Starting phenix.real_space_refine on Thu Sep 26 05:57:51 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ygg_39249/09_2024/8ygg_39249.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ygg_39249/09_2024/8ygg_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ygg_39249/09_2024/8ygg_39249.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ygg_39249/09_2024/8ygg_39249.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ygg_39249/09_2024/8ygg_39249.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ygg_39249/09_2024/8ygg_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-5461/modules/chem_data/mon_lib" Total number of atoms: 12096 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 6048 Number of conformers: 1 Conformer: "" Number of residues, atoms: 745, 6048 Classifications: {'peptide': 745} Link IDs: {'PTRANS': 30, 'TRANS': 714} Chain breaks: 2 Chain: "B" Number of atoms: 6048 Number of conformers: 1 Conformer: "" Number of residues, atoms: 745, 6048 Classifications: {'peptide': 745} Link IDs: {'PTRANS': 30, 'TRANS': 714} Chain breaks: 2 Time building chain proxies: 7.05, per 1000 atoms: 0.58 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: 2.82 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: 1.30 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: 3.77 Time building geometry restraints manager: 3.30 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: 0.00 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: 1.000 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: 0.410 Check model and map are aligned: 0.080 Set scattering table: 0.100 Process input model: 27.910 Find NCS groups from input model: 0.480 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: 0.010 Load rotamer database and sin/cos tables:12.180 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 42.220 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8768 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 12384 Z= 0.184 Angle : 0.650 13.227 16726 Z= 0.371 Chirality : 0.043 0.518 1806 Planarity : 0.003 0.045 2132 Dihedral : 15.453 88.785 4634 Min Nonbonded Distance : 2.233 Molprobity Statistics. All-atom Clashscore : 9.55 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.71 % Favored : 97.23 % Rotamer: Outliers : 2.07 % Allowed : 16.67 % Favored : 81.26 % Cbeta Deviations : 0.07 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.81 (0.23), residues: 1478 helix: 1.73 (0.21), residues: 702 sheet: -1.29 (0.35), residues: 224 loop : -0.09 (0.27), residues: 552 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 856 HIS 0.004 0.000 HIS B1192 PHE 0.016 0.001 PHE B1164 TYR 0.018 0.001 TYR B1033 ARG 0.008 0.000 ARG A 929 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2956 Ramachandran restraints generated. 1478 Oldfield, 0 Emsley, 1478 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2956 Ramachandran restraints generated. 1478 Oldfield, 0 Emsley, 1478 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 1302 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 61 time to evaluate : 1.391 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: 1.1928 time to fit residues: 113.1210 Evaluate side-chains 81 residues out of total 1302 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 61 time to evaluate : 1.319 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8780 moved from start: 0.0901 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 12384 Z= 0.159 Angle : 0.494 8.818 16726 Z= 0.260 Chirality : 0.039 0.147 1806 Planarity : 0.003 0.030 2132 Dihedral : 5.032 55.051 1687 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 6.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 2.61 % Allowed : 15.28 % Favored : 82.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.85 (0.23), residues: 1478 helix: 1.71 (0.20), residues: 708 sheet: -1.21 (0.36), residues: 222 loop : -0.06 (0.28), residues: 548 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B1189 HIS 0.003 0.000 HIS A 650 PHE 0.011 0.001 PHE A1107 TYR 0.014 0.001 TYR B1079 ARG 0.006 0.000 ARG B 662 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2956 Ramachandran restraints generated. 1478 Oldfield, 0 Emsley, 1478 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2956 Ramachandran restraints generated. 1478 Oldfield, 0 Emsley, 1478 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 1302 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 71 time to evaluate : 1.375 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 701 ASP cc_start: 0.9128 (t70) cc_final: 0.8836 (OUTLIER) REVERT: A 987 MET cc_start: 0.9675 (mmm) cc_final: 0.9435 (mmm) REVERT: B 1048 MET cc_start: 0.9232 (mpt) cc_final: 0.9027 (mpp) REVERT: B 1147 LYS cc_start: 0.9503 (tppt) cc_final: 0.9296 (mmmm) outliers start: 34 outliers final: 16 residues processed: 99 average time/residue: 1.1824 time to fit residues: 128.8429 Evaluate side-chains 74 residues out of total 1302 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 59 time to evaluate : 1.389 ------------------------------------------------------------------------------- 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 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 74 optimal weight: 7.9990 chunk 41 optimal weight: 5.9990 chunk 111 optimal weight: 0.0980 chunk 91 optimal weight: 0.5980 chunk 37 optimal weight: 0.9990 chunk 134 optimal weight: 3.9990 chunk 145 optimal weight: 2.9990 chunk 119 optimal weight: 20.0000 chunk 133 optimal weight: 2.9990 chunk 45 optimal weight: 3.9990 chunk 108 optimal weight: 0.8980 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8796 moved from start: 0.1138 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= 0.187 Angle : 0.485 7.690 16726 Z= 0.255 Chirality : 0.039 0.143 1806 Planarity : 0.003 0.033 2132 Dihedral : 4.685 54.997 1670 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 6.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 2.30 % Allowed : 16.05 % Favored : 81.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.94 (0.23), residues: 1478 helix: 1.77 (0.20), residues: 706 sheet: -1.15 (0.36), residues: 222 loop : 0.00 (0.28), residues: 550 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B1189 HIS 0.003 0.000 HIS B 748 PHE 0.008 0.001 PHE A1164 TYR 0.013 0.001 TYR B1079 ARG 0.007 0.000 ARG B1140 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2956 Ramachandran restraints generated. 1478 Oldfield, 0 Emsley, 1478 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2956 Ramachandran restraints generated. 1478 Oldfield, 0 Emsley, 1478 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 1302 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 65 time to evaluate : 1.404 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 856 TRP cc_start: 0.8220 (OUTLIER) cc_final: 0.6672 (m-90) REVERT: A 957 MET cc_start: 0.9449 (mmm) cc_final: 0.9230 (mmm) REVERT: A 987 MET cc_start: 0.9653 (mmm) cc_final: 0.9412 (mmm) REVERT: B 1048 MET cc_start: 0.9277 (OUTLIER) cc_final: 0.9027 (mpp) REVERT: B 1118 LEU cc_start: 0.9256 (mm) cc_final: 0.8926 (pt) outliers start: 30 outliers final: 19 residues processed: 89 average time/residue: 1.1643 time to fit residues: 114.4110 Evaluate side-chains 78 residues out of total 1302 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 57 time to evaluate : 1.385 ------------------------------------------------------------------------------- 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 Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 133 optimal weight: 4.9990 chunk 101 optimal weight: 2.9990 chunk 69 optimal weight: 5.9990 chunk 14 optimal weight: 0.5980 chunk 64 optimal weight: 3.9990 chunk 90 optimal weight: 0.7980 chunk 135 optimal weight: 6.9990 chunk 143 optimal weight: 0.9980 chunk 70 optimal weight: 0.9990 chunk 128 optimal weight: 10.0000 chunk 38 optimal weight: 0.9980 overall best weight: 0.8782 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8793 moved from start: 0.1358 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.114 12384 Z= 0.184 Angle : 0.506 11.587 16726 Z= 0.266 Chirality : 0.039 0.146 1806 Planarity : 0.003 0.028 2132 Dihedral : 4.654 55.828 1670 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 6.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 3.07 % Allowed : 15.51 % Favored : 81.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.94 (0.23), residues: 1478 helix: 1.75 (0.20), residues: 706 sheet: -1.09 (0.36), residues: 222 loop : 0.02 (0.28), residues: 550 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B1189 HIS 0.002 0.000 HIS A1092 PHE 0.010 0.001 PHE B 990 TYR 0.028 0.001 TYR B1029 ARG 0.005 0.000 ARG B1140 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2956 Ramachandran restraints generated. 1478 Oldfield, 0 Emsley, 1478 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2956 Ramachandran restraints generated. 1478 Oldfield, 0 Emsley, 1478 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 1302 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 66 time to evaluate : 1.495 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 856 TRP cc_start: 0.8247 (OUTLIER) cc_final: 0.7615 (m100) REVERT: A 957 MET cc_start: 0.9452 (mmm) cc_final: 0.9211 (mmm) REVERT: B 638 THR cc_start: 0.9646 (OUTLIER) cc_final: 0.9251 (t) REVERT: B 749 MET cc_start: 0.9076 (OUTLIER) cc_final: 0.8402 (mtp) REVERT: B 929 ARG cc_start: 0.9366 (mtm110) cc_final: 0.8510 (ttp80) REVERT: B 1029 TYR cc_start: 0.8266 (p90) cc_final: 0.8054 (p90) REVERT: B 1048 MET cc_start: 0.9279 (OUTLIER) cc_final: 0.9041 (mpp) REVERT: B 1118 LEU cc_start: 0.9259 (mm) cc_final: 0.8940 (pt) REVERT: B 1147 LYS cc_start: 0.9556 (OUTLIER) cc_final: 0.9304 (mmmm) outliers start: 40 outliers final: 19 residues processed: 98 average time/residue: 1.1761 time to fit residues: 127.3208 Evaluate side-chains 84 residues out of total 1302 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 60 time to evaluate : 1.394 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 542 LEU Chi-restraints excluded: chain A residue 579 VAL Chi-restraints excluded: chain A residue 588 VAL Chi-restraints excluded: chain A residue 636 VAL Chi-restraints excluded: chain A residue 669 VAL Chi-restraints excluded: chain A residue 674 THR Chi-restraints excluded: chain A residue 856 TRP Chi-restraints excluded: chain A residue 895 THR Chi-restraints excluded: chain A residue 925 VAL Chi-restraints excluded: chain A residue 931 MET Chi-restraints excluded: chain A residue 983 LEU Chi-restraints excluded: chain A residue 1078 HIS Chi-restraints excluded: chain B residue 443 LEU Chi-restraints excluded: chain B residue 534 ILE Chi-restraints excluded: chain B residue 542 LEU Chi-restraints excluded: chain B residue 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 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 119 optimal weight: 3.9990 chunk 81 optimal weight: 8.9990 chunk 2 optimal weight: 5.9990 chunk 106 optimal weight: 3.9990 chunk 59 optimal weight: 0.9990 chunk 122 optimal weight: 6.9990 chunk 98 optimal weight: 6.9990 chunk 0 optimal weight: 8.9990 chunk 73 optimal weight: 4.9990 chunk 128 optimal weight: 3.9990 chunk 36 optimal weight: 2.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1010 HIS B 523 GLN ** B1192 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8848 moved from start: 0.1759 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.081 12384 Z= 0.433 Angle : 0.606 10.999 16726 Z= 0.312 Chirality : 0.042 0.188 1806 Planarity : 0.004 0.045 2132 Dihedral : 5.003 52.838 1670 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 8.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 3.07 % Allowed : 15.90 % 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: 0.82 (0.23), residues: 1478 helix: 1.70 (0.20), residues: 704 sheet: -1.23 (0.35), residues: 222 loop : -0.07 (0.27), residues: 552 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B1189 HIS 0.004 0.001 HIS B 748 PHE 0.012 0.001 PHE A 596 TYR 0.022 0.001 TYR A 966 ARG 0.010 0.001 ARG A 929 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2956 Ramachandran restraints generated. 1478 Oldfield, 0 Emsley, 1478 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2956 Ramachandran restraints generated. 1478 Oldfield, 0 Emsley, 1478 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 1302 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 58 time to evaluate : 1.424 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 438 GLU cc_start: 0.8024 (tp30) cc_final: 0.7682 (pm20) REVERT: A 856 TRP cc_start: 0.8353 (OUTLIER) cc_final: 0.6984 (m-90) REVERT: A 929 ARG cc_start: 0.9245 (mtp-110) cc_final: 0.9017 (ttp-110) REVERT: A 957 MET cc_start: 0.9421 (mmm) cc_final: 0.9216 (mmm) REVERT: B 929 ARG cc_start: 0.9407 (mtm110) cc_final: 0.8598 (ttp80) REVERT: B 931 MET cc_start: 0.9000 (OUTLIER) cc_final: 0.8741 (ptm) REVERT: B 1029 TYR cc_start: 0.8423 (p90) cc_final: 0.8223 (p90) REVERT: B 1147 LYS cc_start: 0.9579 (OUTLIER) cc_final: 0.9331 (mmmm) REVERT: B 1159 LEU cc_start: 0.9684 (OUTLIER) cc_final: 0.9482 (mm) outliers start: 40 outliers final: 22 residues processed: 90 average time/residue: 1.2377 time to fit residues: 122.5081 Evaluate side-chains 80 residues out of total 1302 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 54 time to evaluate : 1.362 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 542 LEU Chi-restraints excluded: chain A residue 579 VAL Chi-restraints excluded: chain A residue 588 VAL Chi-restraints excluded: chain A residue 636 VAL Chi-restraints excluded: chain A residue 659 LEU Chi-restraints excluded: chain A residue 669 VAL Chi-restraints excluded: chain A residue 674 THR Chi-restraints excluded: chain A residue 856 TRP Chi-restraints excluded: chain A residue 895 THR Chi-restraints excluded: chain A residue 925 VAL Chi-restraints excluded: chain A residue 1078 HIS Chi-restraints excluded: chain 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 789 HIS Chi-restraints excluded: chain B residue 816 THR Chi-restraints excluded: chain B residue 925 VAL Chi-restraints excluded: chain B residue 931 MET Chi-restraints excluded: chain B residue 978 LEU Chi-restraints excluded: chain B residue 1022 ILE Chi-restraints excluded: chain B residue 1061 GLU Chi-restraints excluded: chain B residue 1110 ILE Chi-restraints excluded: chain B residue 1147 LYS Chi-restraints excluded: chain B residue 1159 LEU 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 48 optimal weight: 0.8980 chunk 128 optimal weight: 0.9990 chunk 28 optimal weight: 0.9990 chunk 83 optimal weight: 3.9990 chunk 35 optimal weight: 1.9990 chunk 143 optimal weight: 2.9990 chunk 118 optimal weight: 8.9990 chunk 66 optimal weight: 5.9990 chunk 11 optimal weight: 3.9990 chunk 47 optimal weight: 4.9990 chunk 75 optimal weight: 7.9990 overall best weight: 1.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8823 moved from start: 0.1699 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= 0.238 Angle : 0.532 9.633 16726 Z= 0.273 Chirality : 0.040 0.143 1806 Planarity : 0.003 0.030 2132 Dihedral : 4.899 54.402 1670 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 7.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer: Outliers : 2.84 % Allowed : 16.36 % Favored : 80.80 % 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: 0.90 (0.23), residues: 1478 helix: 1.75 (0.20), residues: 708 sheet: -1.22 (0.35), residues: 222 loop : -0.01 (0.28), residues: 548 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B1189 HIS 0.002 0.000 HIS A1092 PHE 0.008 0.001 PHE B 710 TYR 0.016 0.001 TYR B1029 ARG 0.007 0.000 ARG A 683 *********************** 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 97 residues out of total 1302 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 60 time to evaluate : 1.501 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 438 GLU cc_start: 0.7949 (tp30) cc_final: 0.7668 (pm20) REVERT: A 503 LYS cc_start: 0.9650 (tppp) cc_final: 0.9421 (mmpt) REVERT: A 749 MET cc_start: 0.9440 (mmm) cc_final: 0.8854 (mmm) REVERT: B 848 TYR cc_start: 0.9421 (m-80) cc_final: 0.9185 (m-80) REVERT: B 916 TYR cc_start: 0.8455 (m-10) cc_final: 0.8190 (m-10) REVERT: B 929 ARG cc_start: 0.9413 (mtm110) cc_final: 0.8629 (ttp80) REVERT: B 931 MET cc_start: 0.9053 (OUTLIER) cc_final: 0.8741 (ptm) REVERT: B 1029 TYR cc_start: 0.8411 (p90) cc_final: 0.8210 (p90) REVERT: B 1118 LEU cc_start: 0.9221 (mm) cc_final: 0.8905 (pt) REVERT: B 1147 LYS cc_start: 0.9573 (OUTLIER) cc_final: 0.9323 (mmmm) REVERT: B 1159 LEU cc_start: 0.9684 (OUTLIER) cc_final: 0.9441 (mm) outliers start: 37 outliers final: 25 residues processed: 91 average time/residue: 1.1644 time to fit residues: 116.9070 Evaluate side-chains 88 residues out of total 1302 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 60 time to evaluate : 1.298 ------------------------------------------------------------------------------- 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 789 HIS Chi-restraints excluded: chain B residue 816 THR Chi-restraints excluded: chain B residue 925 VAL Chi-restraints excluded: chain B residue 931 MET Chi-restraints excluded: chain B residue 978 LEU Chi-restraints excluded: chain B residue 1022 ILE Chi-restraints excluded: chain B residue 1061 GLU Chi-restraints excluded: chain B residue 1110 ILE Chi-restraints excluded: chain B residue 1147 LYS Chi-restraints excluded: chain B residue 1159 LEU 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 138 optimal weight: 9.9990 chunk 16 optimal weight: 2.9990 chunk 81 optimal weight: 2.9990 chunk 104 optimal weight: 6.9990 chunk 120 optimal weight: 7.9990 chunk 79 optimal weight: 6.9990 chunk 142 optimal weight: 0.9990 chunk 89 optimal weight: 3.9990 chunk 86 optimal weight: 4.9990 chunk 65 optimal weight: 1.9990 chunk 88 optimal weight: 0.0670 overall best weight: 1.8126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8828 moved from start: 0.1758 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= 0.267 Angle : 0.556 10.807 16726 Z= 0.283 Chirality : 0.040 0.147 1806 Planarity : 0.003 0.030 2132 Dihedral : 4.931 55.292 1670 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 7.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.32 % Favored : 96.68 % Rotamer: Outliers : 2.92 % Allowed : 16.90 % Favored : 80.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.90 (0.23), residues: 1478 helix: 1.75 (0.20), residues: 708 sheet: -1.24 (0.35), residues: 222 loop : -0.00 (0.28), residues: 548 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 856 HIS 0.003 0.000 HIS A1092 PHE 0.009 0.001 PHE A 596 TYR 0.015 0.001 TYR B1029 ARG 0.007 0.000 ARG A 929 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2956 Ramachandran restraints generated. 1478 Oldfield, 0 Emsley, 1478 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2956 Ramachandran restraints generated. 1478 Oldfield, 0 Emsley, 1478 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 1302 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 61 time to evaluate : 1.412 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 438 GLU cc_start: 0.7970 (tp30) cc_final: 0.7664 (pm20) REVERT: A 503 LYS cc_start: 0.9654 (tppp) cc_final: 0.9417 (mmpt) REVERT: A 929 ARG cc_start: 0.8984 (ttp-110) cc_final: 0.8664 (tpm170) REVERT: A 957 MET cc_start: 0.9401 (mmm) cc_final: 0.9173 (mmm) REVERT: B 848 TYR cc_start: 0.9424 (m-80) cc_final: 0.9181 (m-80) REVERT: B 929 ARG cc_start: 0.9417 (mtm110) cc_final: 0.8629 (ttp80) REVERT: B 931 MET cc_start: 0.9058 (OUTLIER) cc_final: 0.8588 (ptm) REVERT: B 957 MET cc_start: 0.9489 (mpp) cc_final: 0.8748 (mpt) REVERT: B 1118 LEU cc_start: 0.9219 (mm) cc_final: 0.8906 (pt) REVERT: B 1133 LEU cc_start: 0.9525 (OUTLIER) cc_final: 0.9243 (mm) REVERT: B 1147 LYS cc_start: 0.9570 (OUTLIER) cc_final: 0.9313 (mmmm) REVERT: B 1159 LEU cc_start: 0.9679 (OUTLIER) cc_final: 0.9431 (mm) outliers start: 38 outliers final: 26 residues processed: 95 average time/residue: 1.1263 time to fit residues: 118.5312 Evaluate side-chains 90 residues out of total 1302 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 60 time to evaluate : 1.353 ------------------------------------------------------------------------------- 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 789 HIS Chi-restraints excluded: chain B residue 816 THR Chi-restraints excluded: chain B residue 895 THR Chi-restraints excluded: chain B residue 925 VAL Chi-restraints excluded: chain B residue 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 1133 LEU Chi-restraints excluded: chain B residue 1147 LYS Chi-restraints excluded: chain B residue 1159 LEU 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 56 optimal weight: 2.9990 chunk 85 optimal weight: 0.8980 chunk 42 optimal weight: 2.9990 chunk 28 optimal weight: 0.7980 chunk 27 optimal weight: 0.7980 chunk 90 optimal weight: 1.9990 chunk 97 optimal weight: 6.9990 chunk 70 optimal weight: 4.9990 chunk 13 optimal weight: 3.9990 chunk 112 optimal weight: 4.9990 chunk 129 optimal weight: 0.8980 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8813 moved from start: 0.1732 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 12384 Z= 0.192 Angle : 0.543 11.583 16726 Z= 0.276 Chirality : 0.039 0.147 1806 Planarity : 0.003 0.031 2132 Dihedral : 4.856 57.031 1670 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 6.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer: Outliers : 2.84 % Allowed : 17.13 % Favored : 80.03 % 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: 0.95 (0.23), residues: 1478 helix: 1.79 (0.20), residues: 708 sheet: -1.20 (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 0.008 0.001 PHE B 710 TYR 0.018 0.001 TYR B1029 ARG 0.006 0.000 ARG A 929 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2956 Ramachandran restraints generated. 1478 Oldfield, 0 Emsley, 1478 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2956 Ramachandran restraints generated. 1478 Oldfield, 0 Emsley, 1478 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 1302 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 64 time to evaluate : 1.259 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 438 GLU cc_start: 0.7929 (tp30) cc_final: 0.7633 (pm20) REVERT: A 503 LYS cc_start: 0.9657 (tppp) cc_final: 0.9399 (mmpt) REVERT: A 929 ARG cc_start: 0.8969 (ttp-110) cc_final: 0.8669 (tpm170) REVERT: A 957 MET cc_start: 0.9431 (mmm) cc_final: 0.9187 (mmm) REVERT: B 929 ARG cc_start: 0.9408 (mtm110) cc_final: 0.9068 (ttp80) REVERT: B 957 MET cc_start: 0.9488 (mpp) cc_final: 0.8737 (mpt) REVERT: B 1048 MET cc_start: 0.9387 (mtm) cc_final: 0.9034 (mpp) REVERT: B 1118 LEU cc_start: 0.9198 (mm) cc_final: 0.8892 (pt) REVERT: B 1133 LEU cc_start: 0.9502 (OUTLIER) cc_final: 0.9219 (mm) REVERT: B 1147 LYS cc_start: 0.9571 (OUTLIER) cc_final: 0.9338 (mmmm) REVERT: B 1159 LEU cc_start: 0.9687 (OUTLIER) cc_final: 0.9434 (mm) outliers start: 37 outliers final: 25 residues processed: 98 average time/residue: 1.1072 time to fit residues: 119.9649 Evaluate side-chains 89 residues out of total 1302 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 61 time to evaluate : 1.409 ------------------------------------------------------------------------------- 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 789 HIS Chi-restraints excluded: chain B residue 816 THR Chi-restraints excluded: chain B residue 895 THR Chi-restraints excluded: chain B residue 925 VAL Chi-restraints excluded: chain B residue 978 LEU Chi-restraints excluded: chain B residue 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 1159 LEU 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 136 optimal weight: 0.0060 chunk 124 optimal weight: 7.9990 chunk 132 optimal weight: 2.9990 chunk 80 optimal weight: 2.9990 chunk 57 optimal weight: 0.9990 chunk 104 optimal weight: 3.9990 chunk 40 optimal weight: 4.9990 chunk 120 optimal weight: 0.3980 chunk 125 optimal weight: 3.9990 chunk 87 optimal weight: 4.9990 chunk 140 optimal weight: 0.0060 overall best weight: 0.8816 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8806 moved from start: 0.1737 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 12384 Z= 0.178 Angle : 0.556 12.428 16726 Z= 0.280 Chirality : 0.039 0.155 1806 Planarity : 0.003 0.040 2132 Dihedral : 4.838 58.981 1670 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 6.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer: Outliers : 2.76 % Allowed : 17.43 % Favored : 79.80 % 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: 1.83 (0.20), residues: 698 sheet: -1.18 (0.35), residues: 222 loop : 0.09 (0.28), residues: 558 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 856 HIS 0.002 0.000 HIS A1092 PHE 0.008 0.001 PHE B 710 TYR 0.014 0.001 TYR B1029 ARG 0.007 0.000 ARG B 662 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2956 Ramachandran restraints generated. 1478 Oldfield, 0 Emsley, 1478 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2956 Ramachandran restraints generated. 1478 Oldfield, 0 Emsley, 1478 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 1302 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 62 time to evaluate : 1.578 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 438 GLU cc_start: 0.7918 (tp30) cc_final: 0.7624 (pm20) REVERT: A 503 LYS cc_start: 0.9663 (tppp) cc_final: 0.9391 (mmpt) REVERT: A 749 MET cc_start: 0.9501 (OUTLIER) cc_final: 0.9284 (mmp) REVERT: A 929 ARG cc_start: 0.8963 (ttp-110) cc_final: 0.8666 (tpm170) REVERT: A 957 MET cc_start: 0.9419 (mmm) cc_final: 0.9158 (mmm) REVERT: B 929 ARG cc_start: 0.9344 (mtm110) cc_final: 0.9128 (ttp80) REVERT: B 1118 LEU cc_start: 0.9177 (mm) cc_final: 0.8893 (pt) REVERT: B 1133 LEU cc_start: 0.9495 (OUTLIER) cc_final: 0.9205 (mm) REVERT: B 1147 LYS cc_start: 0.9555 (OUTLIER) cc_final: 0.9316 (mmmm) REVERT: B 1159 LEU cc_start: 0.9679 (OUTLIER) cc_final: 0.9424 (mm) outliers start: 36 outliers final: 24 residues processed: 94 average time/residue: 1.1874 time to fit residues: 122.9177 Evaluate side-chains 89 residues out of total 1302 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 61 time to evaluate : 1.450 ------------------------------------------------------------------------------- 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 749 MET 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 789 HIS Chi-restraints excluded: chain B residue 816 THR Chi-restraints excluded: chain B residue 895 THR Chi-restraints excluded: chain B residue 925 VAL Chi-restraints excluded: chain B residue 978 LEU Chi-restraints excluded: chain B residue 1061 GLU Chi-restraints excluded: chain B residue 1110 ILE Chi-restraints excluded: chain B residue 1133 LEU Chi-restraints excluded: chain B residue 1147 LYS Chi-restraints excluded: chain B residue 1159 LEU 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 85 optimal weight: 0.9980 chunk 66 optimal weight: 0.0970 chunk 97 optimal weight: 3.9990 chunk 147 optimal weight: 2.9990 chunk 135 optimal weight: 4.9990 chunk 117 optimal weight: 0.3980 chunk 12 optimal weight: 2.9990 chunk 90 optimal weight: 0.3980 chunk 71 optimal weight: 0.8980 chunk 93 optimal weight: 1.9990 chunk 125 optimal weight: 5.9990 overall best weight: 0.5578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8790 moved from start: 0.1741 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 12384 Z= 0.159 Angle : 0.568 12.068 16726 Z= 0.284 Chirality : 0.039 0.145 1806 Planarity : 0.003 0.047 2132 Dihedral : 4.808 58.834 1670 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 7.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 2.15 % Allowed : 17.97 % Favored : 79.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.07 (0.23), residues: 1478 helix: 1.89 (0.20), residues: 686 sheet: -1.14 (0.35), residues: 222 loop : 0.17 (0.27), residues: 570 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 856 HIS 0.003 0.000 HIS B1192 PHE 0.016 0.001 PHE B 959 TYR 0.015 0.001 TYR B1033 ARG 0.011 0.000 ARG B 662 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2956 Ramachandran restraints generated. 1478 Oldfield, 0 Emsley, 1478 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2956 Ramachandran restraints generated. 1478 Oldfield, 0 Emsley, 1478 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 1302 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 68 time to evaluate : 1.414 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 438 GLU cc_start: 0.7862 (tp30) cc_final: 0.7588 (pm20) REVERT: A 503 LYS cc_start: 0.9672 (tppp) cc_final: 0.9372 (mmpt) REVERT: A 893 LYS cc_start: 0.9348 (mppt) cc_final: 0.9073 (tppp) REVERT: A 929 ARG cc_start: 0.8924 (ttp-110) cc_final: 0.8622 (tpm170) REVERT: A 957 MET cc_start: 0.9419 (mmm) cc_final: 0.9156 (mmm) REVERT: B 957 MET cc_start: 0.9447 (mmt) cc_final: 0.8912 (mpt) REVERT: B 1048 MET cc_start: 0.9387 (mtm) cc_final: 0.9028 (mpp) REVERT: B 1118 LEU cc_start: 0.9221 (mm) cc_final: 0.8965 (pt) REVERT: B 1147 LYS cc_start: 0.9569 (OUTLIER) cc_final: 0.9341 (mmmm) REVERT: B 1159 LEU cc_start: 0.9687 (OUTLIER) cc_final: 0.9438 (mm) outliers start: 28 outliers final: 22 residues processed: 93 average time/residue: 1.1688 time to fit residues: 119.9313 Evaluate side-chains 85 residues out of total 1302 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 61 time to evaluate : 1.319 ------------------------------------------------------------------------------- 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 895 THR Chi-restraints excluded: chain B residue 925 VAL Chi-restraints excluded: chain B residue 978 LEU Chi-restraints excluded: chain B residue 1061 GLU Chi-restraints excluded: chain B residue 1147 LYS Chi-restraints excluded: chain B residue 1159 LEU 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 35 optimal weight: 4.9990 chunk 108 optimal weight: 2.9990 chunk 17 optimal weight: 5.9990 chunk 32 optimal weight: 4.9990 chunk 117 optimal weight: 2.9990 chunk 49 optimal weight: 0.8980 chunk 120 optimal weight: 9.9990 chunk 14 optimal weight: 0.9990 chunk 21 optimal weight: 7.9990 chunk 103 optimal weight: 2.9990 chunk 6 optimal weight: 0.7980 overall best weight: 1.7386 ------------------------------------------------------------------------------- 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 = 0.3065 r_free = 0.3065 target = 0.052646 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2680 r_free = 0.2680 target = 0.039597 restraints weight = 44847.643| |-----------------------------------------------------------------------------| r_work (start): 0.2660 rms_B_bonded: 3.49 r_work: 0.2512 rms_B_bonded: 3.92 restraints_weight: 0.5000 r_work (final): 0.2512 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8827 moved from start: 0.1822 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= 0.267 Angle : 0.604 12.039 16726 Z= 0.303 Chirality : 0.040 0.143 1806 Planarity : 0.004 0.050 2132 Dihedral : 4.947 58.992 1670 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 7.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 2.07 % Allowed : 18.05 % Favored : 79.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.04 (0.23), residues: 1478 helix: 1.84 (0.20), residues: 696 sheet: -1.19 (0.35), residues: 222 loop : 0.16 (0.28), residues: 560 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 856 HIS 0.002 0.000 HIS A1092 PHE 0.018 0.001 PHE B 959 TYR 0.019 0.001 TYR B1033 ARG 0.010 0.000 ARG B 662 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3125.82 seconds wall clock time: 56 minutes 16.67 seconds (3376.67 seconds total)