Starting phenix.real_space_refine on Mon Apr 8 12:17:21 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ja0_36123/04_2024/8ja0_36123.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ja0_36123/04_2024/8ja0_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ja0_36123/04_2024/8ja0_36123.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ja0_36123/04_2024/8ja0_36123.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ja0_36123/04_2024/8ja0_36123.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ja0_36123/04_2024/8ja0_36123.pdb" } 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 Residue "A GLU 580": "OE1" <-> "OE2" Residue "A GLU 926": "OE1" <-> "OE2" Residue "D PHE 8": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 57": "OE1" <-> "OE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/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: 10.23, per 1000 atoms: 0.91 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 - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 5.43 Conformation dependent library (CDL) restraints added in 3.4 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: 4.21 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: 5.36 Time building geometry restraints manager: 5.60 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: 100.44 - 107.20: 890 107.20 - 113.95: 6710 113.95 - 120.71: 4828 120.71 - 127.47: 3682 127.47 - 134.22: 270 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 2.440 nonbonded pdb=" O GLN A 919 " pdb=" O2' U B 56 " model vdw 2.194 2.440 nonbonded pdb=" NZ LYS A 390 " pdb=" O PHE A 417 " model vdw 2.210 2.520 nonbonded pdb=" OE2 GLU A 261 " pdb=" OH TYR A 449 " model vdw 2.222 2.440 nonbonded pdb=" O2' A B 17 " pdb=" O4 U B 132 " model vdw 2.245 2.440 ... (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 ========== 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: 3.140 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.080 Construct map_model_manager: 0.020 Extract box with map and model: 8.130 Check model and map are aligned: 0.000 Set scattering table: 0.370 Process input model: 43.370 Find NCS groups from input model: 0.280 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.730 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 58.170 ------------------------------------------------------------------------------- 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= 0.148 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 *********************** 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 fitting. rotamer outliers: 0 poor density : 104 time to evaluate : 1.210 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 104 average time/residue: 0.2524 time to fit residues: 38.0684 Evaluate side-chains 91 residues out of total 960 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 91 time to evaluate : 1.174 ------------------------------------------------------------------------------- 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: 10.0000 chunk 91 optimal weight: 0.5980 chunk 50 optimal weight: 5.9990 chunk 31 optimal weight: 10.0000 chunk 61 optimal weight: 5.9990 chunk 48 optimal weight: 8.9990 chunk 94 optimal weight: 0.8980 chunk 36 optimal weight: 6.9990 chunk 57 optimal weight: 4.9990 chunk 70 optimal weight: 9.9990 chunk 109 optimal weight: 9.9990 overall best weight: 3.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 611 ASN ** A 674 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7932 moved from start: 0.1625 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= 0.348 Angle : 0.691 7.612 16380 Z= 0.348 Chirality : 0.041 0.224 1901 Planarity : 0.005 0.048 1707 Dihedral : 19.472 109.215 2998 Min Nonbonded Distance : 2.132 Molprobity Statistics. All-atom Clashscore : 11.43 Ramachandran Plot: Outliers : 0.73 % Allowed : 7.27 % Favored : 92.00 % Rotamer: Outliers : 2.94 % Allowed : 27.81 % 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: -0.88 (0.25), residues: 1107 helix: 0.63 (0.25), residues: 461 sheet: -0.51 (0.54), residues: 102 loop : -1.71 (0.26), residues: 544 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP A 632 HIS 0.005 0.001 HIS D 27 PHE 0.042 0.002 PHE A 185 TYR 0.020 0.002 TYR A 317 ARG 0.008 0.001 ARG A 646 *********************** 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 116 residues out of total 960 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 89 time to evaluate : 1.217 Fit side-chains REVERT: A 246 LEU cc_start: 0.7869 (OUTLIER) cc_final: 0.7649 (mt) outliers start: 27 outliers final: 16 residues processed: 107 average time/residue: 0.2307 time to fit residues: 36.5484 Evaluate side-chains 94 residues out of total 960 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 77 time to evaluate : 1.168 ------------------------------------------------------------------------------- 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 246 LEU Chi-restraints excluded: chain A residue 249 ASP Chi-restraints excluded: chain A residue 300 THR Chi-restraints excluded: chain A residue 418 ASP 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 670 THR Chi-restraints excluded: chain A residue 969 VAL Chi-restraints excluded: chain A residue 1031 ASN Chi-restraints excluded: chain A residue 1052 VAL Chi-restraints excluded: chain D residue 10 THR Chi-restraints excluded: chain D residue 26 ASN Chi-restraints excluded: chain D residue 47 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 61 optimal weight: 6.9990 chunk 34 optimal weight: 5.9990 chunk 91 optimal weight: 2.9990 chunk 74 optimal weight: 10.0000 chunk 30 optimal weight: 9.9990 chunk 110 optimal weight: 10.0000 chunk 118 optimal weight: 10.0000 chunk 98 optimal weight: 0.0870 chunk 109 optimal weight: 0.9990 chunk 37 optimal weight: 2.9990 chunk 88 optimal weight: 0.8980 overall best weight: 1.5964 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 674 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 822 HIS A 944 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7866 moved from start: 0.1448 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= 0.198 Angle : 0.588 7.204 16380 Z= 0.295 Chirality : 0.037 0.203 1901 Planarity : 0.004 0.047 1707 Dihedral : 19.282 101.276 2998 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 10.35 Ramachandran Plot: Outliers : 0.64 % Allowed : 6.18 % Favored : 93.18 % Rotamer: Outliers : 2.62 % Allowed : 28.46 % 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 (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: -0.69 (0.25), residues: 1107 helix: 0.85 (0.25), residues: 466 sheet: -0.48 (0.53), residues: 102 loop : -1.67 (0.26), residues: 539 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 632 HIS 0.002 0.001 HIS A1002 PHE 0.026 0.001 PHE A 185 TYR 0.016 0.001 TYR A 317 ARG 0.004 0.000 ARG A 646 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 960 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 83 time to evaluate : 1.263 Fit side-chains REVERT: A 246 LEU cc_start: 0.7800 (OUTLIER) cc_final: 0.7599 (mt) outliers start: 24 outliers final: 17 residues processed: 99 average time/residue: 0.2437 time to fit residues: 35.2494 Evaluate side-chains 100 residues out of total 960 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 82 time to evaluate : 1.251 ------------------------------------------------------------------------------- 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 216 PHE Chi-restraints excluded: chain A residue 231 LEU Chi-restraints excluded: chain A residue 246 LEU Chi-restraints excluded: chain A residue 249 ASP Chi-restraints excluded: chain A residue 670 THR 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 1031 ASN Chi-restraints excluded: chain A residue 1052 VAL Chi-restraints excluded: chain D residue 10 THR Chi-restraints excluded: chain D residue 26 ASN Chi-restraints excluded: chain D residue 47 ASP Chi-restraints excluded: chain D residue 58 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 108 optimal weight: 0.6980 chunk 82 optimal weight: 3.9990 chunk 57 optimal weight: 9.9990 chunk 12 optimal weight: 3.9990 chunk 52 optimal weight: 5.9990 chunk 73 optimal weight: 4.9990 chunk 110 optimal weight: 10.0000 chunk 116 optimal weight: 10.0000 chunk 104 optimal weight: 0.0270 chunk 31 optimal weight: 20.0000 chunk 97 optimal weight: 0.9990 overall best weight: 1.9444 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 674 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7877 moved from start: 0.1628 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 11739 Z= 0.219 Angle : 0.587 7.194 16380 Z= 0.294 Chirality : 0.037 0.207 1901 Planarity : 0.004 0.049 1707 Dihedral : 19.223 100.507 2998 Min Nonbonded Distance : 2.202 Molprobity Statistics. All-atom Clashscore : 10.45 Ramachandran Plot: Outliers : 0.55 % Allowed : 7.27 % Favored : 92.18 % Rotamer: Outliers : 3.49 % Allowed : 28.03 % Favored : 68.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.65 (0.25), residues: 1107 helix: 0.89 (0.25), residues: 466 sheet: -0.53 (0.53), residues: 102 loop : -1.64 (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 A1002 PHE 0.026 0.001 PHE A 185 TYR 0.018 0.001 TYR A 317 ARG 0.005 0.000 ARG A 713 *********************** 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 121 residues out of total 960 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 89 time to evaluate : 1.254 Fit side-chains REVERT: A 246 LEU cc_start: 0.7855 (OUTLIER) cc_final: 0.7625 (mt) REVERT: A 580 GLU cc_start: 0.6306 (tm-30) cc_final: 0.6097 (tm-30) REVERT: A 620 TYR cc_start: 0.8050 (t80) cc_final: 0.7594 (t80) outliers start: 32 outliers final: 27 residues processed: 113 average time/residue: 0.2442 time to fit residues: 40.6055 Evaluate side-chains 113 residues out of total 960 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 85 time to evaluate : 1.233 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 SER Chi-restraints excluded: chain A residue 56 ASP Chi-restraints excluded: chain A residue 91 VAL Chi-restraints excluded: chain A residue 102 LEU Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 216 PHE Chi-restraints excluded: chain A residue 231 LEU Chi-restraints excluded: chain A residue 246 LEU Chi-restraints excluded: chain A residue 249 ASP Chi-restraints excluded: chain A residue 310 TYR Chi-restraints excluded: chain A residue 418 ASP Chi-restraints excluded: chain A residue 558 LEU Chi-restraints excluded: chain A residue 667 LEU Chi-restraints excluded: chain A residue 670 THR 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 1031 ASN Chi-restraints excluded: chain A residue 1037 LEU Chi-restraints excluded: chain A residue 1052 VAL Chi-restraints excluded: chain D residue 10 THR Chi-restraints excluded: chain D residue 22 VAL Chi-restraints excluded: chain D residue 26 ASN Chi-restraints excluded: chain D residue 37 SER Chi-restraints excluded: chain D residue 47 ASP Chi-restraints excluded: chain D residue 58 LEU Chi-restraints excluded: chain D residue 79 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 66 optimal weight: 7.9990 chunk 1 optimal weight: 6.9990 chunk 87 optimal weight: 0.0370 chunk 48 optimal weight: 5.9990 chunk 99 optimal weight: 0.0470 chunk 80 optimal weight: 0.9990 chunk 0 optimal weight: 4.9990 chunk 59 optimal weight: 10.0000 chunk 104 optimal weight: 0.2980 chunk 29 optimal weight: 9.9990 chunk 39 optimal weight: 4.9990 overall best weight: 1.2760 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 674 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7834 moved from start: 0.1585 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= 0.174 Angle : 0.553 7.191 16380 Z= 0.277 Chirality : 0.036 0.201 1901 Planarity : 0.004 0.049 1707 Dihedral : 19.113 99.717 2998 Min Nonbonded Distance : 2.208 Molprobity Statistics. All-atom Clashscore : 9.84 Ramachandran Plot: Outliers : 0.55 % Allowed : 6.00 % Favored : 93.45 % Rotamer: Outliers : 2.84 % Allowed : 28.79 % Favored : 68.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.47 (0.26), residues: 1107 helix: 1.05 (0.25), residues: 469 sheet: -0.43 (0.53), residues: 99 loop : -1.56 (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 A1002 PHE 0.019 0.001 PHE A 185 TYR 0.016 0.001 TYR A 317 ARG 0.004 0.000 ARG A 713 *********************** 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 114 residues out of total 960 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 88 time to evaluate : 1.043 Fit side-chains REVERT: A 276 ARG cc_start: 0.7389 (tpt170) cc_final: 0.7135 (tpt170) REVERT: A 580 GLU cc_start: 0.6246 (tm-30) cc_final: 0.6040 (tm-30) REVERT: A 620 TYR cc_start: 0.8055 (t80) cc_final: 0.7638 (t80) outliers start: 26 outliers final: 18 residues processed: 108 average time/residue: 0.2124 time to fit residues: 33.2881 Evaluate side-chains 104 residues out of total 960 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 86 time to evaluate : 1.080 ------------------------------------------------------------------------------- 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 231 LEU Chi-restraints excluded: chain A residue 249 ASP Chi-restraints excluded: chain A residue 310 TYR Chi-restraints excluded: chain A residue 418 ASP Chi-restraints excluded: chain A residue 558 LEU Chi-restraints excluded: chain A residue 670 THR Chi-restraints excluded: chain A residue 673 VAL Chi-restraints excluded: chain A residue 812 GLU Chi-restraints excluded: chain A residue 1009 VAL Chi-restraints excluded: chain A residue 1031 ASN Chi-restraints excluded: chain A residue 1052 VAL Chi-restraints excluded: chain D residue 22 VAL Chi-restraints excluded: chain D residue 26 ASN Chi-restraints excluded: chain D residue 37 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 105 optimal weight: 3.9990 chunk 23 optimal weight: 9.9990 chunk 68 optimal weight: 0.6980 chunk 28 optimal weight: 6.9990 chunk 117 optimal weight: 7.9990 chunk 97 optimal weight: 8.9990 chunk 54 optimal weight: 10.0000 chunk 9 optimal weight: 7.9990 chunk 38 optimal weight: 7.9990 chunk 61 optimal weight: 0.1980 chunk 112 optimal weight: 10.0000 overall best weight: 3.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7951 moved from start: 0.2141 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.064 11739 Z= 0.383 Angle : 0.683 7.705 16380 Z= 0.344 Chirality : 0.041 0.210 1901 Planarity : 0.005 0.049 1707 Dihedral : 19.271 101.974 2998 Min Nonbonded Distance : 2.158 Molprobity Statistics. All-atom Clashscore : 12.37 Ramachandran Plot: Outliers : 0.55 % Allowed : 7.91 % Favored : 91.55 % Rotamer: Outliers : 3.82 % Allowed : 28.14 % Favored : 68.05 % 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: -0.94 (0.25), residues: 1107 helix: 0.62 (0.25), residues: 467 sheet: -0.70 (0.54), residues: 99 loop : -1.77 (0.25), residues: 541 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP A 632 HIS 0.005 0.001 HIS A 414 PHE 0.028 0.002 PHE A 185 TYR 0.021 0.002 TYR A 317 ARG 0.004 0.001 ARG A 713 *********************** 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 121 residues out of total 960 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 86 time to evaluate : 0.992 Fit side-chains REVERT: A 118 LEU cc_start: 0.7160 (OUTLIER) cc_final: 0.6873 (mt) REVERT: A 246 LEU cc_start: 0.7803 (OUTLIER) cc_final: 0.7511 (mt) REVERT: A 620 TYR cc_start: 0.8150 (t80) cc_final: 0.7790 (t80) REVERT: A 819 GLU cc_start: 0.7500 (OUTLIER) cc_final: 0.7077 (mp0) outliers start: 35 outliers final: 25 residues processed: 113 average time/residue: 0.2432 time to fit residues: 39.8806 Evaluate side-chains 110 residues out of total 960 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 82 time to evaluate : 1.112 ------------------------------------------------------------------------------- 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 118 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 249 ASP Chi-restraints excluded: chain A residue 415 ILE Chi-restraints excluded: chain A residue 418 ASP Chi-restraints excluded: chain A residue 505 THR Chi-restraints excluded: chain A residue 558 LEU Chi-restraints excluded: chain A residue 667 LEU Chi-restraints excluded: chain A residue 670 THR Chi-restraints excluded: chain A residue 673 VAL Chi-restraints excluded: chain A residue 812 GLU Chi-restraints excluded: chain A residue 819 GLU Chi-restraints excluded: chain A residue 948 VAL Chi-restraints excluded: chain A residue 969 VAL Chi-restraints excluded: chain A residue 1009 VAL Chi-restraints excluded: chain A residue 1031 ASN Chi-restraints excluded: chain A residue 1052 VAL Chi-restraints excluded: chain D residue 10 THR Chi-restraints excluded: chain D residue 22 VAL Chi-restraints excluded: chain D residue 26 ASN Chi-restraints excluded: chain D residue 37 SER Chi-restraints excluded: chain D residue 47 ASP 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 13 optimal weight: 10.0000 chunk 66 optimal weight: 7.9990 chunk 85 optimal weight: 9.9990 chunk 98 optimal weight: 0.4980 chunk 65 optimal weight: 0.4980 chunk 116 optimal weight: 10.0000 chunk 72 optimal weight: 3.9990 chunk 71 optimal weight: 0.8980 chunk 53 optimal weight: 0.7980 chunk 46 optimal weight: 6.9990 chunk 69 optimal weight: 0.8980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7823 moved from start: 0.1813 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 11739 Z= 0.155 Angle : 0.566 7.839 16380 Z= 0.283 Chirality : 0.036 0.206 1901 Planarity : 0.004 0.049 1707 Dihedral : 19.068 100.781 2998 Min Nonbonded Distance : 2.182 Molprobity Statistics. All-atom Clashscore : 9.84 Ramachandran Plot: Outliers : 0.45 % Allowed : 5.91 % Favored : 93.64 % Rotamer: Outliers : 2.29 % Allowed : 29.23 % Favored : 68.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.54 (0.26), residues: 1107 helix: 0.98 (0.25), residues: 469 sheet: -0.48 (0.54), residues: 99 loop : -1.59 (0.26), residues: 539 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 632 HIS 0.004 0.001 HIS A 414 PHE 0.017 0.001 PHE A 185 TYR 0.016 0.001 TYR A 317 ARG 0.003 0.000 ARG A 713 *********************** 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 fitting. rotamer outliers: 21 poor density : 93 time to evaluate : 1.124 Fit side-chains REVERT: A 246 LEU cc_start: 0.7757 (OUTLIER) cc_final: 0.7513 (mt) REVERT: A 276 ARG cc_start: 0.7450 (tpt170) cc_final: 0.7189 (tpt170) REVERT: A 620 TYR cc_start: 0.8127 (t80) cc_final: 0.7756 (t80) outliers start: 21 outliers final: 15 residues processed: 107 average time/residue: 0.2396 time to fit residues: 37.8582 Evaluate side-chains 104 residues out of total 960 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 88 time to evaluate : 1.131 ------------------------------------------------------------------------------- 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 123 THR Chi-restraints excluded: chain A residue 246 LEU Chi-restraints excluded: chain A residue 249 ASP 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 1009 VAL Chi-restraints excluded: chain A residue 1052 VAL Chi-restraints excluded: chain D residue 10 THR Chi-restraints excluded: chain D residue 22 VAL Chi-restraints excluded: chain D residue 26 ASN Chi-restraints excluded: chain D residue 37 SER Chi-restraints excluded: chain D residue 47 ASP 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 35 optimal weight: 1.9990 chunk 22 optimal weight: 10.0000 chunk 74 optimal weight: 0.4980 chunk 79 optimal weight: 2.9990 chunk 57 optimal weight: 10.0000 chunk 10 optimal weight: 3.9990 chunk 91 optimal weight: 6.9990 chunk 106 optimal weight: 5.9990 chunk 111 optimal weight: 6.9990 chunk 101 optimal weight: 1.9990 chunk 108 optimal weight: 5.9990 overall best weight: 2.2988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 674 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7887 moved from start: 0.1987 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 11739 Z= 0.243 Angle : 0.593 7.756 16380 Z= 0.297 Chirality : 0.038 0.203 1901 Planarity : 0.004 0.050 1707 Dihedral : 19.072 100.130 2998 Min Nonbonded Distance : 2.179 Molprobity Statistics. All-atom Clashscore : 10.54 Ramachandran Plot: Outliers : 0.45 % Allowed : 7.27 % Favored : 92.27 % Rotamer: Outliers : 2.84 % Allowed : 29.12 % Favored : 68.05 % 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: -0.58 (0.26), residues: 1107 helix: 0.97 (0.25), residues: 468 sheet: -0.45 (0.54), residues: 97 loop : -1.64 (0.26), residues: 542 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP A 632 HIS 0.004 0.001 HIS A 414 PHE 0.021 0.001 PHE A 185 TYR 0.018 0.001 TYR A 317 ARG 0.003 0.000 ARG A 713 *********************** 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 114 residues out of total 960 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 88 time to evaluate : 1.151 Fit side-chains REVERT: A 86 LEU cc_start: 0.6987 (OUTLIER) cc_final: 0.6544 (tp) REVERT: A 246 LEU cc_start: 0.7845 (OUTLIER) cc_final: 0.7572 (mt) REVERT: A 276 ARG cc_start: 0.7475 (tpt170) cc_final: 0.7194 (tpt170) REVERT: A 620 TYR cc_start: 0.8127 (t80) cc_final: 0.7828 (t80) outliers start: 26 outliers final: 22 residues processed: 107 average time/residue: 0.2352 time to fit residues: 36.9509 Evaluate side-chains 112 residues out of total 960 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 88 time to evaluate : 1.141 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 ASP Chi-restraints excluded: chain A residue 86 LEU Chi-restraints excluded: chain A residue 91 VAL Chi-restraints excluded: chain A residue 102 LEU Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 216 PHE Chi-restraints excluded: chain A residue 246 LEU Chi-restraints excluded: chain A residue 249 ASP Chi-restraints excluded: chain A residue 310 TYR Chi-restraints excluded: chain A residue 558 LEU Chi-restraints excluded: chain A residue 667 LEU Chi-restraints excluded: chain A residue 670 THR 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 1031 ASN Chi-restraints excluded: chain A residue 1052 VAL Chi-restraints excluded: chain D residue 10 THR Chi-restraints excluded: chain D residue 22 VAL Chi-restraints excluded: chain D residue 26 ASN Chi-restraints excluded: chain D residue 37 SER Chi-restraints excluded: chain D residue 47 ASP 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 111 optimal weight: 7.9990 chunk 65 optimal weight: 1.9990 chunk 47 optimal weight: 2.9990 chunk 85 optimal weight: 9.9990 chunk 33 optimal weight: 1.9990 chunk 98 optimal weight: 0.0030 chunk 102 optimal weight: 10.0000 chunk 108 optimal weight: 0.8980 chunk 71 optimal weight: 0.0570 chunk 114 optimal weight: 5.9990 chunk 70 optimal weight: 0.9990 overall best weight: 0.7912 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 674 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7799 moved from start: 0.1854 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 11739 Z= 0.153 Angle : 0.549 8.618 16380 Z= 0.274 Chirality : 0.036 0.199 1901 Planarity : 0.004 0.050 1707 Dihedral : 18.971 98.795 2998 Min Nonbonded Distance : 2.168 Molprobity Statistics. All-atom Clashscore : 10.35 Ramachandran Plot: Outliers : 0.36 % Allowed : 6.27 % Favored : 93.36 % Rotamer: Outliers : 2.29 % Allowed : 29.44 % Favored : 68.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.35 (0.26), residues: 1107 helix: 1.13 (0.25), residues: 472 sheet: -0.32 (0.54), residues: 99 loop : -1.50 (0.26), residues: 536 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 632 HIS 0.004 0.000 HIS A 414 PHE 0.027 0.001 PHE A 185 TYR 0.016 0.001 TYR A 317 ARG 0.003 0.000 ARG A 713 *********************** 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 117 residues out of total 960 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 96 time to evaluate : 1.186 Fit side-chains REVERT: A 246 LEU cc_start: 0.7803 (OUTLIER) cc_final: 0.7544 (mt) REVERT: A 276 ARG cc_start: 0.7398 (tpt170) cc_final: 0.7111 (tpt170) outliers start: 21 outliers final: 18 residues processed: 112 average time/residue: 0.2273 time to fit residues: 37.4723 Evaluate side-chains 106 residues out of total 960 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 87 time to evaluate : 1.066 ------------------------------------------------------------------------------- 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 246 LEU Chi-restraints excluded: chain A residue 249 ASP Chi-restraints excluded: chain A residue 310 TYR Chi-restraints excluded: chain A residue 558 LEU Chi-restraints excluded: chain A residue 667 LEU Chi-restraints excluded: chain A residue 670 THR 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 22 VAL Chi-restraints excluded: chain D residue 26 ASN Chi-restraints excluded: chain D residue 37 SER 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 54 optimal weight: 9.9990 chunk 79 optimal weight: 0.7980 chunk 120 optimal weight: 10.0000 chunk 110 optimal weight: 10.0000 chunk 95 optimal weight: 7.9990 chunk 9 optimal weight: 3.9990 chunk 74 optimal weight: 0.0000 chunk 58 optimal weight: 6.9990 chunk 76 optimal weight: 0.6980 chunk 102 optimal weight: 8.9990 chunk 29 optimal weight: 8.9990 overall best weight: 2.4988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 674 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7882 moved from start: 0.2061 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.091 11739 Z= 0.263 Angle : 0.599 8.958 16380 Z= 0.300 Chirality : 0.038 0.228 1901 Planarity : 0.004 0.050 1707 Dihedral : 19.028 99.421 2998 Min Nonbonded Distance : 2.186 Molprobity Statistics. All-atom Clashscore : 10.96 Ramachandran Plot: Outliers : 0.36 % Allowed : 7.27 % Favored : 92.36 % Rotamer: Outliers : 2.40 % Allowed : 29.66 % 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 (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: -0.51 (0.26), residues: 1107 helix: 1.04 (0.25), residues: 468 sheet: -0.42 (0.54), residues: 97 loop : -1.62 (0.26), residues: 542 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP A 632 HIS 0.004 0.001 HIS A 414 PHE 0.033 0.002 PHE A 185 TYR 0.017 0.001 TYR A 317 ARG 0.003 0.000 ARG A 713 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 960 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 89 time to evaluate : 1.101 Fit side-chains REVERT: A 86 LEU cc_start: 0.7007 (OUTLIER) cc_final: 0.6569 (tp) REVERT: A 246 LEU cc_start: 0.7903 (OUTLIER) cc_final: 0.7613 (mt) REVERT: A 276 ARG cc_start: 0.7444 (tpt170) cc_final: 0.7106 (tpt170) outliers start: 22 outliers final: 19 residues processed: 106 average time/residue: 0.2235 time to fit residues: 35.3908 Evaluate side-chains 109 residues out of total 960 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 88 time to evaluate : 1.115 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 246 LEU Chi-restraints excluded: chain A residue 249 ASP Chi-restraints excluded: chain A residue 310 TYR Chi-restraints excluded: chain A residue 558 LEU Chi-restraints excluded: chain A residue 667 LEU Chi-restraints excluded: chain A residue 670 THR Chi-restraints excluded: chain A residue 673 VAL Chi-restraints excluded: chain A residue 1009 VAL Chi-restraints excluded: chain A residue 1031 ASN Chi-restraints excluded: chain A residue 1052 VAL Chi-restraints excluded: chain D residue 10 THR Chi-restraints excluded: chain D residue 22 VAL Chi-restraints excluded: chain D residue 26 ASN Chi-restraints excluded: chain D residue 37 SER Chi-restraints excluded: chain D residue 39 VAL 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 88 optimal weight: 2.9990 chunk 14 optimal weight: 0.9990 chunk 26 optimal weight: 9.9990 chunk 96 optimal weight: 5.9990 chunk 40 optimal weight: 7.9990 chunk 98 optimal weight: 6.9990 chunk 12 optimal weight: 5.9990 chunk 17 optimal weight: 0.7980 chunk 84 optimal weight: 0.9990 chunk 5 optimal weight: 0.7980 chunk 69 optimal weight: 0.9990 overall best weight: 0.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 655 GLN ** A 674 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3934 r_free = 0.3934 target = 0.143837 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.110847 restraints weight = 56743.507| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3509 r_free = 0.3509 target = 0.114173 restraints weight = 25613.400| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.114226 restraints weight = 14995.084| |-----------------------------------------------------------------------------| r_work (final): 0.3496 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3496 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3496 r_free = 0.3496 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 = 0.3495 r_free = 0.3495 target_work(ls_wunit_k1) = 0.112 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.3495 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7832 moved from start: 0.1964 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.046 11739 Z= 0.165 Angle : 0.553 9.303 16380 Z= 0.276 Chirality : 0.036 0.209 1901 Planarity : 0.004 0.051 1707 Dihedral : 18.969 99.258 2998 Min Nonbonded Distance : 2.179 Molprobity Statistics. All-atom Clashscore : 9.84 Ramachandran Plot: Outliers : 0.36 % Allowed : 6.36 % Favored : 93.27 % Rotamer: Outliers : 2.51 % Allowed : 29.77 % Favored : 67.72 % 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: 1.17 (0.25), residues: 470 sheet: -0.40 (0.54), residues: 99 loop : -1.47 (0.26), residues: 538 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A 632 HIS 0.004 0.000 HIS A 414 PHE 0.022 0.001 PHE A 185 TYR 0.015 0.001 TYR A 317 ARG 0.003 0.000 ARG A 713 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2181.04 seconds wall clock time: 44 minutes 49.42 seconds (2689.42 seconds total)