Starting phenix.real_space_refine on Wed Feb 12 21:40:38 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7w6p_32331/02_2025/7w6p_32331.cif Found real_map, /net/cci-nas-00/data/ceres_data/7w6p_32331/02_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_32331/02_2025/7w6p_32331.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7w6p_32331/02_2025/7w6p_32331.map" model { file = "/net/cci-nas-00/data/ceres_data/7w6p_32331/02_2025/7w6p_32331.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7w6p_32331/02_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-5592/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: 5.49, per 1000 atoms: 0.65 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: 2.36 Conformation dependent library (CDL) restraints added in 1.1 seconds 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: 0.91 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: 2.44 Time building geometry restraints manager: 2.62 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: 2.690 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: 0.390 Check model and map are aligned: 0.070 Set scattering table: 0.090 Process input model: 22.520 Find NCS groups from input model: 0.100 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:2.930 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.830 ------------------------------------------------------------------------------- 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 to be fit. rotamer outliers: 1 poor density : 96 time to evaluate : 0.815 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: 0.2222 time to fit residues: 29.8078 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 : 0.863 ------------------------------------------------------------------------------- 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 = 47)----------------| | r_work = 0.4152 r_free = 0.4152 target = 0.180240 restraints weight = 10787.872| |-----------------------------------------------------------------------------| r_work (start): 0.4157 rms_B_bonded: 3.09 r_work: 0.4045 rms_B_bonded: 3.71 restraints_weight: 0.5000 r_work (final): 0.4045 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1607 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 to be fit. rotamer outliers: 9 poor density : 68 time to evaluate : 0.838 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 62 HIS cc_start: 0.2182 (t-90) cc_final: 0.1229 (t-90) REVERT: H 47 TRP cc_start: 0.4179 (t60) cc_final: 0.3241 (t60) REVERT: H 218 MET cc_start: -0.0524 (ttt) cc_final: -0.0777 (ptm) REVERT: R 173 TRP cc_start: 0.5339 (m100) cc_final: 0.2447 (t60) REVERT: R 437 ASN cc_start: 0.4160 (m-40) cc_final: 0.2979 (m110) outliers start: 9 outliers final: 5 residues processed: 75 average time/residue: 0.2592 time to fit residues: 27.0254 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 : 0.839 ------------------------------------------------------------------------------- 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: 1.9990 chunk 83 optimal weight: 0.6980 chunk 46 optimal weight: 0.8980 chunk 72 optimal weight: 6.9990 chunk 21 optimal weight: 4.9990 chunk 20 optimal weight: 8.9990 chunk 28 optimal weight: 0.0870 chunk 26 optimal weight: 0.7980 chunk 57 optimal weight: 0.0040 overall best weight: 0.4970 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 437 ASN ** 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 = 0.4547 r_free = 0.4547 target = 0.222966 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.4165 r_free = 0.4165 target = 0.181033 restraints weight = 11002.167| |-----------------------------------------------------------------------------| r_work (start): 0.4169 rms_B_bonded: 3.11 r_work: 0.4055 rms_B_bonded: 3.75 restraints_weight: 0.5000 r_work (final): 0.4055 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1677 moved from start: 0.3161 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 8582 Z= 0.176 Angle : 0.574 6.541 11634 Z= 0.304 Chirality : 0.043 0.161 1331 Planarity : 0.004 0.062 1468 Dihedral : 5.062 55.042 1173 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 12.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.00 % Favored : 95.00 % Rotamer: Outliers : 1.55 % Allowed : 12.76 % Favored : 85.68 % 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: 1.69 (0.27), residues: 365 sheet: -1.39 (0.33), residues: 244 loop : -1.41 (0.29), residues: 452 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP B 82 HIS 0.005 0.001 HIS A 189 PHE 0.021 0.002 PHE R 387 TYR 0.020 0.001 TYR H 178 ARG 0.005 0.000 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 79 residues out of total 925 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 65 time to evaluate : 0.824 Fit side-chains revert: symmetry clash REVERT: A 183 THR cc_start: 0.1131 (OUTLIER) cc_final: 0.0919 (m) REVERT: A 342 ILE cc_start: 0.3935 (mt) cc_final: 0.3479 (mt) REVERT: B 45 MET cc_start: 0.1967 (OUTLIER) cc_final: 0.1455 (ttm) REVERT: H 47 TRP cc_start: 0.3835 (t60) cc_final: 0.3019 (t60) REVERT: H 218 MET cc_start: -0.0771 (ttt) cc_final: -0.1163 (ttt) REVERT: R 138 HIS cc_start: 0.5150 (OUTLIER) cc_final: 0.3676 (m170) REVERT: R 173 TRP cc_start: 0.5453 (m100) cc_final: 0.2484 (t60) REVERT: R 437 ASN cc_start: 0.4102 (m-40) cc_final: 0.2852 (m110) outliers start: 14 outliers final: 6 residues processed: 76 average time/residue: 0.1947 time to fit residues: 21.0822 Evaluate side-chains 70 residues out of total 925 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 61 time to evaluate : 0.841 ------------------------------------------------------------------------------- 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 274 THR Chi-restraints excluded: chain H residue 68 PHE Chi-restraints excluded: chain R residue 50 THR 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 28 optimal weight: 0.9990 chunk 34 optimal weight: 2.9990 chunk 82 optimal weight: 2.9990 chunk 22 optimal weight: 0.6980 chunk 2 optimal weight: 3.9990 chunk 31 optimal weight: 5.9990 chunk 55 optimal weight: 2.9990 chunk 63 optimal weight: 0.3980 chunk 91 optimal weight: 0.7980 chunk 89 optimal weight: 0.6980 chunk 56 optimal weight: 0.3980 overall best weight: 0.5980 ------------------------------------------------------------------------------- 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 R 437 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4681 r_free = 0.4681 target = 0.238997 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4390 r_free = 0.4390 target = 0.204905 restraints weight = 10529.111| |-----------------------------------------------------------------------------| r_work (start): 0.4350 rms_B_bonded: 2.51 r_work: 0.4213 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work (final): 0.4213 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.2001 moved from start: 0.4170 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 8582 Z= 0.179 Angle : 0.596 7.987 11634 Z= 0.313 Chirality : 0.043 0.156 1331 Planarity : 0.004 0.060 1468 Dihedral : 5.071 56.020 1173 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 12.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.00 % Favored : 95.00 % Rotamer: Outliers : 2.44 % Allowed : 14.65 % Favored : 82.91 % 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: -0.51 (0.26), residues: 1061 helix: 1.68 (0.27), residues: 358 sheet: -1.16 (0.34), residues: 235 loop : -1.50 (0.28), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP R 428 HIS 0.006 0.001 HIS A 322 PHE 0.025 0.002 PHE R 406 TYR 0.015 0.002 TYR H 60 ARG 0.004 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 88 residues out of total 925 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 66 time to evaluate : 0.911 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 53 MET cc_start: -0.1396 (ptp) cc_final: -0.3304 (mmp) REVERT: A 248 LEU cc_start: 0.4440 (tt) cc_final: 0.3941 (tp) REVERT: B 286 LEU cc_start: 0.6020 (mp) cc_final: 0.5171 (mp) REVERT: H 47 TRP cc_start: 0.3828 (t60) cc_final: 0.2763 (t60) REVERT: R 138 HIS cc_start: 0.5560 (OUTLIER) cc_final: 0.3762 (m170) REVERT: R 173 TRP cc_start: 0.5439 (m100) cc_final: 0.2660 (t60) outliers start: 22 outliers final: 6 residues processed: 85 average time/residue: 0.2166 time to fit residues: 26.1070 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 : 0.821 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 252 ASP Chi-restraints excluded: chain B residue 33 ILE 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 50 THR Chi-restraints excluded: chain R residue 138 HIS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 66 optimal weight: 5.9990 chunk 90 optimal weight: 0.5980 chunk 105 optimal weight: 1.9990 chunk 42 optimal weight: 1.9990 chunk 56 optimal weight: 2.9990 chunk 41 optimal weight: 0.4980 chunk 95 optimal weight: 0.7980 chunk 58 optimal weight: 0.6980 chunk 83 optimal weight: 0.0010 chunk 59 optimal weight: 6.9990 chunk 55 optimal weight: 3.9990 overall best weight: 0.5186 ------------------------------------------------------------------------------- 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 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 = 0.4672 r_free = 0.4672 target = 0.238300 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4403 r_free = 0.4403 target = 0.206059 restraints weight = 10750.785| |-----------------------------------------------------------------------------| r_work (start): 0.4380 rms_B_bonded: 2.37 r_work: 0.4234 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work (final): 0.4234 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.2041 moved from start: 0.4661 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= 0.157 Angle : 0.576 7.401 11634 Z= 0.302 Chirality : 0.042 0.161 1331 Planarity : 0.004 0.060 1468 Dihedral : 4.729 32.811 1172 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 11.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.62 % Favored : 95.38 % Rotamer: Outliers : 3.11 % Allowed : 14.76 % 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: -0.38 (0.26), residues: 1061 helix: 1.78 (0.27), residues: 358 sheet: -1.08 (0.33), residues: 247 loop : -1.42 (0.29), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP B 339 HIS 0.005 0.001 HIS A 322 PHE 0.015 0.001 PHE R 387 TYR 0.016 0.001 TYR H 178 ARG 0.003 0.000 ARG B 68 *********************** 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 95 residues out of total 925 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 67 time to evaluate : 0.878 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 53 MET cc_start: -0.2007 (ptp) cc_final: -0.3287 (mmp) REVERT: A 248 LEU cc_start: 0.4463 (tt) cc_final: 0.3958 (tp) REVERT: B 261 LEU cc_start: 0.4475 (mm) cc_final: 0.3985 (mt) REVERT: H 47 TRP cc_start: 0.3701 (t60) cc_final: 0.2722 (t60) REVERT: R 138 HIS cc_start: 0.5534 (OUTLIER) cc_final: 0.3594 (m170) REVERT: R 173 TRP cc_start: 0.5511 (m100) cc_final: 0.2606 (t60) outliers start: 28 outliers final: 11 residues processed: 92 average time/residue: 0.1930 time to fit residues: 25.8178 Evaluate side-chains 77 residues out of total 925 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 65 time to evaluate : 0.812 ------------------------------------------------------------------------------- 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 183 HIS Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 274 THR 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 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: 0.9990 chunk 67 optimal weight: 2.9990 chunk 92 optimal weight: 0.9980 chunk 82 optimal weight: 4.9990 chunk 64 optimal weight: 0.0020 chunk 81 optimal weight: 0.9980 chunk 9 optimal weight: 1.9990 chunk 28 optimal weight: 0.8980 chunk 94 optimal weight: 0.0970 chunk 8 optimal weight: 0.5980 chunk 76 optimal weight: 0.3980 overall best weight: 0.3986 ------------------------------------------------------------------------------- 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 = 0.4682 r_free = 0.4682 target = 0.239148 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4428 r_free = 0.4428 target = 0.208022 restraints weight = 10500.186| |-----------------------------------------------------------------------------| r_work (start): 0.4408 rms_B_bonded: 2.18 r_work: 0.4273 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.4124 rms_B_bonded: 4.98 restraints_weight: 0.2500 r_work (final): 0.4124 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.2078 moved from start: 0.5025 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 8582 Z= 0.148 Angle : 0.574 9.250 11634 Z= 0.297 Chirality : 0.042 0.155 1331 Planarity : 0.004 0.059 1468 Dihedral : 4.635 30.220 1172 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 11.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.90 % Favored : 95.10 % Rotamer: Outliers : 1.78 % Allowed : 16.32 % Favored : 81.91 % 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: -0.34 (0.26), residues: 1061 helix: 1.72 (0.27), residues: 362 sheet: -0.97 (0.35), residues: 222 loop : -1.39 (0.28), residues: 477 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 82 HIS 0.006 0.001 HIS A 322 PHE 0.015 0.001 PHE R 220 TYR 0.011 0.001 TYR H 178 ARG 0.009 0.000 ARG B 8 *********************** 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 82 residues out of total 925 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 66 time to evaluate : 0.865 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 53 MET cc_start: -0.1877 (ptp) cc_final: -0.3341 (mmt) REVERT: A 248 LEU cc_start: 0.4472 (tt) cc_final: 0.3994 (tp) REVERT: A 313 ARG cc_start: 0.6951 (mmt180) cc_final: 0.6739 (mmt180) REVERT: A 320 TYR cc_start: 0.2366 (m-80) cc_final: 0.1065 (t80) REVERT: B 261 LEU cc_start: 0.4402 (mm) cc_final: 0.3884 (mt) REVERT: B 286 LEU cc_start: 0.6150 (mp) cc_final: 0.5235 (mp) REVERT: H 47 TRP cc_start: 0.3571 (t60) cc_final: 0.2841 (t60) REVERT: R 138 HIS cc_start: 0.5369 (OUTLIER) cc_final: 0.3596 (m170) REVERT: R 173 TRP cc_start: 0.5531 (m100) cc_final: 0.2637 (t60) outliers start: 16 outliers final: 12 residues processed: 80 average time/residue: 0.2016 time to fit residues: 23.2784 Evaluate side-chains 77 residues out of total 925 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 64 time to evaluate : 0.817 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 199 LEU 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 274 THR Chi-restraints excluded: chain B residue 276 VAL 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 1 optimal weight: 0.9990 chunk 14 optimal weight: 4.9990 chunk 24 optimal weight: 1.9990 chunk 52 optimal weight: 0.5980 chunk 25 optimal weight: 1.9990 chunk 22 optimal weight: 3.9990 chunk 27 optimal weight: 1.9990 chunk 36 optimal weight: 0.8980 chunk 72 optimal weight: 0.3980 chunk 28 optimal weight: 0.8980 chunk 63 optimal weight: 0.7980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.4656 r_free = 0.4656 target = 0.237200 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4386 r_free = 0.4386 target = 0.204529 restraints weight = 11240.190| |-----------------------------------------------------------------------------| r_work (start): 0.4355 rms_B_bonded: 2.59 r_work: 0.4228 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.4228 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.2225 moved from start: 0.5870 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 8582 Z= 0.194 Angle : 0.637 9.062 11634 Z= 0.333 Chirality : 0.043 0.164 1331 Planarity : 0.004 0.060 1468 Dihedral : 5.017 33.964 1172 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 13.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.18 % Favored : 94.82 % Rotamer: Outliers : 2.55 % Allowed : 17.09 % Favored : 80.36 % 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: -0.49 (0.26), residues: 1061 helix: 1.60 (0.27), residues: 359 sheet: -1.08 (0.33), residues: 249 loop : -1.44 (0.29), residues: 453 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP B 82 HIS 0.008 0.002 HIS H 220 PHE 0.021 0.002 PHE R 405 TYR 0.016 0.002 TYR H 178 ARG 0.007 0.001 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 91 residues out of total 925 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 68 time to evaluate : 0.807 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 53 MET cc_start: -0.2642 (ptp) cc_final: -0.3863 (tpt) REVERT: A 320 TYR cc_start: 0.3373 (m-80) cc_final: 0.1438 (t80) REVERT: A 323 MET cc_start: 0.5332 (tpp) cc_final: 0.2816 (mtp) REVERT: B 286 LEU cc_start: 0.6564 (mp) cc_final: 0.5733 (mp) REVERT: G 32 LYS cc_start: 0.5479 (ptpt) cc_final: 0.5226 (mmtt) REVERT: R 102 ILE cc_start: 0.5632 (mt) cc_final: 0.5419 (mt) REVERT: R 125 LEU cc_start: 0.3074 (tp) cc_final: 0.2854 (tt) REVERT: R 138 HIS cc_start: 0.5548 (OUTLIER) cc_final: 0.3677 (m170) REVERT: R 159 LYS cc_start: 0.4341 (mtmt) cc_final: 0.3456 (mptt) REVERT: R 173 TRP cc_start: 0.5743 (m100) cc_final: 0.2444 (t60) outliers start: 23 outliers final: 19 residues processed: 88 average time/residue: 0.2050 time to fit residues: 25.7694 Evaluate side-chains 85 residues out of total 925 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 65 time to evaluate : 0.853 ------------------------------------------------------------------------------- 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 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 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 443 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 9 optimal weight: 7.9990 chunk 52 optimal weight: 1.9990 chunk 55 optimal weight: 0.9990 chunk 61 optimal weight: 2.9990 chunk 31 optimal weight: 5.9990 chunk 50 optimal weight: 3.9990 chunk 53 optimal weight: 7.9990 chunk 73 optimal weight: 1.9990 chunk 96 optimal weight: 0.7980 chunk 7 optimal weight: 0.9990 chunk 40 optimal weight: 6.9990 overall best weight: 1.3588 ------------------------------------------------------------------------------- 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** B 311 HIS B 340 ASN G 59 ASN H 35 HIS R 138 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4719 r_free = 0.4719 target = 0.245248 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4499 r_free = 0.4499 target = 0.218105 restraints weight = 11495.769| |-----------------------------------------------------------------------------| r_work (start): 0.4480 rms_B_bonded: 2.40 r_work: 0.4373 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work (final): 0.4373 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.2715 moved from start: 0.7534 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 8582 Z= 0.299 Angle : 0.807 13.764 11634 Z= 0.421 Chirality : 0.049 0.200 1331 Planarity : 0.005 0.059 1468 Dihedral : 6.296 41.522 1172 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 20.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.88 % Favored : 93.12 % Rotamer: Outliers : 3.00 % Allowed : 17.20 % Favored : 79.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.08 (0.26), residues: 1061 helix: 0.91 (0.27), residues: 366 sheet: -1.48 (0.33), residues: 235 loop : -1.60 (0.29), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.047 0.004 TRP B 82 HIS 0.008 0.002 HIS A 214 PHE 0.025 0.003 PHE R 220 TYR 0.030 0.003 TYR G 40 ARG 0.008 0.001 ARG H 179 *********************** 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 99 residues out of total 925 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 72 time to evaluate : 0.859 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 8 GLU cc_start: 0.4515 (tt0) cc_final: 0.4241 (tt0) REVERT: A 53 MET cc_start: -0.1544 (ptp) cc_final: -0.3591 (tpt) REVERT: R 138 HIS cc_start: 0.5981 (OUTLIER) cc_final: 0.3880 (m170) outliers start: 27 outliers final: 22 residues processed: 94 average time/residue: 0.1789 time to fit residues: 24.8288 Evaluate side-chains 86 residues out of total 925 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 63 time to evaluate : 0.819 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 199 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 62 HIS Chi-restraints excluded: chain B residue 100 VAL 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 184 THR Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain H residue 68 PHE 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 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 105 optimal weight: 4.9990 chunk 14 optimal weight: 1.9990 chunk 69 optimal weight: 1.9990 chunk 8 optimal weight: 0.4980 chunk 4 optimal weight: 0.9980 chunk 36 optimal weight: 0.0870 chunk 3 optimal weight: 0.9980 chunk 33 optimal weight: 9.9990 chunk 81 optimal weight: 0.8980 chunk 50 optimal weight: 1.9990 chunk 100 optimal weight: 6.9990 overall best weight: 0.6958 ------------------------------------------------------------------------------- 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 138 HIS R 437 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4718 r_free = 0.4718 target = 0.244582 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4494 r_free = 0.4494 target = 0.216342 restraints weight = 11300.015| |-----------------------------------------------------------------------------| r_work (start): 0.4479 rms_B_bonded: 2.40 r_work: 0.4367 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work (final): 0.4367 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.2567 moved from start: 0.7637 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 8582 Z= 0.207 Angle : 0.694 8.735 11634 Z= 0.359 Chirality : 0.044 0.172 1331 Planarity : 0.005 0.097 1468 Dihedral : 5.800 44.881 1172 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 15.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.03 % Favored : 93.97 % Rotamer: Outliers : 2.55 % Allowed : 18.20 % Favored : 79.25 % 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: -0.89 (0.26), residues: 1061 helix: 1.30 (0.27), residues: 356 sheet: -1.45 (0.34), residues: 225 loop : -1.61 (0.27), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP B 82 HIS 0.012 0.002 HIS R 138 PHE 0.017 0.002 PHE R 220 TYR 0.021 0.002 TYR H 178 ARG 0.010 0.001 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 91 residues out of total 925 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 68 time to evaluate : 0.939 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 53 MET cc_start: -0.1666 (ptp) cc_final: -0.3644 (tpt) REVERT: A 320 TYR cc_start: 0.4283 (m-80) cc_final: 0.2366 (t80) REVERT: A 323 MET cc_start: 0.5060 (tpp) cc_final: 0.2798 (mtt) REVERT: H 180 MET cc_start: 0.1094 (ptt) cc_final: -0.0560 (mtm) REVERT: R 49 LEU cc_start: 0.6813 (OUTLIER) cc_final: 0.6593 (mm) REVERT: R 138 HIS cc_start: 0.5767 (OUTLIER) cc_final: 0.3716 (m170) outliers start: 23 outliers final: 19 residues processed: 85 average time/residue: 0.1947 time to fit residues: 24.3661 Evaluate side-chains 86 residues out of total 925 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 65 time to evaluate : 0.834 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 199 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 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 H residue 68 PHE Chi-restraints excluded: chain H residue 91 THR Chi-restraints excluded: chain H residue 160 THR Chi-restraints excluded: chain R residue 49 LEU Chi-restraints excluded: chain R residue 87 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 139 LEU 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 8 optimal weight: 0.6980 chunk 92 optimal weight: 2.9990 chunk 31 optimal weight: 0.0770 chunk 55 optimal weight: 0.9990 chunk 34 optimal weight: 0.0670 chunk 84 optimal weight: 5.9990 chunk 6 optimal weight: 0.9990 chunk 47 optimal weight: 3.9990 chunk 24 optimal weight: 1.9990 chunk 64 optimal weight: 3.9990 chunk 91 optimal weight: 0.9980 overall best weight: 0.5678 ------------------------------------------------------------------------------- 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 138 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4715 r_free = 0.4715 target = 0.244276 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4492 r_free = 0.4492 target = 0.215812 restraints weight = 11199.462| |-----------------------------------------------------------------------------| r_work (start): 0.4471 rms_B_bonded: 2.41 r_work: 0.4347 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work (final): 0.4347 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.2547 moved from start: 0.7773 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 8582 Z= 0.187 Angle : 0.666 10.905 11634 Z= 0.341 Chirality : 0.043 0.168 1331 Planarity : 0.004 0.077 1468 Dihedral : 5.565 49.128 1172 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 14.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.31 % Favored : 93.69 % Rotamer: Outliers : 2.33 % Allowed : 19.09 % 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: -0.81 (0.26), residues: 1061 helix: 1.33 (0.27), residues: 362 sheet: -1.38 (0.33), residues: 230 loop : -1.58 (0.28), residues: 469 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP B 82 HIS 0.012 0.002 HIS R 138 PHE 0.014 0.002 PHE R 220 TYR 0.016 0.002 TYR H 178 ARG 0.009 0.000 ARG A 313 ********************** 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 85 residues out of total 925 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 64 time to evaluate : 0.827 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 53 MET cc_start: -0.1703 (ptp) cc_final: -0.3651 (tpt) REVERT: A 320 TYR cc_start: 0.4299 (m-80) cc_final: 0.2314 (t80) REVERT: A 323 MET cc_start: 0.4904 (tpp) cc_final: 0.3001 (mtt) REVERT: B 19 ARG cc_start: 0.6754 (mpt-90) cc_final: 0.6528 (mpt180) REVERT: B 286 LEU cc_start: 0.7042 (OUTLIER) cc_final: 0.6596 (mt) REVERT: G 32 LYS cc_start: 0.6100 (ptpt) cc_final: 0.5712 (mmtt) REVERT: R 49 LEU cc_start: 0.6717 (OUTLIER) cc_final: 0.6515 (mm) REVERT: R 138 HIS cc_start: 0.5647 (OUTLIER) cc_final: 0.3375 (m170) outliers start: 21 outliers final: 17 residues processed: 81 average time/residue: 0.1766 time to fit residues: 21.2916 Evaluate side-chains 84 residues out of total 925 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 64 time to evaluate : 0.860 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 199 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 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 91 THR Chi-restraints excluded: chain H residue 160 THR Chi-restraints excluded: chain R residue 49 LEU Chi-restraints excluded: chain R residue 87 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 139 LEU 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: 6.9990 chunk 93 optimal weight: 0.6980 chunk 10 optimal weight: 1.9990 chunk 18 optimal weight: 0.3980 chunk 83 optimal weight: 0.9990 chunk 55 optimal weight: 0.9990 chunk 26 optimal weight: 0.7980 chunk 34 optimal weight: 3.9990 chunk 94 optimal weight: 5.9990 chunk 31 optimal weight: 0.0770 chunk 2 optimal weight: 0.9980 overall best weight: 0.5938 ------------------------------------------------------------------------------- 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 138 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4727 r_free = 0.4727 target = 0.245338 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4513 r_free = 0.4513 target = 0.218205 restraints weight = 11236.252| |-----------------------------------------------------------------------------| r_work (start): 0.4486 rms_B_bonded: 2.23 r_work: 0.4360 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work (final): 0.4360 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.2559 moved from start: 0.7932 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 8582 Z= 0.183 Angle : 0.650 10.861 11634 Z= 0.333 Chirality : 0.043 0.165 1331 Planarity : 0.004 0.062 1468 Dihedral : 5.538 51.500 1172 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 14.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.22 % Favored : 93.78 % Rotamer: Outliers : 2.55 % Allowed : 19.09 % Favored : 78.36 % 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: -0.82 (0.26), residues: 1061 helix: 1.38 (0.27), residues: 362 sheet: -1.39 (0.33), residues: 230 loop : -1.63 (0.28), residues: 469 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP B 82 HIS 0.009 0.002 HIS R 138 PHE 0.024 0.002 PHE B 278 TYR 0.016 0.002 TYR H 178 ARG 0.008 0.000 ARG A 313 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3939.67 seconds wall clock time: 71 minutes 5.54 seconds (4265.54 seconds total)