Starting phenix.real_space_refine on Tue Sep 24 15:38:23 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7w6p_32331/09_2024/7w6p_32331.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7w6p_32331/09_2024/7w6p_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7w6p_32331/09_2024/7w6p_32331.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7w6p_32331/09_2024/7w6p_32331.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7w6p_32331/09_2024/7w6p_32331.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7w6p_32331/09_2024/7w6p_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-5461/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: 5.16, per 1000 atoms: 0.61 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: 2.16 Conformation dependent library (CDL) restraints added in 973.1 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: 0.88 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: 2.33 Time building geometry restraints manager: 2.49 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: 1.450 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: 0.350 Check model and map are aligned: 0.070 Set scattering table: 0.090 Process input model: 21.490 Find NCS groups from input model: 0.090 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:2.730 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.310 ------------------------------------------------------------------------------- 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 8582 Z= 0.276 Angle : 0.687 9.083 11634 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 *********************** 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 fitting. rotamer outliers: 1 poor density : 96 time to evaluate : 0.823 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: 0.2099 time to fit residues: 28.1685 Evaluate side-chains 72 residues out of total 925 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 71 time to evaluate : 0.836 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1707 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 8582 Z= 0.255 Angle : 0.687 8.736 11634 Z= 0.360 Chirality : 0.046 0.165 1331 Planarity : 0.005 0.058 1468 Dihedral : 5.415 51.501 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 *********************** 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 fitting. rotamer outliers: 9 poor density : 68 time to evaluate : 0.823 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 62 HIS cc_start: 0.2248 (t-90) cc_final: 0.1244 (t-90) REVERT: H 47 TRP cc_start: 0.4124 (t60) cc_final: 0.3673 (t60) REVERT: R 173 TRP cc_start: 0.4843 (m100) cc_final: 0.2296 (t60) REVERT: R 381 GLN cc_start: 0.0678 (mm-40) cc_final: 0.0273 (pp30) REVERT: R 437 ASN cc_start: 0.4581 (m-40) cc_final: 0.3567 (m110) outliers start: 9 outliers final: 5 residues processed: 75 average time/residue: 0.2137 time to fit residues: 22.5987 Evaluate side-chains 65 residues out of total 925 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 60 time to evaluate : 0.880 ------------------------------------------------------------------------------- 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 53 optimal weight: 0.9990 chunk 29 optimal weight: 1.9990 chunk 80 optimal weight: 2.9990 chunk 65 optimal weight: 0.7980 chunk 26 optimal weight: 0.0980 chunk 96 optimal weight: 0.9980 chunk 104 optimal weight: 0.9990 chunk 85 optimal weight: 2.9990 chunk 95 optimal weight: 3.9990 chunk 32 optimal weight: 0.0870 chunk 77 optimal weight: 2.9990 overall best weight: 0.5960 ------------------------------------------------------------------------------- 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 ** R 433 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1886 moved from start: 0.3453 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 8582 Z= 0.187 Angle : 0.594 6.459 11634 Z= 0.315 Chirality : 0.043 0.163 1331 Planarity : 0.004 0.060 1468 Dihedral : 5.131 57.525 1173 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 11.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.00 % Favored : 95.00 % Rotamer: Outliers : 1.89 % Allowed : 12.32 % Favored : 85.79 % 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: -0.58 (0.26), residues: 1061 helix: 1.61 (0.27), residues: 361 sheet: -1.31 (0.33), residues: 236 loop : -1.48 (0.28), residues: 464 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP B 82 HIS 0.005 0.001 HIS A 189 PHE 0.019 0.002 PHE R 387 TYR 0.022 0.002 TYR H 178 ARG 0.005 0.001 ARG H 72 *********************** 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 81 residues out of total 925 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 64 time to evaluate : 0.829 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 183 THR cc_start: 0.1225 (OUTLIER) cc_final: 0.0998 (m) REVERT: A 248 LEU cc_start: 0.3502 (tt) cc_final: 0.3003 (tp) REVERT: A 342 ILE cc_start: 0.4645 (mt) cc_final: 0.4126 (mt) REVERT: B 45 MET cc_start: 0.2776 (OUTLIER) cc_final: 0.2381 (ttm) REVERT: B 266 HIS cc_start: -0.1451 (OUTLIER) cc_final: -0.1710 (m-70) REVERT: H 47 TRP cc_start: 0.3904 (t60) cc_final: 0.3428 (t60) REVERT: R 138 HIS cc_start: 0.5434 (OUTLIER) cc_final: 0.3654 (m170) REVERT: R 173 TRP cc_start: 0.5080 (m100) cc_final: 0.2611 (t60) REVERT: R 381 GLN cc_start: 0.0638 (mm-40) cc_final: 0.0368 (pp30) REVERT: R 437 ASN cc_start: 0.4851 (m-40) cc_final: 0.3896 (m110) outliers start: 17 outliers final: 5 residues processed: 77 average time/residue: 0.1953 time to fit residues: 21.6321 Evaluate side-chains 71 residues out of total 925 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 62 time to evaluate : 0.762 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 183 THR 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 183 HIS Chi-restraints excluded: chain B residue 266 HIS Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain H residue 68 PHE Chi-restraints excluded: chain R residue 138 HIS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 95 optimal weight: 0.9980 chunk 72 optimal weight: 2.9990 chunk 50 optimal weight: 0.9990 chunk 10 optimal weight: 8.9990 chunk 46 optimal weight: 2.9990 chunk 64 optimal weight: 3.9990 chunk 96 optimal weight: 0.9980 chunk 102 optimal weight: 0.0570 chunk 91 optimal weight: 0.8980 chunk 27 optimal weight: 2.9990 chunk 85 optimal weight: 3.9990 overall best weight: 0.7900 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.2168 moved from start: 0.4433 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 8582 Z= 0.205 Angle : 0.620 6.819 11634 Z= 0.328 Chirality : 0.043 0.163 1331 Planarity : 0.004 0.057 1468 Dihedral : 5.226 52.172 1173 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 12.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.47 % Favored : 94.53 % Rotamer: Outliers : 2.77 % Allowed : 14.43 % Favored : 82.80 % 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: -0.60 (0.26), residues: 1061 helix: 1.52 (0.27), residues: 360 sheet: -1.32 (0.33), residues: 233 loop : -1.41 (0.28), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP R 428 HIS 0.007 0.001 HIS H 220 PHE 0.018 0.002 PHE R 387 TYR 0.016 0.002 TYR H 60 ARG 0.005 0.001 ARG H 179 *********************** 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 90 residues out of total 925 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 65 time to evaluate : 0.781 Fit side-chains revert: symmetry clash REVERT: A 53 MET cc_start: -0.1082 (ptp) cc_final: -0.3031 (mmp) REVERT: A 248 LEU cc_start: 0.3744 (tt) cc_final: 0.3157 (tp) REVERT: H 47 TRP cc_start: 0.3947 (t60) cc_final: 0.3138 (t60) REVERT: R 138 HIS cc_start: 0.5787 (OUTLIER) cc_final: 0.3814 (m170) REVERT: R 173 TRP cc_start: 0.5230 (m100) cc_final: 0.2584 (t60) REVERT: R 381 GLN cc_start: 0.0655 (mm-40) cc_final: 0.0385 (pp30) outliers start: 25 outliers final: 8 residues processed: 87 average time/residue: 0.1907 time to fit residues: 24.0756 Evaluate side-chains 69 residues out of total 925 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 60 time to evaluate : 0.820 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 252 ASP Chi-restraints excluded: chain A residue 353 LEU Chi-restraints excluded: chain B residue 33 ILE Chi-restraints excluded: chain B residue 284 LEU Chi-restraints excluded: chain H residue 68 PHE Chi-restraints excluded: chain H residue 91 THR Chi-restraints excluded: chain R residue 95 ILE Chi-restraints excluded: chain R residue 138 HIS Chi-restraints excluded: chain R residue 212 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 58 optimal weight: 0.0070 chunk 1 optimal weight: 0.8980 chunk 76 optimal weight: 1.9990 chunk 42 optimal weight: 2.9990 chunk 87 optimal weight: 1.9990 chunk 70 optimal weight: 2.9990 chunk 0 optimal weight: 1.9990 chunk 52 optimal weight: 0.0970 chunk 91 optimal weight: 2.9990 chunk 25 optimal weight: 2.9990 chunk 34 optimal weight: 1.9990 overall best weight: 1.0000 ------------------------------------------------------------------------------- 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 331 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.2493 moved from start: 0.5774 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 8582 Z= 0.235 Angle : 0.684 7.952 11634 Z= 0.362 Chirality : 0.045 0.175 1331 Planarity : 0.005 0.058 1468 Dihedral : 5.418 33.272 1172 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 14.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.50 % Favored : 93.50 % Rotamer: Outliers : 4.00 % Allowed : 14.76 % Favored : 81.24 % 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: -0.76 (0.26), residues: 1061 helix: 1.41 (0.27), residues: 360 sheet: -1.31 (0.33), residues: 238 loop : -1.58 (0.29), residues: 463 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.003 TRP B 82 HIS 0.007 0.002 HIS H 220 PHE 0.021 0.002 PHE R 405 TYR 0.019 0.002 TYR H 60 ARG 0.009 0.001 ARG H 179 *********************** 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 105 residues out of total 925 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 69 time to evaluate : 0.870 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 320 TYR cc_start: 0.3844 (m-80) cc_final: 0.1849 (t80) REVERT: R 138 HIS cc_start: 0.5954 (OUTLIER) cc_final: 0.3881 (m170) REVERT: R 159 LYS cc_start: 0.4402 (mtmt) cc_final: 0.3939 (mptt) REVERT: R 173 TRP cc_start: 0.5549 (m100) cc_final: 0.2400 (t60) outliers start: 36 outliers final: 22 residues processed: 99 average time/residue: 0.1833 time to fit residues: 26.4062 Evaluate side-chains 89 residues out of total 925 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 66 time to evaluate : 0.856 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 185 ILE Chi-restraints excluded: chain A residue 199 LEU Chi-restraints excluded: chain A residue 226 VAL 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 62 HIS 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 262 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 R residue 49 LEU Chi-restraints excluded: chain R residue 95 ILE Chi-restraints excluded: chain R residue 138 HIS Chi-restraints excluded: chain R residue 154 ILE Chi-restraints excluded: chain R residue 212 VAL Chi-restraints excluded: chain R residue 227 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 92 optimal weight: 1.9990 chunk 20 optimal weight: 9.9990 chunk 60 optimal weight: 6.9990 chunk 25 optimal weight: 1.9990 chunk 102 optimal weight: 0.7980 chunk 85 optimal weight: 0.9990 chunk 47 optimal weight: 0.4980 chunk 8 optimal weight: 0.0970 chunk 33 optimal weight: 0.6980 chunk 53 optimal weight: 8.9990 chunk 98 optimal weight: 3.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- 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** ** A 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 176 GLN ** B 225 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.2432 moved from start: 0.6069 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 8582 Z= 0.179 Angle : 0.623 7.442 11634 Z= 0.326 Chirality : 0.043 0.170 1331 Planarity : 0.004 0.051 1468 Dihedral : 5.052 27.620 1172 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 12.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.84 % Favored : 94.16 % Rotamer: Outliers : 2.11 % Allowed : 18.20 % Favored : 79.69 % 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: -0.63 (0.26), residues: 1061 helix: 1.46 (0.27), residues: 361 sheet: -1.21 (0.32), residues: 256 loop : -1.49 (0.29), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.054 0.002 TRP B 169 HIS 0.012 0.002 HIS B 142 PHE 0.015 0.002 PHE R 405 TYR 0.021 0.002 TYR H 223 ARG 0.003 0.000 ARG H 179 *********************** 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 91 residues out of total 925 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 72 time to evaluate : 0.896 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 320 TYR cc_start: 0.3783 (m-80) cc_final: 0.2111 (t80) REVERT: R 138 HIS cc_start: 0.5758 (OUTLIER) cc_final: 0.3604 (m170) REVERT: R 159 LYS cc_start: 0.4365 (mtmt) cc_final: 0.3918 (mptt) REVERT: R 173 TRP cc_start: 0.5550 (m100) cc_final: 0.2350 (t60) outliers start: 19 outliers final: 15 residues processed: 89 average time/residue: 0.1971 time to fit residues: 25.1085 Evaluate side-chains 82 residues out of total 925 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 66 time to evaluate : 0.780 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 199 LEU Chi-restraints excluded: chain A residue 252 ASP Chi-restraints excluded: chain A residue 353 LEU Chi-restraints excluded: chain B residue 33 ILE 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 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 R residue 95 ILE Chi-restraints excluded: chain R residue 138 HIS Chi-restraints excluded: chain R residue 154 ILE Chi-restraints excluded: chain R residue 212 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 11 optimal weight: 3.9990 chunk 58 optimal weight: 10.0000 chunk 74 optimal weight: 0.0170 chunk 86 optimal weight: 0.0030 chunk 57 optimal weight: 0.0970 chunk 102 optimal weight: 1.9990 chunk 63 optimal weight: 0.7980 chunk 62 optimal weight: 0.9990 chunk 47 optimal weight: 1.9990 chunk 40 optimal weight: 3.9990 chunk 61 optimal weight: 0.9990 overall best weight: 0.3828 ------------------------------------------------------------------------------- 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** ** H 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.2374 moved from start: 0.6274 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 8582 Z= 0.154 Angle : 0.598 9.365 11634 Z= 0.311 Chirality : 0.042 0.166 1331 Planarity : 0.004 0.050 1468 Dihedral : 4.857 26.207 1172 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 11.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.18 % Favored : 94.82 % Rotamer: Outliers : 2.66 % Allowed : 17.76 % Favored : 79.58 % 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: -0.46 (0.26), residues: 1061 helix: 1.72 (0.27), residues: 357 sheet: -1.15 (0.32), residues: 249 loop : -1.44 (0.29), residues: 455 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.059 0.002 TRP B 169 HIS 0.008 0.001 HIS B 142 PHE 0.013 0.001 PHE R 405 TYR 0.016 0.001 TYR H 178 ARG 0.004 0.000 ARG H 179 *********************** 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 89 residues out of total 925 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 65 time to evaluate : 0.975 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 320 TYR cc_start: 0.3782 (m-80) cc_final: 0.2136 (t80) REVERT: B 273 ILE cc_start: 0.0894 (OUTLIER) cc_final: 0.0020 (mp) REVERT: B 286 LEU cc_start: 0.6896 (OUTLIER) cc_final: 0.5790 (mp) REVERT: R 125 LEU cc_start: 0.3789 (tp) cc_final: 0.3580 (tt) REVERT: R 138 HIS cc_start: 0.5527 (OUTLIER) cc_final: 0.3423 (m170) REVERT: R 159 LYS cc_start: 0.4417 (mtmt) cc_final: 0.3784 (mptt) REVERT: R 173 TRP cc_start: 0.5488 (m100) cc_final: 0.2386 (t60) outliers start: 24 outliers final: 16 residues processed: 86 average time/residue: 0.1879 time to fit residues: 23.9862 Evaluate side-chains 84 residues out of total 925 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 65 time to evaluate : 0.915 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 199 LEU Chi-restraints excluded: chain A residue 252 ASP Chi-restraints excluded: chain A residue 353 LEU 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 273 ILE 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 49 LEU Chi-restraints excluded: chain R residue 95 ILE Chi-restraints excluded: chain R residue 124 TYR 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 30 optimal weight: 0.0070 chunk 20 optimal weight: 9.9990 chunk 19 optimal weight: 0.6980 chunk 64 optimal weight: 2.9990 chunk 69 optimal weight: 0.3980 chunk 50 optimal weight: 4.9990 chunk 9 optimal weight: 0.6980 chunk 80 optimal weight: 0.9990 chunk 92 optimal weight: 0.5980 chunk 97 optimal weight: 0.9990 chunk 89 optimal weight: 1.9990 overall best weight: 0.4798 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.2422 moved from start: 0.6557 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 8582 Z= 0.161 Angle : 0.611 9.374 11634 Z= 0.316 Chirality : 0.042 0.167 1331 Planarity : 0.004 0.051 1468 Dihedral : 4.840 26.734 1172 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 11.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.56 % Favored : 94.44 % Rotamer: Outliers : 2.77 % Allowed : 17.43 % Favored : 79.80 % 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: -0.40 (0.26), residues: 1061 helix: 1.66 (0.27), residues: 363 sheet: -1.08 (0.32), residues: 251 loop : -1.38 (0.29), residues: 447 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.050 0.002 TRP B 169 HIS 0.009 0.002 HIS B 142 PHE 0.015 0.001 PHE H 108 TYR 0.017 0.001 TYR H 178 ARG 0.008 0.000 ARG A 313 *********************** 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 92 residues out of total 925 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 67 time to evaluate : 0.764 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 320 TYR cc_start: 0.3908 (m-80) cc_final: 0.2226 (t80) REVERT: A 323 MET cc_start: 0.4475 (tpp) cc_final: 0.2815 (mtt) REVERT: B 217 MET cc_start: 0.2406 (ppp) cc_final: 0.1961 (ppp) REVERT: B 273 ILE cc_start: 0.0776 (OUTLIER) cc_final: -0.0127 (mp) REVERT: B 286 LEU cc_start: 0.7027 (OUTLIER) cc_final: 0.5976 (mp) REVERT: R 138 HIS cc_start: 0.5571 (OUTLIER) cc_final: 0.3457 (m170) REVERT: R 159 LYS cc_start: 0.4544 (mtmt) cc_final: 0.3897 (mptt) REVERT: R 173 TRP cc_start: 0.5504 (m100) cc_final: 0.2663 (t60) outliers start: 25 outliers final: 18 residues processed: 88 average time/residue: 0.1809 time to fit residues: 23.2676 Evaluate side-chains 88 residues out of total 925 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 67 time to evaluate : 0.789 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 199 LEU Chi-restraints excluded: chain A residue 252 ASP Chi-restraints excluded: chain A residue 353 LEU 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 273 ILE 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 138 HIS Chi-restraints excluded: chain R residue 154 ILE Chi-restraints excluded: chain R residue 227 MET Chi-restraints excluded: chain R residue 387 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 95 optimal weight: 0.9990 chunk 97 optimal weight: 0.9990 chunk 57 optimal weight: 0.9990 chunk 41 optimal weight: 7.9990 chunk 74 optimal weight: 0.9980 chunk 29 optimal weight: 0.0770 chunk 86 optimal weight: 1.9990 chunk 90 optimal weight: 3.9990 chunk 94 optimal weight: 8.9990 chunk 62 optimal weight: 0.7980 chunk 100 optimal weight: 0.5980 overall best weight: 0.6940 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.2557 moved from start: 0.7052 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 8582 Z= 0.186 Angle : 0.636 8.058 11634 Z= 0.330 Chirality : 0.043 0.170 1331 Planarity : 0.004 0.051 1468 Dihedral : 5.087 31.147 1172 Min Nonbonded Distance : 2.587 Molprobity Statistics. All-atom Clashscore : 13.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.31 % Favored : 93.69 % Rotamer: Outliers : 2.55 % Allowed : 18.31 % 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: -0.54 (0.26), residues: 1061 helix: 1.56 (0.28), residues: 353 sheet: -1.09 (0.32), residues: 258 loop : -1.44 (0.29), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.047 0.002 TRP B 169 HIS 0.008 0.002 HIS B 142 PHE 0.017 0.002 PHE R 405 TYR 0.016 0.002 TYR H 178 ARG 0.009 0.000 ARG A 313 *********************** 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 87 residues out of total 925 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 64 time to evaluate : 0.899 Fit side-chains REVERT: A 53 MET cc_start: -0.0813 (ptp) cc_final: -0.3065 (mmp) REVERT: A 320 TYR cc_start: 0.4173 (m-80) cc_final: 0.2411 (t80) REVERT: A 323 MET cc_start: 0.5042 (tpp) cc_final: 0.2857 (mtt) REVERT: B 217 MET cc_start: 0.2525 (ppp) cc_final: 0.2034 (ppp) REVERT: B 273 ILE cc_start: 0.0990 (OUTLIER) cc_final: 0.0527 (mp) REVERT: R 138 HIS cc_start: 0.5819 (OUTLIER) cc_final: 0.3750 (m170) outliers start: 23 outliers final: 18 residues processed: 84 average time/residue: 0.1748 time to fit residues: 21.9598 Evaluate side-chains 84 residues out of total 925 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 64 time to evaluate : 0.860 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 252 ASP Chi-restraints excluded: chain A residue 353 LEU 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 273 ILE 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 138 HIS Chi-restraints excluded: chain R residue 154 ILE Chi-restraints excluded: chain R residue 227 MET 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 61 optimal weight: 0.8980 chunk 47 optimal weight: 0.8980 chunk 69 optimal weight: 0.8980 chunk 105 optimal weight: 0.8980 chunk 97 optimal weight: 0.8980 chunk 84 optimal weight: 8.9990 chunk 8 optimal weight: 2.9990 chunk 64 optimal weight: 0.5980 chunk 51 optimal weight: 0.3980 chunk 66 optimal weight: 1.9990 chunk 89 optimal weight: 1.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- 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** A 245 HIS ** B 225 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 340 ASN G 59 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.2633 moved from start: 0.7584 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 8582 Z= 0.190 Angle : 0.647 8.139 11634 Z= 0.334 Chirality : 0.044 0.168 1331 Planarity : 0.005 0.072 1468 Dihedral : 5.335 42.114 1172 Min Nonbonded Distance : 2.578 Molprobity Statistics. All-atom Clashscore : 13.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.84 % Favored : 94.16 % Rotamer: Outliers : 2.44 % Allowed : 18.98 % Favored : 78.58 % 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: -0.69 (0.26), residues: 1061 helix: 1.39 (0.27), residues: 361 sheet: -1.25 (0.32), residues: 242 loop : -1.49 (0.28), residues: 458 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.044 0.003 TRP B 169 HIS 0.009 0.002 HIS B 142 PHE 0.024 0.002 PHE G 61 TYR 0.017 0.002 TYR H 178 ARG 0.008 0.001 ARG B 49 ********************** 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 91 residues out of total 925 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 69 time to evaluate : 0.767 Fit side-chains REVERT: A 53 MET cc_start: -0.0982 (ptp) cc_final: -0.3167 (tpp) REVERT: A 320 TYR cc_start: 0.4344 (m-80) cc_final: 0.2500 (t80) REVERT: A 323 MET cc_start: 0.4784 (tpp) cc_final: 0.2895 (mtt) REVERT: B 217 MET cc_start: 0.2558 (ppp) cc_final: 0.2098 (pmm) REVERT: B 273 ILE cc_start: 0.1014 (OUTLIER) cc_final: 0.0566 (mp) REVERT: H 47 TRP cc_start: 0.3702 (t60) cc_final: 0.3309 (t60) REVERT: R 138 HIS cc_start: 0.5905 (OUTLIER) cc_final: 0.3940 (m170) outliers start: 22 outliers final: 18 residues processed: 87 average time/residue: 0.1607 time to fit residues: 21.3424 Evaluate side-chains 86 residues out of total 925 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 66 time to evaluate : 0.891 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 252 ASP Chi-restraints excluded: chain A residue 353 LEU Chi-restraints excluded: chain B residue 33 ILE 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 273 ILE 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 138 HIS Chi-restraints excluded: chain R residue 154 ILE Chi-restraints excluded: chain R residue 212 VAL Chi-restraints excluded: chain R residue 227 MET 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 25 optimal weight: 1.9990 chunk 77 optimal weight: 4.9990 chunk 12 optimal weight: 2.9990 chunk 23 optimal weight: 0.7980 chunk 84 optimal weight: 0.9980 chunk 35 optimal weight: 0.6980 chunk 86 optimal weight: 1.9990 chunk 10 optimal weight: 1.9990 chunk 15 optimal weight: 3.9990 chunk 73 optimal weight: 2.9990 chunk 4 optimal weight: 0.7980 overall best weight: 1.0582 ------------------------------------------------------------------------------- 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** ** B 225 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 59 ASN R 138 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4741 r_free = 0.4741 target = 0.247843 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4535 r_free = 0.4535 target = 0.222322 restraints weight = 11515.304| |-----------------------------------------------------------------------------| r_work (start): 0.4513 rms_B_bonded: 2.26 r_work: 0.4392 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work (final): 0.4392 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.2707 moved from start: 0.8210 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 8582 Z= 0.237 Angle : 0.714 10.926 11634 Z= 0.370 Chirality : 0.045 0.177 1331 Planarity : 0.005 0.051 1468 Dihedral : 5.879 53.092 1172 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 16.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.31 % Favored : 93.69 % Rotamer: Outliers : 2.44 % Allowed : 19.76 % Favored : 77.80 % 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: -0.85 (0.26), residues: 1061 helix: 1.39 (0.27), residues: 352 sheet: -1.36 (0.32), residues: 251 loop : -1.64 (0.28), residues: 458 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.089 0.004 TRP B 169 HIS 0.010 0.002 HIS B 142 PHE 0.020 0.002 PHE B 278 TYR 0.021 0.002 TYR H 161 ARG 0.010 0.001 ARG A 313 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1940.32 seconds wall clock time: 35 minutes 26.26 seconds (2126.26 seconds total)