Starting phenix.real_space_refine on Wed Sep 17 23:44:26 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ygg_39249/09_2025/8ygg_39249.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ygg_39249/09_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 { model { file = "/net/cci-nas-00/data/ceres_data/8ygg_39249/09_2025/8ygg_39249.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ygg_39249/09_2025/8ygg_39249.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8ygg_39249/09_2025/8ygg_39249.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ygg_39249/09_2025/8ygg_39249.map" } resolution = 2.98 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.041 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/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: 2.95, per 1000 atoms: 0.24 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: 0.97 Conformation dependent library (CDL) restraints added in 519.2 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 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: 0.40 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: 2.31 Time building geometry restraints manager: 1.32 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: 0.02 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: 1.090 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: 0.190 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 12.450 Find NCS groups from input model: 0.170 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.960 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.960 ------------------------------------------------------------------------------- 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 : 9.59 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.81 (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 ARG 0.008 0.000 ARG A 929 TYR 0.018 0.001 TYR B1033 PHE 0.016 0.001 PHE B1164 TRP 0.009 0.001 TRP A 856 HIS 0.004 0.000 HIS B1192 Details of bonding type rmsd covalent geometry : bond 0.00286 (12384) covalent geometry : angle 0.64983 (16726) hydrogen bonds : bond 0.13896 ( 593) hydrogen bonds : angle 5.54698 ( 1656) *********************** 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 : 0.549 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: 0.6405 time to fit residues: 60.1599 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 : 0.514 ------------------------------------------------------------------------------- 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 98 optimal weight: 2.9990 chunk 107 optimal weight: 4.9990 chunk 10 optimal weight: 0.9980 chunk 66 optimal weight: 5.9990 chunk 130 optimal weight: 5.9990 chunk 124 optimal weight: 0.7980 chunk 103 optimal weight: 2.9990 chunk 77 optimal weight: 6.9990 chunk 122 optimal weight: 7.9990 chunk 91 optimal weight: 3.9990 chunk 55 optimal weight: 4.9990 overall best weight: 2.3586 ------------------------------------------------------------------------------- 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 523 GLN B 996 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3061 r_free = 0.3061 target = 0.052426 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2669 r_free = 0.2669 target = 0.039266 restraints weight = 45276.563| |-----------------------------------------------------------------------------| r_work (start): 0.2652 rms_B_bonded: 3.49 r_work: 0.2504 rms_B_bonded: 3.91 restraints_weight: 0.5000 r_work (final): 0.2504 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8822 moved from start: 0.1180 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.059 12384 Z= 0.222 Angle : 0.553 8.422 16726 Z= 0.291 Chirality : 0.041 0.156 1806 Planarity : 0.003 0.029 2132 Dihedral : 5.306 56.586 1687 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 8.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer: Outliers : 2.84 % Allowed : 15.67 % Favored : 81.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.74 (0.23), residues: 1478 helix: 1.64 (0.20), residues: 706 sheet: -1.29 (0.35), residues: 222 loop : -0.12 (0.27), residues: 550 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 662 TYR 0.016 0.001 TYR B1079 PHE 0.015 0.001 PHE A1107 TRP 0.009 0.001 TRP B1189 HIS 0.003 0.001 HIS A1092 Details of bonding type rmsd covalent geometry : bond 0.00502 (12384) covalent geometry : angle 0.55261 (16726) hydrogen bonds : bond 0.04134 ( 593) hydrogen bonds : angle 4.76104 ( 1656) *********************** 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 98 residues out of total 1302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 61 time to evaluate : 0.529 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 701 ASP cc_start: 0.9261 (t70) cc_final: 0.8992 (t0) REVERT: A 856 TRP cc_start: 0.8139 (OUTLIER) cc_final: 0.6700 (m-90) REVERT: A 983 LEU cc_start: 0.9487 (OUTLIER) cc_final: 0.9250 (mt) REVERT: A 987 MET cc_start: 0.9678 (mmm) cc_final: 0.9395 (mmm) REVERT: A 1061 GLU cc_start: 0.9066 (OUTLIER) cc_final: 0.8862 (mp0) REVERT: B 1048 MET cc_start: 0.9269 (mpt) cc_final: 0.9047 (mpp) outliers start: 37 outliers final: 18 residues processed: 92 average time/residue: 0.5896 time to fit residues: 59.4542 Evaluate side-chains 76 residues out of total 1302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 55 time to evaluate : 0.507 ------------------------------------------------------------------------------- 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 1061 GLU 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 1022 ILE Chi-restraints excluded: chain B residue 1061 GLU Chi-restraints excluded: chain B residue 1182 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 92 optimal weight: 0.9990 chunk 96 optimal weight: 2.9990 chunk 31 optimal weight: 2.9990 chunk 143 optimal weight: 0.9980 chunk 108 optimal weight: 0.7980 chunk 85 optimal weight: 0.8980 chunk 66 optimal weight: 0.9980 chunk 24 optimal weight: 0.6980 chunk 45 optimal weight: 4.9990 chunk 113 optimal weight: 1.9990 chunk 61 optimal weight: 8.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 690 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3095 r_free = 0.3095 target = 0.053828 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2711 r_free = 0.2711 target = 0.040638 restraints weight = 44947.240| |-----------------------------------------------------------------------------| r_work (start): 0.2694 rms_B_bonded: 3.54 r_work: 0.2545 rms_B_bonded: 3.96 restraints_weight: 0.5000 r_work (final): 0.2545 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8804 moved from start: 0.1211 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 12384 Z= 0.115 Angle : 0.486 7.863 16726 Z= 0.256 Chirality : 0.039 0.146 1806 Planarity : 0.003 0.030 2132 Dihedral : 5.078 56.821 1676 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 7.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 2.15 % Allowed : 15.82 % Favored : 82.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.87 (0.23), residues: 1478 helix: 1.73 (0.20), residues: 706 sheet: -1.19 (0.35), residues: 222 loop : -0.05 (0.28), residues: 550 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 929 TYR 0.014 0.001 TYR B1079 PHE 0.009 0.001 PHE B 710 TRP 0.009 0.001 TRP B1189 HIS 0.002 0.000 HIS A1092 Details of bonding type rmsd covalent geometry : bond 0.00254 (12384) covalent geometry : angle 0.48566 (16726) hydrogen bonds : bond 0.03647 ( 593) hydrogen bonds : angle 4.55058 ( 1656) *********************** 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 93 residues out of total 1302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 65 time to evaluate : 0.493 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 957 MET cc_start: 0.9407 (mmm) cc_final: 0.9113 (mmm) REVERT: A 983 LEU cc_start: 0.9511 (OUTLIER) cc_final: 0.9259 (mt) REVERT: A 987 MET cc_start: 0.9633 (mmm) cc_final: 0.9412 (mmm) REVERT: B 957 MET cc_start: 0.9611 (mmm) cc_final: 0.9405 (mpp) REVERT: B 1048 MET cc_start: 0.9304 (OUTLIER) cc_final: 0.9041 (mpp) outliers start: 28 outliers final: 18 residues processed: 88 average time/residue: 0.6058 time to fit residues: 58.2027 Evaluate side-chains 79 residues out of total 1302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 59 time to evaluate : 0.401 ------------------------------------------------------------------------------- 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 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 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 1048 MET 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 79 optimal weight: 6.9990 chunk 29 optimal weight: 3.9990 chunk 121 optimal weight: 6.9990 chunk 81 optimal weight: 8.9990 chunk 36 optimal weight: 0.5980 chunk 93 optimal weight: 7.9990 chunk 31 optimal weight: 0.6980 chunk 104 optimal weight: 3.9990 chunk 129 optimal weight: 0.9990 chunk 136 optimal weight: 9.9990 chunk 8 optimal weight: 5.9990 overall best weight: 2.0586 ------------------------------------------------------------------------------- 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 = 0.3054 r_free = 0.3054 target = 0.052200 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2663 r_free = 0.2663 target = 0.039085 restraints weight = 45194.085| |-----------------------------------------------------------------------------| r_work (start): 0.2643 rms_B_bonded: 3.49 r_work: 0.2493 rms_B_bonded: 3.91 restraints_weight: 0.5000 r_work (final): 0.2493 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8826 moved from start: 0.1510 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 12384 Z= 0.198 Angle : 0.520 7.850 16726 Z= 0.273 Chirality : 0.040 0.140 1806 Planarity : 0.003 0.030 2132 Dihedral : 5.111 56.639 1674 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 7.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer: Outliers : 3.07 % Allowed : 15.82 % Favored : 81.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.85 (0.23), residues: 1478 helix: 1.72 (0.20), residues: 708 sheet: -1.20 (0.35), residues: 222 loop : -0.06 (0.28), residues: 548 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 929 TYR 0.015 0.001 TYR A 966 PHE 0.010 0.001 PHE A 596 TRP 0.010 0.001 TRP B1189 HIS 0.003 0.001 HIS A1092 Details of bonding type rmsd covalent geometry : bond 0.00446 (12384) covalent geometry : angle 0.52042 (16726) hydrogen bonds : bond 0.03847 ( 593) hydrogen bonds : angle 4.54141 ( 1656) *********************** 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 102 residues out of total 1302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 62 time to evaluate : 0.500 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 438 GLU cc_start: 0.8037 (tp30) cc_final: 0.7623 (pm20) REVERT: A 749 MET cc_start: 0.9428 (mmm) cc_final: 0.9166 (mmm) REVERT: A 856 TRP cc_start: 0.8193 (OUTLIER) cc_final: 0.6779 (m-90) REVERT: A 957 MET cc_start: 0.9390 (mmm) cc_final: 0.9118 (mmm) REVERT: A 983 LEU cc_start: 0.9505 (OUTLIER) cc_final: 0.9267 (mt) REVERT: B 1048 MET cc_start: 0.9319 (OUTLIER) cc_final: 0.9069 (mpp) outliers start: 40 outliers final: 22 residues processed: 95 average time/residue: 0.6151 time to fit residues: 63.9193 Evaluate side-chains 82 residues out of total 1302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 57 time to evaluate : 0.503 ------------------------------------------------------------------------------- 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 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 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 1048 MET Chi-restraints excluded: chain B residue 1061 GLU Chi-restraints excluded: chain B residue 1110 ILE 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 8 optimal weight: 7.9990 chunk 53 optimal weight: 2.9990 chunk 106 optimal weight: 3.9990 chunk 11 optimal weight: 2.9990 chunk 44 optimal weight: 5.9990 chunk 89 optimal weight: 1.9990 chunk 5 optimal weight: 7.9990 chunk 24 optimal weight: 0.9980 chunk 114 optimal weight: 2.9990 chunk 40 optimal weight: 0.9990 chunk 142 optimal weight: 7.9990 overall best weight: 1.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 540 GLN A1010 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3048 r_free = 0.3048 target = 0.051995 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2659 r_free = 0.2659 target = 0.038949 restraints weight = 45332.509| |-----------------------------------------------------------------------------| r_work (start): 0.2642 rms_B_bonded: 3.44 r_work: 0.2495 rms_B_bonded: 3.87 restraints_weight: 0.5000 r_work (final): 0.2495 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8836 moved from start: 0.1633 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 12384 Z= 0.190 Angle : 0.526 8.247 16726 Z= 0.275 Chirality : 0.040 0.145 1806 Planarity : 0.003 0.040 2132 Dihedral : 5.141 53.505 1674 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 7.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer: Outliers : 3.07 % Allowed : 16.28 % Favored : 80.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.89 (0.23), residues: 1478 helix: 1.75 (0.20), residues: 706 sheet: -1.21 (0.35), residues: 222 loop : -0.04 (0.28), residues: 550 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 929 TYR 0.014 0.001 TYR A 966 PHE 0.009 0.001 PHE B 990 TRP 0.010 0.001 TRP B1189 HIS 0.003 0.001 HIS A1092 Details of bonding type rmsd covalent geometry : bond 0.00430 (12384) covalent geometry : angle 0.52642 (16726) hydrogen bonds : bond 0.03820 ( 593) hydrogen bonds : angle 4.55337 ( 1656) *********************** 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 99 residues out of total 1302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 59 time to evaluate : 0.457 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 438 GLU cc_start: 0.8020 (tp30) cc_final: 0.7646 (pm20) REVERT: A 856 TRP cc_start: 0.8185 (OUTLIER) cc_final: 0.6735 (m-90) REVERT: A 929 ARG cc_start: 0.9408 (mtp-110) cc_final: 0.9184 (ttp-110) REVERT: A 987 MET cc_start: 0.9600 (mmm) cc_final: 0.9360 (mmm) REVERT: B 647 GLU cc_start: 0.9010 (tp30) cc_final: 0.8677 (tp30) REVERT: B 882 LYS cc_start: 0.9425 (OUTLIER) cc_final: 0.9064 (mtpt) REVERT: B 929 ARG cc_start: 0.9391 (mtm110) cc_final: 0.8918 (ttp-110) REVERT: B 1048 MET cc_start: 0.9324 (OUTLIER) cc_final: 0.9068 (mpp) outliers start: 40 outliers final: 21 residues processed: 93 average time/residue: 0.6609 time to fit residues: 66.8071 Evaluate side-chains 80 residues out of total 1302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 56 time to evaluate : 0.507 ------------------------------------------------------------------------------- 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 1064 ILE 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 816 THR Chi-restraints excluded: chain B residue 882 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 1048 MET Chi-restraints excluded: chain B residue 1061 GLU Chi-restraints excluded: chain B residue 1110 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 10 optimal weight: 1.9990 chunk 15 optimal weight: 0.9990 chunk 142 optimal weight: 0.9990 chunk 81 optimal weight: 0.0170 chunk 91 optimal weight: 3.9990 chunk 104 optimal weight: 5.9990 chunk 105 optimal weight: 0.8980 chunk 14 optimal weight: 1.9990 chunk 95 optimal weight: 0.7980 chunk 23 optimal weight: 0.9980 chunk 130 optimal weight: 1.9990 overall best weight: 0.7420 ------------------------------------------------------------------------------- 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 = 0.3084 r_free = 0.3084 target = 0.053475 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2704 r_free = 0.2704 target = 0.040386 restraints weight = 44829.742| |-----------------------------------------------------------------------------| r_work (start): 0.2688 rms_B_bonded: 3.51 r_work: 0.2540 rms_B_bonded: 3.95 restraints_weight: 0.5000 r_work (final): 0.2540 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8808 moved from start: 0.1605 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= 0.108 Angle : 0.499 9.307 16726 Z= 0.256 Chirality : 0.038 0.142 1806 Planarity : 0.003 0.031 2132 Dihedral : 5.044 54.748 1674 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 6.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer: Outliers : 2.76 % Allowed : 16.36 % Favored : 80.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.01 (0.23), residues: 1478 helix: 1.83 (0.20), residues: 710 sheet: -1.17 (0.35), residues: 222 loop : 0.06 (0.28), residues: 546 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 662 TYR 0.012 0.001 TYR A1029 PHE 0.009 0.001 PHE B 710 TRP 0.009 0.001 TRP B1189 HIS 0.002 0.000 HIS A1092 Details of bonding type rmsd covalent geometry : bond 0.00239 (12384) covalent geometry : angle 0.49864 (16726) hydrogen bonds : bond 0.03482 ( 593) hydrogen bonds : angle 4.43166 ( 1656) *********************** 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 101 residues out of total 1302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 65 time to evaluate : 0.499 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 438 GLU cc_start: 0.7901 (tp30) cc_final: 0.7599 (pm20) REVERT: A 503 LYS cc_start: 0.9688 (tppp) cc_final: 0.9435 (mmpt) REVERT: A 987 MET cc_start: 0.9638 (mmm) cc_final: 0.9339 (mmm) REVERT: A 1110 ILE cc_start: 0.9290 (tt) cc_final: 0.9086 (tp) REVERT: B 647 GLU cc_start: 0.9011 (tp30) cc_final: 0.8610 (tp30) REVERT: B 929 ARG cc_start: 0.9436 (mtm110) cc_final: 0.8991 (ttp80) REVERT: B 957 MET cc_start: 0.9598 (mmm) cc_final: 0.8961 (mpt) REVERT: B 1048 MET cc_start: 0.9299 (OUTLIER) cc_final: 0.9031 (mpp) REVERT: B 1118 LEU cc_start: 0.9243 (mm) cc_final: 0.8930 (pt) outliers start: 36 outliers final: 19 residues processed: 94 average time/residue: 0.6094 time to fit residues: 62.5066 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 : 0.469 ------------------------------------------------------------------------------- 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 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 1078 HIS 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 1048 MET Chi-restraints excluded: chain B residue 1061 GLU Chi-restraints excluded: chain B residue 1110 ILE 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 105 optimal weight: 0.8980 chunk 82 optimal weight: 6.9990 chunk 137 optimal weight: 0.9990 chunk 129 optimal weight: 6.9990 chunk 75 optimal weight: 3.9990 chunk 99 optimal weight: 4.9990 chunk 144 optimal weight: 4.9990 chunk 139 optimal weight: 1.9990 chunk 138 optimal weight: 4.9990 chunk 106 optimal weight: 0.9980 chunk 122 optimal weight: 7.9990 overall best weight: 1.7786 ------------------------------------------------------------------------------- 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 = 0.3058 r_free = 0.3058 target = 0.052448 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2667 r_free = 0.2667 target = 0.039291 restraints weight = 45193.537| |-----------------------------------------------------------------------------| r_work (start): 0.2651 rms_B_bonded: 3.48 r_work: 0.2504 rms_B_bonded: 3.91 restraints_weight: 0.5000 r_work (final): 0.2504 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8833 moved from start: 0.1704 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 12384 Z= 0.175 Angle : 0.545 11.099 16726 Z= 0.277 Chirality : 0.040 0.143 1806 Planarity : 0.003 0.036 2132 Dihedral : 4.686 52.958 1668 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 7.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 2.61 % Allowed : 17.05 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.02 (0.23), residues: 1478 helix: 1.85 (0.20), residues: 710 sheet: -1.19 (0.35), residues: 222 loop : 0.06 (0.28), residues: 546 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 929 TYR 0.012 0.001 TYR A 966 PHE 0.009 0.001 PHE A 596 TRP 0.011 0.001 TRP A 856 HIS 0.003 0.000 HIS A1092 Details of bonding type rmsd covalent geometry : bond 0.00397 (12384) covalent geometry : angle 0.54522 (16726) hydrogen bonds : bond 0.03659 ( 593) hydrogen bonds : angle 4.48508 ( 1656) *********************** 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 96 residues out of total 1302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 62 time to evaluate : 0.371 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 438 GLU cc_start: 0.7990 (tp30) cc_final: 0.7656 (pm20) REVERT: A 503 LYS cc_start: 0.9691 (tppp) cc_final: 0.9434 (mmpt) REVERT: A 957 MET cc_start: 0.9297 (mmm) cc_final: 0.8970 (mmm) REVERT: A 987 MET cc_start: 0.9650 (mmm) cc_final: 0.9364 (mmm) REVERT: B 647 GLU cc_start: 0.9033 (tp30) cc_final: 0.8680 (tp30) REVERT: B 1048 MET cc_start: 0.9325 (OUTLIER) cc_final: 0.9065 (mpp) REVERT: B 1118 LEU cc_start: 0.9254 (mm) cc_final: 0.8943 (pt) outliers start: 34 outliers final: 21 residues processed: 92 average time/residue: 0.5651 time to fit residues: 57.2325 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 : 0.504 ------------------------------------------------------------------------------- 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 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 1048 MET Chi-restraints excluded: chain B residue 1061 GLU Chi-restraints excluded: chain B residue 1110 ILE 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 133 optimal weight: 3.9990 chunk 115 optimal weight: 5.9990 chunk 58 optimal weight: 0.7980 chunk 118 optimal weight: 4.9990 chunk 22 optimal weight: 0.7980 chunk 28 optimal weight: 0.7980 chunk 120 optimal weight: 4.9990 chunk 74 optimal weight: 6.9990 chunk 124 optimal weight: 3.9990 chunk 24 optimal weight: 0.9990 chunk 55 optimal weight: 2.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- 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 = 0.052970 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2687 r_free = 0.2687 target = 0.039870 restraints weight = 44654.896| |-----------------------------------------------------------------------------| r_work (start): 0.2668 rms_B_bonded: 3.47 r_work: 0.2522 rms_B_bonded: 3.91 restraints_weight: 0.5000 r_work (final): 0.2522 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8818 moved from start: 0.1738 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= 0.139 Angle : 0.536 10.368 16726 Z= 0.270 Chirality : 0.039 0.157 1806 Planarity : 0.003 0.055 2132 Dihedral : 4.686 56.124 1668 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 7.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 2.92 % Allowed : 16.82 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.03 (0.23), residues: 1478 helix: 1.87 (0.20), residues: 710 sheet: -1.18 (0.35), residues: 222 loop : 0.05 (0.28), residues: 546 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG A 929 TYR 0.013 0.001 TYR B1033 PHE 0.008 0.001 PHE B 710 TRP 0.014 0.001 TRP A 856 HIS 0.003 0.000 HIS A1092 Details of bonding type rmsd covalent geometry : bond 0.00316 (12384) covalent geometry : angle 0.53582 (16726) hydrogen bonds : bond 0.03542 ( 593) hydrogen bonds : angle 4.45232 ( 1656) *********************** 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 98 residues out of total 1302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 60 time to evaluate : 0.441 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 438 GLU cc_start: 0.7951 (tp30) cc_final: 0.7648 (pm20) REVERT: A 503 LYS cc_start: 0.9695 (tppp) cc_final: 0.9418 (mmpt) REVERT: A 929 ARG cc_start: 0.9339 (mtp-110) cc_final: 0.8967 (ttp-110) REVERT: A 957 MET cc_start: 0.9305 (mmm) cc_final: 0.8980 (mmm) REVERT: A 987 MET cc_start: 0.9668 (mmm) cc_final: 0.9377 (mmm) REVERT: B 647 GLU cc_start: 0.9044 (tp30) cc_final: 0.8668 (tp30) REVERT: B 929 ARG cc_start: 0.9467 (mtm110) cc_final: 0.9096 (ttp-110) REVERT: B 957 MET cc_start: 0.9585 (mmm) cc_final: 0.8997 (mpt) REVERT: B 1048 MET cc_start: 0.9306 (OUTLIER) cc_final: 0.9039 (mpp) REVERT: B 1118 LEU cc_start: 0.9217 (mm) cc_final: 0.8914 (pt) outliers start: 38 outliers final: 21 residues processed: 94 average time/residue: 0.5879 time to fit residues: 60.7152 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 : 0.502 ------------------------------------------------------------------------------- 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 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 A residue 1125 ILE 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 1048 MET Chi-restraints excluded: chain B residue 1061 GLU Chi-restraints excluded: chain B residue 1110 ILE 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 84 optimal weight: 5.9990 chunk 41 optimal weight: 0.9980 chunk 87 optimal weight: 4.9990 chunk 131 optimal weight: 0.9980 chunk 21 optimal weight: 0.9980 chunk 108 optimal weight: 3.9990 chunk 88 optimal weight: 2.9990 chunk 141 optimal weight: 3.9990 chunk 43 optimal weight: 2.9990 chunk 125 optimal weight: 9.9990 chunk 5 optimal weight: 9.9990 overall best weight: 1.7984 ------------------------------------------------------------------------------- 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 = 0.3055 r_free = 0.3055 target = 0.052328 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2666 r_free = 0.2666 target = 0.039193 restraints weight = 44949.363| |-----------------------------------------------------------------------------| r_work (start): 0.2647 rms_B_bonded: 3.46 r_work: 0.2499 rms_B_bonded: 3.90 restraints_weight: 0.5000 r_work (final): 0.2499 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8834 moved from start: 0.1797 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 12384 Z= 0.178 Angle : 0.569 10.064 16726 Z= 0.287 Chirality : 0.040 0.148 1806 Planarity : 0.004 0.054 2132 Dihedral : 4.785 59.487 1668 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 7.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 2.07 % Allowed : 17.43 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.99 (0.23), residues: 1478 helix: 1.82 (0.20), residues: 710 sheet: -1.23 (0.35), residues: 222 loop : 0.07 (0.28), residues: 546 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG B 662 TYR 0.016 0.001 TYR B1033 PHE 0.009 0.001 PHE A 596 TRP 0.012 0.001 TRP A 856 HIS 0.003 0.000 HIS A1092 Details of bonding type rmsd covalent geometry : bond 0.00405 (12384) covalent geometry : angle 0.56895 (16726) hydrogen bonds : bond 0.03683 ( 593) hydrogen bonds : angle 4.50624 ( 1656) *********************** 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 88 residues out of total 1302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 61 time to evaluate : 0.398 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 438 GLU cc_start: 0.8001 (tp30) cc_final: 0.7700 (pm20) REVERT: A 503 LYS cc_start: 0.9701 (tppp) cc_final: 0.9418 (mmpt) REVERT: A 701 ASP cc_start: 0.9255 (t70) cc_final: 0.8985 (t0) REVERT: A 929 ARG cc_start: 0.9308 (mtp-110) cc_final: 0.9077 (ttp-110) REVERT: A 957 MET cc_start: 0.9320 (mmm) cc_final: 0.8991 (mmm) REVERT: A 987 MET cc_start: 0.9671 (mmm) cc_final: 0.9378 (mmm) REVERT: B 647 GLU cc_start: 0.9066 (tp30) cc_final: 0.8673 (tp30) REVERT: B 929 ARG cc_start: 0.9437 (mtm110) cc_final: 0.9217 (ttp-110) REVERT: B 957 MET cc_start: 0.9591 (mmm) cc_final: 0.9065 (mpt) REVERT: B 1048 MET cc_start: 0.9320 (OUTLIER) cc_final: 0.9060 (mpp) REVERT: B 1118 LEU cc_start: 0.9222 (mm) cc_final: 0.8930 (pt) outliers start: 27 outliers final: 25 residues processed: 85 average time/residue: 0.5875 time to fit residues: 55.0373 Evaluate side-chains 86 residues out of total 1302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 60 time to evaluate : 0.540 ------------------------------------------------------------------------------- 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 1064 ILE Chi-restraints excluded: chain A residue 1078 HIS Chi-restraints excluded: chain A residue 1125 ILE 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 1022 ILE Chi-restraints excluded: chain B residue 1048 MET 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 1182 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 143 optimal weight: 2.9990 chunk 113 optimal weight: 0.7980 chunk 47 optimal weight: 3.9990 chunk 40 optimal weight: 5.9990 chunk 41 optimal weight: 0.9990 chunk 27 optimal weight: 0.5980 chunk 34 optimal weight: 4.9990 chunk 58 optimal weight: 3.9990 chunk 46 optimal weight: 1.9990 chunk 18 optimal weight: 0.9990 chunk 81 optimal weight: 0.7980 overall best weight: 0.8384 ------------------------------------------------------------------------------- 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 = 0.3084 r_free = 0.3084 target = 0.053397 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2702 r_free = 0.2702 target = 0.040359 restraints weight = 44770.570| |-----------------------------------------------------------------------------| r_work (start): 0.2687 rms_B_bonded: 3.52 r_work: 0.2539 rms_B_bonded: 3.93 restraints_weight: 0.5000 r_work (final): 0.2539 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8799 moved from start: 0.1775 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= 0.117 Angle : 0.560 10.828 16726 Z= 0.279 Chirality : 0.039 0.139 1806 Planarity : 0.003 0.049 2132 Dihedral : 4.677 53.351 1668 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 6.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer: Outliers : 2.15 % Allowed : 17.59 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.02 (0.23), residues: 1478 helix: 1.83 (0.20), residues: 710 sheet: -1.19 (0.35), residues: 222 loop : 0.08 (0.28), residues: 546 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG B 662 TYR 0.018 0.001 TYR B1033 PHE 0.008 0.001 PHE B 710 TRP 0.012 0.001 TRP A 856 HIS 0.002 0.000 HIS A1092 Details of bonding type rmsd covalent geometry : bond 0.00265 (12384) covalent geometry : angle 0.56023 (16726) hydrogen bonds : bond 0.03453 ( 593) hydrogen bonds : angle 4.45675 ( 1656) ********************** 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 94 residues out of total 1302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 66 time to evaluate : 0.500 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 438 GLU cc_start: 0.7941 (tp30) cc_final: 0.7649 (pm20) REVERT: A 503 LYS cc_start: 0.9707 (tppp) cc_final: 0.9415 (mmpt) REVERT: A 701 ASP cc_start: 0.9242 (t70) cc_final: 0.8967 (t0) REVERT: A 929 ARG cc_start: 0.9301 (mtp-110) cc_final: 0.9091 (ttp-110) REVERT: A 957 MET cc_start: 0.9330 (mmm) cc_final: 0.9013 (mmm) REVERT: A 987 MET cc_start: 0.9672 (mmm) cc_final: 0.9363 (mmm) REVERT: B 647 GLU cc_start: 0.9074 (tp30) cc_final: 0.8675 (tp30) REVERT: B 929 ARG cc_start: 0.9443 (mtm110) cc_final: 0.9177 (ttp80) REVERT: B 1048 MET cc_start: 0.9305 (OUTLIER) cc_final: 0.9037 (mpp) REVERT: B 1118 LEU cc_start: 0.9213 (mm) cc_final: 0.8924 (pt) REVERT: B 1147 LYS cc_start: 0.9607 (mmmm) cc_final: 0.9307 (mmmm) outliers start: 28 outliers final: 21 residues processed: 91 average time/residue: 0.6104 time to fit residues: 60.9195 Evaluate side-chains 83 residues out of total 1302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 61 time to evaluate : 0.513 ------------------------------------------------------------------------------- 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 A residue 1125 ILE 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 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 1182 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 108 optimal weight: 6.9990 chunk 20 optimal weight: 4.9990 chunk 28 optimal weight: 0.0170 chunk 145 optimal weight: 0.8980 chunk 96 optimal weight: 3.9990 chunk 101 optimal weight: 0.9980 chunk 19 optimal weight: 3.9990 chunk 105 optimal weight: 0.6980 chunk 48 optimal weight: 3.9990 chunk 139 optimal weight: 1.9990 chunk 54 optimal weight: 3.9990 overall best weight: 0.9220 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 930 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3088 r_free = 0.3088 target = 0.053519 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.2707 r_free = 0.2707 target = 0.040489 restraints weight = 44982.477| |-----------------------------------------------------------------------------| r_work (start): 0.2691 rms_B_bonded: 3.49 r_work: 0.2543 rms_B_bonded: 3.92 restraints_weight: 0.5000 r_work (final): 0.2543 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8810 moved from start: 0.1792 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= 0.124 Angle : 0.568 10.722 16726 Z= 0.283 Chirality : 0.039 0.142 1806 Planarity : 0.003 0.047 2132 Dihedral : 4.612 53.327 1668 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 6.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer: Outliers : 2.00 % Allowed : 17.67 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.00 (0.23), residues: 1478 helix: 1.81 (0.20), residues: 710 sheet: -1.19 (0.35), residues: 222 loop : 0.10 (0.28), residues: 546 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG B 662 TYR 0.021 0.001 TYR B1033 PHE 0.008 0.001 PHE B 710 TRP 0.019 0.001 TRP A 856 HIS 0.002 0.000 HIS A1092 Details of bonding type rmsd covalent geometry : bond 0.00283 (12384) covalent geometry : angle 0.56782 (16726) hydrogen bonds : bond 0.03423 ( 593) hydrogen bonds : angle 4.46573 ( 1656) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2972.90 seconds wall clock time: 51 minutes 49.00 seconds (3109.00 seconds total)