Starting phenix.real_space_refine on Thu Mar 13 15:51:32 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9b5p_44220/03_2025/9b5p_44220.cif Found real_map, /net/cci-nas-00/data/ceres_data/9b5p_44220/03_2025/9b5p_44220.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.08 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9b5p_44220/03_2025/9b5p_44220.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9b5p_44220/03_2025/9b5p_44220.map" model { file = "/net/cci-nas-00/data/ceres_data/9b5p_44220/03_2025/9b5p_44220.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9b5p_44220/03_2025/9b5p_44220.cif" } resolution = 3.08 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.076 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 3 5.49 5 Mg 2 5.21 5 S 41 5.16 5 C 5703 2.51 5 N 1470 2.21 5 O 1716 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib" Total number of atoms: 8935 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 7734 Number of conformers: 1 Conformer: "" Number of residues, atoms: 985, 7734 Classifications: {'peptide': 985} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 55, 'TRANS': 928} Chain breaks: 1 Chain: "C" Number of atoms: 1158 Number of conformers: 1 Conformer: "" Number of residues, atoms: 147, 1158 Classifications: {'peptide': 147} Link IDs: {'PCIS': 1, 'PTRANS': 14, 'TRANS': 131} Chain: "D" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 4 Classifications: {'peptide': 1} Chain: "A" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' MG': 2, 'ATP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "D" Number of atoms: 6 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 6 Unusual residues: {'A1AIV': 1} Classifications: {'undetermined': 1} Time building chain proxies: 6.23, per 1000 atoms: 0.70 Number of scatterers: 8935 At special positions: 0 Unit cell: (82.992, 100.016, 121.296, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 41 16.00 P 3 15.00 Mg 2 11.99 O 1716 8.00 N 1470 7.00 C 5703 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS A 593 " - pdb=" SG CYS C 85 " distance=2.94 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=2, symmetry=0 Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 2.46 Conformation dependent library (CDL) restraints added in 1.0 seconds 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2124 Finding SS restraints... Secondary structure from input PDB file: 48 helices and 9 sheets defined 47.7% alpha, 14.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.13 Creating SS restraints... Processing helix chain 'A' and resid 20 through 25 removed outlier: 3.915A pdb=" N TYR A 25 " --> pdb=" O SER A 21 " (cutoff:3.500A) Processing helix chain 'A' and resid 28 through 36 Processing helix chain 'A' and resid 46 through 60 Processing helix chain 'A' and resid 73 through 79 removed outlier: 3.909A pdb=" N SER A 79 " --> pdb=" O ASP A 76 " (cutoff:3.500A) Processing helix chain 'A' and resid 84 through 88 removed outlier: 3.887A pdb=" N ILE A 88 " --> pdb=" O GLU A 85 " (cutoff:3.500A) Processing helix chain 'A' and resid 91 through 101 removed outlier: 4.483A pdb=" N SER A 98 " --> pdb=" O LYS A 94 " (cutoff:3.500A) removed outlier: 4.645A pdb=" N LYS A 99 " --> pdb=" O VAL A 95 " (cutoff:3.500A) Processing helix chain 'A' and resid 117 through 123 Processing helix chain 'A' and resid 132 through 144 removed outlier: 3.779A pdb=" N PHE A 142 " --> pdb=" O GLU A 138 " (cutoff:3.500A) Processing helix chain 'A' and resid 218 through 224 removed outlier: 3.774A pdb=" N GLY A 224 " --> pdb=" O LEU A 221 " (cutoff:3.500A) Processing helix chain 'A' and resid 267 through 274 removed outlier: 4.468A pdb=" N LYS A 273 " --> pdb=" O ARG A 269 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N ASP A 274 " --> pdb=" O GLU A 270 " (cutoff:3.500A) Processing helix chain 'A' and resid 287 through 305 removed outlier: 3.712A pdb=" N ILE A 293 " --> pdb=" O PRO A 289 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N GLN A 296 " --> pdb=" O HIS A 292 " (cutoff:3.500A) Processing helix chain 'A' and resid 314 through 332 Processing helix chain 'A' and resid 339 through 349 Processing helix chain 'A' and resid 354 through 375 Processing helix chain 'A' and resid 389 through 392 Processing helix chain 'A' and resid 410 through 418 removed outlier: 4.544A pdb=" N VAL A 416 " --> pdb=" O GLY A 412 " (cutoff:3.500A) Processing helix chain 'A' and resid 418 through 427 Processing helix chain 'A' and resid 436 through 450 Processing helix chain 'A' and resid 468 through 474 removed outlier: 3.895A pdb=" N ASN A 473 " --> pdb=" O SER A 470 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N ARG A 474 " --> pdb=" O ASN A 471 " (cutoff:3.500A) Processing helix chain 'A' and resid 479 through 483 Processing helix chain 'A' and resid 486 through 499 removed outlier: 3.520A pdb=" N CYS A 490 " --> pdb=" O LEU A 486 " (cutoff:3.500A) Processing helix chain 'A' and resid 500 through 503 Processing helix chain 'A' and resid 514 through 518 removed outlier: 3.686A pdb=" N GLU A 518 " --> pdb=" O PRO A 515 " (cutoff:3.500A) Processing helix chain 'A' and resid 522 through 527 Processing helix chain 'A' and resid 538 through 553 Processing helix chain 'A' and resid 578 through 582 Processing helix chain 'A' and resid 591 through 597 Processing helix chain 'A' and resid 601 through 618 Processing helix chain 'A' and resid 618 through 628 Processing helix chain 'A' and resid 632 through 641 removed outlier: 3.632A pdb=" N THR A 636 " --> pdb=" O ASN A 632 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N LYS A 639 " --> pdb=" O GLU A 635 " (cutoff:3.500A) Processing helix chain 'A' and resid 643 through 656 Processing helix chain 'A' and resid 662 through 679 removed outlier: 3.603A pdb=" N CYS A 666 " --> pdb=" O SER A 662 " (cutoff:3.500A) Processing helix chain 'A' and resid 679 through 689 Processing helix chain 'A' and resid 718 through 737 Processing helix chain 'A' and resid 743 through 753 removed outlier: 4.017A pdb=" N TYR A 747 " --> pdb=" O ASP A 743 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N GLY A 753 " --> pdb=" O ARG A 749 " (cutoff:3.500A) Processing helix chain 'A' and resid 781 through 794 Processing helix chain 'A' and resid 796 through 800 Processing helix chain 'A' and resid 818 through 834 Processing helix chain 'A' and resid 840 through 849 Processing helix chain 'A' and resid 855 through 876 removed outlier: 3.633A pdb=" N VAL A 871 " --> pdb=" O CYS A 867 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N LYS A 872 " --> pdb=" O LEU A 868 " (cutoff:3.500A) Processing helix chain 'A' and resid 879 through 883 removed outlier: 3.726A pdb=" N TYR A 883 " --> pdb=" O ILE A 880 " (cutoff:3.500A) Processing helix chain 'A' and resid 926 through 937 Processing helix chain 'A' and resid 958 through 966 Processing helix chain 'A' and resid 969 through 979 Processing helix chain 'C' and resid 3 through 16 Processing helix chain 'C' and resid 98 through 112 Processing helix chain 'C' and resid 120 through 130 Processing helix chain 'C' and resid 130 through 145 Processing sheet with id=AA1, first strand: chain 'A' and resid 109 through 111 removed outlier: 6.797A pdb=" N VAL A 64 " --> pdb=" O SER A 110 " (cutoff:3.500A) removed outlier: 6.586A pdb=" N ASN A 39 " --> pdb=" O CYS A 125 " (cutoff:3.500A) removed outlier: 7.956A pdb=" N VAL A 127 " --> pdb=" O ASN A 39 " (cutoff:3.500A) removed outlier: 6.372A pdb=" N LEU A 41 " --> pdb=" O VAL A 127 " (cutoff:3.500A) removed outlier: 6.199A pdb=" N VAL A 126 " --> pdb=" O ILE A 151 " (cutoff:3.500A) removed outlier: 7.685A pdb=" N ALA A 153 " --> pdb=" O VAL A 126 " (cutoff:3.500A) removed outlier: 6.216A pdb=" N VAL A 128 " --> pdb=" O ALA A 153 " (cutoff:3.500A) removed outlier: 8.247A pdb=" N SER A 155 " --> pdb=" O VAL A 128 " (cutoff:3.500A) removed outlier: 4.283A pdb=" N TYR A 385 " --> pdb=" O VAL A 278 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 170 through 172 Processing sheet with id=AA3, first strand: chain 'A' and resid 227 through 228 removed outlier: 4.067A pdb=" N PHE A 209 " --> pdb=" O VAL A 257 " (cutoff:3.500A) removed outlier: 7.380A pdb=" N THR A 195 " --> pdb=" O ALA A 186 " (cutoff:3.500A) removed outlier: 4.517A pdb=" N ILE A 188 " --> pdb=" O VAL A 193 " (cutoff:3.500A) removed outlier: 6.653A pdb=" N VAL A 193 " --> pdb=" O ILE A 188 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 227 through 228 removed outlier: 4.067A pdb=" N PHE A 209 " --> pdb=" O VAL A 257 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 506 through 509 removed outlier: 6.556A pdb=" N ILE A 459 " --> pdb=" O THR A 507 " (cutoff:3.500A) removed outlier: 7.870A pdb=" N TYR A 509 " --> pdb=" O ILE A 459 " (cutoff:3.500A) removed outlier: 6.663A pdb=" N VAL A 461 " --> pdb=" O TYR A 509 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N SER A 460 " --> pdb=" O THR A 430 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N LEU A 531 " --> pdb=" O SER A 429 " (cutoff:3.500A) removed outlier: 4.214A pdb=" N SER A 559 " --> pdb=" O ASN A 534 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 905 through 908 Processing sheet with id=AA7, first strand: chain 'A' and resid 920 through 922 removed outlier: 6.400A pdb=" N TYR A 920 " --> pdb=" O CYS A1009 " (cutoff:3.500A) removed outlier: 6.925A pdb=" N LYS A1011 " --> pdb=" O TYR A 920 " (cutoff:3.500A) removed outlier: 7.007A pdb=" N LEU A 922 " --> pdb=" O LYS A1011 " (cutoff:3.500A) removed outlier: 7.507A pdb=" N VAL A 990 " --> pdb=" O SER A 947 " (cutoff:3.500A) removed outlier: 5.164A pdb=" N SER A 947 " --> pdb=" O VAL A 990 " (cutoff:3.500A) removed outlier: 6.822A pdb=" N GLU A 992 " --> pdb=" O LEU A 945 " (cutoff:3.500A) removed outlier: 4.475A pdb=" N LEU A 945 " --> pdb=" O GLU A 992 " (cutoff:3.500A) removed outlier: 6.626A pdb=" N CYS A 994 " --> pdb=" O THR A 943 " (cutoff:3.500A) removed outlier: 6.855A pdb=" N SER A 947 " --> pdb=" O LEU A 951 " (cutoff:3.500A) removed outlier: 6.169A pdb=" N LEU A 951 " --> pdb=" O SER A 947 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 920 through 922 removed outlier: 6.400A pdb=" N TYR A 920 " --> pdb=" O CYS A1009 " (cutoff:3.500A) removed outlier: 6.925A pdb=" N LYS A1011 " --> pdb=" O TYR A 920 " (cutoff:3.500A) removed outlier: 7.007A pdb=" N LEU A 922 " --> pdb=" O LYS A1011 " (cutoff:3.500A) removed outlier: 4.355A pdb=" N CYS A 995 " --> pdb=" O VAL A1003 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 25 through 26 removed outlier: 6.267A pdb=" N HIS C 32 " --> pdb=" O VAL C 26 " (cutoff:3.500A) 437 hydrogen bonds defined for protein. 1188 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.30 Time building geometry restraints manager: 2.86 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.13 - 1.27: 1512 1.27 - 1.40: 2173 1.40 - 1.54: 5281 1.54 - 1.67: 112 1.67 - 1.81: 62 Bond restraints: 9140 Sorted by residual: bond pdb=" C04 A1AIV D 201 " pdb=" C05 A1AIV D 201 " ideal model delta sigma weight residual 1.453 1.526 -0.073 2.00e-02 2.50e+03 1.35e+01 bond pdb=" C1' ATP A1103 " pdb=" C2' ATP A1103 " ideal model delta sigma weight residual 1.531 1.519 0.012 1.20e-02 6.94e+03 1.06e+00 bond pdb=" C05 A1AIV D 201 " pdb=" N06 A1AIV D 201 " ideal model delta sigma weight residual 1.151 1.133 0.018 2.00e-02 2.50e+03 8.05e-01 bond pdb=" C1' ATP A1103 " pdb=" O4' ATP A1103 " ideal model delta sigma weight residual 1.416 1.406 0.010 1.30e-02 5.92e+03 5.81e-01 bond pdb=" C3' ATP A1103 " pdb=" C4' ATP A1103 " ideal model delta sigma weight residual 1.526 1.532 -0.006 1.10e-02 8.26e+03 2.80e-01 ... (remaining 9135 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.29: 12229 1.29 - 2.57: 82 2.57 - 3.86: 71 3.86 - 5.15: 4 5.15 - 6.44: 4 Bond angle restraints: 12390 Sorted by residual: angle pdb=" C LYS A 381 " pdb=" N GLN A 382 " pdb=" CA GLN A 382 " ideal model delta sigma weight residual 121.70 128.11 -6.41 1.80e+00 3.09e-01 1.27e+01 angle pdb=" C2' ATP A1103 " pdb=" C1' ATP A1103 " pdb=" O4' ATP A1103 " ideal model delta sigma weight residual 106.53 103.12 3.41 1.18e+00 7.24e-01 8.42e+00 angle pdb=" C3' ATP A1103 " pdb=" C4' ATP A1103 " pdb=" C5' ATP A1103 " ideal model delta sigma weight residual 115.19 110.68 4.51 1.76e+00 3.23e-01 6.56e+00 angle pdb=" C2' ATP A1103 " pdb=" C3' ATP A1103 " pdb=" O3' ATP A1103 " ideal model delta sigma weight residual 111.83 105.39 6.44 2.67e+00 1.40e-01 5.82e+00 angle pdb=" C1' ATP A1103 " pdb=" C2' ATP A1103 " pdb=" O2' ATP A1103 " ideal model delta sigma weight residual 110.58 104.42 6.16 2.79e+00 1.28e-01 4.87e+00 ... (remaining 12385 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.75: 5348 17.75 - 35.51: 164 35.51 - 53.26: 32 53.26 - 71.02: 5 71.02 - 88.77: 3 Dihedral angle restraints: 5552 sinusoidal: 2262 harmonic: 3290 Sorted by residual: dihedral pdb=" CB CYS A 593 " pdb=" SG CYS A 593 " pdb=" SG CYS C 85 " pdb=" CB CYS C 85 " ideal model delta sinusoidal sigma weight residual -86.00 -128.67 42.67 1 1.00e+01 1.00e-02 2.54e+01 dihedral pdb=" N LYS A 596 " pdb=" CA LYS A 596 " pdb=" CB LYS A 596 " pdb=" CG LYS A 596 " ideal model delta sinusoidal sigma weight residual -180.00 -121.51 -58.49 3 1.50e+01 4.44e-03 9.47e+00 dihedral pdb=" N GLU A 937 " pdb=" CA GLU A 937 " pdb=" CB GLU A 937 " pdb=" CG GLU A 937 " ideal model delta sinusoidal sigma weight residual -180.00 -123.53 -56.47 3 1.50e+01 4.44e-03 9.40e+00 ... (remaining 5549 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.057: 1219 0.057 - 0.114: 126 0.114 - 0.171: 26 0.171 - 0.228: 1 0.228 - 0.284: 2 Chirality restraints: 1374 Sorted by residual: chirality pdb=" C2' ATP A1103 " pdb=" C1' ATP A1103 " pdb=" C3' ATP A1103 " pdb=" O2' ATP A1103 " both_signs ideal model delta sigma weight residual False -2.68 -2.96 0.28 2.00e-01 2.50e+01 2.02e+00 chirality pdb=" C3' ATP A1103 " pdb=" C2' ATP A1103 " pdb=" C4' ATP A1103 " pdb=" O3' ATP A1103 " both_signs ideal model delta sigma weight residual False -2.63 -2.91 0.27 2.00e-01 2.50e+01 1.88e+00 chirality pdb=" C4' ATP A1103 " pdb=" C3' ATP A1103 " pdb=" C5' ATP A1103 " pdb=" O4' ATP A1103 " both_signs ideal model delta sigma weight residual False -2.49 -2.72 0.23 2.00e-01 2.50e+01 1.28e+00 ... (remaining 1371 not shown) Planarity restraints: 1604 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C SER C 94 " 0.023 5.00e-02 4.00e+02 3.49e-02 1.95e+00 pdb=" N PRO C 95 " -0.060 5.00e-02 4.00e+02 pdb=" CA PRO C 95 " 0.018 5.00e-02 4.00e+02 pdb=" CD PRO C 95 " 0.020 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C HIS C 75 " -0.017 5.00e-02 4.00e+02 2.50e-02 9.98e-01 pdb=" N PRO C 76 " 0.043 5.00e-02 4.00e+02 pdb=" CA PRO C 76 " -0.013 5.00e-02 4.00e+02 pdb=" CD PRO C 76 " -0.014 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU A 922 " 0.015 5.00e-02 4.00e+02 2.30e-02 8.50e-01 pdb=" N PRO A 923 " -0.040 5.00e-02 4.00e+02 pdb=" CA PRO A 923 " 0.012 5.00e-02 4.00e+02 pdb=" CD PRO A 923 " 0.013 5.00e-02 4.00e+02 ... (remaining 1601 not shown) Histogram of nonbonded interaction distances: 2.01 - 2.59: 62 2.59 - 3.16: 7424 3.16 - 3.74: 13052 3.74 - 4.32: 18908 4.32 - 4.90: 32434 Nonbonded interactions: 71880 Sorted by model distance: nonbonded pdb=" OD2 ASP A 465 " pdb="MG MG A1102 " model vdw 2.008 2.170 nonbonded pdb="MG MG A1102 " pdb=" O1B ATP A1103 " model vdw 2.045 2.170 nonbonded pdb="MG MG A1101 " pdb=" O2B ATP A1103 " model vdw 2.117 2.170 nonbonded pdb=" OD2 ASP A 463 " pdb=" O3' ATP A1103 " model vdw 2.198 3.040 nonbonded pdb=" O TYR A 654 " pdb=" OH TYR A 736 " model vdw 2.207 3.040 ... (remaining 71875 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 132.480 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.320 Check model and map are aligned: 0.070 Set scattering table: 0.090 Process input model: 24.760 Find NCS groups from input model: 0.080 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.670 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 160.520 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8136 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 : 0.003 0.073 9140 Z= 0.168 Angle : 0.446 6.436 12390 Z= 0.222 Chirality : 0.041 0.284 1374 Planarity : 0.003 0.035 1604 Dihedral : 9.388 88.774 3425 Min Nonbonded Distance : 2.008 Molprobity Statistics. All-atom Clashscore : 1.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 1.51 % Allowed : 2.02 % Favored : 96.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.43 % Cis-general : 0.09 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.30 (0.26), residues: 1126 helix: 1.80 (0.25), residues: 469 sheet: 0.46 (0.39), residues: 183 loop : 0.18 (0.30), residues: 474 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP A 669 HIS 0.002 0.000 HIS C 75 PHE 0.008 0.001 PHE A 842 TYR 0.007 0.001 TYR A 736 ARG 0.002 0.000 ARG A 409 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 158 time to evaluate : 1.024 Fit side-chains revert: symmetry clash REVERT: A 80 GLN cc_start: 0.8511 (OUTLIER) cc_final: 0.7428 (tm-30) REVERT: A 105 GLN cc_start: 0.8066 (pt0) cc_final: 0.7844 (pt0) REVERT: A 442 MET cc_start: 0.8707 (tpp) cc_final: 0.8075 (mmm) REVERT: A 526 PHE cc_start: 0.9411 (OUTLIER) cc_final: 0.9095 (m-80) REVERT: A 546 ASP cc_start: 0.8223 (t70) cc_final: 0.8012 (t70) REVERT: A 565 LYS cc_start: 0.8962 (mttp) cc_final: 0.8749 (mttm) REVERT: A 596 LYS cc_start: 0.8691 (tmtt) cc_final: 0.8177 (tmtt) REVERT: A 719 ARG cc_start: 0.7623 (ttp-110) cc_final: 0.7416 (ttp80) REVERT: A 832 MET cc_start: 0.8519 (mtp) cc_final: 0.8301 (mtp) REVERT: A 869 GLU cc_start: 0.8094 (OUTLIER) cc_final: 0.7772 (mm-30) REVERT: C 112 ASP cc_start: 0.8272 (p0) cc_final: 0.7818 (p0) outliers start: 15 outliers final: 3 residues processed: 170 average time/residue: 0.3057 time to fit residues: 66.4054 Evaluate side-chains 105 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 99 time to evaluate : 0.973 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 GLN Chi-restraints excluded: chain A residue 526 PHE Chi-restraints excluded: chain A residue 656 VAL Chi-restraints excluded: chain A residue 869 GLU Chi-restraints excluded: chain A residue 1003 VAL Chi-restraints excluded: chain C residue 85 CYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 94 optimal weight: 0.9990 chunk 84 optimal weight: 1.9990 chunk 47 optimal weight: 1.9990 chunk 28 optimal weight: 0.7980 chunk 57 optimal weight: 2.9990 chunk 45 optimal weight: 0.7980 chunk 87 optimal weight: 1.9990 chunk 33 optimal weight: 0.5980 chunk 53 optimal weight: 1.9990 chunk 65 optimal weight: 0.9980 chunk 101 optimal weight: 4.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- 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 = 0.3777 r_free = 0.3777 target = 0.138945 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.102088 restraints weight = 11928.885| |-----------------------------------------------------------------------------| r_work (start): 0.3272 rms_B_bonded: 2.11 r_work: 0.3158 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.3023 rms_B_bonded: 4.22 restraints_weight: 0.2500 r_work (final): 0.3023 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8235 moved from start: 0.1436 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 9140 Z= 0.260 Angle : 0.516 9.355 12390 Z= 0.270 Chirality : 0.043 0.154 1374 Planarity : 0.004 0.038 1604 Dihedral : 6.237 59.483 1257 Min Nonbonded Distance : 1.943 Molprobity Statistics. All-atom Clashscore : 3.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer: Outliers : 1.92 % Allowed : 5.44 % Favored : 92.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.43 % Cis-general : 0.09 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.23 (0.26), residues: 1126 helix: 1.52 (0.24), residues: 486 sheet: 0.80 (0.40), residues: 170 loop : 0.19 (0.30), residues: 470 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 33 HIS 0.009 0.001 HIS C 32 PHE 0.010 0.001 PHE A 842 TYR 0.009 0.001 TYR C 145 ARG 0.005 0.001 ARG C 5 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 103 time to evaluate : 1.145 Fit side-chains revert: symmetry clash REVERT: A 80 GLN cc_start: 0.8519 (OUTLIER) cc_final: 0.7509 (tm-30) REVERT: A 105 GLN cc_start: 0.8358 (pt0) cc_final: 0.8112 (pt0) REVERT: A 179 GLU cc_start: 0.8786 (mm-30) cc_final: 0.7993 (pm20) REVERT: A 442 MET cc_start: 0.8712 (tpp) cc_final: 0.7917 (mmm) REVERT: A 464 MET cc_start: 0.8492 (OUTLIER) cc_final: 0.7496 (pmt) REVERT: A 526 PHE cc_start: 0.9428 (OUTLIER) cc_final: 0.9074 (m-80) REVERT: A 565 LYS cc_start: 0.9058 (mttp) cc_final: 0.8816 (mttm) REVERT: A 596 LYS cc_start: 0.8691 (mmtt) cc_final: 0.8127 (tmtt) REVERT: A 869 GLU cc_start: 0.8267 (OUTLIER) cc_final: 0.7975 (mm-30) REVERT: C 101 LYS cc_start: 0.8392 (mttp) cc_final: 0.8167 (mmtp) REVERT: C 112 ASP cc_start: 0.7977 (p0) cc_final: 0.7646 (p0) outliers start: 19 outliers final: 9 residues processed: 118 average time/residue: 0.3249 time to fit residues: 52.5925 Evaluate side-chains 108 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 95 time to evaluate : 1.165 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 GLN Chi-restraints excluded: chain A residue 184 MET Chi-restraints excluded: chain A residue 331 THR Chi-restraints excluded: chain A residue 461 VAL Chi-restraints excluded: chain A residue 464 MET Chi-restraints excluded: chain A residue 526 PHE Chi-restraints excluded: chain A residue 656 VAL Chi-restraints excluded: chain A residue 675 ASP Chi-restraints excluded: chain A residue 710 THR Chi-restraints excluded: chain A residue 837 THR Chi-restraints excluded: chain A residue 869 GLU Chi-restraints excluded: chain A residue 1003 VAL Chi-restraints excluded: chain C residue 43 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 18 optimal weight: 8.9990 chunk 54 optimal weight: 0.7980 chunk 32 optimal weight: 0.8980 chunk 61 optimal weight: 0.2980 chunk 13 optimal weight: 0.6980 chunk 65 optimal weight: 0.7980 chunk 2 optimal weight: 0.6980 chunk 68 optimal weight: 0.6980 chunk 106 optimal weight: 0.1980 chunk 20 optimal weight: 0.9990 chunk 85 optimal weight: 0.9980 overall best weight: 0.5180 ------------------------------------------------------------------------------- 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 = 0.3779 r_free = 0.3779 target = 0.139524 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.101817 restraints weight = 12114.915| |-----------------------------------------------------------------------------| r_work (start): 0.3272 rms_B_bonded: 2.24 r_work: 0.3150 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.3010 rms_B_bonded: 4.46 restraints_weight: 0.2500 r_work (final): 0.3010 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8214 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 : 0.003 0.032 9140 Z= 0.185 Angle : 0.524 13.843 12390 Z= 0.265 Chirality : 0.042 0.174 1374 Planarity : 0.004 0.042 1604 Dihedral : 6.074 54.954 1256 Min Nonbonded Distance : 1.986 Molprobity Statistics. All-atom Clashscore : 3.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.78 % Favored : 98.22 % Rotamer: Outliers : 1.92 % Allowed : 5.65 % Favored : 92.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.43 % Cis-general : 0.09 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.25 (0.26), residues: 1126 helix: 1.52 (0.24), residues: 486 sheet: 0.88 (0.40), residues: 176 loop : 0.19 (0.30), residues: 464 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 669 HIS 0.004 0.001 HIS C 32 PHE 0.007 0.001 PHE A 842 TYR 0.011 0.001 TYR C 145 ARG 0.004 0.000 ARG C 5 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 108 time to evaluate : 1.000 Fit side-chains revert: symmetry clash REVERT: A 80 GLN cc_start: 0.8530 (OUTLIER) cc_final: 0.7226 (tm-30) REVERT: A 105 GLN cc_start: 0.8348 (pt0) cc_final: 0.8111 (pt0) REVERT: A 154 ASP cc_start: 0.7840 (t0) cc_final: 0.7631 (m-30) REVERT: A 179 GLU cc_start: 0.8799 (mm-30) cc_final: 0.7959 (pm20) REVERT: A 442 MET cc_start: 0.8742 (tpp) cc_final: 0.7936 (mmm) REVERT: A 464 MET cc_start: 0.8447 (OUTLIER) cc_final: 0.7306 (pmt) REVERT: A 526 PHE cc_start: 0.9416 (OUTLIER) cc_final: 0.9046 (m-80) REVERT: A 565 LYS cc_start: 0.9045 (mttp) cc_final: 0.8781 (mttm) REVERT: A 596 LYS cc_start: 0.8538 (mmtt) cc_final: 0.7936 (tmtt) REVERT: A 719 ARG cc_start: 0.7723 (ttp80) cc_final: 0.7397 (tmm-80) REVERT: A 869 GLU cc_start: 0.8229 (OUTLIER) cc_final: 0.7926 (mm-30) REVERT: A 960 LYS cc_start: 0.7304 (tppt) cc_final: 0.6981 (tppt) REVERT: A 964 GLU cc_start: 0.7413 (mm-30) cc_final: 0.7202 (mt-10) REVERT: C 16 ASP cc_start: 0.7962 (p0) cc_final: 0.7207 (t0) REVERT: C 101 LYS cc_start: 0.8396 (mttp) cc_final: 0.8173 (mmtp) outliers start: 19 outliers final: 12 residues processed: 123 average time/residue: 0.2386 time to fit residues: 39.8806 Evaluate side-chains 113 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 97 time to evaluate : 0.987 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 GLN Chi-restraints excluded: chain A residue 184 MET Chi-restraints excluded: chain A residue 213 THR Chi-restraints excluded: chain A residue 331 THR Chi-restraints excluded: chain A residue 390 GLU Chi-restraints excluded: chain A residue 461 VAL Chi-restraints excluded: chain A residue 464 MET Chi-restraints excluded: chain A residue 526 PHE Chi-restraints excluded: chain A residue 593 CYS Chi-restraints excluded: chain A residue 656 VAL Chi-restraints excluded: chain A residue 710 THR Chi-restraints excluded: chain A residue 869 GLU Chi-restraints excluded: chain A residue 1003 VAL Chi-restraints excluded: chain C residue 43 SER Chi-restraints excluded: chain C residue 49 VAL Chi-restraints excluded: chain C residue 85 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 108 optimal weight: 1.9990 chunk 2 optimal weight: 1.9990 chunk 62 optimal weight: 3.9990 chunk 72 optimal weight: 1.9990 chunk 65 optimal weight: 0.9990 chunk 20 optimal weight: 0.9980 chunk 105 optimal weight: 0.6980 chunk 81 optimal weight: 1.9990 chunk 14 optimal weight: 1.9990 chunk 48 optimal weight: 0.9980 chunk 80 optimal weight: 0.7980 overall best weight: 0.8982 ------------------------------------------------------------------------------- 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 = 0.3763 r_free = 0.3763 target = 0.139246 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.100506 restraints weight = 12258.400| |-----------------------------------------------------------------------------| r_work (start): 0.3240 rms_B_bonded: 2.34 r_work: 0.3114 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.2970 rms_B_bonded: 4.60 restraints_weight: 0.2500 r_work (final): 0.2970 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8160 moved from start: 0.1790 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 9140 Z= 0.262 Angle : 0.521 10.617 12390 Z= 0.267 Chirality : 0.043 0.142 1374 Planarity : 0.004 0.042 1604 Dihedral : 6.198 56.894 1256 Min Nonbonded Distance : 1.930 Molprobity Statistics. All-atom Clashscore : 3.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 1.92 % Allowed : 7.26 % Favored : 90.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.43 % Cis-general : 0.09 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.11 (0.26), residues: 1126 helix: 1.42 (0.24), residues: 487 sheet: 0.75 (0.39), residues: 176 loop : 0.11 (0.30), residues: 463 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 141 HIS 0.003 0.001 HIS A 818 PHE 0.009 0.001 PHE A 724 TYR 0.019 0.001 TYR C 145 ARG 0.003 0.000 ARG C 143 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 100 time to evaluate : 1.008 Fit side-chains revert: symmetry clash REVERT: A 80 GLN cc_start: 0.8598 (OUTLIER) cc_final: 0.7537 (tm-30) REVERT: A 105 GLN cc_start: 0.8445 (pt0) cc_final: 0.8191 (pt0) REVERT: A 154 ASP cc_start: 0.7967 (t0) cc_final: 0.7648 (m-30) REVERT: A 179 GLU cc_start: 0.8773 (mm-30) cc_final: 0.7912 (pm20) REVERT: A 205 GLU cc_start: 0.6359 (pm20) cc_final: 0.6099 (pm20) REVERT: A 442 MET cc_start: 0.8821 (tpp) cc_final: 0.8569 (mmm) REVERT: A 464 MET cc_start: 0.8505 (OUTLIER) cc_final: 0.7291 (pmt) REVERT: A 526 PHE cc_start: 0.9413 (OUTLIER) cc_final: 0.9026 (m-80) REVERT: A 565 LYS cc_start: 0.8982 (mttp) cc_final: 0.8729 (mttt) REVERT: A 596 LYS cc_start: 0.8489 (mmtt) cc_final: 0.7850 (tmtt) REVERT: A 719 ARG cc_start: 0.7781 (ttp80) cc_final: 0.7534 (ttp80) REVERT: A 736 TYR cc_start: 0.8014 (m-80) cc_final: 0.7653 (m-10) REVERT: A 869 GLU cc_start: 0.8285 (OUTLIER) cc_final: 0.7982 (mm-30) REVERT: A 964 GLU cc_start: 0.7378 (mm-30) cc_final: 0.7105 (mt-10) REVERT: A 1001 GLU cc_start: 0.7520 (pm20) cc_final: 0.7297 (pm20) REVERT: C 101 LYS cc_start: 0.8427 (mttp) cc_final: 0.8219 (mmtp) REVERT: C 144 LYS cc_start: 0.9023 (ttpp) cc_final: 0.8783 (ttpp) outliers start: 19 outliers final: 13 residues processed: 115 average time/residue: 0.2540 time to fit residues: 39.4422 Evaluate side-chains 112 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 95 time to evaluate : 0.984 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 GLN Chi-restraints excluded: chain A residue 184 MET Chi-restraints excluded: chain A residue 213 THR Chi-restraints excluded: chain A residue 390 GLU Chi-restraints excluded: chain A residue 461 VAL Chi-restraints excluded: chain A residue 462 THR Chi-restraints excluded: chain A residue 464 MET Chi-restraints excluded: chain A residue 526 PHE Chi-restraints excluded: chain A residue 593 CYS Chi-restraints excluded: chain A residue 594 THR Chi-restraints excluded: chain A residue 656 VAL Chi-restraints excluded: chain A residue 710 THR Chi-restraints excluded: chain A residue 869 GLU Chi-restraints excluded: chain A residue 1003 VAL Chi-restraints excluded: chain C residue 43 SER Chi-restraints excluded: chain C residue 49 VAL Chi-restraints excluded: chain C residue 85 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 9 optimal weight: 0.9990 chunk 26 optimal weight: 0.0570 chunk 82 optimal weight: 0.9980 chunk 19 optimal weight: 0.5980 chunk 110 optimal weight: 1.9990 chunk 11 optimal weight: 1.9990 chunk 76 optimal weight: 7.9990 chunk 93 optimal weight: 0.4980 chunk 13 optimal weight: 2.9990 chunk 70 optimal weight: 0.6980 chunk 42 optimal weight: 1.9990 overall best weight: 0.5698 ------------------------------------------------------------------------------- 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 = 0.3776 r_free = 0.3776 target = 0.140206 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.101576 restraints weight = 12128.040| |-----------------------------------------------------------------------------| r_work (start): 0.3259 rms_B_bonded: 2.32 r_work: 0.3136 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.2995 rms_B_bonded: 4.57 restraints_weight: 0.2500 r_work (final): 0.2995 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8141 moved from start: 0.1884 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 9140 Z= 0.192 Angle : 0.492 10.318 12390 Z= 0.252 Chirality : 0.041 0.140 1374 Planarity : 0.004 0.043 1604 Dihedral : 6.042 55.351 1256 Min Nonbonded Distance : 1.976 Molprobity Statistics. All-atom Clashscore : 3.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 1.92 % Allowed : 7.96 % Favored : 90.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.43 % Cis-general : 0.09 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.16 (0.26), residues: 1126 helix: 1.47 (0.24), residues: 487 sheet: 0.73 (0.40), residues: 176 loop : 0.15 (0.31), residues: 463 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 669 HIS 0.002 0.001 HIS A 818 PHE 0.007 0.001 PHE A 613 TYR 0.015 0.001 TYR C 145 ARG 0.004 0.000 ARG A 804 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 106 time to evaluate : 0.984 Fit side-chains revert: symmetry clash REVERT: A 80 GLN cc_start: 0.8575 (OUTLIER) cc_final: 0.7216 (tm-30) REVERT: A 105 GLN cc_start: 0.8425 (pt0) cc_final: 0.8154 (pt0) REVERT: A 154 ASP cc_start: 0.7978 (t0) cc_final: 0.7681 (m-30) REVERT: A 179 GLU cc_start: 0.8733 (mm-30) cc_final: 0.7914 (pm20) REVERT: A 218 MET cc_start: 0.4692 (mmm) cc_final: 0.4338 (mmt) REVERT: A 464 MET cc_start: 0.8475 (OUTLIER) cc_final: 0.7246 (pmt) REVERT: A 526 PHE cc_start: 0.9409 (OUTLIER) cc_final: 0.9024 (m-80) REVERT: A 565 LYS cc_start: 0.8988 (mttp) cc_final: 0.8700 (mttt) REVERT: A 596 LYS cc_start: 0.8461 (mmtt) cc_final: 0.7864 (tmtt) REVERT: A 719 ARG cc_start: 0.7677 (ttp80) cc_final: 0.7311 (tmm-80) REVERT: A 736 TYR cc_start: 0.7963 (m-80) cc_final: 0.7644 (m-10) REVERT: A 869 GLU cc_start: 0.8237 (OUTLIER) cc_final: 0.7927 (mm-30) REVERT: A 960 LYS cc_start: 0.7353 (tppt) cc_final: 0.7009 (tppt) REVERT: A 964 GLU cc_start: 0.7328 (mm-30) cc_final: 0.7068 (mt-10) REVERT: A 1001 GLU cc_start: 0.7649 (pm20) cc_final: 0.7396 (pm20) REVERT: C 12 ASP cc_start: 0.8220 (m-30) cc_final: 0.7998 (m-30) REVERT: C 16 ASP cc_start: 0.7901 (p0) cc_final: 0.7100 (t0) REVERT: C 101 LYS cc_start: 0.8415 (mttp) cc_final: 0.8196 (mmtp) outliers start: 19 outliers final: 14 residues processed: 120 average time/residue: 0.2774 time to fit residues: 44.3626 Evaluate side-chains 117 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 99 time to evaluate : 1.054 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 GLN Chi-restraints excluded: chain A residue 184 MET Chi-restraints excluded: chain A residue 328 ILE Chi-restraints excluded: chain A residue 390 GLU Chi-restraints excluded: chain A residue 461 VAL Chi-restraints excluded: chain A residue 462 THR Chi-restraints excluded: chain A residue 464 MET Chi-restraints excluded: chain A residue 526 PHE Chi-restraints excluded: chain A residue 593 CYS Chi-restraints excluded: chain A residue 594 THR Chi-restraints excluded: chain A residue 656 VAL Chi-restraints excluded: chain A residue 710 THR Chi-restraints excluded: chain A residue 856 CYS Chi-restraints excluded: chain A residue 869 GLU Chi-restraints excluded: chain A residue 1003 VAL Chi-restraints excluded: chain C residue 43 SER Chi-restraints excluded: chain C residue 49 VAL Chi-restraints excluded: chain C residue 85 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 21 optimal weight: 1.9990 chunk 91 optimal weight: 0.8980 chunk 26 optimal weight: 0.9980 chunk 31 optimal weight: 1.9990 chunk 41 optimal weight: 0.0060 chunk 48 optimal weight: 0.6980 chunk 65 optimal weight: 0.6980 chunk 106 optimal weight: 0.4980 chunk 20 optimal weight: 0.7980 chunk 101 optimal weight: 3.9990 chunk 62 optimal weight: 0.9990 overall best weight: 0.5396 ------------------------------------------------------------------------------- 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 = 0.3774 r_free = 0.3774 target = 0.140425 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.101364 restraints weight = 12228.708| |-----------------------------------------------------------------------------| r_work (start): 0.3258 rms_B_bonded: 2.35 r_work: 0.3131 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.2987 rms_B_bonded: 4.64 restraints_weight: 0.2500 r_work (final): 0.2987 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8150 moved from start: 0.1956 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 9140 Z= 0.190 Angle : 0.501 10.595 12390 Z= 0.257 Chirality : 0.042 0.143 1374 Planarity : 0.004 0.043 1604 Dihedral : 6.066 55.250 1256 Min Nonbonded Distance : 1.975 Molprobity Statistics. All-atom Clashscore : 3.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Rotamer: Outliers : 2.12 % Allowed : 7.86 % Favored : 90.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.43 % Cis-general : 0.09 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.18 (0.26), residues: 1126 helix: 1.49 (0.24), residues: 487 sheet: 0.71 (0.39), residues: 176 loop : 0.17 (0.31), residues: 463 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 669 HIS 0.003 0.001 HIS C 32 PHE 0.009 0.001 PHE A 254 TYR 0.015 0.001 TYR C 145 ARG 0.006 0.000 ARG C 5 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 101 time to evaluate : 1.035 Fit side-chains revert: symmetry clash REVERT: A 80 GLN cc_start: 0.8563 (OUTLIER) cc_final: 0.7212 (tm-30) REVERT: A 105 GLN cc_start: 0.8440 (pt0) cc_final: 0.8164 (pt0) REVERT: A 154 ASP cc_start: 0.7931 (t0) cc_final: 0.7677 (m-30) REVERT: A 179 GLU cc_start: 0.8786 (mm-30) cc_final: 0.7944 (pm20) REVERT: A 196 MET cc_start: 0.6455 (mmp) cc_final: 0.5745 (mmm) REVERT: A 254 PHE cc_start: 0.7271 (p90) cc_final: 0.7029 (p90) REVERT: A 464 MET cc_start: 0.8475 (OUTLIER) cc_final: 0.7253 (pmt) REVERT: A 526 PHE cc_start: 0.9411 (OUTLIER) cc_final: 0.9026 (m-80) REVERT: A 565 LYS cc_start: 0.8996 (mttp) cc_final: 0.8708 (mttt) REVERT: A 596 LYS cc_start: 0.8456 (mmtt) cc_final: 0.7867 (tmtt) REVERT: A 736 TYR cc_start: 0.8011 (m-80) cc_final: 0.7737 (m-10) REVERT: A 869 GLU cc_start: 0.8239 (OUTLIER) cc_final: 0.7928 (mm-30) REVERT: A 964 GLU cc_start: 0.7319 (mm-30) cc_final: 0.7050 (mt-10) REVERT: A 1001 GLU cc_start: 0.7710 (pm20) cc_final: 0.7411 (pm20) REVERT: C 16 ASP cc_start: 0.7920 (p0) cc_final: 0.7101 (t0) REVERT: C 101 LYS cc_start: 0.8405 (mttp) cc_final: 0.8189 (mmtp) outliers start: 21 outliers final: 15 residues processed: 116 average time/residue: 0.2456 time to fit residues: 38.6294 Evaluate side-chains 115 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 96 time to evaluate : 0.996 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 GLN Chi-restraints excluded: chain A residue 184 MET Chi-restraints excluded: chain A residue 328 ILE Chi-restraints excluded: chain A residue 390 GLU Chi-restraints excluded: chain A residue 461 VAL Chi-restraints excluded: chain A residue 462 THR Chi-restraints excluded: chain A residue 464 MET Chi-restraints excluded: chain A residue 526 PHE Chi-restraints excluded: chain A residue 593 CYS Chi-restraints excluded: chain A residue 594 THR Chi-restraints excluded: chain A residue 656 VAL Chi-restraints excluded: chain A residue 710 THR Chi-restraints excluded: chain A residue 837 THR Chi-restraints excluded: chain A residue 856 CYS Chi-restraints excluded: chain A residue 869 GLU Chi-restraints excluded: chain A residue 940 LEU Chi-restraints excluded: chain A residue 1003 VAL Chi-restraints excluded: chain C residue 43 SER Chi-restraints excluded: chain C residue 85 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 49 optimal weight: 1.9990 chunk 53 optimal weight: 0.9990 chunk 7 optimal weight: 3.9990 chunk 18 optimal weight: 6.9990 chunk 95 optimal weight: 2.9990 chunk 35 optimal weight: 0.0970 chunk 102 optimal weight: 0.9990 chunk 45 optimal weight: 0.9990 chunk 91 optimal weight: 0.9990 chunk 42 optimal weight: 0.4980 chunk 75 optimal weight: 8.9990 overall best weight: 0.7184 ------------------------------------------------------------------------------- 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 = 0.3770 r_free = 0.3770 target = 0.139799 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.101147 restraints weight = 12244.518| |-----------------------------------------------------------------------------| r_work (start): 0.3252 rms_B_bonded: 2.33 r_work: 0.3128 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.2986 rms_B_bonded: 4.61 restraints_weight: 0.2500 r_work (final): 0.2986 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8158 moved from start: 0.2017 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 9140 Z= 0.224 Angle : 0.513 10.831 12390 Z= 0.262 Chirality : 0.042 0.139 1374 Planarity : 0.004 0.043 1604 Dihedral : 6.139 55.410 1256 Min Nonbonded Distance : 1.954 Molprobity Statistics. All-atom Clashscore : 3.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 2.02 % Allowed : 8.57 % Favored : 89.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.43 % Cis-general : 0.09 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.12 (0.26), residues: 1126 helix: 1.46 (0.24), residues: 487 sheet: 0.66 (0.39), residues: 176 loop : 0.12 (0.31), residues: 463 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 669 HIS 0.003 0.001 HIS A 305 PHE 0.008 0.001 PHE A 724 TYR 0.013 0.001 TYR C 145 ARG 0.006 0.000 ARG C 5 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 101 time to evaluate : 0.963 Fit side-chains revert: symmetry clash REVERT: A 80 GLN cc_start: 0.8585 (OUTLIER) cc_final: 0.7254 (tm-30) REVERT: A 105 GLN cc_start: 0.8426 (pt0) cc_final: 0.8147 (pt0) REVERT: A 154 ASP cc_start: 0.7895 (t0) cc_final: 0.7664 (m-30) REVERT: A 179 GLU cc_start: 0.8778 (mm-30) cc_final: 0.7981 (pm20) REVERT: A 196 MET cc_start: 0.6463 (mmp) cc_final: 0.6127 (mmm) REVERT: A 442 MET cc_start: 0.8811 (tpp) cc_final: 0.8549 (mmm) REVERT: A 464 MET cc_start: 0.8549 (OUTLIER) cc_final: 0.7413 (pmt) REVERT: A 526 PHE cc_start: 0.9417 (OUTLIER) cc_final: 0.9030 (m-80) REVERT: A 565 LYS cc_start: 0.8999 (mttp) cc_final: 0.8707 (mttt) REVERT: A 596 LYS cc_start: 0.8488 (mmtt) cc_final: 0.7902 (tmtt) REVERT: A 869 GLU cc_start: 0.8241 (OUTLIER) cc_final: 0.7932 (mm-30) REVERT: A 1001 GLU cc_start: 0.7740 (pm20) cc_final: 0.7452 (pm20) REVERT: C 16 ASP cc_start: 0.7906 (p0) cc_final: 0.7094 (t0) REVERT: C 101 LYS cc_start: 0.8413 (mttp) cc_final: 0.8192 (mmtp) REVERT: C 122 GLU cc_start: 0.8099 (OUTLIER) cc_final: 0.7783 (pm20) outliers start: 20 outliers final: 15 residues processed: 114 average time/residue: 0.2439 time to fit residues: 37.6061 Evaluate side-chains 118 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 98 time to evaluate : 1.062 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 GLN Chi-restraints excluded: chain A residue 184 MET Chi-restraints excluded: chain A residue 213 THR Chi-restraints excluded: chain A residue 328 ILE Chi-restraints excluded: chain A residue 390 GLU Chi-restraints excluded: chain A residue 461 VAL Chi-restraints excluded: chain A residue 462 THR Chi-restraints excluded: chain A residue 464 MET Chi-restraints excluded: chain A residue 526 PHE Chi-restraints excluded: chain A residue 593 CYS Chi-restraints excluded: chain A residue 594 THR Chi-restraints excluded: chain A residue 656 VAL Chi-restraints excluded: chain A residue 710 THR Chi-restraints excluded: chain A residue 837 THR Chi-restraints excluded: chain A residue 856 CYS Chi-restraints excluded: chain A residue 869 GLU Chi-restraints excluded: chain A residue 1003 VAL Chi-restraints excluded: chain C residue 43 SER Chi-restraints excluded: chain C residue 85 CYS Chi-restraints excluded: chain C residue 122 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 67 optimal weight: 0.8980 chunk 28 optimal weight: 1.9990 chunk 63 optimal weight: 0.9980 chunk 84 optimal weight: 0.9980 chunk 99 optimal weight: 7.9990 chunk 9 optimal weight: 0.0870 chunk 7 optimal weight: 3.9990 chunk 33 optimal weight: 0.9980 chunk 64 optimal weight: 0.9990 chunk 54 optimal weight: 0.9980 chunk 50 optimal weight: 0.9990 overall best weight: 0.7958 ------------------------------------------------------------------------------- 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 = 0.3762 r_free = 0.3762 target = 0.138500 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.100511 restraints weight = 12321.911| |-----------------------------------------------------------------------------| r_work (start): 0.3249 rms_B_bonded: 2.26 r_work: 0.3124 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.2981 rms_B_bonded: 4.50 restraints_weight: 0.2500 r_work (final): 0.2981 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8223 moved from start: 0.2064 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 9140 Z= 0.240 Angle : 0.519 10.322 12390 Z= 0.265 Chirality : 0.042 0.141 1374 Planarity : 0.004 0.043 1604 Dihedral : 6.178 55.687 1256 Min Nonbonded Distance : 1.950 Molprobity Statistics. All-atom Clashscore : 3.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 2.22 % Allowed : 8.77 % Favored : 89.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.43 % Cis-general : 0.09 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.08 (0.26), residues: 1126 helix: 1.43 (0.24), residues: 487 sheet: 0.64 (0.39), residues: 176 loop : 0.10 (0.31), residues: 463 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 669 HIS 0.003 0.001 HIS A 818 PHE 0.010 0.001 PHE A 724 TYR 0.012 0.001 TYR A 736 ARG 0.006 0.000 ARG C 5 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 94 time to evaluate : 1.054 Fit side-chains revert: symmetry clash REVERT: A 80 GLN cc_start: 0.8590 (OUTLIER) cc_final: 0.7304 (tm-30) REVERT: A 154 ASP cc_start: 0.7926 (t0) cc_final: 0.7640 (m-30) REVERT: A 179 GLU cc_start: 0.8788 (mm-30) cc_final: 0.8028 (pm20) REVERT: A 196 MET cc_start: 0.6468 (mmp) cc_final: 0.6140 (mmm) REVERT: A 442 MET cc_start: 0.8776 (tpp) cc_final: 0.8542 (mmm) REVERT: A 464 MET cc_start: 0.8581 (OUTLIER) cc_final: 0.7463 (pmt) REVERT: A 526 PHE cc_start: 0.9423 (OUTLIER) cc_final: 0.9049 (m-80) REVERT: A 543 MET cc_start: 0.8131 (mtm) cc_final: 0.7883 (mtp) REVERT: A 565 LYS cc_start: 0.9033 (mttp) cc_final: 0.8756 (mttt) REVERT: A 596 LYS cc_start: 0.8534 (mmtt) cc_final: 0.8001 (tmtt) REVERT: A 869 GLU cc_start: 0.8239 (OUTLIER) cc_final: 0.7937 (mm-30) REVERT: A 1001 GLU cc_start: 0.7799 (pm20) cc_final: 0.7511 (pm20) REVERT: C 16 ASP cc_start: 0.7883 (p0) cc_final: 0.7027 (t0) REVERT: C 101 LYS cc_start: 0.8439 (mttp) cc_final: 0.8208 (mmtp) REVERT: C 122 GLU cc_start: 0.8108 (OUTLIER) cc_final: 0.7810 (pm20) outliers start: 22 outliers final: 16 residues processed: 110 average time/residue: 0.2700 time to fit residues: 40.3489 Evaluate side-chains 111 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 90 time to evaluate : 1.979 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 GLN Chi-restraints excluded: chain A residue 184 MET Chi-restraints excluded: chain A residue 213 THR Chi-restraints excluded: chain A residue 328 ILE Chi-restraints excluded: chain A residue 390 GLU Chi-restraints excluded: chain A residue 461 VAL Chi-restraints excluded: chain A residue 462 THR Chi-restraints excluded: chain A residue 464 MET Chi-restraints excluded: chain A residue 526 PHE Chi-restraints excluded: chain A residue 568 THR Chi-restraints excluded: chain A residue 593 CYS Chi-restraints excluded: chain A residue 594 THR Chi-restraints excluded: chain A residue 656 VAL Chi-restraints excluded: chain A residue 710 THR Chi-restraints excluded: chain A residue 837 THR Chi-restraints excluded: chain A residue 856 CYS Chi-restraints excluded: chain A residue 869 GLU Chi-restraints excluded: chain A residue 1003 VAL Chi-restraints excluded: chain C residue 43 SER Chi-restraints excluded: chain C residue 85 CYS Chi-restraints excluded: chain C residue 122 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 44 optimal weight: 0.0670 chunk 68 optimal weight: 0.8980 chunk 33 optimal weight: 1.9990 chunk 16 optimal weight: 0.3980 chunk 28 optimal weight: 0.5980 chunk 82 optimal weight: 0.0270 chunk 4 optimal weight: 0.4980 chunk 50 optimal weight: 0.9980 chunk 6 optimal weight: 0.7980 chunk 56 optimal weight: 0.6980 chunk 12 optimal weight: 0.6980 overall best weight: 0.3176 ------------------------------------------------------------------------------- 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 = 0.3788 r_free = 0.3788 target = 0.141865 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.102946 restraints weight = 12241.296| |-----------------------------------------------------------------------------| r_work (start): 0.3275 rms_B_bonded: 2.35 r_work: 0.3150 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.3007 rms_B_bonded: 4.66 restraints_weight: 0.2500 r_work (final): 0.3007 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8123 moved from start: 0.2149 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 9140 Z= 0.151 Angle : 0.494 10.080 12390 Z= 0.251 Chirality : 0.041 0.140 1374 Planarity : 0.004 0.043 1604 Dihedral : 5.926 55.517 1256 Min Nonbonded Distance : 2.018 Molprobity Statistics. All-atom Clashscore : 3.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 1.71 % Allowed : 9.68 % Favored : 88.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.43 % Cis-general : 0.09 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.23 (0.26), residues: 1126 helix: 1.53 (0.24), residues: 488 sheet: 0.80 (0.40), residues: 174 loop : 0.16 (0.31), residues: 464 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 669 HIS 0.002 0.000 HIS A 305 PHE 0.009 0.001 PHE A 613 TYR 0.009 0.001 TYR C 145 ARG 0.004 0.000 ARG C 5 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 102 time to evaluate : 1.075 Fit side-chains revert: symmetry clash REVERT: A 105 GLN cc_start: 0.8425 (pt0) cc_final: 0.8142 (pt0) REVERT: A 154 ASP cc_start: 0.7918 (t0) cc_final: 0.7680 (m-30) REVERT: A 179 GLU cc_start: 0.8794 (mm-30) cc_final: 0.7957 (pm20) REVERT: A 196 MET cc_start: 0.6425 (mmp) cc_final: 0.6079 (mmm) REVERT: A 464 MET cc_start: 0.8488 (OUTLIER) cc_final: 0.7305 (pmt) REVERT: A 565 LYS cc_start: 0.8957 (mttp) cc_final: 0.8671 (mttt) REVERT: A 596 LYS cc_start: 0.8409 (mmtt) cc_final: 0.7875 (tmtt) REVERT: A 869 GLU cc_start: 0.8231 (OUTLIER) cc_final: 0.7946 (mm-30) REVERT: A 1001 GLU cc_start: 0.7714 (pm20) cc_final: 0.7418 (pm20) REVERT: C 16 ASP cc_start: 0.7923 (p0) cc_final: 0.7131 (t0) REVERT: C 101 LYS cc_start: 0.8398 (mttp) cc_final: 0.8147 (mmtp) outliers start: 17 outliers final: 12 residues processed: 115 average time/residue: 0.2806 time to fit residues: 43.3975 Evaluate side-chains 112 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 98 time to evaluate : 1.541 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 GLN Chi-restraints excluded: chain A residue 184 MET Chi-restraints excluded: chain A residue 213 THR Chi-restraints excluded: chain A residue 390 GLU Chi-restraints excluded: chain A residue 461 VAL Chi-restraints excluded: chain A residue 462 THR Chi-restraints excluded: chain A residue 464 MET Chi-restraints excluded: chain A residue 656 VAL Chi-restraints excluded: chain A residue 837 THR Chi-restraints excluded: chain A residue 856 CYS Chi-restraints excluded: chain A residue 869 GLU Chi-restraints excluded: chain A residue 1003 VAL Chi-restraints excluded: chain C residue 43 SER Chi-restraints excluded: chain C residue 85 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 21 optimal weight: 0.0470 chunk 10 optimal weight: 0.9980 chunk 108 optimal weight: 1.9990 chunk 55 optimal weight: 2.9990 chunk 72 optimal weight: 3.9990 chunk 101 optimal weight: 1.9990 chunk 105 optimal weight: 0.5980 chunk 36 optimal weight: 0.8980 chunk 44 optimal weight: 1.9990 chunk 75 optimal weight: 8.9990 chunk 57 optimal weight: 0.0370 overall best weight: 0.5156 ------------------------------------------------------------------------------- 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 = 0.3781 r_free = 0.3781 target = 0.141738 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.102151 restraints weight = 12269.378| |-----------------------------------------------------------------------------| r_work (start): 0.3265 rms_B_bonded: 2.38 r_work: 0.3139 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.2995 rms_B_bonded: 4.69 restraints_weight: 0.2500 r_work (final): 0.2995 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8147 moved from start: 0.2217 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 9140 Z= 0.182 Angle : 0.505 10.266 12390 Z= 0.256 Chirality : 0.041 0.138 1374 Planarity : 0.004 0.043 1604 Dihedral : 5.790 55.714 1254 Min Nonbonded Distance : 1.987 Molprobity Statistics. All-atom Clashscore : 3.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer: Outliers : 1.71 % Allowed : 9.68 % Favored : 88.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.43 % Cis-general : 0.09 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.23 (0.26), residues: 1126 helix: 1.54 (0.24), residues: 488 sheet: 0.78 (0.40), residues: 174 loop : 0.17 (0.31), residues: 464 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP C 93 HIS 0.002 0.001 HIS A 818 PHE 0.009 0.001 PHE A 724 TYR 0.011 0.001 TYR C 145 ARG 0.010 0.000 ARG C 8 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 99 time to evaluate : 0.964 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 105 GLN cc_start: 0.8363 (pt0) cc_final: 0.8118 (pt0) REVERT: A 154 ASP cc_start: 0.7912 (t0) cc_final: 0.7692 (m-30) REVERT: A 179 GLU cc_start: 0.8793 (mm-30) cc_final: 0.7959 (pm20) REVERT: A 196 MET cc_start: 0.6446 (mmp) cc_final: 0.5708 (mmm) REVERT: A 254 PHE cc_start: 0.7379 (p90) cc_final: 0.7105 (p90) REVERT: A 464 MET cc_start: 0.8505 (OUTLIER) cc_final: 0.7317 (pmt) REVERT: A 526 PHE cc_start: 0.9405 (OUTLIER) cc_final: 0.9009 (m-80) REVERT: A 565 LYS cc_start: 0.8972 (mttp) cc_final: 0.8686 (mttt) REVERT: A 596 LYS cc_start: 0.8411 (mmtt) cc_final: 0.7889 (tmtt) REVERT: A 869 GLU cc_start: 0.8249 (OUTLIER) cc_final: 0.7968 (mm-30) REVERT: A 1001 GLU cc_start: 0.7681 (pm20) cc_final: 0.7380 (pm20) REVERT: C 16 ASP cc_start: 0.7904 (p0) cc_final: 0.7096 (t0) REVERT: C 101 LYS cc_start: 0.8469 (mttp) cc_final: 0.8260 (mmtp) outliers start: 17 outliers final: 13 residues processed: 112 average time/residue: 0.2439 time to fit residues: 36.8130 Evaluate side-chains 112 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 96 time to evaluate : 1.112 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 GLN Chi-restraints excluded: chain A residue 184 MET Chi-restraints excluded: chain A residue 213 THR Chi-restraints excluded: chain A residue 390 GLU Chi-restraints excluded: chain A residue 461 VAL Chi-restraints excluded: chain A residue 462 THR Chi-restraints excluded: chain A residue 464 MET Chi-restraints excluded: chain A residue 526 PHE Chi-restraints excluded: chain A residue 568 THR Chi-restraints excluded: chain A residue 656 VAL Chi-restraints excluded: chain A residue 837 THR Chi-restraints excluded: chain A residue 856 CYS Chi-restraints excluded: chain A residue 869 GLU Chi-restraints excluded: chain A residue 1003 VAL Chi-restraints excluded: chain C residue 43 SER Chi-restraints excluded: chain C residue 85 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 10 optimal weight: 1.9990 chunk 106 optimal weight: 0.6980 chunk 31 optimal weight: 0.9980 chunk 44 optimal weight: 0.0970 chunk 20 optimal weight: 4.9990 chunk 73 optimal weight: 0.7980 chunk 76 optimal weight: 0.0570 chunk 29 optimal weight: 0.0870 chunk 105 optimal weight: 0.5980 chunk 96 optimal weight: 1.9990 chunk 5 optimal weight: 0.7980 overall best weight: 0.3074 ------------------------------------------------------------------------------- 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 = 0.3792 r_free = 0.3792 target = 0.142470 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.103307 restraints weight = 12275.330| |-----------------------------------------------------------------------------| r_work (start): 0.3285 rms_B_bonded: 2.37 r_work: 0.3158 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.3014 rms_B_bonded: 4.70 restraints_weight: 0.2500 r_work (final): 0.3014 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8125 moved from start: 0.2267 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 9140 Z= 0.145 Angle : 0.504 10.427 12390 Z= 0.255 Chirality : 0.041 0.138 1374 Planarity : 0.004 0.043 1604 Dihedral : 5.694 55.661 1254 Min Nonbonded Distance : 2.007 Molprobity Statistics. All-atom Clashscore : 3.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 1.41 % Allowed : 10.18 % Favored : 88.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.43 % Cis-general : 0.09 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.32 (0.26), residues: 1126 helix: 1.61 (0.24), residues: 487 sheet: 0.82 (0.40), residues: 174 loop : 0.22 (0.31), residues: 465 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP C 93 HIS 0.002 0.001 HIS A 305 PHE 0.010 0.001 PHE A 254 TYR 0.011 0.001 TYR C 145 ARG 0.012 0.000 ARG C 8 Origin is already at (0, 0, 0), no shifts will be applied Model does not fit in PDB format. =============================================================================== Job complete usr+sys time: 5603.46 seconds wall clock time: 98 minutes 54.76 seconds (5934.76 seconds total)