Starting phenix.real_space_refine on Sat Jun 7 01:58:40 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7w6p_32331/06_2025/7w6p_32331.cif Found real_map, /net/cci-nas-00/data/ceres_data/7w6p_32331/06_2025/7w6p_32331.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.47 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7w6p_32331/06_2025/7w6p_32331.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7w6p_32331/06_2025/7w6p_32331.map" model { file = "/net/cci-nas-00/data/ceres_data/7w6p_32331/06_2025/7w6p_32331.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7w6p_32331/06_2025/7w6p_32331.cif" } resolution = 3.47 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= 0.004 sd= 0.106 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 57 5.16 5 C 5364 2.51 5 N 1435 2.21 5 O 1552 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 45 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 8408 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1604 Number of conformers: 1 Conformer: "" Number of residues, atoms: 204, 1604 Classifications: {'peptide': 204} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 201} Chain breaks: 3 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 2572 Number of conformers: 1 Conformer: "" Number of residues, atoms: 335, 2572 Classifications: {'peptide': 335} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 5, 'TRANS': 329} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "G" Number of atoms: 418 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 418 Classifications: {'peptide': 54} Link IDs: {'PTRANS': 4, 'TRANS': 49} Chain: "H" Number of atoms: 1770 Number of conformers: 1 Conformer: "" Number of residues, atoms: 232, 1770 Classifications: {'peptide': 232} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 10, 'TRANS': 221} Chain breaks: 1 Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 14 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 2} Unresolved non-hydrogen planarities: 12 Chain: "R" Number of atoms: 2027 Number of conformers: 1 Conformer: "" Number of residues, atoms: 258, 2027 Classifications: {'peptide': 258} Incomplete info: {'truncation_to_alanine': 15} Link IDs: {'PTRANS': 9, 'TRANS': 248} Chain breaks: 2 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 71 Unresolved non-hydrogen angles: 87 Unresolved non-hydrogen dihedrals: 67 Planarities with less than four sites: {'PHE:plan': 2, 'GLU:plan': 2, 'ARG:plan': 3, 'TRP:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 47 Chain: "R" Number of atoms: 17 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 17 Unusual residues: {'W96': 1} Classifications: {'undetermined': 1} Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" N LYS H 236 " occ=0.00 ... (7 atoms not shown) pdb=" NZ LYS H 236 " occ=0.00 Time building chain proxies: 5.59, per 1000 atoms: 0.66 Number of scatterers: 8408 At special positions: 0 Unit cell: (88.4, 113.9, 120.7, 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 57 16.00 O 1552 8.00 N 1435 7.00 C 5364 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS H 147 " - pdb=" SG CYS H 217 " distance=2.03 Simple disulfide: pdb=" SG CYS R 121 " - pdb=" SG CYS R 203 " 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: 2.06 Conformation dependent library (CDL) restraints added in 945.1 milliseconds 2122 Ramachandran restraints generated. 1061 Oldfield, 0 Emsley, 1061 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2022 Finding SS restraints... Secondary structure from input PDB file: 22 helices and 12 sheets defined 34.3% alpha, 18.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.86 Creating SS restraints... Processing helix chain 'A' and resid 6 through 30 removed outlier: 3.522A pdb=" N ASN A 22 " --> pdb=" O ALA A 18 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N LEU A 23 " --> pdb=" O ILE A 19 " (cutoff:3.500A) Processing helix chain 'A' and resid 45 through 54 Processing helix chain 'A' and resid 208 through 214 removed outlier: 4.244A pdb=" N TRP A 212 " --> pdb=" O GLU A 208 " (cutoff:3.500A) removed outlier: 4.340A pdb=" N HIS A 214 " --> pdb=" O LYS A 210 " (cutoff:3.500A) Processing helix chain 'A' and resid 215 through 217 No H-bonds generated for 'chain 'A' and resid 215 through 217' Processing helix chain 'A' and resid 242 through 256 Processing helix chain 'A' and resid 296 through 310 Processing helix chain 'A' and resid 330 through 352 removed outlier: 3.768A pdb=" N VAL A 335 " --> pdb=" O ASN A 331 " (cutoff:3.500A) Processing helix chain 'B' and resid 7 through 25 removed outlier: 3.541A pdb=" N CYS B 25 " --> pdb=" O ALA B 21 " (cutoff:3.500A) Processing helix chain 'G' and resid 10 through 24 removed outlier: 3.648A pdb=" N ASN G 24 " --> pdb=" O LYS G 20 " (cutoff:3.500A) Processing helix chain 'G' and resid 29 through 44 Processing helix chain 'H' and resid 28 through 32 Processing helix chain 'R' and resid 47 through 74 removed outlier: 4.132A pdb=" N VAL R 67 " --> pdb=" O VAL R 63 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N PHE R 74 " --> pdb=" O ILE R 70 " (cutoff:3.500A) Processing helix chain 'R' and resid 81 through 83 No H-bonds generated for 'chain 'R' and resid 81 through 83' Processing helix chain 'R' and resid 84 through 108 Proline residue: R 103 - end of helix Processing helix chain 'R' and resid 117 through 151 removed outlier: 3.577A pdb=" N CYS R 121 " --> pdb=" O GLY R 117 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N ILE R 123 " --> pdb=" O ALA R 119 " (cutoff:3.500A) Processing helix chain 'R' and resid 152 through 160 Processing helix chain 'R' and resid 161 through 179 Processing helix chain 'R' and resid 210 through 220 Processing helix chain 'R' and resid 220 through 242 Processing helix chain 'R' and resid 380 through 412 Proline residue: R 404 - end of helix Processing helix chain 'R' and resid 422 through 441 removed outlier: 3.689A pdb=" N SER R 434 " --> pdb=" O GLY R 430 " (cutoff:3.500A) Proline residue: R 438 - end of helix removed outlier: 3.616A pdb=" N TYR R 441 " --> pdb=" O ASN R 437 " (cutoff:3.500A) Processing helix chain 'R' and resid 445 through 457 Processing sheet with id=AA1, first strand: chain 'A' and resid 185 through 192 removed outlier: 6.701A pdb=" N VAL A 34 " --> pdb=" O ARG A 198 " (cutoff:3.500A) removed outlier: 7.648A pdb=" N PHE A 200 " --> pdb=" O VAL A 34 " (cutoff:3.500A) removed outlier: 6.735A pdb=" N LEU A 36 " --> pdb=" O PHE A 200 " (cutoff:3.500A) removed outlier: 7.868A pdb=" N VAL A 202 " --> pdb=" O LEU A 36 " (cutoff:3.500A) removed outlier: 7.457A pdb=" N LEU A 38 " --> pdb=" O VAL A 202 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N ALA A 221 " --> pdb=" O LYS A 35 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 46 through 51 removed outlier: 6.116A pdb=" N THR B 47 " --> pdb=" O ASN B 340 " (cutoff:3.500A) removed outlier: 7.129A pdb=" N ASN B 340 " --> pdb=" O THR B 47 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ARG B 49 " --> pdb=" O ILE B 338 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N ALA B 328 " --> pdb=" O GLY B 319 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63 removed outlier: 6.739A pdb=" N ALA B 73 " --> pdb=" O TYR B 59 " (cutoff:3.500A) removed outlier: 4.106A pdb=" N MET B 61 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 6.467A pdb=" N VAL B 71 " --> pdb=" O MET B 61 " (cutoff:3.500A) removed outlier: 4.732A pdb=" N TRP B 63 " --> pdb=" O LEU B 69 " (cutoff:3.500A) removed outlier: 7.087A pdb=" N LEU B 69 " --> pdb=" O TRP B 63 " (cutoff:3.500A) removed outlier: 4.115A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 6.185A pdb=" N LEU B 79 " --> pdb=" O ALA B 92 " (cutoff:3.500A) removed outlier: 4.348A pdb=" N ALA B 92 " --> pdb=" O LEU B 79 " (cutoff:3.500A) removed outlier: 6.517A pdb=" N ILE B 81 " --> pdb=" O VAL B 90 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 104 through 105 removed outlier: 6.608A pdb=" N CYS B 121 " --> pdb=" O GLU B 138 " (cutoff:3.500A) removed outlier: 5.048A pdb=" N GLU B 138 " --> pdb=" O CYS B 121 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N ILE B 123 " --> pdb=" O SER B 136 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 151 removed outlier: 3.957A pdb=" N THR B 165 " --> pdb=" O SER B 161 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 190 through 192 removed outlier: 3.887A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 6.901A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.511A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 232 through 234 removed outlier: 3.955A pdb=" N PHE B 241 " --> pdb=" O PHE B 253 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N ARG B 251 " --> pdb=" O THR B 243 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N LEU B 252 " --> pdb=" O MET B 262 " (cutoff:3.500A) removed outlier: 4.108A pdb=" N MET B 262 " --> pdb=" O LEU B 252 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 275 through 276 removed outlier: 3.753A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'H' and resid 4 through 6 Processing sheet with id=AB1, first strand: chain 'H' and resid 58 through 60 removed outlier: 3.578A pdb=" N GLU H 46 " --> pdb=" O ARG H 38 " (cutoff:3.500A) removed outlier: 6.520A pdb=" N TRP H 36 " --> pdb=" O VAL H 48 " (cutoff:3.500A) removed outlier: 4.369A pdb=" N TYR H 50 " --> pdb=" O MET H 34 " (cutoff:3.500A) removed outlier: 6.713A pdb=" N MET H 34 " --> pdb=" O TYR H 50 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N VAL H 97 " --> pdb=" O HIS H 35 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N THR H 115 " --> pdb=" O TYR H 94 " (cutoff:3.500A) removed outlier: 4.531A pdb=" N CYS H 96 " --> pdb=" O GLN H 113 " (cutoff:3.500A) removed outlier: 5.966A pdb=" N GLN H 113 " --> pdb=" O CYS H 96 " (cutoff:3.500A) removed outlier: 7.795A pdb=" N ARG H 98 " --> pdb=" O TRP H 111 " (cutoff:3.500A) removed outlier: 6.458A pdb=" N TRP H 111 " --> pdb=" O ARG H 98 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'H' and resid 128 through 129 Processing sheet with id=AB3, first strand: chain 'H' and resid 182 through 183 removed outlier: 5.180A pdb=" N LEU H 175 " --> pdb=" O LEU H 166 " (cutoff:3.500A) removed outlier: 5.875A pdb=" N LEU H 166 " --> pdb=" O LEU H 175 " (cutoff:3.500A) 380 hydrogen bonds defined for protein. 1095 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: 2.38 Time building geometry restraints manager: 2.45 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 1895 1.33 - 1.45: 1924 1.45 - 1.57: 4683 1.57 - 1.69: 1 1.69 - 1.81: 79 Bond restraints: 8582 Sorted by residual: bond pdb=" C1 W96 R 501 " pdb=" N2 W96 R 501 " ideal model delta sigma weight residual 1.374 1.448 -0.074 2.00e-02 2.50e+03 1.37e+01 bond pdb=" C4 W96 R 501 " pdb=" C9 W96 R 501 " ideal model delta sigma weight residual 1.423 1.364 0.059 2.00e-02 2.50e+03 8.76e+00 bond pdb=" C3 W96 R 501 " pdb=" N2 W96 R 501 " ideal model delta sigma weight residual 1.400 1.450 -0.050 2.00e-02 2.50e+03 6.25e+00 bond pdb=" C PHE R 405 " pdb=" O PHE R 405 " ideal model delta sigma weight residual 1.236 1.208 0.028 1.16e-02 7.43e+03 5.84e+00 bond pdb=" N THR B 274 " pdb=" CA THR B 274 " ideal model delta sigma weight residual 1.455 1.487 -0.032 1.38e-02 5.25e+03 5.48e+00 ... (remaining 8577 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.82: 11334 1.82 - 3.63: 244 3.63 - 5.45: 45 5.45 - 7.27: 8 7.27 - 9.08: 3 Bond angle restraints: 11634 Sorted by residual: angle pdb=" CA TYR R 409 " pdb=" CB TYR R 409 " pdb=" CG TYR R 409 " ideal model delta sigma weight residual 113.90 121.85 -7.95 1.80e+00 3.09e-01 1.95e+01 angle pdb=" C PHE R 405 " pdb=" CA PHE R 405 " pdb=" CB PHE R 405 " ideal model delta sigma weight residual 110.95 104.43 6.52 1.55e+00 4.16e-01 1.77e+01 angle pdb=" N PHE R 406 " pdb=" CA PHE R 406 " pdb=" C PHE R 406 " ideal model delta sigma weight residual 111.28 106.81 4.47 1.09e+00 8.42e-01 1.68e+01 angle pdb=" C PHE R 406 " pdb=" N PHE R 407 " pdb=" CA PHE R 407 " ideal model delta sigma weight residual 120.28 115.25 5.03 1.34e+00 5.57e-01 1.41e+01 angle pdb=" C LEU R 100 " pdb=" N VAL R 101 " pdb=" CA VAL R 101 " ideal model delta sigma weight residual 121.97 116.09 5.88 1.80e+00 3.09e-01 1.07e+01 ... (remaining 11629 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.30: 4511 17.30 - 34.60: 451 34.60 - 51.89: 77 51.89 - 69.19: 9 69.19 - 86.49: 6 Dihedral angle restraints: 5054 sinusoidal: 1921 harmonic: 3133 Sorted by residual: dihedral pdb=" CB CYS R 121 " pdb=" SG CYS R 121 " pdb=" SG CYS R 203 " pdb=" CB CYS R 203 " ideal model delta sinusoidal sigma weight residual -86.00 -172.49 86.49 1 1.00e+01 1.00e-02 9.01e+01 dihedral pdb=" CA PHE B 234 " pdb=" C PHE B 234 " pdb=" N PHE B 235 " pdb=" CA PHE B 235 " ideal model delta harmonic sigma weight residual 180.00 155.80 24.20 0 5.00e+00 4.00e-02 2.34e+01 dihedral pdb=" CA LYS B 78 " pdb=" C LYS B 78 " pdb=" N LEU B 79 " pdb=" CA LEU B 79 " ideal model delta harmonic sigma weight residual 180.00 158.64 21.36 0 5.00e+00 4.00e-02 1.82e+01 ... (remaining 5051 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.045: 979 0.045 - 0.090: 272 0.090 - 0.135: 71 0.135 - 0.180: 8 0.180 - 0.225: 1 Chirality restraints: 1331 Sorted by residual: chirality pdb=" CB VAL H 64 " pdb=" CA VAL H 64 " pdb=" CG1 VAL H 64 " pdb=" CG2 VAL H 64 " both_signs ideal model delta sigma weight residual False -2.63 -2.40 -0.23 2.00e-01 2.50e+01 1.27e+00 chirality pdb=" CG LEU B 286 " pdb=" CB LEU B 286 " pdb=" CD1 LEU B 286 " pdb=" CD2 LEU B 286 " both_signs ideal model delta sigma weight residual False -2.59 -2.42 -0.17 2.00e-01 2.50e+01 7.29e-01 chirality pdb=" CA TYR H 223 " pdb=" N TYR H 223 " pdb=" C TYR H 223 " pdb=" CB TYR H 223 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.17 2.00e-01 2.50e+01 6.89e-01 ... (remaining 1328 not shown) Planarity restraints: 1468 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA PRO R 404 " -0.013 2.00e-02 2.50e+03 2.64e-02 6.94e+00 pdb=" C PRO R 404 " 0.046 2.00e-02 2.50e+03 pdb=" O PRO R 404 " -0.017 2.00e-02 2.50e+03 pdb=" N PHE R 405 " -0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA R 98 " -0.012 2.00e-02 2.50e+03 2.48e-02 6.17e+00 pdb=" C ALA R 98 " 0.043 2.00e-02 2.50e+03 pdb=" O ALA R 98 " -0.016 2.00e-02 2.50e+03 pdb=" N THR R 99 " -0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL R 97 " -0.011 2.00e-02 2.50e+03 2.28e-02 5.20e+00 pdb=" C VAL R 97 " 0.039 2.00e-02 2.50e+03 pdb=" O VAL R 97 " -0.015 2.00e-02 2.50e+03 pdb=" N ALA R 98 " -0.013 2.00e-02 2.50e+03 ... (remaining 1465 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 679 2.74 - 3.28: 8787 3.28 - 3.82: 14003 3.82 - 4.36: 16550 4.36 - 4.90: 28573 Nonbonded interactions: 68592 Sorted by model distance: nonbonded pdb=" OE2 GLU A 20 " pdb=" NZ LYS B 89 " model vdw 2.196 3.120 nonbonded pdb=" O ALA A 41 " pdb=" NZ LYS A 46 " model vdw 2.234 3.120 nonbonded pdb=" O TYR B 145 " pdb=" N GLY B 162 " model vdw 2.248 3.120 nonbonded pdb=" O ARG H 67 " pdb=" OG1 THR H 84 " model vdw 2.256 3.040 nonbonded pdb=" O SER B 67 " pdb=" OG SER B 67 " model vdw 2.266 3.040 ... (remaining 68587 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=0.00 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: 1.650 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: 22.220 Find NCS groups from input model: 0.100 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: 0.010 Load rotamer database and sin/cos tables:2.930 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.400 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1027 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 : 0.004 0.074 8584 Z= 0.197 Angle : 0.687 9.083 11638 Z= 0.392 Chirality : 0.044 0.225 1331 Planarity : 0.004 0.056 1468 Dihedral : 13.682 80.650 3026 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 14.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.97 % Favored : 93.03 % Rotamer: Outliers : 0.11 % Allowed : 0.22 % Favored : 99.67 % 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: -0.94 (0.26), residues: 1061 helix: 1.20 (0.28), residues: 344 sheet: -1.72 (0.31), residues: 254 loop : -1.31 (0.29), residues: 463 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP B 169 HIS 0.007 0.001 HIS A 189 PHE 0.028 0.002 PHE B 234 TYR 0.028 0.002 TYR R 409 ARG 0.012 0.000 ARG H 148 Details of bonding type rmsd hydrogen bonds : bond 0.15547 ( 380) hydrogen bonds : angle 6.62969 ( 1095) SS BOND : bond 0.00324 ( 2) SS BOND : angle 0.49980 ( 4) covalent geometry : bond 0.00414 ( 8582) covalent geometry : angle 0.68657 (11634) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2122 Ramachandran restraints generated. 1061 Oldfield, 0 Emsley, 1061 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2122 Ramachandran restraints generated. 1061 Oldfield, 0 Emsley, 1061 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 925 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 96 time to evaluate : 0.804 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 47 TRP cc_start: 0.3248 (t60) cc_final: 0.2947 (t60) REVERT: H 218 MET cc_start: -0.0933 (ttt) cc_final: -0.1655 (ttt) REVERT: R 437 ASN cc_start: 0.3830 (m-40) cc_final: 0.3292 (m-40) outliers start: 1 outliers final: 1 residues processed: 97 average time/residue: 0.2127 time to fit residues: 28.7100 Evaluate side-chains 72 residues out of total 925 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 71 time to evaluate : 0.822 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 274 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 89 optimal weight: 0.9980 chunk 80 optimal weight: 2.9990 chunk 44 optimal weight: 0.9980 chunk 27 optimal weight: 0.7980 chunk 54 optimal weight: 9.9990 chunk 42 optimal weight: 0.7980 chunk 83 optimal weight: 0.8980 chunk 32 optimal weight: 2.9990 chunk 50 optimal weight: 3.9990 chunk 61 optimal weight: 4.9990 chunk 96 optimal weight: 1.9990 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 347 ASN ** B 225 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 159 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4540 r_free = 0.4540 target = 0.222461 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.4152 r_free = 0.4152 target = 0.180228 restraints weight = 10787.874| |-----------------------------------------------------------------------------| r_work (start): 0.4157 rms_B_bonded: 3.08 r_work: 0.4044 rms_B_bonded: 3.72 restraints_weight: 0.5000 r_work (final): 0.4044 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1608 moved from start: 0.2441 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 8584 Z= 0.175 Angle : 0.688 8.736 11638 Z= 0.360 Chirality : 0.046 0.165 1331 Planarity : 0.005 0.058 1468 Dihedral : 5.415 51.502 1173 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 13.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.18 % Favored : 94.82 % Rotamer: Outliers : 1.00 % Allowed : 9.54 % Favored : 89.46 % 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: -0.68 (0.26), residues: 1061 helix: 1.51 (0.27), residues: 366 sheet: -1.57 (0.33), residues: 236 loop : -1.43 (0.28), residues: 459 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.003 TRP B 339 HIS 0.007 0.002 HIS A 189 PHE 0.026 0.002 PHE H 68 TYR 0.016 0.002 TYR H 60 ARG 0.008 0.001 ARG H 38 Details of bonding type rmsd hydrogen bonds : bond 0.04503 ( 380) hydrogen bonds : angle 5.22273 ( 1095) SS BOND : bond 0.01466 ( 2) SS BOND : angle 1.38147 ( 4) covalent geometry : bond 0.00387 ( 8582) covalent geometry : angle 0.68731 (11634) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2122 Ramachandran restraints generated. 1061 Oldfield, 0 Emsley, 1061 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2122 Ramachandran restraints generated. 1061 Oldfield, 0 Emsley, 1061 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 925 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 68 time to evaluate : 0.774 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 62 HIS cc_start: 0.2186 (t-90) cc_final: 0.1231 (t-90) REVERT: H 47 TRP cc_start: 0.4169 (t60) cc_final: 0.3236 (t60) REVERT: H 218 MET cc_start: -0.0528 (ttt) cc_final: -0.0781 (ptm) REVERT: R 173 TRP cc_start: 0.5333 (m100) cc_final: 0.2446 (t60) REVERT: R 437 ASN cc_start: 0.4138 (m-40) cc_final: 0.2965 (m110) outliers start: 9 outliers final: 5 residues processed: 75 average time/residue: 0.2084 time to fit residues: 22.0585 Evaluate side-chains 64 residues out of total 925 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 59 time to evaluate : 0.864 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 252 ASP Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 307 VAL Chi-restraints excluded: chain H residue 93 MET Chi-restraints excluded: chain R residue 135 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 9 optimal weight: 0.8980 chunk 15 optimal weight: 3.9990 chunk 67 optimal weight: 0.9990 chunk 83 optimal weight: 0.6980 chunk 46 optimal weight: 0.4980 chunk 72 optimal weight: 0.0470 chunk 21 optimal weight: 10.0000 chunk 20 optimal weight: 5.9990 chunk 28 optimal weight: 0.0270 chunk 26 optimal weight: 0.9990 chunk 57 optimal weight: 0.0040 overall best weight: 0.2548 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 220 GLN ** B 225 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 433 ASN R 437 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4541 r_free = 0.4541 target = 0.222475 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.4151 r_free = 0.4151 target = 0.179489 restraints weight = 10912.984| |-----------------------------------------------------------------------------| r_work (start): 0.4155 rms_B_bonded: 3.14 r_work: 0.4038 rms_B_bonded: 3.78 restraints_weight: 0.5000 r_work (final): 0.4038 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1501 moved from start: 0.2877 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 8584 Z= 0.112 Angle : 0.551 6.414 11638 Z= 0.290 Chirality : 0.042 0.178 1331 Planarity : 0.004 0.061 1468 Dihedral : 4.918 51.776 1173 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 10.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.62 % Favored : 95.38 % Rotamer: Outliers : 1.11 % Allowed : 12.43 % Favored : 86.46 % 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: -0.44 (0.26), residues: 1061 helix: 1.74 (0.27), residues: 367 sheet: -1.36 (0.32), residues: 253 loop : -1.35 (0.29), residues: 441 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 339 HIS 0.005 0.001 HIS A 189 PHE 0.021 0.001 PHE H 68 TYR 0.018 0.001 TYR H 178 ARG 0.006 0.000 ARG H 179 Details of bonding type rmsd hydrogen bonds : bond 0.03687 ( 380) hydrogen bonds : angle 4.77887 ( 1095) SS BOND : bond 0.00399 ( 2) SS BOND : angle 0.97042 ( 4) covalent geometry : bond 0.00230 ( 8582) covalent geometry : angle 0.55102 (11634) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2122 Ramachandran restraints generated. 1061 Oldfield, 0 Emsley, 1061 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2122 Ramachandran restraints generated. 1061 Oldfield, 0 Emsley, 1061 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 925 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 67 time to evaluate : 0.914 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 183 THR cc_start: 0.1087 (OUTLIER) cc_final: 0.0879 (m) REVERT: A 342 ILE cc_start: 0.3786 (mt) cc_final: 0.3357 (mt) REVERT: B 45 MET cc_start: 0.1849 (OUTLIER) cc_final: 0.1400 (ttm) REVERT: B 285 LEU cc_start: 0.0642 (OUTLIER) cc_final: -0.0119 (tt) REVERT: H 47 TRP cc_start: 0.3699 (t60) cc_final: 0.2891 (t60) REVERT: H 218 MET cc_start: -0.1067 (ttt) cc_final: -0.1426 (ttt) REVERT: R 173 TRP cc_start: 0.5369 (m100) cc_final: 0.2679 (t60) REVERT: R 437 ASN cc_start: 0.3215 (m110) cc_final: 0.2682 (m-40) outliers start: 10 outliers final: 4 residues processed: 75 average time/residue: 0.2201 time to fit residues: 23.8526 Evaluate side-chains 69 residues out of total 925 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 62 time to evaluate : 1.031 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 183 THR Chi-restraints excluded: chain B residue 33 ILE Chi-restraints excluded: chain B residue 45 MET Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 285 LEU Chi-restraints excluded: chain R residue 50 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 28 optimal weight: 4.9990 chunk 34 optimal weight: 3.9990 chunk 82 optimal weight: 2.9990 chunk 22 optimal weight: 0.2980 chunk 2 optimal weight: 2.9990 chunk 31 optimal weight: 4.9990 chunk 55 optimal weight: 0.9990 chunk 63 optimal weight: 0.9980 chunk 91 optimal weight: 0.9990 chunk 89 optimal weight: 2.9990 chunk 56 optimal weight: 0.9980 overall best weight: 0.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 220 GLN ** B 225 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 340 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4674 r_free = 0.4674 target = 0.238686 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4407 r_free = 0.4407 target = 0.206522 restraints weight = 10833.301| |-----------------------------------------------------------------------------| r_work (start): 0.4390 rms_B_bonded: 2.42 r_work: 0.4251 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work (final): 0.4251 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.2129 moved from start: 0.4376 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 8584 Z= 0.155 Angle : 0.662 9.641 11638 Z= 0.349 Chirality : 0.045 0.162 1331 Planarity : 0.005 0.060 1468 Dihedral : 5.373 56.876 1173 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 14.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.56 % Favored : 94.44 % Rotamer: Outliers : 3.11 % Allowed : 13.76 % Favored : 83.13 % 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: -0.72 (0.26), residues: 1061 helix: 1.55 (0.27), residues: 358 sheet: -1.52 (0.33), residues: 234 loop : -1.50 (0.28), residues: 469 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.003 TRP R 402 HIS 0.010 0.002 HIS A 322 PHE 0.039 0.002 PHE R 406 TYR 0.022 0.002 TYR H 60 ARG 0.011 0.001 ARG H 179 Details of bonding type rmsd hydrogen bonds : bond 0.04158 ( 380) hydrogen bonds : angle 5.19281 ( 1095) SS BOND : bond 0.00672 ( 2) SS BOND : angle 0.62854 ( 4) covalent geometry : bond 0.00334 ( 8582) covalent geometry : angle 0.66239 (11634) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2122 Ramachandran restraints generated. 1061 Oldfield, 0 Emsley, 1061 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2122 Ramachandran restraints generated. 1061 Oldfield, 0 Emsley, 1061 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 925 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 66 time to evaluate : 2.232 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 248 LEU cc_start: 0.4442 (tt) cc_final: 0.3914 (tp) REVERT: B 133 VAL cc_start: 0.1602 (OUTLIER) cc_final: 0.1366 (p) REVERT: H 47 TRP cc_start: 0.4059 (t60) cc_final: 0.3012 (t60) REVERT: R 138 HIS cc_start: 0.5842 (OUTLIER) cc_final: 0.3979 (m170) REVERT: R 173 TRP cc_start: 0.5523 (m100) cc_final: 0.2734 (t60) outliers start: 28 outliers final: 7 residues processed: 90 average time/residue: 0.2707 time to fit residues: 36.9713 Evaluate side-chains 69 residues out of total 925 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 60 time to evaluate : 2.651 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 252 ASP Chi-restraints excluded: chain B residue 33 ILE Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 183 HIS Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain H residue 68 PHE Chi-restraints excluded: chain H residue 91 THR Chi-restraints excluded: chain R residue 138 HIS Chi-restraints excluded: chain R residue 406 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 66 optimal weight: 6.9990 chunk 90 optimal weight: 2.9990 chunk 105 optimal weight: 1.9990 chunk 42 optimal weight: 0.6980 chunk 56 optimal weight: 2.9990 chunk 41 optimal weight: 0.1980 chunk 95 optimal weight: 0.1980 chunk 58 optimal weight: 0.0050 chunk 83 optimal weight: 0.2980 chunk 59 optimal weight: 0.6980 chunk 55 optimal weight: 1.9990 overall best weight: 0.2794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 242 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 225 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4677 r_free = 0.4677 target = 0.238749 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4406 r_free = 0.4406 target = 0.205707 restraints weight = 10704.725| |-----------------------------------------------------------------------------| r_work (start): 0.4383 rms_B_bonded: 2.52 r_work: 0.4235 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work (final): 0.4235 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1954 moved from start: 0.4590 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 8584 Z= 0.106 Angle : 0.565 7.850 11638 Z= 0.293 Chirality : 0.041 0.165 1331 Planarity : 0.004 0.063 1468 Dihedral : 4.679 27.821 1172 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 10.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.43 % Favored : 95.57 % Rotamer: Outliers : 2.22 % Allowed : 15.65 % Favored : 82.13 % 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: -0.35 (0.26), residues: 1061 helix: 1.81 (0.27), residues: 360 sheet: -1.11 (0.33), residues: 237 loop : -1.39 (0.29), residues: 464 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 82 HIS 0.006 0.001 HIS A 322 PHE 0.015 0.001 PHE R 387 TYR 0.014 0.001 TYR H 178 ARG 0.003 0.000 ARG H 179 Details of bonding type rmsd hydrogen bonds : bond 0.03493 ( 380) hydrogen bonds : angle 4.76517 ( 1095) SS BOND : bond 0.00266 ( 2) SS BOND : angle 0.77027 ( 4) covalent geometry : bond 0.00218 ( 8582) covalent geometry : angle 0.56484 (11634) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2122 Ramachandran restraints generated. 1061 Oldfield, 0 Emsley, 1061 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2122 Ramachandran restraints generated. 1061 Oldfield, 0 Emsley, 1061 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 925 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 68 time to evaluate : 0.958 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 248 LEU cc_start: 0.4431 (tt) cc_final: 0.3921 (tp) REVERT: B 261 LEU cc_start: 0.4696 (mm) cc_final: 0.4174 (mt) REVERT: B 285 LEU cc_start: 0.0759 (OUTLIER) cc_final: 0.0547 (tp) REVERT: B 286 LEU cc_start: 0.6293 (mp) cc_final: 0.5469 (mp) REVERT: H 47 TRP cc_start: 0.3547 (t60) cc_final: 0.2637 (t60) REVERT: R 138 HIS cc_start: 0.5430 (OUTLIER) cc_final: 0.3601 (m170) REVERT: R 173 TRP cc_start: 0.5502 (m100) cc_final: 0.2612 (t60) outliers start: 20 outliers final: 11 residues processed: 84 average time/residue: 0.2415 time to fit residues: 30.8649 Evaluate side-chains 79 residues out of total 925 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 66 time to evaluate : 1.497 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 252 ASP Chi-restraints excluded: chain B residue 33 ILE Chi-restraints excluded: chain B residue 121 CYS Chi-restraints excluded: chain B residue 183 HIS Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 285 LEU Chi-restraints excluded: chain H residue 68 PHE Chi-restraints excluded: chain H residue 91 THR Chi-restraints excluded: chain H residue 223 TYR Chi-restraints excluded: chain R residue 95 ILE Chi-restraints excluded: chain R residue 138 HIS Chi-restraints excluded: chain R residue 154 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 63 optimal weight: 2.9990 chunk 67 optimal weight: 2.9990 chunk 92 optimal weight: 0.7980 chunk 82 optimal weight: 1.9990 chunk 64 optimal weight: 0.6980 chunk 81 optimal weight: 0.9990 chunk 9 optimal weight: 0.7980 chunk 28 optimal weight: 1.9990 chunk 94 optimal weight: 0.1980 chunk 8 optimal weight: 0.0370 chunk 76 optimal weight: 1.9990 overall best weight: 0.5058 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 242 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 331 ASN ** B 225 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4690 r_free = 0.4690 target = 0.240035 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4434 r_free = 0.4434 target = 0.208882 restraints weight = 10570.946| |-----------------------------------------------------------------------------| r_work (start): 0.4414 rms_B_bonded: 2.30 r_work: 0.4268 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work (final): 0.4268 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.2077 moved from start: 0.5029 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 8584 Z= 0.118 Angle : 0.595 9.027 11638 Z= 0.306 Chirality : 0.042 0.165 1331 Planarity : 0.004 0.059 1468 Dihedral : 4.713 31.491 1172 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 11.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.90 % Favored : 95.10 % Rotamer: Outliers : 2.55 % Allowed : 16.54 % Favored : 80.91 % 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: -0.36 (0.26), residues: 1061 helix: 1.78 (0.27), residues: 359 sheet: -1.02 (0.33), residues: 236 loop : -1.43 (0.29), residues: 466 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 82 HIS 0.006 0.001 HIS A 322 PHE 0.014 0.001 PHE R 387 TYR 0.010 0.001 TYR H 60 ARG 0.005 0.000 ARG B 8 Details of bonding type rmsd hydrogen bonds : bond 0.03591 ( 380) hydrogen bonds : angle 4.76927 ( 1095) SS BOND : bond 0.00387 ( 2) SS BOND : angle 0.64047 ( 4) covalent geometry : bond 0.00248 ( 8582) covalent geometry : angle 0.59453 (11634) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2122 Ramachandran restraints generated. 1061 Oldfield, 0 Emsley, 1061 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2122 Ramachandran restraints generated. 1061 Oldfield, 0 Emsley, 1061 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 925 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 66 time to evaluate : 0.894 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 53 MET cc_start: -0.0126 (ptm) cc_final: -0.2455 (mmp) REVERT: A 248 LEU cc_start: 0.4504 (tt) cc_final: 0.3989 (tp) REVERT: A 320 TYR cc_start: 0.2512 (m-80) cc_final: 0.1079 (t80) REVERT: B 133 VAL cc_start: 0.1470 (OUTLIER) cc_final: 0.1188 (p) REVERT: H 47 TRP cc_start: 0.3731 (t60) cc_final: 0.2855 (t60) REVERT: R 138 HIS cc_start: 0.5565 (OUTLIER) cc_final: 0.3635 (m170) REVERT: R 173 TRP cc_start: 0.5570 (m100) cc_final: 0.2635 (t60) outliers start: 23 outliers final: 14 residues processed: 85 average time/residue: 0.2023 time to fit residues: 24.8189 Evaluate side-chains 80 residues out of total 925 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 64 time to evaluate : 0.867 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 252 ASP Chi-restraints excluded: chain B residue 33 ILE Chi-restraints excluded: chain B residue 62 HIS Chi-restraints excluded: chain B residue 121 CYS Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 183 HIS Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain H residue 68 PHE Chi-restraints excluded: chain H residue 89 GLU Chi-restraints excluded: chain H residue 91 THR Chi-restraints excluded: chain H residue 223 TYR Chi-restraints excluded: chain R residue 95 ILE Chi-restraints excluded: chain R residue 138 HIS Chi-restraints excluded: chain R residue 154 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 1 optimal weight: 0.7980 chunk 14 optimal weight: 2.9990 chunk 24 optimal weight: 1.9990 chunk 52 optimal weight: 0.4980 chunk 25 optimal weight: 0.9980 chunk 22 optimal weight: 1.9990 chunk 27 optimal weight: 0.6980 chunk 36 optimal weight: 0.8980 chunk 72 optimal weight: 1.9990 chunk 28 optimal weight: 0.6980 chunk 63 optimal weight: 0.8980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 242 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 225 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4654 r_free = 0.4654 target = 0.237015 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4365 r_free = 0.4365 target = 0.202732 restraints weight = 11131.998| |-----------------------------------------------------------------------------| r_work (start): 0.4352 rms_B_bonded: 3.01 r_work: 0.4227 rms_B_bonded: 3.52 restraints_weight: 0.5000 r_work (final): 0.4227 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.2187 moved from start: 0.5914 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 8584 Z= 0.135 Angle : 0.648 9.407 11638 Z= 0.335 Chirality : 0.043 0.174 1331 Planarity : 0.005 0.087 1468 Dihedral : 5.075 32.184 1172 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 11.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.18 % Favored : 94.82 % Rotamer: Outliers : 2.22 % Allowed : 17.31 % Favored : 80.47 % 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: -0.54 (0.26), residues: 1061 helix: 1.59 (0.27), residues: 360 sheet: -1.18 (0.32), residues: 253 loop : -1.46 (0.29), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP B 82 HIS 0.007 0.002 HIS A 322 PHE 0.018 0.002 PHE R 220 TYR 0.016 0.002 TYR H 60 ARG 0.008 0.001 ARG B 8 Details of bonding type rmsd hydrogen bonds : bond 0.03858 ( 380) hydrogen bonds : angle 4.93130 ( 1095) SS BOND : bond 0.01801 ( 2) SS BOND : angle 0.82972 ( 4) covalent geometry : bond 0.00286 ( 8582) covalent geometry : angle 0.64747 (11634) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2122 Ramachandran restraints generated. 1061 Oldfield, 0 Emsley, 1061 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2122 Ramachandran restraints generated. 1061 Oldfield, 0 Emsley, 1061 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 925 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 70 time to evaluate : 0.913 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 53 MET cc_start: 0.0016 (ptm) cc_final: -0.2472 (tpt) REVERT: A 248 LEU cc_start: 0.5116 (tt) cc_final: 0.4607 (tp) REVERT: A 313 ARG cc_start: 0.7346 (mmt180) cc_final: 0.6814 (mmt180) REVERT: A 320 TYR cc_start: 0.3207 (m-80) cc_final: 0.1422 (t80) REVERT: A 323 MET cc_start: 0.5280 (tpp) cc_final: 0.2776 (mtt) REVERT: G 32 LYS cc_start: 0.5511 (ptpt) cc_final: 0.5231 (mmtt) REVERT: H 47 TRP cc_start: 0.3923 (t60) cc_final: 0.3133 (t60) REVERT: R 102 ILE cc_start: 0.5729 (mt) cc_final: 0.5523 (mt) REVERT: R 125 LEU cc_start: 0.3301 (tp) cc_final: 0.3084 (tt) REVERT: R 138 HIS cc_start: 0.5535 (OUTLIER) cc_final: 0.3705 (m170) REVERT: R 159 LYS cc_start: 0.4105 (mtmt) cc_final: 0.3237 (mptt) REVERT: R 173 TRP cc_start: 0.5733 (m100) cc_final: 0.2469 (t60) outliers start: 20 outliers final: 16 residues processed: 86 average time/residue: 0.1793 time to fit residues: 22.6876 Evaluate side-chains 84 residues out of total 925 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 67 time to evaluate : 0.783 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 195 LEU Chi-restraints excluded: chain A residue 252 ASP Chi-restraints excluded: chain B residue 33 ILE Chi-restraints excluded: chain B residue 45 MET Chi-restraints excluded: chain B residue 121 CYS Chi-restraints excluded: chain B residue 183 HIS Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain H residue 68 PHE Chi-restraints excluded: chain H residue 89 GLU Chi-restraints excluded: chain H residue 91 THR Chi-restraints excluded: chain H residue 198 THR Chi-restraints excluded: chain H residue 223 TYR Chi-restraints excluded: chain R residue 95 ILE Chi-restraints excluded: chain R residue 138 HIS Chi-restraints excluded: chain R residue 154 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 9 optimal weight: 1.9990 chunk 52 optimal weight: 0.5980 chunk 55 optimal weight: 2.9990 chunk 61 optimal weight: 4.9990 chunk 31 optimal weight: 0.7980 chunk 50 optimal weight: 0.8980 chunk 53 optimal weight: 5.9990 chunk 73 optimal weight: 3.9990 chunk 96 optimal weight: 0.2980 chunk 7 optimal weight: 0.0170 chunk 40 optimal weight: 7.9990 overall best weight: 0.5218 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 242 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 225 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4659 r_free = 0.4659 target = 0.237407 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4394 r_free = 0.4394 target = 0.204841 restraints weight = 11103.386| |-----------------------------------------------------------------------------| r_work (start): 0.4375 rms_B_bonded: 2.67 r_work: 0.4251 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.4251 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.2168 moved from start: 0.6261 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 8584 Z= 0.115 Angle : 0.586 8.402 11638 Z= 0.300 Chirality : 0.042 0.167 1331 Planarity : 0.004 0.056 1468 Dihedral : 4.790 29.354 1172 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 11.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.28 % Favored : 94.72 % Rotamer: Outliers : 2.33 % Allowed : 17.20 % Favored : 80.47 % 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: -0.45 (0.26), residues: 1061 helix: 1.61 (0.27), residues: 361 sheet: -1.09 (0.33), residues: 241 loop : -1.38 (0.29), residues: 459 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 82 HIS 0.005 0.001 HIS A 322 PHE 0.014 0.001 PHE R 387 TYR 0.012 0.001 TYR H 178 ARG 0.004 0.000 ARG B 8 Details of bonding type rmsd hydrogen bonds : bond 0.03559 ( 380) hydrogen bonds : angle 4.78779 ( 1095) SS BOND : bond 0.00299 ( 2) SS BOND : angle 0.74166 ( 4) covalent geometry : bond 0.00241 ( 8582) covalent geometry : angle 0.58611 (11634) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2122 Ramachandran restraints generated. 1061 Oldfield, 0 Emsley, 1061 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2122 Ramachandran restraints generated. 1061 Oldfield, 0 Emsley, 1061 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 925 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 66 time to evaluate : 0.794 Fit side-chains revert: symmetry clash REVERT: A 53 MET cc_start: -0.0007 (ptm) cc_final: -0.2250 (tpp) REVERT: A 313 ARG cc_start: 0.7307 (mmt180) cc_final: 0.6867 (mmt180) REVERT: A 320 TYR cc_start: 0.3378 (m-80) cc_final: 0.1607 (t80) REVERT: B 19 ARG cc_start: 0.6630 (mpt-90) cc_final: 0.6365 (mpt180) REVERT: H 47 TRP cc_start: 0.3686 (t60) cc_final: 0.3011 (t60) REVERT: R 102 ILE cc_start: 0.5779 (mt) cc_final: 0.5572 (mt) REVERT: R 138 HIS cc_start: 0.5389 (OUTLIER) cc_final: 0.3668 (m170) REVERT: R 159 LYS cc_start: 0.4487 (mtmt) cc_final: 0.3565 (mptt) REVERT: R 173 TRP cc_start: 0.5667 (m100) cc_final: 0.2622 (t60) outliers start: 21 outliers final: 18 residues processed: 85 average time/residue: 0.1808 time to fit residues: 22.5711 Evaluate side-chains 84 residues out of total 925 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 65 time to evaluate : 0.801 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 182 THR Chi-restraints excluded: chain A residue 185 ILE Chi-restraints excluded: chain A residue 252 ASP Chi-restraints excluded: chain B residue 33 ILE Chi-restraints excluded: chain B residue 183 HIS Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain B residue 286 LEU Chi-restraints excluded: chain H residue 68 PHE Chi-restraints excluded: chain H residue 89 GLU Chi-restraints excluded: chain H residue 91 THR Chi-restraints excluded: chain H residue 198 THR Chi-restraints excluded: chain H residue 223 TYR Chi-restraints excluded: chain R residue 49 LEU Chi-restraints excluded: chain R residue 95 ILE Chi-restraints excluded: chain R residue 124 TYR Chi-restraints excluded: chain R residue 135 SER Chi-restraints excluded: chain R residue 138 HIS Chi-restraints excluded: chain R residue 154 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 105 optimal weight: 0.9980 chunk 14 optimal weight: 0.9990 chunk 69 optimal weight: 1.9990 chunk 8 optimal weight: 0.0770 chunk 4 optimal weight: 0.9980 chunk 36 optimal weight: 0.9980 chunk 3 optimal weight: 0.6980 chunk 33 optimal weight: 3.9990 chunk 81 optimal weight: 0.8980 chunk 50 optimal weight: 4.9990 chunk 100 optimal weight: 0.8980 overall best weight: 0.7138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 196 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 242 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 225 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 311 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4674 r_free = 0.4674 target = 0.239217 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4421 r_free = 0.4421 target = 0.208338 restraints weight = 11188.118| |-----------------------------------------------------------------------------| r_work (start): 0.4408 rms_B_bonded: 2.79 r_work: 0.4287 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.4287 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.2328 moved from start: 0.6896 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 8584 Z= 0.134 Angle : 0.644 10.074 11638 Z= 0.329 Chirality : 0.043 0.172 1331 Planarity : 0.004 0.058 1468 Dihedral : 5.158 39.115 1172 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 13.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.94 % Favored : 94.06 % Rotamer: Outliers : 2.44 % Allowed : 17.54 % Favored : 80.02 % 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: -0.52 (0.26), residues: 1061 helix: 1.57 (0.27), residues: 361 sheet: -1.26 (0.32), residues: 253 loop : -1.35 (0.30), residues: 447 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP B 82 HIS 0.006 0.002 HIS A 322 PHE 0.015 0.002 PHE R 220 TYR 0.018 0.002 TYR H 178 ARG 0.006 0.000 ARG B 68 Details of bonding type rmsd hydrogen bonds : bond 0.03823 ( 380) hydrogen bonds : angle 4.99999 ( 1095) SS BOND : bond 0.00436 ( 2) SS BOND : angle 0.78038 ( 4) covalent geometry : bond 0.00287 ( 8582) covalent geometry : angle 0.64443 (11634) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2122 Ramachandran restraints generated. 1061 Oldfield, 0 Emsley, 1061 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2122 Ramachandran restraints generated. 1061 Oldfield, 0 Emsley, 1061 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 925 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 67 time to evaluate : 0.871 Fit side-chains revert: symmetry clash REVERT: A 53 MET cc_start: 0.0215 (ptm) cc_final: -0.2113 (tpp) REVERT: A 313 ARG cc_start: 0.7573 (mmt180) cc_final: 0.6851 (mmt180) REVERT: A 320 TYR cc_start: 0.3749 (m-80) cc_final: 0.1884 (t80) REVERT: A 323 MET cc_start: 0.4737 (tpp) cc_final: 0.3100 (mtt) REVERT: B 61 MET cc_start: 0.0955 (mtp) cc_final: 0.0679 (ttp) REVERT: G 32 LYS cc_start: 0.6062 (ptpt) cc_final: 0.5709 (mmtt) REVERT: H 47 TRP cc_start: 0.3341 (t60) cc_final: 0.2785 (t60) REVERT: R 138 HIS cc_start: 0.5596 (OUTLIER) cc_final: 0.3710 (m170) outliers start: 22 outliers final: 21 residues processed: 86 average time/residue: 0.1821 time to fit residues: 23.0347 Evaluate side-chains 88 residues out of total 925 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 66 time to evaluate : 0.807 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 185 ILE Chi-restraints excluded: chain A residue 195 LEU Chi-restraints excluded: chain A residue 252 ASP Chi-restraints excluded: chain B residue 33 ILE Chi-restraints excluded: chain B residue 45 MET Chi-restraints excluded: chain B residue 121 CYS Chi-restraints excluded: chain B residue 160 SER Chi-restraints excluded: chain B residue 183 HIS Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain B residue 286 LEU Chi-restraints excluded: chain H residue 68 PHE Chi-restraints excluded: chain H residue 89 GLU Chi-restraints excluded: chain H residue 91 THR Chi-restraints excluded: chain H residue 198 THR Chi-restraints excluded: chain H residue 223 TYR Chi-restraints excluded: chain R residue 95 ILE Chi-restraints excluded: chain R residue 124 TYR Chi-restraints excluded: chain R residue 135 SER Chi-restraints excluded: chain R residue 138 HIS Chi-restraints excluded: chain R residue 154 ILE Chi-restraints excluded: chain R residue 387 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 8 optimal weight: 0.0770 chunk 92 optimal weight: 2.9990 chunk 31 optimal weight: 0.9990 chunk 55 optimal weight: 0.9980 chunk 34 optimal weight: 0.9980 chunk 84 optimal weight: 5.9990 chunk 6 optimal weight: 0.7980 chunk 47 optimal weight: 0.7980 chunk 24 optimal weight: 1.9990 chunk 64 optimal weight: 1.9990 chunk 91 optimal weight: 0.8980 overall best weight: 0.7138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 196 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 242 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 225 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4711 r_free = 0.4711 target = 0.243608 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4491 r_free = 0.4491 target = 0.215383 restraints weight = 11225.065| |-----------------------------------------------------------------------------| r_work (start): 0.4466 rms_B_bonded: 2.30 r_work: 0.4353 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work (final): 0.4353 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.2387 moved from start: 0.7272 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 8584 Z= 0.130 Angle : 0.629 9.632 11638 Z= 0.321 Chirality : 0.043 0.169 1331 Planarity : 0.004 0.054 1468 Dihedral : 5.221 45.430 1172 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 13.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.94 % Favored : 94.06 % Rotamer: Outliers : 2.77 % Allowed : 17.76 % Favored : 79.47 % 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: -0.56 (0.26), residues: 1061 helix: 1.56 (0.27), residues: 361 sheet: -1.26 (0.32), residues: 243 loop : -1.42 (0.29), residues: 457 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP B 82 HIS 0.005 0.002 HIS A 322 PHE 0.017 0.002 PHE B 278 TYR 0.014 0.001 TYR H 178 ARG 0.005 0.000 ARG B 68 Details of bonding type rmsd hydrogen bonds : bond 0.03776 ( 380) hydrogen bonds : angle 4.98397 ( 1095) SS BOND : bond 0.00414 ( 2) SS BOND : angle 0.82922 ( 4) covalent geometry : bond 0.00276 ( 8582) covalent geometry : angle 0.62933 (11634) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2122 Ramachandran restraints generated. 1061 Oldfield, 0 Emsley, 1061 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2122 Ramachandran restraints generated. 1061 Oldfield, 0 Emsley, 1061 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 925 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 71 time to evaluate : 0.831 Fit side-chains revert: symmetry clash REVERT: A 53 MET cc_start: 0.0464 (ptm) cc_final: -0.1988 (tpp) REVERT: A 320 TYR cc_start: 0.4003 (m-80) cc_final: 0.2133 (t80) REVERT: A 323 MET cc_start: 0.5135 (tpp) cc_final: 0.3107 (mtt) REVERT: G 32 LYS cc_start: 0.6358 (ptpt) cc_final: 0.5963 (mmtt) REVERT: H 47 TRP cc_start: 0.3352 (t60) cc_final: 0.2794 (t60) REVERT: R 138 HIS cc_start: 0.5537 (OUTLIER) cc_final: 0.3747 (m170) outliers start: 25 outliers final: 18 residues processed: 90 average time/residue: 0.1631 time to fit residues: 22.3052 Evaluate side-chains 88 residues out of total 925 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 69 time to evaluate : 0.820 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 185 ILE Chi-restraints excluded: chain A residue 195 LEU Chi-restraints excluded: chain A residue 252 ASP Chi-restraints excluded: chain B residue 45 MET Chi-restraints excluded: chain B residue 160 SER Chi-restraints excluded: chain B residue 183 HIS Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain B residue 286 LEU Chi-restraints excluded: chain H residue 68 PHE Chi-restraints excluded: chain H residue 89 GLU Chi-restraints excluded: chain H residue 91 THR Chi-restraints excluded: chain H residue 198 THR Chi-restraints excluded: chain R residue 95 ILE Chi-restraints excluded: chain R residue 124 TYR Chi-restraints excluded: chain R residue 135 SER Chi-restraints excluded: chain R residue 138 HIS Chi-restraints excluded: chain R residue 154 ILE Chi-restraints excluded: chain R residue 387 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 44 optimal weight: 7.9990 chunk 93 optimal weight: 0.0970 chunk 10 optimal weight: 0.0980 chunk 18 optimal weight: 0.9990 chunk 83 optimal weight: 0.7980 chunk 55 optimal weight: 4.9990 chunk 26 optimal weight: 0.9990 chunk 34 optimal weight: 0.6980 chunk 94 optimal weight: 10.0000 chunk 31 optimal weight: 3.9990 chunk 2 optimal weight: 0.9980 overall best weight: 0.5378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 196 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 242 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 225 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 437 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4720 r_free = 0.4720 target = 0.244497 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4498 r_free = 0.4498 target = 0.216337 restraints weight = 11238.944| |-----------------------------------------------------------------------------| r_work (start): 0.4477 rms_B_bonded: 2.49 r_work: 0.4349 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work (final): 0.4349 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.2402 moved from start: 0.7535 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 8584 Z= 0.121 Angle : 0.623 11.093 11638 Z= 0.316 Chirality : 0.042 0.168 1331 Planarity : 0.004 0.055 1468 Dihedral : 5.169 48.370 1172 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 12.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.28 % Favored : 94.72 % Rotamer: Outliers : 2.22 % Allowed : 18.65 % Favored : 79.13 % 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: -0.51 (0.26), residues: 1061 helix: 1.70 (0.27), residues: 355 sheet: -1.19 (0.32), residues: 242 loop : -1.48 (0.29), residues: 464 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP B 82 HIS 0.006 0.001 HIS A 322 PHE 0.016 0.001 PHE B 278 TYR 0.016 0.001 TYR H 178 ARG 0.003 0.000 ARG B 19 Details of bonding type rmsd hydrogen bonds : bond 0.03638 ( 380) hydrogen bonds : angle 4.85150 ( 1095) SS BOND : bond 0.00317 ( 2) SS BOND : angle 0.81612 ( 4) covalent geometry : bond 0.00260 ( 8582) covalent geometry : angle 0.62249 (11634) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4347.02 seconds wall clock time: 77 minutes 55.93 seconds (4675.93 seconds total)