Starting phenix.real_space_refine on Sat Aug 23 16:06:05 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ja0_36123/08_2025/8ja0_36123.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ja0_36123/08_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_36123/08_2025/8ja0_36123.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ja0_36123/08_2025/8ja0_36123.map" model { file = "/net/cci-nas-00/data/ceres_data/8ja0_36123/08_2025/8ja0_36123.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ja0_36123/08_2025/8ja0_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-2.0-5787/lib/python3.9/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: 4.65, per 1000 atoms: 0.41 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: 0.97 Conformation dependent library (CDL) restraints added in 794.6 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 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: 1.50 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: 2.51 Time building geometry restraints manager: 1.32 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: 1.680 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: 0.250 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 15.910 Find NCS groups from input model: 0.060 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.270 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.310 ------------------------------------------------------------------------------- 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren 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 covalent geometry : bond 0.00225 (11739) covalent geometry : angle 0.57155 (16380) hydrogen bonds : bond 0.14472 ( 461) hydrogen bonds : angle 4.98538 ( 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 : 0.441 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 104 average time/residue: 0.1125 time to fit residues: 17.0460 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 : 0.388 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: A 611 ASN A 944 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3897 r_free = 0.3897 target = 0.140727 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.110382 restraints weight = 47290.913| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.113816 restraints weight = 28833.019| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3509 r_free = 0.3509 target = 0.113841 restraints weight = 15888.559| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3516 r_free = 0.3516 target = 0.114380 restraints weight = 11426.722| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.115626 restraints weight = 10219.200| |-----------------------------------------------------------------------------| r_work (final): 0.3535 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3531 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3531 r_free = 0.3531 target_work(ls_wunit_k1) = 0.114 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3531 r_free = 0.3531 target_work(ls_wunit_k1) = 0.114 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.3531 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7893 moved from start: 0.1669 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.068 11739 Z= 0.307 Angle : 0.745 7.654 16380 Z= 0.378 Chirality : 0.044 0.214 1901 Planarity : 0.006 0.051 1707 Dihedral : 19.505 111.925 2998 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 9.46 Ramachandran Plot: Outliers : 0.73 % Allowed : 7.27 % Favored : 92.00 % Rotamer: Outliers : 2.40 % Allowed : 28.57 % 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 aren not related in a simple way. whole: -0.99 (0.25), residues: 1107 helix: 0.50 (0.24), residues: 466 sheet: -0.60 (0.54), residues: 102 loop : -1.73 (0.26), residues: 539 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 646 TYR 0.022 0.002 TYR A 317 PHE 0.044 0.002 PHE A 185 TRP 0.011 0.002 TRP A 111 HIS 0.005 0.002 HIS D 27 Details of bonding type rmsd covalent geometry : bond 0.00692 (11739) covalent geometry : angle 0.74546 (16380) hydrogen bonds : bond 0.06653 ( 461) hydrogen bonds : angle 4.51692 ( 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 109 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 87 time to evaluate : 0.406 Fit side-chains REVERT: A 246 LEU cc_start: 0.8097 (OUTLIER) cc_final: 0.7756 (mt) outliers start: 22 outliers final: 11 residues processed: 99 average time/residue: 0.1052 time to fit residues: 15.4856 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 : 0.421 ------------------------------------------------------------------------------- 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 300 THR Chi-restraints excluded: chain A residue 423 ILE Chi-restraints excluded: chain A residue 505 THR Chi-restraints excluded: chain A residue 526 ASN Chi-restraints excluded: chain A residue 812 GLU 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 Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 46 optimal weight: 6.9990 chunk 86 optimal weight: 0.7980 chunk 25 optimal weight: 4.9990 chunk 101 optimal weight: 2.9990 chunk 113 optimal weight: 10.0000 chunk 4 optimal weight: 7.9990 chunk 41 optimal weight: 1.9990 chunk 65 optimal weight: 3.9990 chunk 106 optimal weight: 5.9990 chunk 88 optimal weight: 0.8980 chunk 119 optimal weight: 20.0000 overall best weight: 2.1386 ------------------------------------------------------------------------------- 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 = 0.3932 r_free = 0.3932 target = 0.143629 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.112272 restraints weight = 56949.474| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.115183 restraints weight = 28614.207| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.115713 restraints weight = 16841.427| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.115913 restraints weight = 11686.736| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3528 r_free = 0.3528 target = 0.116286 restraints weight = 10862.310| |-----------------------------------------------------------------------------| r_work (final): 0.3529 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3527 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3527 r_free = 0.3527 target_work(ls_wunit_k1) = 0.114 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3527 r_free = 0.3527 target_work(ls_wunit_k1) = 0.114 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.3527 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7889 moved from start: 0.1581 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= 0.158 Angle : 0.617 7.472 16380 Z= 0.310 Chirality : 0.038 0.204 1901 Planarity : 0.004 0.049 1707 Dihedral : 19.284 101.630 2998 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 8.95 Ramachandran Plot: Outliers : 0.55 % Allowed : 6.55 % Favored : 92.91 % Rotamer: Outliers : 2.51 % Allowed : 28.24 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.78 (0.25), residues: 1107 helix: 0.75 (0.25), residues: 465 sheet: -0.60 (0.53), residues: 102 loop : -1.68 (0.26), residues: 540 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 646 TYR 0.017 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 A1002 Details of bonding type rmsd covalent geometry : bond 0.00357 (11739) covalent geometry : angle 0.61690 (16380) hydrogen bonds : bond 0.05052 ( 461) hydrogen bonds : angle 4.13196 ( 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 110 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 87 time to evaluate : 0.429 Fit side-chains REVERT: A 246 LEU cc_start: 0.7992 (OUTLIER) cc_final: 0.7750 (mt) REVERT: A 501 ILE cc_start: 0.8628 (OUTLIER) cc_final: 0.8194 (mp) outliers start: 23 outliers final: 12 residues processed: 103 average time/residue: 0.0948 time to fit residues: 14.4064 Evaluate side-chains 95 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 81 time to evaluate : 0.297 ------------------------------------------------------------------------------- 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 948 VAL Chi-restraints excluded: chain A residue 969 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 Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 15 optimal weight: 0.8980 chunk 88 optimal weight: 3.9990 chunk 13 optimal weight: 10.0000 chunk 5 optimal weight: 0.0470 chunk 90 optimal weight: 0.8980 chunk 92 optimal weight: 3.9990 chunk 51 optimal weight: 5.9990 chunk 114 optimal weight: 7.9990 chunk 120 optimal weight: 10.0000 chunk 103 optimal weight: 0.0970 chunk 64 optimal weight: 4.9990 overall best weight: 1.1878 ------------------------------------------------------------------------------- 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 = 0.142744 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.109750 restraints weight = 59429.971| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.114223 restraints weight = 25415.160| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.113834 restraints weight = 14338.301| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.114277 restraints weight = 9948.818| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.114666 restraints weight = 9042.522| |-----------------------------------------------------------------------------| r_work (final): 0.3493 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3489 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3489 r_free = 0.3489 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 = 0.3489 r_free = 0.3489 target_work(ls_wunit_k1) = 0.111 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.3489 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7833 moved from start: 0.1560 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= 0.122 Angle : 0.586 7.244 16380 Z= 0.294 Chirality : 0.037 0.194 1901 Planarity : 0.004 0.050 1707 Dihedral : 19.183 100.304 2998 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 8.15 Ramachandran Plot: Outliers : 0.55 % Allowed : 6.36 % Favored : 93.09 % Rotamer: Outliers : 2.94 % Allowed : 27.48 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.58 (0.26), residues: 1107 helix: 0.94 (0.25), residues: 465 sheet: -0.53 (0.52), residues: 101 loop : -1.57 (0.26), residues: 541 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 713 TYR 0.016 0.001 TYR A 317 PHE 0.023 0.001 PHE A 185 TRP 0.009 0.001 TRP A 632 HIS 0.003 0.001 HIS A 257 Details of bonding type rmsd covalent geometry : bond 0.00271 (11739) covalent geometry : angle 0.58557 (16380) hydrogen bonds : bond 0.04461 ( 461) hydrogen bonds : angle 3.94280 ( 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 114 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 87 time to evaluate : 0.428 Fit side-chains REVERT: A 246 LEU cc_start: 0.8018 (OUTLIER) cc_final: 0.7803 (mt) REVERT: A 501 ILE cc_start: 0.8511 (OUTLIER) cc_final: 0.8112 (mp) REVERT: A 620 TYR cc_start: 0.8050 (t80) cc_final: 0.7535 (t80) outliers start: 27 outliers final: 16 residues processed: 106 average time/residue: 0.1125 time to fit residues: 17.3601 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 : 0.413 ------------------------------------------------------------------------------- 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 246 LEU Chi-restraints excluded: chain A residue 300 THR Chi-restraints excluded: chain A residue 310 TYR 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 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 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: 4.9990 chunk 25 optimal weight: 3.9990 chunk 15 optimal weight: 4.9990 chunk 66 optimal weight: 8.9990 chunk 59 optimal weight: 5.9990 chunk 46 optimal weight: 3.9990 chunk 86 optimal weight: 2.9990 chunk 105 optimal weight: 2.9990 chunk 99 optimal weight: 0.6980 chunk 60 optimal weight: 0.9980 chunk 69 optimal weight: 0.8980 overall best weight: 1.7184 ------------------------------------------------------------------------------- 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 = 0.3911 r_free = 0.3911 target = 0.142060 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.108748 restraints weight = 46093.957| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.110286 restraints weight = 23658.026| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.111609 restraints weight = 14010.613| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.112198 restraints weight = 10145.880| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.113015 restraints weight = 9316.390| |-----------------------------------------------------------------------------| r_work (final): 0.3477 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3480 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3480 r_free = 0.3480 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 = 0.3480 r_free = 0.3480 target_work(ls_wunit_k1) = 0.111 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.3480 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7853 moved from start: 0.1727 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 11739 Z= 0.139 Angle : 0.583 7.293 16380 Z= 0.292 Chirality : 0.037 0.196 1901 Planarity : 0.004 0.051 1707 Dihedral : 19.121 99.662 2998 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 7.82 Ramachandran Plot: Outliers : 0.55 % Allowed : 6.91 % Favored : 92.55 % Rotamer: Outliers : 2.62 % Allowed : 28.35 % 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 aren not related in a simple way. whole: -0.55 (0.26), residues: 1107 helix: 0.97 (0.25), residues: 468 sheet: -0.53 (0.52), residues: 101 loop : -1.59 (0.26), residues: 538 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 0.022 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 covalent geometry : bond 0.00316 (11739) covalent geometry : angle 0.58349 (16380) hydrogen bonds : bond 0.04651 ( 461) hydrogen bonds : angle 3.90496 ( 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 108 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 84 time to evaluate : 0.421 Fit side-chains REVERT: A 246 LEU cc_start: 0.8069 (OUTLIER) cc_final: 0.7793 (mt) REVERT: A 249 ASP cc_start: 0.7675 (m-30) cc_final: 0.7453 (m-30) REVERT: A 402 ARG cc_start: 0.6713 (mtt-85) cc_final: 0.6224 (mtt90) REVERT: A 501 ILE cc_start: 0.8534 (OUTLIER) cc_final: 0.8136 (mp) REVERT: A 620 TYR cc_start: 0.8044 (t80) cc_final: 0.7653 (t80) outliers start: 24 outliers final: 18 residues processed: 102 average time/residue: 0.1058 time to fit residues: 16.0059 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 : 0.409 ------------------------------------------------------------------------------- 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 246 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 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 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 66 optimal weight: 7.9990 chunk 83 optimal weight: 10.0000 chunk 19 optimal weight: 2.9990 chunk 39 optimal weight: 0.7980 chunk 84 optimal weight: 0.2980 chunk 21 optimal weight: 3.9990 chunk 106 optimal weight: 6.9990 chunk 82 optimal weight: 2.9990 chunk 74 optimal weight: 8.9990 chunk 49 optimal weight: 6.9990 chunk 65 optimal weight: 0.0670 overall best weight: 1.4322 ------------------------------------------------------------------------------- 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 = 0.3922 r_free = 0.3922 target = 0.142915 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.110416 restraints weight = 76248.005| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3528 r_free = 0.3528 target = 0.116220 restraints weight = 32514.405| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3506 r_free = 0.3506 target = 0.115014 restraints weight = 15071.525| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3509 r_free = 0.3509 target = 0.115322 restraints weight = 10256.694| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3513 r_free = 0.3513 target = 0.115557 restraints weight = 9273.251| |-----------------------------------------------------------------------------| r_work (final): 0.3495 ------------------------------------------------------------------------------- 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 | |-----------------------------------------------------------------------------| r_final: 0.3499 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7817 moved from start: 0.1784 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 : 0.572 8.694 16380 Z= 0.285 Chirality : 0.036 0.200 1901 Planarity : 0.004 0.051 1707 Dihedral : 19.033 99.373 2998 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 7.96 Ramachandran Plot: Outliers : 0.55 % Allowed : 6.45 % Favored : 93.00 % Rotamer: Outliers : 2.51 % Allowed : 28.24 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.45 (0.26), residues: 1107 helix: 1.05 (0.25), residues: 469 sheet: -0.46 (0.52), residues: 101 loop : -1.53 (0.26), residues: 537 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 713 TYR 0.017 0.001 TYR A 317 PHE 0.025 0.001 PHE D 8 TRP 0.010 0.001 TRP A 632 HIS 0.003 0.001 HIS A1002 Details of bonding type rmsd covalent geometry : bond 0.00279 (11739) covalent geometry : angle 0.57185 (16380) hydrogen bonds : bond 0.04337 ( 461) hydrogen bonds : angle 3.83042 ( 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 114 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 91 time to evaluate : 0.410 Fit side-chains REVERT: A 246 LEU cc_start: 0.7992 (OUTLIER) cc_final: 0.7757 (mt) REVERT: A 249 ASP cc_start: 0.7600 (m-30) cc_final: 0.7387 (m-30) REVERT: A 501 ILE cc_start: 0.8544 (OUTLIER) cc_final: 0.8210 (mt) REVERT: A 620 TYR cc_start: 0.8055 (t80) cc_final: 0.7749 (t80) outliers start: 23 outliers final: 18 residues processed: 108 average time/residue: 0.1156 time to fit residues: 18.1884 Evaluate side-chains 104 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 84 time to evaluate : 0.412 ------------------------------------------------------------------------------- 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 246 LEU 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 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: 7.9990 chunk 59 optimal weight: 10.0000 chunk 89 optimal weight: 5.9990 chunk 49 optimal weight: 7.9990 chunk 4 optimal weight: 9.9990 chunk 18 optimal weight: 4.9990 chunk 99 optimal weight: 1.9990 chunk 12 optimal weight: 5.9990 chunk 3 optimal weight: 2.9990 chunk 41 optimal weight: 3.9990 chunk 68 optimal weight: 0.9980 overall best weight: 2.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 601 ASN A 611 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3884 r_free = 0.3884 target = 0.139935 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.106022 restraints weight = 61666.607| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.111479 restraints weight = 27009.085| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.110784 restraints weight = 14067.772| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.111220 restraints weight = 10081.406| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.112453 restraints weight = 9196.629| |-----------------------------------------------------------------------------| r_work (final): 0.3468 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3459 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3459 r_free = 0.3459 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 = 0.3459 r_free = 0.3459 target_work(ls_wunit_k1) = 0.109 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.3459 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7884 moved from start: 0.2047 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 11739 Z= 0.201 Angle : 0.635 7.832 16380 Z= 0.319 Chirality : 0.039 0.197 1901 Planarity : 0.005 0.050 1707 Dihedral : 19.093 100.562 2998 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 9.04 Ramachandran Plot: Outliers : 0.45 % Allowed : 7.64 % Favored : 91.91 % Rotamer: Outliers : 2.40 % Allowed : 28.68 % 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 aren not related in a simple way. whole: -0.69 (0.25), residues: 1107 helix: 0.87 (0.25), residues: 468 sheet: -0.64 (0.52), residues: 98 loop : -1.66 (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 0.026 0.002 PHE D 8 TRP 0.018 0.002 TRP A 632 HIS 0.003 0.001 HIS A 822 Details of bonding type rmsd covalent geometry : bond 0.00459 (11739) covalent geometry : angle 0.63485 (16380) hydrogen bonds : bond 0.05323 ( 461) hydrogen bonds : angle 4.03431 ( 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 108 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 86 time to evaluate : 0.421 Fit side-chains REVERT: A 86 LEU cc_start: 0.7003 (OUTLIER) cc_final: 0.6556 (tp) REVERT: A 246 LEU cc_start: 0.8075 (OUTLIER) cc_final: 0.7792 (mt) REVERT: A 620 TYR cc_start: 0.8167 (t80) cc_final: 0.7811 (t80) outliers start: 22 outliers final: 18 residues processed: 101 average time/residue: 0.1169 time to fit residues: 17.2530 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 : 0.309 ------------------------------------------------------------------------------- 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 231 LEU Chi-restraints excluded: chain A residue 246 LEU Chi-restraints excluded: chain A residue 300 THR Chi-restraints excluded: chain A residue 423 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 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 93 optimal weight: 1.9990 chunk 61 optimal weight: 7.9990 chunk 65 optimal weight: 0.9980 chunk 37 optimal weight: 5.9990 chunk 7 optimal weight: 6.9990 chunk 30 optimal weight: 20.0000 chunk 54 optimal weight: 9.9990 chunk 83 optimal weight: 0.9980 chunk 15 optimal weight: 4.9990 chunk 90 optimal weight: 0.9990 chunk 69 optimal weight: 0.9990 overall best weight: 1.1986 ------------------------------------------------------------------------------- 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 = 0.3923 r_free = 0.3923 target = 0.143021 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.109190 restraints weight = 59296.139| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.111030 restraints weight = 24820.601| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3506 r_free = 0.3506 target = 0.114397 restraints weight = 13589.708| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.114394 restraints weight = 9374.466| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.114685 restraints weight = 9113.435| |-----------------------------------------------------------------------------| r_work (final): 0.3499 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3504 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3504 r_free = 0.3504 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 = 0.3504 r_free = 0.3504 target_work(ls_wunit_k1) = 0.112 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.3504 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7823 moved from start: 0.1943 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= 0.120 Angle : 0.578 9.588 16380 Z= 0.289 Chirality : 0.036 0.205 1901 Planarity : 0.004 0.051 1707 Dihedral : 18.989 100.221 2998 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 8.01 Ramachandran Plot: Outliers : 0.45 % Allowed : 6.45 % Favored : 93.09 % Rotamer: Outliers : 2.07 % Allowed : 28.90 % 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 aren not related in a simple way. whole: -0.45 (0.26), residues: 1107 helix: 1.04 (0.25), residues: 469 sheet: -0.45 (0.53), residues: 98 loop : -1.52 (0.26), residues: 540 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 713 TYR 0.017 0.001 TYR A 317 PHE 0.029 0.001 PHE D 8 TRP 0.019 0.001 TRP A 632 HIS 0.002 0.001 HIS A1002 Details of bonding type rmsd covalent geometry : bond 0.00270 (11739) covalent geometry : angle 0.57802 (16380) hydrogen bonds : bond 0.04314 ( 461) hydrogen bonds : angle 3.83700 ( 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 106 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 87 time to evaluate : 0.255 Fit side-chains REVERT: A 246 LEU cc_start: 0.8069 (OUTLIER) cc_final: 0.7813 (mt) REVERT: A 402 ARG cc_start: 0.6707 (mtt-85) cc_final: 0.6377 (mtt90) REVERT: A 620 TYR cc_start: 0.8123 (t80) cc_final: 0.7832 (t80) REVERT: A 819 GLU cc_start: 0.7452 (OUTLIER) cc_final: 0.7022 (mp0) outliers start: 19 outliers final: 16 residues processed: 103 average time/residue: 0.1027 time to fit residues: 15.6230 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 : 0.390 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 246 LEU Chi-restraints excluded: chain A residue 310 TYR Chi-restraints excluded: chain A residue 423 ILE Chi-restraints excluded: chain A residue 558 LEU Chi-restraints excluded: chain A residue 660 ASP 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 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 Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 99 optimal weight: 0.9990 chunk 102 optimal weight: 8.9990 chunk 1 optimal weight: 7.9990 chunk 5 optimal weight: 0.3980 chunk 87 optimal weight: 0.0980 chunk 103 optimal weight: 1.9990 chunk 8 optimal weight: 0.8980 chunk 2 optimal weight: 3.9990 chunk 33 optimal weight: 0.9990 chunk 15 optimal weight: 7.9990 chunk 57 optimal weight: 3.9990 overall best weight: 0.6784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 562 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3956 r_free = 0.3956 target = 0.145486 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.112235 restraints weight = 50253.450| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3550 r_free = 0.3550 target = 0.116839 restraints weight = 22575.427| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3535 r_free = 0.3535 target = 0.116252 restraints weight = 13875.266| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3541 r_free = 0.3541 target = 0.116795 restraints weight = 9646.032| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.117200 restraints weight = 8822.705| |-----------------------------------------------------------------------------| r_work (final): 0.3536 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3541 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3541 r_free = 0.3541 target_work(ls_wunit_k1) = 0.115 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3541 r_free = 0.3541 target_work(ls_wunit_k1) = 0.115 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.3541 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7764 moved from start: 0.1944 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 11739 Z= 0.103 Angle : 0.555 9.272 16380 Z= 0.277 Chirality : 0.035 0.193 1901 Planarity : 0.004 0.051 1707 Dihedral : 18.919 97.593 2998 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 7.64 Ramachandran Plot: Outliers : 0.36 % Allowed : 6.36 % Favored : 93.27 % Rotamer: Outliers : 1.53 % Allowed : 29.88 % 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 aren not related in a simple way. whole: -0.18 (0.26), residues: 1107 helix: 1.25 (0.25), residues: 469 sheet: -0.33 (0.52), residues: 106 loop : -1.37 (0.27), residues: 532 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 713 TYR 0.015 0.001 TYR A 317 PHE 0.038 0.001 PHE A 185 TRP 0.019 0.002 TRP A 632 HIS 0.002 0.000 HIS A1002 Details of bonding type rmsd covalent geometry : bond 0.00228 (11739) covalent geometry : angle 0.55530 (16380) hydrogen bonds : bond 0.03799 ( 461) hydrogen bonds : angle 3.68920 ( 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 110 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 96 time to evaluate : 0.411 Fit side-chains REVERT: A 621 GLU cc_start: 0.8203 (mt-10) cc_final: 0.7927 (mt-10) outliers start: 14 outliers final: 11 residues processed: 109 average time/residue: 0.1106 time to fit residues: 17.6755 Evaluate side-chains 100 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 89 time to evaluate : 0.380 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 558 LEU Chi-restraints excluded: chain A residue 673 VAL Chi-restraints excluded: chain A residue 948 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 37 optimal weight: 0.3980 chunk 69 optimal weight: 2.9990 chunk 52 optimal weight: 0.2980 chunk 26 optimal weight: 20.0000 chunk 0 optimal weight: 8.9990 chunk 105 optimal weight: 3.9990 chunk 7 optimal weight: 5.9990 chunk 72 optimal weight: 0.9980 chunk 50 optimal weight: 0.0770 chunk 56 optimal weight: 5.9990 chunk 51 optimal weight: 0.9990 overall best weight: 0.5540 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 34 ASN A 655 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3968 r_free = 0.3968 target = 0.146320 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.113949 restraints weight = 64380.630| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.118381 restraints weight = 28468.121| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3552 r_free = 0.3552 target = 0.118235 restraints weight = 13942.474| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.118700 restraints weight = 10171.068| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3564 r_free = 0.3564 target = 0.119104 restraints weight = 9310.263| |-----------------------------------------------------------------------------| r_work (final): 0.3548 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3548 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3548 r_free = 0.3548 target_work(ls_wunit_k1) = 0.115 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3548 r_free = 0.3548 target_work(ls_wunit_k1) = 0.115 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.3548 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7745 moved from start: 0.2066 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 11739 Z= 0.100 Angle : 0.550 10.761 16380 Z= 0.273 Chirality : 0.035 0.188 1901 Planarity : 0.004 0.052 1707 Dihedral : 18.879 95.378 2998 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 7.26 Ramachandran Plot: Outliers : 0.36 % Allowed : 5.91 % Favored : 93.73 % Rotamer: Outliers : 1.31 % Allowed : 30.75 % Favored : 67.94 % 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 aren not related in a simple way. whole: -0.18 (0.26), residues: 1107 helix: 1.22 (0.25), residues: 480 sheet: -0.23 (0.52), residues: 106 loop : -1.40 (0.27), residues: 521 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 276 TYR 0.017 0.001 TYR A 140 PHE 0.020 0.001 PHE D 8 TRP 0.015 0.001 TRP A 632 HIS 0.002 0.000 HIS A 201 Details of bonding type rmsd covalent geometry : bond 0.00222 (11739) covalent geometry : angle 0.54991 (16380) hydrogen bonds : bond 0.03683 ( 461) hydrogen bonds : angle 3.62205 ( 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 106 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 94 time to evaluate : 0.424 Fit side-chains REVERT: A 246 LEU cc_start: 0.7969 (OUTLIER) cc_final: 0.7757 (mt) REVERT: A 621 GLU cc_start: 0.8185 (mt-10) cc_final: 0.7921 (mt-10) outliers start: 12 outliers final: 11 residues processed: 105 average time/residue: 0.1029 time to fit residues: 16.2059 Evaluate side-chains 102 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 90 time to evaluate : 0.402 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 231 LEU Chi-restraints excluded: chain A residue 246 LEU 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 673 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 112 optimal weight: 10.0000 chunk 33 optimal weight: 6.9990 chunk 44 optimal weight: 0.5980 chunk 10 optimal weight: 0.0970 chunk 28 optimal weight: 5.9990 chunk 31 optimal weight: 4.9990 chunk 64 optimal weight: 1.9990 chunk 12 optimal weight: 0.9980 chunk 76 optimal weight: 0.7980 chunk 80 optimal weight: 0.1980 chunk 81 optimal weight: 4.9990 overall best weight: 0.5378 ------------------------------------------------------------------------------- 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 = 0.3973 r_free = 0.3973 target = 0.146781 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.113975 restraints weight = 62590.333| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.118093 restraints weight = 27399.145| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3556 r_free = 0.3556 target = 0.118175 restraints weight = 14140.179| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.118937 restraints weight = 10428.524| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3573 r_free = 0.3573 target = 0.119554 restraints weight = 9382.238| |-----------------------------------------------------------------------------| r_work (final): 0.3556 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3556 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3556 r_free = 0.3556 target_work(ls_wunit_k1) = 0.116 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3556 r_free = 0.3556 target_work(ls_wunit_k1) = 0.116 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.3556 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7728 moved from start: 0.2128 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 11739 Z= 0.100 Angle : 0.551 11.194 16380 Z= 0.272 Chirality : 0.035 0.182 1901 Planarity : 0.004 0.051 1707 Dihedral : 18.848 94.200 2998 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 6.98 Ramachandran Plot: Outliers : 0.45 % Allowed : 6.09 % Favored : 93.45 % Rotamer: Outliers : 1.64 % Allowed : 30.43 % Favored : 67.94 % 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 aren not related in a simple way. whole: -0.14 (0.26), residues: 1107 helix: 1.27 (0.25), residues: 478 sheet: -0.21 (0.52), residues: 106 loop : -1.39 (0.27), residues: 523 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 713 TYR 0.012 0.001 TYR A 140 PHE 0.018 0.001 PHE D 8 TRP 0.013 0.001 TRP A 632 HIS 0.002 0.000 HIS A 191 Details of bonding type rmsd covalent geometry : bond 0.00222 (11739) covalent geometry : angle 0.55101 (16380) hydrogen bonds : bond 0.03597 ( 461) hydrogen bonds : angle 3.58140 ( 1235) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2038.21 seconds wall clock time: 35 minutes 54.14 seconds (2154.14 seconds total)