Starting phenix.real_space_refine on Thu Jul 24 21:51:04 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8oif_16891/07_2025/8oif_16891.cif Found real_map, /net/cci-nas-00/data/ceres_data/8oif_16891/07_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_16891/07_2025/8oif_16891.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8oif_16891/07_2025/8oif_16891.map" model { file = "/net/cci-nas-00/data/ceres_data/8oif_16891/07_2025/8oif_16891.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8oif_16891/07_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): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/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 Unusual residues: {'AMP%rna2p': 1} Classifications: {'RNA_mixed': 1} Modifications used: {'rna2p': 1} Time building chain proxies: 4.89, per 1000 atoms: 0.74 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: 1.70 Conformation dependent library (CDL) restraints added in 1.1 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: 0.88 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: 2.13 Time building geometry restraints manager: 2.03 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=" O4' AMP I 201 " ideal model delta sigma weight residual 1.426 1.453 -0.027 2.00e-02 2.50e+03 1.77e+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 ... (remaining 6743 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.90: 9095 1.90 - 3.80: 148 3.80 - 5.69: 32 5.69 - 7.59: 2 7.59 - 9.49: 3 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=" C1' AMP I 201 " pdb=" C2' AMP I 201 " pdb=" C3' AMP I 201 " ideal model delta sigma weight residual 111.00 101.51 9.49 3.00e+00 1.11e-01 1.00e+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 ... (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 - 0.046: 904 0.046 - 0.093: 193 0.093 - 0.139: 34 0.139 - 0.186: 0 0.186 - 0.232: 3 Chirality restraints: 1134 Sorted by residual: chirality pdb=" C3' AMP I 201 " pdb=" C2' AMP I 201 " pdb=" C4' AMP I 201 " pdb=" O3' AMP I 201 " both_signs ideal model delta sigma weight residual False -2.51 -2.74 0.23 2.00e-01 2.50e+01 1.35e+00 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 ... (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: 1.190 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 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: 0.060 Process input model: 20.850 Find NCS groups from input model: 0.120 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.090 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.710 ------------------------------------------------------------------------------- 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 : 0.005 0.247 6750 Z= 0.333 Angle : 0.618 9.489 9282 Z= 0.300 Chirality : 0.040 0.232 1134 Planarity : 0.006 0.115 1191 Dihedral : 13.815 119.684 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 Details of bonding type rmsd hydrogen bonds : bond 0.15334 ( 280) hydrogen bonds : angle 5.30972 ( 759) SS BOND : bond 0.00002 ( 1) SS BOND : angle 0.32219 ( 2) covalent geometry : bond 0.00336 ( 6748) covalent geometry : angle 0.61815 ( 9280) Misc. bond : bond 0.24679 ( 1) *********************** 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 : 0.863 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 33 average time/residue: 0.1101 time to fit residues: 6.4833 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 : 0.632 ------------------------------------------------------------------------------- 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 = 0.089121 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3180 r_free = 0.3180 target = 0.073217 restraints weight = 18400.084| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3209 r_free = 0.3209 target = 0.074600 restraints weight = 11130.034| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3229 r_free = 0.3229 target = 0.075554 restraints weight = 8072.429| |-----------------------------------------------------------------------------| r_work (final): 0.3225 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7940 moved from start: 0.0553 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 6750 Z= 0.107 Angle : 0.563 7.025 9282 Z= 0.267 Chirality : 0.039 0.173 1134 Planarity : 0.005 0.078 1191 Dihedral : 5.240 95.191 989 Min Nonbonded Distance : 2.414 Molprobity Statistics. All-atom Clashscore : 4.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.70 % Favored : 94.30 % Rotamer: Outliers : 1.00 % Allowed : 15.59 % 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: -0.28 (0.29), residues: 912 helix: 1.61 (0.31), residues: 313 sheet: -0.10 (0.46), residues: 136 loop : -1.56 (0.29), residues: 463 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 69 HIS 0.004 0.001 HIS A 286 PHE 0.008 0.001 PHE A1005 TYR 0.009 0.001 TYR A1010 ARG 0.002 0.000 ARG A 616 Details of bonding type rmsd hydrogen bonds : bond 0.03160 ( 280) hydrogen bonds : angle 4.27838 ( 759) SS BOND : bond 0.00042 ( 1) SS BOND : angle 0.32741 ( 2) covalent geometry : bond 0.00250 ( 6748) covalent geometry : angle 0.56260 ( 9280) Misc. bond : bond 0.00033 ( 1) *********************** 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 41 residues out of total 786 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 35 time to evaluate : 0.628 Fit side-chains REVERT: A 1005 PHE cc_start: 0.6371 (OUTLIER) cc_final: 0.5614 (t80) outliers start: 6 outliers final: 3 residues processed: 41 average time/residue: 0.1382 time to fit residues: 8.6921 Evaluate side-chains 39 residues out of total 786 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 35 time to evaluate : 0.615 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 LEU Chi-restraints excluded: chain A residue 167 THR 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: 5.9990 chunk 29 optimal weight: 3.9990 chunk 14 optimal weight: 0.9990 chunk 58 optimal weight: 6.9990 chunk 15 optimal weight: 0.4980 chunk 78 optimal weight: 0.0470 chunk 71 optimal weight: 3.9990 chunk 9 optimal weight: 3.9990 chunk 67 optimal weight: 0.6980 chunk 75 optimal weight: 3.9990 overall best weight: 0.6280 ------------------------------------------------------------------------------- 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 = 0.3511 r_free = 0.3511 target = 0.089959 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3196 r_free = 0.3196 target = 0.074042 restraints weight = 18525.917| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3226 r_free = 0.3226 target = 0.075465 restraints weight = 11158.763| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.076444 restraints weight = 8019.357| |-----------------------------------------------------------------------------| r_work (final): 0.3243 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7913 moved from start: 0.0792 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 6750 Z= 0.090 Angle : 0.537 8.435 9282 Z= 0.251 Chirality : 0.038 0.170 1134 Planarity : 0.005 0.064 1191 Dihedral : 4.112 42.858 989 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 4.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.26 % Favored : 94.74 % Rotamer: Outliers : 1.99 % Allowed : 16.58 % Favored : 81.43 % 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: -0.13 (0.29), residues: 912 helix: 1.69 (0.31), residues: 314 sheet: 0.08 (0.45), residues: 147 loop : -1.50 (0.30), residues: 451 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 614 HIS 0.003 0.001 HIS A 907 PHE 0.005 0.001 PHE A 159 TYR 0.007 0.001 TYR A 603 ARG 0.001 0.000 ARG A 431 Details of bonding type rmsd hydrogen bonds : bond 0.02615 ( 280) hydrogen bonds : angle 3.94601 ( 759) SS BOND : bond 0.00041 ( 1) SS BOND : angle 0.28839 ( 2) covalent geometry : bond 0.00210 ( 6748) covalent geometry : angle 0.53696 ( 9280) Misc. bond : bond 0.00066 ( 1) *********************** 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 51 residues out of total 786 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 39 time to evaluate : 0.738 Fit side-chains REVERT: A 867 GLU cc_start: 0.7725 (mm-30) cc_final: 0.7461 (mm-30) REVERT: A 1005 PHE cc_start: 0.6392 (OUTLIER) cc_final: 0.5576 (t80) outliers start: 12 outliers final: 7 residues processed: 51 average time/residue: 0.1346 time to fit residues: 10.8061 Evaluate side-chains 44 residues out of total 786 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 36 time to evaluate : 0.672 ------------------------------------------------------------------------------- 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 395 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 18 optimal weight: 8.9990 chunk 63 optimal weight: 0.0870 chunk 56 optimal weight: 0.6980 chunk 37 optimal weight: 0.8980 chunk 80 optimal weight: 2.9990 chunk 28 optimal weight: 4.9990 chunk 91 optimal weight: 0.9990 chunk 54 optimal weight: 8.9990 chunk 83 optimal weight: 0.8980 chunk 50 optimal weight: 0.9990 chunk 55 optimal weight: 0.9980 overall best weight: 0.7158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1009 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.089864 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3189 r_free = 0.3189 target = 0.073675 restraints weight = 18702.952| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3222 r_free = 0.3222 target = 0.075217 restraints weight = 10796.544| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3241 r_free = 0.3241 target = 0.076199 restraints weight = 7574.205| |-----------------------------------------------------------------------------| r_work (final): 0.3236 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7921 moved from start: 0.0921 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 6750 Z= 0.094 Angle : 0.542 7.877 9282 Z= 0.253 Chirality : 0.039 0.170 1134 Planarity : 0.005 0.059 1191 Dihedral : 4.015 30.531 989 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 4.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.59 % Favored : 94.41 % Rotamer: Outliers : 1.99 % Allowed : 17.58 % Favored : 80.43 % 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: -0.08 (0.30), residues: 912 helix: 1.75 (0.31), residues: 314 sheet: 0.07 (0.45), residues: 147 loop : -1.47 (0.30), residues: 451 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 L 70 TYR 0.006 0.001 TYR A 603 ARG 0.001 0.000 ARG A 551 Details of bonding type rmsd hydrogen bonds : bond 0.02590 ( 280) hydrogen bonds : angle 3.87518 ( 759) SS BOND : bond 0.00097 ( 1) SS BOND : angle 0.35373 ( 2) covalent geometry : bond 0.00223 ( 6748) covalent geometry : angle 0.54221 ( 9280) Misc. bond : bond 0.00033 ( 1) *********************** 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 46 residues out of total 786 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 34 time to evaluate : 0.659 Fit side-chains REVERT: A 1005 PHE cc_start: 0.6471 (OUTLIER) cc_final: 0.5588 (t80) outliers start: 12 outliers final: 8 residues processed: 46 average time/residue: 0.1091 time to fit residues: 8.4713 Evaluate side-chains 43 residues out of total 786 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 34 time to evaluate : 0.665 ------------------------------------------------------------------------------- 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 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 61 optimal weight: 3.9990 chunk 2 optimal weight: 3.9990 chunk 4 optimal weight: 1.9990 chunk 9 optimal weight: 1.9990 chunk 64 optimal weight: 1.9990 chunk 57 optimal weight: 0.0050 chunk 24 optimal weight: 5.9990 chunk 37 optimal weight: 0.9980 chunk 18 optimal weight: 8.9990 chunk 23 optimal weight: 0.7980 chunk 60 optimal weight: 0.3980 overall best weight: 0.8396 ------------------------------------------------------------------------------- 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 = 0.3507 r_free = 0.3507 target = 0.089702 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3190 r_free = 0.3190 target = 0.073706 restraints weight = 18535.285| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3220 r_free = 0.3220 target = 0.075131 restraints weight = 11094.670| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3240 r_free = 0.3240 target = 0.076082 restraints weight = 8017.583| |-----------------------------------------------------------------------------| r_work (final): 0.3236 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7928 moved from start: 0.0981 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 6750 Z= 0.098 Angle : 0.546 7.742 9282 Z= 0.254 Chirality : 0.039 0.173 1134 Planarity : 0.005 0.055 1191 Dihedral : 4.000 28.712 989 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 4.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.70 % Favored : 94.30 % Rotamer: Outliers : 1.99 % Allowed : 18.24 % Favored : 79.77 % 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: 1.77 (0.31), residues: 314 sheet: 0.04 (0.45), residues: 147 loop : -1.49 (0.30), residues: 451 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP I 123 HIS 0.003 0.001 HIS A 286 PHE 0.005 0.001 PHE A 146 TYR 0.007 0.001 TYR A 603 ARG 0.001 0.000 ARG A 551 Details of bonding type rmsd hydrogen bonds : bond 0.02613 ( 280) hydrogen bonds : angle 3.86268 ( 759) SS BOND : bond 0.00268 ( 1) SS BOND : angle 0.85495 ( 2) covalent geometry : bond 0.00236 ( 6748) covalent geometry : angle 0.54636 ( 9280) Misc. bond : bond 0.00021 ( 1) *********************** 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 46 residues out of total 786 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 34 time to evaluate : 0.795 Fit side-chains REVERT: A 1005 PHE cc_start: 0.6504 (OUTLIER) cc_final: 0.5547 (t80) outliers start: 12 outliers final: 10 residues processed: 46 average time/residue: 0.1131 time to fit residues: 8.8492 Evaluate side-chains 43 residues out of total 786 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 32 time to evaluate : 0.736 ------------------------------------------------------------------------------- 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 3 optimal weight: 0.6980 chunk 76 optimal weight: 0.0170 chunk 23 optimal weight: 0.8980 chunk 35 optimal weight: 3.9990 chunk 22 optimal weight: 7.9990 chunk 55 optimal weight: 0.9990 chunk 36 optimal weight: 3.9990 chunk 52 optimal weight: 0.0070 chunk 17 optimal weight: 0.8980 chunk 90 optimal weight: 8.9990 chunk 32 optimal weight: 0.0970 overall best weight: 0.3434 ------------------------------------------------------------------------------- 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 = 0.3532 r_free = 0.3532 target = 0.091063 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3215 r_free = 0.3215 target = 0.074947 restraints weight = 18223.662| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.076487 restraints weight = 10537.891| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.077503 restraints weight = 7431.788| |-----------------------------------------------------------------------------| r_work (final): 0.3263 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7882 moved from start: 0.1183 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 6750 Z= 0.082 Angle : 0.528 7.506 9282 Z= 0.244 Chirality : 0.038 0.167 1134 Planarity : 0.004 0.054 1191 Dihedral : 3.796 26.231 989 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 4.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.61 % Favored : 95.39 % Rotamer: Outliers : 2.16 % Allowed : 18.74 % 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: -0.00 (0.29), residues: 912 helix: 1.78 (0.31), residues: 317 sheet: 0.07 (0.45), residues: 147 loop : -1.40 (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 0.006 0.000 TYR A 603 ARG 0.001 0.000 ARG A 431 Details of bonding type rmsd hydrogen bonds : bond 0.02209 ( 280) hydrogen bonds : angle 3.69542 ( 759) SS BOND : bond 0.00261 ( 1) SS BOND : angle 0.65585 ( 2) covalent geometry : bond 0.00192 ( 6748) covalent geometry : angle 0.52751 ( 9280) Misc. bond : bond 0.00018 ( 1) *********************** 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 50 residues out of total 786 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 37 time to evaluate : 0.770 Fit side-chains REVERT: A 1005 PHE cc_start: 0.6348 (OUTLIER) cc_final: 0.5588 (t80) outliers start: 13 outliers final: 9 residues processed: 49 average time/residue: 0.1115 time to fit residues: 9.2629 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 : 0.747 ------------------------------------------------------------------------------- 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 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 Chi-restraints excluded: chain L residue 85 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 50 optimal weight: 2.9990 chunk 61 optimal weight: 3.9990 chunk 60 optimal weight: 3.9990 chunk 72 optimal weight: 3.9990 chunk 89 optimal weight: 5.9990 chunk 3 optimal weight: 1.9990 chunk 48 optimal weight: 0.9980 chunk 26 optimal weight: 1.9990 chunk 78 optimal weight: 0.0870 chunk 19 optimal weight: 10.0000 chunk 53 optimal weight: 1.9990 overall best weight: 1.4164 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 50 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.088543 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3164 r_free = 0.3164 target = 0.072476 restraints weight = 18547.532| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3193 r_free = 0.3193 target = 0.073865 restraints weight = 11164.182| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3212 r_free = 0.3212 target = 0.074773 restraints weight = 8104.068| |-----------------------------------------------------------------------------| r_work (final): 0.3208 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7967 moved from start: 0.1078 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 6750 Z= 0.129 Angle : 0.576 8.174 9282 Z= 0.268 Chirality : 0.040 0.177 1134 Planarity : 0.005 0.055 1191 Dihedral : 4.077 25.457 989 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 5.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.36 % Favored : 93.64 % Rotamer: Outliers : 2.49 % Allowed : 18.57 % Favored : 78.94 % 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: -0.26 (0.29), residues: 912 helix: 1.66 (0.31), residues: 317 sheet: -0.22 (0.47), residues: 128 loop : -1.53 (0.29), residues: 467 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 146 TYR 0.008 0.001 TYR A 603 ARG 0.002 0.000 ARG A 85 Details of bonding type rmsd hydrogen bonds : bond 0.03166 ( 280) hydrogen bonds : angle 3.96349 ( 759) SS BOND : bond 0.00069 ( 1) SS BOND : angle 0.44677 ( 2) covalent geometry : bond 0.00311 ( 6748) covalent geometry : angle 0.57601 ( 9280) Misc. bond : bond 0.00007 ( 1) *********************** 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 49 residues out of total 786 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 34 time to evaluate : 0.675 Fit side-chains REVERT: A 1005 PHE cc_start: 0.6682 (OUTLIER) cc_final: 0.5699 (t80) outliers start: 15 outliers final: 12 residues processed: 48 average time/residue: 0.1099 time to fit residues: 8.8495 Evaluate side-chains 45 residues out of total 786 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 32 time to evaluate : 0.693 ------------------------------------------------------------------------------- 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 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 68 ILE Chi-restraints excluded: chain L residue 72 THR Chi-restraints excluded: chain L residue 85 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 43 optimal weight: 1.9990 chunk 38 optimal weight: 5.9990 chunk 20 optimal weight: 4.9990 chunk 69 optimal weight: 0.6980 chunk 18 optimal weight: 0.0970 chunk 68 optimal weight: 3.9990 chunk 84 optimal weight: 5.9990 chunk 13 optimal weight: 2.9990 chunk 76 optimal weight: 4.9990 chunk 54 optimal weight: 0.0170 chunk 31 optimal weight: 2.9990 overall best weight: 1.1620 ------------------------------------------------------------------------------- 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 = 0.3490 r_free = 0.3490 target = 0.088822 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3170 r_free = 0.3170 target = 0.072788 restraints weight = 18501.586| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3200 r_free = 0.3200 target = 0.074183 restraints weight = 11121.567| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3219 r_free = 0.3219 target = 0.075130 restraints weight = 8041.489| |-----------------------------------------------------------------------------| r_work (final): 0.3216 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7959 moved from start: 0.1124 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 6750 Z= 0.115 Angle : 0.567 7.866 9282 Z= 0.265 Chirality : 0.039 0.173 1134 Planarity : 0.005 0.055 1191 Dihedral : 4.052 25.426 989 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 4.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.03 % Favored : 93.97 % Rotamer: Outliers : 2.32 % Allowed : 18.41 % 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: -0.12 (0.29), residues: 912 helix: 1.85 (0.31), residues: 310 sheet: -0.20 (0.47), residues: 128 loop : -1.42 (0.29), residues: 474 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 603 ARG 0.001 0.000 ARG A 85 Details of bonding type rmsd hydrogen bonds : bond 0.02853 ( 280) hydrogen bonds : angle 3.90510 ( 759) SS BOND : bond 0.00509 ( 1) SS BOND : angle 0.56018 ( 2) covalent geometry : bond 0.00278 ( 6748) covalent geometry : angle 0.56665 ( 9280) Misc. bond : bond 0.00004 ( 1) *********************** 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 50 residues out of total 786 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 36 time to evaluate : 0.764 Fit side-chains REVERT: A 75 GLN cc_start: 0.8805 (OUTLIER) cc_final: 0.8491 (tm-30) REVERT: A 1005 PHE cc_start: 0.6704 (OUTLIER) cc_final: 0.5611 (t80) outliers start: 14 outliers final: 11 residues processed: 48 average time/residue: 0.1137 time to fit residues: 9.2196 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 : 0.747 ------------------------------------------------------------------------------- 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 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 Chi-restraints excluded: chain L residue 85 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 81 optimal weight: 30.0000 chunk 68 optimal weight: 2.9990 chunk 42 optimal weight: 0.7980 chunk 75 optimal weight: 8.9990 chunk 18 optimal weight: 0.3980 chunk 69 optimal weight: 0.6980 chunk 91 optimal weight: 6.9990 chunk 41 optimal weight: 0.6980 chunk 79 optimal weight: 0.0370 chunk 23 optimal weight: 1.9990 chunk 28 optimal weight: 0.8980 overall best weight: 0.5258 ------------------------------------------------------------------------------- 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 = 0.3514 r_free = 0.3514 target = 0.090170 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3198 r_free = 0.3198 target = 0.074208 restraints weight = 18605.392| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3229 r_free = 0.3229 target = 0.075645 restraints weight = 11036.019| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.076573 restraints weight = 7937.862| |-----------------------------------------------------------------------------| r_work (final): 0.3244 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7914 moved from start: 0.1260 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 6750 Z= 0.087 Angle : 0.545 7.576 9282 Z= 0.252 Chirality : 0.038 0.184 1134 Planarity : 0.005 0.054 1191 Dihedral : 3.801 25.080 989 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 4.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.15 % Favored : 94.85 % Rotamer: Outliers : 2.65 % Allowed : 18.24 % 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: -0.02 (0.29), residues: 912 helix: 1.89 (0.31), residues: 313 sheet: -0.04 (0.45), residues: 138 loop : -1.42 (0.30), residues: 461 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 604 TYR 0.008 0.001 TYR A 603 ARG 0.001 0.000 ARG A 551 Details of bonding type rmsd hydrogen bonds : bond 0.02312 ( 280) hydrogen bonds : angle 3.71247 ( 759) SS BOND : bond 0.00086 ( 1) SS BOND : angle 0.49610 ( 2) covalent geometry : bond 0.00209 ( 6748) covalent geometry : angle 0.54498 ( 9280) Misc. bond : bond 0.00009 ( 1) *********************** 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 54 residues out of total 786 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 38 time to evaluate : 0.679 Fit side-chains REVERT: A 75 GLN cc_start: 0.8765 (OUTLIER) cc_final: 0.8499 (tm-30) REVERT: A 1005 PHE cc_start: 0.6651 (OUTLIER) cc_final: 0.5653 (t80) outliers start: 16 outliers final: 12 residues processed: 52 average time/residue: 0.1067 time to fit residues: 9.3614 Evaluate side-chains 51 residues out of total 786 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 37 time to evaluate : 0.692 ------------------------------------------------------------------------------- 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 106 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 Chi-restraints excluded: chain L residue 85 ILE 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: 2.9990 chunk 8 optimal weight: 2.9990 chunk 65 optimal weight: 1.9990 chunk 2 optimal weight: 4.9990 chunk 0 optimal weight: 0.6980 chunk 74 optimal weight: 0.9990 chunk 23 optimal weight: 0.8980 chunk 16 optimal weight: 6.9990 chunk 18 optimal weight: 6.9990 chunk 67 optimal weight: 0.9990 overall best weight: 1.1186 ------------------------------------------------------------------------------- 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 = 0.3494 r_free = 0.3494 target = 0.089044 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3173 r_free = 0.3173 target = 0.072985 restraints weight = 18795.418| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3204 r_free = 0.3204 target = 0.074394 restraints weight = 11231.606| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.3224 r_free = 0.3224 target = 0.075345 restraints weight = 8093.996| |-----------------------------------------------------------------------------| r_work (final): 0.3220 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7950 moved from start: 0.1212 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 6750 Z= 0.113 Angle : 0.562 7.808 9282 Z= 0.262 Chirality : 0.039 0.176 1134 Planarity : 0.005 0.054 1191 Dihedral : 3.926 25.342 989 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 5.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.14 % Favored : 93.86 % Rotamer: Outliers : 2.32 % Allowed : 18.74 % Favored : 78.94 % 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: -0.03 (0.29), residues: 912 helix: 1.98 (0.31), residues: 307 sheet: -0.22 (0.47), residues: 129 loop : -1.38 (0.29), residues: 476 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 603 ARG 0.001 0.000 ARG A 85 Details of bonding type rmsd hydrogen bonds : bond 0.02771 ( 280) hydrogen bonds : angle 3.84664 ( 759) SS BOND : bond 0.00162 ( 1) SS BOND : angle 0.64039 ( 2) covalent geometry : bond 0.00273 ( 6748) covalent geometry : angle 0.56224 ( 9280) Misc. bond : bond 0.00014 ( 1) ********************** 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 50 residues out of total 786 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 36 time to evaluate : 0.749 Fit side-chains REVERT: A 75 GLN cc_start: 0.8793 (OUTLIER) cc_final: 0.8491 (tm-30) REVERT: A 1005 PHE cc_start: 0.6706 (OUTLIER) cc_final: 0.5629 (t80) outliers start: 14 outliers final: 12 residues processed: 48 average time/residue: 0.1111 time to fit residues: 8.9957 Evaluate side-chains 50 residues out of total 786 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 36 time to evaluate : 0.740 ------------------------------------------------------------------------------- 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 106 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 Chi-restraints excluded: chain L residue 85 ILE 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: 2.9990 chunk 0 optimal weight: 6.9990 chunk 79 optimal weight: 0.6980 chunk 82 optimal weight: 0.8980 chunk 56 optimal weight: 0.8980 chunk 5 optimal weight: 0.8980 chunk 86 optimal weight: 7.9990 chunk 61 optimal weight: 0.3980 chunk 11 optimal weight: 8.9990 chunk 47 optimal weight: 1.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- 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 = 0.3503 r_free = 0.3503 target = 0.089587 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3184 r_free = 0.3184 target = 0.073498 restraints weight = 18961.518| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3214 r_free = 0.3214 target = 0.074943 restraints weight = 11262.963| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3234 r_free = 0.3234 target = 0.075888 restraints weight = 8102.053| |-----------------------------------------------------------------------------| r_work (final): 0.3231 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7932 moved from start: 0.1273 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 6750 Z= 0.095 Angle : 0.549 7.665 9282 Z= 0.255 Chirality : 0.039 0.176 1134 Planarity : 0.005 0.055 1191 Dihedral : 3.835 25.065 989 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 4.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.37 % Favored : 94.63 % Rotamer: Outliers : 2.65 % Allowed : 18.41 % Favored : 78.94 % 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: 0.01 (0.29), residues: 912 helix: 2.01 (0.31), residues: 307 sheet: -0.20 (0.46), residues: 129 loop : -1.35 (0.29), residues: 476 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 0.005 0.001 PHE A 146 TYR 0.007 0.001 TYR A 603 ARG 0.001 0.000 ARG A 551 Details of bonding type rmsd hydrogen bonds : bond 0.02488 ( 280) hydrogen bonds : angle 3.76179 ( 759) SS BOND : bond 0.00157 ( 1) SS BOND : angle 0.63373 ( 2) covalent geometry : bond 0.00230 ( 6748) covalent geometry : angle 0.54853 ( 9280) Misc. bond : bond 0.00006 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2333.51 seconds wall clock time: 41 minutes 20.92 seconds (2480.92 seconds total)