Starting phenix.real_space_refine on Wed Sep 17 14:01:39 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9b5p_44220/09_2025/9b5p_44220.cif Found real_map, /net/cci-nas-00/data/ceres_data/9b5p_44220/09_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_44220/09_2025/9b5p_44220.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9b5p_44220/09_2025/9b5p_44220.map" model { file = "/net/cci-nas-00/data/ceres_data/9b5p_44220/09_2025/9b5p_44220.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9b5p_44220/09_2025/9b5p_44220.cif" } resolution = 3.08 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/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: 2.30, per 1000 atoms: 0.26 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: 0.93 Conformation dependent library (CDL) restraints added in 341.0 milliseconds Enol-peptide restraints added in 1.2 microseconds 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: 0.52 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: 1.74 Time building geometry restraints manager: 1.18 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: 5.200 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: 0.000 Extract box with map and model: 0.150 Check model and map are aligned: 0.020 Set scattering table: 0.010 Process input model: 10.520 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.430 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.380 ------------------------------------------------------------------------------- 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 : 0.010 0.908 9143 Z= 0.501 Angle : 0.589 41.302 12392 Z= 0.288 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 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 ARG 0.002 0.000 ARG A 409 TYR 0.007 0.001 TYR A 736 PHE 0.008 0.001 PHE A 842 TRP 0.003 0.001 TRP A 669 HIS 0.002 0.000 HIS C 75 Details of bonding type rmsd covalent geometry : bond 0.00256 ( 9140) covalent geometry : angle 0.44640 (12390) SS BOND : bond 0.90787 ( 1) SS BOND : angle 30.24459 ( 2) hydrogen bonds : bond 0.15944 ( 424) hydrogen bonds : angle 5.74370 ( 1188) Misc. bond : bond 0.07729 ( 2) *********************** 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 : 0.368 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: 0.1428 time to fit residues: 30.9918 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 : 0.349 ------------------------------------------------------------------------------- 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 108 optimal weight: 0.7980 chunk 49 optimal weight: 0.8980 chunk 97 optimal weight: 1.9990 chunk 53 optimal weight: 1.9990 chunk 5 optimal weight: 0.4980 chunk 33 optimal weight: 1.9990 chunk 65 optimal weight: 0.9980 chunk 62 optimal weight: 0.9990 chunk 51 optimal weight: 0.9980 chunk 100 optimal weight: 3.9990 chunk 106 optimal weight: 2.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- 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 = 0.3756 r_free = 0.3756 target = 0.138045 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.100540 restraints weight = 12046.976| |-----------------------------------------------------------------------------| r_work (start): 0.3264 rms_B_bonded: 2.20 r_work: 0.3143 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.3002 rms_B_bonded: 4.39 restraints_weight: 0.2500 r_work (final): 0.3002 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8234 moved from start: 0.1463 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 9143 Z= 0.160 Angle : 0.516 9.214 12392 Z= 0.270 Chirality : 0.043 0.151 1374 Planarity : 0.004 0.039 1604 Dihedral : 6.230 58.236 1257 Min Nonbonded Distance : 1.940 Molprobity Statistics. All-atom Clashscore : 3.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer: Outliers : 2.02 % Allowed : 5.44 % Favored : 92.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.43 % Cis-general : 0.09 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.23 (0.26), residues: 1126 helix: 1.52 (0.24), residues: 486 sheet: 0.80 (0.40), residues: 170 loop : 0.18 (0.30), residues: 470 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C 5 TYR 0.008 0.001 TYR C 145 PHE 0.010 0.001 PHE A 842 TRP 0.006 0.001 TRP C 33 HIS 0.005 0.001 HIS C 32 Details of bonding type rmsd covalent geometry : bond 0.00390 ( 9140) covalent geometry : angle 0.51379 (12390) SS BOND : bond 0.01732 ( 1) SS BOND : angle 3.41195 ( 2) hydrogen bonds : bond 0.04596 ( 424) hydrogen bonds : angle 4.51031 ( 1188) Misc. bond : bond 0.00059 ( 2) *********************** 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 124 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 104 time to evaluate : 0.378 Fit side-chains revert: symmetry clash REVERT: A 80 GLN cc_start: 0.8544 (OUTLIER) cc_final: 0.7520 (tm-30) REVERT: A 105 GLN cc_start: 0.8366 (pt0) cc_final: 0.8117 (pt0) REVERT: A 165 ASP cc_start: 0.8850 (OUTLIER) cc_final: 0.8646 (t0) REVERT: A 179 GLU cc_start: 0.8789 (mm-30) cc_final: 0.7962 (pm20) REVERT: A 442 MET cc_start: 0.8733 (tpp) cc_final: 0.7918 (mmm) REVERT: A 464 MET cc_start: 0.8504 (OUTLIER) cc_final: 0.7363 (pmt) REVERT: A 526 PHE cc_start: 0.9430 (OUTLIER) cc_final: 0.9073 (m-80) REVERT: A 565 LYS cc_start: 0.9050 (mttp) cc_final: 0.8801 (mttm) REVERT: A 596 LYS cc_start: 0.8680 (mmtt) cc_final: 0.8098 (tmtt) REVERT: A 869 GLU cc_start: 0.8281 (OUTLIER) cc_final: 0.7991 (mm-30) REVERT: C 101 LYS cc_start: 0.8397 (mttp) cc_final: 0.8179 (mmtp) REVERT: C 112 ASP cc_start: 0.7932 (p0) cc_final: 0.7661 (p0) outliers start: 20 outliers final: 10 residues processed: 120 average time/residue: 0.1291 time to fit residues: 20.8852 Evaluate side-chains 108 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 93 time to evaluate : 0.357 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 GLN Chi-restraints excluded: chain A residue 165 ASP 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 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 51 optimal weight: 0.9980 chunk 34 optimal weight: 0.6980 chunk 10 optimal weight: 0.6980 chunk 108 optimal weight: 2.9990 chunk 69 optimal weight: 0.7980 chunk 75 optimal weight: 0.0060 chunk 90 optimal weight: 0.7980 chunk 109 optimal weight: 3.9990 chunk 37 optimal weight: 0.9980 chunk 66 optimal weight: 0.9980 chunk 21 optimal weight: 3.9990 overall best weight: 0.5996 ------------------------------------------------------------------------------- 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 = 0.139256 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3298 r_free = 0.3298 target = 0.101496 restraints weight = 11980.065| |-----------------------------------------------------------------------------| r_work (start): 0.3268 rms_B_bonded: 2.23 r_work: 0.3147 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.3005 rms_B_bonded: 4.45 restraints_weight: 0.2500 r_work (final): 0.3005 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8215 moved from start: 0.1674 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 9143 Z= 0.130 Angle : 0.525 13.679 12392 Z= 0.266 Chirality : 0.042 0.149 1374 Planarity : 0.004 0.041 1604 Dihedral : 6.109 55.534 1256 Min Nonbonded Distance : 1.976 Molprobity Statistics. All-atom Clashscore : 3.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Rotamer: Outliers : 2.02 % Allowed : 5.85 % Favored : 92.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.43 % Cis-general : 0.09 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.20 (0.26), residues: 1126 helix: 1.50 (0.24), residues: 487 sheet: 0.85 (0.40), residues: 176 loop : 0.14 (0.30), residues: 463 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 5 TYR 0.021 0.001 TYR A 736 PHE 0.007 0.001 PHE A 842 TRP 0.006 0.001 TRP A 669 HIS 0.004 0.001 HIS C 32 Details of bonding type rmsd covalent geometry : bond 0.00308 ( 9140) covalent geometry : angle 0.52412 (12390) SS BOND : bond 0.02171 ( 1) SS BOND : angle 2.63008 ( 2) hydrogen bonds : bond 0.04033 ( 424) hydrogen bonds : angle 4.32843 ( 1188) Misc. bond : bond 0.00201 ( 2) *********************** 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 126 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 106 time to evaluate : 0.363 Fit side-chains revert: symmetry clash REVERT: A 80 GLN cc_start: 0.8561 (OUTLIER) cc_final: 0.7265 (tm-30) REVERT: A 105 GLN cc_start: 0.8385 (pt0) cc_final: 0.8144 (pt0) REVERT: A 154 ASP cc_start: 0.7838 (t0) cc_final: 0.7629 (m-30) REVERT: A 165 ASP cc_start: 0.8848 (OUTLIER) cc_final: 0.8622 (t0) REVERT: A 179 GLU cc_start: 0.8795 (mm-30) cc_final: 0.7982 (pm20) REVERT: A 205 GLU cc_start: 0.6437 (pm20) cc_final: 0.6206 (pm20) REVERT: A 442 MET cc_start: 0.8754 (tpp) cc_final: 0.7926 (mmm) REVERT: A 464 MET cc_start: 0.8469 (OUTLIER) cc_final: 0.7344 (pmt) REVERT: A 526 PHE cc_start: 0.9419 (OUTLIER) cc_final: 0.9053 (m-80) REVERT: A 565 LYS cc_start: 0.9041 (mttp) cc_final: 0.8775 (mttm) REVERT: A 596 LYS cc_start: 0.8553 (mmtt) cc_final: 0.7947 (tmtt) REVERT: A 719 ARG cc_start: 0.7684 (ttp80) cc_final: 0.7355 (tmm-80) REVERT: A 869 GLU cc_start: 0.8272 (OUTLIER) cc_final: 0.7968 (mm-30) REVERT: A 960 LYS cc_start: 0.7313 (tppt) cc_final: 0.6985 (tppt) REVERT: A 964 GLU cc_start: 0.7404 (mm-30) cc_final: 0.7178 (mt-10) REVERT: A 1001 GLU cc_start: 0.7681 (pt0) cc_final: 0.7442 (pm20) REVERT: C 16 ASP cc_start: 0.7931 (p0) cc_final: 0.7163 (t0) REVERT: C 101 LYS cc_start: 0.8430 (mttp) cc_final: 0.8210 (mmtp) outliers start: 20 outliers final: 12 residues processed: 122 average time/residue: 0.1145 time to fit residues: 18.9865 Evaluate side-chains 114 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 97 time to evaluate : 0.407 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 GLN Chi-restraints excluded: chain A residue 165 ASP 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 3 optimal weight: 0.9980 chunk 80 optimal weight: 0.8980 chunk 64 optimal weight: 5.9990 chunk 90 optimal weight: 0.7980 chunk 15 optimal weight: 1.9990 chunk 104 optimal weight: 3.9990 chunk 53 optimal weight: 1.9990 chunk 100 optimal weight: 0.7980 chunk 93 optimal weight: 5.9990 chunk 74 optimal weight: 5.9990 chunk 68 optimal weight: 3.9990 overall best weight: 1.0982 ------------------------------------------------------------------------------- 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 = 0.3750 r_free = 0.3750 target = 0.137307 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3263 r_free = 0.3263 target = 0.099311 restraints weight = 12303.613| |-----------------------------------------------------------------------------| r_work (start): 0.3237 rms_B_bonded: 2.25 r_work: 0.3112 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.2970 rms_B_bonded: 4.47 restraints_weight: 0.2500 r_work (final): 0.2970 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8265 moved from start: 0.1825 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 9143 Z= 0.190 Angle : 0.538 10.472 12392 Z= 0.276 Chirality : 0.044 0.148 1374 Planarity : 0.004 0.042 1604 Dihedral : 6.321 58.510 1256 Min Nonbonded Distance : 1.913 Molprobity Statistics. All-atom Clashscore : 3.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 2.22 % Allowed : 7.26 % Favored : 90.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.43 % Cis-general : 0.09 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.02 (0.26), residues: 1126 helix: 1.37 (0.24), residues: 486 sheet: 0.67 (0.40), residues: 176 loop : 0.06 (0.30), residues: 464 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 409 TYR 0.022 0.001 TYR A 736 PHE 0.010 0.001 PHE A1007 TRP 0.007 0.001 TRP A 669 HIS 0.004 0.001 HIS A 818 Details of bonding type rmsd covalent geometry : bond 0.00474 ( 9140) covalent geometry : angle 0.53695 (12390) SS BOND : bond 0.02368 ( 1) SS BOND : angle 2.08340 ( 2) hydrogen bonds : bond 0.04364 ( 424) hydrogen bonds : angle 4.37555 ( 1188) Misc. bond : bond 0.00046 ( 2) *********************** 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 118 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 96 time to evaluate : 0.424 Fit side-chains revert: symmetry clash REVERT: A 105 GLN cc_start: 0.8423 (pt0) cc_final: 0.8179 (pt0) REVERT: A 179 GLU cc_start: 0.8799 (mm-30) cc_final: 0.7987 (pm20) REVERT: A 442 MET cc_start: 0.8780 (tpp) cc_final: 0.8563 (mmm) REVERT: A 464 MET cc_start: 0.8576 (OUTLIER) cc_final: 0.7418 (pmt) REVERT: A 526 PHE cc_start: 0.9431 (OUTLIER) cc_final: 0.9071 (m-80) REVERT: A 565 LYS cc_start: 0.9082 (mttp) cc_final: 0.8829 (mttt) REVERT: A 596 LYS cc_start: 0.8611 (mmtt) cc_final: 0.8033 (tmtt) REVERT: A 869 GLU cc_start: 0.8298 (OUTLIER) cc_final: 0.7994 (mm-30) REVERT: A 964 GLU cc_start: 0.7428 (mm-30) cc_final: 0.7203 (mt-10) REVERT: C 101 LYS cc_start: 0.8459 (mttp) cc_final: 0.8255 (mmtp) outliers start: 22 outliers final: 17 residues processed: 115 average time/residue: 0.1166 time to fit residues: 18.2332 Evaluate side-chains 108 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 88 time to evaluate : 0.351 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 GLN Chi-restraints excluded: chain A residue 165 ASP 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 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 38 optimal weight: 0.3980 chunk 110 optimal weight: 0.5980 chunk 98 optimal weight: 0.9990 chunk 35 optimal weight: 0.9980 chunk 80 optimal weight: 0.6980 chunk 93 optimal weight: 0.8980 chunk 40 optimal weight: 0.7980 chunk 24 optimal weight: 1.9990 chunk 66 optimal weight: 0.5980 chunk 48 optimal weight: 0.7980 chunk 64 optimal weight: 2.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- 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 = 0.3769 r_free = 0.3769 target = 0.139690 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.100871 restraints weight = 12283.787| |-----------------------------------------------------------------------------| r_work (start): 0.3247 rms_B_bonded: 2.33 r_work: 0.3120 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.2977 rms_B_bonded: 4.60 restraints_weight: 0.2500 r_work (final): 0.2977 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8156 moved from start: 0.1919 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 9143 Z= 0.130 Angle : 0.509 10.590 12392 Z= 0.261 Chirality : 0.042 0.142 1374 Planarity : 0.004 0.043 1604 Dihedral : 6.237 55.482 1256 Min Nonbonded Distance : 1.966 Molprobity Statistics. All-atom Clashscore : 3.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 2.12 % Allowed : 7.96 % Favored : 89.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.43 % Cis-general : 0.09 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.07 (0.26), residues: 1126 helix: 1.42 (0.24), residues: 487 sheet: 0.63 (0.40), residues: 176 loop : 0.10 (0.31), residues: 463 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 804 TYR 0.017 0.001 TYR C 145 PHE 0.010 0.001 PHE A 724 TRP 0.006 0.001 TRP A 669 HIS 0.003 0.001 HIS C 32 Details of bonding type rmsd covalent geometry : bond 0.00314 ( 9140) covalent geometry : angle 0.50883 (12390) SS BOND : bond 0.01610 ( 1) SS BOND : angle 1.61221 ( 2) hydrogen bonds : bond 0.03869 ( 424) hydrogen bonds : angle 4.26837 ( 1188) Misc. bond : bond 0.00024 ( 2) *********************** 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 115 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 94 time to evaluate : 0.356 Fit side-chains REVERT: A 80 GLN cc_start: 0.8587 (OUTLIER) cc_final: 0.7484 (tm-30) REVERT: A 105 GLN cc_start: 0.8459 (pt0) cc_final: 0.8202 (pt0) REVERT: A 154 ASP cc_start: 0.7971 (t0) cc_final: 0.7673 (m-30) REVERT: A 179 GLU cc_start: 0.8770 (mm-30) cc_final: 0.7923 (pm20) REVERT: A 218 MET cc_start: 0.4677 (mmm) cc_final: 0.4348 (mmt) REVERT: A 464 MET cc_start: 0.8518 (OUTLIER) cc_final: 0.7340 (pmt) REVERT: A 526 PHE cc_start: 0.9406 (OUTLIER) cc_final: 0.9022 (m-80) REVERT: A 565 LYS cc_start: 0.8982 (mttp) cc_final: 0.8701 (mttt) REVERT: A 596 LYS cc_start: 0.8480 (mmtt) cc_final: 0.7879 (tmtt) REVERT: A 719 ARG cc_start: 0.7684 (ttp80) cc_final: 0.7363 (tmm-80) REVERT: A 869 GLU cc_start: 0.8240 (OUTLIER) cc_final: 0.7924 (mm-30) REVERT: C 16 ASP cc_start: 0.7886 (p0) cc_final: 0.7102 (t0) REVERT: C 101 LYS cc_start: 0.8431 (mttp) cc_final: 0.8218 (mmtp) outliers start: 21 outliers final: 14 residues processed: 109 average time/residue: 0.1209 time to fit residues: 17.6508 Evaluate side-chains 109 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 91 time to evaluate : 0.349 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 GLN Chi-restraints excluded: chain A residue 165 ASP 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 498 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 940 LEU 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 28 optimal weight: 1.9990 chunk 44 optimal weight: 1.9990 chunk 56 optimal weight: 1.9990 chunk 0 optimal weight: 2.9990 chunk 20 optimal weight: 0.7980 chunk 93 optimal weight: 1.9990 chunk 88 optimal weight: 1.9990 chunk 43 optimal weight: 0.5980 chunk 109 optimal weight: 0.6980 chunk 40 optimal weight: 0.6980 chunk 61 optimal weight: 3.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- 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 = 0.3723 r_free = 0.3723 target = 0.137096 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.101885 restraints weight = 12135.320| |-----------------------------------------------------------------------------| r_work (start): 0.3254 rms_B_bonded: 2.23 r_work: 0.3119 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.2978 rms_B_bonded: 4.23 restraints_weight: 0.2500 r_work (final): 0.2978 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8271 moved from start: 0.2020 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 9143 Z= 0.171 Angle : 0.529 10.476 12392 Z= 0.272 Chirality : 0.043 0.149 1374 Planarity : 0.004 0.043 1604 Dihedral : 6.326 56.992 1256 Min Nonbonded Distance : 1.934 Molprobity Statistics. All-atom Clashscore : 3.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 2.72 % Allowed : 7.36 % Favored : 89.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.43 % Cis-general : 0.09 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.97 (0.26), residues: 1126 helix: 1.35 (0.24), residues: 487 sheet: 0.47 (0.39), residues: 181 loop : 0.07 (0.31), residues: 458 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 804 TYR 0.015 0.001 TYR A 736 PHE 0.009 0.001 PHE A1007 TRP 0.006 0.001 TRP A 669 HIS 0.003 0.001 HIS A 818 Details of bonding type rmsd covalent geometry : bond 0.00422 ( 9140) covalent geometry : angle 0.52899 (12390) SS BOND : bond 0.01705 ( 1) SS BOND : angle 1.74613 ( 2) hydrogen bonds : bond 0.04126 ( 424) hydrogen bonds : angle 4.36111 ( 1188) Misc. bond : bond 0.00014 ( 2) *********************** 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 118 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 91 time to evaluate : 0.378 Fit side-chains revert: symmetry clash REVERT: A 179 GLU cc_start: 0.8810 (mm-30) cc_final: 0.8044 (pm20) REVERT: A 442 MET cc_start: 0.8704 (tpp) cc_final: 0.8494 (mmm) REVERT: A 464 MET cc_start: 0.8476 (OUTLIER) cc_final: 0.7305 (pmt) REVERT: A 526 PHE cc_start: 0.9429 (OUTLIER) cc_final: 0.9061 (m-80) REVERT: A 565 LYS cc_start: 0.9083 (mttp) cc_final: 0.8819 (mttt) REVERT: A 596 LYS cc_start: 0.8607 (mmtt) cc_final: 0.8052 (tmtt) REVERT: A 869 GLU cc_start: 0.8257 (OUTLIER) cc_final: 0.7945 (mm-30) REVERT: A 964 GLU cc_start: 0.7273 (mm-30) cc_final: 0.6930 (mt-10) REVERT: C 16 ASP cc_start: 0.7887 (p0) cc_final: 0.7058 (t0) REVERT: C 101 LYS cc_start: 0.8443 (mttp) cc_final: 0.8216 (mmtp) REVERT: C 122 GLU cc_start: 0.8162 (OUTLIER) cc_final: 0.7937 (pm20) outliers start: 27 outliers final: 18 residues processed: 112 average time/residue: 0.1194 time to fit residues: 18.1074 Evaluate side-chains 111 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 89 time to evaluate : 0.327 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 165 ASP Chi-restraints excluded: chain A residue 213 THR Chi-restraints excluded: chain A residue 328 ILE 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 746 ILE 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 944 MET 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 76 optimal weight: 0.9980 chunk 72 optimal weight: 3.9990 chunk 52 optimal weight: 0.6980 chunk 111 optimal weight: 0.7980 chunk 11 optimal weight: 0.9980 chunk 81 optimal weight: 0.7980 chunk 86 optimal weight: 0.8980 chunk 10 optimal weight: 0.6980 chunk 17 optimal weight: 5.9990 chunk 84 optimal weight: 0.9980 chunk 45 optimal weight: 0.8980 overall best weight: 0.7780 ------------------------------------------------------------------------------- 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 = 0.3725 r_free = 0.3725 target = 0.137462 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3255 r_free = 0.3255 target = 0.100526 restraints weight = 12132.170| |-----------------------------------------------------------------------------| r_work (start): 0.3224 rms_B_bonded: 2.18 r_work: 0.3095 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.2954 rms_B_bonded: 4.43 restraints_weight: 0.2500 r_work (final): 0.2954 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8291 moved from start: 0.2074 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 9143 Z= 0.149 Angle : 0.524 10.267 12392 Z= 0.269 Chirality : 0.042 0.140 1374 Planarity : 0.004 0.044 1604 Dihedral : 5.952 56.012 1253 Min Nonbonded Distance : 1.950 Molprobity Statistics. All-atom Clashscore : 3.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 2.62 % Allowed : 8.37 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.02 (0.26), residues: 1126 helix: 1.36 (0.24), residues: 487 sheet: 0.59 (0.40), residues: 176 loop : 0.09 (0.31), residues: 463 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 804 TYR 0.014 0.001 TYR C 145 PHE 0.009 0.001 PHE A 724 TRP 0.005 0.001 TRP A 669 HIS 0.003 0.001 HIS C 32 Details of bonding type rmsd covalent geometry : bond 0.00365 ( 9140) covalent geometry : angle 0.52333 (12390) SS BOND : bond 0.01582 ( 1) SS BOND : angle 1.68218 ( 2) hydrogen bonds : bond 0.03971 ( 424) hydrogen bonds : angle 4.31604 ( 1188) Misc. bond : bond 0.00075 ( 2) *********************** 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 117 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 91 time to evaluate : 0.385 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 154 ASP cc_start: 0.7629 (m-30) cc_final: 0.7373 (m-30) REVERT: A 179 GLU cc_start: 0.8826 (mm-30) cc_final: 0.8059 (pm20) REVERT: A 464 MET cc_start: 0.8477 (OUTLIER) cc_final: 0.7297 (pmt) REVERT: A 526 PHE cc_start: 0.9426 (OUTLIER) cc_final: 0.9063 (m-80) REVERT: A 565 LYS cc_start: 0.9076 (mttp) cc_final: 0.8822 (mttt) REVERT: A 596 LYS cc_start: 0.8621 (mmtt) cc_final: 0.8084 (tmtt) REVERT: A 869 GLU cc_start: 0.8261 (OUTLIER) cc_final: 0.7957 (mm-30) REVERT: C 16 ASP cc_start: 0.7871 (p0) cc_final: 0.7050 (t0) REVERT: C 101 LYS cc_start: 0.8432 (mttp) cc_final: 0.8175 (mmtp) REVERT: C 122 GLU cc_start: 0.8141 (OUTLIER) cc_final: 0.7864 (pm20) outliers start: 26 outliers final: 20 residues processed: 111 average time/residue: 0.1204 time to fit residues: 18.0272 Evaluate side-chains 111 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 87 time to evaluate : 0.417 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 GLN Chi-restraints excluded: chain A residue 165 ASP 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 746 ILE 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 45 TYR 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 51 optimal weight: 1.9990 chunk 104 optimal weight: 0.0370 chunk 44 optimal weight: 0.0870 chunk 29 optimal weight: 4.9990 chunk 13 optimal weight: 1.9990 chunk 36 optimal weight: 0.9980 chunk 15 optimal weight: 0.6980 chunk 47 optimal weight: 2.9990 chunk 55 optimal weight: 1.9990 chunk 16 optimal weight: 2.9990 chunk 75 optimal weight: 9.9990 overall best weight: 0.7638 ------------------------------------------------------------------------------- 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 = 0.3724 r_free = 0.3724 target = 0.137427 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.102283 restraints weight = 12120.090| |-----------------------------------------------------------------------------| r_work (start): 0.3244 rms_B_bonded: 2.21 r_work: 0.3111 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.2973 rms_B_bonded: 4.23 restraints_weight: 0.2500 r_work (final): 0.2973 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8271 moved from start: 0.2122 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 9143 Z= 0.147 Angle : 0.528 10.466 12392 Z= 0.269 Chirality : 0.042 0.139 1374 Planarity : 0.004 0.044 1604 Dihedral : 5.921 55.814 1253 Min Nonbonded Distance : 1.957 Molprobity Statistics. All-atom Clashscore : 3.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 2.42 % Allowed : 8.57 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.01 (0.26), residues: 1126 helix: 1.38 (0.24), residues: 487 sheet: 0.57 (0.39), residues: 176 loop : 0.08 (0.31), residues: 463 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 804 TYR 0.012 0.001 TYR A 736 PHE 0.009 0.001 PHE A 724 TRP 0.006 0.001 TRP A 669 HIS 0.003 0.001 HIS A 818 Details of bonding type rmsd covalent geometry : bond 0.00359 ( 9140) covalent geometry : angle 0.52742 (12390) SS BOND : bond 0.01437 ( 1) SS BOND : angle 1.49596 ( 2) hydrogen bonds : bond 0.03913 ( 424) hydrogen bonds : angle 4.30371 ( 1188) Misc. bond : bond 0.00009 ( 2) *********************** 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 114 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 90 time to evaluate : 0.365 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 154 ASP cc_start: 0.7585 (m-30) cc_final: 0.7330 (m-30) REVERT: A 179 GLU cc_start: 0.8816 (mm-30) cc_final: 0.8050 (pm20) REVERT: A 464 MET cc_start: 0.8470 (OUTLIER) cc_final: 0.7293 (pmt) REVERT: A 526 PHE cc_start: 0.9422 (OUTLIER) cc_final: 0.9063 (m-80) REVERT: A 565 LYS cc_start: 0.9088 (mttp) cc_final: 0.8815 (mttt) REVERT: A 596 LYS cc_start: 0.8577 (mmtt) cc_final: 0.8055 (tmtt) REVERT: A 869 GLU cc_start: 0.8221 (OUTLIER) cc_final: 0.7913 (mm-30) REVERT: C 16 ASP cc_start: 0.7860 (p0) cc_final: 0.7017 (t0) REVERT: C 101 LYS cc_start: 0.8426 (mttp) cc_final: 0.8175 (mmtp) REVERT: C 122 GLU cc_start: 0.8098 (OUTLIER) cc_final: 0.7820 (pm20) outliers start: 24 outliers final: 18 residues processed: 106 average time/residue: 0.1200 time to fit residues: 17.1339 Evaluate side-chains 110 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 88 time to evaluate : 0.350 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 GLN Chi-restraints excluded: chain A residue 165 ASP 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 746 ILE 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 87 optimal weight: 1.9990 chunk 42 optimal weight: 0.9990 chunk 84 optimal weight: 0.8980 chunk 10 optimal weight: 0.7980 chunk 61 optimal weight: 2.9990 chunk 100 optimal weight: 2.9990 chunk 26 optimal weight: 0.8980 chunk 95 optimal weight: 0.8980 chunk 107 optimal weight: 2.9990 chunk 39 optimal weight: 1.9990 chunk 67 optimal weight: 0.7980 overall best weight: 0.8580 ------------------------------------------------------------------------------- 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 = 0.3724 r_free = 0.3724 target = 0.137412 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.100571 restraints weight = 12115.464| |-----------------------------------------------------------------------------| r_work (start): 0.3220 rms_B_bonded: 2.17 r_work: 0.3093 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.2952 rms_B_bonded: 4.42 restraints_weight: 0.2500 r_work (final): 0.2952 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8292 moved from start: 0.2150 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 9143 Z= 0.159 Angle : 0.534 10.782 12392 Z= 0.272 Chirality : 0.042 0.141 1374 Planarity : 0.004 0.044 1604 Dihedral : 5.939 56.549 1253 Min Nonbonded Distance : 1.943 Molprobity Statistics. All-atom Clashscore : 3.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 2.62 % Allowed : 8.77 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.98 (0.26), residues: 1126 helix: 1.36 (0.24), residues: 487 sheet: 0.56 (0.40), residues: 176 loop : 0.05 (0.30), residues: 463 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 804 TYR 0.013 0.001 TYR C 145 PHE 0.010 0.001 PHE A 724 TRP 0.006 0.001 TRP A 669 HIS 0.003 0.001 HIS A 818 Details of bonding type rmsd covalent geometry : bond 0.00393 ( 9140) covalent geometry : angle 0.53355 (12390) SS BOND : bond 0.01323 ( 1) SS BOND : angle 1.62107 ( 2) hydrogen bonds : bond 0.03968 ( 424) hydrogen bonds : angle 4.30810 ( 1188) Misc. bond : bond 0.00029 ( 2) *********************** 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: 26 poor density : 93 time to evaluate : 0.363 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 154 ASP cc_start: 0.7580 (m-30) cc_final: 0.7326 (m-30) REVERT: A 179 GLU cc_start: 0.8830 (mm-30) cc_final: 0.8063 (pm20) REVERT: A 442 MET cc_start: 0.8667 (tpp) cc_final: 0.8448 (mmm) REVERT: A 464 MET cc_start: 0.8517 (OUTLIER) cc_final: 0.7379 (pmt) REVERT: A 526 PHE cc_start: 0.9428 (OUTLIER) cc_final: 0.9127 (m-80) REVERT: A 565 LYS cc_start: 0.9106 (mttp) cc_final: 0.8834 (mttt) REVERT: A 596 LYS cc_start: 0.8604 (mmtt) cc_final: 0.8096 (tmtt) REVERT: A 754 TYR cc_start: 0.7768 (t80) cc_final: 0.7555 (t80) REVERT: A 869 GLU cc_start: 0.8260 (OUTLIER) cc_final: 0.7960 (mm-30) REVERT: A 964 GLU cc_start: 0.7275 (mm-30) cc_final: 0.6972 (mt-10) REVERT: C 16 ASP cc_start: 0.7861 (p0) cc_final: 0.7024 (t0) REVERT: C 101 LYS cc_start: 0.8438 (mttp) cc_final: 0.8185 (mmtp) REVERT: C 122 GLU cc_start: 0.8109 (OUTLIER) cc_final: 0.7819 (pm20) outliers start: 26 outliers final: 21 residues processed: 112 average time/residue: 0.1180 time to fit residues: 17.7954 Evaluate side-chains 114 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 89 time to evaluate : 0.351 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 GLN Chi-restraints excluded: chain A residue 165 ASP 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 524 GLU 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 746 ILE 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 45 TYR Chi-restraints excluded: chain C residue 85 CYS Chi-restraints excluded: chain C residue 122 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 8 optimal weight: 1.9990 chunk 18 optimal weight: 2.9990 chunk 49 optimal weight: 0.9980 chunk 110 optimal weight: 0.9980 chunk 109 optimal weight: 0.0000 chunk 86 optimal weight: 0.7980 chunk 66 optimal weight: 0.9980 chunk 102 optimal weight: 0.0980 chunk 1 optimal weight: 0.5980 chunk 10 optimal weight: 0.9980 chunk 42 optimal weight: 0.5980 overall best weight: 0.4184 ------------------------------------------------------------------------------- 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 = 0.3735 r_free = 0.3735 target = 0.138523 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.101487 restraints weight = 11972.132| |-----------------------------------------------------------------------------| r_work (start): 0.3241 rms_B_bonded: 2.17 r_work: 0.3119 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.2975 rms_B_bonded: 4.43 restraints_weight: 0.2500 r_work (final): 0.2975 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8268 moved from start: 0.2187 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 9143 Z= 0.112 Angle : 0.520 10.991 12392 Z= 0.264 Chirality : 0.041 0.143 1374 Planarity : 0.004 0.044 1604 Dihedral : 5.837 53.826 1253 Min Nonbonded Distance : 1.979 Molprobity Statistics. All-atom Clashscore : 3.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer: Outliers : 2.32 % Allowed : 9.07 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.07 (0.26), residues: 1126 helix: 1.43 (0.24), residues: 486 sheet: 0.62 (0.39), residues: 176 loop : 0.10 (0.31), residues: 464 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 645 TYR 0.013 0.001 TYR C 145 PHE 0.009 0.001 PHE A 724 TRP 0.032 0.001 TRP C 93 HIS 0.002 0.001 HIS C 32 Details of bonding type rmsd covalent geometry : bond 0.00261 ( 9140) covalent geometry : angle 0.51979 (12390) SS BOND : bond 0.01125 ( 1) SS BOND : angle 1.31399 ( 2) hydrogen bonds : bond 0.03629 ( 424) hydrogen bonds : angle 4.22852 ( 1188) Misc. bond : bond 0.00025 ( 2) ********************** 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 117 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 94 time to evaluate : 0.369 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 154 ASP cc_start: 0.7523 (m-30) cc_final: 0.7274 (m-30) REVERT: A 179 GLU cc_start: 0.8861 (mm-30) cc_final: 0.8090 (pm20) REVERT: A 464 MET cc_start: 0.8508 (OUTLIER) cc_final: 0.7386 (pmt) REVERT: A 526 PHE cc_start: 0.9423 (OUTLIER) cc_final: 0.9059 (m-80) REVERT: A 565 LYS cc_start: 0.9090 (mttp) cc_final: 0.8823 (mttt) REVERT: A 596 LYS cc_start: 0.8637 (mmtt) cc_final: 0.8153 (tmtt) REVERT: A 869 GLU cc_start: 0.8222 (OUTLIER) cc_final: 0.7921 (mm-30) REVERT: A 960 LYS cc_start: 0.7600 (tppt) cc_final: 0.7298 (tppt) REVERT: A 964 GLU cc_start: 0.7247 (mm-30) cc_final: 0.7025 (mt-10) REVERT: C 16 ASP cc_start: 0.7896 (p0) cc_final: 0.7085 (t0) REVERT: C 101 LYS cc_start: 0.8432 (mttp) cc_final: 0.8206 (mmtp) REVERT: C 122 GLU cc_start: 0.8060 (OUTLIER) cc_final: 0.7775 (pm20) outliers start: 23 outliers final: 18 residues processed: 111 average time/residue: 0.1207 time to fit residues: 18.0222 Evaluate side-chains 113 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 91 time to evaluate : 0.370 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 GLN 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 524 GLU 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 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 45 TYR Chi-restraints excluded: chain C residue 85 CYS Chi-restraints excluded: chain C residue 122 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 7 optimal weight: 0.4980 chunk 87 optimal weight: 0.9990 chunk 0 optimal weight: 2.9990 chunk 76 optimal weight: 0.9980 chunk 101 optimal weight: 0.8980 chunk 5 optimal weight: 0.9990 chunk 49 optimal weight: 1.9990 chunk 30 optimal weight: 1.9990 chunk 62 optimal weight: 2.9990 chunk 21 optimal weight: 4.9990 chunk 108 optimal weight: 0.7980 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 = 0.3725 r_free = 0.3725 target = 0.137518 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.100675 restraints weight = 11959.444| |-----------------------------------------------------------------------------| r_work (start): 0.3220 rms_B_bonded: 2.17 r_work: 0.3097 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.2957 rms_B_bonded: 4.38 restraints_weight: 0.2500 r_work (final): 0.2957 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8283 moved from start: 0.2205 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 9143 Z= 0.156 Angle : 0.537 11.008 12392 Z= 0.273 Chirality : 0.042 0.140 1374 Planarity : 0.004 0.043 1604 Dihedral : 5.900 56.357 1253 Min Nonbonded Distance : 1.941 Molprobity Statistics. All-atom Clashscore : 4.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 2.32 % Allowed : 9.17 % Favored : 88.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.43 % Cis-general : 0.09 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.00 (0.26), residues: 1126 helix: 1.37 (0.24), residues: 486 sheet: 0.59 (0.40), residues: 176 loop : 0.06 (0.30), residues: 464 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 8 TYR 0.013 0.001 TYR C 145 PHE 0.010 0.001 PHE A 724 TRP 0.020 0.001 TRP C 93 HIS 0.003 0.001 HIS A 818 Details of bonding type rmsd covalent geometry : bond 0.00387 ( 9140) covalent geometry : angle 0.53706 (12390) SS BOND : bond 0.01298 ( 1) SS BOND : angle 1.58065 ( 2) hydrogen bonds : bond 0.03938 ( 424) hydrogen bonds : angle 4.30150 ( 1188) Misc. bond : bond 0.00025 ( 2) Origin is already at (0, 0, 0), no shifts will be applied Model does not fit in PDB format. =============================================================================== Job complete usr+sys time: 2625.79 seconds wall clock time: 45 minutes 21.61 seconds (2721.61 seconds total)