Starting phenix.real_space_refine on Sat Mar 16 22:19:52 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8b9i_15932/03_2024/8b9i_15932_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8b9i_15932/03_2024/8b9i_15932.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.95 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8b9i_15932/03_2024/8b9i_15932.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8b9i_15932/03_2024/8b9i_15932.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8b9i_15932/03_2024/8b9i_15932_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8b9i_15932/03_2024/8b9i_15932_updated.pdb" } resolution = 2.95 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= 0.012 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 7861 atoms to isotropic. 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: 8 Type Number sf(0) Gaussians Al 1 5.89 5 P 13 5.49 5 Mg 1 5.21 5 S 48 5.16 5 C 5043 2.51 5 N 1381 2.21 5 O 1535 1.98 5 F 4 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 153": "OE1" <-> "OE2" Residue "A GLU 392": "OE1" <-> "OE2" Residue "A GLU 456": "OE1" <-> "OE2" Residue "A GLU 508": "OE1" <-> "OE2" Residue "A GLU 585": "OE1" <-> "OE2" Residue "A GLU 632": "OE1" <-> "OE2" Residue "A GLU 641": "OE1" <-> "OE2" Residue "A GLU 698": "OE1" <-> "OE2" Residue "A GLU 704": "OE1" <-> "OE2" Residue "A GLU 790": "OE1" <-> "OE2" Residue "A GLU 804": "OE1" <-> "OE2" Residue "A GLU 835": "OE1" <-> "OE2" Residue "A GLU 842": "OE1" <-> "OE2" Residue "A GLU 851": "OE1" <-> "OE2" Residue "A GLU 896": "OE1" <-> "OE2" Residue "A GLU 978": "OE1" <-> "OE2" Residue "A GLU 1025": "OE1" <-> "OE2" Residue "A GLU 1054": "OE1" <-> "OE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 8026 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 7784 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 984, 7781 Classifications: {'peptide': 984} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 49, 'TRANS': 932} Chain breaks: 2 Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 12 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 9 Conformer: "B" Number of residues, atoms: 984, 7781 Classifications: {'peptide': 984} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 49, 'TRANS': 932} Chain breaks: 2 Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 12 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 9 bond proxies already assigned to first conformer: 7927 Chain: "C" Number of atoms: 204 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 204 Classifications: {'RNA': 11} Modifications used: {'rna3p_pyr': 10} Link IDs: {'rna3p': 10} Unresolved chain link dihedrals: 1 Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 27 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {' U:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "A" Number of atoms: 37 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 37 Unusual residues: {' MG': 1, 'ADP': 1, 'ALF': 1} Classifications: {'undetermined': 3, 'water': 4} Link IDs: {None: 6} Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Time building chain proxies: 8.30, per 1000 atoms: 1.03 Number of scatterers: 8026 At special positions: 0 Unit cell: (83.022, 96.174, 104.394, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 8 Type Number sf(0) S 48 16.00 P 13 15.00 Al 1 13.00 Mg 1 11.99 F 4 9.00 O 1535 8.00 N 1381 7.00 C 5043 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 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=0, symmetry=0 Time building additional restraints: 3.22 Conformation dependent library (CDL) restraints added in 2.5 seconds 1954 Ramachandran restraints generated. 977 Oldfield, 0 Emsley, 977 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1880 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 46 helices and 7 sheets defined 45.4% alpha, 12.2% beta 0 base pairs and 3 stacking pairs defined. Time for finding SS restraints: 3.54 Creating SS restraints... Processing helix chain 'A' and resid 147 through 154 Processing helix chain 'A' and resid 160 through 162 No H-bonds generated for 'chain 'A' and resid 160 through 162' Processing helix chain 'A' and resid 167 through 181 removed outlier: 4.193A pdb=" N LYS A 171 " --> pdb=" O ILE A 167 " (cutoff:3.500A) removed outlier: 5.778A pdb=" N GLU A 172 " --> pdb=" O GLU A 168 " (cutoff:3.500A) Processing helix chain 'A' and resid 224 through 241 Processing helix chain 'A' and resid 269 through 282 Processing helix chain 'A' and resid 289 through 291 No H-bonds generated for 'chain 'A' and resid 289 through 291' Processing helix chain 'A' and resid 353 through 370 Processing helix chain 'A' and resid 372 through 383 removed outlier: 3.613A pdb=" N LYS A 383 " --> pdb=" O GLU A 379 " (cutoff:3.500A) Processing helix chain 'A' and resid 385 through 388 No H-bonds generated for 'chain 'A' and resid 385 through 388' Processing helix chain 'A' and resid 390 through 399 Processing helix chain 'A' and resid 413 through 427 removed outlier: 4.589A pdb=" N ALA A 418 " --> pdb=" O THR A 414 " (cutoff:3.500A) removed outlier: 4.562A pdb=" N GLN A 419 " --> pdb=" O THR A 415 " (cutoff:3.500A) Processing helix chain 'A' and resid 431 through 433 No H-bonds generated for 'chain 'A' and resid 431 through 433' Processing helix chain 'A' and resid 443 through 456 Processing helix chain 'A' and resid 487 through 496 removed outlier: 4.243A pdb=" N GLU A 495 " --> pdb=" O LEU A 491 " (cutoff:3.500A) removed outlier: 4.797A pdb=" N ALA A 496 " --> pdb=" O ARG A 492 " (cutoff:3.500A) Processing helix chain 'A' and resid 509 through 511 No H-bonds generated for 'chain 'A' and resid 509 through 511' Processing helix chain 'A' and resid 514 through 529 Processing helix chain 'A' and resid 544 through 550 Processing helix chain 'A' and resid 571 through 578 Processing helix chain 'A' and resid 584 through 592 removed outlier: 3.733A pdb=" N ARG A 590 " --> pdb=" O SER A 586 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N GLU A 592 " --> pdb=" O ARG A 588 " (cutoff:3.500A) Processing helix chain 'A' and resid 621 through 629 Processing helix chain 'A' and resid 637 through 650 Processing helix chain 'A' and resid 663 through 675 Processing helix chain 'A' and resid 677 through 680 No H-bonds generated for 'chain 'A' and resid 677 through 680' Processing helix chain 'A' and resid 696 through 702 removed outlier: 3.998A pdb=" N VAL A 702 " --> pdb=" O GLU A 698 " (cutoff:3.500A) Processing helix chain 'A' and resid 718 through 721 Processing helix chain 'A' and resid 759 through 768 removed outlier: 3.664A pdb=" N ARG A 768 " --> pdb=" O GLN A 764 " (cutoff:3.500A) Processing helix chain 'A' and resid 783 through 788 Processing helix chain 'A' and resid 796 through 798 No H-bonds generated for 'chain 'A' and resid 796 through 798' Processing helix chain 'A' and resid 803 through 812 Processing helix chain 'A' and resid 817 through 822 Processing helix chain 'A' and resid 830 through 842 Processing helix chain 'A' and resid 854 through 860 Processing helix chain 'A' and resid 866 through 878 Processing helix chain 'A' and resid 881 through 892 Processing helix chain 'A' and resid 909 through 915 removed outlier: 4.220A pdb=" N SER A 915 " --> pdb=" O GLN A 911 " (cutoff:3.500A) Processing helix chain 'A' and resid 921 through 938 Processing helix chain 'A' and resid 940 through 950 Processing helix chain 'A' and resid 954 through 974 Processing helix chain 'A' and resid 978 through 980 No H-bonds generated for 'chain 'A' and resid 978 through 980' Processing helix chain 'A' and resid 995 through 1007 removed outlier: 3.722A pdb=" N CYS A1005 " --> pdb=" O LEU A1001 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N LEU A1006 " --> pdb=" O ALA A1002 " (cutoff:3.500A) Processing helix chain 'A' and resid 1024 through 1026 No H-bonds generated for 'chain 'A' and resid 1024 through 1026' Processing helix chain 'A' and resid 1071 through 1076 Processing helix chain 'A' and resid 1102 through 1124 removed outlier: 3.932A pdb=" N LEU A1111 " --> pdb=" O LYS A1107 " (cutoff:3.500A) removed outlier: 4.280A pdb=" N LYS A1112 " --> pdb=" O ILE A1108 " (cutoff:3.500A) Proline residue: A1113 - end of helix Processing helix chain 'A' and resid 1126 through 1128 No H-bonds generated for 'chain 'A' and resid 1126 through 1128' Processing helix chain 'A' and resid 1134 through 1147 Processing helix chain 'A' and resid 1149 through 1152 removed outlier: 4.474A pdb=" N GLY A1152 " --> pdb=" O LYS A1149 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1149 through 1152' Processing sheet with id= A, first strand: chain 'A' and resid 188 through 192 removed outlier: 3.702A pdb=" N ARG A 213 " --> pdb=" O VAL A 208 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 555 through 559 removed outlier: 6.696A pdb=" N VAL A 535 " --> pdb=" O VAL A 403 " (cutoff:3.500A) removed outlier: 7.815A pdb=" N ILE A 405 " --> pdb=" O VAL A 535 " (cutoff:3.500A) removed outlier: 6.483A pdb=" N LEU A 537 " --> pdb=" O ILE A 405 " (cutoff:3.500A) removed outlier: 7.734A pdb=" N GLY A 407 " --> pdb=" O LEU A 537 " (cutoff:3.500A) removed outlier: 5.961A pdb=" N SER A 539 " --> pdb=" O GLY A 407 " (cutoff:3.500A) removed outlier: 6.606A pdb=" N ALA A 481 " --> pdb=" O ILE A 436 " (cutoff:3.500A) removed outlier: 7.847A pdb=" N VAL A 438 " --> pdb=" O ALA A 481 " (cutoff:3.500A) removed outlier: 6.213A pdb=" N LEU A 483 " --> pdb=" O VAL A 438 " (cutoff:3.500A) removed outlier: 7.352A pdb=" N GLN A 440 " --> pdb=" O LEU A 483 " (cutoff:3.500A) removed outlier: 6.522A pdb=" N CYS A 485 " --> pdb=" O GLN A 440 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N THR A 486 " --> pdb=" O SER A 468 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 566 through 569 removed outlier: 7.189A pdb=" N GLY A 775 " --> pdb=" O GLN A 567 " (cutoff:3.500A) removed outlier: 8.610A pdb=" N PHE A 569 " --> pdb=" O GLY A 775 " (cutoff:3.500A) removed outlier: 6.625A pdb=" N CYS A 777 " --> pdb=" O PHE A 569 " (cutoff:3.500A) removed outlier: 6.864A pdb=" N ALA A 655 " --> pdb=" O VAL A 730 " (cutoff:3.500A) removed outlier: 5.473A pdb=" N VAL A 732 " --> pdb=" O ALA A 655 " (cutoff:3.500A) removed outlier: 6.482A pdb=" N LEU A 657 " --> pdb=" O VAL A 732 " (cutoff:3.500A) removed outlier: 5.144A pdb=" N ASP A 734 " --> pdb=" O LEU A 657 " (cutoff:3.500A) removed outlier: 6.580A pdb=" N PHE A 659 " --> pdb=" O ASP A 734 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 737 through 744 Processing sheet with id= E, first strand: chain 'A' and resid 1049 through 1051 removed outlier: 6.967A pdb=" N LYS A1020 " --> pdb=" O LYS A1016 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'A' and resid 1054 through 1057 removed outlier: 3.671A pdb=" N GLU A1054 " --> pdb=" O LYS A1064 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'A' and resid 1082 through 1084 327 hydrogen bonds defined for protein. 954 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 3 stacking parallelities Total time for adding SS restraints: 2.52 Time building geometry restraints manager: 3.52 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.42: 3326 1.42 - 1.62: 4786 1.62 - 1.83: 78 1.83 - 2.03: 0 2.03 - 2.23: 1 Bond restraints: 8191 Sorted by residual: bond pdb=" C GLY A 346 " pdb=" N LEU A 348 " ideal model delta sigma weight residual 1.329 2.234 -0.905 1.40e-02 5.10e+03 4.17e+03 bond pdb=" F3 ALF A1203 " pdb="AL ALF A1203 " ideal model delta sigma weight residual 1.685 1.782 -0.097 2.00e-02 2.50e+03 2.35e+01 bond pdb=" F2 ALF A1203 " pdb="AL ALF A1203 " ideal model delta sigma weight residual 1.685 1.781 -0.096 2.00e-02 2.50e+03 2.33e+01 bond pdb=" F1 ALF A1203 " pdb="AL ALF A1203 " ideal model delta sigma weight residual 1.684 1.779 -0.095 2.00e-02 2.50e+03 2.28e+01 bond pdb=" F4 ALF A1203 " pdb="AL ALF A1203 " ideal model delta sigma weight residual 1.686 1.779 -0.093 2.00e-02 2.50e+03 2.18e+01 ... (remaining 8186 not shown) Histogram of bond angle deviations from ideal: 89.59 - 107.64: 378 107.64 - 125.70: 10640 125.70 - 143.75: 125 143.75 - 161.81: 0 161.81 - 179.86: 2 Bond angle restraints: 11145 Sorted by residual: angle pdb=" F1 ALF A1203 " pdb="AL ALF A1203 " pdb=" F2 ALF A1203 " ideal model delta sigma weight residual 108.68 179.45 -70.77 3.00e+00 1.11e-01 5.57e+02 angle pdb=" F3 ALF A1203 " pdb="AL ALF A1203 " pdb=" F4 ALF A1203 " ideal model delta sigma weight residual 109.63 179.86 -70.23 3.00e+00 1.11e-01 5.48e+02 angle pdb=" CA PRO A 560 " pdb=" N PRO A 560 " pdb=" CD PRO A 560 " ideal model delta sigma weight residual 112.00 98.49 13.51 1.40e+00 5.10e-01 9.32e+01 angle pdb=" CA GLY A 346 " pdb=" C GLY A 346 " pdb=" N LEU A 348 " ideal model delta sigma weight residual 115.32 103.41 11.91 1.42e+00 4.96e-01 7.03e+01 angle pdb=" C GLY A 346 " pdb=" N LEU A 348 " pdb=" CA LEU A 348 " ideal model delta sigma weight residual 121.70 135.74 -14.04 1.80e+00 3.09e-01 6.08e+01 ... (remaining 11140 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.51: 4768 33.51 - 67.02: 252 67.02 - 100.52: 26 100.52 - 134.03: 1 134.03 - 167.54: 3 Dihedral angle restraints: 5050 sinusoidal: 2164 harmonic: 2886 Sorted by residual: dihedral pdb=" O4' U C 6 " pdb=" C1' U C 6 " pdb=" N1 U C 6 " pdb=" C2 U C 6 " ideal model delta sinusoidal sigma weight residual -160.00 7.54 -167.54 1 1.50e+01 4.44e-03 8.43e+01 dihedral pdb=" C5' ADP A1201 " pdb=" O5' ADP A1201 " pdb=" PA ADP A1201 " pdb=" O2A ADP A1201 " ideal model delta sinusoidal sigma weight residual 300.00 144.92 155.08 1 2.00e+01 2.50e-03 4.58e+01 dihedral pdb=" O2A ADP A1201 " pdb=" O3A ADP A1201 " pdb=" PA ADP A1201 " pdb=" PB ADP A1201 " ideal model delta sinusoidal sigma weight residual -60.00 90.48 -150.48 1 2.00e+01 2.50e-03 4.49e+01 ... (remaining 5047 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.050: 994 0.050 - 0.100: 226 0.100 - 0.150: 62 0.150 - 0.200: 3 0.200 - 0.251: 2 Chirality restraints: 1287 Sorted by residual: chirality pdb=" CB ILE A 719 " pdb=" CA ILE A 719 " pdb=" CG1 ILE A 719 " pdb=" CG2 ILE A 719 " both_signs ideal model delta sigma weight residual False 2.64 2.39 0.25 2.00e-01 2.50e+01 1.57e+00 chirality pdb=" CG LEU A 201 " pdb=" CB LEU A 201 " pdb=" CD1 LEU A 201 " pdb=" CD2 LEU A 201 " both_signs ideal model delta sigma weight residual False -2.59 -2.36 -0.23 2.00e-01 2.50e+01 1.30e+00 chirality pdb=" CA ILE A 343 " pdb=" N ILE A 343 " pdb=" C ILE A 343 " pdb=" CB ILE A 343 " both_signs ideal model delta sigma weight residual False 2.43 2.62 -0.19 2.00e-01 2.50e+01 8.89e-01 ... (remaining 1284 not shown) Planarity restraints: 1401 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLY A 346 " -0.113 2.00e-02 2.50e+03 1.97e-01 3.90e+02 pdb=" C GLY A 346 " 0.337 2.00e-02 2.50e+03 pdb=" O GLY A 346 " -0.159 2.00e-02 2.50e+03 pdb=" N LEU A 348 " -0.065 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C VAL A 559 " 0.068 5.00e-02 4.00e+02 9.48e-02 1.44e+01 pdb=" N PRO A 560 " -0.163 5.00e-02 4.00e+02 pdb=" CA PRO A 560 " 0.043 5.00e-02 4.00e+02 pdb=" CD PRO A 560 " 0.052 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ASN A 342 " 0.014 2.00e-02 2.50e+03 2.81e-02 7.92e+00 pdb=" C ASN A 342 " -0.049 2.00e-02 2.50e+03 pdb=" O ASN A 342 " 0.019 2.00e-02 2.50e+03 pdb=" N ILE A 343 " 0.016 2.00e-02 2.50e+03 ... (remaining 1398 not shown) Histogram of nonbonded interaction distances: 1.96 - 2.55: 68 2.55 - 3.14: 6239 3.14 - 3.73: 13248 3.73 - 4.31: 18523 4.31 - 4.90: 29800 Nonbonded interactions: 67878 Sorted by model distance: nonbonded pdb="MG MG A1202 " pdb=" O HOH A1302 " model vdw 1.963 2.170 nonbonded pdb=" F2 ALF A1203 " pdb=" O HOH A1301 " model vdw 2.099 2.390 nonbonded pdb=" F2 ALF A1203 " pdb=" O HOH A1302 " model vdw 2.146 2.390 nonbonded pdb=" OE1 GLN A 576 " pdb=" OG1 THR A 623 " model vdw 2.187 2.440 nonbonded pdb=" O3B ADP A1201 " pdb=" O HOH A1301 " model vdw 2.196 2.440 ... (remaining 67873 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== 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=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.960 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.080 Construct map_model_manager: 0.010 Extract box with map and model: 3.830 Check model and map are aligned: 0.110 Set scattering table: 0.070 Process input model: 30.510 Find NCS groups from input model: 0.220 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:11.360 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 47.190 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7395 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 : 0.011 0.905 8191 Z= 0.964 Angle : 1.242 70.773 11145 Z= 0.516 Chirality : 0.046 0.251 1287 Planarity : 0.008 0.197 1401 Dihedral : 19.476 167.540 3170 Min Nonbonded Distance : 1.963 Molprobity Statistics. All-atom Clashscore : 11.55 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.59 % Favored : 96.31 % Rotamer: Outliers : 2.31 % Allowed : 30.40 % Favored : 67.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.96 % 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: 0.95 (0.28), residues: 977 helix: 1.73 (0.24), residues: 457 sheet: -0.38 (0.42), residues: 161 loop : -0.21 (0.36), residues: 359 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 663 HIS 0.004 0.001 HIS A 746 PHE 0.016 0.002 PHE A 878 TYR 0.012 0.001 TYR A 890 ARG 0.007 0.000 ARG A 624 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1954 Ramachandran restraints generated. 977 Oldfield, 0 Emsley, 977 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1954 Ramachandran restraints generated. 977 Oldfield, 0 Emsley, 977 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 866 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 132 time to evaluate : 1.009 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 294 ILE cc_start: 0.8506 (OUTLIER) cc_final: 0.8107 (pp) outliers start: 20 outliers final: 9 residues processed: 150 average time/residue: 1.2166 time to fit residues: 193.3049 Evaluate side-chains 77 residues out of total 866 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 67 time to evaluate : 1.024 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 158 ASN Chi-restraints excluded: chain A residue 293 LYS Chi-restraints excluded: chain A residue 294 ILE Chi-restraints excluded: chain A residue 297 ASP Chi-restraints excluded: chain A residue 363 SER Chi-restraints excluded: chain A residue 527 VAL Chi-restraints excluded: chain A residue 581 VAL Chi-restraints excluded: chain A residue 792 ASN Chi-restraints excluded: chain A residue 929 SER Chi-restraints excluded: chain A residue 1058 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 83 optimal weight: 0.9990 chunk 75 optimal weight: 2.9990 chunk 41 optimal weight: 4.9990 chunk 25 optimal weight: 0.8980 chunk 50 optimal weight: 2.9990 chunk 40 optimal weight: 0.9990 chunk 77 optimal weight: 6.9990 chunk 30 optimal weight: 0.4980 chunk 47 optimal weight: 2.9990 chunk 57 optimal weight: 4.9990 chunk 89 optimal weight: 2.9990 overall best weight: 1.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 212 ASN A 332 GLN A 339 HIS A 567 GLN A 621 GLN A 911 GLN A 953 GLN A 973 GLN A1037 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7506 moved from start: 0.2144 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.090 8191 Z= 0.246 Angle : 0.666 9.964 11145 Z= 0.325 Chirality : 0.044 0.198 1287 Planarity : 0.005 0.054 1401 Dihedral : 12.593 167.758 1254 Min Nonbonded Distance : 1.867 Molprobity Statistics. All-atom Clashscore : 12.18 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.58 % Favored : 96.32 % Rotamer: Outliers : 5.43 % Allowed : 28.79 % Favored : 65.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.96 % Cis-general : 0.11 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.01 (0.28), residues: 979 helix: 1.82 (0.24), residues: 458 sheet: -0.30 (0.40), residues: 174 loop : -0.28 (0.37), residues: 347 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 335 HIS 0.004 0.001 HIS A 691 PHE 0.016 0.001 PHE A 667 TYR 0.009 0.001 TYR A 437 ARG 0.014 0.001 ARG A 844 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1958 Ramachandran restraints generated. 979 Oldfield, 0 Emsley, 979 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1958 Ramachandran restraints generated. 979 Oldfield, 0 Emsley, 979 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 866 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 72 time to evaluate : 1.016 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 257 ASP cc_start: 0.6255 (OUTLIER) cc_final: 0.5999 (p0) REVERT: A 297 ASP cc_start: 0.6850 (OUTLIER) cc_final: 0.5958 (p0) outliers start: 46 outliers final: 14 residues processed: 111 average time/residue: 1.0103 time to fit residues: 120.7148 Evaluate side-chains 74 residues out of total 866 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 58 time to evaluate : 0.900 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 161 ILE Chi-restraints excluded: chain A residue 235 LEU Chi-restraints excluded: chain A residue 257 ASP Chi-restraints excluded: chain A residue 292 ILE Chi-restraints excluded: chain A residue 293 LYS Chi-restraints excluded: chain A residue 294 ILE Chi-restraints excluded: chain A residue 297 ASP Chi-restraints excluded: chain A residue 581 VAL Chi-restraints excluded: chain A residue 627 MET Chi-restraints excluded: chain A residue 722 THR Chi-restraints excluded: chain A residue 729 ILE Chi-restraints excluded: chain A residue 762 LEU Chi-restraints excluded: chain A residue 792 ASN Chi-restraints excluded: chain A residue 998 ASP Chi-restraints excluded: chain A residue 1058 THR Chi-restraints excluded: chain A residue 1148 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 49 optimal weight: 2.9990 chunk 27 optimal weight: 0.9990 chunk 74 optimal weight: 8.9990 chunk 61 optimal weight: 4.9990 chunk 24 optimal weight: 1.9990 chunk 90 optimal weight: 8.9990 chunk 97 optimal weight: 0.8980 chunk 80 optimal weight: 0.0030 chunk 89 optimal weight: 0.8980 chunk 30 optimal weight: 3.9990 chunk 72 optimal weight: 1.9990 overall best weight: 0.9594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 212 ASN ** A 510 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 664 ASN ** A 746 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7510 moved from start: 0.2625 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 8191 Z= 0.209 Angle : 0.624 8.320 11145 Z= 0.306 Chirality : 0.043 0.171 1287 Planarity : 0.005 0.050 1401 Dihedral : 12.289 161.809 1249 Min Nonbonded Distance : 1.964 Molprobity Statistics. All-atom Clashscore : 10.87 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.48 % Favored : 96.42 % Rotamer: Outliers : 3.58 % Allowed : 29.71 % Favored : 66.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.96 % Cis-general : 0.11 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.05 (0.28), residues: 979 helix: 1.85 (0.25), residues: 457 sheet: -0.22 (0.40), residues: 175 loop : -0.27 (0.36), residues: 347 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 335 HIS 0.003 0.001 HIS A 746 PHE 0.015 0.001 PHE A 667 TYR 0.048 0.001 TYR A1009 ARG 0.011 0.001 ARG A 844 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1958 Ramachandran restraints generated. 979 Oldfield, 0 Emsley, 979 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1958 Ramachandran restraints generated. 979 Oldfield, 0 Emsley, 979 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 866 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 63 time to evaluate : 0.949 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 297 ASP cc_start: 0.6771 (OUTLIER) cc_final: 0.5972 (p0) outliers start: 30 outliers final: 15 residues processed: 88 average time/residue: 1.0929 time to fit residues: 103.4646 Evaluate side-chains 75 residues out of total 866 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 59 time to evaluate : 0.822 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 148 ASP Chi-restraints excluded: chain A residue 167 ILE Chi-restraints excluded: chain A residue 235 LEU Chi-restraints excluded: chain A residue 294 ILE Chi-restraints excluded: chain A residue 297 ASP Chi-restraints excluded: chain A residue 415 THR Chi-restraints excluded: chain A residue 444 ILE Chi-restraints excluded: chain A residue 447 ILE Chi-restraints excluded: chain A residue 581 VAL Chi-restraints excluded: chain A residue 729 ILE Chi-restraints excluded: chain A residue 762 LEU Chi-restraints excluded: chain A residue 763 GLU Chi-restraints excluded: chain A residue 892 SER Chi-restraints excluded: chain A residue 998 ASP Chi-restraints excluded: chain A residue 1058 THR Chi-restraints excluded: chain A residue 1150 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 88 optimal weight: 1.9990 chunk 67 optimal weight: 0.8980 chunk 46 optimal weight: 0.6980 chunk 9 optimal weight: 0.9980 chunk 42 optimal weight: 6.9990 chunk 60 optimal weight: 4.9990 chunk 90 optimal weight: 4.9990 chunk 95 optimal weight: 5.9990 chunk 47 optimal weight: 3.9990 chunk 85 optimal weight: 5.9990 chunk 25 optimal weight: 0.5980 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 212 ASN A 440 GLN ** A 510 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 746 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1032 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7523 moved from start: 0.2926 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 8191 Z= 0.205 Angle : 0.615 8.953 11145 Z= 0.300 Chirality : 0.043 0.174 1287 Planarity : 0.005 0.048 1401 Dihedral : 12.001 160.051 1243 Min Nonbonded Distance : 1.941 Molprobity Statistics. All-atom Clashscore : 10.49 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.68 % Favored : 96.22 % Rotamer: Outliers : 4.05 % Allowed : 29.13 % Favored : 66.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.96 % Cis-general : 0.11 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.07 (0.28), residues: 979 helix: 1.88 (0.25), residues: 456 sheet: -0.21 (0.39), residues: 180 loop : -0.27 (0.36), residues: 343 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 335 HIS 0.003 0.001 HIS A 746 PHE 0.014 0.001 PHE A 667 TYR 0.061 0.002 TYR A1009 ARG 0.006 0.001 ARG A 844 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1958 Ramachandran restraints generated. 979 Oldfield, 0 Emsley, 979 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1958 Ramachandran restraints generated. 979 Oldfield, 0 Emsley, 979 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 866 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 62 time to evaluate : 0.920 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 297 ASP cc_start: 0.6754 (OUTLIER) cc_final: 0.5986 (p0) outliers start: 34 outliers final: 15 residues processed: 89 average time/residue: 1.0753 time to fit residues: 102.8418 Evaluate side-chains 71 residues out of total 866 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 55 time to evaluate : 0.997 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 148 ASP Chi-restraints excluded: chain A residue 167 ILE Chi-restraints excluded: chain A residue 235 LEU Chi-restraints excluded: chain A residue 294 ILE Chi-restraints excluded: chain A residue 297 ASP Chi-restraints excluded: chain A residue 444 ILE Chi-restraints excluded: chain A residue 581 VAL Chi-restraints excluded: chain A residue 729 ILE Chi-restraints excluded: chain A residue 762 LEU Chi-restraints excluded: chain A residue 763 GLU Chi-restraints excluded: chain A residue 792 ASN Chi-restraints excluded: chain A residue 871 MET Chi-restraints excluded: chain A residue 892 SER Chi-restraints excluded: chain A residue 998 ASP Chi-restraints excluded: chain A residue 1058 THR Chi-restraints excluded: chain A residue 1150 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 79 optimal weight: 1.9990 chunk 54 optimal weight: 6.9990 chunk 1 optimal weight: 7.9990 chunk 71 optimal weight: 0.8980 chunk 39 optimal weight: 3.9990 chunk 81 optimal weight: 9.9990 chunk 66 optimal weight: 1.9990 chunk 0 optimal weight: 5.9990 chunk 48 optimal weight: 0.8980 chunk 85 optimal weight: 7.9990 chunk 24 optimal weight: 2.9990 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 746 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 953 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7578 moved from start: 0.3138 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 8191 Z= 0.268 Angle : 0.634 9.860 11145 Z= 0.311 Chirality : 0.044 0.199 1287 Planarity : 0.005 0.046 1401 Dihedral : 11.991 162.557 1243 Min Nonbonded Distance : 1.716 Molprobity Statistics. All-atom Clashscore : 10.62 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.37 % Favored : 96.52 % Rotamer: Outliers : 3.24 % Allowed : 30.17 % Favored : 66.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.96 % Cis-general : 0.11 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.07 (0.28), residues: 979 helix: 1.84 (0.24), residues: 457 sheet: -0.12 (0.40), residues: 175 loop : -0.29 (0.36), residues: 347 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 335 HIS 0.003 0.001 HIS A 691 PHE 0.014 0.001 PHE A 667 TYR 0.034 0.002 TYR A1009 ARG 0.009 0.001 ARG A 184 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1958 Ramachandran restraints generated. 979 Oldfield, 0 Emsley, 979 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1958 Ramachandran restraints generated. 979 Oldfield, 0 Emsley, 979 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 866 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 59 time to evaluate : 0.785 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 297 ASP cc_start: 0.6901 (OUTLIER) cc_final: 0.6211 (p0) outliers start: 27 outliers final: 17 residues processed: 81 average time/residue: 1.0723 time to fit residues: 93.6778 Evaluate side-chains 77 residues out of total 866 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 59 time to evaluate : 0.960 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 161 ILE Chi-restraints excluded: chain A residue 167 ILE Chi-restraints excluded: chain A residue 235 LEU Chi-restraints excluded: chain A residue 297 ASP Chi-restraints excluded: chain A residue 444 ILE Chi-restraints excluded: chain A residue 447 ILE Chi-restraints excluded: chain A residue 581 VAL Chi-restraints excluded: chain A residue 729 ILE Chi-restraints excluded: chain A residue 762 LEU Chi-restraints excluded: chain A residue 763 GLU Chi-restraints excluded: chain A residue 792 ASN Chi-restraints excluded: chain A residue 821 LEU Chi-restraints excluded: chain A residue 892 SER Chi-restraints excluded: chain A residue 997 LEU Chi-restraints excluded: chain A residue 998 ASP Chi-restraints excluded: chain A residue 1058 THR Chi-restraints excluded: chain A residue 1076 LEU Chi-restraints excluded: chain A residue 1150 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 32 optimal weight: 0.9980 chunk 86 optimal weight: 0.4980 chunk 18 optimal weight: 0.0020 chunk 56 optimal weight: 4.9990 chunk 23 optimal weight: 3.9990 chunk 95 optimal weight: 2.9990 chunk 79 optimal weight: 3.9990 chunk 44 optimal weight: 5.9990 chunk 7 optimal weight: 8.9990 chunk 31 optimal weight: 4.9990 chunk 50 optimal weight: 3.9990 overall best weight: 1.6992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 746 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7587 moved from start: 0.3359 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 8191 Z= 0.262 Angle : 0.633 10.587 11145 Z= 0.308 Chirality : 0.044 0.206 1287 Planarity : 0.004 0.044 1401 Dihedral : 11.898 162.988 1241 Min Nonbonded Distance : 1.850 Molprobity Statistics. All-atom Clashscore : 10.37 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.58 % Favored : 96.32 % Rotamer: Outliers : 3.58 % Allowed : 29.83 % Favored : 66.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.96 % Cis-general : 0.11 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.07 (0.28), residues: 979 helix: 1.84 (0.25), residues: 457 sheet: -0.17 (0.40), residues: 175 loop : -0.26 (0.37), residues: 347 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 335 HIS 0.003 0.001 HIS A 746 PHE 0.019 0.001 PHE A 155 TYR 0.044 0.002 TYR A1009 ARG 0.006 0.001 ARG A 184 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1958 Ramachandran restraints generated. 979 Oldfield, 0 Emsley, 979 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1958 Ramachandran restraints generated. 979 Oldfield, 0 Emsley, 979 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 866 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 58 time to evaluate : 0.905 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 297 ASP cc_start: 0.6966 (OUTLIER) cc_final: 0.6284 (p0) outliers start: 30 outliers final: 20 residues processed: 83 average time/residue: 1.0077 time to fit residues: 90.3912 Evaluate side-chains 76 residues out of total 866 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 55 time to evaluate : 0.945 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 148 ASP Chi-restraints excluded: chain A residue 161 ILE Chi-restraints excluded: chain A residue 167 ILE Chi-restraints excluded: chain A residue 235 LEU Chi-restraints excluded: chain A residue 292 ILE Chi-restraints excluded: chain A residue 297 ASP Chi-restraints excluded: chain A residue 415 THR Chi-restraints excluded: chain A residue 444 ILE Chi-restraints excluded: chain A residue 447 ILE Chi-restraints excluded: chain A residue 557 LEU Chi-restraints excluded: chain A residue 581 VAL Chi-restraints excluded: chain A residue 729 ILE Chi-restraints excluded: chain A residue 762 LEU Chi-restraints excluded: chain A residue 792 ASN Chi-restraints excluded: chain A residue 821 LEU Chi-restraints excluded: chain A residue 871 MET Chi-restraints excluded: chain A residue 892 SER Chi-restraints excluded: chain A residue 997 LEU Chi-restraints excluded: chain A residue 998 ASP Chi-restraints excluded: chain A residue 1058 THR Chi-restraints excluded: chain A residue 1150 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 92 optimal weight: 1.9990 chunk 10 optimal weight: 0.0980 chunk 54 optimal weight: 5.9990 chunk 69 optimal weight: 0.7980 chunk 80 optimal weight: 2.9990 chunk 53 optimal weight: 0.1980 chunk 95 optimal weight: 1.9990 chunk 59 optimal weight: 4.9990 chunk 58 optimal weight: 0.9980 chunk 44 optimal weight: 0.8980 chunk 38 optimal weight: 0.1980 overall best weight: 0.4380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 510 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 746 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7512 moved from start: 0.3563 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 8191 Z= 0.171 Angle : 0.619 11.502 11145 Z= 0.298 Chirality : 0.042 0.201 1287 Planarity : 0.004 0.044 1401 Dihedral : 11.673 154.374 1241 Min Nonbonded Distance : 2.042 Molprobity Statistics. All-atom Clashscore : 10.18 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.17 % Favored : 96.73 % Rotamer: Outliers : 3.12 % Allowed : 30.40 % Favored : 66.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.96 % Cis-general : 0.11 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.08 (0.28), residues: 979 helix: 1.87 (0.25), residues: 456 sheet: -0.01 (0.41), residues: 164 loop : -0.36 (0.36), residues: 359 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 663 HIS 0.003 0.000 HIS A 746 PHE 0.018 0.001 PHE A 155 TYR 0.038 0.001 TYR A1009 ARG 0.005 0.000 ARG A 844 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1958 Ramachandran restraints generated. 979 Oldfield, 0 Emsley, 979 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1958 Ramachandran restraints generated. 979 Oldfield, 0 Emsley, 979 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 866 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 62 time to evaluate : 0.932 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 297 ASP cc_start: 0.6991 (OUTLIER) cc_final: 0.6385 (p0) outliers start: 26 outliers final: 10 residues processed: 84 average time/residue: 0.9237 time to fit residues: 84.3171 Evaluate side-chains 74 residues out of total 866 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 63 time to evaluate : 0.876 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 148 ASP Chi-restraints excluded: chain A residue 235 LEU Chi-restraints excluded: chain A residue 297 ASP Chi-restraints excluded: chain A residue 444 ILE Chi-restraints excluded: chain A residue 581 VAL Chi-restraints excluded: chain A residue 729 ILE Chi-restraints excluded: chain A residue 762 LEU Chi-restraints excluded: chain A residue 871 MET Chi-restraints excluded: chain A residue 998 ASP Chi-restraints excluded: chain A residue 1058 THR Chi-restraints excluded: chain A residue 1076 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 56 optimal weight: 0.3980 chunk 28 optimal weight: 1.9990 chunk 18 optimal weight: 8.9990 chunk 60 optimal weight: 0.7980 chunk 65 optimal weight: 1.9990 chunk 47 optimal weight: 1.9990 chunk 8 optimal weight: 10.0000 chunk 75 optimal weight: 0.9990 chunk 86 optimal weight: 2.9990 chunk 91 optimal weight: 0.6980 chunk 83 optimal weight: 3.9990 overall best weight: 0.9784 ------------------------------------------------------------------------------- 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: 0.7546 moved from start: 0.3693 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 8191 Z= 0.209 Angle : 0.635 11.972 11145 Z= 0.306 Chirality : 0.043 0.237 1287 Planarity : 0.004 0.042 1401 Dihedral : 11.582 155.895 1241 Min Nonbonded Distance : 1.957 Molprobity Statistics. All-atom Clashscore : 10.49 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.68 % Favored : 96.22 % Rotamer: Outliers : 1.62 % Allowed : 32.49 % Favored : 65.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.96 % Cis-general : 0.11 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.08 (0.28), residues: 979 helix: 1.84 (0.25), residues: 456 sheet: -0.10 (0.40), residues: 175 loop : -0.26 (0.37), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 663 HIS 0.003 0.001 HIS A 746 PHE 0.014 0.001 PHE A 667 TYR 0.017 0.001 TYR A 360 ARG 0.004 0.000 ARG A 624 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1958 Ramachandran restraints generated. 979 Oldfield, 0 Emsley, 979 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1958 Ramachandran restraints generated. 979 Oldfield, 0 Emsley, 979 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 866 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 59 time to evaluate : 0.946 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 297 ASP cc_start: 0.7035 (OUTLIER) cc_final: 0.6444 (p0) outliers start: 13 outliers final: 11 residues processed: 69 average time/residue: 0.9614 time to fit residues: 72.1791 Evaluate side-chains 68 residues out of total 866 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 56 time to evaluate : 0.863 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 148 ASP Chi-restraints excluded: chain A residue 235 LEU Chi-restraints excluded: chain A residue 297 ASP Chi-restraints excluded: chain A residue 444 ILE Chi-restraints excluded: chain A residue 581 VAL Chi-restraints excluded: chain A residue 729 ILE Chi-restraints excluded: chain A residue 762 LEU Chi-restraints excluded: chain A residue 792 ASN Chi-restraints excluded: chain A residue 871 MET Chi-restraints excluded: chain A residue 998 ASP Chi-restraints excluded: chain A residue 1058 THR Chi-restraints excluded: chain A residue 1076 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 88 optimal weight: 5.9990 chunk 91 optimal weight: 3.9990 chunk 53 optimal weight: 4.9990 chunk 38 optimal weight: 3.9990 chunk 69 optimal weight: 0.9980 chunk 27 optimal weight: 3.9990 chunk 80 optimal weight: 3.9990 chunk 84 optimal weight: 0.9980 chunk 58 optimal weight: 2.9990 chunk 94 optimal weight: 0.9980 chunk 57 optimal weight: 0.9990 overall best weight: 1.3984 ------------------------------------------------------------------------------- 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: 0.7575 moved from start: 0.3759 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 8191 Z= 0.239 Angle : 0.643 12.535 11145 Z= 0.310 Chirality : 0.044 0.254 1287 Planarity : 0.004 0.043 1401 Dihedral : 11.506 158.936 1241 Min Nonbonded Distance : 1.942 Molprobity Statistics. All-atom Clashscore : 11.12 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.68 % Favored : 96.22 % Rotamer: Outliers : 1.85 % Allowed : 32.37 % Favored : 65.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.96 % Cis-general : 0.11 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.07 (0.28), residues: 979 helix: 1.81 (0.25), residues: 456 sheet: -0.12 (0.40), residues: 175 loop : -0.23 (0.37), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 663 HIS 0.003 0.001 HIS A 691 PHE 0.013 0.001 PHE A 667 TYR 0.032 0.001 TYR A1009 ARG 0.004 0.000 ARG A 844 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1958 Ramachandran restraints generated. 979 Oldfield, 0 Emsley, 979 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1958 Ramachandran restraints generated. 979 Oldfield, 0 Emsley, 979 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 866 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 57 time to evaluate : 0.878 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 297 ASP cc_start: 0.7046 (OUTLIER) cc_final: 0.6489 (p0) outliers start: 15 outliers final: 9 residues processed: 68 average time/residue: 1.0561 time to fit residues: 77.3650 Evaluate side-chains 67 residues out of total 866 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 57 time to evaluate : 0.888 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 148 ASP Chi-restraints excluded: chain A residue 235 LEU Chi-restraints excluded: chain A residue 297 ASP Chi-restraints excluded: chain A residue 444 ILE Chi-restraints excluded: chain A residue 581 VAL Chi-restraints excluded: chain A residue 762 LEU Chi-restraints excluded: chain A residue 871 MET Chi-restraints excluded: chain A residue 998 ASP Chi-restraints excluded: chain A residue 1058 THR Chi-restraints excluded: chain A residue 1076 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 44 optimal weight: 1.9990 chunk 65 optimal weight: 0.0770 chunk 98 optimal weight: 8.9990 chunk 90 optimal weight: 0.0370 chunk 78 optimal weight: 0.8980 chunk 8 optimal weight: 1.9990 chunk 60 optimal weight: 0.7980 chunk 48 optimal weight: 1.9990 chunk 62 optimal weight: 0.9980 chunk 83 optimal weight: 1.9990 chunk 24 optimal weight: 4.9990 overall best weight: 0.5616 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 510 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7522 moved from start: 0.3869 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 8191 Z= 0.185 Angle : 0.638 12.928 11145 Z= 0.308 Chirality : 0.043 0.253 1287 Planarity : 0.004 0.042 1401 Dihedral : 11.434 153.726 1241 Min Nonbonded Distance : 1.928 Molprobity Statistics. All-atom Clashscore : 10.99 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.58 % Favored : 96.32 % Rotamer: Outliers : 1.16 % Allowed : 32.95 % Favored : 65.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.96 % Cis-general : 0.11 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.05 (0.28), residues: 979 helix: 1.76 (0.25), residues: 456 sheet: -0.06 (0.40), residues: 175 loop : -0.23 (0.36), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 663 HIS 0.003 0.001 HIS A 746 PHE 0.013 0.001 PHE A 667 TYR 0.011 0.001 TYR A 360 ARG 0.005 0.000 ARG A1059 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1958 Ramachandran restraints generated. 979 Oldfield, 0 Emsley, 979 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1958 Ramachandran restraints generated. 979 Oldfield, 0 Emsley, 979 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 866 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 57 time to evaluate : 1.032 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 297 ASP cc_start: 0.7054 (OUTLIER) cc_final: 0.6510 (p0) REVERT: A 627 MET cc_start: 0.6018 (tpt) cc_final: 0.5279 (tpt) outliers start: 9 outliers final: 8 residues processed: 64 average time/residue: 1.1403 time to fit residues: 78.5980 Evaluate side-chains 65 residues out of total 866 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 56 time to evaluate : 0.986 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 235 LEU Chi-restraints excluded: chain A residue 297 ASP Chi-restraints excluded: chain A residue 444 ILE Chi-restraints excluded: chain A residue 581 VAL Chi-restraints excluded: chain A residue 762 LEU Chi-restraints excluded: chain A residue 871 MET Chi-restraints excluded: chain A residue 998 ASP Chi-restraints excluded: chain A residue 1058 THR Chi-restraints excluded: chain A residue 1076 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 72 optimal weight: 2.9990 chunk 11 optimal weight: 7.9990 chunk 21 optimal weight: 1.9990 chunk 78 optimal weight: 1.9990 chunk 32 optimal weight: 0.9980 chunk 80 optimal weight: 0.5980 chunk 9 optimal weight: 3.9990 chunk 14 optimal weight: 0.0030 chunk 69 optimal weight: 0.8980 chunk 4 optimal weight: 3.9990 chunk 56 optimal weight: 5.9990 overall best weight: 0.8992 ------------------------------------------------------------------------------- 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 = 0.3405 r_free = 0.3405 target = 0.086075 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2989 r_free = 0.2989 target = 0.064003 restraints weight = 22491.702| |-----------------------------------------------------------------------------| r_work (start): 0.2994 rms_B_bonded: 4.30 r_work: 0.2812 rms_B_bonded: 4.92 restraints_weight: 0.5000 r_work (final): 0.2812 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2818 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2818 r_free = 0.2818 target_work(ls_wunit_k1) = 0.057 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2818 r_free = 0.2818 target_work(ls_wunit_k1) = 0.057 | | occupancies: max = 1.00 min = 0.08 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.2818 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8377 moved from start: 0.3903 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 8191 Z= 0.204 Angle : 0.652 12.731 11145 Z= 0.313 Chirality : 0.043 0.265 1287 Planarity : 0.004 0.041 1401 Dihedral : 11.398 154.334 1241 Min Nonbonded Distance : 1.898 Molprobity Statistics. All-atom Clashscore : 10.87 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.78 % Favored : 96.11 % Rotamer: Outliers : 1.62 % Allowed : 32.49 % Favored : 65.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.96 % Cis-general : 0.11 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.08 (0.28), residues: 979 helix: 1.80 (0.25), residues: 456 sheet: -0.08 (0.40), residues: 175 loop : -0.22 (0.37), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 663 HIS 0.003 0.001 HIS A 746 PHE 0.013 0.001 PHE A 667 TYR 0.031 0.001 TYR A 360 ARG 0.004 0.000 ARG A1059 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2755.89 seconds wall clock time: 49 minutes 52.18 seconds (2992.18 seconds total)