Starting phenix.real_space_refine on Wed Jul 30 06:18:52 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9eda_47942/07_2025/9eda_47942.cif Found real_map, /net/cci-nas-00/data/ceres_data/9eda_47942/07_2025/9eda_47942.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.88 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9eda_47942/07_2025/9eda_47942.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9eda_47942/07_2025/9eda_47942.map" model { file = "/net/cci-nas-00/data/ceres_data/9eda_47942/07_2025/9eda_47942.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9eda_47942/07_2025/9eda_47942.cif" } resolution = 2.88 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.009 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: 5 Type Number sf(0) Gaussians P 138 5.49 5 S 17 5.16 5 C 7190 2.51 5 N 2110 2.21 5 O 2624 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 21 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib" Total number of atoms: 12079 Number of models: 1 Model: "" Number of chains: 6 Chain: "B" Number of atoms: 1995 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 1995 Classifications: {'RNA': 93} Modifications used: {'rna2p_pur': 6, 'rna2p_pyr': 6, 'rna3p_pur': 50, 'rna3p_pyr': 31} Link IDs: {'rna2p': 12, 'rna3p': 80} Chain: "C" Number of atoms: 346 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 346 Classifications: {'DNA': 17} Link IDs: {'rna3p': 16} Chain: "D" Number of atoms: 332 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 332 Classifications: {'DNA': 16} Link IDs: {'rna3p': 15} Chain: "c" Number of atoms: 239 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 239 Classifications: {'DNA': 12} Link IDs: {'rna3p': 11} Chain: "A" Number of atoms: 9166 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1150, 9166 Classifications: {'peptide': 1150} Incomplete info: {'truncation_to_alanine': 53} Link IDs: {'PTRANS': 32, 'TRANS': 1117} Chain breaks: 4 Unresolved non-hydrogen bonds: 221 Unresolved non-hydrogen angles: 261 Unresolved non-hydrogen dihedrals: 190 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'GLN:plan1': 2, 'TYR:plan': 3, 'ASN:plan1': 1, 'ASP:plan': 4, 'GLU:plan': 12, 'ARG:plan': 6} Unresolved non-hydrogen planarities: 122 Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Time building chain proxies: 8.90, per 1000 atoms: 0.74 Number of scatterers: 12079 At special positions: 0 Unit cell: (85.8196, 136.645, 124.147, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 17 16.00 P 138 15.00 O 2624 8.00 N 2110 7.00 C 7190 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.88 Conformation dependent library (CDL) restraints added in 1.2 seconds 2280 Ramachandran restraints generated. 1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2188 Finding SS restraints... Secondary structure from input PDB file: 54 helices and 6 sheets defined 54.4% alpha, 7.6% beta 51 base pairs and 88 stacking pairs defined. Time for finding SS restraints: 4.31 Creating SS restraints... Processing helix chain 'A' and resid 59 through 95 removed outlier: 5.046A pdb=" N ASN A 88 " --> pdb=" O GLU A 84 " (cutoff:3.500A) removed outlier: 5.644A pdb=" N GLU A 89 " --> pdb=" O ILE A 85 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N LYS A 92 " --> pdb=" O ASN A 88 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N ASP A 95 " --> pdb=" O ALA A 91 " (cutoff:3.500A) Processing helix chain 'A' and resid 96 through 103 Processing helix chain 'A' and resid 121 through 132 Processing helix chain 'A' and resid 134 through 145 removed outlier: 3.778A pdb=" N LEU A 138 " --> pdb=" O THR A 134 " (cutoff:3.500A) Processing helix chain 'A' and resid 150 through 164 Processing helix chain 'A' and resid 180 through 196 removed outlier: 3.537A pdb=" N LEU A 184 " --> pdb=" O ASP A 180 " (cutoff:3.500A) Processing helix chain 'A' and resid 207 through 213 Processing helix chain 'A' and resid 217 through 229 Processing helix chain 'A' and resid 236 through 247 Processing helix chain 'A' and resid 252 through 257 removed outlier: 3.556A pdb=" N PHE A 256 " --> pdb=" O PHE A 252 " (cutoff:3.500A) Processing helix chain 'A' and resid 270 through 283 Processing helix chain 'A' and resid 286 through 304 removed outlier: 3.784A pdb=" N ASP A 304 " --> pdb=" O ILE A 300 " (cutoff:3.500A) Processing helix chain 'A' and resid 315 through 343 Processing helix chain 'A' and resid 344 through 346 No H-bonds generated for 'chain 'A' and resid 344 through 346' Processing helix chain 'A' and resid 347 through 352 Processing helix chain 'A' and resid 358 through 364 Processing helix chain 'A' and resid 368 through 382 Proline residue: A 378 - end of helix Processing helix chain 'A' and resid 386 through 395 Processing helix chain 'A' and resid 404 through 410 removed outlier: 3.724A pdb=" N GLY A 408 " --> pdb=" O PHE A 405 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N SER A 409 " --> pdb=" O ASP A 406 " (cutoff:3.500A) Processing helix chain 'A' and resid 411 through 427 removed outlier: 4.129A pdb=" N HIS A 415 " --> pdb=" O PRO A 411 " (cutoff:3.500A) Processing helix chain 'A' and resid 430 through 436 removed outlier: 4.017A pdb=" N LYS A 434 " --> pdb=" O TYR A 430 " (cutoff:3.500A) Processing helix chain 'A' and resid 436 through 446 Processing helix chain 'A' and resid 477 through 482 Processing helix chain 'A' and resid 483 through 496 removed outlier: 3.984A pdb=" N MET A 495 " --> pdb=" O PHE A 491 " (cutoff:3.500A) Processing helix chain 'A' and resid 512 through 525 Processing helix chain 'A' and resid 541 through 556 removed outlier: 3.684A pdb=" N PHE A 553 " --> pdb=" O VAL A 549 " (cutoff:3.500A) removed outlier: 4.458A pdb=" N LYS A 554 " --> pdb=" O ASP A 550 " (cutoff:3.500A) Processing helix chain 'A' and resid 560 through 568 Processing helix chain 'A' and resid 591 through 602 Processing helix chain 'A' and resid 612 through 626 Processing helix chain 'A' and resid 628 through 637 removed outlier: 4.194A pdb=" N ARG A 635 " --> pdb=" O MET A 631 " (cutoff:3.500A) Processing helix chain 'A' and resid 638 through 640 No H-bonds generated for 'chain 'A' and resid 638 through 640' Processing helix chain 'A' and resid 644 through 654 Processing helix chain 'A' and resid 663 through 668 removed outlier: 3.700A pdb=" N ILE A 667 " --> pdb=" O SER A 663 " (cutoff:3.500A) Processing helix chain 'A' and resid 678 through 685 Processing helix chain 'A' and resid 692 through 697 Processing helix chain 'A' and resid 703 through 714 Processing helix chain 'A' and resid 719 through 726 Processing helix chain 'A' and resid 730 through 751 removed outlier: 3.582A pdb=" N MET A 751 " --> pdb=" O LEU A 747 " (cutoff:3.500A) Processing helix chain 'A' and resid 926 through 940 Processing helix chain 'A' and resid 959 through 969 removed outlier: 3.822A pdb=" N VAL A 963 " --> pdb=" O LYS A 959 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N PHE A 966 " --> pdb=" O LEU A 962 " (cutoff:3.500A) Processing helix chain 'A' and resid 981 through 1001 Processing helix chain 'A' and resid 1078 through 1088 Processing helix chain 'A' and resid 1127 through 1132 Processing helix chain 'A' and resid 1170 through 1177 removed outlier: 3.685A pdb=" N ASN A1177 " --> pdb=" O SER A1173 " (cutoff:3.500A) Processing helix chain 'A' and resid 1177 through 1186 Processing helix chain 'A' and resid 1191 through 1195 Processing helix chain 'A' and resid 1229 through 1240 Processing helix chain 'A' and resid 1248 through 1262 Processing helix chain 'A' and resid 1263 through 1280 removed outlier: 4.335A pdb=" N ASP A1267 " --> pdb=" O LYS A1263 " (cutoff:3.500A) Processing helix chain 'A' and resid 1283 through 1297 Processing helix chain 'A' and resid 1301 through 1312 Processing helix chain 'A' and resid 1313 through 1316 Processing helix chain 'A' and resid 1341 through 1344 Processing helix chain 'A' and resid 1363 through 1365 No H-bonds generated for 'chain 'A' and resid 1363 through 1365' Processing sheet with id=AA1, first strand: chain 'A' and resid 955 through 957 removed outlier: 6.211A pdb=" N ILE A 759 " --> pdb=" O ILE A 956 " (cutoff:3.500A) removed outlier: 6.446A pdb=" N ILE A 7 " --> pdb=" O VAL A 760 " (cutoff:3.500A) removed outlier: 8.186A pdb=" N GLU A 762 " --> pdb=" O ILE A 7 " (cutoff:3.500A) removed outlier: 6.661A pdb=" N LEU A 9 " --> pdb=" O GLU A 762 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 42 through 46 removed outlier: 9.907A pdb=" N GLU A1357 " --> pdb=" O LYS A 31 " (cutoff:3.500A) removed outlier: 6.839A pdb=" N LYS A 33 " --> pdb=" O GLU A1357 " (cutoff:3.500A) removed outlier: 7.834A pdb=" N ARG A1359 " --> pdb=" O LYS A 33 " (cutoff:3.500A) removed outlier: 6.226A pdb=" N LEU A 35 " --> pdb=" O ARG A1359 " (cutoff:3.500A) removed outlier: 7.712A pdb=" N ASP A1361 " --> pdb=" O LEU A 35 " (cutoff:3.500A) removed outlier: 4.124A pdb=" N LEU A1203 " --> pdb=" O ILE A1348 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 538 through 539 removed outlier: 3.835A pdb=" N TYR A 529 " --> pdb=" O ALA A 538 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 1063 through 1064 removed outlier: 3.967A pdb=" N TRP A1074 " --> pdb=" O GLU A1064 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 1156 through 1167 Processing sheet with id=AA6, first strand: chain 'A' and resid 1324 through 1326 removed outlier: 3.587A pdb=" N PHE A1324 " --> pdb=" O ILE A1331 " (cutoff:3.500A) 444 hydrogen bonds defined for protein. 1293 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 123 hydrogen bonds 242 hydrogen bond angles 0 basepair planarities 51 basepair parallelities 88 stacking parallelities Total time for adding SS restraints: 6.53 Time building geometry restraints manager: 3.47 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2562 1.33 - 1.46: 3593 1.46 - 1.58: 6131 1.58 - 1.70: 274 1.70 - 1.83: 32 Bond restraints: 12592 Sorted by residual: bond pdb=" N ASN A 726 " pdb=" CA ASN A 726 " ideal model delta sigma weight residual 1.457 1.495 -0.038 1.32e-02 5.74e+03 8.26e+00 bond pdb=" N ILE A 226 " pdb=" CA ILE A 226 " ideal model delta sigma weight residual 1.459 1.496 -0.037 1.30e-02 5.92e+03 8.06e+00 bond pdb=" N ILE A 927 " pdb=" CA ILE A 927 " ideal model delta sigma weight residual 1.461 1.493 -0.032 1.19e-02 7.06e+03 7.35e+00 bond pdb=" N LYS A1156 " pdb=" CA LYS A1156 " ideal model delta sigma weight residual 1.454 1.487 -0.032 1.27e-02 6.20e+03 6.49e+00 bond pdb=" N MET A 694 " pdb=" CA MET A 694 " ideal model delta sigma weight residual 1.459 1.490 -0.031 1.23e-02 6.61e+03 6.43e+00 ... (remaining 12587 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.58: 17173 2.58 - 5.15: 359 5.15 - 7.73: 78 7.73 - 10.31: 17 10.31 - 12.88: 8 Bond angle restraints: 17635 Sorted by residual: angle pdb=" CA LYS A1192 " pdb=" CB LYS A1192 " pdb=" CG LYS A1192 " ideal model delta sigma weight residual 114.10 124.86 -10.76 2.00e+00 2.50e-01 2.89e+01 angle pdb=" CA GLN A1364 " pdb=" CB GLN A1364 " pdb=" CG GLN A1364 " ideal model delta sigma weight residual 114.10 123.73 -9.63 2.00e+00 2.50e-01 2.32e+01 angle pdb=" N GLU A 24 " pdb=" CA GLU A 24 " pdb=" C GLU A 24 " ideal model delta sigma weight residual 113.20 107.56 5.64 1.21e+00 6.83e-01 2.18e+01 angle pdb=" CA TYR A 451 " pdb=" CB TYR A 451 " pdb=" CG TYR A 451 " ideal model delta sigma weight residual 113.90 122.29 -8.39 1.80e+00 3.09e-01 2.17e+01 angle pdb=" CB GLN A1364 " pdb=" CG GLN A1364 " pdb=" CD GLN A1364 " ideal model delta sigma weight residual 112.60 120.42 -7.82 1.70e+00 3.46e-01 2.12e+01 ... (remaining 17630 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.06: 6361 18.06 - 36.11: 736 36.11 - 54.17: 306 54.17 - 72.23: 139 72.23 - 90.28: 28 Dihedral angle restraints: 7570 sinusoidal: 4197 harmonic: 3373 Sorted by residual: dihedral pdb=" CA GLU A 627 " pdb=" C GLU A 627 " pdb=" N ASP A 628 " pdb=" CA ASP A 628 " ideal model delta harmonic sigma weight residual 180.00 153.75 26.25 0 5.00e+00 4.00e-02 2.76e+01 dihedral pdb=" CA PRO A 449 " pdb=" C PRO A 449 " pdb=" N TYR A 450 " pdb=" CA TYR A 450 " ideal model delta harmonic sigma weight residual 180.00 155.55 24.45 0 5.00e+00 4.00e-02 2.39e+01 dihedral pdb=" CA LEU A 625 " pdb=" C LEU A 625 " pdb=" N PHE A 626 " pdb=" CA PHE A 626 " ideal model delta harmonic sigma weight residual -180.00 -156.22 -23.78 0 5.00e+00 4.00e-02 2.26e+01 ... (remaining 7567 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.124: 2002 0.124 - 0.248: 46 0.248 - 0.371: 2 0.371 - 0.495: 3 0.495 - 0.619: 7 Chirality restraints: 2060 Sorted by residual: chirality pdb=" P DT c 4 " pdb=" OP1 DT c 4 " pdb=" OP2 DT c 4 " pdb=" O5' DT c 4 " both_signs ideal model delta sigma weight residual True 2.35 -2.96 -0.62 2.00e-01 2.50e+01 9.58e+00 chirality pdb=" P DT c 9 " pdb=" OP1 DT c 9 " pdb=" OP2 DT c 9 " pdb=" O5' DT c 9 " both_signs ideal model delta sigma weight residual True 2.35 -2.88 -0.53 2.00e-01 2.50e+01 7.09e+00 chirality pdb=" P DA c 8 " pdb=" OP1 DA c 8 " pdb=" OP2 DA c 8 " pdb=" O5' DA c 8 " both_signs ideal model delta sigma weight residual True 2.35 -2.88 -0.53 2.00e-01 2.50e+01 7.04e+00 ... (remaining 2057 not shown) Planarity restraints: 1751 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG A 655 " -0.480 9.50e-02 1.11e+02 2.15e-01 2.84e+01 pdb=" NE ARG A 655 " 0.030 2.00e-02 2.50e+03 pdb=" CZ ARG A 655 " 0.002 2.00e-02 2.50e+03 pdb=" NH1 ARG A 655 " 0.005 2.00e-02 2.50e+03 pdb=" NH2 ARG A 655 " -0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 661 " -0.361 9.50e-02 1.11e+02 1.62e-01 1.61e+01 pdb=" NE ARG A 661 " 0.023 2.00e-02 2.50e+03 pdb=" CZ ARG A 661 " 0.001 2.00e-02 2.50e+03 pdb=" NH1 ARG A 661 " 0.004 2.00e-02 2.50e+03 pdb=" NH2 ARG A 661 " -0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 518 " -0.012 2.00e-02 2.50e+03 2.33e-02 9.53e+00 pdb=" CG PHE A 518 " 0.052 2.00e-02 2.50e+03 pdb=" CD1 PHE A 518 " -0.020 2.00e-02 2.50e+03 pdb=" CD2 PHE A 518 " -0.024 2.00e-02 2.50e+03 pdb=" CE1 PHE A 518 " -0.002 2.00e-02 2.50e+03 pdb=" CE2 PHE A 518 " 0.002 2.00e-02 2.50e+03 pdb=" CZ PHE A 518 " 0.004 2.00e-02 2.50e+03 ... (remaining 1748 not shown) Histogram of nonbonded interaction distances: 2.19 - 2.73: 892 2.73 - 3.28: 11375 3.28 - 3.82: 21732 3.82 - 4.36: 26854 4.36 - 4.90: 40655 Nonbonded interactions: 101508 Sorted by model distance: nonbonded pdb=" OH TYR A 451 " pdb=" OD2 ASP A 628 " model vdw 2.193 3.040 nonbonded pdb=" O2' A B 47 " pdb=" O LEU A 101 " model vdw 2.207 3.040 nonbonded pdb=" OG SER A 512 " pdb=" OE2 GLU A 617 " model vdw 2.217 3.040 nonbonded pdb=" O ILE A 667 " pdb=" OG1 THR A 678 " model vdw 2.225 3.040 nonbonded pdb=" CG2 VAL A 530 " pdb=" CB PRO A 537 " model vdw 2.241 3.860 ... (remaining 101503 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== 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: 7.160 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.500 Check model and map are aligned: 0.080 Set scattering table: 0.120 Process input model: 35.700 Find NCS groups from input model: 0.100 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:12.470 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 56.190 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7594 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 : 0.006 0.062 12592 Z= 0.272 Angle : 0.981 12.883 17635 Z= 0.521 Chirality : 0.060 0.619 2060 Planarity : 0.009 0.215 1751 Dihedral : 19.256 90.285 5382 Min Nonbonded Distance : 2.193 Molprobity Statistics. All-atom Clashscore : 7.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer: Outliers : 0.41 % Allowed : 27.33 % Favored : 72.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.21 (0.23), residues: 1140 helix: -0.50 (0.20), residues: 560 sheet: -0.30 (0.48), residues: 117 loop : -1.16 (0.26), residues: 463 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP A 659 HIS 0.012 0.002 HIS A 160 PHE 0.052 0.003 PHE A 518 TYR 0.041 0.003 TYR A 271 ARG 0.015 0.001 ARG A 586 Details of bonding type rmsd hydrogen bonds : bond 0.14734 ( 567) hydrogen bonds : angle 6.22377 ( 1535) covalent geometry : bond 0.00553 (12592) covalent geometry : angle 0.98108 (17635) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2280 Ramachandran restraints generated. 1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2280 Ramachandran restraints generated. 1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 1030 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 118 time to evaluate : 1.061 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 26 LYS cc_start: 0.7204 (mtpp) cc_final: 0.6886 (ptpp) REVERT: A 209 LYS cc_start: 0.8911 (ttmm) cc_final: 0.8536 (tptp) REVERT: A 284 ASP cc_start: 0.8286 (p0) cc_final: 0.7728 (t0) REVERT: A 288 ASP cc_start: 0.8716 (m-30) cc_final: 0.8301 (t0) REVERT: A 383 MET cc_start: 0.7425 (mtp) cc_final: 0.7040 (mtm) REVERT: A 599 LYS cc_start: 0.8904 (mptt) cc_final: 0.8596 (mmtm) REVERT: A 618 ASP cc_start: 0.8019 (t0) cc_final: 0.7609 (t0) REVERT: A 702 LEU cc_start: 0.6082 (mm) cc_final: 0.5767 (mm) REVERT: A 762 GLU cc_start: 0.7398 (pt0) cc_final: 0.6698 (tt0) REVERT: A 1151 LYS cc_start: 0.8044 (ttmm) cc_final: 0.7777 (mttm) REVERT: A 1170 GLU cc_start: 0.8414 (mt-10) cc_final: 0.8092 (mt-10) REVERT: A 1176 LYS cc_start: 0.8511 (ttmm) cc_final: 0.8104 (tmmt) REVERT: A 1177 ASN cc_start: 0.8696 (OUTLIER) cc_final: 0.8142 (t0) REVERT: A 1258 PHE cc_start: 0.6027 (t80) cc_final: 0.5687 (t80) REVERT: A 1261 GLN cc_start: 0.8830 (pt0) cc_final: 0.8570 (pt0) outliers start: 4 outliers final: 1 residues processed: 121 average time/residue: 1.1217 time to fit residues: 149.1222 Evaluate side-chains 95 residues out of total 1030 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 93 time to evaluate : 1.181 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 264 LEU Chi-restraints excluded: chain A residue 1177 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 107 optimal weight: 0.9980 chunk 96 optimal weight: 3.9990 chunk 53 optimal weight: 0.7980 chunk 32 optimal weight: 0.0970 chunk 64 optimal weight: 4.9990 chunk 51 optimal weight: 0.0980 chunk 99 optimal weight: 0.9980 chunk 38 optimal weight: 4.9990 chunk 60 optimal weight: 0.0980 chunk 74 optimal weight: 0.6980 chunk 115 optimal weight: 0.0980 overall best weight: 0.2178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 160 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 235 ASN A 709 GLN A1364 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4080 r_free = 0.4080 target = 0.147593 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3564 r_free = 0.3564 target = 0.108678 restraints weight = 21632.240| |-----------------------------------------------------------------------------| r_work (start): 0.3519 rms_B_bonded: 2.29 r_work: 0.3412 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work (final): 0.3412 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7799 moved from start: 0.1426 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 12592 Z= 0.124 Angle : 0.556 6.952 17635 Z= 0.298 Chirality : 0.036 0.153 2060 Planarity : 0.004 0.037 1751 Dihedral : 19.120 90.604 3126 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 8.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.84 % Favored : 98.16 % Rotamer: Outliers : 3.38 % Allowed : 23.23 % Favored : 73.39 % 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: -0.22 (0.24), residues: 1140 helix: 0.50 (0.21), residues: 575 sheet: -0.19 (0.49), residues: 117 loop : -0.88 (0.27), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A1074 HIS 0.005 0.001 HIS A 160 PHE 0.016 0.002 PHE A 518 TYR 0.029 0.001 TYR A 451 ARG 0.006 0.001 ARG A 586 Details of bonding type rmsd hydrogen bonds : bond 0.03815 ( 567) hydrogen bonds : angle 4.34462 ( 1535) covalent geometry : bond 0.00259 (12592) covalent geometry : angle 0.55646 (17635) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2280 Ramachandran restraints generated. 1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2280 Ramachandran restraints generated. 1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 1030 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 118 time to evaluate : 1.188 Fit side-chains REVERT: A 26 LYS cc_start: 0.6970 (mtpp) cc_final: 0.6760 (ptpp) REVERT: A 118 ILE cc_start: 0.7749 (OUTLIER) cc_final: 0.7480 (mm) REVERT: A 122 ILE cc_start: 0.7937 (OUTLIER) cc_final: 0.7403 (mp) REVERT: A 209 LYS cc_start: 0.8913 (ttmm) cc_final: 0.8539 (tptp) REVERT: A 288 ASP cc_start: 0.8770 (m-30) cc_final: 0.8480 (t0) REVERT: A 383 MET cc_start: 0.7632 (mtp) cc_final: 0.7266 (mtm) REVERT: A 618 ASP cc_start: 0.8379 (t0) cc_final: 0.7786 (t0) REVERT: A 648 MET cc_start: 0.7869 (mtm) cc_final: 0.7664 (mtt) REVERT: A 702 LEU cc_start: 0.5877 (OUTLIER) cc_final: 0.5565 (mm) REVERT: A 762 GLU cc_start: 0.7187 (pt0) cc_final: 0.6628 (tt0) REVERT: A 1177 ASN cc_start: 0.8545 (OUTLIER) cc_final: 0.7832 (p0) REVERT: A 1261 GLN cc_start: 0.8794 (pt0) cc_final: 0.8547 (pt0) outliers start: 33 outliers final: 10 residues processed: 144 average time/residue: 1.0761 time to fit residues: 174.7560 Evaluate side-chains 102 residues out of total 1030 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 88 time to evaluate : 2.147 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 VAL Chi-restraints excluded: chain A residue 62 THR Chi-restraints excluded: chain A residue 118 ILE Chi-restraints excluded: chain A residue 122 ILE Chi-restraints excluded: chain A residue 396 GLU Chi-restraints excluded: chain A residue 561 VAL Chi-restraints excluded: chain A residue 614 ASP Chi-restraints excluded: chain A residue 652 LYS Chi-restraints excluded: chain A residue 702 LEU Chi-restraints excluded: chain A residue 750 VAL Chi-restraints excluded: chain A residue 1083 VAL Chi-restraints excluded: chain A residue 1088 SER Chi-restraints excluded: chain A residue 1177 ASN Chi-restraints excluded: chain A residue 1339 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 68 optimal weight: 8.9990 chunk 77 optimal weight: 0.7980 chunk 95 optimal weight: 5.9990 chunk 96 optimal weight: 0.9990 chunk 53 optimal weight: 2.9990 chunk 17 optimal weight: 0.9980 chunk 31 optimal weight: 0.1980 chunk 2 optimal weight: 2.9990 chunk 67 optimal weight: 3.9990 chunk 98 optimal weight: 3.9990 chunk 16 optimal weight: 1.9990 overall best weight: 0.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3969 r_free = 0.3969 target = 0.138564 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.097832 restraints weight = 21779.976| |-----------------------------------------------------------------------------| r_work (start): 0.3341 rms_B_bonded: 2.26 r_work: 0.3226 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work: 0.3109 rms_B_bonded: 4.93 restraints_weight: 0.2500 r_work (final): 0.3109 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8130 moved from start: 0.2824 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 12592 Z= 0.225 Angle : 0.613 6.811 17635 Z= 0.327 Chirality : 0.040 0.218 2060 Planarity : 0.004 0.040 1751 Dihedral : 19.259 93.329 3124 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 8.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 4.09 % Allowed : 23.75 % Favored : 72.16 % 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: 0.04 (0.24), residues: 1140 helix: 0.68 (0.21), residues: 576 sheet: 0.22 (0.52), residues: 98 loop : -0.76 (0.28), residues: 466 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP A1074 HIS 0.011 0.001 HIS A 160 PHE 0.022 0.002 PHE A 105 TYR 0.021 0.002 TYR A 451 ARG 0.005 0.001 ARG A 403 Details of bonding type rmsd hydrogen bonds : bond 0.04395 ( 567) hydrogen bonds : angle 4.38957 ( 1535) covalent geometry : bond 0.00492 (12592) covalent geometry : angle 0.61325 (17635) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2280 Ramachandran restraints generated. 1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2280 Ramachandran restraints generated. 1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 1030 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 96 time to evaluate : 1.267 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 26 LYS cc_start: 0.7107 (mtpp) cc_final: 0.6603 (ptpp) REVERT: A 103 GLU cc_start: 0.7446 (OUTLIER) cc_final: 0.6777 (pt0) REVERT: A 122 ILE cc_start: 0.8244 (OUTLIER) cc_final: 0.8010 (tp) REVERT: A 179 SER cc_start: 0.8133 (p) cc_final: 0.7883 (m) REVERT: A 209 LYS cc_start: 0.8900 (ttmm) cc_final: 0.8593 (tptp) REVERT: A 288 ASP cc_start: 0.8820 (m-30) cc_final: 0.8542 (t0) REVERT: A 331 ASP cc_start: 0.8854 (t0) cc_final: 0.8619 (t0) REVERT: A 618 ASP cc_start: 0.8687 (t0) cc_final: 0.8257 (t0) REVERT: A 702 LEU cc_start: 0.6061 (mm) cc_final: 0.5414 (mm) REVERT: A 762 GLU cc_start: 0.7424 (pt0) cc_final: 0.6946 (tt0) REVERT: A 976 ARG cc_start: 0.7924 (ptp90) cc_final: 0.7534 (ptp90) REVERT: A 1177 ASN cc_start: 0.8568 (OUTLIER) cc_final: 0.7771 (p0) REVERT: A 1261 GLN cc_start: 0.8815 (pt0) cc_final: 0.8595 (pt0) REVERT: A 1307 GLU cc_start: 0.6758 (tt0) cc_final: 0.6222 (pt0) outliers start: 40 outliers final: 15 residues processed: 125 average time/residue: 1.0309 time to fit residues: 143.0561 Evaluate side-chains 105 residues out of total 1030 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 87 time to evaluate : 1.111 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 VAL Chi-restraints excluded: chain A residue 103 GLU Chi-restraints excluded: chain A residue 122 ILE Chi-restraints excluded: chain A residue 278 LEU Chi-restraints excluded: chain A residue 305 ILE Chi-restraints excluded: chain A residue 561 VAL Chi-restraints excluded: chain A residue 597 LEU Chi-restraints excluded: chain A residue 652 LYS Chi-restraints excluded: chain A residue 721 HIS Chi-restraints excluded: chain A residue 750 VAL Chi-restraints excluded: chain A residue 975 VAL Chi-restraints excluded: chain A residue 1088 SER Chi-restraints excluded: chain A residue 1135 ASP Chi-restraints excluded: chain A residue 1177 ASN Chi-restraints excluded: chain A residue 1312 LEU Chi-restraints excluded: chain A residue 1318 LEU Chi-restraints excluded: chain A residue 1338 SER Chi-restraints excluded: chain A residue 1342 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 45 optimal weight: 0.9990 chunk 50 optimal weight: 1.9990 chunk 44 optimal weight: 0.9980 chunk 27 optimal weight: 0.7980 chunk 123 optimal weight: 0.8980 chunk 5 optimal weight: 1.9990 chunk 28 optimal weight: 0.8980 chunk 111 optimal weight: 1.9990 chunk 17 optimal weight: 1.9990 chunk 49 optimal weight: 0.8980 chunk 122 optimal weight: 0.8980 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1364 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3972 r_free = 0.3972 target = 0.138543 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.097610 restraints weight = 21479.264| |-----------------------------------------------------------------------------| r_work (start): 0.3354 rms_B_bonded: 2.24 r_work: 0.3240 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work: 0.3126 rms_B_bonded: 4.90 restraints_weight: 0.2500 r_work (final): 0.3126 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8127 moved from start: 0.3436 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 12592 Z= 0.187 Angle : 0.556 7.789 17635 Z= 0.296 Chirality : 0.038 0.183 2060 Planarity : 0.004 0.031 1751 Dihedral : 19.232 94.168 3124 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 7.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 3.99 % Allowed : 23.95 % Favored : 72.06 % 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: 0.21 (0.25), residues: 1140 helix: 0.82 (0.22), residues: 578 sheet: -0.16 (0.49), residues: 117 loop : -0.57 (0.29), residues: 445 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A1074 HIS 0.007 0.001 HIS A 160 PHE 0.020 0.002 PHE A 518 TYR 0.014 0.001 TYR A 271 ARG 0.005 0.001 ARG A 403 Details of bonding type rmsd hydrogen bonds : bond 0.03762 ( 567) hydrogen bonds : angle 4.22685 ( 1535) covalent geometry : bond 0.00417 (12592) covalent geometry : angle 0.55632 (17635) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2280 Ramachandran restraints generated. 1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2280 Ramachandran restraints generated. 1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 1030 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 99 time to evaluate : 1.171 Fit side-chains revert: symmetry clash REVERT: A 26 LYS cc_start: 0.7179 (mtpp) cc_final: 0.6580 (ptpp) REVERT: A 103 GLU cc_start: 0.7443 (OUTLIER) cc_final: 0.6760 (pt0) REVERT: A 209 LYS cc_start: 0.8858 (ttmm) cc_final: 0.8553 (tptp) REVERT: A 288 ASP cc_start: 0.8742 (m-30) cc_final: 0.8540 (t0) REVERT: A 290 PHE cc_start: 0.7847 (m-80) cc_final: 0.7617 (m-80) REVERT: A 618 ASP cc_start: 0.8594 (t0) cc_final: 0.8162 (t0) REVERT: A 702 LEU cc_start: 0.6145 (mm) cc_final: 0.5647 (mm) REVERT: A 708 ILE cc_start: 0.8178 (pt) cc_final: 0.7910 (pp) REVERT: A 762 GLU cc_start: 0.7447 (pt0) cc_final: 0.6973 (tt0) REVERT: A 976 ARG cc_start: 0.7900 (ptp90) cc_final: 0.7331 (ptp90) REVERT: A 1177 ASN cc_start: 0.8534 (OUTLIER) cc_final: 0.7780 (p0) REVERT: A 1307 GLU cc_start: 0.6612 (tt0) cc_final: 0.6258 (mt-10) outliers start: 39 outliers final: 15 residues processed: 128 average time/residue: 1.0553 time to fit residues: 149.6783 Evaluate side-chains 102 residues out of total 1030 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 85 time to evaluate : 1.096 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 VAL Chi-restraints excluded: chain A residue 23 ASP Chi-restraints excluded: chain A residue 103 GLU Chi-restraints excluded: chain A residue 264 LEU Chi-restraints excluded: chain A residue 278 LEU Chi-restraints excluded: chain A residue 308 VAL Chi-restraints excluded: chain A residue 404 THR Chi-restraints excluded: chain A residue 561 VAL Chi-restraints excluded: chain A residue 652 LYS Chi-restraints excluded: chain A residue 750 VAL Chi-restraints excluded: chain A residue 975 VAL Chi-restraints excluded: chain A residue 1088 SER Chi-restraints excluded: chain A residue 1135 ASP Chi-restraints excluded: chain A residue 1177 ASN Chi-restraints excluded: chain A residue 1312 LEU Chi-restraints excluded: chain A residue 1338 SER Chi-restraints excluded: chain A residue 1357 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 44 optimal weight: 0.9980 chunk 32 optimal weight: 10.0000 chunk 80 optimal weight: 0.9980 chunk 16 optimal weight: 2.9990 chunk 107 optimal weight: 0.9990 chunk 87 optimal weight: 0.7980 chunk 14 optimal weight: 1.9990 chunk 8 optimal weight: 4.9990 chunk 15 optimal weight: 0.8980 chunk 29 optimal weight: 0.9990 chunk 9 optimal weight: 3.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 116 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 695 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 698 HIS A 709 GLN A1262 HIS A1272 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4038 r_free = 0.4038 target = 0.141840 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.100382 restraints weight = 21600.455| |-----------------------------------------------------------------------------| r_work (start): 0.3424 rms_B_bonded: 2.17 r_work: 0.3313 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.3197 rms_B_bonded: 4.70 restraints_weight: 0.2500 r_work (final): 0.3197 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8405 moved from start: 0.3888 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 12592 Z= 0.198 Angle : 0.561 7.215 17635 Z= 0.300 Chirality : 0.038 0.168 2060 Planarity : 0.004 0.033 1751 Dihedral : 19.252 94.715 3124 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 7.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 4.09 % Allowed : 23.64 % Favored : 72.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.24 (0.25), residues: 1140 helix: 0.94 (0.22), residues: 577 sheet: -0.08 (0.51), residues: 101 loop : -0.71 (0.28), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A1074 HIS 0.007 0.001 HIS A 160 PHE 0.019 0.002 PHE A1105 TYR 0.018 0.002 TYR A 155 ARG 0.009 0.001 ARG A 221 Details of bonding type rmsd hydrogen bonds : bond 0.03966 ( 567) hydrogen bonds : angle 4.24149 ( 1535) covalent geometry : bond 0.00437 (12592) covalent geometry : angle 0.56083 (17635) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2280 Ramachandran restraints generated. 1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2280 Ramachandran restraints generated. 1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 1030 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 94 time to evaluate : 1.224 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 26 LYS cc_start: 0.7638 (mtpp) cc_final: 0.7001 (ptpp) REVERT: A 43 ILE cc_start: 0.8719 (OUTLIER) cc_final: 0.8346 (tt) REVERT: A 103 GLU cc_start: 0.7545 (OUTLIER) cc_final: 0.7170 (pt0) REVERT: A 209 LYS cc_start: 0.8943 (ttmm) cc_final: 0.8574 (tptp) REVERT: A 221 ARG cc_start: 0.7766 (ttm110) cc_final: 0.7406 (ttm110) REVERT: A 290 PHE cc_start: 0.7926 (m-80) cc_final: 0.7696 (m-80) REVERT: A 404 THR cc_start: 0.8624 (OUTLIER) cc_final: 0.8358 (p) REVERT: A 479 GLU cc_start: 0.8471 (OUTLIER) cc_final: 0.8250 (mp0) REVERT: A 599 LYS cc_start: 0.8925 (OUTLIER) cc_final: 0.8643 (mmtm) REVERT: A 642 LEU cc_start: 0.8089 (OUTLIER) cc_final: 0.7657 (tp) REVERT: A 702 LEU cc_start: 0.6298 (OUTLIER) cc_final: 0.5776 (mm) REVERT: A 708 ILE cc_start: 0.8380 (pt) cc_final: 0.8090 (pp) REVERT: A 762 GLU cc_start: 0.7596 (OUTLIER) cc_final: 0.7274 (tt0) REVERT: A 976 ARG cc_start: 0.8097 (ptp90) cc_final: 0.7543 (ptp90) REVERT: A 1177 ASN cc_start: 0.8648 (OUTLIER) cc_final: 0.8093 (p0) REVERT: A 1307 GLU cc_start: 0.6981 (tt0) cc_final: 0.6440 (pt0) outliers start: 40 outliers final: 17 residues processed: 123 average time/residue: 1.2236 time to fit residues: 165.9642 Evaluate side-chains 112 residues out of total 1030 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 86 time to evaluate : 1.170 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 SER Chi-restraints excluded: chain A residue 16 VAL Chi-restraints excluded: chain A residue 21 ILE Chi-restraints excluded: chain A residue 23 ASP Chi-restraints excluded: chain A residue 43 ILE Chi-restraints excluded: chain A residue 103 GLU Chi-restraints excluded: chain A residue 189 VAL Chi-restraints excluded: chain A residue 264 LEU Chi-restraints excluded: chain A residue 278 LEU Chi-restraints excluded: chain A residue 308 VAL Chi-restraints excluded: chain A residue 404 THR Chi-restraints excluded: chain A residue 479 GLU Chi-restraints excluded: chain A residue 561 VAL Chi-restraints excluded: chain A residue 599 LYS Chi-restraints excluded: chain A residue 642 LEU Chi-restraints excluded: chain A residue 652 LYS Chi-restraints excluded: chain A residue 702 LEU Chi-restraints excluded: chain A residue 750 VAL Chi-restraints excluded: chain A residue 762 GLU Chi-restraints excluded: chain A residue 975 VAL Chi-restraints excluded: chain A residue 1088 SER Chi-restraints excluded: chain A residue 1135 ASP Chi-restraints excluded: chain A residue 1177 ASN Chi-restraints excluded: chain A residue 1213 MET Chi-restraints excluded: chain A residue 1312 LEU Chi-restraints excluded: chain A residue 1338 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 52 optimal weight: 0.0980 chunk 62 optimal weight: 0.9980 chunk 82 optimal weight: 0.9980 chunk 32 optimal weight: 0.0470 chunk 33 optimal weight: 0.9990 chunk 65 optimal weight: 0.0010 chunk 83 optimal weight: 0.0670 chunk 89 optimal weight: 0.4980 chunk 53 optimal weight: 0.6980 chunk 97 optimal weight: 2.9990 chunk 7 optimal weight: 5.9990 overall best weight: 0.1422 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 695 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1272 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4021 r_free = 0.4021 target = 0.142153 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.102014 restraints weight = 21839.629| |-----------------------------------------------------------------------------| r_work (start): 0.3422 rms_B_bonded: 2.26 r_work: 0.3309 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work: 0.3194 rms_B_bonded: 4.97 restraints_weight: 0.2500 r_work (final): 0.3194 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8043 moved from start: 0.4070 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 12592 Z= 0.105 Angle : 0.508 8.482 17635 Z= 0.269 Chirality : 0.035 0.179 2060 Planarity : 0.003 0.029 1751 Dihedral : 19.019 92.996 3124 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 7.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 2.25 % Allowed : 24.97 % Favored : 72.77 % 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: 0.63 (0.25), residues: 1140 helix: 1.34 (0.22), residues: 578 sheet: -0.08 (0.50), residues: 118 loop : -0.61 (0.29), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 476 HIS 0.004 0.001 HIS A 160 PHE 0.011 0.001 PHE A 606 TYR 0.013 0.001 TYR A 271 ARG 0.004 0.000 ARG A 976 Details of bonding type rmsd hydrogen bonds : bond 0.03131 ( 567) hydrogen bonds : angle 3.98768 ( 1535) covalent geometry : bond 0.00217 (12592) covalent geometry : angle 0.50775 (17635) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2280 Ramachandran restraints generated. 1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2280 Ramachandran restraints generated. 1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 1030 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 96 time to evaluate : 2.364 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 26 LYS cc_start: 0.7107 (mtpp) cc_final: 0.6559 (ptpp) REVERT: A 103 GLU cc_start: 0.7449 (OUTLIER) cc_final: 0.6601 (pt0) REVERT: A 195 LEU cc_start: 0.8538 (OUTLIER) cc_final: 0.8330 (mm) REVERT: A 209 LYS cc_start: 0.8836 (ttmm) cc_final: 0.8522 (tptp) REVERT: A 290 PHE cc_start: 0.7820 (m-80) cc_final: 0.7589 (m-80) REVERT: A 520 VAL cc_start: 0.8974 (t) cc_final: 0.8753 (p) REVERT: A 599 LYS cc_start: 0.8835 (mptt) cc_final: 0.8541 (mmtm) REVERT: A 697 ILE cc_start: 0.9103 (pp) cc_final: 0.8889 (pp) REVERT: A 702 LEU cc_start: 0.6122 (OUTLIER) cc_final: 0.5647 (mm) REVERT: A 708 ILE cc_start: 0.8149 (pt) cc_final: 0.7920 (pp) REVERT: A 762 GLU cc_start: 0.7145 (OUTLIER) cc_final: 0.6753 (tt0) REVERT: A 976 ARG cc_start: 0.7809 (ptp90) cc_final: 0.7364 (ptp90) REVERT: A 1170 GLU cc_start: 0.8669 (mt-10) cc_final: 0.8287 (pt0) outliers start: 22 outliers final: 5 residues processed: 110 average time/residue: 1.3648 time to fit residues: 165.4053 Evaluate side-chains 96 residues out of total 1030 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 87 time to evaluate : 1.343 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 VAL Chi-restraints excluded: chain A residue 103 GLU Chi-restraints excluded: chain A residue 195 LEU Chi-restraints excluded: chain A residue 246 LEU Chi-restraints excluded: chain A residue 278 LEU Chi-restraints excluded: chain A residue 308 VAL Chi-restraints excluded: chain A residue 702 LEU Chi-restraints excluded: chain A residue 762 GLU Chi-restraints excluded: chain A residue 1338 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 30 optimal weight: 2.9990 chunk 79 optimal weight: 1.9990 chunk 45 optimal weight: 0.9990 chunk 115 optimal weight: 4.9990 chunk 98 optimal weight: 4.9990 chunk 10 optimal weight: 1.9990 chunk 120 optimal weight: 2.9990 chunk 111 optimal weight: 0.9990 chunk 14 optimal weight: 2.9990 chunk 53 optimal weight: 1.9990 chunk 28 optimal weight: 0.7980 overall best weight: 1.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 116 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 695 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1272 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4016 r_free = 0.4016 target = 0.140130 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.098095 restraints weight = 21645.059| |-----------------------------------------------------------------------------| r_work (start): 0.3392 rms_B_bonded: 2.21 r_work: 0.3281 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.3165 rms_B_bonded: 4.71 restraints_weight: 0.2500 r_work (final): 0.3165 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8442 moved from start: 0.4375 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.048 12592 Z= 0.270 Angle : 0.614 9.210 17635 Z= 0.323 Chirality : 0.041 0.162 2060 Planarity : 0.004 0.068 1751 Dihedral : 19.311 95.371 3122 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 7.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 2.76 % Allowed : 25.18 % Favored : 72.06 % 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: 0.35 (0.25), residues: 1140 helix: 1.13 (0.22), residues: 577 sheet: -0.17 (0.52), residues: 101 loop : -0.77 (0.28), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A1074 HIS 0.006 0.001 HIS A 698 PHE 0.023 0.002 PHE A 105 TYR 0.021 0.002 TYR A 155 ARG 0.014 0.001 ARG A 221 Details of bonding type rmsd hydrogen bonds : bond 0.04417 ( 567) hydrogen bonds : angle 4.23413 ( 1535) covalent geometry : bond 0.00598 (12592) covalent geometry : angle 0.61353 (17635) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2280 Ramachandran restraints generated. 1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2280 Ramachandran restraints generated. 1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 1030 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 83 time to evaluate : 1.404 Fit side-chains revert: symmetry clash REVERT: A 26 LYS cc_start: 0.7604 (mtpp) cc_final: 0.6972 (ptpp) REVERT: A 43 ILE cc_start: 0.8772 (OUTLIER) cc_final: 0.8425 (tt) REVERT: A 103 GLU cc_start: 0.7598 (OUTLIER) cc_final: 0.7148 (pt0) REVERT: A 209 LYS cc_start: 0.8933 (ttmm) cc_final: 0.8599 (tptp) REVERT: A 290 PHE cc_start: 0.7982 (m-80) cc_final: 0.7725 (m-80) REVERT: A 390 LEU cc_start: 0.8758 (OUTLIER) cc_final: 0.8432 (mm) REVERT: A 404 THR cc_start: 0.8717 (OUTLIER) cc_final: 0.8449 (p) REVERT: A 479 GLU cc_start: 0.8468 (OUTLIER) cc_final: 0.8247 (mp0) REVERT: A 702 LEU cc_start: 0.6591 (mm) cc_final: 0.6021 (mm) REVERT: A 708 ILE cc_start: 0.8467 (pt) cc_final: 0.8198 (pp) REVERT: A 762 GLU cc_start: 0.7631 (OUTLIER) cc_final: 0.7349 (tt0) REVERT: A 976 ARG cc_start: 0.8056 (ptp90) cc_final: 0.7649 (ptp90) REVERT: A 1307 GLU cc_start: 0.7009 (tt0) cc_final: 0.6428 (pt0) outliers start: 27 outliers final: 13 residues processed: 106 average time/residue: 1.4026 time to fit residues: 162.2763 Evaluate side-chains 97 residues out of total 1030 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 78 time to evaluate : 1.204 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 VAL Chi-restraints excluded: chain A residue 23 ASP Chi-restraints excluded: chain A residue 43 ILE Chi-restraints excluded: chain A residue 103 GLU Chi-restraints excluded: chain A residue 124 ASP Chi-restraints excluded: chain A residue 195 LEU Chi-restraints excluded: chain A residue 246 LEU Chi-restraints excluded: chain A residue 264 LEU Chi-restraints excluded: chain A residue 278 LEU Chi-restraints excluded: chain A residue 308 VAL Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 404 THR Chi-restraints excluded: chain A residue 479 GLU Chi-restraints excluded: chain A residue 762 GLU Chi-restraints excluded: chain A residue 975 VAL Chi-restraints excluded: chain A residue 1163 LEU Chi-restraints excluded: chain A residue 1312 LEU Chi-restraints excluded: chain A residue 1338 SER Chi-restraints excluded: chain A residue 1342 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 125 optimal weight: 0.7980 chunk 34 optimal weight: 3.9990 chunk 56 optimal weight: 0.6980 chunk 20 optimal weight: 0.5980 chunk 13 optimal weight: 0.9990 chunk 8 optimal weight: 4.9990 chunk 61 optimal weight: 0.9980 chunk 74 optimal weight: 0.9990 chunk 117 optimal weight: 0.7980 chunk 126 optimal weight: 0.7980 chunk 114 optimal weight: 4.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 695 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1272 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4041 r_free = 0.4041 target = 0.142050 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.100570 restraints weight = 21853.776| |-----------------------------------------------------------------------------| r_work (start): 0.3431 rms_B_bonded: 2.19 r_work: 0.3321 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.3206 rms_B_bonded: 4.71 restraints_weight: 0.2500 r_work (final): 0.3206 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8399 moved from start: 0.4491 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 12592 Z= 0.166 Angle : 0.550 10.732 17635 Z= 0.290 Chirality : 0.037 0.161 2060 Planarity : 0.004 0.061 1751 Dihedral : 19.219 94.268 3122 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 7.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Rotamer: Outliers : 3.07 % Allowed : 24.67 % Favored : 72.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.45 (0.25), residues: 1140 helix: 1.22 (0.22), residues: 577 sheet: -0.21 (0.51), residues: 101 loop : -0.70 (0.28), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A1074 HIS 0.005 0.001 HIS A 160 PHE 0.017 0.002 PHE A1105 TYR 0.013 0.001 TYR A 271 ARG 0.014 0.001 ARG A 221 Details of bonding type rmsd hydrogen bonds : bond 0.03657 ( 567) hydrogen bonds : angle 4.12781 ( 1535) covalent geometry : bond 0.00368 (12592) covalent geometry : angle 0.54960 (17635) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2280 Ramachandran restraints generated. 1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2280 Ramachandran restraints generated. 1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 1030 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 84 time to evaluate : 1.233 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 26 LYS cc_start: 0.7580 (mtpp) cc_final: 0.6924 (ptpp) REVERT: A 43 ILE cc_start: 0.8739 (OUTLIER) cc_final: 0.8456 (tt) REVERT: A 103 GLU cc_start: 0.7509 (OUTLIER) cc_final: 0.7111 (pt0) REVERT: A 145 SER cc_start: 0.8652 (OUTLIER) cc_final: 0.8320 (t) REVERT: A 195 LEU cc_start: 0.8593 (OUTLIER) cc_final: 0.8371 (mm) REVERT: A 209 LYS cc_start: 0.8903 (ttmm) cc_final: 0.8582 (tptp) REVERT: A 290 PHE cc_start: 0.7951 (m-80) cc_final: 0.7687 (m-80) REVERT: A 390 LEU cc_start: 0.8741 (OUTLIER) cc_final: 0.8439 (mm) REVERT: A 642 LEU cc_start: 0.8142 (OUTLIER) cc_final: 0.7660 (tp) REVERT: A 702 LEU cc_start: 0.6563 (OUTLIER) cc_final: 0.6003 (mm) REVERT: A 708 ILE cc_start: 0.8462 (pt) cc_final: 0.8199 (pp) REVERT: A 762 GLU cc_start: 0.7533 (OUTLIER) cc_final: 0.7244 (tt0) REVERT: A 976 ARG cc_start: 0.8049 (ptp90) cc_final: 0.7634 (ptp90) REVERT: A 1307 GLU cc_start: 0.6942 (tt0) cc_final: 0.6567 (mt-10) outliers start: 30 outliers final: 13 residues processed: 108 average time/residue: 1.2175 time to fit residues: 144.1435 Evaluate side-chains 102 residues out of total 1030 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 81 time to evaluate : 1.213 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 VAL Chi-restraints excluded: chain A residue 43 ILE Chi-restraints excluded: chain A residue 103 GLU Chi-restraints excluded: chain A residue 145 SER Chi-restraints excluded: chain A residue 195 LEU Chi-restraints excluded: chain A residue 246 LEU Chi-restraints excluded: chain A residue 264 LEU Chi-restraints excluded: chain A residue 278 LEU Chi-restraints excluded: chain A residue 301 LEU Chi-restraints excluded: chain A residue 308 VAL Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 404 THR Chi-restraints excluded: chain A residue 642 LEU Chi-restraints excluded: chain A residue 677 LYS Chi-restraints excluded: chain A residue 702 LEU Chi-restraints excluded: chain A residue 750 VAL Chi-restraints excluded: chain A residue 762 GLU Chi-restraints excluded: chain A residue 975 VAL Chi-restraints excluded: chain A residue 1088 SER Chi-restraints excluded: chain A residue 1312 LEU Chi-restraints excluded: chain A residue 1338 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 78 optimal weight: 2.9990 chunk 6 optimal weight: 3.9990 chunk 123 optimal weight: 1.9990 chunk 69 optimal weight: 5.9990 chunk 90 optimal weight: 0.5980 chunk 119 optimal weight: 0.9990 chunk 89 optimal weight: 0.5980 chunk 2 optimal weight: 2.9990 chunk 46 optimal weight: 1.9990 chunk 107 optimal weight: 0.0970 chunk 110 optimal weight: 0.9980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 695 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1272 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3982 r_free = 0.3982 target = 0.138008 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.097260 restraints weight = 21573.742| |-----------------------------------------------------------------------------| r_work (start): 0.3350 rms_B_bonded: 2.18 r_work: 0.3239 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.3124 rms_B_bonded: 4.76 restraints_weight: 0.2500 r_work (final): 0.3124 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8302 moved from start: 0.4637 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 12592 Z= 0.155 Angle : 0.548 10.371 17635 Z= 0.289 Chirality : 0.037 0.188 2060 Planarity : 0.003 0.056 1751 Dihedral : 19.135 94.240 3122 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 6.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer: Outliers : 2.97 % Allowed : 24.46 % Favored : 72.57 % 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 (0.25), residues: 1140 helix: 1.30 (0.22), residues: 576 sheet: -0.22 (0.52), residues: 99 loop : -0.68 (0.28), residues: 465 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A1074 HIS 0.005 0.001 HIS A 412 PHE 0.014 0.001 PHE A1105 TYR 0.015 0.001 TYR A 155 ARG 0.015 0.000 ARG A 221 Details of bonding type rmsd hydrogen bonds : bond 0.03574 ( 567) hydrogen bonds : angle 4.08909 ( 1535) covalent geometry : bond 0.00342 (12592) covalent geometry : angle 0.54774 (17635) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2280 Ramachandran restraints generated. 1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2280 Ramachandran restraints generated. 1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 1030 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 85 time to evaluate : 1.127 Fit side-chains revert: symmetry clash REVERT: A 26 LYS cc_start: 0.7428 (mtpp) cc_final: 0.6685 (ptpp) REVERT: A 103 GLU cc_start: 0.7475 (OUTLIER) cc_final: 0.6937 (pt0) REVERT: A 145 SER cc_start: 0.8664 (OUTLIER) cc_final: 0.8258 (t) REVERT: A 195 LEU cc_start: 0.8588 (OUTLIER) cc_final: 0.8366 (mm) REVERT: A 209 LYS cc_start: 0.8885 (ttmm) cc_final: 0.8565 (tptt) REVERT: A 221 ARG cc_start: 0.7666 (ttm110) cc_final: 0.7321 (ttm110) REVERT: A 290 PHE cc_start: 0.7966 (m-80) cc_final: 0.7687 (m-80) REVERT: A 390 LEU cc_start: 0.8573 (OUTLIER) cc_final: 0.8271 (mm) REVERT: A 642 LEU cc_start: 0.8196 (OUTLIER) cc_final: 0.7804 (tp) REVERT: A 702 LEU cc_start: 0.6615 (OUTLIER) cc_final: 0.6082 (mm) REVERT: A 708 ILE cc_start: 0.8398 (pt) cc_final: 0.8182 (pp) REVERT: A 762 GLU cc_start: 0.7451 (OUTLIER) cc_final: 0.7136 (tt0) REVERT: A 976 ARG cc_start: 0.7935 (ptp90) cc_final: 0.7485 (ptp90) REVERT: A 1170 GLU cc_start: 0.8671 (mt-10) cc_final: 0.8402 (pt0) REVERT: A 1307 GLU cc_start: 0.6755 (tt0) cc_final: 0.6391 (mt-10) outliers start: 29 outliers final: 12 residues processed: 108 average time/residue: 1.4026 time to fit residues: 166.5522 Evaluate side-chains 99 residues out of total 1030 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 80 time to evaluate : 1.405 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 VAL Chi-restraints excluded: chain A residue 103 GLU Chi-restraints excluded: chain A residue 145 SER Chi-restraints excluded: chain A residue 195 LEU Chi-restraints excluded: chain A residue 246 LEU Chi-restraints excluded: chain A residue 264 LEU Chi-restraints excluded: chain A residue 278 LEU Chi-restraints excluded: chain A residue 301 LEU Chi-restraints excluded: chain A residue 308 VAL Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 404 THR Chi-restraints excluded: chain A residue 642 LEU Chi-restraints excluded: chain A residue 702 LEU Chi-restraints excluded: chain A residue 750 VAL Chi-restraints excluded: chain A residue 762 GLU Chi-restraints excluded: chain A residue 975 VAL Chi-restraints excluded: chain A residue 1163 LEU Chi-restraints excluded: chain A residue 1312 LEU Chi-restraints excluded: chain A residue 1338 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 16 optimal weight: 0.6980 chunk 122 optimal weight: 0.6980 chunk 27 optimal weight: 1.9990 chunk 38 optimal weight: 5.9990 chunk 51 optimal weight: 0.5980 chunk 43 optimal weight: 0.9980 chunk 4 optimal weight: 1.9990 chunk 54 optimal weight: 0.5980 chunk 63 optimal weight: 1.9990 chunk 58 optimal weight: 0.1980 chunk 80 optimal weight: 0.9980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 695 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1272 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3988 r_free = 0.3988 target = 0.138513 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.097748 restraints weight = 21584.250| |-----------------------------------------------------------------------------| r_work (start): 0.3363 rms_B_bonded: 2.19 r_work: 0.3252 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.3137 rms_B_bonded: 4.77 restraints_weight: 0.2500 r_work (final): 0.3137 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8290 moved from start: 0.4741 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 12592 Z= 0.143 Angle : 0.543 10.110 17635 Z= 0.286 Chirality : 0.036 0.171 2060 Planarity : 0.003 0.057 1751 Dihedral : 19.102 93.909 3122 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 7.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 2.46 % Allowed : 25.38 % Favored : 72.16 % 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 (0.25), residues: 1140 helix: 1.32 (0.22), residues: 576 sheet: -0.11 (0.52), residues: 99 loop : -0.68 (0.28), residues: 465 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A1074 HIS 0.006 0.001 HIS A 698 PHE 0.014 0.001 PHE A1105 TYR 0.014 0.001 TYR A 155 ARG 0.014 0.001 ARG A 221 Details of bonding type rmsd hydrogen bonds : bond 0.03483 ( 567) hydrogen bonds : angle 4.07601 ( 1535) covalent geometry : bond 0.00314 (12592) covalent geometry : angle 0.54298 (17635) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2280 Ramachandran restraints generated. 1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2280 Ramachandran restraints generated. 1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 1030 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 80 time to evaluate : 1.166 Fit side-chains revert: symmetry clash REVERT: A 26 LYS cc_start: 0.7421 (mtpp) cc_final: 0.6632 (ptpp) REVERT: A 103 GLU cc_start: 0.7450 (OUTLIER) cc_final: 0.6943 (pt0) REVERT: A 145 SER cc_start: 0.8640 (OUTLIER) cc_final: 0.8242 (t) REVERT: A 195 LEU cc_start: 0.8626 (OUTLIER) cc_final: 0.8403 (mm) REVERT: A 209 LYS cc_start: 0.8894 (ttmm) cc_final: 0.8596 (tptt) REVERT: A 229 LEU cc_start: 0.8127 (mm) cc_final: 0.7511 (mt) REVERT: A 290 PHE cc_start: 0.7938 (m-80) cc_final: 0.7700 (m-80) REVERT: A 390 LEU cc_start: 0.8555 (OUTLIER) cc_final: 0.8259 (mm) REVERT: A 504 ASN cc_start: 0.8196 (p0) cc_final: 0.7937 (t0) REVERT: A 642 LEU cc_start: 0.8210 (OUTLIER) cc_final: 0.7824 (tp) REVERT: A 702 LEU cc_start: 0.6632 (OUTLIER) cc_final: 0.6034 (mm) REVERT: A 708 ILE cc_start: 0.8428 (pt) cc_final: 0.8218 (pp) REVERT: A 762 GLU cc_start: 0.7396 (OUTLIER) cc_final: 0.7113 (tt0) REVERT: A 976 ARG cc_start: 0.7927 (ptp90) cc_final: 0.7472 (ptp90) REVERT: A 1089 MET cc_start: 0.8842 (ttm) cc_final: 0.8627 (ttm) REVERT: A 1170 GLU cc_start: 0.8668 (mt-10) cc_final: 0.8432 (pt0) REVERT: A 1262 HIS cc_start: 0.8003 (m90) cc_final: 0.6687 (m90) REVERT: A 1307 GLU cc_start: 0.6728 (tt0) cc_final: 0.6370 (mt-10) outliers start: 24 outliers final: 12 residues processed: 97 average time/residue: 1.2060 time to fit residues: 128.3791 Evaluate side-chains 94 residues out of total 1030 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 75 time to evaluate : 1.252 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 VAL Chi-restraints excluded: chain A residue 103 GLU Chi-restraints excluded: chain A residue 145 SER Chi-restraints excluded: chain A residue 195 LEU Chi-restraints excluded: chain A residue 246 LEU Chi-restraints excluded: chain A residue 264 LEU Chi-restraints excluded: chain A residue 278 LEU Chi-restraints excluded: chain A residue 301 LEU Chi-restraints excluded: chain A residue 308 VAL Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 404 THR Chi-restraints excluded: chain A residue 642 LEU Chi-restraints excluded: chain A residue 702 LEU Chi-restraints excluded: chain A residue 750 VAL Chi-restraints excluded: chain A residue 762 GLU Chi-restraints excluded: chain A residue 975 VAL Chi-restraints excluded: chain A residue 1163 LEU Chi-restraints excluded: chain A residue 1213 MET Chi-restraints excluded: chain A residue 1312 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 91 optimal weight: 0.9980 chunk 20 optimal weight: 0.5980 chunk 9 optimal weight: 3.9990 chunk 98 optimal weight: 0.7980 chunk 126 optimal weight: 2.9990 chunk 40 optimal weight: 0.8980 chunk 64 optimal weight: 4.9990 chunk 58 optimal weight: 0.1980 chunk 81 optimal weight: 0.7980 chunk 88 optimal weight: 4.9990 chunk 69 optimal weight: 0.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 255 ASN ** A 695 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1272 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3983 r_free = 0.3983 target = 0.138117 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.097256 restraints weight = 21507.774| |-----------------------------------------------------------------------------| r_work (start): 0.3354 rms_B_bonded: 2.18 r_work: 0.3243 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work: 0.3128 rms_B_bonded: 4.77 restraints_weight: 0.2500 r_work (final): 0.3128 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8301 moved from start: 0.4816 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 12592 Z= 0.156 Angle : 0.557 10.154 17635 Z= 0.292 Chirality : 0.037 0.155 2060 Planarity : 0.003 0.036 1751 Dihedral : 19.112 94.002 3122 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 7.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 2.35 % Allowed : 25.49 % Favored : 72.16 % 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 (0.25), residues: 1140 helix: 1.30 (0.22), residues: 576 sheet: -0.08 (0.53), residues: 99 loop : -0.69 (0.29), residues: 465 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A1074 HIS 0.006 0.001 HIS A 698 PHE 0.015 0.001 PHE A1105 TYR 0.014 0.001 TYR A 155 ARG 0.010 0.001 ARG A 221 Details of bonding type rmsd hydrogen bonds : bond 0.03565 ( 567) hydrogen bonds : angle 4.10428 ( 1535) covalent geometry : bond 0.00344 (12592) covalent geometry : angle 0.55718 (17635) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10436.60 seconds wall clock time: 185 minutes 4.48 seconds (11104.48 seconds total)