Starting phenix.real_space_refine on Sat Dec 9 14:35:20 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8oma_16972/12_2023/8oma_16972_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8oma_16972/12_2023/8oma_16972.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.29 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8oma_16972/12_2023/8oma_16972.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8oma_16972/12_2023/8oma_16972.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8oma_16972/12_2023/8oma_16972_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8oma_16972/12_2023/8oma_16972_updated.pdb" } resolution = 3.29 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= 0.001 sd= 0.024 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: 6 Type Number sf(0) Gaussians P 40 5.49 5 Mg 1 5.21 5 S 52 5.16 5 C 7099 2.51 5 N 1952 2.21 5 O 2235 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 188": "OE1" <-> "OE2" Residue "A ARG 389": "NH1" <-> "NH2" Residue "A GLU 480": "OE1" <-> "OE2" Residue "A GLU 571": "OE1" <-> "OE2" Residue "A GLU 590": "OE1" <-> "OE2" Residue "A GLU 643": "OE1" <-> "OE2" Residue "A GLU 698": "OE1" <-> "OE2" Residue "A GLU 728": "OE1" <-> "OE2" Residue "A GLU 852": "OE1" <-> "OE2" Residue "A GLU 902": "OE1" <-> "OE2" Residue "B GLU 651": "OE1" <-> "OE2" Residue "B GLU 732": "OE1" <-> "OE2" Residue "B GLU 812": "OE1" <-> "OE2" Residue "B GLU 926": "OE1" <-> "OE2" Residue "B GLU 1124": "OE1" <-> "OE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/chem_data/mon_lib" Total number of atoms: 11379 Number of models: 1 Model: "" Number of chains: 6 Chain: "C" Number of atoms: 351 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 351 Classifications: {'DNA': 17} Link IDs: {'rna3p': 16} Chain: "D" Number of atoms: 346 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 346 Classifications: {'DNA': 17} Link IDs: {'rna3p': 16} Chain: "A" Number of atoms: 5990 Number of conformers: 1 Conformer: "" Number of residues, atoms: 760, 5990 Classifications: {'peptide': 760} Link IDs: {'PTRANS': 21, 'TRANS': 738} Chain breaks: 4 Chain: "B" Number of atoms: 4629 Number of conformers: 1 Conformer: "" Number of residues, atoms: 577, 4629 Classifications: {'peptide': 577} Link IDs: {'PTRANS': 17, 'TRANS': 559} Chain breaks: 2 Chain: "A" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 6.50, per 1000 atoms: 0.57 Number of scatterers: 11379 At special positions: 0 Unit cell: (94.1626, 107.876, 173.698, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 52 16.00 P 40 15.00 Mg 1 11.99 O 2235 8.00 N 1952 7.00 C 7099 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 - 3.50 Amino acid : False - 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=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 5.20 Conformation dependent library (CDL) restraints added in 2.0 seconds 2642 Ramachandran restraints generated. 1321 Oldfield, 0 Emsley, 1321 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2530 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 52 helices and 11 sheets defined 51.2% alpha, 7.2% beta 17 base pairs and 29 stacking pairs defined. Time for finding SS restraints: 5.46 Creating SS restraints... Processing helix chain 'A' and resid 185 through 192 Processing helix chain 'A' and resid 208 through 219 removed outlier: 4.023A pdb=" N LYS A 212 " --> pdb=" O GLY A 208 " (cutoff:3.500A) Processing helix chain 'A' and resid 229 through 231 No H-bonds generated for 'chain 'A' and resid 229 through 231' Processing helix chain 'A' and resid 237 through 244 Processing helix chain 'A' and resid 248 through 250 No H-bonds generated for 'chain 'A' and resid 248 through 250' Processing helix chain 'A' and resid 255 through 257 No H-bonds generated for 'chain 'A' and resid 255 through 257' Processing helix chain 'A' and resid 259 through 261 No H-bonds generated for 'chain 'A' and resid 259 through 261' Processing helix chain 'A' and resid 264 through 276 Processing helix chain 'A' and resid 283 through 285 No H-bonds generated for 'chain 'A' and resid 283 through 285' Processing helix chain 'A' and resid 304 through 309 Processing helix chain 'A' and resid 326 through 330 Processing helix chain 'A' and resid 336 through 347 Processing helix chain 'A' and resid 353 through 368 Processing helix chain 'A' and resid 370 through 378 Processing helix chain 'A' and resid 387 through 395 Processing helix chain 'A' and resid 401 through 423 Proline residue: A 415 - end of helix Processing helix chain 'A' and resid 430 through 456 Proline residue: A 439 - end of helix removed outlier: 4.778A pdb=" N LYS A 449 " --> pdb=" O SER A 445 " (cutoff:3.500A) removed outlier: 4.955A pdb=" N PHE A 450 " --> pdb=" O ASP A 446 " (cutoff:3.500A) Processing helix chain 'A' and resid 460 through 464 Processing helix chain 'A' and resid 476 through 503 Processing helix chain 'A' and resid 554 through 614 removed outlier: 4.769A pdb=" N GLU A 580 " --> pdb=" O ALA A 576 " (cutoff:3.500A) removed outlier: 4.474A pdb=" N ASN A 583 " --> pdb=" O LYS A 579 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N TYR A 588 " --> pdb=" O ILE A 584 " (cutoff:3.500A) removed outlier: 4.477A pdb=" N VAL A 589 " --> pdb=" O SER A 585 " (cutoff:3.500A) removed outlier: 5.745A pdb=" N GLU A 590 " --> pdb=" O SER A 586 " (cutoff:3.500A) Proline residue: A 591 - end of helix Processing helix chain 'A' and resid 675 through 691 Processing helix chain 'A' and resid 724 through 738 Processing helix chain 'A' and resid 757 through 772 Processing helix chain 'A' and resid 787 through 792 Processing helix chain 'A' and resid 827 through 833 Processing helix chain 'A' and resid 838 through 850 Processing helix chain 'A' and resid 879 through 893 Processing helix chain 'A' and resid 901 through 918 Processing helix chain 'A' and resid 921 through 929 removed outlier: 3.716A pdb=" N ILE A 926 " --> pdb=" O PHE A 922 " (cutoff:3.500A) Processing helix chain 'B' and resid 539 through 544 Processing helix chain 'B' and resid 560 through 564 Processing helix chain 'B' and resid 570 through 580 Processing helix chain 'B' and resid 587 through 601 Processing helix chain 'B' and resid 607 through 616 Processing helix chain 'B' and resid 623 through 629 Processing helix chain 'B' and resid 635 through 662 Proline residue: B 657 - end of helix Processing helix chain 'B' and resid 666 through 678 removed outlier: 3.954A pdb=" N ILE B 672 " --> pdb=" O LEU B 668 " (cutoff:3.500A) Proline residue: B 676 - end of helix Processing helix chain 'B' and resid 680 through 687 removed outlier: 3.858A pdb=" N GLU B 683 " --> pdb=" O SER B 680 " (cutoff:3.500A) removed outlier: 5.098A pdb=" N HIS B 684 " --> pdb=" O PRO B 681 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N LEU B 686 " --> pdb=" O GLU B 683 " (cutoff:3.500A) Processing helix chain 'B' and resid 691 through 696 Processing helix chain 'B' and resid 706 through 708 No H-bonds generated for 'chain 'B' and resid 706 through 708' Processing helix chain 'B' and resid 710 through 737 removed outlier: 3.707A pdb=" N ARG B 715 " --> pdb=" O LEU B 711 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N GLN B 731 " --> pdb=" O ARG B 727 " (cutoff:3.500A) removed outlier: 4.696A pdb=" N GLU B 732 " --> pdb=" O MET B 728 " (cutoff:3.500A) Processing helix chain 'B' and resid 759 through 761 No H-bonds generated for 'chain 'B' and resid 759 through 761' Processing helix chain 'B' and resid 783 through 843 removed outlier: 4.049A pdb=" N HIS B 817 " --> pdb=" O LYS B 813 " (cutoff:3.500A) removed outlier: 4.388A pdb=" N HIS B 819 " --> pdb=" O SER B 815 " (cutoff:3.500A) removed outlier: 5.747A pdb=" N SER B 820 " --> pdb=" O GLU B 816 " (cutoff:3.500A) Processing helix chain 'B' and resid 865 through 870 Processing helix chain 'B' and resid 902 through 918 Processing helix chain 'B' and resid 945 through 947 No H-bonds generated for 'chain 'B' and resid 945 through 947' Processing helix chain 'B' and resid 951 through 965 Processing helix chain 'B' and resid 983 through 999 Processing helix chain 'B' and resid 1017 through 1020 No H-bonds generated for 'chain 'B' and resid 1017 through 1020' Processing helix chain 'B' and resid 1069 through 1075 Processing helix chain 'B' and resid 1080 through 1110 Processing helix chain 'B' and resid 1116 through 1123 Processing sheet with id= A, first strand: chain 'A' and resid 223 through 227 removed outlier: 3.746A pdb=" N LEU A 201 " --> pdb=" O THR A 225 " (cutoff:3.500A) removed outlier: 8.375A pdb=" N MET A 152 " --> pdb=" O PRO A 202 " (cutoff:3.500A) removed outlier: 4.543A pdb=" N VAL A 147 " --> pdb=" O VAL A 166 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N VAL A 166 " --> pdb=" O VAL A 147 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N GLN A 160 " --> pdb=" O SER A 153 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 513 through 516 Processing sheet with id= C, first strand: chain 'A' and resid 539 through 541 Processing sheet with id= D, first strand: chain 'A' and resid 632 through 635 removed outlier: 3.698A pdb=" N SER A 699 " --> pdb=" O LYS A 635 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'A' and resid 797 through 800 removed outlier: 6.701A pdb=" N PHE A 664 " --> pdb=" O ASN A 798 " (cutoff:3.500A) removed outlier: 7.626A pdb=" N LEU A 800 " --> pdb=" O PHE A 664 " (cutoff:3.500A) removed outlier: 6.518A pdb=" N ILE A 666 " --> pdb=" O LEU A 800 " (cutoff:3.500A) removed outlier: 6.108A pdb=" N CYS A 778 " --> pdb=" O HIS A 665 " (cutoff:3.500A) removed outlier: 7.210A pdb=" N ILE A 667 " --> pdb=" O CYS A 778 " (cutoff:3.500A) removed outlier: 6.198A pdb=" N PHE A 780 " --> pdb=" O ILE A 667 " (cutoff:3.500A) removed outlier: 7.117A pdb=" N CYS A 707 " --> pdb=" O LEU A 744 " (cutoff:3.500A) removed outlier: 7.647A pdb=" N ILE A 746 " --> pdb=" O CYS A 707 " (cutoff:3.500A) removed outlier: 6.663A pdb=" N LEU A 709 " --> pdb=" O ILE A 746 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'A' and resid 804 through 807 Processing sheet with id= G, first strand: chain 'B' and resid 754 through 756 Processing sheet with id= H, first strand: chain 'B' and resid 857 through 860 Processing sheet with id= I, first strand: chain 'B' and resid 891 through 896 Processing sheet with id= J, first strand: chain 'B' and resid 935 through 937 removed outlier: 6.313A pdb=" N LEU B 971 " --> pdb=" O PHE B 936 " (cutoff:3.500A) removed outlier: 6.470A pdb=" N LEU B1004 " --> pdb=" O VAL B 972 " (cutoff:3.500A) No H-bonds generated for sheet with id= J Processing sheet with id= K, first strand: chain 'B' and resid 1032 through 1034 removed outlier: 3.749A pdb=" N THR B1054 " --> pdb=" O LEU B1033 " (cutoff:3.500A) 503 hydrogen bonds defined for protein. 1476 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 42 hydrogen bonds 84 hydrogen bond angles 0 basepair planarities 17 basepair parallelities 29 stacking parallelities Total time for adding SS restraints: 4.49 Time building geometry restraints manager: 5.54 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 3522 1.34 - 1.48: 2877 1.48 - 1.61: 5153 1.61 - 1.75: 2 1.75 - 1.88: 84 Bond restraints: 11638 Sorted by residual: bond pdb=" CA SER A 637 " pdb=" CB SER A 637 " ideal model delta sigma weight residual 1.529 1.460 0.069 1.66e-02 3.63e+03 1.73e+01 bond pdb=" CE1 HIS B 864 " pdb=" NE2 HIS B 864 " ideal model delta sigma weight residual 1.321 1.354 -0.033 1.00e-02 1.00e+04 1.09e+01 bond pdb=" CA SER B 920 " pdb=" CB SER B 920 " ideal model delta sigma weight residual 1.528 1.480 0.048 1.48e-02 4.57e+03 1.07e+01 bond pdb=" CG MET B 953 " pdb=" SD MET B 953 " ideal model delta sigma weight residual 1.803 1.884 -0.081 2.50e-02 1.60e+03 1.04e+01 bond pdb=" CD ARG B 938 " pdb=" NE ARG B 938 " ideal model delta sigma weight residual 1.458 1.419 0.039 1.40e-02 5.10e+03 7.95e+00 ... (remaining 11633 not shown) Histogram of bond angle deviations from ideal: 98.17 - 106.10: 411 106.10 - 114.04: 6493 114.04 - 121.97: 6403 121.97 - 129.91: 2482 129.91 - 137.84: 67 Bond angle restraints: 15856 Sorted by residual: angle pdb=" C5' ATP B2000 " pdb=" O5' ATP B2000 " pdb=" PA ATP B2000 " ideal model delta sigma weight residual 121.27 113.20 8.07 1.00e+00 1.00e+00 6.50e+01 angle pdb=" N THR B 951 " pdb=" CA THR B 951 " pdb=" CB THR B 951 " ideal model delta sigma weight residual 109.72 117.37 -7.65 1.70e+00 3.46e-01 2.02e+01 angle pdb=" C ARG A 711 " pdb=" CA ARG A 711 " pdb=" CB ARG A 711 " ideal model delta sigma weight residual 111.70 117.20 -5.50 1.31e+00 5.83e-01 1.77e+01 angle pdb=" C PRO A 652 " pdb=" CA PRO A 652 " pdb=" CB PRO A 652 " ideal model delta sigma weight residual 111.23 106.06 5.17 1.28e+00 6.10e-01 1.63e+01 angle pdb=" N GLY A 692 " pdb=" CA GLY A 692 " pdb=" C GLY A 692 " ideal model delta sigma weight residual 114.95 109.31 5.64 1.41e+00 5.03e-01 1.60e+01 ... (remaining 15851 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.96: 5764 17.96 - 35.92: 869 35.92 - 53.88: 323 53.88 - 71.85: 66 71.85 - 89.81: 18 Dihedral angle restraints: 7040 sinusoidal: 3145 harmonic: 3895 Sorted by residual: dihedral pdb=" CA GLY A 504 " pdb=" C GLY A 504 " pdb=" N LEU A 505 " pdb=" CA LEU A 505 " ideal model delta harmonic sigma weight residual 180.00 -152.34 -27.66 0 5.00e+00 4.00e-02 3.06e+01 dihedral pdb=" CA MET B 728 " pdb=" C MET B 728 " pdb=" N HIS B 729 " pdb=" CA HIS B 729 " ideal model delta harmonic sigma weight residual 180.00 155.28 24.72 0 5.00e+00 4.00e-02 2.44e+01 dihedral pdb=" CA SER B1067 " pdb=" C SER B1067 " pdb=" N TYR B1068 " pdb=" CA TYR B1068 " ideal model delta harmonic sigma weight residual -180.00 -155.91 -24.09 0 5.00e+00 4.00e-02 2.32e+01 ... (remaining 7037 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.076: 1034 0.076 - 0.152: 625 0.152 - 0.228: 128 0.228 - 0.304: 25 0.304 - 0.380: 7 Chirality restraints: 1819 Sorted by residual: chirality pdb=" CA ARG A 171 " pdb=" N ARG A 171 " pdb=" C ARG A 171 " pdb=" CB ARG A 171 " both_signs ideal model delta sigma weight residual False 2.51 2.13 0.38 2.00e-01 2.50e+01 3.62e+00 chirality pdb=" CG LEU B 640 " pdb=" CB LEU B 640 " pdb=" CD1 LEU B 640 " pdb=" CD2 LEU B 640 " both_signs ideal model delta sigma weight residual False -2.59 -2.22 -0.37 2.00e-01 2.50e+01 3.48e+00 chirality pdb=" CB THR B 951 " pdb=" CA THR B 951 " pdb=" OG1 THR B 951 " pdb=" CG2 THR B 951 " both_signs ideal model delta sigma weight residual False 2.55 2.20 0.36 2.00e-01 2.50e+01 3.15e+00 ... (remaining 1816 not shown) Planarity restraints: 1897 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG B 938 " 0.406 9.50e-02 1.11e+02 1.82e-01 2.25e+01 pdb=" NE ARG B 938 " -0.034 2.00e-02 2.50e+03 pdb=" CZ ARG B 938 " 0.020 2.00e-02 2.50e+03 pdb=" NH1 ARG B 938 " -0.010 2.00e-02 2.50e+03 pdb=" NH2 ARG B 938 " 0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR B 991 " -0.032 2.00e-02 2.50e+03 1.72e-02 5.92e+00 pdb=" CG TYR B 991 " 0.017 2.00e-02 2.50e+03 pdb=" CD1 TYR B 991 " 0.025 2.00e-02 2.50e+03 pdb=" CD2 TYR B 991 " 0.008 2.00e-02 2.50e+03 pdb=" CE1 TYR B 991 " -0.006 2.00e-02 2.50e+03 pdb=" CE2 TYR B 991 " 0.010 2.00e-02 2.50e+03 pdb=" CZ TYR B 991 " -0.008 2.00e-02 2.50e+03 pdb=" OH TYR B 991 " -0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE B1007 " 0.027 2.00e-02 2.50e+03 1.78e-02 5.55e+00 pdb=" CG PHE B1007 " -0.013 2.00e-02 2.50e+03 pdb=" CD1 PHE B1007 " -0.019 2.00e-02 2.50e+03 pdb=" CD2 PHE B1007 " -0.021 2.00e-02 2.50e+03 pdb=" CE1 PHE B1007 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 PHE B1007 " 0.002 2.00e-02 2.50e+03 pdb=" CZ PHE B1007 " 0.023 2.00e-02 2.50e+03 ... (remaining 1894 not shown) Histogram of nonbonded interaction distances: 1.88 - 2.48: 88 2.48 - 3.09: 8264 3.09 - 3.69: 19511 3.69 - 4.30: 27317 4.30 - 4.90: 42566 Nonbonded interactions: 97746 Sorted by model distance: nonbonded pdb=" O2G ATP B2000 " pdb="MG MG B2001 " model vdw 1.878 2.170 nonbonded pdb=" OG SER B 903 " pdb="MG MG B2001 " model vdw 2.000 2.170 nonbonded pdb=" OG1 THR A 335 " pdb=" OD2 ASP A 603 " model vdw 2.112 2.440 nonbonded pdb=" O LYS A 565 " pdb=" OG1 THR A 568 " model vdw 2.174 2.440 nonbonded pdb=" OD1 ASN A 186 " pdb=" NE2 GLN A 348 " model vdw 2.178 2.520 ... (remaining 97741 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.03 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: 2.810 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: 7.320 Check model and map are aligned: 0.160 Set scattering table: 0.110 Process input model: 38.320 Find NCS groups from input model: 0.310 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.600 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 51.680 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6894 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 : 0.008 0.081 11638 Z= 0.494 Angle : 1.304 8.981 15856 Z= 0.857 Chirality : 0.094 0.380 1819 Planarity : 0.007 0.182 1897 Dihedral : 19.919 89.807 4510 Min Nonbonded Distance : 1.878 Molprobity Statistics. All-atom Clashscore : 28.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.87 % Favored : 92.13 % Rotamer: Outliers : 2.97 % Allowed : 22.71 % Favored : 74.32 % Cbeta Deviations : 0.08 % 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: -1.51 (0.22), residues: 1321 helix: 0.08 (0.18), residues: 716 sheet: -2.00 (0.41), residues: 145 loop : -2.34 (0.27), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.005 TRP A 764 HIS 0.016 0.003 HIS B 647 PHE 0.027 0.005 PHE B1007 TYR 0.032 0.005 TYR B 991 ARG 0.025 0.002 ARG B 938 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2642 Ramachandran restraints generated. 1321 Oldfield, 0 Emsley, 1321 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2642 Ramachandran restraints generated. 1321 Oldfield, 0 Emsley, 1321 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 252 residues out of total 1180 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 217 time to evaluate : 1.262 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 35 outliers final: 17 residues processed: 236 average time/residue: 0.3411 time to fit residues: 106.7055 Evaluate side-chains 206 residues out of total 1180 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 189 time to evaluate : 1.254 Switching outliers to nearest non-outliers outliers start: 17 outliers final: 0 residues processed: 17 average time/residue: 0.1536 time to fit residues: 6.2930 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 113 optimal weight: 0.0970 chunk 102 optimal weight: 0.9990 chunk 56 optimal weight: 0.0870 chunk 34 optimal weight: 0.9980 chunk 69 optimal weight: 0.4980 chunk 54 optimal weight: 0.6980 chunk 105 optimal weight: 0.6980 chunk 40 optimal weight: 0.0870 chunk 64 optimal weight: 0.8980 chunk 78 optimal weight: 0.6980 chunk 122 optimal weight: 1.9990 overall best weight: 0.2934 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 324 GLN ** A 348 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 413 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 518 GLN A 566 ASN ** A 574 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 596 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 846 GLN B 551 GLN B 647 HIS B 729 HIS ** B 898 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 908 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1027 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1120 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6798 moved from start: 0.1309 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 11638 Z= 0.203 Angle : 0.648 11.189 15856 Z= 0.343 Chirality : 0.042 0.193 1819 Planarity : 0.004 0.073 1897 Dihedral : 17.756 89.854 1859 Min Nonbonded Distance : 1.937 Molprobity Statistics. All-atom Clashscore : 22.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.98 % Favored : 94.02 % Rotamer: Outliers : 3.14 % Allowed : 22.03 % Favored : 74.83 % 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: -0.88 (0.23), residues: 1321 helix: 0.51 (0.19), residues: 713 sheet: -2.03 (0.39), residues: 171 loop : -1.69 (0.30), residues: 437 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 807 HIS 0.009 0.001 HIS B 729 PHE 0.040 0.002 PHE A 286 TYR 0.014 0.001 TYR A 815 ARG 0.006 0.000 ARG A 631 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2642 Ramachandran restraints generated. 1321 Oldfield, 0 Emsley, 1321 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2642 Ramachandran restraints generated. 1321 Oldfield, 0 Emsley, 1321 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 248 residues out of total 1180 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 211 time to evaluate : 1.184 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 37 outliers final: 24 residues processed: 228 average time/residue: 0.2997 time to fit residues: 91.5759 Evaluate side-chains 215 residues out of total 1180 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 191 time to evaluate : 1.235 Switching outliers to nearest non-outliers outliers start: 24 outliers final: 0 residues processed: 24 average time/residue: 0.1376 time to fit residues: 7.2487 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 68 optimal weight: 3.9990 chunk 38 optimal weight: 8.9990 chunk 102 optimal weight: 0.1980 chunk 83 optimal weight: 0.2980 chunk 33 optimal weight: 0.2980 chunk 122 optimal weight: 0.0030 chunk 132 optimal weight: 4.9990 chunk 109 optimal weight: 0.0970 chunk 121 optimal weight: 1.9990 chunk 41 optimal weight: 5.9990 chunk 98 optimal weight: 0.0870 overall best weight: 0.1366 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 324 GLN ** A 348 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 413 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 574 GLN ** A 596 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 639 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 846 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 647 HIS ** B 898 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 908 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1027 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6754 moved from start: 0.1839 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 11638 Z= 0.178 Angle : 0.611 7.487 15856 Z= 0.327 Chirality : 0.041 0.242 1819 Planarity : 0.004 0.077 1897 Dihedral : 17.524 85.662 1859 Min Nonbonded Distance : 1.988 Molprobity Statistics. All-atom Clashscore : 20.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.36 % Favored : 93.64 % Rotamer: Outliers : 2.03 % Allowed : 23.73 % Favored : 74.24 % 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: -0.55 (0.23), residues: 1321 helix: 0.76 (0.19), residues: 714 sheet: -1.70 (0.40), residues: 171 loop : -1.58 (0.30), residues: 436 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 807 HIS 0.007 0.001 HIS B 647 PHE 0.038 0.001 PHE A 286 TYR 0.014 0.001 TYR B1028 ARG 0.006 0.001 ARG B 796 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2642 Ramachandran restraints generated. 1321 Oldfield, 0 Emsley, 1321 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2642 Ramachandran restraints generated. 1321 Oldfield, 0 Emsley, 1321 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 225 residues out of total 1180 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 201 time to evaluate : 1.118 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 24 outliers final: 9 residues processed: 216 average time/residue: 0.2730 time to fit residues: 81.4324 Evaluate side-chains 184 residues out of total 1180 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 175 time to evaluate : 1.224 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 0.1460 time to fit residues: 3.9453 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 121 optimal weight: 0.2980 chunk 92 optimal weight: 0.9990 chunk 63 optimal weight: 2.9990 chunk 13 optimal weight: 0.9980 chunk 58 optimal weight: 1.9990 chunk 82 optimal weight: 0.5980 chunk 123 optimal weight: 0.4980 chunk 130 optimal weight: 1.9990 chunk 64 optimal weight: 2.9990 chunk 116 optimal weight: 0.6980 chunk 35 optimal weight: 1.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 348 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 413 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 596 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 829 HIS A 846 GLN B 549 GLN B 647 HIS ** B 731 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 817 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 898 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 908 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1027 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6836 moved from start: 0.2067 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 11638 Z= 0.220 Angle : 0.639 11.932 15856 Z= 0.339 Chirality : 0.042 0.196 1819 Planarity : 0.004 0.078 1897 Dihedral : 17.456 87.688 1859 Min Nonbonded Distance : 1.920 Molprobity Statistics. All-atom Clashscore : 20.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.28 % Favored : 93.72 % Rotamer: Outliers : 2.71 % Allowed : 24.58 % Favored : 72.71 % 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: -0.54 (0.23), residues: 1321 helix: 0.72 (0.19), residues: 720 sheet: -1.61 (0.41), residues: 169 loop : -1.56 (0.31), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 764 HIS 0.004 0.001 HIS B 817 PHE 0.027 0.002 PHE A 286 TYR 0.016 0.001 TYR B 877 ARG 0.005 0.000 ARG B 938 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2642 Ramachandran restraints generated. 1321 Oldfield, 0 Emsley, 1321 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2642 Ramachandran restraints generated. 1321 Oldfield, 0 Emsley, 1321 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 227 residues out of total 1180 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 195 time to evaluate : 1.226 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 32 outliers final: 12 residues processed: 215 average time/residue: 0.3039 time to fit residues: 88.7082 Evaluate side-chains 188 residues out of total 1180 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 176 time to evaluate : 1.078 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 0 residues processed: 12 average time/residue: 0.1392 time to fit residues: 4.7491 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 108 optimal weight: 2.9990 chunk 74 optimal weight: 8.9990 chunk 1 optimal weight: 20.0000 chunk 97 optimal weight: 3.9990 chunk 53 optimal weight: 0.9990 chunk 111 optimal weight: 1.9990 chunk 90 optimal weight: 0.9980 chunk 0 optimal weight: 10.0000 chunk 66 optimal weight: 1.9990 chunk 117 optimal weight: 0.9980 chunk 32 optimal weight: 1.9990 overall best weight: 1.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 395 GLN ** A 413 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 846 GLN B 647 HIS ** B 817 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 898 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 908 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1027 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1029 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6966 moved from start: 0.2604 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.074 11638 Z= 0.372 Angle : 0.740 10.444 15856 Z= 0.397 Chirality : 0.046 0.196 1819 Planarity : 0.005 0.082 1897 Dihedral : 17.459 85.818 1859 Min Nonbonded Distance : 1.834 Molprobity Statistics. All-atom Clashscore : 27.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.49 % Favored : 92.51 % Rotamer: Outliers : 2.63 % Allowed : 25.00 % Favored : 72.37 % 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: -1.14 (0.23), residues: 1321 helix: 0.24 (0.19), residues: 734 sheet: -1.88 (0.44), residues: 149 loop : -1.94 (0.28), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 764 HIS 0.012 0.001 HIS B1029 PHE 0.035 0.003 PHE A 436 TYR 0.020 0.002 TYR B 877 ARG 0.006 0.001 ARG B 779 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2642 Ramachandran restraints generated. 1321 Oldfield, 0 Emsley, 1321 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2642 Ramachandran restraints generated. 1321 Oldfield, 0 Emsley, 1321 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 220 residues out of total 1180 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 189 time to evaluate : 1.245 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 31 outliers final: 10 residues processed: 210 average time/residue: 0.2822 time to fit residues: 80.8913 Evaluate side-chains 194 residues out of total 1180 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 184 time to evaluate : 1.177 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 0 residues processed: 10 average time/residue: 0.1543 time to fit residues: 4.0578 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 43 optimal weight: 0.9980 chunk 117 optimal weight: 0.9980 chunk 25 optimal weight: 0.9980 chunk 76 optimal weight: 1.9990 chunk 32 optimal weight: 0.9990 chunk 130 optimal weight: 0.9980 chunk 108 optimal weight: 0.6980 chunk 60 optimal weight: 0.6980 chunk 10 optimal weight: 0.6980 chunk 68 optimal weight: 1.9990 chunk 125 optimal weight: 2.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 324 GLN ** A 413 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 647 HIS B 684 HIS B 817 HIS ** B 898 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 908 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1027 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6921 moved from start: 0.2874 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 11638 Z= 0.266 Angle : 0.680 9.768 15856 Z= 0.362 Chirality : 0.044 0.264 1819 Planarity : 0.004 0.084 1897 Dihedral : 17.363 89.633 1859 Min Nonbonded Distance : 1.894 Molprobity Statistics. All-atom Clashscore : 24.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.28 % Favored : 93.72 % Rotamer: Outliers : 3.22 % Allowed : 25.08 % Favored : 71.69 % 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: 1321 helix: 0.42 (0.19), residues: 731 sheet: -1.83 (0.44), residues: 144 loop : -2.00 (0.28), residues: 446 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 764 HIS 0.007 0.001 HIS B 684 PHE 0.026 0.002 PHE A 436 TYR 0.026 0.002 TYR B1057 ARG 0.010 0.001 ARG B 779 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2642 Ramachandran restraints generated. 1321 Oldfield, 0 Emsley, 1321 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2642 Ramachandran restraints generated. 1321 Oldfield, 0 Emsley, 1321 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 227 residues out of total 1180 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 189 time to evaluate : 1.265 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 38 outliers final: 16 residues processed: 213 average time/residue: 0.2868 time to fit residues: 83.4237 Evaluate side-chains 198 residues out of total 1180 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 182 time to evaluate : 1.237 Switching outliers to nearest non-outliers outliers start: 16 outliers final: 0 residues processed: 16 average time/residue: 0.1365 time to fit residues: 5.5605 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 14 optimal weight: 0.9990 chunk 74 optimal weight: 10.0000 chunk 95 optimal weight: 2.9990 chunk 73 optimal weight: 3.9990 chunk 109 optimal weight: 0.8980 chunk 72 optimal weight: 0.7980 chunk 130 optimal weight: 0.9980 chunk 81 optimal weight: 0.9980 chunk 79 optimal weight: 0.6980 chunk 60 optimal weight: 0.9990 chunk 80 optimal weight: 0.5980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 846 GLN B 647 HIS B 852 GLN ** B 898 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 908 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1027 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6922 moved from start: 0.3153 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 11638 Z= 0.266 Angle : 0.714 12.142 15856 Z= 0.375 Chirality : 0.045 0.384 1819 Planarity : 0.004 0.081 1897 Dihedral : 17.333 88.096 1859 Min Nonbonded Distance : 1.896 Molprobity Statistics. All-atom Clashscore : 25.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.36 % Favored : 93.64 % Rotamer: Outliers : 1.95 % Allowed : 26.36 % Favored : 71.69 % 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: 1321 helix: 0.46 (0.19), residues: 728 sheet: -1.89 (0.44), residues: 144 loop : -1.94 (0.28), residues: 449 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 764 HIS 0.005 0.001 HIS A 829 PHE 0.032 0.002 PHE B 571 TYR 0.016 0.002 TYR B 877 ARG 0.011 0.001 ARG B 779 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2642 Ramachandran restraints generated. 1321 Oldfield, 0 Emsley, 1321 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2642 Ramachandran restraints generated. 1321 Oldfield, 0 Emsley, 1321 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 1180 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 184 time to evaluate : 1.319 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 23 outliers final: 11 residues processed: 202 average time/residue: 0.3009 time to fit residues: 83.1972 Evaluate side-chains 185 residues out of total 1180 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 174 time to evaluate : 1.178 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 0 residues processed: 11 average time/residue: 0.1127 time to fit residues: 4.0929 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 51 optimal weight: 1.9990 chunk 77 optimal weight: 4.9990 chunk 39 optimal weight: 20.0000 chunk 25 optimal weight: 1.9990 chunk 82 optimal weight: 0.1980 chunk 88 optimal weight: 0.8980 chunk 64 optimal weight: 3.9990 chunk 12 optimal weight: 0.0030 chunk 102 optimal weight: 0.6980 chunk 118 optimal weight: 0.9980 chunk 124 optimal weight: 0.7980 overall best weight: 0.5190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 647 HIS ** B 898 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1027 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6885 moved from start: 0.3329 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 11638 Z= 0.227 Angle : 0.691 12.354 15856 Z= 0.361 Chirality : 0.044 0.347 1819 Planarity : 0.004 0.077 1897 Dihedral : 17.251 87.774 1859 Min Nonbonded Distance : 1.925 Molprobity Statistics. All-atom Clashscore : 23.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.43 % Favored : 93.57 % Rotamer: Outliers : 1.10 % Allowed : 27.88 % Favored : 71.02 % 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: -0.76 (0.23), residues: 1321 helix: 0.60 (0.19), residues: 728 sheet: -1.84 (0.44), residues: 143 loop : -1.81 (0.28), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 807 HIS 0.006 0.001 HIS B 729 PHE 0.029 0.002 PHE B 571 TYR 0.019 0.002 TYR A 815 ARG 0.012 0.001 ARG B1103 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2642 Ramachandran restraints generated. 1321 Oldfield, 0 Emsley, 1321 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2642 Ramachandran restraints generated. 1321 Oldfield, 0 Emsley, 1321 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 1180 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 188 time to evaluate : 1.234 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 13 outliers final: 5 residues processed: 195 average time/residue: 0.3062 time to fit residues: 80.8562 Evaluate side-chains 184 residues out of total 1180 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 179 time to evaluate : 1.272 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.1935 time to fit residues: 3.3171 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 113 optimal weight: 0.7980 chunk 121 optimal weight: 0.2980 chunk 124 optimal weight: 0.6980 chunk 72 optimal weight: 1.9990 chunk 52 optimal weight: 0.9980 chunk 95 optimal weight: 3.9990 chunk 37 optimal weight: 7.9990 chunk 109 optimal weight: 0.0070 chunk 114 optimal weight: 1.9990 chunk 120 optimal weight: 0.7980 chunk 79 optimal weight: 0.9980 overall best weight: 0.5198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 898 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1027 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6883 moved from start: 0.3513 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 11638 Z= 0.225 Angle : 0.724 14.571 15856 Z= 0.372 Chirality : 0.045 0.411 1819 Planarity : 0.005 0.077 1897 Dihedral : 17.212 88.372 1859 Min Nonbonded Distance : 1.921 Molprobity Statistics. All-atom Clashscore : 23.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.43 % Favored : 93.57 % Rotamer: Outliers : 0.51 % Allowed : 28.31 % Favored : 71.19 % 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: -0.64 (0.23), residues: 1321 helix: 0.66 (0.19), residues: 722 sheet: -1.77 (0.45), residues: 142 loop : -1.67 (0.29), residues: 457 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 807 HIS 0.005 0.001 HIS A 785 PHE 0.035 0.002 PHE B 784 TYR 0.013 0.002 TYR A 408 ARG 0.016 0.001 ARG B1103 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2642 Ramachandran restraints generated. 1321 Oldfield, 0 Emsley, 1321 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2642 Ramachandran restraints generated. 1321 Oldfield, 0 Emsley, 1321 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 1180 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 189 time to evaluate : 1.316 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 6 outliers final: 4 residues processed: 194 average time/residue: 0.3233 time to fit residues: 83.8234 Evaluate side-chains 188 residues out of total 1180 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 184 time to evaluate : 1.196 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.1789 time to fit residues: 3.3534 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 128 optimal weight: 0.1980 chunk 78 optimal weight: 0.8980 chunk 60 optimal weight: 0.0020 chunk 89 optimal weight: 0.8980 chunk 134 optimal weight: 0.9990 chunk 123 optimal weight: 1.9990 chunk 107 optimal weight: 0.5980 chunk 11 optimal weight: 2.9990 chunk 82 optimal weight: 0.7980 chunk 65 optimal weight: 0.3980 chunk 85 optimal weight: 0.0870 overall best weight: 0.2566 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 829 HIS A 846 GLN B 647 HIS ** B 729 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 898 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 908 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1027 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6837 moved from start: 0.3733 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 11638 Z= 0.204 Angle : 0.731 14.667 15856 Z= 0.376 Chirality : 0.045 0.421 1819 Planarity : 0.005 0.073 1897 Dihedral : 17.144 86.969 1859 Min Nonbonded Distance : 1.970 Molprobity Statistics. All-atom Clashscore : 22.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.75 % Favored : 94.25 % Rotamer: Outliers : 0.51 % Allowed : 28.05 % Favored : 71.44 % 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: -0.56 (0.24), residues: 1321 helix: 0.69 (0.19), residues: 722 sheet: -1.64 (0.45), residues: 143 loop : -1.59 (0.29), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 807 HIS 0.007 0.001 HIS A 428 PHE 0.041 0.002 PHE B 784 TYR 0.017 0.002 TYR A 815 ARG 0.011 0.001 ARG B 796 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2642 Ramachandran restraints generated. 1321 Oldfield, 0 Emsley, 1321 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2642 Ramachandran restraints generated. 1321 Oldfield, 0 Emsley, 1321 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 1180 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 178 time to evaluate : 1.115 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 6 outliers final: 5 residues processed: 180 average time/residue: 0.3137 time to fit residues: 75.8438 Evaluate side-chains 176 residues out of total 1180 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 171 time to evaluate : 1.241 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.1196 time to fit residues: 2.9051 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 114 optimal weight: 0.5980 chunk 32 optimal weight: 0.5980 chunk 98 optimal weight: 1.9990 chunk 15 optimal weight: 0.9990 chunk 29 optimal weight: 3.9990 chunk 107 optimal weight: 1.9990 chunk 44 optimal weight: 1.9990 chunk 110 optimal weight: 0.0040 chunk 13 optimal weight: 0.6980 chunk 19 optimal weight: 1.9990 chunk 94 optimal weight: 0.9980 overall best weight: 0.5792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 582 GLN ** B 729 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 898 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 908 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1027 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4911 r_free = 0.4911 target = 0.219406 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.4594 r_free = 0.4594 target = 0.187623 restraints weight = 18503.539| |-----------------------------------------------------------------------------| r_work (start): 0.4518 rms_B_bonded: 3.59 r_work: 0.4383 rms_B_bonded: 4.42 restraints_weight: 0.5000 r_work (final): 0.4383 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4381 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4381 r_free = 0.4381 target_work(ls_wunit_k1) = 0.168 | | occupancies: max = 1.00 min = 0.03 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4381 r_free = 0.4381 target_work(ls_wunit_k1) = 0.168 | | occupancies: max = 1.00 min = 0.68 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.4381 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5914 moved from start: 0.3919 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 11638 Z= 0.244 Angle : 0.762 15.216 15856 Z= 0.396 Chirality : 0.046 0.427 1819 Planarity : 0.005 0.071 1897 Dihedral : 17.139 87.656 1859 Min Nonbonded Distance : 1.915 Molprobity Statistics. All-atom Clashscore : 24.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.74 % Favored : 93.26 % Rotamer: Outliers : 0.59 % Allowed : 28.14 % Favored : 71.27 % 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: -0.53 (0.24), residues: 1321 helix: 0.74 (0.19), residues: 716 sheet: -1.60 (0.45), residues: 143 loop : -1.59 (0.29), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP B 562 HIS 0.008 0.001 HIS B 729 PHE 0.050 0.002 PHE B 784 TYR 0.020 0.002 TYR A 522 ARG 0.024 0.001 ARG A 524 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3147.28 seconds wall clock time: 57 minutes 36.90 seconds (3456.90 seconds total)