Starting phenix.real_space_refine on Mon Mar 11 11:14:21 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pd3_17599/03_2024/8pd3_17599.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pd3_17599/03_2024/8pd3_17599.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pd3_17599/03_2024/8pd3_17599.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pd3_17599/03_2024/8pd3_17599.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pd3_17599/03_2024/8pd3_17599.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pd3_17599/03_2024/8pd3_17599.pdb" } resolution = 3.3 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= 0.027 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 41 5.16 5 C 5303 2.51 5 N 1346 2.21 5 O 1431 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 740": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 848": "OE1" <-> "OE2" Residue "A GLU 911": "OE1" <-> "OE2" Residue "A GLU 954": "OE1" <-> "OE2" Residue "A PHE 982": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1009": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1071": "OE1" <-> "OE2" Residue "A TYR 1125": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1178": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 8121 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 8121 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1028, 8121 Classifications: {'peptide': 1028} Link IDs: {'PTRANS': 30, 'TRANS': 997} Chain breaks: 5 Time building chain proxies: 4.80, per 1000 atoms: 0.59 Number of scatterers: 8121 At special positions: 0 Unit cell: (79.42, 113.696, 125.4, 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 41 16.00 O 1431 8.00 N 1346 7.00 C 5303 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=0, symmetry=0 Time building additional restraints: 3.32 Conformation dependent library (CDL) restraints added in 1.6 seconds 2032 Ramachandran restraints generated. 1016 Oldfield, 0 Emsley, 1016 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1940 Finding SS restraints... Secondary structure from input PDB file: 46 helices and 4 sheets defined 76.7% alpha, 5.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.98 Creating SS restraints... Processing helix chain 'A' and resid 76 through 95 removed outlier: 3.945A pdb=" N PHE A 80 " --> pdb=" O LYS A 76 " (cutoff:3.500A) Processing helix chain 'A' and resid 101 through 118 removed outlier: 3.971A pdb=" N VAL A 105 " --> pdb=" O PRO A 101 " (cutoff:3.500A) Processing helix chain 'A' and resid 120 through 132 removed outlier: 3.582A pdb=" N GLU A 124 " --> pdb=" O VAL A 120 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N HIS A 126 " --> pdb=" O LEU A 122 " (cutoff:3.500A) removed outlier: 4.965A pdb=" N ASP A 129 " --> pdb=" O GLU A 125 " (cutoff:3.500A) removed outlier: 5.078A pdb=" N VAL A 130 " --> pdb=" O HIS A 126 " (cutoff:3.500A) Processing helix chain 'A' and resid 134 through 154 removed outlier: 4.412A pdb=" N GLN A 140 " --> pdb=" O HIS A 136 " (cutoff:3.500A) Proline residue: A 144 - end of helix removed outlier: 3.985A pdb=" N MET A 154 " --> pdb=" O SER A 150 " (cutoff:3.500A) Processing helix chain 'A' and resid 155 through 161 Processing helix chain 'A' and resid 162 through 171 removed outlier: 3.561A pdb=" N VAL A 166 " --> pdb=" O SER A 162 " (cutoff:3.500A) Processing helix chain 'A' and resid 171 through 188 Processing helix chain 'A' and resid 194 through 206 Processing helix chain 'A' and resid 210 through 221 removed outlier: 3.996A pdb=" N LEU A 216 " --> pdb=" O ALA A 212 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N ASP A 219 " --> pdb=" O ALA A 215 " (cutoff:3.500A) Processing helix chain 'A' and resid 225 through 254 removed outlier: 3.742A pdb=" N ILE A 229 " --> pdb=" O GLN A 225 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N VAL A 243 " --> pdb=" O GLY A 239 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N LYS A 250 " --> pdb=" O ASN A 246 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N MET A 251 " --> pdb=" O VAL A 247 " (cutoff:3.500A) Processing helix chain 'A' and resid 260 through 273 Processing helix chain 'A' and resid 273 through 291 Processing helix chain 'A' and resid 296 through 318 removed outlier: 3.594A pdb=" N GLU A 300 " --> pdb=" O ASP A 296 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N TYR A 312 " --> pdb=" O THR A 308 " (cutoff:3.500A) Processing helix chain 'A' and resid 322 through 337 Processing helix chain 'A' and resid 338 through 341 Processing helix chain 'A' and resid 342 through 376 removed outlier: 3.632A pdb=" N PHE A 348 " --> pdb=" O GLU A 344 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N ARG A 351 " --> pdb=" O VAL A 347 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N THR A 373 " --> pdb=" O GLY A 369 " (cutoff:3.500A) Processing helix chain 'A' and resid 381 through 411 removed outlier: 3.885A pdb=" N TRP A 385 " --> pdb=" O ASP A 381 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N PHE A 386 " --> pdb=" O LYS A 382 " (cutoff:3.500A) Proline residue: A 408 - end of helix Processing helix chain 'A' and resid 418 through 428 Processing helix chain 'A' and resid 432 through 446 Processing helix chain 'A' and resid 449 through 469 removed outlier: 4.224A pdb=" N SER A 453 " --> pdb=" O ASP A 449 " (cutoff:3.500A) Processing helix chain 'A' and resid 469 through 481 removed outlier: 4.836A pdb=" N GLN A 475 " --> pdb=" O ALA A 471 " (cutoff:3.500A) removed outlier: 5.437A pdb=" N THR A 476 " --> pdb=" O THR A 472 " (cutoff:3.500A) Processing helix chain 'A' and resid 487 through 513 Processing helix chain 'A' and resid 514 through 519 removed outlier: 6.265A pdb=" N PHE A 517 " --> pdb=" O SER A 514 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N ALA A 519 " --> pdb=" O ARG A 516 " (cutoff:3.500A) Processing helix chain 'A' and resid 522 through 530 Processing helix chain 'A' and resid 571 through 600 Processing helix chain 'A' and resid 604 through 620 Processing helix chain 'A' and resid 627 through 636 removed outlier: 4.438A pdb=" N LYS A 633 " --> pdb=" O ASP A 629 " (cutoff:3.500A) removed outlier: 5.104A pdb=" N SER A 634 " --> pdb=" O ASP A 630 " (cutoff:3.500A) removed outlier: 4.253A pdb=" N TRP A 635 " --> pdb=" O LEU A 631 " (cutoff:3.500A) Processing helix chain 'A' and resid 639 through 653 removed outlier: 3.504A pdb=" N TRP A 643 " --> pdb=" O GLY A 639 " (cutoff:3.500A) Processing helix chain 'A' and resid 678 through 706 removed outlier: 4.342A pdb=" N VAL A 682 " --> pdb=" O MET A 678 " (cutoff:3.500A) removed outlier: 4.982A pdb=" N VAL A 693 " --> pdb=" O VAL A 689 " (cutoff:3.500A) Proline residue: A 694 - end of helix removed outlier: 4.405A pdb=" N PHE A 699 " --> pdb=" O ILE A 695 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N VAL A 701 " --> pdb=" O MET A 697 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N LYS A 704 " --> pdb=" O VAL A 700 " (cutoff:3.500A) Processing helix chain 'A' and resid 726 through 755 removed outlier: 3.753A pdb=" N ASP A 730 " --> pdb=" O GLN A 726 " (cutoff:3.500A) removed outlier: 5.694A pdb=" N ALA A 731 " --> pdb=" O LYS A 727 " (cutoff:3.500A) removed outlier: 4.363A pdb=" N LEU A 732 " --> pdb=" O ILE A 728 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N ARG A 733 " --> pdb=" O GLU A 729 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N TYR A 737 " --> pdb=" O ARG A 733 " (cutoff:3.500A) Processing helix chain 'A' and resid 756 through 760 removed outlier: 3.944A pdb=" N ILE A 759 " --> pdb=" O ARG A 756 " (cutoff:3.500A) Processing helix chain 'A' and resid 761 through 784 removed outlier: 3.936A pdb=" N LYS A 765 " --> pdb=" O SER A 761 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N PHE A 766 " --> pdb=" O HIS A 762 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ASP A 767 " --> pdb=" O TRP A 763 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N LEU A 771 " --> pdb=" O ASP A 767 " (cutoff:3.500A) Processing helix chain 'A' and resid 794 through 797 Processing helix chain 'A' and resid 798 through 811 removed outlier: 3.911A pdb=" N ARG A 806 " --> pdb=" O PHE A 802 " (cutoff:3.500A) removed outlier: 4.584A pdb=" N ARG A 809 " --> pdb=" O LEU A 805 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N LEU A 811 " --> pdb=" O GLY A 807 " (cutoff:3.500A) Processing helix chain 'A' and resid 813 through 852 Proline residue: A 819 - end of helix removed outlier: 3.600A pdb=" N LYS A 852 " --> pdb=" O GLU A 848 " (cutoff:3.500A) Processing helix chain 'A' and resid 853 through 857 Processing helix chain 'A' and resid 860 through 889 removed outlier: 3.630A pdb=" N GLN A 877 " --> pdb=" O THR A 873 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N GLN A 886 " --> pdb=" O LEU A 882 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N ARG A 887 " --> pdb=" O GLY A 883 " (cutoff:3.500A) Processing helix chain 'A' and resid 889 through 919 Processing helix chain 'A' and resid 923 through 942 removed outlier: 3.526A pdb=" N THR A 933 " --> pdb=" O LYS A 929 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N LEU A 941 " --> pdb=" O LYS A 937 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N MET A 942 " --> pdb=" O MET A 938 " (cutoff:3.500A) Processing helix chain 'A' and resid 952 through 959 removed outlier: 3.641A pdb=" N LEU A 956 " --> pdb=" O PRO A 952 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N LEU A 957 " --> pdb=" O PRO A 953 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N LYS A 958 " --> pdb=" O GLU A 954 " (cutoff:3.500A) Processing helix chain 'A' and resid 960 through 964 Processing helix chain 'A' and resid 966 through 977 Processing helix chain 'A' and resid 1043 through 1050 Processing helix chain 'A' and resid 1070 through 1080 Processing helix chain 'A' and resid 1085 through 1107 removed outlier: 3.617A pdb=" N ARG A1097 " --> pdb=" O VAL A1093 " (cutoff:3.500A) Proline residue: A1101 - end of helix Processing helix chain 'A' and resid 1113 through 1123 removed outlier: 3.710A pdb=" N ARG A1123 " --> pdb=" O LEU A1119 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 978 through 982 removed outlier: 6.460A pdb=" N GLN A1064 " --> pdb=" O VAL A1002 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 987 through 989 removed outlier: 6.816A pdb=" N VAL A 987 " --> pdb=" O CYS A1059 " (cutoff:3.500A) removed outlier: 6.911A pdb=" N CYS A1059 " --> pdb=" O VAL A 987 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N VAL A 989 " --> pdb=" O VAL A1057 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 1125 through 1126 removed outlier: 6.689A pdb=" N ARG A1185 " --> pdb=" O ILE A1148 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N ASP A1144 " --> pdb=" O VAL A1189 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 1134 through 1136 570 hydrogen bonds defined for protein. 1668 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.57 Time building geometry restraints manager: 3.56 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 2574 1.35 - 1.46: 1857 1.46 - 1.58: 3772 1.58 - 1.70: 0 1.70 - 1.81: 76 Bond restraints: 8279 Sorted by residual: bond pdb=" N LEU A 70 " pdb=" CA LEU A 70 " ideal model delta sigma weight residual 1.458 1.490 -0.032 1.90e-02 2.77e+03 2.86e+00 bond pdb=" CA ILE A 488 " pdb=" CB ILE A 488 " ideal model delta sigma weight residual 1.534 1.524 0.010 6.80e-03 2.16e+04 2.26e+00 bond pdb=" CB GLU A1071 " pdb=" CG GLU A1071 " ideal model delta sigma weight residual 1.520 1.550 -0.030 3.00e-02 1.11e+03 9.92e-01 bond pdb=" CB GLU A 994 " pdb=" CG GLU A 994 " ideal model delta sigma weight residual 1.520 1.548 -0.028 3.00e-02 1.11e+03 8.91e-01 bond pdb=" CB ARG A 733 " pdb=" CG ARG A 733 " ideal model delta sigma weight residual 1.520 1.547 -0.027 3.00e-02 1.11e+03 8.25e-01 ... (remaining 8274 not shown) Histogram of bond angle deviations from ideal: 100.16 - 106.93: 195 106.93 - 113.69: 4835 113.69 - 120.46: 3315 120.46 - 127.22: 2799 127.22 - 133.99: 85 Bond angle restraints: 11229 Sorted by residual: angle pdb=" N VAL A 130 " pdb=" CA VAL A 130 " pdb=" C VAL A 130 " ideal model delta sigma weight residual 112.12 109.15 2.97 8.40e-01 1.42e+00 1.25e+01 angle pdb=" C LEU A 817 " pdb=" N ILE A 818 " pdb=" CA ILE A 818 " ideal model delta sigma weight residual 120.24 122.24 -2.00 6.30e-01 2.52e+00 1.00e+01 angle pdb=" C ILE A 818 " pdb=" CA ILE A 818 " pdb=" CB ILE A 818 " ideal model delta sigma weight residual 114.35 111.02 3.33 1.06e+00 8.90e-01 9.90e+00 angle pdb=" CA ARG A 733 " pdb=" CB ARG A 733 " pdb=" CG ARG A 733 " ideal model delta sigma weight residual 114.10 119.90 -5.80 2.00e+00 2.50e-01 8.40e+00 angle pdb=" CB MET A 925 " pdb=" CG MET A 925 " pdb=" SD MET A 925 " ideal model delta sigma weight residual 112.70 120.60 -7.90 3.00e+00 1.11e-01 6.94e+00 ... (remaining 11224 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.71: 4439 16.71 - 33.43: 400 33.43 - 50.14: 83 50.14 - 66.85: 14 66.85 - 83.57: 7 Dihedral angle restraints: 4943 sinusoidal: 1952 harmonic: 2991 Sorted by residual: dihedral pdb=" CA ARG A1162 " pdb=" C ARG A1162 " pdb=" N SER A1163 " pdb=" CA SER A1163 " ideal model delta harmonic sigma weight residual -180.00 -155.64 -24.36 0 5.00e+00 4.00e-02 2.37e+01 dihedral pdb=" CA LEU A 805 " pdb=" C LEU A 805 " pdb=" N ARG A 806 " pdb=" CA ARG A 806 " ideal model delta harmonic sigma weight residual 180.00 157.21 22.79 0 5.00e+00 4.00e-02 2.08e+01 dihedral pdb=" CA ASN A 448 " pdb=" C ASN A 448 " pdb=" N ASP A 449 " pdb=" CA ASP A 449 " ideal model delta harmonic sigma weight residual 180.00 160.52 19.48 0 5.00e+00 4.00e-02 1.52e+01 ... (remaining 4940 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.032: 873 0.032 - 0.063: 326 0.063 - 0.095: 110 0.095 - 0.127: 37 0.127 - 0.158: 4 Chirality restraints: 1350 Sorted by residual: chirality pdb=" CA ILE A 948 " pdb=" N ILE A 948 " pdb=" C ILE A 948 " pdb=" CB ILE A 948 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.16 2.00e-01 2.50e+01 6.25e-01 chirality pdb=" CA ILE A 742 " pdb=" N ILE A 742 " pdb=" C ILE A 742 " pdb=" CB ILE A 742 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.48e-01 chirality pdb=" CA ASN A 448 " pdb=" N ASN A 448 " pdb=" C ASN A 448 " pdb=" CB ASN A 448 " both_signs ideal model delta sigma weight residual False 2.51 2.38 0.13 2.00e-01 2.50e+01 4.47e-01 ... (remaining 1347 not shown) Planarity restraints: 1383 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL A 120 " 0.045 5.00e-02 4.00e+02 6.77e-02 7.33e+00 pdb=" N PRO A 121 " -0.117 5.00e-02 4.00e+02 pdb=" CA PRO A 121 " 0.035 5.00e-02 4.00e+02 pdb=" CD PRO A 121 " 0.037 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER A1163 " 0.029 5.00e-02 4.00e+02 4.46e-02 3.18e+00 pdb=" N PRO A1164 " -0.077 5.00e-02 4.00e+02 pdb=" CA PRO A1164 " 0.023 5.00e-02 4.00e+02 pdb=" CD PRO A1164 " 0.025 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 733 " 0.142 9.50e-02 1.11e+02 6.37e-02 2.57e+00 pdb=" NE ARG A 733 " -0.010 2.00e-02 2.50e+03 pdb=" CZ ARG A 733 " 0.003 2.00e-02 2.50e+03 pdb=" NH1 ARG A 733 " -0.003 2.00e-02 2.50e+03 pdb=" NH2 ARG A 733 " 0.003 2.00e-02 2.50e+03 ... (remaining 1380 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.76: 1377 2.76 - 3.30: 8397 3.30 - 3.83: 12765 3.83 - 4.37: 15061 4.37 - 4.90: 26259 Nonbonded interactions: 63859 Sorted by model distance: nonbonded pdb=" N GLU A 954 " pdb=" OE1 GLU A 954 " model vdw 2.227 2.520 nonbonded pdb=" N GLU A 994 " pdb=" OE1 GLU A 994 " model vdw 2.228 2.520 nonbonded pdb=" O PHE A 254 " pdb=" NE2 GLN A 256 " model vdw 2.248 2.520 nonbonded pdb=" OD1 ASN A 237 " pdb=" N ASP A 238 " model vdw 2.270 2.520 nonbonded pdb=" N GLU A1071 " pdb=" OE1 GLU A1071 " model vdw 2.273 2.520 ... (remaining 63854 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=1.00 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: 2.230 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: 6.130 Check model and map are aligned: 0.150 Set scattering table: 0.090 Process input model: 26.150 Find NCS groups from input model: 0.220 Set up NCS constraints: 0.030 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:2.590 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.600 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7334 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 0.035 8279 Z= 0.180 Angle : 0.560 7.902 11229 Z= 0.307 Chirality : 0.039 0.158 1350 Planarity : 0.004 0.068 1383 Dihedral : 13.667 83.567 3003 Min Nonbonded Distance : 2.227 Molprobity Statistics. All-atom Clashscore : 4.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.28 % Favored : 98.72 % Rotamer: Outliers : 0.00 % Allowed : 10.86 % Favored : 89.14 % 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: 0.70 (0.26), residues: 1016 helix: 0.81 (0.19), residues: 725 sheet: 0.93 (0.84), residues: 38 loop : -0.35 (0.37), residues: 253 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 635 HIS 0.006 0.001 HIS A 132 PHE 0.018 0.001 PHE A 740 TYR 0.010 0.001 TYR A1178 ARG 0.007 0.001 ARG A 573 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2032 Ramachandran restraints generated. 1016 Oldfield, 0 Emsley, 1016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2032 Ramachandran restraints generated. 1016 Oldfield, 0 Emsley, 1016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 219 residues out of total 884 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 219 time to evaluate : 0.979 Fit side-chains REVERT: A 113 LEU cc_start: 0.7467 (tt) cc_final: 0.7187 (tp) REVERT: A 128 ARG cc_start: 0.7103 (ttm170) cc_final: 0.6867 (ttm-80) REVERT: A 160 MET cc_start: 0.6836 (mmt) cc_final: 0.6409 (mmm) REVERT: A 176 VAL cc_start: 0.7544 (p) cc_final: 0.7255 (m) REVERT: A 346 GLU cc_start: 0.6953 (tt0) cc_final: 0.6704 (tt0) REVERT: A 375 LYS cc_start: 0.7810 (mtmt) cc_final: 0.7339 (mtmm) REVERT: A 385 TRP cc_start: 0.7977 (m100) cc_final: 0.7460 (m100) REVERT: A 579 MET cc_start: 0.6806 (tpt) cc_final: 0.6169 (tpt) REVERT: A 624 GLN cc_start: 0.7425 (mm-40) cc_final: 0.6997 (mm-40) REVERT: A 684 ILE cc_start: 0.7616 (mm) cc_final: 0.7388 (mt) REVERT: A 697 MET cc_start: 0.6534 (mmm) cc_final: 0.5858 (mmm) REVERT: A 852 LYS cc_start: 0.8200 (mmtm) cc_final: 0.7998 (mmmt) REVERT: A 972 PHE cc_start: 0.7776 (t80) cc_final: 0.7446 (t80) REVERT: A 1054 ASN cc_start: 0.8049 (t0) cc_final: 0.7819 (t0) REVERT: A 1133 HIS cc_start: 0.6011 (t70) cc_final: 0.5781 (t-90) REVERT: A 1173 LYS cc_start: 0.7030 (ttmt) cc_final: 0.6603 (ttmm) REVERT: A 1183 GLU cc_start: 0.7767 (tt0) cc_final: 0.7538 (tt0) REVERT: A 1185 ARG cc_start: 0.7807 (mmm160) cc_final: 0.7465 (mmm160) outliers start: 0 outliers final: 0 residues processed: 219 average time/residue: 0.2484 time to fit residues: 69.6459 Evaluate side-chains 205 residues out of total 884 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 205 time to evaluate : 0.879 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 86 optimal weight: 2.9990 chunk 77 optimal weight: 3.9990 chunk 42 optimal weight: 1.9990 chunk 26 optimal weight: 0.8980 chunk 52 optimal weight: 0.7980 chunk 41 optimal weight: 3.9990 chunk 79 optimal weight: 0.6980 chunk 30 optimal weight: 2.9990 chunk 48 optimal weight: 0.5980 chunk 59 optimal weight: 4.9990 chunk 92 optimal weight: 0.7980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 256 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 374 GLN A 636 GLN A 691 ASN A 886 GLN A 981 HIS A1114 GLN A1120 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7347 moved from start: 0.1584 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 8279 Z= 0.237 Angle : 0.545 7.251 11229 Z= 0.291 Chirality : 0.041 0.167 1350 Planarity : 0.004 0.060 1383 Dihedral : 4.180 19.275 1097 Min Nonbonded Distance : 2.207 Molprobity Statistics. All-atom Clashscore : 3.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.38 % Favored : 98.62 % Rotamer: Outliers : 1.70 % Allowed : 13.24 % Favored : 85.07 % 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: 1.65 (0.26), residues: 1016 helix: 1.48 (0.19), residues: 738 sheet: 1.15 (1.05), residues: 28 loop : 0.10 (0.40), residues: 250 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 278 HIS 0.003 0.001 HIS A1133 PHE 0.016 0.002 PHE A1136 TYR 0.014 0.001 TYR A 267 ARG 0.005 0.001 ARG A 903 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2032 Ramachandran restraints generated. 1016 Oldfield, 0 Emsley, 1016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2032 Ramachandran restraints generated. 1016 Oldfield, 0 Emsley, 1016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 223 residues out of total 884 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 208 time to evaluate : 0.957 Fit side-chains REVERT: A 160 MET cc_start: 0.6836 (mmt) cc_final: 0.6473 (mmm) REVERT: A 176 VAL cc_start: 0.7363 (p) cc_final: 0.7000 (m) REVERT: A 217 LEU cc_start: 0.7249 (mp) cc_final: 0.6944 (mp) REVERT: A 375 LYS cc_start: 0.7745 (mtmt) cc_final: 0.7456 (mtmm) REVERT: A 385 TRP cc_start: 0.7884 (m100) cc_final: 0.7652 (m100) REVERT: A 579 MET cc_start: 0.6841 (tpt) cc_final: 0.6426 (tpt) REVERT: A 624 GLN cc_start: 0.7468 (mm-40) cc_final: 0.6875 (tt0) REVERT: A 684 ILE cc_start: 0.7682 (mm) cc_final: 0.7458 (mt) REVERT: A 697 MET cc_start: 0.6639 (mmm) cc_final: 0.5966 (mmm) REVERT: A 736 ASN cc_start: 0.6880 (m-40) cc_final: 0.6420 (m-40) REVERT: A 852 LYS cc_start: 0.8246 (mmtm) cc_final: 0.8008 (mmmt) REVERT: A 856 ARG cc_start: 0.7182 (mtp180) cc_final: 0.6935 (mtm110) REVERT: A 857 MET cc_start: 0.7658 (tpp) cc_final: 0.7438 (tpp) REVERT: A 958 LYS cc_start: 0.7626 (ttpp) cc_final: 0.7012 (ttpp) REVERT: A 990 ARG cc_start: 0.7217 (ttm110) cc_final: 0.6479 (ttm110) REVERT: A 1054 ASN cc_start: 0.8091 (t0) cc_final: 0.7841 (t0) REVERT: A 1058 THR cc_start: 0.8088 (m) cc_final: 0.7804 (p) REVERT: A 1173 LYS cc_start: 0.7193 (ttmt) cc_final: 0.6851 (ttmm) outliers start: 15 outliers final: 5 residues processed: 218 average time/residue: 0.2437 time to fit residues: 68.6720 Evaluate side-chains 205 residues out of total 884 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 200 time to evaluate : 0.868 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 220 LEU Chi-restraints excluded: chain A residue 273 VAL Chi-restraints excluded: chain A residue 401 MET Chi-restraints excluded: chain A residue 424 ILE Chi-restraints excluded: chain A residue 640 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 51 optimal weight: 0.7980 chunk 28 optimal weight: 0.5980 chunk 77 optimal weight: 2.9990 chunk 63 optimal weight: 6.9990 chunk 25 optimal weight: 0.7980 chunk 92 optimal weight: 0.7980 chunk 100 optimal weight: 3.9990 chunk 82 optimal weight: 0.8980 chunk 31 optimal weight: 2.9990 chunk 74 optimal weight: 1.9990 chunk 91 optimal weight: 1.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 256 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 374 GLN ** A 691 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 832 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7357 moved from start: 0.2064 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 8279 Z= 0.228 Angle : 0.499 6.426 11229 Z= 0.266 Chirality : 0.040 0.174 1350 Planarity : 0.004 0.053 1383 Dihedral : 3.981 18.173 1097 Min Nonbonded Distance : 2.192 Molprobity Statistics. All-atom Clashscore : 4.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.18 % Favored : 98.82 % Rotamer: Outliers : 2.04 % Allowed : 13.57 % Favored : 84.39 % 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: 1.79 (0.26), residues: 1016 helix: 1.70 (0.19), residues: 725 sheet: 0.78 (0.97), residues: 28 loop : -0.10 (0.38), residues: 263 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 278 HIS 0.008 0.001 HIS A1133 PHE 0.015 0.001 PHE A1136 TYR 0.009 0.001 TYR A 309 ARG 0.006 0.000 ARG A 887 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2032 Ramachandran restraints generated. 1016 Oldfield, 0 Emsley, 1016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2032 Ramachandran restraints generated. 1016 Oldfield, 0 Emsley, 1016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 223 residues out of total 884 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 205 time to evaluate : 0.949 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 160 MET cc_start: 0.6980 (mmt) cc_final: 0.6625 (mmm) REVERT: A 176 VAL cc_start: 0.7283 (p) cc_final: 0.6944 (m) REVERT: A 217 LEU cc_start: 0.7234 (mp) cc_final: 0.6913 (mp) REVERT: A 375 LYS cc_start: 0.7834 (mtmt) cc_final: 0.7498 (mtmm) REVERT: A 383 MET cc_start: 0.6769 (mmp) cc_final: 0.6445 (mmp) REVERT: A 579 MET cc_start: 0.6771 (tpt) cc_final: 0.6439 (tpt) REVERT: A 584 LEU cc_start: 0.7941 (mt) cc_final: 0.7692 (mm) REVERT: A 630 ASP cc_start: 0.7553 (m-30) cc_final: 0.7303 (m-30) REVERT: A 684 ILE cc_start: 0.7687 (mm) cc_final: 0.7455 (mt) REVERT: A 697 MET cc_start: 0.6560 (mmm) cc_final: 0.5972 (mmm) REVERT: A 758 TYR cc_start: 0.6557 (t80) cc_final: 0.6299 (t80) REVERT: A 856 ARG cc_start: 0.7148 (mtp180) cc_final: 0.6930 (mtp-110) REVERT: A 857 MET cc_start: 0.7653 (tpp) cc_final: 0.7325 (tpt) REVERT: A 887 ARG cc_start: 0.7865 (mtp85) cc_final: 0.7423 (mtp85) REVERT: A 958 LYS cc_start: 0.7668 (ttpp) cc_final: 0.7020 (ttpp) REVERT: A 990 ARG cc_start: 0.7290 (ttm110) cc_final: 0.6530 (ttm110) REVERT: A 1058 THR cc_start: 0.8075 (m) cc_final: 0.7714 (p) REVERT: A 1061 THR cc_start: 0.8184 (m) cc_final: 0.7928 (p) REVERT: A 1143 GLU cc_start: 0.6692 (mm-30) cc_final: 0.6476 (mm-30) REVERT: A 1173 LYS cc_start: 0.7239 (ttmt) cc_final: 0.6882 (ttmm) outliers start: 18 outliers final: 11 residues processed: 216 average time/residue: 0.2268 time to fit residues: 64.6324 Evaluate side-chains 211 residues out of total 884 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 200 time to evaluate : 0.850 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 127 THR Chi-restraints excluded: chain A residue 200 MET Chi-restraints excluded: chain A residue 220 LEU Chi-restraints excluded: chain A residue 257 LEU Chi-restraints excluded: chain A residue 347 VAL Chi-restraints excluded: chain A residue 401 MET Chi-restraints excluded: chain A residue 430 LEU Chi-restraints excluded: chain A residue 640 ILE Chi-restraints excluded: chain A residue 652 ILE Chi-restraints excluded: chain A residue 1063 VAL Chi-restraints excluded: chain A residue 1142 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 69 optimal weight: 0.9980 chunk 48 optimal weight: 2.9990 chunk 10 optimal weight: 0.9980 chunk 44 optimal weight: 0.9990 chunk 62 optimal weight: 0.0370 chunk 93 optimal weight: 1.9990 chunk 98 optimal weight: 2.9990 chunk 88 optimal weight: 1.9990 chunk 26 optimal weight: 0.4980 chunk 82 optimal weight: 0.8980 chunk 55 optimal weight: 8.9990 overall best weight: 0.6858 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 165 GLN ** A 256 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 374 GLN A 691 ASN A 832 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7354 moved from start: 0.2294 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 8279 Z= 0.204 Angle : 0.479 7.161 11229 Z= 0.253 Chirality : 0.039 0.171 1350 Planarity : 0.004 0.050 1383 Dihedral : 3.848 17.778 1097 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 5.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.18 % Favored : 98.82 % Rotamer: Outliers : 2.83 % Allowed : 14.59 % Favored : 82.58 % 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: 2.00 (0.26), residues: 1016 helix: 1.84 (0.19), residues: 725 sheet: 0.78 (0.95), residues: 33 loop : 0.04 (0.38), residues: 258 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 278 HIS 0.005 0.001 HIS A1120 PHE 0.013 0.001 PHE A1136 TYR 0.008 0.001 TYR A 309 ARG 0.004 0.000 ARG A 887 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2032 Ramachandran restraints generated. 1016 Oldfield, 0 Emsley, 1016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2032 Ramachandran restraints generated. 1016 Oldfield, 0 Emsley, 1016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 232 residues out of total 884 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 207 time to evaluate : 0.914 Fit side-chains REVERT: A 160 MET cc_start: 0.7063 (mmt) cc_final: 0.6706 (mmm) REVERT: A 176 VAL cc_start: 0.7300 (p) cc_final: 0.6973 (m) REVERT: A 217 LEU cc_start: 0.7249 (mp) cc_final: 0.6902 (mp) REVERT: A 375 LYS cc_start: 0.7861 (mtmt) cc_final: 0.7529 (mtmm) REVERT: A 383 MET cc_start: 0.6764 (mmp) cc_final: 0.6540 (mmp) REVERT: A 579 MET cc_start: 0.6747 (tpt) cc_final: 0.6433 (tpt) REVERT: A 584 LEU cc_start: 0.7906 (mt) cc_final: 0.7697 (mm) REVERT: A 624 GLN cc_start: 0.7404 (mm-40) cc_final: 0.6868 (tt0) REVERT: A 630 ASP cc_start: 0.7551 (m-30) cc_final: 0.7304 (m-30) REVERT: A 684 ILE cc_start: 0.7704 (mm) cc_final: 0.7428 (mt) REVERT: A 758 TYR cc_start: 0.6627 (t80) cc_final: 0.6415 (t80) REVERT: A 856 ARG cc_start: 0.7151 (mtp180) cc_final: 0.6803 (mtp180) REVERT: A 857 MET cc_start: 0.7652 (tpp) cc_final: 0.7375 (tpp) REVERT: A 877 GLN cc_start: 0.8309 (tt0) cc_final: 0.8100 (tt0) REVERT: A 887 ARG cc_start: 0.7878 (mtp85) cc_final: 0.7432 (mtp85) REVERT: A 958 LYS cc_start: 0.7709 (ttpp) cc_final: 0.7036 (ttpp) REVERT: A 990 ARG cc_start: 0.7337 (ttm110) cc_final: 0.6697 (ttm110) REVERT: A 1054 ASN cc_start: 0.8092 (t0) cc_final: 0.7839 (t0) REVERT: A 1058 THR cc_start: 0.8091 (m) cc_final: 0.7694 (p) REVERT: A 1061 THR cc_start: 0.8225 (m) cc_final: 0.7976 (p) REVERT: A 1173 LYS cc_start: 0.7225 (ttmt) cc_final: 0.6882 (ttmm) REVERT: A 1186 LEU cc_start: 0.8206 (tp) cc_final: 0.7953 (tp) outliers start: 25 outliers final: 18 residues processed: 222 average time/residue: 0.2244 time to fit residues: 65.3796 Evaluate side-chains 226 residues out of total 884 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 208 time to evaluate : 0.887 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 127 THR Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 154 MET Chi-restraints excluded: chain A residue 200 MET Chi-restraints excluded: chain A residue 257 LEU Chi-restraints excluded: chain A residue 269 LEU Chi-restraints excluded: chain A residue 273 VAL Chi-restraints excluded: chain A residue 347 VAL Chi-restraints excluded: chain A residue 401 MET Chi-restraints excluded: chain A residue 417 LEU Chi-restraints excluded: chain A residue 430 LEU Chi-restraints excluded: chain A residue 506 ASN Chi-restraints excluded: chain A residue 640 ILE Chi-restraints excluded: chain A residue 652 ILE Chi-restraints excluded: chain A residue 822 ILE Chi-restraints excluded: chain A residue 837 TYR Chi-restraints excluded: chain A residue 865 ARG Chi-restraints excluded: chain A residue 1142 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 1 optimal weight: 1.9990 chunk 73 optimal weight: 0.5980 chunk 40 optimal weight: 0.6980 chunk 84 optimal weight: 0.9990 chunk 68 optimal weight: 1.9990 chunk 0 optimal weight: 2.9990 chunk 50 optimal weight: 0.0970 chunk 88 optimal weight: 0.0270 chunk 24 optimal weight: 0.9980 chunk 33 optimal weight: 0.7980 chunk 19 optimal weight: 2.9990 overall best weight: 0.4436 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 256 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 374 GLN A 691 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7339 moved from start: 0.2528 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 8279 Z= 0.159 Angle : 0.458 7.525 11229 Z= 0.241 Chirality : 0.038 0.156 1350 Planarity : 0.004 0.046 1383 Dihedral : 3.720 18.139 1097 Min Nonbonded Distance : 2.180 Molprobity Statistics. All-atom Clashscore : 5.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.08 % Favored : 98.92 % Rotamer: Outliers : 2.83 % Allowed : 15.27 % Favored : 81.90 % 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: 2.28 (0.27), residues: 1016 helix: 2.08 (0.19), residues: 721 sheet: 0.79 (0.82), residues: 43 loop : 0.05 (0.39), residues: 252 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 353 HIS 0.004 0.001 HIS A1133 PHE 0.019 0.001 PHE A 972 TYR 0.007 0.001 TYR A 309 ARG 0.003 0.000 ARG A 887 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2032 Ramachandran restraints generated. 1016 Oldfield, 0 Emsley, 1016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2032 Ramachandran restraints generated. 1016 Oldfield, 0 Emsley, 1016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 234 residues out of total 884 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 209 time to evaluate : 0.946 Fit side-chains revert: symmetry clash REVERT: A 160 MET cc_start: 0.7040 (mmt) cc_final: 0.6681 (mmm) REVERT: A 176 VAL cc_start: 0.7271 (p) cc_final: 0.6959 (m) REVERT: A 217 LEU cc_start: 0.7201 (mp) cc_final: 0.6862 (mp) REVERT: A 375 LYS cc_start: 0.7832 (mtmt) cc_final: 0.7474 (mtmm) REVERT: A 383 MET cc_start: 0.6813 (mmp) cc_final: 0.6411 (mmp) REVERT: A 624 GLN cc_start: 0.7387 (mm-40) cc_final: 0.6866 (tt0) REVERT: A 630 ASP cc_start: 0.7532 (m-30) cc_final: 0.7297 (m-30) REVERT: A 684 ILE cc_start: 0.7698 (mm) cc_final: 0.7470 (mt) REVERT: A 697 MET cc_start: 0.6786 (mmm) cc_final: 0.6383 (tmm) REVERT: A 736 ASN cc_start: 0.7096 (m-40) cc_final: 0.6739 (m-40) REVERT: A 758 TYR cc_start: 0.6639 (t80) cc_final: 0.6333 (t80) REVERT: A 856 ARG cc_start: 0.7150 (mtp180) cc_final: 0.6795 (mtp180) REVERT: A 857 MET cc_start: 0.7677 (tpp) cc_final: 0.7391 (tpp) REVERT: A 877 GLN cc_start: 0.8332 (tt0) cc_final: 0.8092 (tt0) REVERT: A 881 GLU cc_start: 0.8181 (mm-30) cc_final: 0.7779 (mt-10) REVERT: A 887 ARG cc_start: 0.7878 (mtp85) cc_final: 0.7454 (mtp85) REVERT: A 958 LYS cc_start: 0.7720 (ttpp) cc_final: 0.7027 (ttpp) REVERT: A 990 ARG cc_start: 0.7371 (ttm110) cc_final: 0.6619 (ttm110) REVERT: A 1037 THR cc_start: 0.8402 (t) cc_final: 0.8065 (m) REVERT: A 1054 ASN cc_start: 0.8053 (t0) cc_final: 0.7812 (t0) REVERT: A 1173 LYS cc_start: 0.7231 (ttmt) cc_final: 0.6873 (tttp) outliers start: 25 outliers final: 19 residues processed: 223 average time/residue: 0.2272 time to fit residues: 66.6042 Evaluate side-chains 220 residues out of total 884 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 201 time to evaluate : 0.930 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 127 THR Chi-restraints excluded: chain A residue 200 MET Chi-restraints excluded: chain A residue 257 LEU Chi-restraints excluded: chain A residue 269 LEU Chi-restraints excluded: chain A residue 273 VAL Chi-restraints excluded: chain A residue 347 VAL Chi-restraints excluded: chain A residue 401 MET Chi-restraints excluded: chain A residue 417 LEU Chi-restraints excluded: chain A residue 430 LEU Chi-restraints excluded: chain A residue 479 ARG Chi-restraints excluded: chain A residue 506 ASN Chi-restraints excluded: chain A residue 640 ILE Chi-restraints excluded: chain A residue 652 ILE Chi-restraints excluded: chain A residue 691 ASN Chi-restraints excluded: chain A residue 809 ARG Chi-restraints excluded: chain A residue 810 MET Chi-restraints excluded: chain A residue 822 ILE Chi-restraints excluded: chain A residue 837 TYR Chi-restraints excluded: chain A residue 865 ARG Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 57 optimal weight: 6.9990 chunk 24 optimal weight: 0.3980 chunk 98 optimal weight: 3.9990 chunk 81 optimal weight: 0.7980 chunk 45 optimal weight: 0.6980 chunk 8 optimal weight: 0.9980 chunk 32 optimal weight: 0.9990 chunk 51 optimal weight: 0.5980 chunk 95 optimal weight: 0.7980 chunk 11 optimal weight: 0.5980 chunk 56 optimal weight: 0.8980 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 256 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 374 GLN A 832 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7347 moved from start: 0.2595 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 8279 Z= 0.189 Angle : 0.460 9.166 11229 Z= 0.242 Chirality : 0.039 0.140 1350 Planarity : 0.004 0.047 1383 Dihedral : 3.694 18.069 1097 Min Nonbonded Distance : 2.180 Molprobity Statistics. All-atom Clashscore : 5.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.08 % Favored : 98.92 % Rotamer: Outliers : 2.83 % Allowed : 15.84 % Favored : 81.33 % 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: 2.32 (0.27), residues: 1016 helix: 2.09 (0.19), residues: 726 sheet: 0.92 (0.97), residues: 33 loop : 0.07 (0.39), residues: 257 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 278 HIS 0.005 0.001 HIS A1120 PHE 0.016 0.001 PHE A 254 TYR 0.015 0.001 TYR A 267 ARG 0.003 0.000 ARG A 887 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2032 Ramachandran restraints generated. 1016 Oldfield, 0 Emsley, 1016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2032 Ramachandran restraints generated. 1016 Oldfield, 0 Emsley, 1016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 228 residues out of total 884 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 203 time to evaluate : 0.868 Fit side-chains REVERT: A 160 MET cc_start: 0.7009 (mmt) cc_final: 0.6651 (mmm) REVERT: A 176 VAL cc_start: 0.7254 (p) cc_final: 0.6943 (m) REVERT: A 217 LEU cc_start: 0.7189 (mp) cc_final: 0.6848 (mp) REVERT: A 375 LYS cc_start: 0.7866 (mtmt) cc_final: 0.7501 (mtmm) REVERT: A 383 MET cc_start: 0.6809 (mmp) cc_final: 0.6404 (mmp) REVERT: A 579 MET cc_start: 0.6769 (tpt) cc_final: 0.6409 (tpt) REVERT: A 624 GLN cc_start: 0.7412 (mm-40) cc_final: 0.6826 (tt0) REVERT: A 630 ASP cc_start: 0.7544 (m-30) cc_final: 0.7319 (m-30) REVERT: A 684 ILE cc_start: 0.7723 (mm) cc_final: 0.7415 (mt) REVERT: A 697 MET cc_start: 0.6806 (mmm) cc_final: 0.6438 (tmm) REVERT: A 736 ASN cc_start: 0.7115 (m-40) cc_final: 0.6741 (m-40) REVERT: A 758 TYR cc_start: 0.6646 (t80) cc_final: 0.6364 (t80) REVERT: A 856 ARG cc_start: 0.7155 (mtp180) cc_final: 0.6842 (mtp180) REVERT: A 857 MET cc_start: 0.7676 (tpp) cc_final: 0.7475 (tpp) REVERT: A 877 GLN cc_start: 0.8343 (tt0) cc_final: 0.8100 (tt0) REVERT: A 881 GLU cc_start: 0.8184 (mm-30) cc_final: 0.7777 (mt-10) REVERT: A 887 ARG cc_start: 0.7884 (mtp85) cc_final: 0.7537 (mtp85) REVERT: A 958 LYS cc_start: 0.7751 (ttpp) cc_final: 0.7060 (ttpp) REVERT: A 990 ARG cc_start: 0.7366 (ttm110) cc_final: 0.6699 (ttm110) REVERT: A 1037 THR cc_start: 0.8432 (t) cc_final: 0.8106 (m) REVERT: A 1054 ASN cc_start: 0.8047 (t0) cc_final: 0.7807 (t0) REVERT: A 1061 THR cc_start: 0.8272 (m) cc_final: 0.8052 (p) REVERT: A 1125 TYR cc_start: 0.7901 (p90) cc_final: 0.7514 (p90) REVERT: A 1173 LYS cc_start: 0.7239 (ttmt) cc_final: 0.6883 (tttp) outliers start: 25 outliers final: 19 residues processed: 215 average time/residue: 0.2250 time to fit residues: 63.5094 Evaluate side-chains 223 residues out of total 884 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 204 time to evaluate : 0.928 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 127 THR Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 154 MET Chi-restraints excluded: chain A residue 200 MET Chi-restraints excluded: chain A residue 257 LEU Chi-restraints excluded: chain A residue 269 LEU Chi-restraints excluded: chain A residue 273 VAL Chi-restraints excluded: chain A residue 296 ASP Chi-restraints excluded: chain A residue 347 VAL Chi-restraints excluded: chain A residue 401 MET Chi-restraints excluded: chain A residue 417 LEU Chi-restraints excluded: chain A residue 430 LEU Chi-restraints excluded: chain A residue 479 ARG Chi-restraints excluded: chain A residue 506 ASN Chi-restraints excluded: chain A residue 640 ILE Chi-restraints excluded: chain A residue 652 ILE Chi-restraints excluded: chain A residue 822 ILE Chi-restraints excluded: chain A residue 837 TYR Chi-restraints excluded: chain A residue 865 ARG Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 72 optimal weight: 1.9990 chunk 55 optimal weight: 5.9990 chunk 83 optimal weight: 1.9990 chunk 98 optimal weight: 0.0070 chunk 61 optimal weight: 0.9990 chunk 59 optimal weight: 0.8980 chunk 45 optimal weight: 0.5980 chunk 60 optimal weight: 1.9990 chunk 39 optimal weight: 0.5980 chunk 58 optimal weight: 0.5980 chunk 29 optimal weight: 0.7980 overall best weight: 0.5198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 685 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7340 moved from start: 0.2704 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 8279 Z= 0.169 Angle : 0.451 7.456 11229 Z= 0.238 Chirality : 0.038 0.135 1350 Planarity : 0.004 0.047 1383 Dihedral : 3.632 18.039 1097 Min Nonbonded Distance : 2.170 Molprobity Statistics. All-atom Clashscore : 5.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.38 % Favored : 98.62 % Rotamer: Outliers : 2.71 % Allowed : 16.52 % Favored : 80.77 % 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: 2.51 (0.27), residues: 1016 helix: 2.22 (0.19), residues: 717 sheet: 0.93 (0.97), residues: 33 loop : 0.26 (0.39), residues: 266 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 278 HIS 0.004 0.001 HIS A1120 PHE 0.014 0.001 PHE A 254 TYR 0.013 0.001 TYR A 267 ARG 0.008 0.000 ARG A 161 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2032 Ramachandran restraints generated. 1016 Oldfield, 0 Emsley, 1016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2032 Ramachandran restraints generated. 1016 Oldfield, 0 Emsley, 1016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 229 residues out of total 884 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 205 time to evaluate : 1.018 Fit side-chains REVERT: A 160 MET cc_start: 0.6754 (mmt) cc_final: 0.6390 (mmm) REVERT: A 176 VAL cc_start: 0.7240 (p) cc_final: 0.6937 (m) REVERT: A 217 LEU cc_start: 0.7173 (mp) cc_final: 0.6797 (mp) REVERT: A 375 LYS cc_start: 0.7849 (mtmt) cc_final: 0.7471 (mtmm) REVERT: A 383 MET cc_start: 0.6818 (mmp) cc_final: 0.6401 (mmp) REVERT: A 443 GLU cc_start: 0.7462 (tp30) cc_final: 0.7243 (tm-30) REVERT: A 579 MET cc_start: 0.6705 (tpt) cc_final: 0.6404 (tpt) REVERT: A 584 LEU cc_start: 0.7941 (mm) cc_final: 0.7677 (mp) REVERT: A 624 GLN cc_start: 0.7409 (mm-40) cc_final: 0.6829 (tt0) REVERT: A 630 ASP cc_start: 0.7565 (m-30) cc_final: 0.7326 (m-30) REVERT: A 684 ILE cc_start: 0.7686 (mm) cc_final: 0.7381 (mt) REVERT: A 697 MET cc_start: 0.6836 (mmm) cc_final: 0.6470 (tmm) REVERT: A 736 ASN cc_start: 0.7103 (m-40) cc_final: 0.6716 (m-40) REVERT: A 758 TYR cc_start: 0.6665 (t80) cc_final: 0.6343 (t80) REVERT: A 856 ARG cc_start: 0.7144 (mtp180) cc_final: 0.6843 (mtm110) REVERT: A 857 MET cc_start: 0.7687 (tpp) cc_final: 0.7470 (tpp) REVERT: A 877 GLN cc_start: 0.8337 (tt0) cc_final: 0.8098 (tt0) REVERT: A 881 GLU cc_start: 0.8179 (mm-30) cc_final: 0.7777 (mt-10) REVERT: A 887 ARG cc_start: 0.7864 (mtp85) cc_final: 0.7570 (mtp85) REVERT: A 958 LYS cc_start: 0.7759 (ttpp) cc_final: 0.7053 (ttpp) REVERT: A 990 ARG cc_start: 0.7382 (ttm110) cc_final: 0.6746 (ttm110) REVERT: A 1037 THR cc_start: 0.8395 (t) cc_final: 0.8072 (m) REVERT: A 1054 ASN cc_start: 0.8022 (t0) cc_final: 0.7781 (t0) REVERT: A 1125 TYR cc_start: 0.7894 (p90) cc_final: 0.7514 (p90) REVERT: A 1173 LYS cc_start: 0.7252 (ttmt) cc_final: 0.6914 (tttp) REVERT: A 1182 GLU cc_start: 0.7796 (mm-30) cc_final: 0.7591 (mm-30) outliers start: 24 outliers final: 22 residues processed: 218 average time/residue: 0.2291 time to fit residues: 65.6211 Evaluate side-chains 224 residues out of total 884 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 202 time to evaluate : 0.920 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 127 THR Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 154 MET Chi-restraints excluded: chain A residue 200 MET Chi-restraints excluded: chain A residue 257 LEU Chi-restraints excluded: chain A residue 269 LEU Chi-restraints excluded: chain A residue 273 VAL Chi-restraints excluded: chain A residue 296 ASP Chi-restraints excluded: chain A residue 347 VAL Chi-restraints excluded: chain A residue 401 MET Chi-restraints excluded: chain A residue 417 LEU Chi-restraints excluded: chain A residue 430 LEU Chi-restraints excluded: chain A residue 479 ARG Chi-restraints excluded: chain A residue 506 ASN Chi-restraints excluded: chain A residue 640 ILE Chi-restraints excluded: chain A residue 652 ILE Chi-restraints excluded: chain A residue 810 MET Chi-restraints excluded: chain A residue 822 ILE Chi-restraints excluded: chain A residue 837 TYR Chi-restraints excluded: chain A residue 865 ARG Chi-restraints excluded: chain A residue 979 LEU Chi-restraints excluded: chain A residue 1142 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 19 optimal weight: 0.9990 chunk 62 optimal weight: 4.9990 chunk 66 optimal weight: 0.4980 chunk 48 optimal weight: 2.9990 chunk 9 optimal weight: 2.9990 chunk 77 optimal weight: 3.9990 chunk 89 optimal weight: 0.9980 chunk 94 optimal weight: 2.9990 chunk 85 optimal weight: 0.6980 chunk 91 optimal weight: 0.9990 chunk 55 optimal weight: 0.7980 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 600 HIS ** A 685 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7354 moved from start: 0.2734 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 8279 Z= 0.225 Angle : 0.477 10.031 11229 Z= 0.250 Chirality : 0.039 0.137 1350 Planarity : 0.004 0.048 1383 Dihedral : 3.683 18.632 1097 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 5.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.57 % Favored : 98.43 % Rotamer: Outliers : 2.49 % Allowed : 16.97 % Favored : 80.54 % 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: 2.36 (0.27), residues: 1016 helix: 2.11 (0.19), residues: 723 sheet: 0.91 (0.98), residues: 33 loop : 0.19 (0.39), residues: 260 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 278 HIS 0.006 0.001 HIS A1133 PHE 0.013 0.001 PHE A 254 TYR 0.010 0.001 TYR A 267 ARG 0.006 0.000 ARG A 161 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2032 Ramachandran restraints generated. 1016 Oldfield, 0 Emsley, 1016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2032 Ramachandran restraints generated. 1016 Oldfield, 0 Emsley, 1016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 227 residues out of total 884 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 205 time to evaluate : 0.898 Fit side-chains REVERT: A 160 MET cc_start: 0.7043 (mmt) cc_final: 0.6692 (mmm) REVERT: A 176 VAL cc_start: 0.7251 (p) cc_final: 0.6944 (m) REVERT: A 217 LEU cc_start: 0.7167 (mp) cc_final: 0.6804 (mp) REVERT: A 375 LYS cc_start: 0.7848 (mtmt) cc_final: 0.7444 (mtmm) REVERT: A 383 MET cc_start: 0.6839 (mmp) cc_final: 0.6396 (mmp) REVERT: A 443 GLU cc_start: 0.7461 (tp30) cc_final: 0.7237 (tm-30) REVERT: A 579 MET cc_start: 0.6740 (tpt) cc_final: 0.6413 (tpt) REVERT: A 624 GLN cc_start: 0.7488 (mm-40) cc_final: 0.6879 (tt0) REVERT: A 630 ASP cc_start: 0.7579 (m-30) cc_final: 0.7340 (m-30) REVERT: A 684 ILE cc_start: 0.7707 (mm) cc_final: 0.7411 (mt) REVERT: A 697 MET cc_start: 0.6883 (mmm) cc_final: 0.6518 (tmm) REVERT: A 736 ASN cc_start: 0.7097 (m-40) cc_final: 0.6707 (m-40) REVERT: A 856 ARG cc_start: 0.7129 (mtp180) cc_final: 0.6814 (mtm110) REVERT: A 857 MET cc_start: 0.7681 (tpp) cc_final: 0.7467 (tpp) REVERT: A 877 GLN cc_start: 0.8349 (tt0) cc_final: 0.8085 (tt0) REVERT: A 881 GLU cc_start: 0.8189 (mm-30) cc_final: 0.7771 (mt-10) REVERT: A 887 ARG cc_start: 0.7876 (mtp85) cc_final: 0.7569 (mtp85) REVERT: A 958 LYS cc_start: 0.7753 (ttpp) cc_final: 0.7051 (ttpp) REVERT: A 1037 THR cc_start: 0.8402 (t) cc_final: 0.8082 (m) REVERT: A 1125 TYR cc_start: 0.7877 (p90) cc_final: 0.7499 (p90) REVERT: A 1173 LYS cc_start: 0.7256 (ttmt) cc_final: 0.6949 (ttmm) REVERT: A 1182 GLU cc_start: 0.7777 (mm-30) cc_final: 0.7565 (mm-30) outliers start: 22 outliers final: 21 residues processed: 215 average time/residue: 0.2281 time to fit residues: 64.3112 Evaluate side-chains 224 residues out of total 884 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 203 time to evaluate : 0.921 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 127 THR Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 154 MET Chi-restraints excluded: chain A residue 200 MET Chi-restraints excluded: chain A residue 257 LEU Chi-restraints excluded: chain A residue 269 LEU Chi-restraints excluded: chain A residue 273 VAL Chi-restraints excluded: chain A residue 296 ASP Chi-restraints excluded: chain A residue 347 VAL Chi-restraints excluded: chain A residue 401 MET Chi-restraints excluded: chain A residue 417 LEU Chi-restraints excluded: chain A residue 430 LEU Chi-restraints excluded: chain A residue 479 ARG Chi-restraints excluded: chain A residue 506 ASN Chi-restraints excluded: chain A residue 640 ILE Chi-restraints excluded: chain A residue 652 ILE Chi-restraints excluded: chain A residue 810 MET Chi-restraints excluded: chain A residue 822 ILE Chi-restraints excluded: chain A residue 837 TYR Chi-restraints excluded: chain A residue 865 ARG Chi-restraints excluded: chain A residue 1061 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 39 optimal weight: 0.9980 chunk 71 optimal weight: 0.7980 chunk 28 optimal weight: 0.0870 chunk 82 optimal weight: 0.7980 chunk 86 optimal weight: 3.9990 chunk 91 optimal weight: 0.7980 chunk 60 optimal weight: 3.9990 chunk 96 optimal weight: 0.9990 chunk 59 optimal weight: 0.9990 chunk 45 optimal weight: 0.7980 chunk 67 optimal weight: 0.8980 overall best weight: 0.6558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 685 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7347 moved from start: 0.2792 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 8279 Z= 0.196 Angle : 0.466 6.905 11229 Z= 0.245 Chirality : 0.039 0.174 1350 Planarity : 0.004 0.048 1383 Dihedral : 3.668 18.555 1097 Min Nonbonded Distance : 2.166 Molprobity Statistics. All-atom Clashscore : 5.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.48 % Favored : 98.52 % Rotamer: Outliers : 2.71 % Allowed : 17.19 % Favored : 80.09 % 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: 2.39 (0.26), residues: 1016 helix: 2.11 (0.19), residues: 728 sheet: 0.85 (0.96), residues: 33 loop : 0.20 (0.39), residues: 255 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 278 HIS 0.005 0.001 HIS A1133 PHE 0.012 0.001 PHE A 254 TYR 0.009 0.001 TYR A 267 ARG 0.008 0.000 ARG A 161 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2032 Ramachandran restraints generated. 1016 Oldfield, 0 Emsley, 1016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2032 Ramachandran restraints generated. 1016 Oldfield, 0 Emsley, 1016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 231 residues out of total 884 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 207 time to evaluate : 0.936 Fit side-chains REVERT: A 160 MET cc_start: 0.6814 (mmt) cc_final: 0.6454 (mmm) REVERT: A 176 VAL cc_start: 0.7241 (p) cc_final: 0.6943 (m) REVERT: A 217 LEU cc_start: 0.7199 (mp) cc_final: 0.6853 (mp) REVERT: A 375 LYS cc_start: 0.7851 (mtmt) cc_final: 0.7450 (mtmm) REVERT: A 383 MET cc_start: 0.6832 (mmp) cc_final: 0.6386 (mmp) REVERT: A 443 GLU cc_start: 0.7474 (tp30) cc_final: 0.7245 (tm-30) REVERT: A 579 MET cc_start: 0.6719 (tpt) cc_final: 0.6448 (tpt) REVERT: A 584 LEU cc_start: 0.7926 (mm) cc_final: 0.7659 (mp) REVERT: A 624 GLN cc_start: 0.7453 (mm-40) cc_final: 0.6833 (tt0) REVERT: A 630 ASP cc_start: 0.7585 (m-30) cc_final: 0.7343 (m-30) REVERT: A 684 ILE cc_start: 0.7706 (mm) cc_final: 0.7329 (mt) REVERT: A 697 MET cc_start: 0.6882 (mmm) cc_final: 0.6524 (tmm) REVERT: A 736 ASN cc_start: 0.7091 (m-40) cc_final: 0.6706 (m-40) REVERT: A 769 PHE cc_start: 0.6475 (t80) cc_final: 0.6229 (t80) REVERT: A 812 ARG cc_start: 0.7904 (ptm-80) cc_final: 0.7371 (ttt180) REVERT: A 856 ARG cc_start: 0.7140 (mtp180) cc_final: 0.6819 (mtm110) REVERT: A 857 MET cc_start: 0.7669 (tpp) cc_final: 0.7448 (tpp) REVERT: A 877 GLN cc_start: 0.8382 (tt0) cc_final: 0.8128 (tt0) REVERT: A 881 GLU cc_start: 0.8187 (mm-30) cc_final: 0.7775 (mt-10) REVERT: A 887 ARG cc_start: 0.7910 (mtp85) cc_final: 0.7596 (mtp85) REVERT: A 958 LYS cc_start: 0.7754 (ttpp) cc_final: 0.7042 (ttpp) REVERT: A 1037 THR cc_start: 0.8380 (t) cc_final: 0.8064 (m) REVERT: A 1125 TYR cc_start: 0.7839 (p90) cc_final: 0.7445 (p90) REVERT: A 1173 LYS cc_start: 0.7258 (ttmt) cc_final: 0.6949 (ttmm) REVERT: A 1182 GLU cc_start: 0.7780 (mm-30) cc_final: 0.7569 (mm-30) outliers start: 24 outliers final: 23 residues processed: 219 average time/residue: 0.2310 time to fit residues: 66.0355 Evaluate side-chains 227 residues out of total 884 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 204 time to evaluate : 0.883 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 127 THR Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 154 MET Chi-restraints excluded: chain A residue 200 MET Chi-restraints excluded: chain A residue 257 LEU Chi-restraints excluded: chain A residue 269 LEU Chi-restraints excluded: chain A residue 273 VAL Chi-restraints excluded: chain A residue 296 ASP Chi-restraints excluded: chain A residue 347 VAL Chi-restraints excluded: chain A residue 401 MET Chi-restraints excluded: chain A residue 417 LEU Chi-restraints excluded: chain A residue 430 LEU Chi-restraints excluded: chain A residue 479 ARG Chi-restraints excluded: chain A residue 506 ASN Chi-restraints excluded: chain A residue 640 ILE Chi-restraints excluded: chain A residue 652 ILE Chi-restraints excluded: chain A residue 810 MET Chi-restraints excluded: chain A residue 822 ILE Chi-restraints excluded: chain A residue 837 TYR Chi-restraints excluded: chain A residue 865 ARG Chi-restraints excluded: chain A residue 979 LEU Chi-restraints excluded: chain A residue 1061 THR Chi-restraints excluded: chain A residue 1171 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 101 optimal weight: 0.6980 chunk 93 optimal weight: 0.8980 chunk 80 optimal weight: 0.8980 chunk 8 optimal weight: 1.9990 chunk 62 optimal weight: 4.9990 chunk 49 optimal weight: 0.9980 chunk 64 optimal weight: 0.4980 chunk 86 optimal weight: 2.9990 chunk 24 optimal weight: 0.9990 chunk 74 optimal weight: 0.9990 chunk 11 optimal weight: 1.9990 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 685 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1074 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7355 moved from start: 0.2817 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 8279 Z= 0.227 Angle : 0.481 8.495 11229 Z= 0.252 Chirality : 0.039 0.141 1350 Planarity : 0.004 0.048 1383 Dihedral : 3.683 18.509 1097 Min Nonbonded Distance : 2.160 Molprobity Statistics. All-atom Clashscore : 5.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.67 % Favored : 98.33 % Rotamer: Outliers : 2.60 % Allowed : 17.76 % Favored : 79.64 % 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: 2.33 (0.26), residues: 1016 helix: 2.07 (0.19), residues: 729 sheet: 0.85 (0.97), residues: 33 loop : 0.18 (0.39), residues: 254 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 278 HIS 0.006 0.001 HIS A1120 PHE 0.012 0.001 PHE A 254 TYR 0.010 0.001 TYR A 267 ARG 0.009 0.000 ARG A 161 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2032 Ramachandran restraints generated. 1016 Oldfield, 0 Emsley, 1016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2032 Ramachandran restraints generated. 1016 Oldfield, 0 Emsley, 1016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 228 residues out of total 884 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 205 time to evaluate : 0.862 Fit side-chains REVERT: A 160 MET cc_start: 0.6979 (mmt) cc_final: 0.6624 (mmm) REVERT: A 176 VAL cc_start: 0.7195 (p) cc_final: 0.6901 (m) REVERT: A 217 LEU cc_start: 0.7185 (mp) cc_final: 0.6840 (mp) REVERT: A 375 LYS cc_start: 0.7850 (mtmt) cc_final: 0.7465 (mtmm) REVERT: A 383 MET cc_start: 0.6873 (mmp) cc_final: 0.6420 (mmp) REVERT: A 579 MET cc_start: 0.6728 (tpt) cc_final: 0.6447 (tpt) REVERT: A 584 LEU cc_start: 0.7933 (mm) cc_final: 0.7679 (mp) REVERT: A 609 ARG cc_start: 0.7388 (mtp180) cc_final: 0.7142 (mtm-85) REVERT: A 624 GLN cc_start: 0.7473 (mm-40) cc_final: 0.6851 (tt0) REVERT: A 630 ASP cc_start: 0.7598 (m-30) cc_final: 0.7361 (m-30) REVERT: A 684 ILE cc_start: 0.7711 (mm) cc_final: 0.7348 (mt) REVERT: A 697 MET cc_start: 0.6888 (mmm) cc_final: 0.6525 (tmm) REVERT: A 736 ASN cc_start: 0.7132 (m-40) cc_final: 0.6745 (m-40) REVERT: A 812 ARG cc_start: 0.7939 (ptm-80) cc_final: 0.7433 (ttt180) REVERT: A 856 ARG cc_start: 0.7138 (mtp180) cc_final: 0.6809 (mtm110) REVERT: A 857 MET cc_start: 0.7666 (tpp) cc_final: 0.7443 (tpp) REVERT: A 877 GLN cc_start: 0.8391 (tt0) cc_final: 0.8125 (tt0) REVERT: A 881 GLU cc_start: 0.8187 (mm-30) cc_final: 0.7767 (mt-10) REVERT: A 887 ARG cc_start: 0.7933 (mtp85) cc_final: 0.7611 (mtp85) REVERT: A 931 GLU cc_start: 0.7242 (tt0) cc_final: 0.6910 (mt-10) REVERT: A 958 LYS cc_start: 0.7753 (ttpp) cc_final: 0.7039 (ttpp) REVERT: A 1037 THR cc_start: 0.8401 (t) cc_final: 0.8087 (m) REVERT: A 1125 TYR cc_start: 0.7918 (p90) cc_final: 0.7497 (p90) REVERT: A 1173 LYS cc_start: 0.7276 (ttmt) cc_final: 0.6985 (ttmm) REVERT: A 1182 GLU cc_start: 0.7760 (mm-30) cc_final: 0.7546 (mm-30) outliers start: 23 outliers final: 23 residues processed: 217 average time/residue: 0.2359 time to fit residues: 66.7142 Evaluate side-chains 229 residues out of total 884 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 206 time to evaluate : 0.893 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 127 THR Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 154 MET Chi-restraints excluded: chain A residue 200 MET Chi-restraints excluded: chain A residue 257 LEU Chi-restraints excluded: chain A residue 269 LEU Chi-restraints excluded: chain A residue 273 VAL Chi-restraints excluded: chain A residue 296 ASP Chi-restraints excluded: chain A residue 347 VAL Chi-restraints excluded: chain A residue 401 MET Chi-restraints excluded: chain A residue 417 LEU Chi-restraints excluded: chain A residue 430 LEU Chi-restraints excluded: chain A residue 479 ARG Chi-restraints excluded: chain A residue 506 ASN Chi-restraints excluded: chain A residue 640 ILE Chi-restraints excluded: chain A residue 652 ILE Chi-restraints excluded: chain A residue 810 MET Chi-restraints excluded: chain A residue 822 ILE Chi-restraints excluded: chain A residue 837 TYR Chi-restraints excluded: chain A residue 865 ARG Chi-restraints excluded: chain A residue 979 LEU Chi-restraints excluded: chain A residue 1061 THR Chi-restraints excluded: chain A residue 1171 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 22 optimal weight: 1.9990 chunk 81 optimal weight: 0.6980 chunk 33 optimal weight: 0.7980 chunk 83 optimal weight: 2.9990 chunk 10 optimal weight: 0.6980 chunk 14 optimal weight: 0.8980 chunk 71 optimal weight: 0.6980 chunk 4 optimal weight: 3.9990 chunk 58 optimal weight: 6.9990 chunk 92 optimal weight: 0.6980 chunk 54 optimal weight: 0.5980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 374 GLN ** A 685 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1074 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3655 r_free = 0.3655 target = 0.134645 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.112355 restraints weight = 10958.980| |-----------------------------------------------------------------------------| r_work (start): 0.3330 rms_B_bonded: 1.87 r_work: 0.3203 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.3042 rms_B_bonded: 4.11 restraints_weight: 0.2500 r_work (final): 0.3042 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7793 moved from start: 0.2872 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 8279 Z= 0.200 Angle : 0.470 8.101 11229 Z= 0.247 Chirality : 0.039 0.135 1350 Planarity : 0.004 0.048 1383 Dihedral : 3.658 18.507 1097 Min Nonbonded Distance : 2.162 Molprobity Statistics. All-atom Clashscore : 5.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.48 % Favored : 98.52 % Rotamer: Outliers : 2.83 % Allowed : 17.31 % Favored : 79.86 % 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: 2.38 (0.27), residues: 1016 helix: 2.10 (0.19), residues: 730 sheet: 0.82 (0.97), residues: 33 loop : 0.19 (0.39), residues: 253 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 278 HIS 0.005 0.001 HIS A1133 PHE 0.023 0.001 PHE A 769 TYR 0.009 0.001 TYR A 267 ARG 0.009 0.000 ARG A 161 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2266.16 seconds wall clock time: 41 minutes 34.37 seconds (2494.37 seconds total)