Starting phenix.real_space_refine on Wed Feb 12 11:30:05 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7wu2_32817/02_2025/7wu2_32817.cif Found real_map, /net/cci-nas-00/data/ceres_data/7wu2_32817/02_2025/7wu2_32817.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7wu2_32817/02_2025/7wu2_32817.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7wu2_32817/02_2025/7wu2_32817.map" model { file = "/net/cci-nas-00/data/ceres_data/7wu2_32817/02_2025/7wu2_32817.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7wu2_32817/02_2025/7wu2_32817.cif" } resolution = 2.8 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= 0.002 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: 4 Type Number sf(0) Gaussians S 50 5.16 5 C 4968 2.51 5 N 1361 2.21 5 O 1450 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 2 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib" Total number of atoms: 7829 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 1734 Number of conformers: 1 Conformer: "" Number of residues, atoms: 210, 1734 Classifications: {'peptide': 210} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 6, 'TRANS': 203} Chain breaks: 1 Unresolved non-hydrogen bonds: 19 Unresolved non-hydrogen angles: 21 Unresolved non-hydrogen dihedrals: 17 Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "B" Number of atoms: 2586 Number of conformers: 1 Conformer: "" Number of residues, atoms: 339, 2586 Classifications: {'peptide': 339} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 5, 'TRANS': 333} Unresolved non-hydrogen bonds: 21 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 16 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 3, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 17 Chain: "C" Number of atoms: 423 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 423 Classifications: {'peptide': 56} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 4, 'TRANS': 51} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "N" Number of atoms: 971 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 971 Classifications: {'peptide': 128} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 5, 'TRANS': 122} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "R" Number of atoms: 2115 Number of conformers: 1 Conformer: "" Number of residues, atoms: 277, 2115 Classifications: {'peptide': 277} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 7, 'TRANS': 269} Unresolved non-hydrogen bonds: 28 Unresolved non-hydrogen angles: 36 Unresolved non-hydrogen dihedrals: 25 Planarities with less than four sites: {'TYR:plan': 1, 'GLU:plan': 1, 'ASP:plan': 1, 'ASN:plan1': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 22 Time building chain proxies: 4.89, per 1000 atoms: 0.62 Number of scatterers: 7829 At special positions: 0 Unit cell: (106.029, 118.881, 83.538, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 50 16.00 O 1450 8.00 N 1361 7.00 C 4968 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS N 22 " - pdb=" SG CYS N 96 " distance=2.03 Simple disulfide: pdb=" SG CYS N 99 " - pdb=" SG CYS N 107 " distance=2.02 Simple disulfide: pdb=" SG CYS R 632 " - pdb=" SG CYS R 704 " 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=0, symmetry=0 Time building additional restraints: 1.87 Conformation dependent library (CDL) restraints added in 1.2 seconds 1996 Ramachandran restraints generated. 998 Oldfield, 0 Emsley, 998 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1892 Finding SS restraints... Secondary structure from input PDB file: 32 helices and 10 sheets defined 40.5% alpha, 20.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.87 Creating SS restraints... Processing helix chain 'A' and resid 26 through 40 Processing helix chain 'A' and resid 53 through 57 removed outlier: 3.904A pdb=" N VAL A 57 " --> pdb=" O SER A 54 " (cutoff:3.500A) Processing helix chain 'A' and resid 233 through 239 removed outlier: 3.675A pdb=" N ASN A 239 " --> pdb=" O GLN A 236 " (cutoff:3.500A) Processing helix chain 'A' and resid 265 through 278 Processing helix chain 'A' and resid 293 through 304 removed outlier: 3.520A pdb=" N LEU A 297 " --> pdb=" O LYS A 293 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N GLY A 304 " --> pdb=" O LYS A 300 " (cutoff:3.500A) Processing helix chain 'A' and resid 307 through 312 removed outlier: 4.196A pdb=" N TYR A 311 " --> pdb=" O LYS A 307 " (cutoff:3.500A) Processing helix chain 'A' and resid 313 through 316 removed outlier: 3.860A pdb=" N ALA A 316 " --> pdb=" O PRO A 313 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 313 through 316' Processing helix chain 'A' and resid 331 through 352 removed outlier: 3.613A pdb=" N ILE A 348 " --> pdb=" O GLU A 344 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N SER A 352 " --> pdb=" O ILE A 348 " (cutoff:3.500A) Processing helix chain 'A' and resid 370 through 391 Processing helix chain 'B' and resid 3 through 26 Processing helix chain 'B' and resid 29 through 34 removed outlier: 3.733A pdb=" N ILE B 33 " --> pdb=" O THR B 29 " (cutoff:3.500A) Processing helix chain 'C' and resid 8 through 25 removed outlier: 4.305A pdb=" N ILE C 25 " --> pdb=" O MET C 21 " (cutoff:3.500A) Processing helix chain 'C' and resid 29 through 44 removed outlier: 3.532A pdb=" N ALA C 33 " --> pdb=" O LYS C 29 " (cutoff:3.500A) Processing helix chain 'C' and resid 45 through 48 Processing helix chain 'N' and resid 28 through 32 removed outlier: 3.606A pdb=" N TYR N 32 " --> pdb=" O PHE N 29 " (cutoff:3.500A) Processing helix chain 'N' and resid 87 through 91 removed outlier: 3.503A pdb=" N THR N 91 " --> pdb=" O PRO N 88 " (cutoff:3.500A) Processing helix chain 'R' and resid 559 through 591 Processing helix chain 'R' and resid 592 through 594 No H-bonds generated for 'chain 'R' and resid 592 through 594' Processing helix chain 'R' and resid 601 through 623 Processing helix chain 'R' and resid 629 through 662 removed outlier: 4.006A pdb=" N VAL R 637 " --> pdb=" O GLN R 633 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ALA R 646 " --> pdb=" O PHE R 642 " (cutoff:3.500A) Processing helix chain 'R' and resid 671 through 680 Processing helix chain 'R' and resid 680 through 694 removed outlier: 3.706A pdb=" N LEU R 684 " --> pdb=" O TRP R 680 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N PHE R 693 " --> pdb=" O ILE R 689 " (cutoff:3.500A) Processing helix chain 'R' and resid 713 through 737 Proline residue: R 719 - end of helix Processing helix chain 'R' and resid 738 through 745 Processing helix chain 'R' and resid 745 through 750 removed outlier: 4.002A pdb=" N HIS R 749 " --> pdb=" O ASN R 745 " (cutoff:3.500A) Processing helix chain 'R' and resid 752 through 764 removed outlier: 3.967A pdb=" N LYS R 756 " --> pdb=" O PRO R 752 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N LEU R 757 " --> pdb=" O SER R 753 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N THR R 758 " --> pdb=" O ALA R 754 " (cutoff:3.500A) Processing helix chain 'R' and resid 764 through 770 removed outlier: 4.572A pdb=" N ILE R 768 " --> pdb=" O VAL R 764 " (cutoff:3.500A) Processing helix chain 'R' and resid 773 through 778 removed outlier: 3.822A pdb=" N VAL R 777 " --> pdb=" O TRP R 773 " (cutoff:3.500A) Processing helix chain 'R' and resid 779 through 781 No H-bonds generated for 'chain 'R' and resid 779 through 781' Processing helix chain 'R' and resid 783 through 797 removed outlier: 3.647A pdb=" N PHE R 787 " --> pdb=" O CYS R 783 " (cutoff:3.500A) Processing helix chain 'R' and resid 797 through 807 Processing helix chain 'R' and resid 810 through 821 Processing sheet with id=AA1, first strand: chain 'A' and resid 209 through 214 removed outlier: 6.251A pdb=" N HIS A 41 " --> pdb=" O HIS A 220 " (cutoff:3.500A) removed outlier: 7.592A pdb=" N PHE A 222 " --> pdb=" O HIS A 41 " (cutoff:3.500A) removed outlier: 6.602A pdb=" N LEU A 43 " --> pdb=" O PHE A 222 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N ALA A 243 " --> pdb=" O ARG A 42 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 47 through 52 removed outlier: 3.759A pdb=" N ARG B 49 " --> pdb=" O ILE B 338 " (cutoff:3.500A) removed outlier: 4.490A pdb=" N PHE B 335 " --> pdb=" O SER B 331 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63 removed outlier: 6.714A pdb=" N ALA B 73 " --> pdb=" O TYR B 59 " (cutoff:3.500A) removed outlier: 4.233A pdb=" N MET B 61 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 6.702A pdb=" N VAL B 71 " --> pdb=" O MET B 61 " (cutoff:3.500A) removed outlier: 5.174A pdb=" N TRP B 63 " --> pdb=" O LEU B 69 " (cutoff:3.500A) removed outlier: 7.292A pdb=" N LEU B 69 " --> pdb=" O TRP B 63 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 6.405A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 6.015A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 104 through 105 removed outlier: 6.393A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 6.481A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 151 removed outlier: 3.556A pdb=" N CYS B 148 " --> pdb=" O SER B 160 " (cutoff:3.500A) removed outlier: 4.199A pdb=" N THR B 165 " --> pdb=" O SER B 161 " (cutoff:3.500A) removed outlier: 6.512A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 6.363A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 187 through 192 removed outlier: 7.047A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.599A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 6.917A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 5.466A pdb=" N LEU B 192 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 7.675A pdb=" N LEU B 198 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 6.850A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.572A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.448A pdb=" N CYS B 250 " --> pdb=" O THR B 263 " (cutoff:3.500A) removed outlier: 4.379A pdb=" N THR B 263 " --> pdb=" O CYS B 250 " (cutoff:3.500A) removed outlier: 6.545A pdb=" N LEU B 252 " --> pdb=" O LEU B 261 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ASP B 254 " --> pdb=" O GLN B 259 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N GLN B 259 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 273 through 278 removed outlier: 4.046A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) removed outlier: 6.636A pdb=" N CYS B 294 " --> pdb=" O VAL B 307 " (cutoff:3.500A) removed outlier: 4.637A pdb=" N VAL B 307 " --> pdb=" O CYS B 294 " (cutoff:3.500A) removed outlier: 6.560A pdb=" N VAL B 296 " --> pdb=" O ALA B 305 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'N' and resid 3 through 8 Processing sheet with id=AB1, first strand: chain 'N' and resid 10 through 12 removed outlier: 6.017A pdb=" N GLY N 10 " --> pdb=" O THR N 125 " (cutoff:3.500A) removed outlier: 5.990A pdb=" N ARG N 38 " --> pdb=" O TRP N 47 " (cutoff:3.500A) removed outlier: 5.208A pdb=" N TRP N 47 " --> pdb=" O ARG N 38 " (cutoff:3.500A) 384 hydrogen bonds defined for protein. 1104 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: 2.69 Time building geometry restraints manager: 2.21 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2552 1.34 - 1.46: 1364 1.46 - 1.58: 4006 1.58 - 1.70: 0 1.70 - 1.82: 70 Bond restraints: 7992 Sorted by residual: bond pdb=" N ARG A 265 " pdb=" CA ARG A 265 " ideal model delta sigma weight residual 1.457 1.488 -0.031 1.35e-02 5.49e+03 5.23e+00 bond pdb=" N ASN A 254 " pdb=" CA ASN A 254 " ideal model delta sigma weight residual 1.460 1.487 -0.027 1.22e-02 6.72e+03 5.05e+00 bond pdb=" N TYR A 253 " pdb=" CA TYR A 253 " ideal model delta sigma weight residual 1.458 1.489 -0.031 1.42e-02 4.96e+03 4.84e+00 bond pdb=" N ASN A 50 " pdb=" CA ASN A 50 " ideal model delta sigma weight residual 1.457 1.470 -0.013 1.29e-02 6.01e+03 1.03e+00 bond pdb=" CA ASN A 50 " pdb=" CB ASN A 50 " ideal model delta sigma weight residual 1.530 1.547 -0.017 1.69e-02 3.50e+03 1.02e+00 ... (remaining 7987 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.89: 10714 1.89 - 3.78: 109 3.78 - 5.66: 16 5.66 - 7.55: 3 7.55 - 9.44: 3 Bond angle restraints: 10845 Sorted by residual: angle pdb=" C ASP A 49 " pdb=" N ASN A 50 " pdb=" CA ASN A 50 " ideal model delta sigma weight residual 121.54 130.98 -9.44 1.91e+00 2.74e-01 2.44e+01 angle pdb=" CB ARG B 8 " pdb=" CG ARG B 8 " pdb=" CD ARG B 8 " ideal model delta sigma weight residual 111.30 119.21 -7.91 2.30e+00 1.89e-01 1.18e+01 angle pdb=" C ASN R 546 " pdb=" N PHE R 547 " pdb=" CA PHE R 547 " ideal model delta sigma weight residual 121.54 127.92 -6.38 1.91e+00 2.74e-01 1.12e+01 angle pdb=" N GLU A 299 " pdb=" CA GLU A 299 " pdb=" CB GLU A 299 " ideal model delta sigma weight residual 110.28 114.62 -4.34 1.55e+00 4.16e-01 7.84e+00 angle pdb=" N ASN A 50 " pdb=" CA ASN A 50 " pdb=" CB ASN A 50 " ideal model delta sigma weight residual 110.49 115.04 -4.55 1.69e+00 3.50e-01 7.25e+00 ... (remaining 10840 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.88: 4345 17.88 - 35.75: 321 35.75 - 53.63: 47 53.63 - 71.51: 9 71.51 - 89.38: 7 Dihedral angle restraints: 4729 sinusoidal: 1800 harmonic: 2929 Sorted by residual: dihedral pdb=" CB CYS R 632 " pdb=" SG CYS R 632 " pdb=" SG CYS R 704 " pdb=" CB CYS R 704 " ideal model delta sinusoidal sigma weight residual -86.00 -132.06 46.06 1 1.00e+01 1.00e-02 2.94e+01 dihedral pdb=" CB CYS N 99 " pdb=" SG CYS N 99 " pdb=" SG CYS N 107 " pdb=" CB CYS N 107 " ideal model delta sinusoidal sigma weight residual -86.00 -42.57 -43.43 1 1.00e+01 1.00e-02 2.63e+01 dihedral pdb=" CA CYS N 99 " pdb=" C CYS N 99 " pdb=" N PRO N 100 " pdb=" CA PRO N 100 " ideal model delta harmonic sigma weight residual 180.00 -160.12 -19.88 0 5.00e+00 4.00e-02 1.58e+01 ... (remaining 4726 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.037: 876 0.037 - 0.075: 263 0.075 - 0.112: 73 0.112 - 0.149: 22 0.149 - 0.186: 2 Chirality restraints: 1236 Sorted by residual: chirality pdb=" CA ASN A 50 " pdb=" N ASN A 50 " pdb=" C ASN A 50 " pdb=" CB ASN A 50 " both_signs ideal model delta sigma weight residual False 2.51 2.32 0.19 2.00e-01 2.50e+01 8.68e-01 chirality pdb=" CB VAL N 110 " pdb=" CA VAL N 110 " pdb=" CG1 VAL N 110 " pdb=" CG2 VAL N 110 " both_signs ideal model delta sigma weight residual False -2.63 -2.45 -0.18 2.00e-01 2.50e+01 8.18e-01 chirality pdb=" CA THR R 630 " pdb=" N THR R 630 " pdb=" C THR R 630 " pdb=" CB THR R 630 " both_signs ideal model delta sigma weight residual False 2.53 2.38 0.15 2.00e-01 2.50e+01 5.44e-01 ... (remaining 1233 not shown) Planarity restraints: 1385 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASP A 49 " -0.010 2.00e-02 2.50e+03 1.99e-02 3.94e+00 pdb=" C ASP A 49 " 0.034 2.00e-02 2.50e+03 pdb=" O ASP A 49 " -0.013 2.00e-02 2.50e+03 pdb=" N ASN A 50 " -0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASP A 252 " 0.009 2.00e-02 2.50e+03 1.75e-02 3.06e+00 pdb=" C ASP A 252 " -0.030 2.00e-02 2.50e+03 pdb=" O ASP A 252 " 0.011 2.00e-02 2.50e+03 pdb=" N TYR A 253 " 0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ARG R 598 " 0.007 2.00e-02 2.50e+03 1.40e-02 1.95e+00 pdb=" C ARG R 598 " -0.024 2.00e-02 2.50e+03 pdb=" O ARG R 598 " 0.009 2.00e-02 2.50e+03 pdb=" N ASN R 599 " 0.008 2.00e-02 2.50e+03 ... (remaining 1382 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 516 2.74 - 3.28: 7936 3.28 - 3.82: 13282 3.82 - 4.36: 15829 4.36 - 4.90: 27202 Nonbonded interactions: 64765 Sorted by model distance: nonbonded pdb=" O THR R 596 " pdb=" ND2 ASN R 599 " model vdw 2.200 3.120 nonbonded pdb=" OD1 ASP B 163 " pdb=" OG1 THR B 165 " model vdw 2.217 3.040 nonbonded pdb=" O ASP R 696 " pdb=" OG1 THR R 700 " model vdw 2.262 3.040 nonbonded pdb=" NE2 GLN B 220 " pdb=" OD1 ASP B 258 " model vdw 2.307 3.120 nonbonded pdb=" O ILE B 58 " pdb=" OG SER B 316 " model vdw 2.314 3.040 ... (remaining 64760 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.280 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: 0.310 Check model and map are aligned: 0.060 Set scattering table: 0.070 Process input model: 21.560 Find NCS groups from input model: 0.070 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: 0.000 Load rotamer database and sin/cos tables:12.690 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.080 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7354 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 : 0.002 0.031 7992 Z= 0.130 Angle : 0.513 9.441 10845 Z= 0.275 Chirality : 0.041 0.186 1236 Planarity : 0.003 0.040 1385 Dihedral : 12.858 89.384 2828 Min Nonbonded Distance : 2.200 Molprobity Statistics. All-atom Clashscore : 6.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.10 % Favored : 97.90 % Rotamer: Outliers : 0.00 % Allowed : 0.36 % Favored : 99.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.79 (0.27), residues: 998 helix: 1.38 (0.29), residues: 369 sheet: 0.65 (0.34), residues: 224 loop : -0.27 (0.31), residues: 405 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 169 HIS 0.009 0.001 HIS B 266 PHE 0.010 0.001 PHE N 29 TYR 0.013 0.001 TYR R 789 ARG 0.009 0.000 ARG B 8 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1996 Ramachandran restraints generated. 998 Oldfield, 0 Emsley, 998 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1996 Ramachandran restraints generated. 998 Oldfield, 0 Emsley, 998 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 856 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 155 time to evaluate : 0.872 Fit side-chains REVERT: A 55 THR cc_start: 0.7759 (m) cc_final: 0.7467 (p) REVERT: A 307 LYS cc_start: 0.7889 (mmtt) cc_final: 0.7655 (mmmt) REVERT: A 343 ASP cc_start: 0.6462 (m-30) cc_final: 0.6038 (m-30) REVERT: R 804 LEU cc_start: 0.8517 (tt) cc_final: 0.8243 (tp) outliers start: 0 outliers final: 0 residues processed: 155 average time/residue: 1.1700 time to fit residues: 193.0991 Evaluate side-chains 122 residues out of total 856 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 122 time to evaluate : 0.999 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 82 optimal weight: 1.9990 chunk 74 optimal weight: 2.9990 chunk 41 optimal weight: 3.9990 chunk 25 optimal weight: 2.9990 chunk 50 optimal weight: 3.9990 chunk 39 optimal weight: 0.9990 chunk 76 optimal weight: 0.0670 chunk 29 optimal weight: 0.9990 chunk 46 optimal weight: 3.9990 chunk 57 optimal weight: 3.9990 chunk 88 optimal weight: 1.9990 overall best weight: 1.2126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 254 ASN A 371 ASN B 32 GLN B 175 GLN B 266 HIS N 31 ASN R 562 HIS R 600 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3945 r_free = 0.3945 target = 0.168129 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.132275 restraints weight = 8096.432| |-----------------------------------------------------------------------------| r_work (start): 0.3540 rms_B_bonded: 1.67 r_work: 0.3360 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.3217 rms_B_bonded: 4.12 restraints_weight: 0.2500 r_work (final): 0.3217 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7967 moved from start: 0.2688 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.059 7992 Z= 0.318 Angle : 0.632 8.490 10845 Z= 0.336 Chirality : 0.045 0.148 1236 Planarity : 0.004 0.044 1385 Dihedral : 4.567 30.029 1095 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 5.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer: Outliers : 3.82 % Allowed : 9.67 % Favored : 86.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.70 % 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: 0.96 (0.27), residues: 998 helix: 1.82 (0.28), residues: 356 sheet: 0.41 (0.34), residues: 216 loop : -0.18 (0.31), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP B 339 HIS 0.013 0.002 HIS A 357 PHE 0.018 0.002 PHE R 665 TYR 0.025 0.002 TYR B 59 ARG 0.006 0.001 ARG B 8 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1996 Ramachandran restraints generated. 998 Oldfield, 0 Emsley, 998 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1996 Ramachandran restraints generated. 998 Oldfield, 0 Emsley, 998 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 856 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 120 time to evaluate : 0.838 Fit side-chains REVERT: A 38 ARG cc_start: 0.8483 (OUTLIER) cc_final: 0.6924 (mtt180) REVERT: B 156 GLN cc_start: 0.8776 (OUTLIER) cc_final: 0.8572 (pt0) REVERT: B 274 THR cc_start: 0.8860 (m) cc_final: 0.8660 (m) REVERT: N 31 ASN cc_start: 0.8422 (m-40) cc_final: 0.8118 (m-40) outliers start: 32 outliers final: 14 residues processed: 135 average time/residue: 1.0865 time to fit residues: 156.8518 Evaluate side-chains 123 residues out of total 856 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 107 time to evaluate : 0.909 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 ARG Chi-restraints excluded: chain A residue 229 ASP Chi-restraints excluded: chain A residue 306 SER Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 156 GLN Chi-restraints excluded: chain B residue 177 THR Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain C residue 21 MET Chi-restraints excluded: chain N residue 59 SER Chi-restraints excluded: chain N residue 110 VAL Chi-restraints excluded: chain R residue 586 VAL Chi-restraints excluded: chain R residue 660 MET Chi-restraints excluded: chain R residue 700 THR Chi-restraints excluded: chain R residue 771 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 31 optimal weight: 1.9990 chunk 42 optimal weight: 2.9990 chunk 57 optimal weight: 0.8980 chunk 96 optimal weight: 0.9980 chunk 48 optimal weight: 2.9990 chunk 80 optimal weight: 0.8980 chunk 55 optimal weight: 4.9990 chunk 27 optimal weight: 3.9990 chunk 60 optimal weight: 2.9990 chunk 12 optimal weight: 1.9990 chunk 67 optimal weight: 0.8980 overall best weight: 1.1382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 32 GLN B 75 GLN B 175 GLN B 266 HIS R 562 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3934 r_free = 0.3934 target = 0.167111 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3521 r_free = 0.3521 target = 0.131303 restraints weight = 8220.824| |-----------------------------------------------------------------------------| r_work (start): 0.3512 rms_B_bonded: 1.72 r_work: 0.3347 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.3205 rms_B_bonded: 3.92 restraints_weight: 0.2500 r_work (final): 0.3205 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7982 moved from start: 0.3071 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 7992 Z= 0.283 Angle : 0.579 10.177 10845 Z= 0.310 Chirality : 0.043 0.171 1236 Planarity : 0.004 0.043 1385 Dihedral : 4.508 32.362 1095 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 5.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 4.53 % Allowed : 15.04 % Favored : 80.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.70 % 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: 0.80 (0.27), residues: 998 helix: 1.76 (0.28), residues: 361 sheet: 0.43 (0.34), residues: 214 loop : -0.44 (0.30), residues: 423 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 82 HIS 0.009 0.001 HIS A 357 PHE 0.012 0.002 PHE B 199 TYR 0.015 0.002 TYR A 391 ARG 0.004 0.001 ARG B 46 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1996 Ramachandran restraints generated. 998 Oldfield, 0 Emsley, 998 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1996 Ramachandran restraints generated. 998 Oldfield, 0 Emsley, 998 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 856 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 106 time to evaluate : 0.744 Fit side-chains REVERT: A 229 ASP cc_start: 0.7780 (OUTLIER) cc_final: 0.7555 (p0) REVERT: A 268 GLU cc_start: 0.7902 (tm-30) cc_final: 0.7329 (tt0) REVERT: A 314 GLU cc_start: 0.8219 (OUTLIER) cc_final: 0.7506 (mm-30) REVERT: B 156 GLN cc_start: 0.8685 (OUTLIER) cc_final: 0.8420 (pt0) REVERT: N 77 ASN cc_start: 0.7943 (m-40) cc_final: 0.7673 (m-40) REVERT: R 635 MET cc_start: 0.6307 (OUTLIER) cc_final: 0.6053 (ppp) outliers start: 38 outliers final: 17 residues processed: 125 average time/residue: 1.1569 time to fit residues: 154.0356 Evaluate side-chains 121 residues out of total 856 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 100 time to evaluate : 0.856 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 THR Chi-restraints excluded: chain A residue 229 ASP Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 306 SER Chi-restraints excluded: chain A residue 314 GLU Chi-restraints excluded: chain A residue 334 VAL Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 156 GLN Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain C residue 46 LYS Chi-restraints excluded: chain N residue 59 SER Chi-restraints excluded: chain N residue 96 CYS Chi-restraints excluded: chain R residue 586 VAL Chi-restraints excluded: chain R residue 635 MET Chi-restraints excluded: chain R residue 660 MET Chi-restraints excluded: chain R residue 692 SER Chi-restraints excluded: chain R residue 700 THR Chi-restraints excluded: chain R residue 777 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 89 optimal weight: 3.9990 chunk 49 optimal weight: 0.9980 chunk 21 optimal weight: 5.9990 chunk 9 optimal weight: 2.9990 chunk 47 optimal weight: 0.0870 chunk 76 optimal weight: 1.9990 chunk 63 optimal weight: 0.9980 chunk 33 optimal weight: 0.1980 chunk 67 optimal weight: 0.6980 chunk 38 optimal weight: 0.0570 chunk 51 optimal weight: 3.9990 overall best weight: 0.4076 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 32 GLN B 175 GLN B 266 HIS R 562 HIS R 600 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3957 r_free = 0.3957 target = 0.169596 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.133205 restraints weight = 8148.706| |-----------------------------------------------------------------------------| r_work (start): 0.3556 rms_B_bonded: 1.70 r_work: 0.3396 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.3255 rms_B_bonded: 4.08 restraints_weight: 0.2500 r_work (final): 0.3255 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7932 moved from start: 0.3015 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 7992 Z= 0.154 Angle : 0.491 7.908 10845 Z= 0.263 Chirality : 0.040 0.147 1236 Planarity : 0.003 0.039 1385 Dihedral : 4.145 30.986 1095 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 4.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % Rotamer: Outliers : 3.34 % Allowed : 17.30 % Favored : 79.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.70 % 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: 0.98 (0.27), residues: 998 helix: 2.02 (0.28), residues: 363 sheet: 0.42 (0.34), residues: 214 loop : -0.40 (0.30), residues: 421 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 82 HIS 0.004 0.001 HIS A 357 PHE 0.012 0.001 PHE A 212 TYR 0.007 0.001 TYR N 95 ARG 0.004 0.000 ARG A 317 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1996 Ramachandran restraints generated. 998 Oldfield, 0 Emsley, 998 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1996 Ramachandran restraints generated. 998 Oldfield, 0 Emsley, 998 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 856 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 109 time to evaluate : 0.908 Fit side-chains REVERT: B 134 ARG cc_start: 0.6668 (OUTLIER) cc_final: 0.6098 (ptp90) REVERT: B 155 ASN cc_start: 0.7064 (t0) cc_final: 0.6838 (t0) REVERT: B 156 GLN cc_start: 0.8627 (OUTLIER) cc_final: 0.8354 (pt0) REVERT: N 57 SER cc_start: 0.7771 (t) cc_final: 0.7417 (m) REVERT: N 77 ASN cc_start: 0.7951 (m-40) cc_final: 0.7706 (m-40) REVERT: R 695 MET cc_start: 0.7309 (ttt) cc_final: 0.6603 (ttm) outliers start: 28 outliers final: 10 residues processed: 124 average time/residue: 1.1128 time to fit residues: 147.3082 Evaluate side-chains 112 residues out of total 856 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 100 time to evaluate : 0.901 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 THR Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 306 SER Chi-restraints excluded: chain A residue 334 VAL Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 134 ARG Chi-restraints excluded: chain B residue 156 GLN Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain N residue 59 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 89 optimal weight: 3.9990 chunk 71 optimal weight: 6.9990 chunk 54 optimal weight: 0.0030 chunk 55 optimal weight: 5.9990 chunk 86 optimal weight: 10.0000 chunk 91 optimal weight: 0.0570 chunk 26 optimal weight: 1.9990 chunk 35 optimal weight: 1.9990 chunk 2 optimal weight: 1.9990 chunk 65 optimal weight: 0.7980 chunk 84 optimal weight: 1.9990 overall best weight: 0.9712 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 32 GLN B 175 GLN R 562 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3925 r_free = 0.3925 target = 0.166343 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.129070 restraints weight = 8006.768| |-----------------------------------------------------------------------------| r_work (start): 0.3491 rms_B_bonded: 1.76 r_work: 0.3327 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.3183 rms_B_bonded: 3.98 restraints_weight: 0.2500 r_work (final): 0.3183 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7998 moved from start: 0.3326 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 7992 Z= 0.251 Angle : 0.554 10.023 10845 Z= 0.295 Chirality : 0.043 0.149 1236 Planarity : 0.004 0.042 1385 Dihedral : 4.425 30.936 1095 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 5.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % Rotamer: Outliers : 3.70 % Allowed : 18.14 % Favored : 78.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.70 % 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: 0.83 (0.26), residues: 998 helix: 1.90 (0.28), residues: 362 sheet: 0.36 (0.33), residues: 214 loop : -0.49 (0.30), residues: 422 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 82 HIS 0.006 0.001 HIS A 357 PHE 0.012 0.002 PHE B 199 TYR 0.015 0.001 TYR N 95 ARG 0.004 0.000 ARG A 317 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1996 Ramachandran restraints generated. 998 Oldfield, 0 Emsley, 998 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1996 Ramachandran restraints generated. 998 Oldfield, 0 Emsley, 998 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 856 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 101 time to evaluate : 0.932 Fit side-chains REVERT: A 268 GLU cc_start: 0.7895 (tm-30) cc_final: 0.7365 (tt0) REVERT: C 48 ASP cc_start: 0.8520 (t0) cc_final: 0.8313 (t0) REVERT: N 43 LYS cc_start: 0.7565 (mtpp) cc_final: 0.6785 (mmtp) REVERT: N 77 ASN cc_start: 0.7983 (m-40) cc_final: 0.7718 (m-40) REVERT: R 735 THR cc_start: 0.7684 (m) cc_final: 0.7394 (p) outliers start: 31 outliers final: 15 residues processed: 120 average time/residue: 1.1427 time to fit residues: 146.4551 Evaluate side-chains 112 residues out of total 856 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 97 time to evaluate : 0.803 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 THR Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 306 SER Chi-restraints excluded: chain A residue 334 VAL Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain N residue 59 SER Chi-restraints excluded: chain N residue 96 CYS Chi-restraints excluded: chain R residue 692 SER Chi-restraints excluded: chain R residue 700 THR Chi-restraints excluded: chain R residue 766 LEU Chi-restraints excluded: chain R residue 777 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 1 optimal weight: 2.9990 chunk 21 optimal weight: 9.9990 chunk 22 optimal weight: 1.9990 chunk 86 optimal weight: 9.9990 chunk 38 optimal weight: 2.9990 chunk 70 optimal weight: 2.9990 chunk 94 optimal weight: 2.9990 chunk 42 optimal weight: 3.9990 chunk 8 optimal weight: 1.9990 chunk 67 optimal weight: 0.9990 chunk 34 optimal weight: 0.8980 overall best weight: 1.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 278 ASN B 88 ASN B 175 GLN R 562 HIS R 600 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3885 r_free = 0.3885 target = 0.162238 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.125057 restraints weight = 8056.827| |-----------------------------------------------------------------------------| r_work (start): 0.3447 rms_B_bonded: 1.77 r_work: 0.3281 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.3137 rms_B_bonded: 3.88 restraints_weight: 0.2500 r_work (final): 0.3137 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8048 moved from start: 0.3819 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.059 7992 Z= 0.409 Angle : 0.651 10.080 10845 Z= 0.348 Chirality : 0.046 0.168 1236 Planarity : 0.004 0.044 1385 Dihedral : 4.885 37.358 1095 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 5.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.51 % Favored : 96.49 % Rotamer: Outliers : 4.06 % Allowed : 18.38 % Favored : 77.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.70 % 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: 0.44 (0.26), residues: 998 helix: 1.45 (0.27), residues: 362 sheet: 0.27 (0.33), residues: 222 loop : -0.68 (0.30), residues: 414 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.003 TRP B 82 HIS 0.007 0.001 HIS A 357 PHE 0.015 0.002 PHE A 208 TYR 0.018 0.002 TYR N 95 ARG 0.004 0.001 ARG N 72 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1996 Ramachandran restraints generated. 998 Oldfield, 0 Emsley, 998 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1996 Ramachandran restraints generated. 998 Oldfield, 0 Emsley, 998 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 856 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 101 time to evaluate : 0.820 Fit side-chains REVERT: A 268 GLU cc_start: 0.7970 (tm-30) cc_final: 0.7407 (tt0) REVERT: B 156 GLN cc_start: 0.8623 (OUTLIER) cc_final: 0.8368 (mt0) REVERT: R 735 THR cc_start: 0.7940 (m) cc_final: 0.7685 (p) outliers start: 34 outliers final: 21 residues processed: 123 average time/residue: 1.1195 time to fit residues: 146.6994 Evaluate side-chains 121 residues out of total 856 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 99 time to evaluate : 0.810 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 THR Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 306 SER Chi-restraints excluded: chain A residue 334 VAL Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 156 GLN Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain C residue 46 LYS Chi-restraints excluded: chain N residue 59 SER Chi-restraints excluded: chain N residue 96 CYS Chi-restraints excluded: chain N residue 110 VAL Chi-restraints excluded: chain R residue 576 LEU Chi-restraints excluded: chain R residue 692 SER Chi-restraints excluded: chain R residue 695 MET Chi-restraints excluded: chain R residue 700 THR Chi-restraints excluded: chain R residue 757 LEU Chi-restraints excluded: chain R residue 766 LEU Chi-restraints excluded: chain R residue 771 THR Chi-restraints excluded: chain R residue 777 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 9 optimal weight: 1.9990 chunk 55 optimal weight: 1.9990 chunk 6 optimal weight: 0.9980 chunk 37 optimal weight: 0.6980 chunk 66 optimal weight: 0.0980 chunk 21 optimal weight: 5.9990 chunk 63 optimal weight: 0.0970 chunk 49 optimal weight: 2.9990 chunk 82 optimal weight: 0.6980 chunk 71 optimal weight: 4.9990 chunk 11 optimal weight: 0.7980 overall best weight: 0.4778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 175 GLN R 562 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3943 r_free = 0.3943 target = 0.168190 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.131266 restraints weight = 8068.509| |-----------------------------------------------------------------------------| r_work (start): 0.3528 rms_B_bonded: 1.78 r_work: 0.3348 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.3202 rms_B_bonded: 4.22 restraints_weight: 0.2500 r_work (final): 0.3202 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7985 moved from start: 0.3600 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 7992 Z= 0.167 Angle : 0.497 6.985 10845 Z= 0.268 Chirality : 0.041 0.148 1236 Planarity : 0.003 0.039 1385 Dihedral : 4.343 35.938 1095 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 4.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % Rotamer: Outliers : 3.10 % Allowed : 19.81 % Favored : 77.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.70 % 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: 0.81 (0.27), residues: 998 helix: 1.89 (0.28), residues: 362 sheet: 0.38 (0.33), residues: 212 loop : -0.55 (0.30), residues: 424 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP B 169 HIS 0.004 0.001 HIS A 357 PHE 0.013 0.001 PHE A 212 TYR 0.009 0.001 TYR R 602 ARG 0.003 0.000 ARG A 317 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1996 Ramachandran restraints generated. 998 Oldfield, 0 Emsley, 998 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1996 Ramachandran restraints generated. 998 Oldfield, 0 Emsley, 998 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 856 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 101 time to evaluate : 0.950 Fit side-chains REVERT: A 38 ARG cc_start: 0.8409 (mmt180) cc_final: 0.8179 (mmt90) REVERT: A 268 GLU cc_start: 0.7934 (tm-30) cc_final: 0.7396 (tt0) REVERT: N 43 LYS cc_start: 0.7593 (mtpp) cc_final: 0.6788 (mmtp) REVERT: N 77 ASN cc_start: 0.7993 (m-40) cc_final: 0.7744 (m-40) REVERT: R 735 THR cc_start: 0.8044 (m) cc_final: 0.7792 (p) outliers start: 26 outliers final: 14 residues processed: 118 average time/residue: 1.2002 time to fit residues: 151.1508 Evaluate side-chains 110 residues out of total 856 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 96 time to evaluate : 0.868 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 THR Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 306 SER Chi-restraints excluded: chain A residue 334 VAL Chi-restraints excluded: chain A residue 367 VAL Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain N residue 59 SER Chi-restraints excluded: chain N residue 96 CYS Chi-restraints excluded: chain R residue 566 LEU Chi-restraints excluded: chain R residue 700 THR Chi-restraints excluded: chain R residue 777 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 79 optimal weight: 0.0170 chunk 80 optimal weight: 0.9990 chunk 17 optimal weight: 1.9990 chunk 44 optimal weight: 1.9990 chunk 55 optimal weight: 4.9990 chunk 9 optimal weight: 0.8980 chunk 46 optimal weight: 0.6980 chunk 71 optimal weight: 3.9990 chunk 75 optimal weight: 1.9990 chunk 70 optimal weight: 2.9990 chunk 81 optimal weight: 0.9980 overall best weight: 0.7220 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 175 GLN R 562 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3925 r_free = 0.3925 target = 0.166323 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.128848 restraints weight = 8094.042| |-----------------------------------------------------------------------------| r_work (start): 0.3506 rms_B_bonded: 1.77 r_work: 0.3339 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.3194 rms_B_bonded: 4.07 restraints_weight: 0.2500 r_work (final): 0.3194 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7996 moved from start: 0.3673 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 7992 Z= 0.209 Angle : 0.530 9.527 10845 Z= 0.282 Chirality : 0.042 0.156 1236 Planarity : 0.003 0.039 1385 Dihedral : 4.373 37.044 1095 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 4.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.61 % Favored : 96.39 % Rotamer: Outliers : 2.51 % Allowed : 20.76 % Favored : 76.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.70 % 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: 0.83 (0.26), residues: 998 helix: 1.91 (0.28), residues: 362 sheet: 0.38 (0.33), residues: 212 loop : -0.53 (0.30), residues: 424 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 82 HIS 0.005 0.001 HIS A 357 PHE 0.012 0.001 PHE B 199 TYR 0.011 0.001 TYR N 95 ARG 0.006 0.000 ARG A 317 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1996 Ramachandran restraints generated. 998 Oldfield, 0 Emsley, 998 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1996 Ramachandran restraints generated. 998 Oldfield, 0 Emsley, 998 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 856 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 99 time to evaluate : 0.948 Fit side-chains REVERT: A 268 GLU cc_start: 0.7907 (tm-30) cc_final: 0.7370 (tt0) REVERT: N 43 LYS cc_start: 0.7577 (mtpp) cc_final: 0.6786 (mmtp) REVERT: N 77 ASN cc_start: 0.8031 (m-40) cc_final: 0.7768 (m-40) REVERT: R 735 THR cc_start: 0.8012 (m) cc_final: 0.7764 (p) outliers start: 21 outliers final: 15 residues processed: 112 average time/residue: 1.1870 time to fit residues: 141.5592 Evaluate side-chains 113 residues out of total 856 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 98 time to evaluate : 0.855 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 THR Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 306 SER Chi-restraints excluded: chain A residue 334 VAL Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain N residue 59 SER Chi-restraints excluded: chain N residue 96 CYS Chi-restraints excluded: chain R residue 566 LEU Chi-restraints excluded: chain R residue 692 SER Chi-restraints excluded: chain R residue 695 MET Chi-restraints excluded: chain R residue 700 THR Chi-restraints excluded: chain R residue 777 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 29 optimal weight: 1.9990 chunk 91 optimal weight: 2.9990 chunk 39 optimal weight: 3.9990 chunk 62 optimal weight: 0.7980 chunk 41 optimal weight: 0.9990 chunk 86 optimal weight: 10.0000 chunk 54 optimal weight: 10.0000 chunk 66 optimal weight: 0.5980 chunk 87 optimal weight: 4.9990 chunk 42 optimal weight: 0.8980 chunk 9 optimal weight: 0.7980 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 175 GLN R 562 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3920 r_free = 0.3920 target = 0.165783 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.128540 restraints weight = 8200.594| |-----------------------------------------------------------------------------| r_work (start): 0.3486 rms_B_bonded: 1.80 r_work: 0.3299 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.3152 rms_B_bonded: 4.27 restraints_weight: 0.2500 r_work (final): 0.3152 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8019 moved from start: 0.3721 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 7992 Z= 0.223 Angle : 0.536 8.955 10845 Z= 0.286 Chirality : 0.042 0.157 1236 Planarity : 0.004 0.039 1385 Dihedral : 4.401 36.300 1095 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 4.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.51 % Favored : 96.49 % Rotamer: Outliers : 2.51 % Allowed : 21.12 % Favored : 76.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.70 % 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: 0.84 (0.27), residues: 998 helix: 1.92 (0.27), residues: 362 sheet: 0.36 (0.34), residues: 213 loop : -0.50 (0.30), residues: 423 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 82 HIS 0.005 0.001 HIS A 357 PHE 0.012 0.001 PHE B 199 TYR 0.012 0.001 TYR N 95 ARG 0.007 0.000 ARG A 317 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1996 Ramachandran restraints generated. 998 Oldfield, 0 Emsley, 998 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1996 Ramachandran restraints generated. 998 Oldfield, 0 Emsley, 998 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 856 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 99 time to evaluate : 0.886 Fit side-chains REVERT: A 38 ARG cc_start: 0.8396 (mmt180) cc_final: 0.8164 (mmt90) REVERT: A 268 GLU cc_start: 0.7950 (tm-30) cc_final: 0.7409 (tt0) REVERT: B 46 ARG cc_start: 0.7987 (mpt180) cc_final: 0.7606 (mmt-90) REVERT: N 43 LYS cc_start: 0.7596 (mtpp) cc_final: 0.6819 (mmtp) REVERT: N 77 ASN cc_start: 0.8021 (m-40) cc_final: 0.7784 (m-40) REVERT: R 735 THR cc_start: 0.8029 (m) cc_final: 0.7782 (p) outliers start: 21 outliers final: 16 residues processed: 112 average time/residue: 1.1523 time to fit residues: 137.6006 Evaluate side-chains 114 residues out of total 856 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 98 time to evaluate : 0.937 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 THR Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 306 SER Chi-restraints excluded: chain A residue 334 VAL Chi-restraints excluded: chain A residue 367 VAL Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain N residue 59 SER Chi-restraints excluded: chain N residue 96 CYS Chi-restraints excluded: chain R residue 566 LEU Chi-restraints excluded: chain R residue 695 MET Chi-restraints excluded: chain R residue 700 THR Chi-restraints excluded: chain R residue 757 LEU Chi-restraints excluded: chain R residue 777 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 70 optimal weight: 2.9990 chunk 90 optimal weight: 0.9990 chunk 38 optimal weight: 3.9990 chunk 60 optimal weight: 2.9990 chunk 36 optimal weight: 0.6980 chunk 83 optimal weight: 2.9990 chunk 22 optimal weight: 7.9990 chunk 65 optimal weight: 0.6980 chunk 84 optimal weight: 0.7980 chunk 32 optimal weight: 0.6980 chunk 43 optimal weight: 0.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 175 GLN R 562 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3922 r_free = 0.3922 target = 0.166083 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.128918 restraints weight = 8129.634| |-----------------------------------------------------------------------------| r_work (start): 0.3492 rms_B_bonded: 1.79 r_work: 0.3308 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.3162 rms_B_bonded: 4.24 restraints_weight: 0.2500 r_work (final): 0.3162 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8014 moved from start: 0.3734 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 7992 Z= 0.215 Angle : 0.529 8.412 10845 Z= 0.282 Chirality : 0.042 0.159 1236 Planarity : 0.004 0.039 1385 Dihedral : 4.374 36.503 1095 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 4.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.71 % Favored : 96.29 % Rotamer: Outliers : 2.39 % Allowed : 21.36 % Favored : 76.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.70 % 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: 0.85 (0.27), residues: 998 helix: 1.94 (0.27), residues: 362 sheet: 0.34 (0.34), residues: 214 loop : -0.49 (0.30), residues: 422 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 82 HIS 0.005 0.001 HIS A 357 PHE 0.012 0.001 PHE B 199 TYR 0.011 0.001 TYR N 95 ARG 0.007 0.000 ARG A 317 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1996 Ramachandran restraints generated. 998 Oldfield, 0 Emsley, 998 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1996 Ramachandran restraints generated. 998 Oldfield, 0 Emsley, 998 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 856 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 100 time to evaluate : 0.828 Fit side-chains REVERT: A 268 GLU cc_start: 0.7942 (tm-30) cc_final: 0.7407 (tt0) REVERT: N 43 LYS cc_start: 0.7546 (mtpp) cc_final: 0.6799 (mmtp) REVERT: N 77 ASN cc_start: 0.8024 (m-40) cc_final: 0.7789 (m-40) REVERT: R 735 THR cc_start: 0.8031 (m) cc_final: 0.7788 (p) outliers start: 20 outliers final: 17 residues processed: 112 average time/residue: 1.1747 time to fit residues: 140.0478 Evaluate side-chains 118 residues out of total 856 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 101 time to evaluate : 0.905 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 THR Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 306 SER Chi-restraints excluded: chain A residue 334 VAL Chi-restraints excluded: chain A residue 367 VAL Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain N residue 59 SER Chi-restraints excluded: chain N residue 96 CYS Chi-restraints excluded: chain R residue 566 LEU Chi-restraints excluded: chain R residue 692 SER Chi-restraints excluded: chain R residue 695 MET Chi-restraints excluded: chain R residue 700 THR Chi-restraints excluded: chain R residue 757 LEU Chi-restraints excluded: chain R residue 777 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 80 optimal weight: 0.8980 chunk 33 optimal weight: 1.9990 chunk 66 optimal weight: 1.9990 chunk 32 optimal weight: 0.9990 chunk 23 optimal weight: 10.0000 chunk 40 optimal weight: 0.5980 chunk 47 optimal weight: 2.9990 chunk 7 optimal weight: 0.8980 chunk 28 optimal weight: 0.9980 chunk 96 optimal weight: 0.6980 chunk 24 optimal weight: 4.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 175 GLN R 562 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3920 r_free = 0.3920 target = 0.165858 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3497 r_free = 0.3497 target = 0.128754 restraints weight = 8170.374| |-----------------------------------------------------------------------------| r_work (start): 0.3490 rms_B_bonded: 1.76 r_work: 0.3303 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.3157 rms_B_bonded: 4.22 restraints_weight: 0.2500 r_work (final): 0.3157 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8016 moved from start: 0.3752 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 7992 Z= 0.222 Angle : 0.534 8.260 10845 Z= 0.285 Chirality : 0.042 0.159 1236 Planarity : 0.004 0.039 1385 Dihedral : 4.396 36.532 1095 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 5.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Rotamer: Outliers : 2.27 % Allowed : 21.48 % Favored : 76.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.70 % 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: 0.85 (0.27), residues: 998 helix: 1.93 (0.27), residues: 362 sheet: 0.34 (0.34), residues: 214 loop : -0.48 (0.30), residues: 422 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 82 HIS 0.004 0.001 HIS A 357 PHE 0.012 0.001 PHE B 199 TYR 0.012 0.001 TYR N 95 ARG 0.007 0.000 ARG A 317 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6191.51 seconds wall clock time: 110 minutes 0.17 seconds (6600.17 seconds total)