Starting phenix.real_space_refine on Thu Jul 31 07:12:01 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ja0_36123/07_2025/8ja0_36123.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ja0_36123/07_2025/8ja0_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8ja0_36123/07_2025/8ja0_36123.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ja0_36123/07_2025/8ja0_36123.map" model { file = "/net/cci-nas-00/data/ceres_data/8ja0_36123/07_2025/8ja0_36123.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ja0_36123/07_2025/8ja0_36123.cif" } resolution = 3.52 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.171 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/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: {'GLN:plan1': 1, 'HIS:plan': 2, 'ASN:plan1': 1, 'ASP:plan': 1, 'PHE:plan': 2, 'GLU:plan': 9, 'ARG:plan': 9} 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: {'GLN:plan1': 1, 'HIS:plan': 2, 'ASN:plan1': 1, 'ASP:plan': 1, 'PHE:plan': 2, 'GLU:plan': 9, 'ARG:plan': 9} 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: 10.74, per 1000 atoms: 0.95 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: 2.68 Conformation dependent library (CDL) restraints added in 2.3 seconds 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: 4.27 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: 4.80 Time building geometry restraints manager: 3.25 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: 6310 23.85 - 47.69: 708 47.69 - 71.54: 252 71.54 - 95.39: 44 95.39 - 119.24: 3 Dihedral angle restraints: 7317 sinusoidal: 4067 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 7314 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: 1.380 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.100 Construct map_model_manager: 0.010 Extract box with map and model: 0.510 Check model and map are aligned: 0.100 Set scattering table: 0.120 Process input model: 38.100 Find NCS groups from input model: 0.130 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.990 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 43.520 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7730 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 : 20.778 119.236 5209 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.68 (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 TRP 0.016 0.001 TRP A 632 HIS 0.002 0.000 HIS A 843 PHE 0.024 0.001 PHE D 8 TYR 0.012 0.001 TYR A 317 ARG 0.009 0.000 ARG A 646 Details of bonding type rmsd hydrogen bonds : bond 0.14472 ( 461) hydrogen bonds : angle 4.98538 ( 1235) covalent geometry : bond 0.00225 (11739) covalent geometry : angle 0.57155 (16380) *********************** 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 : 1.045 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 104 average time/residue: 0.2328 time to fit residues: 35.3038 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 : 1.013 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 102 optimal weight: 8.9990 chunk 91 optimal weight: 0.8980 chunk 50 optimal weight: 3.9990 chunk 31 optimal weight: 8.9990 chunk 61 optimal weight: 5.9990 chunk 48 optimal weight: 7.9990 chunk 94 optimal weight: 0.9980 chunk 36 optimal weight: 6.9990 chunk 57 optimal weight: 0.9990 chunk 70 optimal weight: 0.9980 chunk 109 optimal weight: 9.9990 overall best weight: 1.5784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3934 r_free = 0.3934 target = 0.143030 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.110259 restraints weight = 61013.048| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.114194 restraints weight = 26803.209| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.113788 restraints weight = 16315.051| |-----------------------------------------------------------------------------| r_work (final): 0.3493 ------------------------------------------------------------------------------- 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 | |-----------------------------------------------------------------------------| r_final: 0.3491 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7815 moved from start: 0.0902 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 11739 Z= 0.135 Angle : 0.580 8.386 16380 Z= 0.290 Chirality : 0.037 0.189 1901 Planarity : 0.004 0.051 1707 Dihedral : 19.362 113.355 2998 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 7.73 Ramachandran Plot: Outliers : 0.64 % Allowed : 5.73 % Favored : 93.64 % Rotamer: Outliers : 1.74 % Allowed : 27.92 % Favored : 70.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.52 (0.26), residues: 1107 helix: 0.84 (0.25), residues: 479 sheet: -0.32 (0.52), residues: 110 loop : -1.51 (0.27), residues: 518 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 279 HIS 0.003 0.001 HIS A 201 PHE 0.028 0.001 PHE A 185 TYR 0.016 0.001 TYR A 317 ARG 0.009 0.000 ARG A 646 Details of bonding type rmsd hydrogen bonds : bond 0.04876 ( 461) hydrogen bonds : angle 4.08369 ( 1235) covalent geometry : bond 0.00298 (11739) covalent geometry : angle 0.58032 (16380) *********************** 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 106 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 90 time to evaluate : 1.191 Fit side-chains outliers start: 16 outliers final: 8 residues processed: 97 average time/residue: 0.2239 time to fit residues: 32.8217 Evaluate side-chains 91 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 83 time to evaluate : 1.312 ------------------------------------------------------------------------------- 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 102 LEU Chi-restraints excluded: chain A residue 231 LEU Chi-restraints excluded: chain A residue 423 ILE 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=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 90 optimal weight: 5.9990 chunk 87 optimal weight: 5.9990 chunk 107 optimal weight: 0.0270 chunk 83 optimal weight: 2.9990 chunk 1 optimal weight: 6.9990 chunk 64 optimal weight: 0.9990 chunk 7 optimal weight: 7.9990 chunk 45 optimal weight: 2.9990 chunk 82 optimal weight: 0.7980 chunk 102 optimal weight: 9.9990 chunk 35 optimal weight: 1.9990 overall best weight: 1.3644 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 611 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3928 r_free = 0.3928 target = 0.142685 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.109864 restraints weight = 55134.323| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.114171 restraints weight = 25234.451| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.113737 restraints weight = 14681.045| |-----------------------------------------------------------------------------| r_work (final): 0.3488 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3488 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3488 r_free = 0.3488 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 = 0.3488 r_free = 0.3488 target_work(ls_wunit_k1) = 0.111 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.3488 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7814 moved from start: 0.1217 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 11739 Z= 0.123 Angle : 0.567 7.247 16380 Z= 0.283 Chirality : 0.036 0.199 1901 Planarity : 0.004 0.050 1707 Dihedral : 19.165 99.377 2998 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 7.68 Ramachandran Plot: Outliers : 0.55 % Allowed : 6.36 % Favored : 93.09 % Rotamer: Outliers : 1.64 % Allowed : 28.68 % Favored : 69.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.32 (0.26), residues: 1107 helix: 1.08 (0.25), residues: 469 sheet: -0.30 (0.51), residues: 109 loop : -1.41 (0.27), residues: 529 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 632 HIS 0.002 0.001 HIS A 201 PHE 0.027 0.001 PHE A 185 TYR 0.015 0.001 TYR A 317 ARG 0.004 0.000 ARG A 713 Details of bonding type rmsd hydrogen bonds : bond 0.04448 ( 461) hydrogen bonds : angle 3.89395 ( 1235) covalent geometry : bond 0.00275 (11739) covalent geometry : angle 0.56689 (16380) *********************** 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 105 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 90 time to evaluate : 1.153 Fit side-chains REVERT: A 276 ARG cc_start: 0.7321 (tpt170) cc_final: 0.7048 (tpt170) REVERT: A 402 ARG cc_start: 0.6661 (mtt-85) cc_final: 0.6174 (mtt90) REVERT: A 801 ASP cc_start: 0.7503 (p0) cc_final: 0.7295 (p0) outliers start: 15 outliers final: 10 residues processed: 97 average time/residue: 0.2371 time to fit residues: 34.2302 Evaluate side-chains 94 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 84 time to evaluate : 1.005 ------------------------------------------------------------------------------- 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 231 LEU Chi-restraints excluded: chain A residue 310 TYR Chi-restraints excluded: chain A residue 423 ILE Chi-restraints excluded: chain A residue 649 LYS Chi-restraints excluded: chain A residue 969 VAL Chi-restraints excluded: chain A residue 1052 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 87 optimal weight: 6.9990 chunk 53 optimal weight: 10.0000 chunk 41 optimal weight: 0.9980 chunk 91 optimal weight: 6.9990 chunk 43 optimal weight: 0.9990 chunk 19 optimal weight: 4.9990 chunk 67 optimal weight: 4.9990 chunk 90 optimal weight: 4.9990 chunk 101 optimal weight: 2.9990 chunk 46 optimal weight: 2.9990 chunk 36 optimal weight: 7.9990 overall best weight: 2.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 422 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3895 r_free = 0.3895 target = 0.140755 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.107096 restraints weight = 56847.296| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.112333 restraints weight = 25911.360| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.111577 restraints weight = 14215.770| |-----------------------------------------------------------------------------| r_work (final): 0.3451 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3455 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3455 r_free = 0.3455 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 = 0.3455 r_free = 0.3455 target_work(ls_wunit_k1) = 0.109 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.3455 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7896 moved from start: 0.1638 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 11739 Z= 0.182 Angle : 0.621 7.303 16380 Z= 0.313 Chirality : 0.038 0.200 1901 Planarity : 0.005 0.050 1707 Dihedral : 19.184 100.377 2998 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 8.48 Ramachandran Plot: Outliers : 0.55 % Allowed : 6.82 % Favored : 92.64 % Rotamer: Outliers : 2.40 % Allowed : 28.24 % Favored : 69.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.50 (0.26), residues: 1107 helix: 1.02 (0.25), residues: 460 sheet: -0.48 (0.52), residues: 101 loop : -1.52 (0.26), residues: 546 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 111 HIS 0.003 0.001 HIS A 201 PHE 0.032 0.002 PHE A 185 TYR 0.016 0.001 TYR A 317 ARG 0.005 0.000 ARG A 713 Details of bonding type rmsd hydrogen bonds : bond 0.05262 ( 461) hydrogen bonds : angle 4.04680 ( 1235) covalent geometry : bond 0.00411 (11739) covalent geometry : angle 0.62091 (16380) *********************** 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 107 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 85 time to evaluate : 1.003 Fit side-chains REVERT: A 276 ARG cc_start: 0.7398 (tpt170) cc_final: 0.7089 (tpt170) outliers start: 22 outliers final: 14 residues processed: 99 average time/residue: 0.2273 time to fit residues: 32.9765 Evaluate side-chains 97 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 83 time to evaluate : 1.003 ------------------------------------------------------------------------------- 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 231 LEU Chi-restraints excluded: chain A residue 310 TYR Chi-restraints excluded: chain A residue 423 ILE 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 1052 VAL Chi-restraints excluded: chain D residue 10 THR Chi-restraints excluded: chain D residue 47 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 74 optimal weight: 2.9990 chunk 100 optimal weight: 3.9990 chunk 10 optimal weight: 0.9980 chunk 3 optimal weight: 2.9990 chunk 15 optimal weight: 10.0000 chunk 98 optimal weight: 8.9990 chunk 93 optimal weight: 5.9990 chunk 67 optimal weight: 4.9990 chunk 17 optimal weight: 3.9990 chunk 71 optimal weight: 0.7980 chunk 109 optimal weight: 7.9990 overall best weight: 2.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 822 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3897 r_free = 0.3897 target = 0.141053 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.107018 restraints weight = 45872.795| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.109156 restraints weight = 21834.777| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.111448 restraints weight = 12471.753| |-----------------------------------------------------------------------------| r_work (final): 0.3462 ------------------------------------------------------------------------------- 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 | |-----------------------------------------------------------------------------| r_final: 0.3464 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7872 moved from start: 0.1752 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 11739 Z= 0.166 Angle : 0.605 7.270 16380 Z= 0.304 Chirality : 0.038 0.208 1901 Planarity : 0.004 0.050 1707 Dihedral : 19.143 101.060 2998 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 8.62 Ramachandran Plot: Outliers : 0.55 % Allowed : 6.64 % Favored : 92.82 % Rotamer: Outliers : 2.18 % Allowed : 28.35 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.57 (0.25), residues: 1107 helix: 0.94 (0.25), residues: 467 sheet: -0.49 (0.52), residues: 101 loop : -1.58 (0.26), residues: 539 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 632 HIS 0.003 0.001 HIS A 354 PHE 0.029 0.002 PHE A 185 TYR 0.018 0.001 TYR A 317 ARG 0.004 0.000 ARG A 713 Details of bonding type rmsd hydrogen bonds : bond 0.04951 ( 461) hydrogen bonds : angle 3.99002 ( 1235) covalent geometry : bond 0.00377 (11739) covalent geometry : angle 0.60536 (16380) *********************** 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 110 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 90 time to evaluate : 1.089 Fit side-chains REVERT: A 276 ARG cc_start: 0.7365 (tpt170) cc_final: 0.7052 (tpt170) REVERT: A 501 ILE cc_start: 0.8533 (OUTLIER) cc_final: 0.8118 (mp) outliers start: 20 outliers final: 14 residues processed: 104 average time/residue: 0.2400 time to fit residues: 36.5921 Evaluate side-chains 101 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 86 time to evaluate : 1.050 ------------------------------------------------------------------------------- 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 231 LEU Chi-restraints excluded: chain A residue 300 THR Chi-restraints excluded: chain A residue 310 TYR Chi-restraints excluded: chain A residue 501 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 1052 VAL Chi-restraints excluded: chain D residue 10 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 98 optimal weight: 0.7980 chunk 104 optimal weight: 1.9990 chunk 37 optimal weight: 5.9990 chunk 0 optimal weight: 6.9990 chunk 84 optimal weight: 4.9990 chunk 9 optimal weight: 4.9990 chunk 99 optimal weight: 0.0670 chunk 45 optimal weight: 0.8980 chunk 88 optimal weight: 2.9990 chunk 70 optimal weight: 6.9990 chunk 58 optimal weight: 10.0000 overall best weight: 1.3522 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3919 r_free = 0.3919 target = 0.142686 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.108599 restraints weight = 55211.387| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.113278 restraints weight = 23912.680| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3486 r_free = 0.3486 target = 0.112936 restraints weight = 13715.353| |-----------------------------------------------------------------------------| r_work (final): 0.3476 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3477 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3477 r_free = 0.3477 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 = 0.3477 r_free = 0.3477 target_work(ls_wunit_k1) = 0.110 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.3477 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7846 moved from start: 0.1754 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 11739 Z= 0.124 Angle : 0.581 7.491 16380 Z= 0.291 Chirality : 0.036 0.201 1901 Planarity : 0.004 0.050 1707 Dihedral : 19.060 100.393 2998 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 7.92 Ramachandran Plot: Outliers : 0.55 % Allowed : 6.36 % Favored : 93.09 % Rotamer: Outliers : 2.18 % Allowed : 28.68 % Favored : 69.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.41 (0.26), residues: 1107 helix: 1.06 (0.25), residues: 468 sheet: -0.45 (0.52), residues: 101 loop : -1.47 (0.26), residues: 538 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 632 HIS 0.002 0.001 HIS A 354 PHE 0.024 0.001 PHE D 8 TYR 0.017 0.001 TYR A 317 ARG 0.003 0.000 ARG A 713 Details of bonding type rmsd hydrogen bonds : bond 0.04410 ( 461) hydrogen bonds : angle 3.84489 ( 1235) covalent geometry : bond 0.00279 (11739) covalent geometry : angle 0.58118 (16380) *********************** 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: 20 poor density : 89 time to evaluate : 1.108 Fit side-chains REVERT: A 276 ARG cc_start: 0.7338 (tpt170) cc_final: 0.7043 (tpt170) REVERT: A 402 ARG cc_start: 0.6714 (mtt-85) cc_final: 0.6204 (mtt90) REVERT: A 501 ILE cc_start: 0.8493 (OUTLIER) cc_final: 0.8146 (mp) outliers start: 20 outliers final: 14 residues processed: 104 average time/residue: 0.2277 time to fit residues: 35.6149 Evaluate side-chains 100 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 85 time to evaluate : 1.084 ------------------------------------------------------------------------------- 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 231 LEU Chi-restraints excluded: chain A residue 310 TYR Chi-restraints excluded: chain A residue 501 ILE 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 79 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 74 optimal weight: 6.9990 chunk 6 optimal weight: 0.7980 chunk 118 optimal weight: 10.0000 chunk 116 optimal weight: 10.0000 chunk 102 optimal weight: 5.9990 chunk 105 optimal weight: 3.9990 chunk 87 optimal weight: 0.9980 chunk 64 optimal weight: 0.7980 chunk 4 optimal weight: 9.9990 chunk 120 optimal weight: 8.9990 chunk 96 optimal weight: 7.9990 overall best weight: 2.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3891 r_free = 0.3891 target = 0.140593 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.106562 restraints weight = 60984.114| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.111461 restraints weight = 26516.693| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.111014 restraints weight = 14405.119| |-----------------------------------------------------------------------------| r_work (final): 0.3444 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3440 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3440 r_free = 0.3440 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 = 0.3440 r_free = 0.3440 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.3440 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7900 moved from start: 0.1952 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= 0.177 Angle : 0.619 8.659 16380 Z= 0.311 Chirality : 0.038 0.204 1901 Planarity : 0.004 0.050 1707 Dihedral : 19.082 100.220 2998 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 8.43 Ramachandran Plot: Outliers : 0.45 % Allowed : 7.64 % Favored : 91.91 % Rotamer: Outliers : 2.73 % Allowed : 28.03 % Favored : 69.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.57 (0.26), residues: 1107 helix: 0.95 (0.25), residues: 468 sheet: -0.62 (0.53), residues: 98 loop : -1.56 (0.26), residues: 541 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 632 HIS 0.003 0.001 HIS A 822 PHE 0.025 0.002 PHE D 8 TYR 0.019 0.002 TYR A 317 ARG 0.003 0.000 ARG A 713 Details of bonding type rmsd hydrogen bonds : bond 0.05088 ( 461) hydrogen bonds : angle 3.97366 ( 1235) covalent geometry : bond 0.00403 (11739) covalent geometry : angle 0.61855 (16380) *********************** 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 114 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 89 time to evaluate : 1.175 Fit side-chains REVERT: A 249 ASP cc_start: 0.7627 (m-30) cc_final: 0.7387 (m-30) REVERT: A 276 ARG cc_start: 0.7400 (tpt170) cc_final: 0.7067 (tpt170) REVERT: A 501 ILE cc_start: 0.8585 (OUTLIER) cc_final: 0.8158 (mp) outliers start: 25 outliers final: 20 residues processed: 106 average time/residue: 0.2265 time to fit residues: 35.2559 Evaluate side-chains 105 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 84 time to evaluate : 1.115 ------------------------------------------------------------------------------- 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 300 THR Chi-restraints excluded: chain A residue 310 TYR Chi-restraints excluded: chain A residue 501 ILE Chi-restraints excluded: chain A residue 558 LEU Chi-restraints excluded: chain A residue 573 ILE 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 948 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 79 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 105 optimal weight: 2.9990 chunk 102 optimal weight: 10.0000 chunk 116 optimal weight: 10.0000 chunk 12 optimal weight: 3.9990 chunk 2 optimal weight: 3.9990 chunk 70 optimal weight: 4.9990 chunk 91 optimal weight: 5.9990 chunk 69 optimal weight: 0.9980 chunk 45 optimal weight: 2.9990 chunk 67 optimal weight: 4.9990 chunk 32 optimal weight: 0.8980 overall best weight: 2.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3893 r_free = 0.3893 target = 0.140649 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.106853 restraints weight = 67101.708| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.111876 restraints weight = 27152.789| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.111397 restraints weight = 14309.952| |-----------------------------------------------------------------------------| r_work (final): 0.3449 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3449 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3449 r_free = 0.3449 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 = 0.3449 r_free = 0.3449 target_work(ls_wunit_k1) = 0.109 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.3449 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7890 moved from start: 0.2060 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 11739 Z= 0.169 Angle : 0.615 9.093 16380 Z= 0.308 Chirality : 0.038 0.203 1901 Planarity : 0.004 0.050 1707 Dihedral : 19.065 101.068 2998 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 8.43 Ramachandran Plot: Outliers : 0.45 % Allowed : 7.27 % Favored : 92.27 % Rotamer: Outliers : 2.73 % Allowed : 27.81 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.59 (0.25), residues: 1107 helix: 0.92 (0.25), residues: 467 sheet: -0.64 (0.53), residues: 98 loop : -1.56 (0.26), residues: 542 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 632 HIS 0.003 0.001 HIS A 822 PHE 0.027 0.002 PHE D 8 TYR 0.020 0.001 TYR A 317 ARG 0.003 0.000 ARG A 713 Details of bonding type rmsd hydrogen bonds : bond 0.04975 ( 461) hydrogen bonds : angle 3.97090 ( 1235) covalent geometry : bond 0.00383 (11739) covalent geometry : angle 0.61502 (16380) *********************** 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 112 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 87 time to evaluate : 1.103 Fit side-chains REVERT: A 249 ASP cc_start: 0.7629 (m-30) cc_final: 0.7405 (m-30) REVERT: A 276 ARG cc_start: 0.7396 (tpt170) cc_final: 0.7064 (tpt170) REVERT: A 501 ILE cc_start: 0.8589 (OUTLIER) cc_final: 0.8066 (mp) outliers start: 25 outliers final: 22 residues processed: 105 average time/residue: 0.2356 time to fit residues: 36.2925 Evaluate side-chains 108 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 85 time to evaluate : 1.025 ------------------------------------------------------------------------------- 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 300 THR Chi-restraints excluded: chain A residue 310 TYR Chi-restraints excluded: chain A residue 501 ILE Chi-restraints excluded: chain A residue 526 ASN Chi-restraints excluded: chain A residue 558 LEU Chi-restraints excluded: chain A residue 573 ILE 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 948 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 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 50 optimal weight: 0.3980 chunk 55 optimal weight: 9.9990 chunk 52 optimal weight: 1.9990 chunk 69 optimal weight: 7.9990 chunk 116 optimal weight: 10.0000 chunk 101 optimal weight: 0.8980 chunk 103 optimal weight: 8.9990 chunk 23 optimal weight: 0.6980 chunk 65 optimal weight: 3.9990 chunk 39 optimal weight: 4.9990 chunk 109 optimal weight: 4.9990 overall best weight: 1.5984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3913 r_free = 0.3913 target = 0.142172 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.108515 restraints weight = 61485.209| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.113372 restraints weight = 26074.403| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.113039 restraints weight = 13498.498| |-----------------------------------------------------------------------------| r_work (final): 0.3474 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3478 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3478 r_free = 0.3478 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 = 0.3478 r_free = 0.3478 target_work(ls_wunit_k1) = 0.111 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.3478 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7852 moved from start: 0.2002 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 11739 Z= 0.134 Angle : 0.591 10.224 16380 Z= 0.297 Chirality : 0.037 0.208 1901 Planarity : 0.004 0.050 1707 Dihedral : 19.013 100.625 2998 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 8.62 Ramachandran Plot: Outliers : 0.36 % Allowed : 6.91 % Favored : 92.73 % Rotamer: Outliers : 2.29 % Allowed : 27.92 % Favored : 69.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.41 (0.26), residues: 1107 helix: 1.06 (0.25), residues: 467 sheet: -0.49 (0.53), residues: 101 loop : -1.45 (0.26), residues: 539 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP A 632 HIS 0.002 0.001 HIS A 502 PHE 0.037 0.001 PHE A 185 TYR 0.018 0.001 TYR A 317 ARG 0.003 0.000 ARG A 713 Details of bonding type rmsd hydrogen bonds : bond 0.04478 ( 461) hydrogen bonds : angle 3.86785 ( 1235) covalent geometry : bond 0.00306 (11739) covalent geometry : angle 0.59149 (16380) *********************** 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 110 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 89 time to evaluate : 1.172 Fit side-chains REVERT: A 276 ARG cc_start: 0.7367 (tpt170) cc_final: 0.7081 (tpt170) REVERT: A 402 ARG cc_start: 0.6699 (mtt-85) cc_final: 0.6362 (mtt90) outliers start: 21 outliers final: 17 residues processed: 104 average time/residue: 0.2271 time to fit residues: 35.1616 Evaluate side-chains 101 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 84 time to evaluate : 1.088 ------------------------------------------------------------------------------- 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 185 PHE Chi-restraints excluded: chain A residue 231 LEU Chi-restraints excluded: chain A residue 300 THR Chi-restraints excluded: chain A residue 558 LEU Chi-restraints excluded: chain A residue 573 ILE 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 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 90 optimal weight: 2.9990 chunk 99 optimal weight: 0.9990 chunk 56 optimal weight: 9.9990 chunk 58 optimal weight: 9.9990 chunk 28 optimal weight: 6.9990 chunk 27 optimal weight: 0.3980 chunk 16 optimal weight: 6.9990 chunk 69 optimal weight: 5.9990 chunk 52 optimal weight: 9.9990 chunk 74 optimal weight: 10.0000 chunk 18 optimal weight: 0.9980 overall best weight: 2.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 34 ASN A 422 GLN ** A 655 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.141038 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.107203 restraints weight = 66261.450| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.111510 restraints weight = 27735.850| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.111333 restraints weight = 14309.518| |-----------------------------------------------------------------------------| r_work (final): 0.3449 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3447 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3447 r_free = 0.3447 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 = 0.3447 r_free = 0.3447 target_work(ls_wunit_k1) = 0.109 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.3447 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7888 moved from start: 0.2124 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 11739 Z= 0.166 Angle : 0.616 9.362 16380 Z= 0.308 Chirality : 0.038 0.203 1901 Planarity : 0.004 0.050 1707 Dihedral : 19.030 100.223 2998 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 8.52 Ramachandran Plot: Outliers : 0.36 % Allowed : 7.64 % Favored : 92.00 % Rotamer: Outliers : 2.18 % Allowed : 28.24 % Favored : 69.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.52 (0.26), residues: 1107 helix: 0.99 (0.25), residues: 467 sheet: -0.59 (0.53), residues: 98 loop : -1.53 (0.26), residues: 542 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP A 632 HIS 0.003 0.001 HIS A 822 PHE 0.029 0.002 PHE A 185 TYR 0.019 0.001 TYR A 317 ARG 0.003 0.000 ARG A 713 Details of bonding type rmsd hydrogen bonds : bond 0.04885 ( 461) hydrogen bonds : angle 3.91711 ( 1235) covalent geometry : bond 0.00378 (11739) covalent geometry : angle 0.61615 (16380) ********************** 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 103 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 83 time to evaluate : 1.123 Fit side-chains REVERT: A 249 ASP cc_start: 0.7676 (m-30) cc_final: 0.7448 (m-30) REVERT: A 276 ARG cc_start: 0.7387 (tpt170) cc_final: 0.7075 (tpt170) outliers start: 20 outliers final: 18 residues processed: 96 average time/residue: 0.2180 time to fit residues: 31.6273 Evaluate side-chains 101 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 83 time to evaluate : 1.121 ------------------------------------------------------------------------------- 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 300 THR Chi-restraints excluded: chain A residue 526 ASN Chi-restraints excluded: chain A residue 558 LEU Chi-restraints excluded: chain A residue 573 ILE 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 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 105 optimal weight: 2.9990 chunk 73 optimal weight: 2.9990 chunk 61 optimal weight: 5.9990 chunk 50 optimal weight: 0.9990 chunk 0 optimal weight: 7.9990 chunk 42 optimal weight: 0.0060 chunk 1 optimal weight: 0.9980 chunk 28 optimal weight: 8.9990 chunk 95 optimal weight: 4.9990 chunk 11 optimal weight: 5.9990 chunk 49 optimal weight: 6.9990 overall best weight: 1.6002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 655 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3913 r_free = 0.3913 target = 0.142227 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.108454 restraints weight = 44045.624| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.110684 restraints weight = 20832.795| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.113664 restraints weight = 12101.325| |-----------------------------------------------------------------------------| r_work (final): 0.3490 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3490 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3490 r_free = 0.3490 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 = 0.3490 r_free = 0.3490 target_work(ls_wunit_k1) = 0.111 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.3490 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7833 moved from start: 0.2067 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 11739 Z= 0.136 Angle : 0.594 11.046 16380 Z= 0.297 Chirality : 0.037 0.207 1901 Planarity : 0.004 0.051 1707 Dihedral : 19.011 100.562 2998 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 8.43 Ramachandran Plot: Outliers : 0.36 % Allowed : 7.00 % Favored : 92.64 % Rotamer: Outliers : 1.96 % Allowed : 28.24 % Favored : 69.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.37 (0.26), residues: 1107 helix: 1.09 (0.25), residues: 467 sheet: -0.47 (0.53), residues: 101 loop : -1.43 (0.26), residues: 539 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP A 632 HIS 0.002 0.001 HIS A 822 PHE 0.025 0.001 PHE A 185 TYR 0.018 0.001 TYR A 317 ARG 0.003 0.000 ARG A 713 Details of bonding type rmsd hydrogen bonds : bond 0.04495 ( 461) hydrogen bonds : angle 3.84323 ( 1235) covalent geometry : bond 0.00311 (11739) covalent geometry : angle 0.59399 (16380) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3878.59 seconds wall clock time: 67 minutes 52.18 seconds (4072.18 seconds total)