Starting phenix.real_space_refine on Fri Jul 3 08:48:50 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8ja0_36123/07_2026/8ja0_36123.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ja0_36123/07_2026/8ja0_36123.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.52 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/8ja0_36123/07_2026/8ja0_36123.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8ja0_36123/07_2026/8ja0_36123.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8ja0_36123/07_2026/8ja0_36123.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ja0_36123/07_2026/8ja0_36123.map" model { file = "/net/cci-nas-00/data/ceres_data/8ja0_36123/07_2026/8ja0_36123.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ja0_36123/07_2026/8ja0_36123.cif" } resolution = 3.52 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.171 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 2216 atoms to isotropic. 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 115 5.49 5 S 25 5.16 5 C 6695 2.51 5 N 2028 2.21 5 O 2428 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 4 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 11291 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 8168 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 1027, 8144 Classifications: {'peptide': 1027} Incomplete info: {'truncation_to_alanine': 48} Link IDs: {'PTRANS': 43, 'TRANS': 983} Chain breaks: 5 Unresolved non-hydrogen bonds: 198 Unresolved non-hydrogen angles: 234 Unresolved non-hydrogen dihedrals: 170 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'GLU:plan': 9, 'ARG:plan': 9, 'HIS:plan': 2, 'ASP:plan': 1, 'ASN:plan1': 1, 'GLN:plan1': 1, 'PHE:plan': 2} Unresolved non-hydrogen planarities: 113 Conformer: "B" Number of residues, atoms: 1027, 8144 Classifications: {'peptide': 1027} Incomplete info: {'truncation_to_alanine': 48} Link IDs: {'PTRANS': 43, 'TRANS': 983} Chain breaks: 5 Unresolved non-hydrogen bonds: 198 Unresolved non-hydrogen angles: 234 Unresolved non-hydrogen dihedrals: 170 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'GLU:plan': 9, 'ARG:plan': 9, 'HIS:plan': 2, 'ASP:plan': 1, 'ASN:plan1': 1, 'GLN:plan1': 1, 'PHE:plan': 2} Unresolved non-hydrogen planarities: 113 bond proxies already assigned to first conformer: 8271 Chain: "D" Number of atoms: 692 Number of conformers: 1 Conformer: "" Number of residues, atoms: 87, 692 Classifications: {'peptide': 87} Link IDs: {'PTRANS': 2, 'TRANS': 84} Chain: "B" Number of atoms: 2431 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 2431 Classifications: {'RNA': 115} Modifications used: {'rna2p_pur': 6, 'rna2p_pyr': 5, 'rna3p_pur': 47, 'rna3p_pyr': 57} Link IDs: {'rna2p': 11, 'rna3p': 103} Chain breaks: 1 Residues with excluded nonbonded symmetry interactions: 2 residue: pdb=" N AARG A 398 " occ=0.39 ... (20 atoms not shown) pdb=" NH2BARG A 398 " occ=0.61 residue: pdb=" N AARG A 538 " occ=0.87 ... (20 atoms not shown) pdb=" NH2BARG A 538 " occ=0.13 Time building chain proxies: 3.70, per 1000 atoms: 0.33 Number of scatterers: 11291 At special positions: 0 Unit cell: (108.8, 111.35, 141.95, 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 25 16.00 P 115 15.00 O 2428 8.00 N 2028 7.00 C 6695 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: 1.10 Conformation dependent library (CDL) restraints added in 807.9 milliseconds 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2108 Finding SS restraints... Secondary structure from input PDB file: 42 helices and 9 sheets defined 45.8% alpha, 8.9% beta 35 base pairs and 62 stacking pairs defined. Time for finding SS restraints: 1.41 Creating SS restraints... Processing helix chain 'A' and resid 60 through 89 Processing helix chain 'A' and resid 93 through 97 Processing helix chain 'A' and resid 109 through 115 Processing helix chain 'A' and resid 123 through 137 removed outlier: 3.756A pdb=" N SER A 128 " --> pdb=" O PRO A 124 " (cutoff:3.500A) removed outlier: 4.266A pdb=" N ALA A 129 " --> pdb=" O LEU A 125 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N VAL A 130 " --> pdb=" O GLU A 126 " (cutoff:3.500A) Processing helix chain 'A' and resid 156 through 170 Processing helix chain 'A' and resid 176 through 184 Processing helix chain 'A' and resid 204 through 223 removed outlier: 3.819A pdb=" N PHE A 222 " --> pdb=" O LYS A 218 " (cutoff:3.500A) Processing helix chain 'A' and resid 228 through 240 Processing helix chain 'A' and resid 271 through 285 removed outlier: 3.935A pdb=" N ASN A 285 " --> pdb=" O THR A 281 " (cutoff:3.500A) Processing helix chain 'A' and resid 298 through 306 removed outlier: 4.002A pdb=" N THR A 304 " --> pdb=" O THR A 300 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N MET A 306 " --> pdb=" O ARG A 302 " (cutoff:3.500A) Processing helix chain 'A' and resid 316 through 325 removed outlier: 3.755A pdb=" N ALA A 320 " --> pdb=" O THR A 316 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N ARG A 321 " --> pdb=" O TYR A 317 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N LEU A 323 " --> pdb=" O GLN A 319 " (cutoff:3.500A) Processing helix chain 'A' and resid 351 through 363 removed outlier: 3.976A pdb=" N GLU A 363 " --> pdb=" O ALA A 359 " (cutoff:3.500A) Processing helix chain 'A' and resid 375 through 389 Processing helix chain 'A' and resid 391 through 399 Processing helix chain 'A' and resid 404 through 412 removed outlier: 3.630A pdb=" N LEU A 408 " --> pdb=" O GLN A 404 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N GLU A 409 " --> pdb=" O PRO A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 424 through 437 removed outlier: 3.563A pdb=" N ARG A 429 " --> pdb=" O LEU A 425 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N ARG A 430 " --> pdb=" O LYS A 426 " (cutoff:3.500A) Proline residue: A 433 - end of helix Processing helix chain 'A' and resid 440 through 449 Processing helix chain 'A' and resid 474 through 495 Processing helix chain 'A' and resid 512 through 541 removed outlier: 4.062A pdb=" N GLU A 539 " --> pdb=" O ALA A 535 " (cutoff:3.500A) removed outlier: 4.227A pdb=" N TYR A 540 " --> pdb=" O LYS A 536 " (cutoff:3.500A) removed outlier: 4.201A pdb=" N PHE A 541 " --> pdb=" O PHE A 537 " (cutoff:3.500A) Processing helix chain 'A' and resid 549 through 562 Processing helix chain 'A' and resid 591 through 596 Processing helix chain 'A' and resid 618 through 622 Processing helix chain 'A' and resid 629 through 640 removed outlier: 4.163A pdb=" N PHE A 635 " --> pdb=" O GLU A 631 " (cutoff:3.500A) Processing helix chain 'A' and resid 645 through 650 Processing helix chain 'A' and resid 660 through 667 Processing helix chain 'A' and resid 671 through 684 Processing helix chain 'A' and resid 700 through 711 Processing helix chain 'A' and resid 722 through 732 removed outlier: 3.682A pdb=" N ASP A 726 " --> pdb=" O HIS A 722 " (cutoff:3.500A) Processing helix chain 'A' and resid 734 through 750 removed outlier: 3.727A pdb=" N MET A 750 " --> pdb=" O ARG A 746 " (cutoff:3.500A) Processing helix chain 'A' and resid 778 through 789 removed outlier: 3.761A pdb=" N GLU A 782 " --> pdb=" O PHE A 778 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N MET A 784 " --> pdb=" O ALA A 780 " (cutoff:3.500A) Processing helix chain 'A' and resid 802 through 814 Processing helix chain 'A' and resid 817 through 821 removed outlier: 4.130A pdb=" N VAL A 821 " --> pdb=" O PRO A 818 " (cutoff:3.500A) Processing helix chain 'A' and resid 868 through 873 removed outlier: 3.934A pdb=" N GLU A 873 " --> pdb=" O LEU A 869 " (cutoff:3.500A) Processing helix chain 'A' and resid 881 through 893 removed outlier: 3.686A pdb=" N TYR A 885 " --> pdb=" O GLU A 881 " (cutoff:3.500A) Processing helix chain 'A' and resid 898 through 903 Processing helix chain 'A' and resid 965 through 972 Processing helix chain 'A' and resid 984 through 988 Processing helix chain 'D' and resid 13 through 19 Processing helix chain 'D' and resid 20 through 23 Processing helix chain 'D' and resid 24 through 44 Proline residue: D 30 - end of helix Processing helix chain 'D' and resid 46 through 51 removed outlier: 4.118A pdb=" N LYS D 50 " --> pdb=" O ARG D 46 " (cutoff:3.500A) Processing helix chain 'D' and resid 57 through 85 Processing sheet with id=AA1, first strand: chain 'A' and resid 695 through 697 removed outlier: 6.675A pdb=" N ILE A 501 " --> pdb=" O PHE A 696 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N ARG A 500 " --> pdb=" O TYR A 11 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N ASP A 40 " --> pdb=" O MET A 26 " (cutoff:3.500A) removed outlier: 6.804A pdb=" N GLU A 28 " --> pdb=" O LEU A 38 " (cutoff:3.500A) removed outlier: 6.076A pdb=" N LEU A 38 " --> pdb=" O GLU A 28 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 267 through 268 removed outlier: 3.922A pdb=" N ALA A 267 " --> pdb=" O VAL A 421 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 288 through 289 Processing sheet with id=AA4, first strand: chain 'A' and resid 586 through 588 Processing sheet with id=AA5, first strand: chain 'A' and resid 858 through 863 Processing sheet with id=AA6, first strand: chain 'A' and resid 933 through 935 Processing sheet with id=AA7, first strand: chain 'A' and resid 958 through 964 removed outlier: 3.772A pdb=" N PHE A 999 " --> pdb=" O VAL A 952 " (cutoff:3.500A) removed outlier: 6.558A pdb=" N GLU A 954 " --> pdb=" O PHE A 997 " (cutoff:3.500A) removed outlier: 5.658A pdb=" N PHE A 997 " --> pdb=" O GLU A 954 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 977 through 978 Processing sheet with id=AA9, first strand: chain 'A' and resid 1046 through 1050 removed outlier: 3.664A pdb=" N ILE A1032 " --> pdb=" O LEU A1047 " (cutoff:3.500A) removed outlier: 4.302A pdb=" N GLY A1049 " --> pdb=" O ILE A1030 " (cutoff:3.500A) removed outlier: 6.375A pdb=" N ILE A1030 " --> pdb=" O GLY A1049 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N SER A1022 " --> pdb=" O ASN A1031 " (cutoff:3.500A) removed outlier: 6.109A pdb=" N ARG A1033 " --> pdb=" O PHE A1020 " (cutoff:3.500A) removed outlier: 5.652A pdb=" N PHE A1020 " --> pdb=" O ARG A1033 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N ASP A1005 " --> pdb=" O PHE A1020 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N LEU A1006 " --> pdb=" O TYR A1061 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N SER A1057 " --> pdb=" O ILE A1010 " (cutoff:3.500A) 375 hydrogen bonds defined for protein. 1075 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 86 hydrogen bonds 160 hydrogen bond angles 0 basepair planarities 35 basepair parallelities 62 stacking parallelities Total time for adding SS restraints: 2.35 Time building geometry restraints manager: 1.42 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 3324 1.34 - 1.46: 2893 1.46 - 1.58: 5251 1.58 - 1.70: 228 1.70 - 1.82: 43 Bond restraints: 11739 Sorted by residual: bond pdb=" CA LYS A 269 " pdb=" CB LYS A 269 " ideal model delta sigma weight residual 1.524 1.543 -0.019 1.31e-02 5.83e+03 2.19e+00 bond pdb=" N AARG A 538 " pdb=" CA AARG A 538 " ideal model delta sigma weight residual 1.458 1.474 -0.017 1.42e-02 4.96e+03 1.38e+00 bond pdb=" N BARG A 538 " pdb=" CA BARG A 538 " ideal model delta sigma weight residual 1.458 1.474 -0.017 1.42e-02 4.96e+03 1.38e+00 bond pdb=" CG GLU D 65 " pdb=" CD GLU D 65 " ideal model delta sigma weight residual 1.516 1.541 -0.025 2.50e-02 1.60e+03 1.02e+00 bond pdb=" CA ASP A 597 " pdb=" C ASP A 597 " ideal model delta sigma weight residual 1.523 1.539 -0.016 1.61e-02 3.86e+03 1.02e+00 ... (remaining 11734 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.36: 16208 2.36 - 4.72: 150 4.72 - 7.09: 18 7.09 - 9.45: 2 9.45 - 11.81: 2 Bond angle restraints: 16380 Sorted by residual: angle pdb=" C PRO A 309 " pdb=" N TYR A 310 " pdb=" CA TYR A 310 " ideal model delta sigma weight residual 121.54 129.29 -7.75 1.91e+00 2.74e-01 1.65e+01 angle pdb=" CB MET A 350 " pdb=" CG MET A 350 " pdb=" SD MET A 350 " ideal model delta sigma weight residual 112.70 124.51 -11.81 3.00e+00 1.11e-01 1.55e+01 angle pdb=" N LYS A 269 " pdb=" CA LYS A 269 " pdb=" C LYS A 269 " ideal model delta sigma weight residual 111.81 106.41 5.40 1.44e+00 4.82e-01 1.41e+01 angle pdb=" CA GLU A 580 " pdb=" CB GLU A 580 " pdb=" CG GLU A 580 " ideal model delta sigma weight residual 114.10 120.69 -6.59 2.00e+00 2.50e-01 1.09e+01 angle pdb=" C ILE A 573 " pdb=" N ASN A 574 " pdb=" CA ASN A 574 " ideal model delta sigma weight residual 121.54 127.77 -6.23 1.91e+00 2.74e-01 1.06e+01 ... (remaining 16375 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.85: 6163 23.85 - 47.69: 614 47.69 - 71.54: 125 71.54 - 95.39: 14 95.39 - 119.24: 3 Dihedral angle restraints: 6919 sinusoidal: 3669 harmonic: 3250 Sorted by residual: dihedral pdb=" O4' A B 76 " pdb=" C1' A B 76 " pdb=" N9 A B 76 " pdb=" C4 A B 76 " ideal model delta sinusoidal sigma weight residual 68.00 145.09 -77.09 1 1.70e+01 3.46e-03 2.58e+01 dihedral pdb=" O4' A B 45 " pdb=" C1' A B 45 " pdb=" N9 A B 45 " pdb=" C4 A B 45 " ideal model delta sinusoidal sigma weight residual 68.00 135.83 -67.83 1 1.70e+01 3.46e-03 2.07e+01 dihedral pdb=" O4' C B 42 " pdb=" C1' C B 42 " pdb=" N1 C B 42 " pdb=" C2 C B 42 " ideal model delta sinusoidal sigma weight residual -128.00 -74.29 -53.71 1 1.70e+01 3.46e-03 1.36e+01 ... (remaining 6916 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.050: 1654 0.050 - 0.101: 212 0.101 - 0.151: 31 0.151 - 0.202: 3 0.202 - 0.252: 1 Chirality restraints: 1901 Sorted by residual: chirality pdb=" CB ILE A 382 " pdb=" CA ILE A 382 " pdb=" CG1 ILE A 382 " pdb=" CG2 ILE A 382 " both_signs ideal model delta sigma weight residual False 2.64 2.39 0.25 2.00e-01 2.50e+01 1.59e+00 chirality pdb=" C1' A B 119 " pdb=" O4' A B 119 " pdb=" C2' A B 119 " pdb=" N9 A B 119 " both_signs ideal model delta sigma weight residual False 2.46 2.27 0.19 2.00e-01 2.50e+01 8.96e-01 chirality pdb=" P A B 78 " pdb=" OP1 A B 78 " pdb=" OP2 A B 78 " pdb=" O5' A B 78 " both_signs ideal model delta sigma weight residual True 2.41 -2.60 -0.19 2.00e-01 2.50e+01 8.94e-01 ... (remaining 1898 not shown) Planarity restraints: 1707 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR A 123 " -0.032 5.00e-02 4.00e+02 4.93e-02 3.88e+00 pdb=" N PRO A 124 " 0.085 5.00e-02 4.00e+02 pdb=" CA PRO A 124 " -0.025 5.00e-02 4.00e+02 pdb=" CD PRO A 124 " -0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR A 109 " -0.032 5.00e-02 4.00e+02 4.85e-02 3.76e+00 pdb=" N PRO A 110 " 0.084 5.00e-02 4.00e+02 pdb=" CA PRO A 110 " -0.025 5.00e-02 4.00e+02 pdb=" CD PRO A 110 " -0.027 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA GLU A 580 " 0.009 2.00e-02 2.50e+03 1.86e-02 3.48e+00 pdb=" C GLU A 580 " -0.032 2.00e-02 2.50e+03 pdb=" O GLU A 580 " 0.012 2.00e-02 2.50e+03 pdb=" N LYS A 581 " 0.011 2.00e-02 2.50e+03 ... (remaining 1704 not shown) Histogram of nonbonded interaction distances: 2.19 - 2.73: 767 2.73 - 3.27: 10703 3.27 - 3.81: 18933 3.81 - 4.36: 22219 4.36 - 4.90: 35720 Nonbonded interactions: 88342 Sorted by model distance: nonbonded pdb=" O THR A 237 " pdb=" OG1 THR A 241 " model vdw 2.187 3.040 nonbonded pdb=" O GLN A 919 " pdb=" O2' U B 56 " model vdw 2.194 3.040 nonbonded pdb=" NZ LYS A 390 " pdb=" O PHE A 417 " model vdw 2.210 3.120 nonbonded pdb=" OE2 GLU A 261 " pdb=" OH TYR A 449 " model vdw 2.222 3.040 nonbonded pdb=" O2' A B 17 " pdb=" O4 U B 132 " model vdw 2.245 3.040 ... (remaining 88337 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=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.570 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.030 Construct map_model_manager: 0.000 Extract box with map and model: 0.240 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 14.650 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.360 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.980 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7898 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 : 0.002 0.030 11739 Z= 0.109 Angle : 0.572 11.811 16380 Z= 0.290 Chirality : 0.035 0.252 1901 Planarity : 0.004 0.049 1707 Dihedral : 17.763 119.236 4811 Min Nonbonded Distance : 2.187 Molprobity Statistics. All-atom Clashscore : 9.41 Ramachandran Plot: Outliers : 0.64 % Allowed : 5.64 % Favored : 93.73 % Rotamer: Outliers : 0.00 % Allowed : 28.90 % Favored : 71.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.68 (0.26), residues: 1107 helix: 0.66 (0.25), residues: 465 sheet: -0.17 (0.54), residues: 104 loop : -1.53 (0.26), residues: 538 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 646 TYR 0.012 0.001 TYR A 317 PHE 0.024 0.001 PHE D 8 TRP 0.016 0.001 TRP A 632 HIS 0.002 0.000 HIS A 843 Details of bonding type rmsd/Z covalent geometry : bond 0.00225 / 0.11 (11739) covalent geometry : angle 0.57155 / 0.29 (16380) hydrogen bonds : bond 0.14472 / 10.05 ( 461) hydrogen bonds : angle 4.98538 / 3.78 ( 1235) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 104 time to evaluate : 0.440 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 104 average time/residue: 0.1071 time to fit residues: 16.3344 Evaluate side-chains 91 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 91 time to evaluate : 0.385 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 108 optimal weight: 10.0000 chunk 49 optimal weight: 5.9990 chunk 97 optimal weight: 7.9990 chunk 113 optimal weight: 10.0000 chunk 53 optimal weight: 9.9990 chunk 5 optimal weight: 0.9990 chunk 33 optimal weight: 8.9990 chunk 65 optimal weight: 0.3980 chunk 62 optimal weight: 8.9990 chunk 51 optimal weight: 9.9990 chunk 117 optimal weight: 7.9990 overall best weight: 4.6788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 611 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3889 r_free = 0.3889 target = 0.140162 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.109634 restraints weight = 47187.103| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3497 r_free = 0.3497 target = 0.112532 restraints weight = 29375.648| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.112881 restraints weight = 16636.261| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.113426 restraints weight = 11892.391| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3508 r_free = 0.3508 target = 0.114021 restraints weight = 10658.261| |-----------------------------------------------------------------------------| r_work (final): 0.3516 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3516 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3516 r_free = 0.3516 target_work(ls_wunit_k1) = 0.113 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3516 r_free = 0.3516 target_work(ls_wunit_k1) = 0.113 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (6 function evaluations) r_final: 0.3516 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8059 moved from start: 0.1812 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.067 11739 Z= 0.301 Angle : 0.752 8.028 16380 Z= 0.381 Chirality : 0.044 0.215 1901 Planarity : 0.006 0.054 1707 Dihedral : 13.330 111.082 2600 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 9.93 Ramachandran Plot: Outliers : 0.64 % Allowed : 7.82 % Favored : 91.55 % Rotamer: Outliers : 2.73 % Allowed : 28.24 % Favored : 69.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.05 (0.25), residues: 1107 helix: 0.45 (0.24), residues: 465 sheet: -0.63 (0.54), residues: 102 loop : -1.78 (0.25), residues: 540 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 646 TYR 0.022 0.002 TYR A 317 PHE 0.045 0.002 PHE A 185 TRP 0.009 0.002 TRP A 111 HIS 0.005 0.002 HIS A1002 Details of bonding type rmsd/Z covalent geometry : bond 0.00680 / 0.30 (11739) covalent geometry : angle 0.75154 / 0.38 (16380) hydrogen bonds : bond 0.06880 / 4.81 ( 461) hydrogen bonds : angle 4.54656 / 3.32 ( 1235) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 89 time to evaluate : 0.421 Fit side-chains revert: symmetry clash REVERT: A 246 LEU cc_start: 0.8068 (OUTLIER) cc_final: 0.7741 (mt) outliers start: 25 outliers final: 11 residues processed: 103 average time/residue: 0.0951 time to fit residues: 14.5935 Evaluate side-chains 91 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 79 time to evaluate : 0.378 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 SER Chi-restraints excluded: chain A residue 56 ASP Chi-restraints excluded: chain A residue 246 LEU Chi-restraints excluded: chain A residue 261 GLU Chi-restraints excluded: chain A residue 300 THR Chi-restraints excluded: chain A residue 505 THR Chi-restraints excluded: chain A residue 526 ASN Chi-restraints excluded: chain A residue 881 GLU Chi-restraints excluded: chain A residue 969 VAL Chi-restraints excluded: chain A residue 1052 VAL Chi-restraints excluded: chain D residue 10 THR Chi-restraints excluded: chain D residue 47 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 46 optimal weight: 2.9990 chunk 86 optimal weight: 1.9990 chunk 25 optimal weight: 5.9990 chunk 101 optimal weight: 0.9980 chunk 113 optimal weight: 10.0000 chunk 4 optimal weight: 3.9990 chunk 41 optimal weight: 4.9990 chunk 65 optimal weight: 2.9990 chunk 106 optimal weight: 1.9990 chunk 88 optimal weight: 0.8980 chunk 119 optimal weight: 20.0000 overall best weight: 1.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 822 HIS A 944 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3898 r_free = 0.3898 target = 0.141089 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.107356 restraints weight = 57601.743| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.109243 restraints weight = 25750.182| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.112282 restraints weight = 13928.851| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.112345 restraints weight = 9837.775| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.112580 restraints weight = 9597.072| |-----------------------------------------------------------------------------| r_work (final): 0.3464 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3472 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3472 r_free = 0.3472 target_work(ls_wunit_k1) = 0.110 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3472 r_free = 0.3472 target_work(ls_wunit_k1) = 0.110 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3472 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8025 moved from start: 0.1592 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 11739 Z= 0.145 Angle : 0.612 7.424 16380 Z= 0.308 Chirality : 0.038 0.204 1901 Planarity : 0.004 0.049 1707 Dihedral : 12.888 101.934 2600 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 8.24 Ramachandran Plot: Outliers : 0.55 % Allowed : 6.27 % Favored : 93.18 % Rotamer: Outliers : 2.29 % Allowed : 28.24 % Favored : 69.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.78 (0.25), residues: 1107 helix: 0.77 (0.25), residues: 465 sheet: -0.76 (0.52), residues: 104 loop : -1.66 (0.26), residues: 538 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 646 TYR 0.017 0.001 TYR A 317 PHE 0.026 0.001 PHE A 185 TRP 0.009 0.001 TRP A 632 HIS 0.002 0.001 HIS A1002 Details of bonding type rmsd/Z covalent geometry : bond 0.00325 / 0.14 (11739) covalent geometry : angle 0.61198 / 0.31 (16380) hydrogen bonds : bond 0.04977 / 3.53 ( 461) hydrogen bonds : angle 4.12497 / 3.03 ( 1235) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 86 time to evaluate : 0.381 Fit side-chains REVERT: A 246 LEU cc_start: 0.8009 (OUTLIER) cc_final: 0.7777 (mt) REVERT: A 501 ILE cc_start: 0.8504 (OUTLIER) cc_final: 0.8101 (mp) outliers start: 21 outliers final: 12 residues processed: 100 average time/residue: 0.1047 time to fit residues: 15.3671 Evaluate side-chains 93 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 79 time to evaluate : 0.342 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 SER Chi-restraints excluded: chain A residue 56 ASP Chi-restraints excluded: chain A residue 91 VAL Chi-restraints excluded: chain A residue 102 LEU Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 216 PHE Chi-restraints excluded: chain A residue 246 LEU Chi-restraints excluded: chain A residue 501 ILE Chi-restraints excluded: chain A residue 673 VAL Chi-restraints excluded: chain A residue 709 PHE Chi-restraints excluded: chain A residue 948 VAL Chi-restraints excluded: chain A residue 969 VAL Chi-restraints excluded: chain A residue 1052 VAL Chi-restraints excluded: chain D residue 10 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 15 optimal weight: 0.9990 chunk 88 optimal weight: 2.9990 chunk 13 optimal weight: 10.0000 chunk 5 optimal weight: 0.8980 chunk 90 optimal weight: 5.9990 chunk 92 optimal weight: 4.9990 chunk 51 optimal weight: 0.3980 chunk 114 optimal weight: 7.9990 chunk 120 optimal weight: 10.0000 chunk 103 optimal weight: 5.9990 chunk 64 optimal weight: 4.9990 overall best weight: 2.0586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3893 r_free = 0.3893 target = 0.140814 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.107755 restraints weight = 59812.964| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.110671 restraints weight = 27010.828| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.110896 restraints weight = 16527.714| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.111858 restraints weight = 11202.922| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.112427 restraints weight = 9980.546| |-----------------------------------------------------------------------------| r_work (final): 0.3464 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3464 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3464 r_free = 0.3464 target_work(ls_wunit_k1) = 0.110 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3464 r_free = 0.3464 target_work(ls_wunit_k1) = 0.110 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3464 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8041 moved from start: 0.1745 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 11739 Z= 0.155 Angle : 0.607 7.259 16380 Z= 0.305 Chirality : 0.038 0.209 1901 Planarity : 0.004 0.050 1707 Dihedral : 12.717 100.489 2600 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 8.85 Ramachandran Plot: Outliers : 0.55 % Allowed : 6.91 % Favored : 92.55 % Rotamer: Outliers : 3.16 % Allowed : 27.92 % Favored : 68.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.72 (0.26), residues: 1107 helix: 0.83 (0.25), residues: 468 sheet: -0.77 (0.52), residues: 103 loop : -1.64 (0.26), residues: 536 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 713 TYR 0.019 0.001 TYR A 317 PHE 0.028 0.001 PHE A 185 TRP 0.009 0.001 TRP A 632 HIS 0.003 0.001 HIS A 822 Details of bonding type rmsd/Z covalent geometry : bond 0.00352 / 0.16 (11739) covalent geometry : angle 0.60658 / 0.31 (16380) hydrogen bonds : bond 0.04963 / 3.52 ( 461) hydrogen bonds : angle 4.03475 / 2.96 ( 1235) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 84 time to evaluate : 0.421 Fit side-chains REVERT: A 246 LEU cc_start: 0.8046 (OUTLIER) cc_final: 0.7817 (mt) REVERT: A 276 ARG cc_start: 0.7369 (tpt170) cc_final: 0.7085 (tpt170) REVERT: A 501 ILE cc_start: 0.8577 (OUTLIER) cc_final: 0.8166 (mp) REVERT: A 620 TYR cc_start: 0.8066 (t80) cc_final: 0.7599 (t80) outliers start: 29 outliers final: 21 residues processed: 106 average time/residue: 0.1033 time to fit residues: 16.2206 Evaluate side-chains 104 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 81 time to evaluate : 0.333 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 SER Chi-restraints excluded: chain A residue 56 ASP Chi-restraints excluded: chain A residue 91 VAL Chi-restraints excluded: chain A residue 102 LEU Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 216 PHE Chi-restraints excluded: chain A residue 231 LEU Chi-restraints excluded: chain A residue 246 LEU Chi-restraints excluded: chain A residue 260 PHE Chi-restraints excluded: chain A residue 300 THR Chi-restraints excluded: chain A residue 423 ILE Chi-restraints excluded: chain A residue 501 ILE Chi-restraints excluded: chain A residue 558 LEU Chi-restraints excluded: chain A residue 667 LEU Chi-restraints excluded: chain A residue 673 VAL Chi-restraints excluded: chain A residue 948 VAL Chi-restraints excluded: chain A residue 969 VAL Chi-restraints excluded: chain A residue 1009 VAL Chi-restraints excluded: chain A residue 1037 LEU Chi-restraints excluded: chain A residue 1052 VAL Chi-restraints excluded: chain D residue 10 THR Chi-restraints excluded: chain D residue 58 LEU Chi-restraints excluded: chain D residue 79 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 76 optimal weight: 6.9990 chunk 25 optimal weight: 0.9990 chunk 15 optimal weight: 7.9990 chunk 66 optimal weight: 9.9990 chunk 59 optimal weight: 5.9990 chunk 46 optimal weight: 6.9990 chunk 86 optimal weight: 0.9990 chunk 105 optimal weight: 2.9990 chunk 99 optimal weight: 5.9990 chunk 60 optimal weight: 3.9990 chunk 69 optimal weight: 4.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 601 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3874 r_free = 0.3874 target = 0.139391 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.105727 restraints weight = 46058.550| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.106971 restraints weight = 21038.591| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.109852 restraints weight = 12975.732| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.109556 restraints weight = 9788.825| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.110231 restraints weight = 9099.495| |-----------------------------------------------------------------------------| r_work (final): 0.3438 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3437 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3437 r_free = 0.3437 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3437 r_free = 0.3437 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3437 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8080 moved from start: 0.1972 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 11739 Z= 0.192 Angle : 0.634 7.214 16380 Z= 0.320 Chirality : 0.039 0.208 1901 Planarity : 0.005 0.050 1707 Dihedral : 12.725 100.975 2600 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 9.13 Ramachandran Plot: Outliers : 0.55 % Allowed : 7.27 % Favored : 92.18 % Rotamer: Outliers : 3.49 % Allowed : 27.70 % Favored : 68.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.83 (0.25), residues: 1107 helix: 0.76 (0.25), residues: 468 sheet: -0.74 (0.53), residues: 98 loop : -1.74 (0.26), residues: 541 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 713 TYR 0.020 0.002 TYR A 317 PHE 0.025 0.002 PHE A 185 TRP 0.011 0.001 TRP A 632 HIS 0.003 0.001 HIS A 822 Details of bonding type rmsd/Z covalent geometry : bond 0.00435 / 0.19 (11739) covalent geometry : angle 0.63410 / 0.32 (16380) hydrogen bonds : bond 0.05370 / 3.80 ( 461) hydrogen bonds : angle 4.14030 / 3.04 ( 1235) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 86 time to evaluate : 0.344 Fit side-chains REVERT: A 246 LEU cc_start: 0.8075 (OUTLIER) cc_final: 0.7802 (mt) REVERT: A 249 ASP cc_start: 0.7689 (m-30) cc_final: 0.7469 (m-30) REVERT: A 276 ARG cc_start: 0.7361 (tpt170) cc_final: 0.7020 (tpt170) outliers start: 32 outliers final: 23 residues processed: 111 average time/residue: 0.1019 time to fit residues: 16.7249 Evaluate side-chains 107 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 83 time to evaluate : 0.372 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 SER Chi-restraints excluded: chain A residue 56 ASP Chi-restraints excluded: chain A residue 91 VAL Chi-restraints excluded: chain A residue 102 LEU Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 216 PHE Chi-restraints excluded: chain A residue 231 LEU Chi-restraints excluded: chain A residue 246 LEU Chi-restraints excluded: chain A residue 260 PHE Chi-restraints excluded: chain A residue 300 THR Chi-restraints excluded: chain A residue 310 TYR Chi-restraints excluded: chain A residue 558 LEU Chi-restraints excluded: chain A residue 667 LEU Chi-restraints excluded: chain A residue 673 VAL Chi-restraints excluded: chain A residue 948 VAL Chi-restraints excluded: chain A residue 969 VAL Chi-restraints excluded: chain A residue 1009 VAL Chi-restraints excluded: chain A residue 1037 LEU Chi-restraints excluded: chain A residue 1052 VAL Chi-restraints excluded: chain D residue 10 THR Chi-restraints excluded: chain D residue 39 VAL Chi-restraints excluded: chain D residue 47 ASP Chi-restraints excluded: chain D residue 58 LEU Chi-restraints excluded: chain D residue 79 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 66 optimal weight: 8.9990 chunk 83 optimal weight: 6.9990 chunk 19 optimal weight: 1.9990 chunk 39 optimal weight: 5.9990 chunk 84 optimal weight: 0.2980 chunk 21 optimal weight: 1.9990 chunk 106 optimal weight: 3.9990 chunk 82 optimal weight: 5.9990 chunk 74 optimal weight: 7.9990 chunk 49 optimal weight: 7.9990 chunk 65 optimal weight: 1.9990 overall best weight: 2.0588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3892 r_free = 0.3892 target = 0.140701 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.108314 restraints weight = 76228.084| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.112560 restraints weight = 29716.948| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.111765 restraints weight = 17104.794| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.112873 restraints weight = 10843.024| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.113300 restraints weight = 9510.218| |-----------------------------------------------------------------------------| r_work (final): 0.3469 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3460 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3460 r_free = 0.3460 target_work(ls_wunit_k1) = 0.110 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3460 r_free = 0.3460 target_work(ls_wunit_k1) = 0.110 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3460 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8027 moved from start: 0.1961 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 11739 Z= 0.153 Angle : 0.604 7.811 16380 Z= 0.303 Chirality : 0.038 0.209 1901 Planarity : 0.004 0.050 1707 Dihedral : 12.528 100.739 2600 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 8.38 Ramachandran Plot: Outliers : 0.55 % Allowed : 7.36 % Favored : 92.09 % Rotamer: Outliers : 2.62 % Allowed : 28.79 % Favored : 68.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.69 (0.26), residues: 1107 helix: 0.87 (0.25), residues: 468 sheet: -0.79 (0.52), residues: 103 loop : -1.63 (0.26), residues: 536 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 713 TYR 0.020 0.001 TYR A 317 PHE 0.022 0.001 PHE A 185 TRP 0.010 0.001 TRP A 632 HIS 0.003 0.001 HIS A1002 Details of bonding type rmsd/Z covalent geometry : bond 0.00348 / 0.15 (11739) covalent geometry : angle 0.60351 / 0.30 (16380) hydrogen bonds : bond 0.04841 / 3.44 ( 461) hydrogen bonds : angle 4.00941 / 2.94 ( 1235) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 85 time to evaluate : 0.250 Fit side-chains REVERT: A 86 LEU cc_start: 0.6974 (OUTLIER) cc_final: 0.6548 (tp) REVERT: A 246 LEU cc_start: 0.8042 (OUTLIER) cc_final: 0.7809 (mt) REVERT: A 276 ARG cc_start: 0.7372 (tpt170) cc_final: 0.7052 (tpt170) outliers start: 24 outliers final: 21 residues processed: 102 average time/residue: 0.0899 time to fit residues: 13.4977 Evaluate side-chains 105 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 82 time to evaluate : 0.383 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 SER Chi-restraints excluded: chain A residue 56 ASP Chi-restraints excluded: chain A residue 86 LEU Chi-restraints excluded: chain A residue 91 VAL Chi-restraints excluded: chain A residue 102 LEU Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 216 PHE Chi-restraints excluded: chain A residue 231 LEU Chi-restraints excluded: chain A residue 246 LEU Chi-restraints excluded: chain A residue 260 PHE Chi-restraints excluded: chain A residue 300 THR Chi-restraints excluded: chain A residue 310 TYR Chi-restraints excluded: chain A residue 415 ILE Chi-restraints excluded: chain A residue 558 LEU Chi-restraints excluded: chain A residue 673 VAL Chi-restraints excluded: chain A residue 948 VAL Chi-restraints excluded: chain A residue 969 VAL Chi-restraints excluded: chain A residue 1009 VAL Chi-restraints excluded: chain A residue 1037 LEU Chi-restraints excluded: chain A residue 1052 VAL Chi-restraints excluded: chain D residue 10 THR Chi-restraints excluded: chain D residue 58 LEU Chi-restraints excluded: chain D residue 79 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 60 optimal weight: 5.9990 chunk 59 optimal weight: 10.0000 chunk 89 optimal weight: 6.9990 chunk 49 optimal weight: 6.9990 chunk 4 optimal weight: 9.9990 chunk 18 optimal weight: 4.9990 chunk 99 optimal weight: 5.9990 chunk 12 optimal weight: 5.9990 chunk 3 optimal weight: 3.9990 chunk 41 optimal weight: 3.9990 chunk 68 optimal weight: 0.9980 overall best weight: 3.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 611 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3889 r_free = 0.3889 target = 0.140520 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.109313 restraints weight = 60394.148| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.111694 restraints weight = 34916.208| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.112633 restraints weight = 19479.934| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3491 r_free = 0.3491 target = 0.113207 restraints weight = 13477.457| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.113777 restraints weight = 12070.153| |-----------------------------------------------------------------------------| r_work (final): 0.3499 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3499 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3499 r_free = 0.3499 target_work(ls_wunit_k1) = 0.112 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3499 r_free = 0.3499 target_work(ls_wunit_k1) = 0.112 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3499 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8080 moved from start: 0.2291 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.065 11739 Z= 0.255 Angle : 0.695 8.157 16380 Z= 0.352 Chirality : 0.041 0.205 1901 Planarity : 0.005 0.049 1707 Dihedral : 12.803 102.111 2600 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 9.70 Ramachandran Plot: Outliers : 0.45 % Allowed : 8.27 % Favored : 91.27 % Rotamer: Outliers : 3.49 % Allowed : 28.14 % Favored : 68.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.02 (0.25), residues: 1107 helix: 0.57 (0.25), residues: 468 sheet: -0.90 (0.53), residues: 99 loop : -1.80 (0.26), residues: 540 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG A 63 TYR 0.023 0.002 TYR A 317 PHE 0.027 0.002 PHE A 185 TRP 0.012 0.002 TRP A 632 HIS 0.004 0.001 HIS A 822 Details of bonding type rmsd/Z covalent geometry : bond 0.00580 / 0.25 (11739) covalent geometry : angle 0.69525 / 0.35 (16380) hydrogen bonds : bond 0.06086 / 4.30 ( 461) hydrogen bonds : angle 4.32291 / 3.17 ( 1235) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 87 time to evaluate : 0.357 Fit side-chains REVERT: A 86 LEU cc_start: 0.7013 (OUTLIER) cc_final: 0.6523 (tp) REVERT: A 246 LEU cc_start: 0.8120 (OUTLIER) cc_final: 0.7829 (mt) REVERT: A 276 ARG cc_start: 0.7609 (tpt170) cc_final: 0.7297 (tpt170) REVERT: A 541 PHE cc_start: 0.4486 (OUTLIER) cc_final: 0.4262 (t80) REVERT: A 819 GLU cc_start: 0.7392 (OUTLIER) cc_final: 0.6975 (mp0) outliers start: 32 outliers final: 21 residues processed: 112 average time/residue: 0.1046 time to fit residues: 17.0534 Evaluate side-chains 108 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 83 time to evaluate : 0.342 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 SER Chi-restraints excluded: chain A residue 56 ASP Chi-restraints excluded: chain A residue 86 LEU Chi-restraints excluded: chain A residue 91 VAL Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 216 PHE Chi-restraints excluded: chain A residue 246 LEU Chi-restraints excluded: chain A residue 260 PHE Chi-restraints excluded: chain A residue 300 THR Chi-restraints excluded: chain A residue 526 ASN Chi-restraints excluded: chain A residue 541 PHE Chi-restraints excluded: chain A residue 558 LEU Chi-restraints excluded: chain A residue 667 LEU Chi-restraints excluded: chain A residue 673 VAL Chi-restraints excluded: chain A residue 812 GLU Chi-restraints excluded: chain A residue 819 GLU Chi-restraints excluded: chain A residue 948 VAL Chi-restraints excluded: chain A residue 969 VAL Chi-restraints excluded: chain A residue 1009 VAL Chi-restraints excluded: chain A residue 1037 LEU Chi-restraints excluded: chain A residue 1052 VAL Chi-restraints excluded: chain D residue 10 THR Chi-restraints excluded: chain D residue 39 VAL Chi-restraints excluded: chain D residue 58 LEU Chi-restraints excluded: chain D residue 79 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 93 optimal weight: 2.9990 chunk 61 optimal weight: 0.7980 chunk 65 optimal weight: 3.9990 chunk 37 optimal weight: 9.9990 chunk 7 optimal weight: 5.9990 chunk 30 optimal weight: 0.7980 chunk 54 optimal weight: 8.9990 chunk 83 optimal weight: 8.9990 chunk 15 optimal weight: 2.9990 chunk 90 optimal weight: 1.9990 chunk 69 optimal weight: 4.9990 overall best weight: 1.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3887 r_free = 0.3887 target = 0.140388 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.106747 restraints weight = 59146.941| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.108175 restraints weight = 25483.199| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.111485 restraints weight = 14155.906| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.111498 restraints weight = 9823.522| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.111695 restraints weight = 9624.978| |-----------------------------------------------------------------------------| r_work (final): 0.3456 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3456 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3456 r_free = 0.3456 target_work(ls_wunit_k1) = 0.109 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3456 r_free = 0.3456 target_work(ls_wunit_k1) = 0.109 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3456 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8046 moved from start: 0.2149 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 11739 Z= 0.149 Angle : 0.614 9.414 16380 Z= 0.308 Chirality : 0.038 0.208 1901 Planarity : 0.004 0.050 1707 Dihedral : 12.528 101.816 2600 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 8.85 Ramachandran Plot: Outliers : 0.45 % Allowed : 7.09 % Favored : 92.45 % Rotamer: Outliers : 2.40 % Allowed : 28.79 % Favored : 68.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.77 (0.26), residues: 1107 helix: 0.79 (0.25), residues: 468 sheet: -0.84 (0.52), residues: 103 loop : -1.65 (0.26), residues: 536 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 713 TYR 0.020 0.001 TYR A 317 PHE 0.023 0.001 PHE A 185 TRP 0.013 0.001 TRP A 632 HIS 0.003 0.001 HIS A1002 Details of bonding type rmsd/Z covalent geometry : bond 0.00337 / 0.15 (11739) covalent geometry : angle 0.61412 / 0.31 (16380) hydrogen bonds : bond 0.04864 / 3.47 ( 461) hydrogen bonds : angle 4.03898 / 2.95 ( 1235) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 87 time to evaluate : 0.385 Fit side-chains REVERT: A 86 LEU cc_start: 0.6971 (OUTLIER) cc_final: 0.6477 (tp) REVERT: A 246 LEU cc_start: 0.8103 (OUTLIER) cc_final: 0.7839 (mt) REVERT: A 819 GLU cc_start: 0.7474 (OUTLIER) cc_final: 0.7033 (mp0) outliers start: 22 outliers final: 17 residues processed: 105 average time/residue: 0.1032 time to fit residues: 15.8646 Evaluate side-chains 102 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 82 time to evaluate : 0.407 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 SER Chi-restraints excluded: chain A residue 56 ASP Chi-restraints excluded: chain A residue 86 LEU Chi-restraints excluded: chain A residue 91 VAL Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 216 PHE Chi-restraints excluded: chain A residue 246 LEU Chi-restraints excluded: chain A residue 260 PHE Chi-restraints excluded: chain A residue 526 ASN Chi-restraints excluded: chain A residue 558 LEU Chi-restraints excluded: chain A residue 673 VAL Chi-restraints excluded: chain A residue 819 GLU Chi-restraints excluded: chain A residue 948 VAL Chi-restraints excluded: chain A residue 969 VAL Chi-restraints excluded: chain A residue 1009 VAL Chi-restraints excluded: chain A residue 1037 LEU Chi-restraints excluded: chain A residue 1052 VAL Chi-restraints excluded: chain D residue 10 THR Chi-restraints excluded: chain D residue 58 LEU Chi-restraints excluded: chain D residue 79 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 99 optimal weight: 4.9990 chunk 102 optimal weight: 3.9990 chunk 1 optimal weight: 6.9990 chunk 5 optimal weight: 0.9990 chunk 87 optimal weight: 8.9990 chunk 103 optimal weight: 0.5980 chunk 8 optimal weight: 3.9990 chunk 2 optimal weight: 0.6980 chunk 33 optimal weight: 0.8980 chunk 15 optimal weight: 3.9990 chunk 57 optimal weight: 5.9990 overall best weight: 1.4384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3905 r_free = 0.3905 target = 0.141694 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.107956 restraints weight = 50449.889| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.109854 restraints weight = 22037.086| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.113120 restraints weight = 12733.653| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.113052 restraints weight = 9012.550| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.113199 restraints weight = 8786.981| |-----------------------------------------------------------------------------| r_work (final): 0.3483 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3482 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3482 r_free = 0.3482 target_work(ls_wunit_k1) = 0.111 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3482 r_free = 0.3482 target_work(ls_wunit_k1) = 0.111 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3482 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8002 moved from start: 0.2065 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 11739 Z= 0.130 Angle : 0.592 8.561 16380 Z= 0.296 Chirality : 0.037 0.202 1901 Planarity : 0.004 0.051 1707 Dihedral : 12.307 99.672 2600 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 8.43 Ramachandran Plot: Outliers : 0.45 % Allowed : 7.36 % Favored : 92.18 % Rotamer: Outliers : 2.40 % Allowed : 29.01 % Favored : 68.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.59 (0.26), residues: 1107 helix: 0.94 (0.25), residues: 469 sheet: -0.80 (0.52), residues: 103 loop : -1.55 (0.26), residues: 535 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 713 TYR 0.018 0.001 TYR A 317 PHE 0.018 0.001 PHE A 185 TRP 0.012 0.001 TRP A 632 HIS 0.003 0.001 HIS A1002 Details of bonding type rmsd/Z covalent geometry : bond 0.00296 / 0.13 (11739) covalent geometry : angle 0.59159 / 0.30 (16380) hydrogen bonds : bond 0.04427 / 3.16 ( 461) hydrogen bonds : angle 3.88243 / 2.84 ( 1235) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 90 time to evaluate : 0.510 Fit side-chains REVERT: A 86 LEU cc_start: 0.6962 (OUTLIER) cc_final: 0.6575 (tp) REVERT: A 246 LEU cc_start: 0.8166 (OUTLIER) cc_final: 0.7851 (mt) REVERT: A 348 MET cc_start: 0.7442 (tmm) cc_final: 0.7108 (tmm) outliers start: 22 outliers final: 16 residues processed: 107 average time/residue: 0.1078 time to fit residues: 17.0289 Evaluate side-chains 102 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 84 time to evaluate : 0.379 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 SER Chi-restraints excluded: chain A residue 56 ASP Chi-restraints excluded: chain A residue 86 LEU Chi-restraints excluded: chain A residue 91 VAL Chi-restraints excluded: chain A residue 102 LEU Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 216 PHE Chi-restraints excluded: chain A residue 246 LEU Chi-restraints excluded: chain A residue 260 PHE Chi-restraints excluded: chain A residue 558 LEU Chi-restraints excluded: chain A residue 673 VAL Chi-restraints excluded: chain A residue 969 VAL Chi-restraints excluded: chain A residue 1009 VAL Chi-restraints excluded: chain A residue 1052 VAL Chi-restraints excluded: chain D residue 10 THR Chi-restraints excluded: chain D residue 39 VAL Chi-restraints excluded: chain D residue 58 LEU Chi-restraints excluded: chain D residue 79 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 37 optimal weight: 6.9990 chunk 69 optimal weight: 8.9990 chunk 52 optimal weight: 5.9990 chunk 26 optimal weight: 20.0000 chunk 0 optimal weight: 6.9990 chunk 105 optimal weight: 2.9990 chunk 7 optimal weight: 7.9990 chunk 72 optimal weight: 1.9990 chunk 50 optimal weight: 4.9990 chunk 56 optimal weight: 10.0000 chunk 51 optimal weight: 5.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3886 r_free = 0.3886 target = 0.140091 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.109184 restraints weight = 61597.108| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.111303 restraints weight = 35336.000| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.112221 restraints weight = 19147.539| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3486 r_free = 0.3486 target = 0.112839 restraints weight = 13553.027| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.113294 restraints weight = 12087.291| |-----------------------------------------------------------------------------| r_work (final): 0.3491 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3491 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3491 r_free = 0.3491 target_work(ls_wunit_k1) = 0.111 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3491 r_free = 0.3491 target_work(ls_wunit_k1) = 0.111 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3491 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8097 moved from start: 0.2522 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.068 11739 Z= 0.280 Angle : 0.729 8.534 16380 Z= 0.369 Chirality : 0.043 0.198 1901 Planarity : 0.006 0.050 1707 Dihedral : 12.748 101.462 2600 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 10.45 Ramachandran Plot: Outliers : 0.45 % Allowed : 8.27 % Favored : 91.27 % Rotamer: Outliers : 2.62 % Allowed : 28.90 % Favored : 68.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.11 (0.25), residues: 1107 helix: 0.49 (0.24), residues: 475 sheet: -0.99 (0.53), residues: 99 loop : -1.86 (0.26), residues: 533 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 63 TYR 0.024 0.002 TYR A 317 PHE 0.029 0.002 PHE A 185 TRP 0.029 0.002 TRP A 632 HIS 0.005 0.002 HIS A 563 Details of bonding type rmsd/Z covalent geometry : bond 0.00638 / 0.28 (11739) covalent geometry : angle 0.72868 / 0.37 (16380) hydrogen bonds : bond 0.06358 / 4.49 ( 461) hydrogen bonds : angle 4.38307 / 3.20 ( 1235) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 87 time to evaluate : 0.379 Fit side-chains REVERT: A 86 LEU cc_start: 0.7050 (OUTLIER) cc_final: 0.6549 (tp) REVERT: A 246 LEU cc_start: 0.8114 (OUTLIER) cc_final: 0.7801 (mt) REVERT: A 541 PHE cc_start: 0.4473 (OUTLIER) cc_final: 0.4239 (t80) REVERT: A 620 TYR cc_start: 0.8094 (t80) cc_final: 0.7843 (t80) outliers start: 24 outliers final: 18 residues processed: 105 average time/residue: 0.0902 time to fit residues: 14.2731 Evaluate side-chains 106 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 85 time to evaluate : 0.250 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 SER Chi-restraints excluded: chain A residue 56 ASP Chi-restraints excluded: chain A residue 86 LEU Chi-restraints excluded: chain A residue 91 VAL Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 216 PHE Chi-restraints excluded: chain A residue 246 LEU Chi-restraints excluded: chain A residue 260 PHE Chi-restraints excluded: chain A residue 310 TYR Chi-restraints excluded: chain A residue 526 ASN Chi-restraints excluded: chain A residue 541 PHE Chi-restraints excluded: chain A residue 558 LEU Chi-restraints excluded: chain A residue 673 VAL Chi-restraints excluded: chain A residue 969 VAL Chi-restraints excluded: chain A residue 1009 VAL Chi-restraints excluded: chain A residue 1052 VAL Chi-restraints excluded: chain D residue 10 THR Chi-restraints excluded: chain D residue 39 VAL Chi-restraints excluded: chain D residue 47 ASP Chi-restraints excluded: chain D residue 58 LEU Chi-restraints excluded: chain D residue 79 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 112 optimal weight: 10.0000 chunk 33 optimal weight: 3.9990 chunk 44 optimal weight: 0.9990 chunk 10 optimal weight: 0.9980 chunk 28 optimal weight: 6.9990 chunk 31 optimal weight: 10.0000 chunk 64 optimal weight: 0.9990 chunk 12 optimal weight: 1.9990 chunk 76 optimal weight: 0.8980 chunk 80 optimal weight: 0.0170 chunk 81 optimal weight: 0.6980 overall best weight: 0.7220 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3914 r_free = 0.3914 target = 0.142317 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.108736 restraints weight = 58235.235| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.113351 restraints weight = 25110.436| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3486 r_free = 0.3486 target = 0.112863 restraints weight = 14745.214| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.113497 restraints weight = 10212.369| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.114747 restraints weight = 9237.421| |-----------------------------------------------------------------------------| r_work (final): 0.3494 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3497 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3497 r_free = 0.3497 target_work(ls_wunit_k1) = 0.112 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3497 r_free = 0.3497 target_work(ls_wunit_k1) = 0.112 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3497 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7980 moved from start: 0.2234 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 11739 Z= 0.118 Angle : 0.606 8.939 16380 Z= 0.304 Chirality : 0.037 0.213 1901 Planarity : 0.004 0.051 1707 Dihedral : 12.360 101.967 2600 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 8.71 Ramachandran Plot: Outliers : 0.45 % Allowed : 6.09 % Favored : 93.45 % Rotamer: Outliers : 1.42 % Allowed : 30.21 % Favored : 68.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.64 (0.26), residues: 1107 helix: 0.86 (0.25), residues: 473 sheet: -0.66 (0.53), residues: 103 loop : -1.61 (0.26), residues: 531 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 713 TYR 0.018 0.001 TYR A 317 PHE 0.012 0.001 PHE A 185 TRP 0.022 0.002 TRP A 632 HIS 0.003 0.001 HIS A 201 Details of bonding type rmsd/Z covalent geometry : bond 0.00262 / 0.12 (11739) covalent geometry : angle 0.60594 / 0.30 (16380) hydrogen bonds : bond 0.04364 / 3.11 ( 461) hydrogen bonds : angle 3.94759 / 2.88 ( 1235) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1954.36 seconds wall clock time: 34 minutes 29.70 seconds (2069.70 seconds total)