Starting phenix.real_space_refine on Thu Nov 14 15:48:23 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8oif_16891/11_2024/8oif_16891.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8oif_16891/11_2024/8oif_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8oif_16891/11_2024/8oif_16891.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8oif_16891/11_2024/8oif_16891.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8oif_16891/11_2024/8oif_16891.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8oif_16891/11_2024/8oif_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-5513/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: 4.67, per 1000 atoms: 0.71 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: 1.84 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: 0.89 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: 2.11 Time building geometry restraints manager: 2.13 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: 1.490 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.280 Check model and map are aligned: 0.060 Set scattering table: 0.060 Process input model: 20.290 Find NCS groups from input model: 0.060 Set up NCS constraints: 0.030 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: 0.010 Load rotamer database and sin/cos tables:3.220 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.510 ------------------------------------------------------------------------------- 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 : 0.828 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 33 average time/residue: 0.1345 time to fit residues: 7.5963 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 : 0.717 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7948 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 : 0.764 Fit side-chains REVERT: A 469 MET cc_start: 0.6890 (pmm) cc_final: 0.6263 (pmm) REVERT: A 1005 PHE cc_start: 0.6349 (OUTLIER) cc_final: 0.5603 (t80) outliers start: 8 outliers final: 3 residues processed: 43 average time/residue: 0.1557 time to fit residues: 10.2098 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 : 0.751 ------------------------------------------------------------------------------- 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 46 optimal weight: 3.9990 chunk 25 optimal weight: 0.5980 chunk 69 optimal weight: 2.9990 chunk 56 optimal weight: 3.9990 chunk 23 optimal weight: 0.8980 chunk 83 optimal weight: 0.9990 chunk 90 optimal weight: 0.1980 chunk 74 optimal weight: 0.5980 chunk 82 optimal weight: 0.8980 chunk 28 optimal weight: 0.9980 chunk 67 optimal weight: 0.7980 overall best weight: 0.6180 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7921 moved from start: 0.0784 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= 0.144 Angle : 0.538 9.611 9280 Z= 0.251 Chirality : 0.038 0.174 1134 Planarity : 0.005 0.068 1191 Dihedral : 5.415 88.628 989 Min Nonbonded Distance : 2.602 Molprobity Statistics. All-atom Clashscore : 4.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.26 % Favored : 94.74 % Rotamer: Outliers : 1.66 % Allowed : 16.92 % 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: -0.12 (0.29), residues: 912 helix: 1.69 (0.31), residues: 314 sheet: 0.11 (0.45), residues: 146 loop : -1.49 (0.30), residues: 452 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP I 123 HIS 0.003 0.001 HIS A 907 PHE 0.005 0.001 PHE A 159 TYR 0.006 0.001 TYR A 603 ARG 0.001 0.000 ARG A 882 *********************** 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 49 residues out of total 786 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 39 time to evaluate : 0.848 Fit side-chains REVERT: A 469 MET cc_start: 0.6870 (pmm) cc_final: 0.6273 (pmm) REVERT: A 1005 PHE cc_start: 0.6391 (OUTLIER) cc_final: 0.5578 (t80) outliers start: 10 outliers final: 5 residues processed: 49 average time/residue: 0.1394 time to fit residues: 10.9231 Evaluate side-chains 43 residues out of total 786 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 37 time to evaluate : 0.816 ------------------------------------------------------------------------------- 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 82 optimal weight: 0.0570 chunk 62 optimal weight: 1.9990 chunk 43 optimal weight: 0.8980 chunk 9 optimal weight: 1.9990 chunk 39 optimal weight: 0.8980 chunk 56 optimal weight: 0.8980 chunk 83 optimal weight: 3.9990 chunk 88 optimal weight: 2.9990 chunk 79 optimal weight: 4.9990 chunk 23 optimal weight: 0.7980 chunk 74 optimal weight: 0.9990 overall best weight: 0.7098 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7926 moved from start: 0.0887 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 6748 Z= 0.152 Angle : 0.538 8.007 9280 Z= 0.252 Chirality : 0.038 0.176 1134 Planarity : 0.005 0.058 1191 Dihedral : 4.958 67.290 989 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 4.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.70 % Favored : 94.30 % Rotamer: Outliers : 1.99 % Allowed : 17.74 % Favored : 80.27 % 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: -0.09 (0.29), residues: 912 helix: 1.74 (0.31), residues: 314 sheet: 0.06 (0.45), residues: 146 loop : -1.47 (0.30), residues: 452 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 0.002 0.000 ARG A 501 *********************** 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 47 residues out of total 786 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 35 time to evaluate : 0.766 Fit side-chains REVERT: A 469 MET cc_start: 0.6901 (pmm) cc_final: 0.6254 (pmm) REVERT: A 1005 PHE cc_start: 0.6443 (OUTLIER) cc_final: 0.5556 (t80) outliers start: 12 outliers final: 7 residues processed: 47 average time/residue: 0.1358 time to fit residues: 9.9129 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 : 0.734 ------------------------------------------------------------------------------- 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 50 optimal weight: 2.9990 chunk 1 optimal weight: 2.9990 chunk 66 optimal weight: 0.5980 chunk 36 optimal weight: 3.9990 chunk 75 optimal weight: 0.0870 chunk 61 optimal weight: 2.9990 chunk 0 optimal weight: 6.9990 chunk 45 optimal weight: 1.9990 chunk 79 optimal weight: 3.9990 chunk 22 optimal weight: 9.9990 chunk 29 optimal weight: 0.9990 overall best weight: 1.3364 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7978 moved from start: 0.0938 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 6748 Z= 0.204 Angle : 0.569 8.012 9280 Z= 0.268 Chirality : 0.039 0.172 1134 Planarity : 0.005 0.056 1191 Dihedral : 4.634 46.725 989 Min Nonbonded Distance : 2.385 Molprobity Statistics. All-atom Clashscore : 5.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.36 % Favored : 93.64 % Rotamer: Outliers : 2.16 % Allowed : 18.08 % 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: -0.26 (0.29), residues: 912 helix: 1.69 (0.31), residues: 314 sheet: -0.09 (0.49), residues: 121 loop : -1.56 (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 146 TYR 0.009 0.001 TYR A 603 ARG 0.002 0.000 ARG A 545 *********************** 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 47 residues out of total 786 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 34 time to evaluate : 1.101 Fit side-chains REVERT: A 469 MET cc_start: 0.7007 (pmm) cc_final: 0.6371 (pmm) REVERT: A 1005 PHE cc_start: 0.6631 (OUTLIER) cc_final: 0.5497 (t80) outliers start: 13 outliers final: 11 residues processed: 46 average time/residue: 0.1513 time to fit residues: 11.8245 Evaluate side-chains 43 residues out of total 786 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 31 time to evaluate : 0.854 ------------------------------------------------------------------------------- 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 Chi-restraints excluded: chain L residue 85 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 80 optimal weight: 6.9990 chunk 17 optimal weight: 0.9980 chunk 52 optimal weight: 0.4980 chunk 21 optimal weight: 0.9980 chunk 89 optimal weight: 1.9990 chunk 73 optimal weight: 0.8980 chunk 41 optimal weight: 1.9990 chunk 7 optimal weight: 0.7980 chunk 29 optimal weight: 2.9990 chunk 46 optimal weight: 5.9990 chunk 85 optimal weight: 0.0040 overall best weight: 0.6392 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7934 moved from start: 0.1073 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 6748 Z= 0.147 Angle : 0.534 7.537 9280 Z= 0.250 Chirality : 0.038 0.160 1134 Planarity : 0.005 0.056 1191 Dihedral : 4.334 46.991 989 Min Nonbonded Distance : 2.569 Molprobity Statistics. All-atom Clashscore : 4.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.15 % Favored : 94.85 % 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: -0.11 (0.29), residues: 912 helix: 1.76 (0.31), residues: 316 sheet: 0.02 (0.47), residues: 131 loop : -1.48 (0.29), residues: 465 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 0.001 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 47 residues out of total 786 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 34 time to evaluate : 0.827 Fit side-chains REVERT: A 469 MET cc_start: 0.7009 (pmm) cc_final: 0.6442 (pmm) REVERT: A 1005 PHE cc_start: 0.6595 (OUTLIER) cc_final: 0.5568 (t80) outliers start: 13 outliers final: 9 residues processed: 46 average time/residue: 0.1176 time to fit residues: 9.1416 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 : 0.842 ------------------------------------------------------------------------------- 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 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 10 optimal weight: 0.9990 chunk 50 optimal weight: 1.9990 chunk 65 optimal weight: 0.8980 chunk 74 optimal weight: 0.2980 chunk 49 optimal weight: 0.8980 chunk 88 optimal weight: 0.8980 chunk 55 optimal weight: 0.7980 chunk 54 optimal weight: 2.9990 chunk 40 optimal weight: 2.9990 chunk 35 optimal weight: 3.9990 chunk 52 optimal weight: 0.0370 overall best weight: 0.5858 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7925 moved from start: 0.1175 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 6748 Z= 0.143 Angle : 0.537 8.140 9280 Z= 0.248 Chirality : 0.038 0.169 1134 Planarity : 0.005 0.055 1191 Dihedral : 4.236 47.576 989 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 4.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.37 % Favored : 94.63 % 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: -0.06 (0.29), residues: 912 helix: 1.87 (0.31), residues: 313 sheet: -0.10 (0.43), residues: 152 loop : -1.48 (0.30), residues: 447 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 0.008 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 50 residues out of total 786 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 36 time to evaluate : 0.763 Fit side-chains REVERT: A 469 MET cc_start: 0.7034 (pmm) cc_final: 0.6384 (pmm) REVERT: A 1005 PHE cc_start: 0.6570 (OUTLIER) cc_final: 0.5654 (t80) outliers start: 14 outliers final: 12 residues processed: 49 average time/residue: 0.1167 time to fit residues: 9.6409 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 : 0.735 ------------------------------------------------------------------------------- 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 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 26 optimal weight: 0.5980 chunk 17 optimal weight: 1.9990 chunk 56 optimal weight: 0.8980 chunk 60 optimal weight: 1.9990 chunk 43 optimal weight: 0.4980 chunk 8 optimal weight: 0.9980 chunk 69 optimal weight: 0.9990 chunk 80 optimal weight: 0.4980 chunk 84 optimal weight: 3.9990 chunk 77 optimal weight: 2.9990 chunk 82 optimal weight: 0.8980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7926 moved from start: 0.1210 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= 0.152 Angle : 0.542 7.684 9280 Z= 0.252 Chirality : 0.038 0.165 1134 Planarity : 0.005 0.055 1191 Dihedral : 4.222 47.861 989 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 4.95 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: -0.04 (0.29), residues: 912 helix: 1.89 (0.31), residues: 313 sheet: -0.15 (0.43), residues: 153 loop : -1.44 (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 62 PHE 0.006 0.001 PHE A 159 TYR 0.005 0.001 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 53 residues out of total 786 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 38 time to evaluate : 0.968 Fit side-chains REVERT: A 469 MET cc_start: 0.7056 (pmm) cc_final: 0.6393 (pmm) REVERT: A 1005 PHE cc_start: 0.6558 (OUTLIER) cc_final: 0.5642 (t80) outliers start: 15 outliers final: 11 residues processed: 51 average time/residue: 0.1118 time to fit residues: 9.6678 Evaluate side-chains 49 residues out of total 786 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 37 time to evaluate : 0.794 ------------------------------------------------------------------------------- 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 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 84 optimal weight: 2.9990 chunk 49 optimal weight: 0.9990 chunk 35 optimal weight: 2.9990 chunk 64 optimal weight: 0.1980 chunk 25 optimal weight: 0.0970 chunk 74 optimal weight: 0.9990 chunk 78 optimal weight: 0.0270 chunk 82 optimal weight: 0.9990 chunk 54 optimal weight: 0.2980 chunk 87 optimal weight: 1.9990 chunk 53 optimal weight: 3.9990 overall best weight: 0.3238 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 62 HIS A 891 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7898 moved from start: 0.1330 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 6748 Z= 0.140 Angle : 0.538 7.563 9280 Z= 0.250 Chirality : 0.038 0.173 1134 Planarity : 0.005 0.055 1191 Dihedral : 4.136 48.103 989 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 4.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.15 % Favored : 94.85 % 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: 0.12 (0.30), residues: 912 helix: 2.08 (0.31), residues: 307 sheet: -0.09 (0.44), residues: 153 loop : -1.33 (0.30), residues: 452 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 551 *********************** 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: 15 poor density : 39 time to evaluate : 0.783 Fit side-chains REVERT: A 469 MET cc_start: 0.7021 (pmm) cc_final: 0.6367 (pmm) REVERT: A 1005 PHE cc_start: 0.6398 (OUTLIER) cc_final: 0.5556 (t80) outliers start: 15 outliers final: 10 residues processed: 51 average time/residue: 0.1128 time to fit residues: 9.7202 Evaluate side-chains 50 residues out of total 786 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 39 time to evaluate : 0.831 ------------------------------------------------------------------------------- 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 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 41 optimal weight: 4.9990 chunk 60 optimal weight: 0.8980 chunk 91 optimal weight: 6.9990 chunk 84 optimal weight: 2.9990 chunk 72 optimal weight: 4.9990 chunk 7 optimal weight: 0.5980 chunk 56 optimal weight: 2.9990 chunk 44 optimal weight: 0.6980 chunk 57 optimal weight: 0.7980 chunk 77 optimal weight: 4.9990 chunk 22 optimal weight: 10.0000 overall best weight: 1.1982 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7962 moved from start: 0.1237 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 6748 Z= 0.195 Angle : 0.569 8.087 9280 Z= 0.267 Chirality : 0.039 0.182 1134 Planarity : 0.005 0.055 1191 Dihedral : 4.355 47.950 989 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 5.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.36 % Favored : 93.64 % Rotamer: Outliers : 1.82 % Allowed : 19.07 % 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: -0.05 (0.29), residues: 912 helix: 1.95 (0.31), residues: 310 sheet: -0.24 (0.47), residues: 128 loop : -1.40 (0.29), residues: 474 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 568 HIS 0.004 0.001 HIS A 286 PHE 0.007 0.001 PHE A 146 TYR 0.006 0.001 TYR A 596 ARG 0.002 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 48 residues out of total 786 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 37 time to evaluate : 0.759 Fit side-chains REVERT: A 469 MET cc_start: 0.7091 (pmm) cc_final: 0.6466 (pmm) REVERT: A 1005 PHE cc_start: 0.6731 (OUTLIER) cc_final: 0.5748 (t80) outliers start: 11 outliers final: 10 residues processed: 46 average time/residue: 0.1144 time to fit residues: 8.8862 Evaluate side-chains 48 residues out of total 786 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 37 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 167 THR 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 67 optimal weight: 5.9990 chunk 10 optimal weight: 3.9990 chunk 20 optimal weight: 1.9990 chunk 73 optimal weight: 0.5980 chunk 30 optimal weight: 0.8980 chunk 75 optimal weight: 8.9990 chunk 9 optimal weight: 0.9980 chunk 13 optimal weight: 0.9980 chunk 64 optimal weight: 2.9990 chunk 4 optimal weight: 0.0970 chunk 52 optimal weight: 1.9990 overall best weight: 0.7178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 887 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.089726 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3186 r_free = 0.3186 target = 0.073696 restraints weight = 18546.707| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3216 r_free = 0.3216 target = 0.075099 restraints weight = 11088.392| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3236 r_free = 0.3236 target = 0.076033 restraints weight = 8039.542| |-----------------------------------------------------------------------------| r_work (final): 0.3234 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7927 moved from start: 0.1313 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= 0.158 Angle : 0.549 7.789 9280 Z= 0.257 Chirality : 0.039 0.177 1134 Planarity : 0.005 0.056 1191 Dihedral : 4.261 48.046 989 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 5.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.37 % Favored : 94.63 % Rotamer: Outliers : 1.82 % Allowed : 19.24 % 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: 0.04 (0.29), residues: 912 helix: 2.03 (0.31), residues: 307 sheet: -0.10 (0.45), residues: 138 loop : -1.38 (0.30), residues: 467 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 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1547.52 seconds wall clock time: 29 minutes 10.25 seconds (1750.25 seconds total)