Starting phenix.real_space_refine on Tue Feb 11 21:43:16 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8oif_16891/02_2025/8oif_16891.cif Found real_map, /net/cci-nas-00/data/ceres_data/8oif_16891/02_2025/8oif_16891.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8oif_16891/02_2025/8oif_16891.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8oif_16891/02_2025/8oif_16891.map" model { file = "/net/cci-nas-00/data/ceres_data/8oif_16891/02_2025/8oif_16891.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8oif_16891/02_2025/8oif_16891.cif" } resolution = 3.5 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= 0.003 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: 5 Type Number sf(0) Gaussians P 1 5.49 5 S 20 5.16 5 C 4237 2.51 5 N 1166 2.21 5 O 1165 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 8 residue(s): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib" Total number of atoms: 6589 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 4939 Number of conformers: 1 Conformer: "" Number of residues, atoms: 704, 4939 Classifications: {'peptide': 704} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 124} Link IDs: {'PTRANS': 41, 'TRANS': 662} Chain breaks: 8 Unresolved non-hydrogen bonds: 509 Unresolved non-hydrogen angles: 631 Unresolved non-hydrogen dihedrals: 411 Unresolved non-hydrogen chiralities: 16 Planarities with less than four sites: {'GLN:plan1': 20, 'ASP:plan': 19, 'TYR:plan': 1, 'TRP:plan': 1, 'HIS:plan': 5, 'PHE:plan': 2, 'GLU:plan': 31, 'ARG:plan': 14} Unresolved non-hydrogen planarities: 384 Chain: "I" Number of atoms: 560 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 560 Classifications: {'peptide': 79} Incomplete info: {'truncation_to_alanine': 17} Link IDs: {'PTRANS': 4, 'TRANS': 74} Unresolved non-hydrogen bonds: 67 Unresolved non-hydrogen angles: 81 Unresolved non-hydrogen dihedrals: 53 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 5, 'ARG:plan': 2, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 47 Chain: "L" Number of atoms: 1067 Number of conformers: 1 Conformer: "" Number of residues, atoms: 151, 1067 Classifications: {'peptide': 151} Incomplete info: {'truncation_to_alanine': 42} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 132} Unresolved non-hydrogen bonds: 171 Unresolved non-hydrogen angles: 206 Unresolved non-hydrogen dihedrals: 143 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLN:plan1': 2, 'TYR:plan': 1, 'ASN:plan1': 2, 'ASP:plan': 5, 'PHE:plan': 2, 'GLU:plan': 9, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 109 Chain: "I" Number of atoms: 23 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 23 Classifications: {'RNA': 1} Modifications used: {'rna2p': 1} Time building chain proxies: 4.84, per 1000 atoms: 0.73 Number of scatterers: 6589 At special positions: 0 Unit cell: (110.656, 118.317, 82.5664, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 20 16.00 P 1 15.00 O 1165 8.00 N 1166 7.00 C 4237 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS A 599 " - pdb=" SG CYS L 86 " distance=2.03 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=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 1.77 Conformation dependent library (CDL) restraints added in 1.0 seconds 1824 Ramachandran restraints generated. 912 Oldfield, 0 Emsley, 912 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1748 Finding SS restraints... Secondary structure from input PDB file: 31 helices and 8 sheets defined 37.9% alpha, 12.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.84 Creating SS restraints... Processing helix chain 'A' and resid 42 through 55 Processing helix chain 'A' and resid 68 through 72 Processing helix chain 'A' and resid 86 through 100 removed outlier: 4.417A pdb=" N GLU A 93 " --> pdb=" O GLU A 89 " (cutoff:3.500A) removed outlier: 4.579A pdb=" N LEU A 94 " --> pdb=" O ALA A 90 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N LEU A 98 " --> pdb=" O LEU A 94 " (cutoff:3.500A) removed outlier: 4.244A pdb=" N ASN A 99 " --> pdb=" O LEU A 95 " (cutoff:3.500A) Processing helix chain 'A' and resid 115 through 119 Processing helix chain 'A' and resid 130 through 143 Processing helix chain 'A' and resid 266 through 271 Processing helix chain 'A' and resid 281 through 305 removed outlier: 4.411A pdb=" N HIS A 285 " --> pdb=" O SER A 281 " (cutoff:3.500A) removed outlier: 4.145A pdb=" N HIS A 286 " --> pdb=" O GLN A 282 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N ALA A 287 " --> pdb=" O GLU A 283 " (cutoff:3.500A) Processing helix chain 'A' and resid 312 through 324 removed outlier: 3.579A pdb=" N ALA A 316 " --> pdb=" O ASP A 312 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N GLU A 317 " --> pdb=" O PRO A 313 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N THR A 318 " --> pdb=" O VAL A 314 " (cutoff:3.500A) Processing helix chain 'A' and resid 342 through 353 Processing helix chain 'A' and resid 357 through 375 Processing helix chain 'A' and resid 415 through 420 Processing helix chain 'A' and resid 423 through 433 removed outlier: 3.507A pdb=" N GLN A 427 " --> pdb=" O GLY A 423 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N ARG A 432 " --> pdb=" O GLU A 428 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N GLN A 433 " --> pdb=" O LYS A 429 " (cutoff:3.500A) Processing helix chain 'A' and resid 441 through 455 removed outlier: 3.723A pdb=" N GLU A 446 " --> pdb=" O ALA A 442 " (cutoff:3.500A) Processing helix chain 'A' and resid 473 through 480 removed outlier: 3.615A pdb=" N SER A 478 " --> pdb=" O SER A 475 " (cutoff:3.500A) Processing helix chain 'A' and resid 484 through 488 removed outlier: 3.741A pdb=" N VAL A 488 " --> pdb=" O SER A 485 " (cutoff:3.500A) Processing helix chain 'A' and resid 491 through 504 removed outlier: 3.638A pdb=" N VAL A 495 " --> pdb=" O PRO A 491 " (cutoff:3.500A) Processing helix chain 'A' and resid 525 through 532 removed outlier: 3.977A pdb=" N ARG A 531 " --> pdb=" O ASN A 527 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N VAL A 532 " --> pdb=" O PHE A 528 " (cutoff:3.500A) Processing helix chain 'A' and resid 542 through 556 Processing helix chain 'A' and resid 585 through 592 removed outlier: 3.531A pdb=" N SER A 591 " --> pdb=" O SER A 587 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N GLU A 592 " --> pdb=" O ALA A 588 " (cutoff:3.500A) Processing helix chain 'A' and resid 611 through 615 Processing helix chain 'A' and resid 853 through 872 removed outlier: 3.746A pdb=" N THR A 857 " --> pdb=" O ILE A 853 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N LYS A 870 " --> pdb=" O LEU A 866 " (cutoff:3.500A) Processing helix chain 'A' and resid 889 through 891 No H-bonds generated for 'chain 'A' and resid 889 through 891' Processing helix chain 'A' and resid 927 through 939 Processing helix chain 'A' and resid 959 through 967 removed outlier: 3.609A pdb=" N HIS A 966 " --> pdb=" O LYS A 962 " (cutoff:3.500A) Processing helix chain 'A' and resid 970 through 979 Processing helix chain 'I' and resid 103 through 116 removed outlier: 3.680A pdb=" N LEU I 107 " --> pdb=" O THR I 103 " (cutoff:3.500A) Processing helix chain 'I' and resid 136 through 141 removed outlier: 4.384A pdb=" N TYR I 140 " --> pdb=" O PRO I 136 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N GLY I 141 " --> pdb=" O LEU I 137 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 136 through 141' Processing helix chain 'L' and resid 4 through 17 removed outlier: 4.081A pdb=" N VAL L 8 " --> pdb=" O SER L 4 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N GLU L 12 " --> pdb=" O VAL L 8 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N ASP L 13 " --> pdb=" O LYS L 9 " (cutoff:3.500A) Processing helix chain 'L' and resid 100 through 114 removed outlier: 3.732A pdb=" N VAL L 104 " --> pdb=" O LYS L 100 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N ARG L 114 " --> pdb=" O VAL L 110 " (cutoff:3.500A) Processing helix chain 'L' and resid 122 through 132 removed outlier: 3.637A pdb=" N ASP L 127 " --> pdb=" O MET L 123 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N LEU L 128 " --> pdb=" O ASP L 124 " (cutoff:3.500A) Processing helix chain 'L' and resid 132 through 147 removed outlier: 3.570A pdb=" N PHE L 136 " --> pdb=" O ASN L 132 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N GLU L 141 " --> pdb=" O ARG L 137 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N GLU L 142 " --> pdb=" O LYS L 138 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 105 through 106 removed outlier: 6.207A pdb=" N LEU A 59 " --> pdb=" O VAL A 105 " (cutoff:3.500A) removed outlier: 6.340A pdb=" N VAL A 35 " --> pdb=" O THR A 60 " (cutoff:3.500A) removed outlier: 7.880A pdb=" N HIS A 62 " --> pdb=" O VAL A 35 " (cutoff:3.500A) removed outlier: 6.671A pdb=" N VAL A 37 " --> pdb=" O HIS A 62 " (cutoff:3.500A) removed outlier: 6.989A pdb=" N ARG A 34 " --> pdb=" O VAL A 121 " (cutoff:3.500A) removed outlier: 8.399A pdb=" N VAL A 123 " --> pdb=" O ARG A 34 " (cutoff:3.500A) removed outlier: 6.438A pdb=" N LEU A 36 " --> pdb=" O VAL A 123 " (cutoff:3.500A) removed outlier: 7.986A pdb=" N THR A 125 " --> pdb=" O LEU A 36 " (cutoff:3.500A) removed outlier: 6.481A pdb=" N SER A 38 " --> pdb=" O THR A 125 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N VAL A 155 " --> pdb=" O ARG A 152 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 166 through 168 Processing sheet with id=AA3, first strand: chain 'A' and resid 178 through 179 removed outlier: 3.721A pdb=" N VAL A 209 " --> pdb=" O ARG A 226 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 509 through 512 removed outlier: 6.511A pdb=" N TYR A 435 " --> pdb=" O THR A 465 " (cutoff:3.500A) removed outlier: 8.056A pdb=" N VAL A 467 " --> pdb=" O TYR A 435 " (cutoff:3.500A) removed outlier: 6.443A pdb=" N LEU A 437 " --> pdb=" O VAL A 467 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N ALA A 562 " --> pdb=" O ALA A 537 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 904 through 906 Processing sheet with id=AA6, first strand: chain 'A' and resid 917 through 919 removed outlier: 6.543A pdb=" N LEU A 917 " --> pdb=" O HIS A1009 " (cutoff:3.500A) removed outlier: 6.984A pdb=" N GLU A1011 " --> pdb=" O LEU A 917 " (cutoff:3.500A) removed outlier: 7.059A pdb=" N VAL A 919 " --> pdb=" O GLU A1011 " (cutoff:3.500A) removed outlier: 6.956A pdb=" N LEU A 946 " --> pdb=" O LEU A 953 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'I' and resid 93 through 98 Processing sheet with id=AA8, first strand: chain 'L' and resid 23 through 26 removed outlier: 4.248A pdb=" N LEU L 25 " --> pdb=" O HIS L 36 " (cutoff:3.500A) removed outlier: 6.423A pdb=" N HIS L 36 " --> pdb=" O LEU L 25 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N ALA L 37 " --> pdb=" O LEU L 53 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N LEU L 53 " --> pdb=" O ALA L 37 " (cutoff:3.500A) 280 hydrogen bonds defined for protein. 759 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: 1.98 Time building geometry restraints manager: 1.99 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 2169 1.34 - 1.46: 1537 1.46 - 1.58: 3014 1.58 - 1.70: 1 1.70 - 1.82: 27 Bond restraints: 6748 Sorted by residual: bond pdb=" CG PRO A 382 " pdb=" CD PRO A 382 " ideal model delta sigma weight residual 1.503 1.549 -0.046 3.40e-02 8.65e+02 1.85e+00 bond pdb=" C LEU A 456 " pdb=" N GLY A 457 " ideal model delta sigma weight residual 1.331 1.311 0.020 1.46e-02 4.69e+03 1.82e+00 bond pdb=" C4 AMP I 201 " pdb=" C5 AMP I 201 " ideal model delta sigma weight residual 1.490 1.466 0.024 2.00e-02 2.50e+03 1.43e+00 bond pdb=" CB PRO A 382 " pdb=" CG PRO A 382 " ideal model delta sigma weight residual 1.492 1.551 -0.059 5.00e-02 4.00e+02 1.41e+00 bond pdb=" CA GLU A 113 " pdb=" CB GLU A 113 " ideal model delta sigma weight residual 1.524 1.536 -0.012 1.31e-02 5.83e+03 8.95e-01 ... (remaining 6743 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.87: 9103 1.87 - 3.73: 144 3.73 - 5.60: 29 5.60 - 7.46: 3 7.46 - 9.33: 1 Bond angle restraints: 9280 Sorted by residual: angle pdb=" CA PRO A 382 " pdb=" N PRO A 382 " pdb=" CD PRO A 382 " ideal model delta sigma weight residual 112.00 106.39 5.61 1.40e+00 5.10e-01 1.61e+01 angle pdb=" N VAL A 102 " pdb=" CA VAL A 102 " pdb=" C VAL A 102 " ideal model delta sigma weight residual 113.71 109.95 3.76 9.50e-01 1.11e+00 1.57e+01 angle pdb=" CG1 ILE L 55 " pdb=" CB ILE L 55 " pdb=" CG2 ILE L 55 " ideal model delta sigma weight residual 110.70 101.37 9.33 3.00e+00 1.11e-01 9.67e+00 angle pdb=" N GLU A 113 " pdb=" CA GLU A 113 " pdb=" C GLU A 113 " ideal model delta sigma weight residual 111.81 107.53 4.28 1.44e+00 4.82e-01 8.84e+00 angle pdb=" CB MET A 54 " pdb=" CG MET A 54 " pdb=" SD MET A 54 " ideal model delta sigma weight residual 112.70 119.83 -7.13 3.00e+00 1.11e-01 5.64e+00 ... (remaining 9275 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.94: 3753 23.94 - 47.87: 193 47.87 - 71.81: 10 71.81 - 95.75: 1 95.75 - 119.68: 1 Dihedral angle restraints: 3958 sinusoidal: 1265 harmonic: 2693 Sorted by residual: dihedral pdb=" C5' AMP I 201 " pdb=" O5' AMP I 201 " pdb=" P AMP I 201 " pdb=" O3P AMP I 201 " ideal model delta sinusoidal sigma weight residual -60.00 -179.68 119.68 1 2.00e+01 2.50e-03 3.59e+01 dihedral pdb=" CA HIS A 907 " pdb=" C HIS A 907 " pdb=" N HIS A 908 " pdb=" CA HIS A 908 " ideal model delta harmonic sigma weight residual 180.00 154.83 25.17 0 5.00e+00 4.00e-02 2.53e+01 dihedral pdb=" CA PHE A 906 " pdb=" C PHE A 906 " pdb=" N HIS A 907 " pdb=" CA HIS A 907 " ideal model delta harmonic sigma weight residual 180.00 -161.21 -18.79 0 5.00e+00 4.00e-02 1.41e+01 ... (remaining 3955 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.042: 870 0.042 - 0.085: 206 0.085 - 0.127: 55 0.127 - 0.169: 1 0.169 - 0.211: 2 Chirality restraints: 1134 Sorted by residual: chirality pdb=" CB ILE L 55 " pdb=" CA ILE L 55 " pdb=" CG1 ILE L 55 " pdb=" CG2 ILE L 55 " both_signs ideal model delta sigma weight residual False 2.64 2.86 -0.21 2.00e-01 2.50e+01 1.12e+00 chirality pdb=" CB ILE L 68 " pdb=" CA ILE L 68 " pdb=" CG1 ILE L 68 " pdb=" CG2 ILE L 68 " both_signs ideal model delta sigma weight residual False 2.64 2.85 -0.20 2.00e-01 2.50e+01 1.02e+00 chirality pdb=" CA ILE L 55 " pdb=" N ILE L 55 " pdb=" C ILE L 55 " pdb=" CB ILE L 55 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.53e-01 ... (remaining 1131 not shown) Planarity restraints: 1191 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C MET A 381 " 0.078 5.00e-02 4.00e+02 1.15e-01 2.11e+01 pdb=" N PRO A 382 " -0.199 5.00e-02 4.00e+02 pdb=" CA PRO A 382 " 0.060 5.00e-02 4.00e+02 pdb=" CD PRO A 382 " 0.061 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA A 594 " 0.043 5.00e-02 4.00e+02 6.48e-02 6.73e+00 pdb=" N PRO A 595 " -0.112 5.00e-02 4.00e+02 pdb=" CA PRO A 595 " 0.034 5.00e-02 4.00e+02 pdb=" CD PRO A 595 " 0.036 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU A 395 " -0.037 5.00e-02 4.00e+02 5.59e-02 5.00e+00 pdb=" N PRO A 396 " 0.097 5.00e-02 4.00e+02 pdb=" CA PRO A 396 " -0.029 5.00e-02 4.00e+02 pdb=" CD PRO A 396 " -0.031 5.00e-02 4.00e+02 ... (remaining 1188 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 1320 2.78 - 3.31: 5865 3.31 - 3.84: 10156 3.84 - 4.37: 10721 4.37 - 4.90: 20038 Nonbonded interactions: 48100 Sorted by model distance: nonbonded pdb=" OG1 THR I 125 " pdb=" OD1 ASN I 151 " model vdw 2.246 3.040 nonbonded pdb=" OH TYR L 46 " pdb=" O TYR L 75 " model vdw 2.252 3.040 nonbonded pdb=" O THR A 927 " pdb=" OG SER A 930 " model vdw 2.259 3.040 nonbonded pdb=" OG SER I 112 " pdb=" O VAL I 117 " model vdw 2.280 3.040 nonbonded pdb=" O ASN A 527 " pdb=" OG SER A 530 " model vdw 2.302 3.040 ... (remaining 48095 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.900 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: 0.300 Check model and map are aligned: 0.050 Set scattering table: 0.070 Process input model: 19.770 Find NCS groups from input model: 0.060 Set up NCS constraints: 0.020 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:2.890 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.060 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7973 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 0.059 6748 Z= 0.227 Angle : 0.595 9.327 9280 Z= 0.295 Chirality : 0.039 0.211 1134 Planarity : 0.006 0.115 1191 Dihedral : 13.828 119.684 2207 Min Nonbonded Distance : 2.246 Molprobity Statistics. All-atom Clashscore : 6.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.80 % Favored : 93.20 % Rotamer: Outliers : 0.00 % Allowed : 12.11 % Favored : 87.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.59 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.42 (0.29), residues: 912 helix: 1.47 (0.31), residues: 316 sheet: -0.16 (0.45), residues: 137 loop : -1.65 (0.29), residues: 459 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP I 123 HIS 0.005 0.001 HIS A 286 PHE 0.009 0.001 PHE A 483 TYR 0.008 0.001 TYR A 596 ARG 0.003 0.000 ARG A 85 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1824 Ramachandran restraints generated. 912 Oldfield, 0 Emsley, 912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1824 Ramachandran restraints generated. 912 Oldfield, 0 Emsley, 912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 33 residues out of total 786 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 33 time to evaluate : 0.757 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 33 average time/residue: 0.1290 time to fit residues: 7.2641 Evaluate side-chains 32 residues out of total 786 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 32 time to evaluate : 0.807 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 77 optimal weight: 5.9990 chunk 69 optimal weight: 0.9980 chunk 38 optimal weight: 6.9990 chunk 23 optimal weight: 0.7980 chunk 47 optimal weight: 0.8980 chunk 37 optimal weight: 0.8980 chunk 72 optimal weight: 0.9980 chunk 27 optimal weight: 1.9990 chunk 43 optimal weight: 0.9980 chunk 53 optimal weight: 10.0000 chunk 83 optimal weight: 0.9990 overall best weight: 0.9180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1009 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.089158 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3179 r_free = 0.3179 target = 0.073224 restraints weight = 18414.745| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3208 r_free = 0.3208 target = 0.074601 restraints weight = 11113.459| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3228 r_free = 0.3228 target = 0.075534 restraints weight = 8071.889| |-----------------------------------------------------------------------------| r_work (final): 0.3224 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7940 moved from start: 0.0550 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 6748 Z= 0.169 Angle : 0.553 7.044 9280 Z= 0.264 Chirality : 0.039 0.168 1134 Planarity : 0.005 0.078 1191 Dihedral : 6.109 111.011 989 Min Nonbonded Distance : 2.565 Molprobity Statistics. All-atom Clashscore : 4.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.70 % Favored : 94.30 % Rotamer: Outliers : 1.33 % Allowed : 15.26 % Favored : 83.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.59 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.29 (0.29), residues: 912 helix: 1.59 (0.31), residues: 313 sheet: -0.10 (0.46), residues: 136 loop : -1.55 (0.29), residues: 463 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 69 HIS 0.004 0.001 HIS A 286 PHE 0.007 0.001 PHE A1005 TYR 0.009 0.001 TYR A1010 ARG 0.001 0.000 ARG A 616 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1824 Ramachandran restraints generated. 912 Oldfield, 0 Emsley, 912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1824 Ramachandran restraints generated. 912 Oldfield, 0 Emsley, 912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 43 residues out of total 786 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 35 time to evaluate : 0.755 Fit side-chains REVERT: A 469 MET cc_start: 0.6888 (pmm) cc_final: 0.6238 (pmm) REVERT: A 1005 PHE cc_start: 0.6361 (OUTLIER) cc_final: 0.5611 (t80) outliers start: 8 outliers final: 3 residues processed: 43 average time/residue: 0.1489 time to fit residues: 9.8909 Evaluate side-chains 40 residues out of total 786 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 36 time to evaluate : 0.760 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 167 THR Chi-restraints excluded: chain A residue 578 VAL Chi-restraints excluded: chain A residue 1005 PHE Chi-restraints excluded: chain L residue 72 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 37 optimal weight: 0.8980 chunk 54 optimal weight: 8.9990 chunk 29 optimal weight: 3.9990 chunk 14 optimal weight: 1.9990 chunk 58 optimal weight: 5.9990 chunk 15 optimal weight: 0.0170 chunk 78 optimal weight: 4.9990 chunk 71 optimal weight: 3.9990 chunk 9 optimal weight: 2.9990 chunk 67 optimal weight: 0.7980 chunk 75 optimal weight: 3.9990 overall best weight: 1.3422 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1009 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.088248 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3158 r_free = 0.3158 target = 0.072225 restraints weight = 18650.498| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3188 r_free = 0.3188 target = 0.073623 restraints weight = 11278.233| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3208 r_free = 0.3208 target = 0.074567 restraints weight = 8139.520| |-----------------------------------------------------------------------------| r_work (final): 0.3204 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7972 moved from start: 0.0722 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 6748 Z= 0.202 Angle : 0.572 10.196 9280 Z= 0.270 Chirality : 0.039 0.174 1134 Planarity : 0.005 0.071 1191 Dihedral : 5.695 92.817 989 Min Nonbonded Distance : 2.600 Molprobity Statistics. All-atom Clashscore : 4.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.36 % Favored : 93.64 % Rotamer: Outliers : 1.49 % Allowed : 17.25 % Favored : 81.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.59 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.34 (0.29), residues: 912 helix: 1.57 (0.31), residues: 314 sheet: -0.04 (0.49), residues: 121 loop : -1.59 (0.29), residues: 477 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP I 123 HIS 0.005 0.001 HIS A 286 PHE 0.007 0.001 PHE A 389 TYR 0.007 0.001 TYR A 596 ARG 0.001 0.000 ARG A 85 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1824 Ramachandran restraints generated. 912 Oldfield, 0 Emsley, 912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1824 Ramachandran restraints generated. 912 Oldfield, 0 Emsley, 912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 44 residues out of total 786 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 35 time to evaluate : 0.776 Fit side-chains REVERT: A 469 MET cc_start: 0.6989 (pmm) cc_final: 0.6289 (pmm) REVERT: A 1005 PHE cc_start: 0.6632 (OUTLIER) cc_final: 0.5575 (t80) outliers start: 9 outliers final: 5 residues processed: 44 average time/residue: 0.1142 time to fit residues: 8.7206 Evaluate side-chains 39 residues out of total 786 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 33 time to evaluate : 0.718 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 167 THR Chi-restraints excluded: chain A residue 395 LEU Chi-restraints excluded: chain A residue 467 VAL Chi-restraints excluded: chain A residue 1005 PHE Chi-restraints excluded: chain L residue 72 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 18 optimal weight: 10.0000 chunk 63 optimal weight: 0.6980 chunk 56 optimal weight: 3.9990 chunk 37 optimal weight: 1.9990 chunk 80 optimal weight: 0.5980 chunk 28 optimal weight: 3.9990 chunk 91 optimal weight: 2.9990 chunk 54 optimal weight: 7.9990 chunk 83 optimal weight: 3.9990 chunk 50 optimal weight: 1.9990 chunk 55 optimal weight: 2.9990 overall best weight: 1.6586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1009 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.087454 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3140 r_free = 0.3140 target = 0.071324 restraints weight = 18902.318| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3170 r_free = 0.3170 target = 0.072686 restraints weight = 11441.118| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3190 r_free = 0.3190 target = 0.073603 restraints weight = 8308.122| |-----------------------------------------------------------------------------| r_work (final): 0.3186 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8002 moved from start: 0.0930 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 6748 Z= 0.236 Angle : 0.586 8.950 9280 Z= 0.280 Chirality : 0.040 0.163 1134 Planarity : 0.005 0.063 1191 Dihedral : 5.242 62.208 989 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 5.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.80 % Favored : 93.20 % Rotamer: Outliers : 2.32 % Allowed : 16.92 % Favored : 80.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.59 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.43 (0.29), residues: 912 helix: 1.51 (0.31), residues: 314 sheet: -0.08 (0.49), residues: 121 loop : -1.65 (0.29), residues: 477 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP I 123 HIS 0.007 0.001 HIS A 286 PHE 0.008 0.001 PHE A 389 TYR 0.009 0.001 TYR A 596 ARG 0.002 0.000 ARG A 545 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1824 Ramachandran restraints generated. 912 Oldfield, 0 Emsley, 912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1824 Ramachandran restraints generated. 912 Oldfield, 0 Emsley, 912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 45 residues out of total 786 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 31 time to evaluate : 0.752 Fit side-chains REVERT: A 469 MET cc_start: 0.7094 (pmm) cc_final: 0.6325 (pmm) REVERT: A 1005 PHE cc_start: 0.6878 (OUTLIER) cc_final: 0.5624 (t80) outliers start: 14 outliers final: 10 residues processed: 45 average time/residue: 0.1097 time to fit residues: 9.4562 Evaluate side-chains 42 residues out of total 786 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 31 time to evaluate : 0.695 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 61 LEU Chi-restraints excluded: chain A residue 167 THR Chi-restraints excluded: chain A residue 361 VAL Chi-restraints excluded: chain A residue 395 LEU Chi-restraints excluded: chain A residue 438 VAL Chi-restraints excluded: chain A residue 464 LEU Chi-restraints excluded: chain A residue 467 VAL Chi-restraints excluded: chain A residue 578 VAL Chi-restraints excluded: chain A residue 1005 PHE Chi-restraints excluded: chain L residue 72 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 61 optimal weight: 5.9990 chunk 2 optimal weight: 0.2980 chunk 4 optimal weight: 0.8980 chunk 9 optimal weight: 1.9990 chunk 64 optimal weight: 2.9990 chunk 57 optimal weight: 0.6980 chunk 24 optimal weight: 2.9990 chunk 37 optimal weight: 0.9980 chunk 18 optimal weight: 0.0870 chunk 23 optimal weight: 0.9990 chunk 60 optimal weight: 6.9990 overall best weight: 0.5958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1009 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.089298 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3181 r_free = 0.3181 target = 0.073309 restraints weight = 18719.818| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3211 r_free = 0.3211 target = 0.074712 restraints weight = 11228.467| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3232 r_free = 0.3232 target = 0.075665 restraints weight = 8126.000| |-----------------------------------------------------------------------------| r_work (final): 0.3227 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7938 moved from start: 0.1019 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 6748 Z= 0.145 Angle : 0.533 7.385 9280 Z= 0.251 Chirality : 0.038 0.143 1134 Planarity : 0.005 0.057 1191 Dihedral : 4.514 46.887 989 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 4.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.15 % Favored : 94.85 % Rotamer: Outliers : 2.16 % Allowed : 18.57 % Favored : 79.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.59 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.21 (0.29), residues: 912 helix: 1.71 (0.31), residues: 314 sheet: -0.04 (0.49), residues: 122 loop : -1.52 (0.29), residues: 476 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP I 123 HIS 0.004 0.001 HIS A 554 PHE 0.006 0.001 PHE A 159 TYR 0.007 0.001 TYR A 603 ARG 0.001 0.000 ARG A 551 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1824 Ramachandran restraints generated. 912 Oldfield, 0 Emsley, 912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1824 Ramachandran restraints generated. 912 Oldfield, 0 Emsley, 912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 49 residues out of total 786 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 36 time to evaluate : 0.704 Fit side-chains REVERT: A 469 MET cc_start: 0.7049 (pmm) cc_final: 0.6383 (pmm) REVERT: A 1005 PHE cc_start: 0.6713 (OUTLIER) cc_final: 0.5631 (t80) outliers start: 13 outliers final: 9 residues processed: 49 average time/residue: 0.1090 time to fit residues: 9.0485 Evaluate side-chains 44 residues out of total 786 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 34 time to evaluate : 0.808 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 61 LEU Chi-restraints excluded: chain A residue 167 THR Chi-restraints excluded: chain A residue 361 VAL Chi-restraints excluded: chain A residue 395 LEU Chi-restraints excluded: chain A residue 464 LEU Chi-restraints excluded: chain A residue 467 VAL Chi-restraints excluded: chain A residue 578 VAL Chi-restraints excluded: chain A residue 1005 PHE Chi-restraints excluded: chain L residue 72 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 3 optimal weight: 0.4980 chunk 76 optimal weight: 0.0070 chunk 23 optimal weight: 0.9990 chunk 35 optimal weight: 3.9990 chunk 22 optimal weight: 6.9990 chunk 55 optimal weight: 0.7980 chunk 36 optimal weight: 1.9990 chunk 52 optimal weight: 0.0020 chunk 17 optimal weight: 1.9990 chunk 90 optimal weight: 8.9990 chunk 32 optimal weight: 0.9980 overall best weight: 0.4606 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1009 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.090070 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3199 r_free = 0.3199 target = 0.074170 restraints weight = 18384.375| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3230 r_free = 0.3230 target = 0.075602 restraints weight = 11034.024| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3249 r_free = 0.3249 target = 0.076550 restraints weight = 7968.241| |-----------------------------------------------------------------------------| r_work (final): 0.3247 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7914 moved from start: 0.1134 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 6748 Z= 0.142 Angle : 0.528 7.499 9280 Z= 0.248 Chirality : 0.038 0.167 1134 Planarity : 0.005 0.056 1191 Dihedral : 4.272 47.209 989 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 4.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.26 % Favored : 94.74 % Rotamer: Outliers : 2.49 % Allowed : 18.41 % Favored : 79.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.59 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.09 (0.29), residues: 912 helix: 1.80 (0.31), residues: 314 sheet: -0.07 (0.43), residues: 152 loop : -1.47 (0.30), residues: 446 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP I 123 HIS 0.003 0.001 HIS A 554 PHE 0.005 0.001 PHE A 159 TYR 0.005 0.001 TYR A 603 ARG 0.001 0.000 ARG A 551 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1824 Ramachandran restraints generated. 912 Oldfield, 0 Emsley, 912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1824 Ramachandran restraints generated. 912 Oldfield, 0 Emsley, 912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 52 residues out of total 786 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 37 time to evaluate : 0.728 Fit side-chains REVERT: A 75 GLN cc_start: 0.8751 (OUTLIER) cc_final: 0.8521 (tm-30) REVERT: A 469 MET cc_start: 0.7005 (pmm) cc_final: 0.6283 (pmm) REVERT: A 1005 PHE cc_start: 0.6597 (OUTLIER) cc_final: 0.5574 (t80) outliers start: 15 outliers final: 10 residues processed: 51 average time/residue: 0.1134 time to fit residues: 9.6042 Evaluate side-chains 47 residues out of total 786 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 35 time to evaluate : 0.776 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 61 LEU Chi-restraints excluded: chain A residue 75 GLN Chi-restraints excluded: chain A residue 167 THR Chi-restraints excluded: chain A residue 361 VAL Chi-restraints excluded: chain A residue 395 LEU Chi-restraints excluded: chain A residue 438 VAL Chi-restraints excluded: chain A residue 464 LEU Chi-restraints excluded: chain A residue 467 VAL Chi-restraints excluded: chain A residue 578 VAL Chi-restraints excluded: chain A residue 1005 PHE Chi-restraints excluded: chain L residue 72 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 50 optimal weight: 0.9990 chunk 61 optimal weight: 0.8980 chunk 60 optimal weight: 0.4980 chunk 72 optimal weight: 1.9990 chunk 89 optimal weight: 7.9990 chunk 3 optimal weight: 0.5980 chunk 48 optimal weight: 1.9990 chunk 26 optimal weight: 0.9990 chunk 78 optimal weight: 0.8980 chunk 19 optimal weight: 8.9990 chunk 53 optimal weight: 5.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1009 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.089601 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3189 r_free = 0.3189 target = 0.073710 restraints weight = 18464.087| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3220 r_free = 0.3220 target = 0.075142 restraints weight = 11057.866| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.076083 restraints weight = 7962.227| |-----------------------------------------------------------------------------| r_work (final): 0.3235 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7929 moved from start: 0.1157 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 6748 Z= 0.156 Angle : 0.539 7.991 9280 Z= 0.250 Chirality : 0.038 0.181 1134 Planarity : 0.005 0.056 1191 Dihedral : 4.270 47.455 989 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 5.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.48 % Favored : 94.52 % Rotamer: Outliers : 2.65 % Allowed : 18.91 % Favored : 78.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.59 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.10 (0.29), residues: 912 helix: 1.81 (0.31), residues: 313 sheet: -0.06 (0.44), residues: 151 loop : -1.50 (0.30), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP I 123 HIS 0.003 0.001 HIS A 286 PHE 0.006 0.001 PHE A 159 TYR 0.007 0.001 TYR A 603 ARG 0.001 0.000 ARG A 551 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1824 Ramachandran restraints generated. 912 Oldfield, 0 Emsley, 912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1824 Ramachandran restraints generated. 912 Oldfield, 0 Emsley, 912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 52 residues out of total 786 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 36 time to evaluate : 0.718 Fit side-chains REVERT: A 469 MET cc_start: 0.7105 (pmm) cc_final: 0.6358 (pmm) REVERT: A 1005 PHE cc_start: 0.6613 (OUTLIER) cc_final: 0.5592 (t80) outliers start: 16 outliers final: 11 residues processed: 51 average time/residue: 0.1112 time to fit residues: 9.5018 Evaluate side-chains 47 residues out of total 786 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 35 time to evaluate : 0.701 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 61 LEU Chi-restraints excluded: chain A residue 167 THR Chi-restraints excluded: chain A residue 168 VAL Chi-restraints excluded: chain A residue 361 VAL Chi-restraints excluded: chain A residue 395 LEU Chi-restraints excluded: chain A residue 438 VAL Chi-restraints excluded: chain A residue 464 LEU Chi-restraints excluded: chain A residue 467 VAL Chi-restraints excluded: chain A residue 578 VAL Chi-restraints excluded: chain A residue 1005 PHE Chi-restraints excluded: chain L residue 72 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 43 optimal weight: 0.7980 chunk 38 optimal weight: 3.9990 chunk 20 optimal weight: 0.7980 chunk 69 optimal weight: 3.9990 chunk 18 optimal weight: 0.3980 chunk 68 optimal weight: 0.5980 chunk 84 optimal weight: 4.9990 chunk 13 optimal weight: 0.0370 chunk 76 optimal weight: 0.7980 chunk 54 optimal weight: 0.0980 chunk 31 optimal weight: 0.9990 overall best weight: 0.3858 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 891 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.090824 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3216 r_free = 0.3216 target = 0.075002 restraints weight = 18373.408| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.3246 r_free = 0.3246 target = 0.076451 restraints weight = 10946.263| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.077356 restraints weight = 7850.282| |-----------------------------------------------------------------------------| r_work (final): 0.3261 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7891 moved from start: 0.1310 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 6748 Z= 0.135 Angle : 0.526 7.647 9280 Z= 0.243 Chirality : 0.038 0.160 1134 Planarity : 0.004 0.055 1191 Dihedral : 4.108 48.068 989 Min Nonbonded Distance : 2.567 Molprobity Statistics. All-atom Clashscore : 5.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.82 % Favored : 95.18 % Rotamer: Outliers : 2.82 % Allowed : 18.74 % Favored : 78.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.59 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.02 (0.29), residues: 912 helix: 1.93 (0.31), residues: 311 sheet: -0.07 (0.43), residues: 153 loop : -1.41 (0.30), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP I 123 HIS 0.003 0.001 HIS A 554 PHE 0.005 0.001 PHE A 159 TYR 0.004 0.000 TYR A 603 ARG 0.001 0.000 ARG A 551 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1824 Ramachandran restraints generated. 912 Oldfield, 0 Emsley, 912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1824 Ramachandran restraints generated. 912 Oldfield, 0 Emsley, 912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 58 residues out of total 786 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 41 time to evaluate : 0.696 Fit side-chains REVERT: A 75 GLN cc_start: 0.8752 (OUTLIER) cc_final: 0.8501 (tm-30) REVERT: A 469 MET cc_start: 0.7084 (pmm) cc_final: 0.6305 (pmm) REVERT: A 1005 PHE cc_start: 0.6435 (OUTLIER) cc_final: 0.5454 (t80) outliers start: 17 outliers final: 11 residues processed: 56 average time/residue: 0.1291 time to fit residues: 11.2371 Evaluate side-chains 52 residues out of total 786 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 39 time to evaluate : 0.801 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 61 LEU Chi-restraints excluded: chain A residue 75 GLN Chi-restraints excluded: chain A residue 167 THR Chi-restraints excluded: chain A residue 168 VAL Chi-restraints excluded: chain A residue 261 THR Chi-restraints excluded: chain A residue 438 VAL Chi-restraints excluded: chain A residue 464 LEU Chi-restraints excluded: chain A residue 467 VAL Chi-restraints excluded: chain A residue 503 LEU Chi-restraints excluded: chain A residue 578 VAL Chi-restraints excluded: chain A residue 1005 PHE Chi-restraints excluded: chain L residue 72 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 81 optimal weight: 4.9990 chunk 68 optimal weight: 2.9990 chunk 42 optimal weight: 2.9990 chunk 75 optimal weight: 3.9990 chunk 18 optimal weight: 10.0000 chunk 69 optimal weight: 0.9980 chunk 91 optimal weight: 2.9990 chunk 41 optimal weight: 2.9990 chunk 79 optimal weight: 4.9990 chunk 23 optimal weight: 0.8980 chunk 28 optimal weight: 0.9980 overall best weight: 1.7784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 50 ASN A 887 HIS ** A1009 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.087828 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3146 r_free = 0.3146 target = 0.071693 restraints weight = 18820.468| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3176 r_free = 0.3176 target = 0.073070 restraints weight = 11365.747| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3195 r_free = 0.3195 target = 0.073995 restraints weight = 8256.260| |-----------------------------------------------------------------------------| r_work (final): 0.3191 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7989 moved from start: 0.1217 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 6748 Z= 0.247 Angle : 0.592 7.877 9280 Z= 0.279 Chirality : 0.040 0.174 1134 Planarity : 0.005 0.056 1191 Dihedral : 4.530 47.535 989 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 5.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.69 % Favored : 93.31 % Rotamer: Outliers : 2.99 % Allowed : 18.57 % Favored : 78.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.59 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.20 (0.29), residues: 912 helix: 1.80 (0.31), residues: 310 sheet: -0.28 (0.47), residues: 127 loop : -1.48 (0.29), residues: 475 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP I 123 HIS 0.005 0.001 HIS A 286 PHE 0.008 0.001 PHE A1005 TYR 0.008 0.001 TYR A 603 ARG 0.003 0.000 ARG A 85 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1824 Ramachandran restraints generated. 912 Oldfield, 0 Emsley, 912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1824 Ramachandran restraints generated. 912 Oldfield, 0 Emsley, 912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 53 residues out of total 786 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 35 time to evaluate : 0.739 Fit side-chains REVERT: A 75 GLN cc_start: 0.8847 (OUTLIER) cc_final: 0.8510 (tm-30) REVERT: A 469 MET cc_start: 0.7138 (pmm) cc_final: 0.6417 (pmm) REVERT: A 867 GLU cc_start: 0.7681 (mm-30) cc_final: 0.7377 (mm-30) REVERT: A 1005 PHE cc_start: 0.6832 (OUTLIER) cc_final: 0.5686 (t80) outliers start: 18 outliers final: 15 residues processed: 52 average time/residue: 0.1157 time to fit residues: 10.1231 Evaluate side-chains 52 residues out of total 786 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 35 time to evaluate : 0.796 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 61 LEU Chi-restraints excluded: chain A residue 75 GLN Chi-restraints excluded: chain A residue 105 VAL Chi-restraints excluded: chain A residue 167 THR Chi-restraints excluded: chain A residue 168 VAL Chi-restraints excluded: chain A residue 191 ILE Chi-restraints excluded: chain A residue 361 VAL Chi-restraints excluded: chain A residue 438 VAL Chi-restraints excluded: chain A residue 464 LEU Chi-restraints excluded: chain A residue 467 VAL Chi-restraints excluded: chain A residue 503 LEU Chi-restraints excluded: chain A residue 578 VAL Chi-restraints excluded: chain A residue 871 VAL Chi-restraints excluded: chain A residue 1005 PHE Chi-restraints excluded: chain I residue 103 THR Chi-restraints excluded: chain L residue 72 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 35 optimal weight: 2.9990 chunk 84 optimal weight: 0.7980 chunk 8 optimal weight: 0.5980 chunk 65 optimal weight: 4.9990 chunk 2 optimal weight: 5.9990 chunk 0 optimal weight: 1.9990 chunk 74 optimal weight: 5.9990 chunk 23 optimal weight: 3.9990 chunk 16 optimal weight: 5.9990 chunk 18 optimal weight: 0.0000 chunk 67 optimal weight: 5.9990 overall best weight: 1.2788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1009 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.088280 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3156 r_free = 0.3156 target = 0.072160 restraints weight = 18895.218| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3187 r_free = 0.3187 target = 0.073556 restraints weight = 11353.570| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3205 r_free = 0.3205 target = 0.074463 restraints weight = 8225.846| |-----------------------------------------------------------------------------| r_work (final): 0.3201 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7976 moved from start: 0.1259 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 6748 Z= 0.197 Angle : 0.572 8.010 9280 Z= 0.268 Chirality : 0.039 0.178 1134 Planarity : 0.005 0.057 1191 Dihedral : 4.506 47.831 989 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 5.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.92 % Favored : 94.08 % Rotamer: Outliers : 2.16 % Allowed : 19.40 % Favored : 78.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.59 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.21 (0.29), residues: 912 helix: 1.83 (0.31), residues: 310 sheet: -0.35 (0.47), residues: 127 loop : -1.49 (0.29), residues: 475 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP I 123 HIS 0.004 0.001 HIS A 286 PHE 0.006 0.001 PHE A 146 TYR 0.006 0.001 TYR A 596 ARG 0.001 0.000 ARG A 85 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1824 Ramachandran restraints generated. 912 Oldfield, 0 Emsley, 912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1824 Ramachandran restraints generated. 912 Oldfield, 0 Emsley, 912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 49 residues out of total 786 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 36 time to evaluate : 0.720 Fit side-chains REVERT: A 75 GLN cc_start: 0.8827 (OUTLIER) cc_final: 0.8495 (tm-30) REVERT: A 469 MET cc_start: 0.7177 (pmm) cc_final: 0.6447 (pmm) REVERT: A 867 GLU cc_start: 0.7600 (mm-30) cc_final: 0.7300 (mm-30) REVERT: A 1005 PHE cc_start: 0.6789 (OUTLIER) cc_final: 0.5548 (t80) outliers start: 13 outliers final: 11 residues processed: 48 average time/residue: 0.1102 time to fit residues: 8.9270 Evaluate side-chains 48 residues out of total 786 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 35 time to evaluate : 0.708 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 61 LEU Chi-restraints excluded: chain A residue 75 GLN Chi-restraints excluded: chain A residue 105 VAL Chi-restraints excluded: chain A residue 167 THR Chi-restraints excluded: chain A residue 168 VAL Chi-restraints excluded: chain A residue 361 VAL Chi-restraints excluded: chain A residue 438 VAL Chi-restraints excluded: chain A residue 464 LEU Chi-restraints excluded: chain A residue 467 VAL Chi-restraints excluded: chain A residue 578 VAL Chi-restraints excluded: chain A residue 1005 PHE Chi-restraints excluded: chain L residue 72 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 87 optimal weight: 3.9990 chunk 76 optimal weight: 0.9990 chunk 0 optimal weight: 6.9990 chunk 79 optimal weight: 5.9990 chunk 82 optimal weight: 0.3980 chunk 56 optimal weight: 2.9990 chunk 5 optimal weight: 3.9990 chunk 86 optimal weight: 0.0030 chunk 61 optimal weight: 4.9990 chunk 11 optimal weight: 1.9990 chunk 47 optimal weight: 0.5980 overall best weight: 0.7994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1009 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.089063 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3175 r_free = 0.3175 target = 0.073034 restraints weight = 18818.697| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3205 r_free = 0.3205 target = 0.074445 restraints weight = 11160.486| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3224 r_free = 0.3224 target = 0.075368 restraints weight = 8059.886| |-----------------------------------------------------------------------------| r_work (final): 0.3219 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7948 moved from start: 0.1312 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 6748 Z= 0.161 Angle : 0.554 7.600 9280 Z= 0.258 Chirality : 0.039 0.172 1134 Planarity : 0.005 0.056 1191 Dihedral : 4.388 48.025 989 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 5.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.70 % Favored : 94.30 % Rotamer: Outliers : 2.49 % Allowed : 19.24 % Favored : 78.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.59 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.12 (0.29), residues: 912 helix: 1.94 (0.31), residues: 307 sheet: -0.34 (0.46), residues: 128 loop : -1.43 (0.29), residues: 477 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP I 123 HIS 0.003 0.001 HIS A 286 PHE 0.006 0.001 PHE A 159 TYR 0.008 0.001 TYR A 603 ARG 0.001 0.000 ARG A 551 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2171.87 seconds wall clock time: 39 minutes 44.21 seconds (2384.21 seconds total)