THR Chi-restraints excluded: chain A residue 925 VAL Chi-restraints excluded: chain A residue 1027 SER Chi-restraints excluded: chain A residue 1078 HIS Chi-restraints excluded: chain B residue 443 LEU Chi-restraints excluded: chain B residue 534 ILE Chi-restraints excluded: chain B residue 542 LEU Chi-restraints excluded: chain B residue 669 VAL Chi-restraints excluded: chain B residue 749 MET Chi-restraints excluded: chain B residue 816 THR Chi-restraints excluded: chain B residue 925 VAL Chi-restraints excluded: chain B residue 978 LEU Chi-restraints excluded: chain B residue 1061 GLU Chi-restraints excluded: chain B residue 1110 ILE Chi-restraints excluded: chain B residue 1147 LYS Chi-restraints excluded: chain B residue 1182 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 66 optimal weight: 2.9990 chunk 147 optimal weight: 4.9990 chunk 42 optimal weight: 1.9990 chunk 16 optimal weight: 6.9990 chunk 73 optimal weight: 4.9990 chunk 102 optimal weight: 0.9980 chunk 3 optimal weight: 0.9980 chunk 79 optimal weight: 7.9990 chunk 7 optimal weight: 0.6980 chunk 143 optimal weight: 2.9990 chunk 39 optimal weight: 0.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 506 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3086 r_free = 0.3086 target = 0.053462 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2703 r_free = 0.2703 target = 0.040384 restraints weight = 45411.589| |-----------------------------------------------------------------------------| r_work (start): 0.2686 rms_B_bonded: 3.54 r_work: 0.2538 rms_B_bonded: 3.97 restraints_weight: 0.5000 r_work (final): 0.2538 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8812 moved from start: 0.1663 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 12384 Z= 0.196 Angle : 0.535 10.056 16726 Z= 0.271 Chirality : 0.039 0.142 1806 Planarity : 0.003 0.028 2132 Dihedral : 4.734 56.472 1670 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 6.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer: Outliers : 2.76 % Allowed : 16.82 % Favored : 80.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.02 (0.23), residues: 1478 helix: 1.82 (0.20), residues: 708 sheet: -1.09 (0.35), residues: 222 loop : 0.06 (0.28), residues: 548 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 856 HIS 0.002 0.000 HIS A1092 PHE 0.017 0.001 PHE B 959 TYR 0.014 0.001 TYR B1029 ARG 0.006 0.000 ARG A 929 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2956 Ramachandran restraints generated. 1478 Oldfield, 0 Emsley, 1478 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2956 Ramachandran restraints generated. 1478 Oldfield, 0 Emsley, 1478 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 1302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 65 time to evaluate : 1.310 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 438 GLU cc_start: 0.7894 (tp30) cc_final: 0.7626 (pm20) REVERT: A 503 LYS cc_start: 0.9696 (tppp) cc_final: 0.9415 (mmpt) REVERT: A 929 ARG cc_start: 0.9034 (ttp-110) cc_final: 0.8694 (tpm170) REVERT: A 957 MET cc_start: 0.9355 (mmm) cc_final: 0.9012 (mmm) REVERT: A 987 MET cc_start: 0.9672 (mmm) cc_final: 0.9371 (mmm) REVERT: B 749 MET cc_start: 0.9133 (OUTLIER) cc_final: 0.8284 (mtp) REVERT: B 929 ARG cc_start: 0.9382 (mtm110) cc_final: 0.9162 (ttp80) REVERT: B 1110 ILE cc_start: 0.9281 (OUTLIER) cc_final: 0.9058 (tp) REVERT: B 1118 LEU cc_start: 0.9219 (mm) cc_final: 0.8940 (pt) REVERT: B 1147 LYS cc_start: 0.9585 (OUTLIER) cc_final: 0.9349 (mmmm) outliers start: 36 outliers final: 21 residues processed: 95 average time/residue: 1.2132 time to fit residues: 126.7088 Evaluate side-chains 84 residues out of total 1302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 60 time to evaluate : 1.309 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 542 LEU Chi-restraints excluded: chain A residue 579 VAL Chi-restraints excluded: chain A residue 588 VAL Chi-restraints excluded: chain A residue 636 VAL Chi-restraints excluded: chain A residue 659 LEU Chi-restraints excluded: chain A residue 669 VAL Chi-restraints excluded: chain A residue 674 THR Chi-restraints excluded: chain A residue 895 THR Chi-restraints excluded: chain A residue 925 VAL Chi-restraints excluded: chain A residue 931 MET Chi-restraints excluded: chain A residue 1027 SER Chi-restraints excluded: chain A residue 1078 HIS Chi-restraints excluded: chain B residue 443 LEU Chi-restraints excluded: chain B residue 534 ILE Chi-restraints excluded: chain B residue 669 VAL Chi-restraints excluded: chain B residue 749 MET Chi-restraints excluded: chain B residue 816 THR Chi-restraints excluded: chain B residue 895 THR Chi-restraints excluded: chain B residue 925 VAL Chi-restraints excluded: chain B residue 978 LEU Chi-restraints excluded: chain B residue 1061 GLU Chi-restraints excluded: chain B residue 1110 ILE Chi-restraints excluded: chain B residue 1147 LYS Chi-restraints excluded: chain B residue 1182 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 41 optimal weight: 4.9990 chunk 141 optimal weight: 9.9990 chunk 58 optimal weight: 0.9990 chunk 5 optimal weight: 8.9990 chunk 139 optimal weight: 0.0770 chunk 102 optimal weight: 5.9990 chunk 56 optimal weight: 2.9990 chunk 45 optimal weight: 7.9990 chunk 4 optimal weight: 5.9990 chunk 118 optimal weight: 6.9990 chunk 54 optimal weight: 8.9990 overall best weight: 3.0146 ------------------------------------------------------------------------------- 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 = 0.3026 r_free = 0.3026 target = 0.051245 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2630 r_free = 0.2630 target = 0.038092 restraints weight = 45733.099| |-----------------------------------------------------------------------------| r_work (start): 0.2612 rms_B_bonded: 3.47 r_work: 0.2464 rms_B_bonded: 3.89 restraints_weight: 0.5000 r_work (final): 0.2464 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8844 moved from start: 0.1942 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.074 12384 Z= 0.415 Angle : 0.643 10.485 16726 Z= 0.326 Chirality : 0.042 0.146 1806 Planarity : 0.004 0.049 2132 Dihedral : 5.114 56.535 1670 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 8.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 2.30 % Allowed : 17.51 % Favored : 80.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.87 (0.23), residues: 1478 helix: 1.70 (0.20), residues: 708 sheet: -1.22 (0.34), residues: 222 loop : 0.01 (0.28), residues: 548 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 856 HIS 0.003 0.001 HIS B 748 PHE 0.022 0.001 PHE B 959 TYR 0.023 0.001 TYR A 966 ARG 0.007 0.000 ARG B 662 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2956 Ramachandran restraints generated. 1478 Oldfield, 0 Emsley, 1478 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2956 Ramachandran restraints generated. 1478 Oldfield, 0 Emsley, 1478 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 1302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 61 time to evaluate : 1.555 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 438 GLU cc_start: 0.8052 (tp30) cc_final: 0.7747 (pm20) REVERT: A 503 LYS cc_start: 0.9697 (tppp) cc_final: 0.9433 (mmpt) REVERT: A 929 ARG cc_start: 0.9052 (ttp-110) cc_final: 0.8722 (tpm170) REVERT: A 957 MET cc_start: 0.9327 (mmm) cc_final: 0.9024 (mmm) REVERT: A 987 MET cc_start: 0.9663 (mmm) cc_final: 0.9366 (mmm) REVERT: B 929 ARG cc_start: 0.9433 (mtm110) cc_final: 0.9229 (ttp80) REVERT: B 1048 MET cc_start: 0.9463 (mtm) cc_final: 0.9069 (mpp) REVERT: B 1147 LYS cc_start: 0.9606 (OUTLIER) cc_final: 0.9357 (mmmm) outliers start: 30 outliers final: 22 residues processed: 87 average time/residue: 1.2387 time to fit residues: 118.4433 Evaluate side-chains 82 residues out of total 1302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 59 time to evaluate : 1.359 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 534 ILE Chi-restraints excluded: chain A residue 542 LEU Chi-restraints excluded: chain A residue 579 VAL Chi-restraints excluded: chain A residue 588 VAL Chi-restraints excluded: chain A residue 636 VAL Chi-restraints excluded: chain A residue 659 LEU Chi-restraints excluded: chain A residue 669 VAL Chi-restraints excluded: chain A residue 674 THR Chi-restraints excluded: chain A residue 895 THR Chi-restraints excluded: chain A residue 925 VAL Chi-restraints excluded: chain A residue 1078 HIS Chi-restraints excluded: chain B residue 443 LEU Chi-restraints excluded: chain B residue 534 ILE Chi-restraints excluded: chain B residue 669 VAL Chi-restraints excluded: chain B residue 816 THR Chi-restraints excluded: chain B residue 895 THR Chi-restraints excluded: chain B residue 925 VAL Chi-restraints excluded: chain B residue 978 LEU Chi-restraints excluded: chain B residue 1061 GLU Chi-restraints excluded: chain B residue 1073 ASP Chi-restraints excluded: chain B residue 1110 ILE Chi-restraints excluded: chain B residue 1147 LYS Chi-restraints excluded: chain B residue 1182 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 3 optimal weight: 3.9990 chunk 127 optimal weight: 4.9990 chunk 72 optimal weight: 0.6980 chunk 12 optimal weight: 0.8980 chunk 59 optimal weight: 3.9990 chunk 133 optimal weight: 5.9990 chunk 47 optimal weight: 1.9990 chunk 1 optimal weight: 5.9990 chunk 7 optimal weight: 3.9990 chunk 17 optimal weight: 0.9980 chunk 80 optimal weight: 0.5980 overall best weight: 1.0382 ------------------------------------------------------------------------------- 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 = 0.3071 r_free = 0.3071 target = 0.052850 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2686 r_free = 0.2686 target = 0.039804 restraints weight = 44853.073| |-----------------------------------------------------------------------------| r_work (start): 0.2670 rms_B_bonded: 3.48 r_work: 0.2522 rms_B_bonded: 3.90 restraints_weight: 0.5000 r_work (final): 0.2522 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8817 moved from start: 0.1810 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 12384 Z= 0.196 Angle : 0.576 10.928 16726 Z= 0.291 Chirality : 0.040 0.142 1806 Planarity : 0.003 0.033 2132 Dihedral : 4.976 58.541 1670 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 7.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer: Outliers : 1.92 % Allowed : 17.82 % Favored : 80.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.93 (0.23), residues: 1478 helix: 1.75 (0.20), residues: 708 sheet: -1.21 (0.35), residues: 222 loop : 0.05 (0.28), residues: 548 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 856 HIS 0.003 0.000 HIS A1092 PHE 0.022 0.001 PHE B 959 TYR 0.018 0.001 TYR B1029 ARG 0.008 0.000 ARG B 662 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2956 Ramachandran restraints generated. 1478 Oldfield, 0 Emsley, 1478 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2956 Ramachandran restraints generated. 1478 Oldfield, 0 Emsley, 1478 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 1302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 63 time to evaluate : 1.558 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 438 GLU cc_start: 0.7964 (tp30) cc_final: 0.7735 (pm20) REVERT: A 503 LYS cc_start: 0.9702 (tppp) cc_final: 0.9427 (mmpt) REVERT: A 749 MET cc_start: 0.9448 (mmm) cc_final: 0.9174 (mmm) REVERT: A 929 ARG cc_start: 0.9043 (ttp-110) cc_final: 0.8687 (tpm170) REVERT: A 957 MET cc_start: 0.9330 (mmm) cc_final: 0.9017 (mmm) REVERT: A 987 MET cc_start: 0.9660 (mmm) cc_final: 0.9346 (mmm) REVERT: B 957 MET cc_start: 0.9500 (mpp) cc_final: 0.8738 (mpt) REVERT: B 1048 MET cc_start: 0.9411 (mtm) cc_final: 0.9034 (mpp) REVERT: B 1118 LEU cc_start: 0.9183 (mm) cc_final: 0.8871 (pt) REVERT: B 1147 LYS cc_start: 0.9604 (OUTLIER) cc_final: 0.9371 (mmmm) outliers start: 25 outliers final: 20 residues processed: 85 average time/residue: 1.2541 time to fit residues: 117.3287 Evaluate side-chains 82 residues out of total 1302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 61 time to evaluate : 1.391 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 534 ILE Chi-restraints excluded: chain A residue 542 LEU Chi-restraints excluded: chain A residue 579 VAL Chi-restraints excluded: chain A residue 588 VAL Chi-restraints excluded: chain A residue 636 VAL Chi-restraints excluded: chain A residue 659 LEU Chi-restraints excluded: chain A residue 669 VAL Chi-restraints excluded: chain A residue 674 THR Chi-restraints excluded: chain A residue 895 THR Chi-restraints excluded: chain A residue 925 VAL Chi-restraints excluded: chain A residue 1078 HIS Chi-restraints excluded: chain B residue 443 LEU Chi-restraints excluded: chain B residue 534 ILE Chi-restraints excluded: chain B residue 669 VAL Chi-restraints excluded: chain B residue 816 THR Chi-restraints excluded: chain B residue 895 THR Chi-restraints excluded: chain B residue 925 VAL Chi-restraints excluded: chain B residue 1061 GLU Chi-restraints excluded: chain B residue 1110 ILE Chi-restraints excluded: chain B residue 1147 LYS Chi-restraints excluded: chain B residue 1182 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 23 optimal weight: 0.6980 chunk 12 optimal weight: 2.9990 chunk 126 optimal weight: 3.9990 chunk 52 optimal weight: 2.9990 chunk 31 optimal weight: 0.6980 chunk 102 optimal weight: 1.9990 chunk 136 optimal weight: 6.9990 chunk 54 optimal weight: 2.9990 chunk 131 optimal weight: 0.0050 chunk 94 optimal weight: 3.9990 chunk 56 optimal weight: 3.9990 overall best weight: 1.2798 ------------------------------------------------------------------------------- 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 = 0.3066 r_free = 0.3066 target = 0.052677 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2678 r_free = 0.2678 target = 0.039587 restraints weight = 45148.894| |-----------------------------------------------------------------------------| r_work (start): 0.2665 rms_B_bonded: 3.50 r_work: 0.2518 rms_B_bonded: 3.92 restraints_weight: 0.5000 r_work (final): 0.2518 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8819 moved from start: 0.1835 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 12384 Z= 0.221 Angle : 0.589 10.744 16726 Z= 0.296 Chirality : 0.040 0.143 1806 Planarity : 0.003 0.046 2132 Dihedral : 4.859 59.782 1668 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 7.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 2.00 % Allowed : 17.90 % Favored : 80.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.92 (0.23), residues: 1478 helix: 1.73 (0.20), residues: 708 sheet: -1.23 (0.35), residues: 222 loop : 0.07 (0.28), residues: 548 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 856 HIS 0.003 0.000 HIS A1092 PHE 0.021 0.001 PHE B 959 TYR 0.019 0.001 TYR B1033 ARG 0.011 0.000 ARG B 929 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6253.41 seconds wall clock time: 112 minutes 3.86 seconds (6723.86 seconds total)