Starting phenix.real_space_refine on Wed Jul 30 11:21:07 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ygg_39249/07_2025/8ygg_39249.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ygg_39249/07_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_39249/07_2025/8ygg_39249.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ygg_39249/07_2025/8ygg_39249.map" model { file = "/net/cci-nas-00/data/ceres_data/8ygg_39249/07_2025/8ygg_39249.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ygg_39249/07_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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/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: 6.79, per 1000 atoms: 0.56 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: 2.47 Conformation dependent library (CDL) restraints added in 1.4 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: 1.33 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: 3.74 Time building geometry restraints manager: 2.99 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: 0.05 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: 0.400 Check model and map are aligned: 0.080 Set scattering table: 0.100 Process input model: 27.240 Find NCS groups from input model: 0.350 Set up NCS constraints: 0.040 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:11.190 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 40.250 ------------------------------------------------------------------------------- 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= 0.156 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 Details of bonding type rmsd hydrogen bonds : bond 0.13896 ( 593) hydrogen bonds : angle 5.54698 ( 1656) covalent geometry : bond 0.00286 (12384) covalent geometry : angle 0.64983 (16726) *********************** 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 : 1.435 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: 1.2407 time to fit residues: 117.3430 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 : 1.430 ------------------------------------------------------------------------------- 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 = 0.3128 r_free = 0.3128 target = 0.055012 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2752 r_free = 0.2752 target = 0.041928 restraints weight = 43988.931| |-----------------------------------------------------------------------------| r_work (start): 0.2736 rms_B_bonded: 3.52 r_work: 0.2589 rms_B_bonded: 3.96 restraints_weight: 0.5000 r_work (final): 0.2589 ------------------------------------------------------------------------------- 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= 0.113 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 Details of bonding type rmsd hydrogen bonds : bond 0.03690 ( 593) hydrogen bonds : angle 4.64248 ( 1656) covalent geometry : bond 0.00247 (12384) covalent geometry : angle 0.49408 (16726) *********************** 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 : 1.438 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 701 ASP cc_start: 0.9164 (t70) cc_final: 0.8877 (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: 0.9262 (mpt) cc_final: 0.9059 (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: 1.2523 time to fit residues: 136.0751 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 : 1.472 ------------------------------------------------------------------------------- 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: 6.9990 chunk 83 optimal weight: 0.7980 chunk 59 optimal weight: 3.9990 chunk 79 optimal weight: 9.9990 chunk 63 optimal weight: 3.9990 chunk 128 optimal weight: 6.9990 chunk 11 optimal weight: 0.9990 chunk 29 optimal weight: 3.9990 chunk 109 optimal weight: 1.9990 overall best weight: 1.2986 ------------------------------------------------------------------------------- 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 = 0.3099 r_free = 0.3099 target = 0.053938 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2710 r_free = 0.2710 target = 0.040623 restraints weight = 45031.358| |-----------------------------------------------------------------------------| r_work (start): 0.2698 rms_B_bonded: 3.57 r_work: 0.2548 rms_B_bonded: 4.00 restraints_weight: 0.5000 r_work (final): 0.2548 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8808 moved from start: 0.1144 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 12384 Z= 0.140 Angle : 0.493 7.785 16726 Z= 0.259 Chirality : 0.039 0.145 1806 Planarity : 0.003 0.031 2132 Dihedral : 4.713 55.118 1670 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 7.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 2.30 % Allowed : 15.98 % Favored : 81.72 % 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: 1.77 (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 0.008 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 Details of bonding type rmsd hydrogen bonds : bond 0.03614 ( 593) hydrogen bonds : angle 4.50814 ( 1656) covalent geometry : bond 0.00315 (12384) covalent geometry : angle 0.49322 (16726) *********************** 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 91 residues out of total 1302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 61 time to evaluate : 1.272 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 749 MET cc_start: 0.9461 (mmm) cc_final: 0.9013 (mmm) REVERT: A 856 TRP cc_start: 0.8103 (OUTLIER) cc_final: 0.6666 (m-90) REVERT: A 957 MET cc_start: 0.9397 (mmm) cc_final: 0.9059 (mmm) REVERT: A 983 LEU cc_start: 0.9503 (OUTLIER) cc_final: 0.9227 (mt) REVERT: A 987 MET cc_start: 0.9649 (mmm) cc_final: 0.9429 (mmm) REVERT: B 1048 MET cc_start: 0.9309 (OUTLIER) cc_final: 0.9061 (mpp) outliers start: 30 outliers final: 19 residues processed: 85 average time/residue: 1.3718 time to fit residues: 128.0453 Evaluate side-chains 80 residues out of total 1302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 58 time to evaluate : 1.462 ------------------------------------------------------------------------------- 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 1048 MET Chi-restraints excluded: chain B residue 1061 GLU Chi-restraints excluded: chain B residue 1182 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 128 optimal weight: 0.9990 chunk 59 optimal weight: 0.5980 chunk 27 optimal weight: 2.9990 chunk 136 optimal weight: 0.9980 chunk 52 optimal weight: 2.9990 chunk 81 optimal weight: 9.9990 chunk 6 optimal weight: 0.8980 chunk 134 optimal weight: 0.9990 chunk 107 optimal weight: 5.9990 chunk 12 optimal weight: 3.9990 chunk 133 optimal weight: 3.9990 overall best weight: 0.8984 ------------------------------------------------------------------------------- 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 = 0.3109 r_free = 0.3109 target = 0.054279 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2726 r_free = 0.2726 target = 0.041066 restraints weight = 44417.472| |-----------------------------------------------------------------------------| r_work (start): 0.2711 rms_B_bonded: 3.53 r_work: 0.2563 rms_B_bonded: 3.96 restraints_weight: 0.5000 r_work (final): 0.2563 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8798 moved from start: 0.1336 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 12384 Z= 0.121 Angle : 0.509 10.344 16726 Z= 0.267 Chirality : 0.039 0.146 1806 Planarity : 0.003 0.028 2132 Dihedral : 4.671 56.179 1670 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 6.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer: Outliers : 3.15 % Allowed : 15.44 % 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: 0.93 (0.23), residues: 1478 helix: 1.75 (0.20), residues: 706 sheet: -1.09 (0.36), residues: 222 loop : 0.00 (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 A1092 PHE 0.010 0.001 PHE B 990 TYR 0.012 0.001 TYR B1079 ARG 0.005 0.000 ARG B1140 Details of bonding type rmsd hydrogen bonds : bond 0.03516 ( 593) hydrogen bonds : angle 4.43166 ( 1656) covalent geometry : bond 0.00265 (12384) covalent geometry : angle 0.50924 (16726) *********************** 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 108 residues out of total 1302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 67 time to evaluate : 1.641 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 749 MET cc_start: 0.9417 (mmm) cc_final: 0.9146 (mmm) REVERT: A 957 MET cc_start: 0.9419 (mmm) cc_final: 0.9099 (mmm) REVERT: A 983 LEU cc_start: 0.9508 (OUTLIER) cc_final: 0.9223 (mt) REVERT: B 638 THR cc_start: 0.9627 (OUTLIER) cc_final: 0.9212 (t) REVERT: B 749 MET cc_start: 0.9115 (OUTLIER) cc_final: 0.8430 (mtp) REVERT: B 929 ARG cc_start: 0.9364 (mtm110) cc_final: 0.8581 (ttp80) REVERT: B 1048 MET cc_start: 0.9293 (OUTLIER) cc_final: 0.9047 (mpp) REVERT: B 1118 LEU cc_start: 0.9287 (mm) cc_final: 0.8966 (pt) REVERT: B 1147 LYS cc_start: 0.9597 (OUTLIER) cc_final: 0.9348 (mmmm) outliers start: 41 outliers final: 17 residues processed: 99 average time/residue: 1.4660 time to fit residues: 159.3526 Evaluate side-chains 82 residues out of total 1302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 60 time to evaluate : 2.928 ------------------------------------------------------------------------------- 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 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 638 THR 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 978 LEU Chi-restraints excluded: chain B residue 1048 MET Chi-restraints excluded: chain B residue 1061 GLU Chi-restraints excluded: chain B residue 1147 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 45 optimal weight: 5.9990 chunk 85 optimal weight: 2.9990 chunk 123 optimal weight: 0.0040 chunk 71 optimal weight: 4.9990 chunk 83 optimal weight: 8.9990 chunk 13 optimal weight: 0.9980 chunk 132 optimal weight: 4.9990 chunk 0 optimal weight: 8.9990 chunk 92 optimal weight: 1.9990 chunk 34 optimal weight: 4.9990 chunk 87 optimal weight: 5.9990 overall best weight: 2.1998 ------------------------------------------------------------------------------- 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 = 0.3053 r_free = 0.3053 target = 0.052191 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2658 r_free = 0.2658 target = 0.038889 restraints weight = 45108.636| |-----------------------------------------------------------------------------| r_work (start): 0.2642 rms_B_bonded: 3.53 r_work: 0.2493 rms_B_bonded: 3.95 restraints_weight: 0.5000 r_work (final): 0.2493 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8839 moved from start: 0.1598 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 12384 Z= 0.209 Angle : 0.550 10.968 16726 Z= 0.284 Chirality : 0.041 0.179 1806 Planarity : 0.004 0.048 2132 Dihedral : 4.845 52.828 1670 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 7.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 2.76 % Allowed : 16.21 % 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: 0.91 (0.23), residues: 1478 helix: 1.77 (0.20), residues: 704 sheet: -1.14 (0.35), residues: 222 loop : -0.03 (0.28), residues: 552 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 856 HIS 0.003 0.001 HIS A1092 PHE 0.010 0.001 PHE A 596 TYR 0.016 0.001 TYR A 966 ARG 0.009 0.000 ARG A 929 Details of bonding type rmsd hydrogen bonds : bond 0.03811 ( 593) hydrogen bonds : angle 4.53049 ( 1656) covalent geometry : bond 0.00472 (12384) covalent geometry : angle 0.55001 (16726) *********************** 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 96 residues out of total 1302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 60 time to evaluate : 1.426 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 438 GLU cc_start: 0.8010 (tp30) cc_final: 0.7683 (pm20) REVERT: A 503 LYS cc_start: 0.9684 (tppp) cc_final: 0.9440 (mmpt) REVERT: A 856 TRP cc_start: 0.8162 (OUTLIER) cc_final: 0.6807 (m-90) REVERT: A 987 MET cc_start: 0.9593 (mmm) cc_final: 0.9337 (mmm) REVERT: B 929 ARG cc_start: 0.9378 (mtm110) cc_final: 0.8550 (ttp80) REVERT: B 931 MET cc_start: 0.8938 (OUTLIER) cc_final: 0.8540 (ptm) REVERT: B 1048 MET cc_start: 0.9315 (OUTLIER) cc_final: 0.9063 (mpp) REVERT: B 1118 LEU cc_start: 0.9250 (mm) cc_final: 0.8945 (pt) REVERT: B 1147 LYS cc_start: 0.9604 (OUTLIER) cc_final: 0.9360 (mmmm) outliers start: 36 outliers final: 22 residues processed: 90 average time/residue: 1.1961 time to fit residues: 118.6900 Evaluate side-chains 83 residues out of total 1302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 57 time to evaluate : 1.307 ------------------------------------------------------------------------------- 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 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 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 931 MET Chi-restraints excluded: chain B residue 978 LEU Chi-restraints excluded: chain B residue 1022 ILE Chi-restraints excluded: chain B residue 1048 MET 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: 2.9990 chunk 129 optimal weight: 0.8980 chunk 120 optimal weight: 5.9990 chunk 135 optimal weight: 5.9990 chunk 25 optimal weight: 3.9990 chunk 23 optimal weight: 0.9990 chunk 37 optimal weight: 3.9990 chunk 67 optimal weight: 0.8980 chunk 111 optimal weight: 2.9990 chunk 21 optimal weight: 3.9990 chunk 94 optimal weight: 2.9990 overall best weight: 1.7586 ------------------------------------------------------------------------------- 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 = 0.3060 r_free = 0.3060 target = 0.052438 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2667 r_free = 0.2667 target = 0.039153 restraints weight = 45548.687| |-----------------------------------------------------------------------------| r_work (start): 0.2649 rms_B_bonded: 3.54 r_work: 0.2499 rms_B_bonded: 3.95 restraints_weight: 0.5000 r_work (final): 0.2499 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8832 moved from start: 0.1634 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 12384 Z= 0.172 Angle : 0.529 9.697 16726 Z= 0.273 Chirality : 0.040 0.143 1806 Planarity : 0.003 0.030 2132 Dihedral : 4.855 53.102 1670 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 7.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 3.00 % Allowed : 16.05 % Favored : 80.95 % 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: 1.77 (0.20), residues: 708 sheet: -1.16 (0.35), residues: 222 loop : 0.00 (0.28), residues: 548 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B1189 HIS 0.003 0.000 HIS A1092 PHE 0.008 0.001 PHE A 596 TYR 0.012 0.001 TYR B1079 ARG 0.007 0.000 ARG A 683 Details of bonding type rmsd hydrogen bonds : bond 0.03705 ( 593) hydrogen bonds : angle 4.51225 ( 1656) covalent geometry : bond 0.00388 (12384) covalent geometry : angle 0.52899 (16726) *********************** 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 100 residues out of total 1302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 61 time to evaluate : 1.430 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 438 GLU cc_start: 0.7992 (tp30) cc_final: 0.7707 (pm20) REVERT: A 503 LYS cc_start: 0.9688 (tppp) cc_final: 0.9439 (mmpt) REVERT: A 929 ARG cc_start: 0.9092 (ttp-110) cc_final: 0.8677 (tpm170) REVERT: A 987 MET cc_start: 0.9605 (mmm) cc_final: 0.9341 (mmm) REVERT: B 848 TYR cc_start: 0.9435 (m-80) cc_final: 0.9223 (m-80) REVERT: B 929 ARG cc_start: 0.9382 (mtm110) cc_final: 0.8598 (ttp80) REVERT: B 931 MET cc_start: 0.9002 (OUTLIER) cc_final: 0.8550 (ptm) REVERT: B 1118 LEU cc_start: 0.9249 (mm) cc_final: 0.8941 (pt) REVERT: B 1147 LYS cc_start: 0.9603 (OUTLIER) cc_final: 0.9363 (mmmm) outliers start: 39 outliers final: 24 residues processed: 93 average time/residue: 1.1686 time to fit residues: 119.8418 Evaluate side-chains 87 residues out of total 1302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 61 time to evaluate : 1.401 ------------------------------------------------------------------------------- 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 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 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 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 32 optimal weight: 0.9990 chunk 116 optimal weight: 0.6980 chunk 75 optimal weight: 0.0770 chunk 119 optimal weight: 2.9990 chunk 141 optimal weight: 7.9990 chunk 12 optimal weight: 3.9990 chunk 9 optimal weight: 3.9990 chunk 121 optimal weight: 7.9990 chunk 84 optimal weight: 0.9990 chunk 56 optimal weight: 2.9990 chunk 130 optimal weight: 0.2980 overall best weight: 0.6142 ------------------------------------------------------------------------------- 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 = 0.3102 r_free = 0.3102 target = 0.054053 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2724 r_free = 0.2724 target = 0.041006 restraints weight = 44548.925| |-----------------------------------------------------------------------------| r_work (start): 0.2710 rms_B_bonded: 3.53 r_work: 0.2564 rms_B_bonded: 3.95 restraints_weight: 0.5000 r_work (final): 0.2564 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8796 moved from start: 0.1598 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= 0.104 Angle : 0.511 9.170 16726 Z= 0.260 Chirality : 0.039 0.145 1806 Planarity : 0.003 0.030 2132 Dihedral : 4.701 55.375 1670 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 6.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 2.76 % Allowed : 16.74 % 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: 1.00 (0.23), residues: 1478 helix: 1.82 (0.20), residues: 708 sheet: -1.09 (0.35), residues: 222 loop : 0.02 (0.28), residues: 548 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 856 HIS 0.003 0.000 HIS A 748 PHE 0.008 0.001 PHE B 710 TYR 0.012 0.001 TYR A1029 ARG 0.008 0.000 ARG B 662 Details of bonding type rmsd hydrogen bonds : bond 0.03363 ( 593) hydrogen bonds : angle 4.40537 ( 1656) covalent geometry : bond 0.00229 (12384) covalent geometry : angle 0.51088 (16726) *********************** 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 103 residues out of total 1302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 67 time to evaluate : 1.318 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 438 GLU cc_start: 0.7900 (tp30) cc_final: 0.7575 (pm20) REVERT: A 503 LYS cc_start: 0.9679 (tppp) cc_final: 0.9411 (mmpt) REVERT: A 749 MET cc_start: 0.9429 (mmm) cc_final: 0.9216 (mmp) REVERT: A 929 ARG cc_start: 0.9071 (ttp-110) cc_final: 0.8686 (tpm170) REVERT: A 957 MET cc_start: 0.9323 (mmm) cc_final: 0.9040 (mmm) REVERT: A 987 MET cc_start: 0.9665 (mmm) cc_final: 0.9353 (mmm) REVERT: B 878 LYS cc_start: 0.9291 (OUTLIER) cc_final: 0.9016 (ttpp) REVERT: B 929 ARG cc_start: 0.9340 (mtm110) cc_final: 0.8991 (ttp80) REVERT: B 957 MET cc_start: 0.9459 (OUTLIER) cc_final: 0.8836 (mpt) REVERT: B 1048 MET cc_start: 0.9417 (mtm) cc_final: 0.9036 (mpp) REVERT: B 1118 LEU cc_start: 0.9212 (mm) cc_final: 0.8936 (pt) REVERT: B 1147 LYS cc_start: 0.9587 (OUTLIER) cc_final: 0.9358 (mmmm) outliers start: 36 outliers final: 21 residues processed: 97 average time/residue: 1.1044 time to fit residues: 118.3311 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 : 1.443 ------------------------------------------------------------------------------- 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 542 LEU Chi-restraints excluded: chain B residue 669 VAL Chi-restraints excluded: chain B residue 816 THR Chi-restraints excluded: chain B residue 878 LYS Chi-restraints excluded: chain B residue 925 VAL Chi-restraints excluded: chain B residue 957 MET 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 66 optimal weight: 1.9990 chunk 147 optimal weight: 4.9990 chunk 42 optimal weight: 3.9990 chunk 16 optimal weight: 4.9990 chunk 73 optimal weight: 4.9990 chunk 102 optimal weight: 2.9990 chunk 3 optimal weight: 0.9990 chunk 79 optimal weight: 0.9980 chunk 7 optimal weight: 2.9990 chunk 143 optimal weight: 3.9990 chunk 39 optimal weight: 0.8980 overall best weight: 1.5786 ------------------------------------------------------------------------------- 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 = 0.052715 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2679 r_free = 0.2679 target = 0.039621 restraints weight = 45596.268| |-----------------------------------------------------------------------------| r_work (start): 0.2666 rms_B_bonded: 3.50 r_work: 0.2517 rms_B_bonded: 3.94 restraints_weight: 0.5000 r_work (final): 0.2517 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8814 moved from start: 0.1693 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 12384 Z= 0.162 Angle : 0.543 9.177 16726 Z= 0.277 Chirality : 0.040 0.143 1806 Planarity : 0.003 0.030 2132 Dihedral : 4.783 55.877 1670 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 7.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer: Outliers : 2.92 % Allowed : 16.67 % 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: 1.00 (0.23), residues: 1478 helix: 1.81 (0.20), residues: 708 sheet: -1.09 (0.35), residues: 222 loop : 0.04 (0.28), residues: 548 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 856 HIS 0.002 0.000 HIS A1092 PHE 0.009 0.001 PHE A 596 TYR 0.013 0.001 TYR B1033 ARG 0.006 0.000 ARG A 683 Details of bonding type rmsd hydrogen bonds : bond 0.03586 ( 593) hydrogen bonds : angle 4.42622 ( 1656) covalent geometry : bond 0.00367 (12384) covalent geometry : angle 0.54275 (16726) *********************** 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 97 residues out of total 1302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 59 time to evaluate : 1.517 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 438 GLU cc_start: 0.7951 (tp30) cc_final: 0.7688 (pm20) REVERT: A 503 LYS cc_start: 0.9700 (tppp) cc_final: 0.9417 (mmpt) REVERT: A 929 ARG cc_start: 0.9046 (ttp-110) cc_final: 0.8716 (tpm170) REVERT: A 957 MET cc_start: 0.9349 (mmm) cc_final: 0.9010 (mmm) REVERT: A 987 MET cc_start: 0.9668 (mmm) cc_final: 0.9364 (mmm) REVERT: B 878 LYS cc_start: 0.9348 (OUTLIER) cc_final: 0.9125 (ttpp) REVERT: B 929 ARG cc_start: 0.9385 (mtm110) cc_final: 0.9167 (ttp80) REVERT: B 957 MET cc_start: 0.9489 (OUTLIER) cc_final: 0.8721 (mpt) REVERT: B 1048 MET cc_start: 0.9472 (mtm) cc_final: 0.9103 (mpp) REVERT: B 1110 ILE cc_start: 0.9288 (OUTLIER) cc_final: 0.9068 (tp) REVERT: B 1118 LEU cc_start: 0.9228 (mm) cc_final: 0.8934 (pt) REVERT: B 1133 LEU cc_start: 0.9513 (OUTLIER) cc_final: 0.9201 (mm) REVERT: B 1147 LYS cc_start: 0.9600 (OUTLIER) cc_final: 0.9379 (mmmm) outliers start: 38 outliers final: 24 residues processed: 92 average time/residue: 1.1730 time to fit residues: 119.2658 Evaluate side-chains 88 residues out of total 1302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 59 time to evaluate : 1.313 ------------------------------------------------------------------------------- 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 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 542 LEU Chi-restraints excluded: chain B residue 669 VAL Chi-restraints excluded: chain B residue 816 THR Chi-restraints excluded: chain B residue 878 LYS Chi-restraints excluded: chain B residue 925 VAL Chi-restraints excluded: chain B residue 957 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 1078 HIS Chi-restraints excluded: chain B residue 1110 ILE Chi-restraints excluded: chain B residue 1133 LEU 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: 4.9990 chunk 58 optimal weight: 0.8980 chunk 5 optimal weight: 9.9990 chunk 139 optimal weight: 4.9990 chunk 102 optimal weight: 0.0870 chunk 56 optimal weight: 0.9990 chunk 45 optimal weight: 0.5980 chunk 4 optimal weight: 5.9990 chunk 118 optimal weight: 7.9990 chunk 54 optimal weight: 4.9990 overall best weight: 1.5162 ------------------------------------------------------------------------------- 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 = 0.3068 r_free = 0.3068 target = 0.052751 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2680 r_free = 0.2680 target = 0.039602 restraints weight = 45136.214| |-----------------------------------------------------------------------------| r_work (start): 0.2663 rms_B_bonded: 3.52 r_work: 0.2515 rms_B_bonded: 3.94 restraints_weight: 0.5000 r_work (final): 0.2515 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8824 moved from start: 0.1734 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 12384 Z= 0.157 Angle : 0.554 9.703 16726 Z= 0.282 Chirality : 0.040 0.142 1806 Planarity : 0.003 0.035 2132 Dihedral : 4.856 57.017 1670 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 7.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer: Outliers : 2.53 % Allowed : 17.13 % Favored : 80.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.98 (0.23), residues: 1478 helix: 1.79 (0.20), residues: 708 sheet: -1.12 (0.35), residues: 222 loop : 0.04 (0.28), residues: 548 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 856 HIS 0.002 0.000 HIS A1092 PHE 0.013 0.001 PHE B 959 TYR 0.016 0.001 TYR B1033 ARG 0.006 0.000 ARG B 662 Details of bonding type rmsd hydrogen bonds : bond 0.03609 ( 593) hydrogen bonds : angle 4.43685 ( 1656) covalent geometry : bond 0.00356 (12384) covalent geometry : angle 0.55437 (16726) *********************** 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 97 residues out of total 1302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 64 time to evaluate : 1.514 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 438 GLU cc_start: 0.7959 (tp30) cc_final: 0.7706 (pm20) REVERT: A 503 LYS cc_start: 0.9702 (tppp) cc_final: 0.9418 (mmpt) REVERT: A 749 MET cc_start: 0.9446 (mmm) cc_final: 0.9174 (mmm) REVERT: A 929 ARG cc_start: 0.9045 (ttp-110) cc_final: 0.8710 (tpm170) REVERT: A 957 MET cc_start: 0.9331 (mmm) cc_final: 0.9014 (mmm) REVERT: A 987 MET cc_start: 0.9664 (mmm) cc_final: 0.9360 (mmm) REVERT: B 878 LYS cc_start: 0.9325 (OUTLIER) cc_final: 0.9112 (ttpp) REVERT: B 1048 MET cc_start: 0.9464 (mtm) cc_final: 0.9084 (mpp) REVERT: B 1118 LEU cc_start: 0.9202 (mm) cc_final: 0.8916 (pt) REVERT: B 1133 LEU cc_start: 0.9505 (OUTLIER) cc_final: 0.9205 (mm) REVERT: B 1147 LYS cc_start: 0.9592 (OUTLIER) cc_final: 0.9360 (mmmm) outliers start: 33 outliers final: 22 residues processed: 93 average time/residue: 1.1586 time to fit residues: 118.9751 Evaluate side-chains 87 residues out of total 1302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 62 time to evaluate : 1.407 ------------------------------------------------------------------------------- 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 669 VAL Chi-restraints excluded: chain B residue 816 THR Chi-restraints excluded: chain B residue 878 LYS Chi-restraints excluded: chain B residue 925 VAL 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 1133 LEU 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: 0.8980 chunk 127 optimal weight: 1.9990 chunk 72 optimal weight: 3.9990 chunk 12 optimal weight: 2.9990 chunk 59 optimal weight: 0.9990 chunk 133 optimal weight: 0.6980 chunk 47 optimal weight: 3.9990 chunk 1 optimal weight: 5.9990 chunk 7 optimal weight: 5.9990 chunk 17 optimal weight: 4.9990 chunk 80 optimal weight: 2.9990 overall best weight: 1.5186 ------------------------------------------------------------------------------- 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 = 0.3068 r_free = 0.3068 target = 0.052659 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2680 r_free = 0.2680 target = 0.039572 restraints weight = 45033.667| |-----------------------------------------------------------------------------| r_work (start): 0.2663 rms_B_bonded: 3.51 r_work: 0.2514 rms_B_bonded: 3.93 restraints_weight: 0.5000 r_work (final): 0.2514 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8825 moved from start: 0.1765 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 12384 Z= 0.159 Angle : 0.574 10.800 16726 Z= 0.291 Chirality : 0.040 0.143 1806 Planarity : 0.004 0.046 2132 Dihedral : 4.913 58.176 1670 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 7.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 2.15 % Allowed : 17.36 % 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: 0.96 (0.23), residues: 1478 helix: 1.76 (0.20), residues: 708 sheet: -1.16 (0.35), residues: 222 loop : 0.07 (0.28), residues: 548 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 856 HIS 0.003 0.000 HIS A1092 PHE 0.013 0.001 PHE B 959 TYR 0.020 0.001 TYR B1033 ARG 0.012 0.000 ARG B 662 Details of bonding type rmsd hydrogen bonds : bond 0.03602 ( 593) hydrogen bonds : angle 4.42254 ( 1656) covalent geometry : bond 0.00364 (12384) covalent geometry : angle 0.57418 (16726) ********************** 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 93 residues out of total 1302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 65 time to evaluate : 1.331 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 438 GLU cc_start: 0.7945 (tp30) cc_final: 0.7718 (pm20) REVERT: A 503 LYS cc_start: 0.9711 (tppp) cc_final: 0.9420 (mmpt) REVERT: A 749 MET cc_start: 0.9442 (mmm) cc_final: 0.9177 (mmm) REVERT: A 893 LYS cc_start: 0.9396 (mppt) cc_final: 0.9043 (tppp) REVERT: A 929 ARG cc_start: 0.9026 (ttp-110) cc_final: 0.8674 (tpm170) REVERT: A 957 MET cc_start: 0.9321 (mmm) cc_final: 0.9007 (mmm) REVERT: A 987 MET cc_start: 0.9661 (mmm) cc_final: 0.9352 (mmm) REVERT: B 647 GLU cc_start: 0.9007 (tp30) cc_final: 0.8576 (tp30) REVERT: B 957 MET cc_start: 0.9468 (mmt) cc_final: 0.8865 (mpt) REVERT: B 1048 MET cc_start: 0.9470 (mtm) cc_final: 0.9009 (mpp) REVERT: B 1118 LEU cc_start: 0.9200 (mm) cc_final: 0.8917 (pt) REVERT: B 1133 LEU cc_start: 0.9510 (OUTLIER) cc_final: 0.9202 (mm) REVERT: B 1147 LYS cc_start: 0.9594 (OUTLIER) cc_final: 0.9371 (mmmm) outliers start: 28 outliers final: 23 residues processed: 90 average time/residue: 1.2148 time to fit residues: 120.2627 Evaluate side-chains 84 residues out of total 1302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 59 time to evaluate : 1.397 ------------------------------------------------------------------------------- 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 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 816 THR Chi-restraints excluded: chain B residue 925 VAL 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 1133 LEU 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: 0.8980 chunk 12 optimal weight: 2.9990 chunk 126 optimal weight: 2.9990 chunk 52 optimal weight: 2.9990 chunk 31 optimal weight: 0.9990 chunk 102 optimal weight: 0.6980 chunk 136 optimal weight: 3.9990 chunk 54 optimal weight: 0.1980 chunk 131 optimal weight: 1.9990 chunk 94 optimal weight: 1.9990 chunk 56 optimal weight: 4.9990 overall best weight: 0.9584 ------------------------------------------------------------------------------- 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 = 0.3084 r_free = 0.3084 target = 0.053359 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2700 r_free = 0.2700 target = 0.040263 restraints weight = 45005.048| |-----------------------------------------------------------------------------| r_work (start): 0.2684 rms_B_bonded: 3.52 r_work: 0.2535 rms_B_bonded: 3.96 restraints_weight: 0.5000 r_work (final): 0.2535 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8810 moved from start: 0.1776 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= 0.127 Angle : 0.574 10.572 16726 Z= 0.289 Chirality : 0.039 0.141 1806 Planarity : 0.003 0.037 2132 Dihedral : 4.909 59.463 1670 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 6.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 2.30 % Allowed : 17.43 % 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: 0.96 (0.23), residues: 1478 helix: 1.76 (0.20), residues: 708 sheet: -1.15 (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 0.002 0.000 HIS A1092 PHE 0.014 0.001 PHE B 959 TYR 0.021 0.001 TYR B1033 ARG 0.011 0.000 ARG B 662 Details of bonding type rmsd hydrogen bonds : bond 0.03496 ( 593) hydrogen bonds : angle 4.43513 ( 1656) covalent geometry : bond 0.00290 (12384) covalent geometry : angle 0.57380 (16726) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6865.75 seconds wall clock time: 121 minutes 11.82 seconds (7271.82 seconds total)