Starting phenix.real_space_refine on Wed Sep 17 11:24:00 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7w6p_32331/09_2025/7w6p_32331.cif Found real_map, /net/cci-nas-00/data/ceres_data/7w6p_32331/09_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_32331/09_2025/7w6p_32331.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7w6p_32331/09_2025/7w6p_32331.map" model { file = "/net/cci-nas-00/data/ceres_data/7w6p_32331/09_2025/7w6p_32331.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7w6p_32331/09_2025/7w6p_32331.cif" } resolution = 3.47 write_initial_geo_file = False refinement { macro_cycles = 10 } 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/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: {'GLU:plan': 2, 'PHE:plan': 2, 'ARG:plan': 3, 'ASP:plan': 1, 'TRP: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: 2.17, per 1000 atoms: 0.26 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: 0.72 Conformation dependent library (CDL) restraints added in 420.4 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 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: 0.33 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: 1.34 Time building geometry restraints manager: 0.96 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: 2.150 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: 0.150 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 9.500 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.020 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:1.290 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.210 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1027 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.074 8584 Z= 0.197 Angle : 0.687 9.083 11638 Z= 0.392 Chirality : 0.044 0.225 1331 Planarity : 0.004 0.056 1468 Dihedral : 13.682 80.650 3026 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 14.53 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. 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 ARG 0.012 0.000 ARG H 148 TYR 0.028 0.002 TYR R 409 PHE 0.028 0.002 PHE B 234 TRP 0.028 0.001 TRP B 169 HIS 0.007 0.001 HIS A 189 Details of bonding type rmsd covalent geometry : bond 0.00414 ( 8582) covalent geometry : angle 0.68657 (11634) SS BOND : bond 0.00324 ( 2) SS BOND : angle 0.49980 ( 4) hydrogen bonds : bond 0.15547 ( 380) hydrogen bonds : angle 6.62969 ( 1095) *********************** 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 : 0.309 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: 0.1015 time to fit residues: 13.6807 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 : 0.303 ------------------------------------------------------------------------------- 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 49 optimal weight: 0.0370 chunk 97 optimal weight: 0.9980 chunk 53 optimal weight: 9.9990 chunk 5 optimal weight: 0.3980 chunk 33 optimal weight: 2.9990 chunk 65 optimal weight: 5.9990 chunk 62 optimal weight: 0.3980 chunk 51 optimal weight: 0.0870 chunk 100 optimal weight: 0.5980 chunk 38 optimal weight: 1.9990 chunk 61 optimal weight: 0.8980 overall best weight: 0.3036 ------------------------------------------------------------------------------- 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** H 159 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 = 0.4546 r_free = 0.4546 target = 0.223730 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4194 r_free = 0.4194 target = 0.182107 restraints weight = 10741.838| |-----------------------------------------------------------------------------| r_work (start): 0.4169 rms_B_bonded: 3.34 r_work: 0.4032 rms_B_bonded: 3.80 restraints_weight: 0.5000 r_work (final): 0.4032 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1233 moved from start: 0.1916 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 8584 Z= 0.125 Angle : 0.605 8.295 11638 Z= 0.315 Chirality : 0.043 0.151 1331 Planarity : 0.004 0.060 1468 Dihedral : 5.065 46.065 1173 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 11.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.43 % Favored : 95.57 % Rotamer: Outliers : 0.55 % Allowed : 8.55 % Favored : 90.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.50 (0.26), residues: 1061 helix: 1.73 (0.27), residues: 366 sheet: -1.45 (0.32), residues: 250 loop : -1.39 (0.29), residues: 445 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG H 72 TYR 0.017 0.002 TYR R 409 PHE 0.024 0.002 PHE R 387 TRP 0.031 0.002 TRP B 339 HIS 0.006 0.001 HIS A 189 Details of bonding type rmsd covalent geometry : bond 0.00258 ( 8582) covalent geometry : angle 0.60379 (11634) SS BOND : bond 0.01272 ( 2) SS BOND : angle 1.79144 ( 4) hydrogen bonds : bond 0.04119 ( 380) hydrogen bonds : angle 4.93451 ( 1095) *********************** 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 73 residues out of total 925 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 68 time to evaluate : 0.306 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 62 HIS cc_start: 0.1677 (t-90) cc_final: 0.1147 (t-90) REVERT: H 47 TRP cc_start: 0.3926 (t60) cc_final: 0.3018 (t60) REVERT: R 437 ASN cc_start: 0.2647 (m110) cc_final: 0.2445 (m-40) outliers start: 5 outliers final: 2 residues processed: 71 average time/residue: 0.0987 time to fit residues: 9.9794 Evaluate side-chains 64 residues out of total 925 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 62 time to evaluate : 0.396 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 252 ASP Chi-restraints excluded: chain B residue 274 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 19 optimal weight: 2.9990 chunk 68 optimal weight: 0.0050 chunk 72 optimal weight: 3.9990 chunk 46 optimal weight: 0.8980 chunk 102 optimal weight: 2.9990 chunk 30 optimal weight: 0.3980 chunk 3 optimal weight: 0.5980 chunk 10 optimal weight: 4.9990 chunk 71 optimal weight: 0.8980 chunk 13 optimal weight: 2.9990 chunk 84 optimal weight: 2.9990 overall best weight: 0.5594 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4618 r_free = 0.4618 target = 0.233184 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4296 r_free = 0.4296 target = 0.194944 restraints weight = 10795.738| |-----------------------------------------------------------------------------| r_work (start): 0.4245 rms_B_bonded: 2.72 r_work: 0.4115 rms_B_bonded: 3.32 restraints_weight: 0.5000 r_work (final): 0.4115 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1648 moved from start: 0.2982 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 8584 Z= 0.127 Angle : 0.594 7.289 11638 Z= 0.313 Chirality : 0.043 0.160 1331 Planarity : 0.004 0.061 1468 Dihedral : 5.006 48.869 1173 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 12.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.18 % Favored : 94.82 % Rotamer: Outliers : 1.44 % Allowed : 12.43 % Favored : 86.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.45 (0.26), residues: 1061 helix: 1.70 (0.27), residues: 363 sheet: -1.23 (0.34), residues: 226 loop : -1.41 (0.28), residues: 472 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 68 TYR 0.017 0.002 TYR R 409 PHE 0.018 0.002 PHE R 387 TRP 0.031 0.002 TRP B 339 HIS 0.006 0.001 HIS A 322 Details of bonding type rmsd covalent geometry : bond 0.00272 ( 8582) covalent geometry : angle 0.59371 (11634) SS BOND : bond 0.00533 ( 2) SS BOND : angle 1.20761 ( 4) hydrogen bonds : bond 0.03744 ( 380) hydrogen bonds : angle 4.90317 ( 1095) *********************** 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 to be fit. rotamer outliers: 13 poor density : 68 time to evaluate : 0.326 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 183 THR cc_start: 0.1190 (OUTLIER) cc_final: 0.0978 (m) REVERT: B 19 ARG cc_start: 0.4991 (tpt170) cc_final: 0.4729 (mpt-90) REVERT: B 285 LEU cc_start: 0.0676 (OUTLIER) cc_final: -0.0103 (tt) REVERT: H 47 TRP cc_start: 0.4307 (t60) cc_final: 0.3234 (t60) REVERT: R 138 HIS cc_start: 0.5070 (OUTLIER) cc_final: 0.3649 (m170) REVERT: R 173 TRP cc_start: 0.5367 (m100) cc_final: 0.2437 (t60) REVERT: R 437 ASN cc_start: 0.3501 (m110) cc_final: 0.2592 (m110) outliers start: 13 outliers final: 7 residues processed: 80 average time/residue: 0.0997 time to fit residues: 11.1888 Evaluate side-chains 74 residues out of total 925 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 64 time to evaluate : 0.364 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 183 THR Chi-restraints excluded: chain A residue 252 ASP Chi-restraints excluded: chain A residue 348 LEU Chi-restraints excluded: chain B residue 33 ILE Chi-restraints excluded: chain B residue 183 HIS Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 285 LEU Chi-restraints excluded: chain R residue 50 THR Chi-restraints excluded: chain R residue 135 SER 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 105 optimal weight: 4.9990 chunk 38 optimal weight: 0.8980 chunk 48 optimal weight: 2.9990 chunk 39 optimal weight: 0.9980 chunk 19 optimal weight: 0.5980 chunk 14 optimal weight: 0.0170 chunk 71 optimal weight: 0.5980 chunk 99 optimal weight: 1.9990 chunk 89 optimal weight: 3.9990 chunk 97 optimal weight: 2.9990 chunk 80 optimal weight: 2.9990 overall best weight: 0.6218 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 331 ASN B 62 HIS B 340 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4683 r_free = 0.4683 target = 0.239417 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4382 r_free = 0.4382 target = 0.203962 restraints weight = 10634.138| |-----------------------------------------------------------------------------| r_work (start): 0.4344 rms_B_bonded: 2.59 r_work: 0.4193 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.4193 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1943 moved from start: 0.4002 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 8584 Z= 0.127 Angle : 0.586 6.906 11638 Z= 0.308 Chirality : 0.043 0.178 1331 Planarity : 0.004 0.061 1468 Dihedral : 4.959 51.083 1173 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 12.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.81 % Favored : 95.19 % Rotamer: Outliers : 2.00 % Allowed : 14.98 % Favored : 83.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.43 (0.26), residues: 1061 helix: 1.71 (0.27), residues: 361 sheet: -1.09 (0.34), residues: 227 loop : -1.46 (0.28), residues: 473 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 8 TYR 0.014 0.001 TYR H 60 PHE 0.016 0.001 PHE R 220 TRP 0.016 0.002 TRP B 63 HIS 0.007 0.001 HIS B 62 Details of bonding type rmsd covalent geometry : bond 0.00269 ( 8582) covalent geometry : angle 0.58648 (11634) SS BOND : bond 0.00513 ( 2) SS BOND : angle 0.49674 ( 4) hydrogen bonds : bond 0.03652 ( 380) hydrogen bonds : angle 4.82637 ( 1095) *********************** 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 81 residues out of total 925 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 63 time to evaluate : 0.324 Fit side-chains revert: symmetry clash REVERT: A 183 THR cc_start: 0.1288 (OUTLIER) cc_final: 0.1074 (m) REVERT: A 248 LEU cc_start: 0.4403 (tt) cc_final: 0.3924 (tp) REVERT: A 342 ILE cc_start: 0.4616 (mt) cc_final: 0.4062 (mt) REVERT: B 45 MET cc_start: 0.2840 (mtp) cc_final: 0.2119 (ttm) REVERT: H 47 TRP cc_start: 0.4011 (t60) cc_final: 0.3054 (t60) REVERT: H 218 MET cc_start: -0.0421 (ttt) cc_final: -0.0907 (ttp) REVERT: R 138 HIS cc_start: 0.5451 (OUTLIER) cc_final: 0.3973 (m170) REVERT: R 173 TRP cc_start: 0.5437 (m100) cc_final: 0.2652 (t60) outliers start: 18 outliers final: 8 residues processed: 79 average time/residue: 0.0886 time to fit residues: 10.2823 Evaluate side-chains 70 residues out of total 925 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 60 time to evaluate : 0.298 ------------------------------------------------------------------------------- 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 61 MET Chi-restraints excluded: chain B residue 274 THR 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 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 2 optimal weight: 3.9990 chunk 33 optimal weight: 4.9990 chunk 38 optimal weight: 3.9990 chunk 22 optimal weight: 0.5980 chunk 67 optimal weight: 7.9990 chunk 104 optimal weight: 0.1980 chunk 76 optimal weight: 0.9990 chunk 101 optimal weight: 2.9990 chunk 58 optimal weight: 0.0370 chunk 68 optimal weight: 0.3980 chunk 46 optimal weight: 10.0000 overall best weight: 0.4460 ------------------------------------------------------------------------------- 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** R 437 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4679 r_free = 0.4679 target = 0.238636 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4396 r_free = 0.4396 target = 0.205125 restraints weight = 10659.854| |-----------------------------------------------------------------------------| r_work (start): 0.4378 rms_B_bonded: 2.46 r_work: 0.4232 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work (final): 0.4232 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1950 moved from start: 0.4380 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 8584 Z= 0.111 Angle : 0.559 7.501 11638 Z= 0.292 Chirality : 0.041 0.157 1331 Planarity : 0.004 0.062 1468 Dihedral : 4.905 50.578 1173 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 11.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.90 % Favored : 95.10 % Rotamer: Outliers : 3.11 % Allowed : 14.32 % Favored : 82.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.29 (0.26), residues: 1061 helix: 1.79 (0.27), residues: 361 sheet: -0.99 (0.34), residues: 233 loop : -1.36 (0.28), residues: 467 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 314 TYR 0.014 0.001 TYR H 178 PHE 0.018 0.001 PHE B 234 TRP 0.011 0.001 TRP B 82 HIS 0.006 0.001 HIS A 322 Details of bonding type rmsd covalent geometry : bond 0.00233 ( 8582) covalent geometry : angle 0.55906 (11634) SS BOND : bond 0.00362 ( 2) SS BOND : angle 0.54497 ( 4) hydrogen bonds : bond 0.03504 ( 380) hydrogen bonds : angle 4.71971 ( 1095) *********************** 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 94 residues out of total 925 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 66 time to evaluate : 0.330 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 183 THR cc_start: 0.1513 (OUTLIER) cc_final: 0.1236 (m) REVERT: A 248 LEU cc_start: 0.4409 (tt) cc_final: 0.3914 (tp) REVERT: A 342 ILE cc_start: 0.4539 (mt) cc_final: 0.4088 (mt) REVERT: B 19 ARG cc_start: 0.4928 (tpt170) cc_final: 0.4591 (mpt-90) REVERT: B 261 LEU cc_start: 0.4838 (mm) cc_final: 0.4402 (mt) REVERT: B 285 LEU cc_start: 0.0840 (OUTLIER) cc_final: 0.0613 (tp) REVERT: H 47 TRP cc_start: 0.3688 (t60) cc_final: 0.2711 (t60) REVERT: H 154 LEU cc_start: 0.6019 (tt) cc_final: 0.5443 (tp) REVERT: H 218 MET cc_start: -0.0290 (ttp) cc_final: -0.1642 (ttp) REVERT: R 138 HIS cc_start: 0.5351 (OUTLIER) cc_final: 0.3786 (m170) REVERT: R 173 TRP cc_start: 0.5489 (m100) cc_final: 0.2424 (t60) outliers start: 28 outliers final: 11 residues processed: 90 average time/residue: 0.0889 time to fit residues: 11.5434 Evaluate side-chains 77 residues out of total 925 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 63 time to evaluate : 0.319 ------------------------------------------------------------------------------- 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 112 VAL Chi-restraints excluded: chain B residue 153 ASP Chi-restraints excluded: chain B residue 183 HIS Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 285 LEU Chi-restraints excluded: chain H residue 68 PHE Chi-restraints excluded: chain H residue 91 THR Chi-restraints excluded: chain H residue 223 TYR Chi-restraints excluded: chain R residue 95 ILE Chi-restraints excluded: chain R residue 135 SER Chi-restraints excluded: chain R residue 138 HIS Chi-restraints excluded: chain R residue 139 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 21 optimal weight: 0.0770 chunk 103 optimal weight: 0.9980 chunk 49 optimal weight: 1.9990 chunk 82 optimal weight: 0.8980 chunk 80 optimal weight: 4.9990 chunk 72 optimal weight: 3.9990 chunk 99 optimal weight: 2.9990 chunk 8 optimal weight: 0.9990 chunk 46 optimal weight: 1.9990 chunk 16 optimal weight: 3.9990 chunk 31 optimal weight: 2.9990 overall best weight: 0.9942 ------------------------------------------------------------------------------- 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** ** H 219 GLN ** 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 = 0.4663 r_free = 0.4663 target = 0.238610 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4395 r_free = 0.4395 target = 0.206336 restraints weight = 11382.633| |-----------------------------------------------------------------------------| r_work (start): 0.4360 rms_B_bonded: 2.63 r_work: 0.4238 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.4238 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.2311 moved from start: 0.5677 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 8584 Z= 0.168 Angle : 0.691 9.371 11638 Z= 0.363 Chirality : 0.045 0.185 1331 Planarity : 0.005 0.059 1468 Dihedral : 5.351 33.787 1172 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 15.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.03 % Favored : 93.97 % Rotamer: Outliers : 2.55 % Allowed : 16.54 % Favored : 80.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.62 (0.26), residues: 1061 helix: 1.54 (0.27), residues: 359 sheet: -1.30 (0.33), residues: 231 loop : -1.48 (0.28), residues: 471 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 68 TYR 0.022 0.002 TYR H 60 PHE 0.019 0.002 PHE G 61 TRP 0.024 0.003 TRP B 82 HIS 0.011 0.002 HIS H 220 Details of bonding type rmsd covalent geometry : bond 0.00370 ( 8582) covalent geometry : angle 0.69130 (11634) SS BOND : bond 0.00702 ( 2) SS BOND : angle 0.63617 ( 4) hydrogen bonds : bond 0.04318 ( 380) hydrogen bonds : angle 5.33118 ( 1095) *********************** 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 to be fit. rotamer outliers: 23 poor density : 68 time to evaluate : 0.331 Fit side-chains revert: symmetry clash REVERT: A 53 MET cc_start: 0.0171 (ptm) cc_final: -0.2070 (tpt) REVERT: A 183 THR cc_start: 0.2002 (OUTLIER) cc_final: 0.1774 (m) REVERT: A 313 ARG cc_start: 0.7302 (mmt180) cc_final: 0.6950 (mmt180) REVERT: A 320 TYR cc_start: 0.3345 (m-80) cc_final: 0.1396 (t80) REVERT: B 183 HIS cc_start: 0.2002 (OUTLIER) cc_final: 0.0703 (t70) REVERT: H 47 TRP cc_start: 0.4072 (t60) cc_final: 0.3120 (t60) REVERT: H 218 MET cc_start: 0.0197 (ttp) cc_final: -0.1417 (ttp) REVERT: R 102 ILE cc_start: 0.5740 (mt) cc_final: 0.5514 (mt) REVERT: R 138 HIS cc_start: 0.5742 (OUTLIER) cc_final: 0.4181 (m170) REVERT: R 159 LYS cc_start: 0.4459 (mtmt) cc_final: 0.3684 (mptt) REVERT: R 173 TRP cc_start: 0.5713 (m100) cc_final: 0.2608 (t60) outliers start: 23 outliers final: 11 residues processed: 87 average time/residue: 0.0909 time to fit residues: 11.4733 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 : 0.311 ------------------------------------------------------------------------------- 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 183 HIS 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 135 SER 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 89 optimal weight: 1.9990 chunk 44 optimal weight: 5.9990 chunk 20 optimal weight: 10.0000 chunk 37 optimal weight: 4.9990 chunk 104 optimal weight: 0.9990 chunk 43 optimal weight: 0.4980 chunk 75 optimal weight: 0.5980 chunk 55 optimal weight: 0.9990 chunk 73 optimal weight: 0.7980 chunk 62 optimal weight: 1.9990 chunk 87 optimal weight: 0.5980 overall best weight: 0.6982 ------------------------------------------------------------------------------- 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** B 311 HIS ** H 39 GLN ** 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 = 0.4665 r_free = 0.4665 target = 0.238834 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4364 r_free = 0.4364 target = 0.203847 restraints weight = 11316.435| |-----------------------------------------------------------------------------| r_work (start): 0.4361 rms_B_bonded: 3.18 r_work: 0.4232 rms_B_bonded: 3.75 restraints_weight: 0.5000 r_work (final): 0.4232 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.2218 moved from start: 0.6049 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 8584 Z= 0.128 Angle : 0.631 17.582 11638 Z= 0.321 Chirality : 0.043 0.175 1331 Planarity : 0.004 0.061 1468 Dihedral : 5.060 28.088 1172 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 12.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.09 % Favored : 94.91 % Rotamer: Outliers : 2.77 % Allowed : 18.65 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.54 (0.26), residues: 1061 helix: 1.57 (0.27), residues: 361 sheet: -1.16 (0.34), residues: 241 loop : -1.47 (0.29), residues: 459 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG H 179 TYR 0.021 0.002 TYR H 223 PHE 0.015 0.002 PHE R 405 TRP 0.021 0.002 TRP B 82 HIS 0.006 0.002 HIS A 322 Details of bonding type rmsd covalent geometry : bond 0.00274 ( 8582) covalent geometry : angle 0.63117 (11634) SS BOND : bond 0.00490 ( 2) SS BOND : angle 0.70149 ( 4) hydrogen bonds : bond 0.03756 ( 380) hydrogen bonds : angle 5.05305 ( 1095) *********************** 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 95 residues out of total 925 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 70 time to evaluate : 0.309 Fit side-chains revert: symmetry clash REVERT: A 53 MET cc_start: 0.0399 (ptm) cc_final: -0.2009 (tpp) REVERT: A 183 THR cc_start: 0.2078 (OUTLIER) cc_final: 0.1771 (m) REVERT: A 248 LEU cc_start: 0.4997 (tt) cc_final: 0.4719 (tp) REVERT: A 313 ARG cc_start: 0.7396 (mmt180) cc_final: 0.7187 (mmt180) REVERT: A 320 TYR cc_start: 0.3236 (m-80) cc_final: 0.1479 (t80) REVERT: H 47 TRP cc_start: 0.3818 (t60) cc_final: 0.2852 (t60) REVERT: H 154 LEU cc_start: 0.6548 (tt) cc_final: 0.6227 (tp) REVERT: R 102 ILE cc_start: 0.5768 (mt) cc_final: 0.5555 (mt) REVERT: R 125 LEU cc_start: 0.3522 (tp) cc_final: 0.3302 (tt) REVERT: R 138 HIS cc_start: 0.5488 (OUTLIER) cc_final: 0.4041 (m170) REVERT: R 159 LYS cc_start: 0.4400 (mtmt) cc_final: 0.3468 (mptt) REVERT: R 173 TRP cc_start: 0.5731 (m100) cc_final: 0.2462 (t60) outliers start: 25 outliers final: 18 residues processed: 92 average time/residue: 0.0871 time to fit residues: 11.6751 Evaluate side-chains 87 residues out of total 925 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 67 time to evaluate : 0.304 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 183 THR Chi-restraints excluded: chain A residue 222 ILE 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 183 HIS Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain B residue 285 LEU Chi-restraints excluded: chain H residue 68 PHE Chi-restraints excluded: chain H residue 91 THR Chi-restraints excluded: chain H residue 198 THR Chi-restraints excluded: chain R residue 95 ILE Chi-restraints excluded: chain R residue 135 SER 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 387 PHE 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 49 optimal weight: 2.9990 chunk 3 optimal weight: 1.9990 chunk 45 optimal weight: 3.9990 chunk 37 optimal weight: 1.9990 chunk 97 optimal weight: 0.8980 chunk 15 optimal weight: 0.8980 chunk 41 optimal weight: 3.9990 chunk 14 optimal weight: 4.9990 chunk 53 optimal weight: 0.8980 chunk 11 optimal weight: 0.9990 chunk 84 optimal weight: 9.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- 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 62 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 225 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 340 ASN G 59 ASN H 219 GLN R 138 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4686 r_free = 0.4686 target = 0.241257 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4397 r_free = 0.4397 target = 0.208476 restraints weight = 11329.751| |-----------------------------------------------------------------------------| r_work (start): 0.4389 rms_B_bonded: 2.92 r_work: 0.4287 rms_B_bonded: 3.54 restraints_weight: 0.5000 r_work (final): 0.4287 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.2528 moved from start: 0.7183 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 8584 Z= 0.177 Angle : 0.732 16.438 11638 Z= 0.382 Chirality : 0.047 0.185 1331 Planarity : 0.005 0.067 1468 Dihedral : 5.793 29.489 1172 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 16.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.79 % Favored : 93.21 % Rotamer: Outliers : 3.00 % Allowed : 18.42 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.82 (0.26), residues: 1061 helix: 1.40 (0.27), residues: 351 sheet: -1.36 (0.33), residues: 243 loop : -1.58 (0.28), residues: 467 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 68 TYR 0.024 0.002 TYR G 40 PHE 0.021 0.003 PHE R 405 TRP 0.039 0.003 TRP B 82 HIS 0.009 0.002 HIS B 62 Details of bonding type rmsd covalent geometry : bond 0.00391 ( 8582) covalent geometry : angle 0.73193 (11634) SS BOND : bond 0.00672 ( 2) SS BOND : angle 1.05054 ( 4) hydrogen bonds : bond 0.04589 ( 380) hydrogen bonds : angle 5.47097 ( 1095) *********************** 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 94 residues out of total 925 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 67 time to evaluate : 0.318 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 53 MET cc_start: 0.1232 (ptm) cc_final: -0.1531 (tpp) REVERT: A 183 THR cc_start: 0.2700 (OUTLIER) cc_final: 0.2210 (m) REVERT: A 323 MET cc_start: 0.5177 (tpp) cc_final: 0.2700 (mtt) REVERT: H 47 TRP cc_start: 0.3599 (t60) cc_final: 0.2817 (t60) REVERT: R 138 HIS cc_start: 0.5894 (OUTLIER) cc_final: 0.4217 (m170) REVERT: R 159 LYS cc_start: 0.4350 (mtmt) cc_final: 0.3318 (mptt) outliers start: 27 outliers final: 20 residues processed: 90 average time/residue: 0.0703 time to fit residues: 9.4967 Evaluate side-chains 81 residues out of total 925 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 59 time to evaluate : 0.296 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 183 THR Chi-restraints excluded: chain A residue 222 ILE 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 276 VAL Chi-restraints excluded: chain B residue 285 LEU Chi-restraints excluded: chain B residue 286 LEU Chi-restraints excluded: chain H residue 68 PHE Chi-restraints excluded: chain H residue 89 GLU Chi-restraints excluded: chain H residue 91 THR Chi-restraints excluded: chain H residue 198 THR Chi-restraints excluded: chain H residue 219 GLN Chi-restraints excluded: chain R residue 49 LEU Chi-restraints excluded: chain R residue 95 ILE Chi-restraints excluded: chain R residue 124 TYR Chi-restraints excluded: chain R residue 135 SER Chi-restraints excluded: chain R residue 138 HIS Chi-restraints excluded: chain R residue 154 ILE Chi-restraints excluded: chain R residue 212 VAL 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 27 optimal weight: 0.9990 chunk 21 optimal weight: 10.0000 chunk 89 optimal weight: 0.9980 chunk 103 optimal weight: 0.9980 chunk 28 optimal weight: 0.6980 chunk 72 optimal weight: 5.9990 chunk 82 optimal weight: 6.9990 chunk 52 optimal weight: 0.0670 chunk 102 optimal weight: 0.9990 chunk 65 optimal weight: 3.9990 chunk 78 optimal weight: 2.9990 overall best weight: 0.7520 ------------------------------------------------------------------------------- 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 62 HIS ** B 225 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 59 ASN ** H 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 138 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4688 r_free = 0.4688 target = 0.241411 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.4400 r_free = 0.4400 target = 0.208922 restraints weight = 11319.111| |-----------------------------------------------------------------------------| r_work (start): 0.4392 rms_B_bonded: 2.80 r_work: 0.4292 rms_B_bonded: 3.41 restraints_weight: 0.5000 r_work (final): 0.4292 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.2484 moved from start: 0.7341 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 8584 Z= 0.139 Angle : 0.662 15.688 11638 Z= 0.341 Chirality : 0.044 0.181 1331 Planarity : 0.004 0.054 1468 Dihedral : 5.501 32.333 1172 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 15.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.75 % Favored : 94.25 % Rotamer: Outliers : 3.00 % Allowed : 18.98 % Favored : 78.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.75 (0.26), residues: 1061 helix: 1.43 (0.27), residues: 354 sheet: -1.37 (0.33), residues: 234 loop : -1.53 (0.28), residues: 473 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG H 179 TYR 0.016 0.002 TYR H 178 PHE 0.018 0.002 PHE B 278 TRP 0.029 0.002 TRP B 82 HIS 0.012 0.002 HIS R 138 Details of bonding type rmsd covalent geometry : bond 0.00298 ( 8582) covalent geometry : angle 0.66207 (11634) SS BOND : bond 0.00501 ( 2) SS BOND : angle 1.15240 ( 4) hydrogen bonds : bond 0.04110 ( 380) hydrogen bonds : angle 5.17879 ( 1095) *********************** 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 to be fit. rotamer outliers: 27 poor density : 60 time to evaluate : 0.305 Fit side-chains revert: symmetry clash REVERT: A 53 MET cc_start: 0.1029 (ptm) cc_final: -0.1645 (tpp) REVERT: A 183 THR cc_start: 0.2747 (OUTLIER) cc_final: 0.2470 (m) REVERT: A 320 TYR cc_start: 0.4094 (m-80) cc_final: 0.2337 (t80) REVERT: A 323 MET cc_start: 0.5263 (tpp) cc_final: 0.2740 (mtt) REVERT: B 19 ARG cc_start: 0.6908 (mpt-90) cc_final: 0.6680 (mpt180) REVERT: B 217 MET cc_start: 0.2505 (pmm) cc_final: 0.2234 (pmm) REVERT: B 273 ILE cc_start: 0.0860 (OUTLIER) cc_final: 0.0056 (mp) REVERT: H 47 TRP cc_start: 0.3376 (t60) cc_final: 0.2676 (t60) REVERT: H 179 ARG cc_start: 0.1151 (mmt90) cc_final: 0.0920 (mmm-85) REVERT: R 49 LEU cc_start: 0.6628 (OUTLIER) cc_final: 0.6426 (mm) REVERT: R 138 HIS cc_start: 0.5585 (OUTLIER) cc_final: 0.3769 (m170) outliers start: 27 outliers final: 21 residues processed: 84 average time/residue: 0.0757 time to fit residues: 9.6631 Evaluate side-chains 85 residues out of total 925 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 60 time to evaluate : 0.363 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 183 THR Chi-restraints excluded: chain A residue 222 ILE 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 183 HIS Chi-restraints excluded: chain B residue 273 ILE Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain B residue 285 LEU 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 198 THR Chi-restraints excluded: chain H residue 223 TYR Chi-restraints excluded: chain R residue 49 LEU Chi-restraints excluded: chain R residue 95 ILE Chi-restraints excluded: chain R residue 124 TYR Chi-restraints excluded: chain R residue 135 SER Chi-restraints excluded: chain R residue 138 HIS Chi-restraints excluded: chain R residue 139 LEU Chi-restraints excluded: chain R residue 154 ILE Chi-restraints excluded: chain R residue 212 VAL 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 11 optimal weight: 7.9990 chunk 43 optimal weight: 0.6980 chunk 15 optimal weight: 0.9990 chunk 24 optimal weight: 1.9990 chunk 37 optimal weight: 0.8980 chunk 103 optimal weight: 4.9990 chunk 39 optimal weight: 0.6980 chunk 83 optimal weight: 3.9990 chunk 105 optimal weight: 0.3980 chunk 49 optimal weight: 0.9980 chunk 19 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** ** B 62 HIS ** 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 = 0.4690 r_free = 0.4690 target = 0.241892 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4408 r_free = 0.4408 target = 0.209787 restraints weight = 11244.375| |-----------------------------------------------------------------------------| r_work (start): 0.4403 rms_B_bonded: 2.76 r_work: 0.4301 rms_B_bonded: 3.39 restraints_weight: 0.5000 r_work (final): 0.4301 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.2491 moved from start: 0.7530 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 8584 Z= 0.137 Angle : 0.649 15.134 11638 Z= 0.335 Chirality : 0.044 0.180 1331 Planarity : 0.004 0.057 1468 Dihedral : 5.471 35.472 1172 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 15.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.50 % Favored : 93.50 % Rotamer: Outliers : 2.89 % Allowed : 19.53 % Favored : 77.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.74 (0.26), residues: 1061 helix: 1.43 (0.27), residues: 354 sheet: -1.25 (0.34), residues: 232 loop : -1.59 (0.27), residues: 475 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 150 TYR 0.017 0.002 TYR B 59 PHE 0.017 0.002 PHE B 278 TRP 0.029 0.002 TRP B 82 HIS 0.013 0.002 HIS R 138 Details of bonding type rmsd covalent geometry : bond 0.00297 ( 8582) covalent geometry : angle 0.64889 (11634) SS BOND : bond 0.00475 ( 2) SS BOND : angle 0.94844 ( 4) hydrogen bonds : bond 0.04060 ( 380) hydrogen bonds : angle 5.13172 ( 1095) ********************** 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 88 residues out of total 925 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 62 time to evaluate : 0.314 Fit side-chains revert: symmetry clash REVERT: A 53 MET cc_start: 0.1243 (ptm) cc_final: -0.1497 (tpp) REVERT: A 183 THR cc_start: 0.2982 (OUTLIER) cc_final: 0.2712 (m) REVERT: A 320 TYR cc_start: 0.4239 (m-80) cc_final: 0.2342 (t80) REVERT: A 323 MET cc_start: 0.5456 (tpp) cc_final: 0.2937 (mtt) REVERT: B 61 MET cc_start: 0.1291 (ptp) cc_final: 0.0574 (ptp) REVERT: B 217 MET cc_start: 0.2541 (pmm) cc_final: 0.2246 (pmm) REVERT: B 273 ILE cc_start: 0.0886 (OUTLIER) cc_final: 0.0464 (mp) REVERT: H 47 TRP cc_start: 0.3270 (t60) cc_final: 0.2630 (t60) REVERT: R 138 HIS cc_start: 0.5609 (OUTLIER) cc_final: 0.3675 (m170) outliers start: 26 outliers final: 21 residues processed: 85 average time/residue: 0.0742 time to fit residues: 9.6476 Evaluate side-chains 86 residues out of total 925 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 62 time to evaluate : 0.266 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 183 THR Chi-restraints excluded: chain A residue 222 ILE 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 183 HIS Chi-restraints excluded: chain B residue 273 ILE Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain B residue 285 LEU 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 198 THR Chi-restraints excluded: chain H residue 223 TYR Chi-restraints excluded: chain R residue 95 ILE Chi-restraints excluded: chain R residue 124 TYR Chi-restraints excluded: chain R residue 135 SER Chi-restraints excluded: chain R residue 138 HIS Chi-restraints excluded: chain R residue 139 LEU Chi-restraints excluded: chain R residue 154 ILE Chi-restraints excluded: chain R residue 212 VAL Chi-restraints excluded: chain R residue 387 PHE Chi-restraints excluded: chain R residue 443 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 100 optimal weight: 0.0170 chunk 77 optimal weight: 0.6980 chunk 42 optimal weight: 0.6980 chunk 6 optimal weight: 0.5980 chunk 33 optimal weight: 5.9990 chunk 93 optimal weight: 0.6980 chunk 86 optimal weight: 0.9990 chunk 21 optimal weight: 9.9990 chunk 24 optimal weight: 0.9980 chunk 75 optimal weight: 1.9990 chunk 47 optimal weight: 1.9990 overall best weight: 0.5418 ------------------------------------------------------------------------------- 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 = 0.4695 r_free = 0.4695 target = 0.242519 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4415 r_free = 0.4415 target = 0.210219 restraints weight = 11170.687| |-----------------------------------------------------------------------------| r_work (start): 0.4410 rms_B_bonded: 2.76 r_work: 0.4308 rms_B_bonded: 3.38 restraints_weight: 0.5000 r_work (final): 0.4308 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.2444 moved from start: 0.7653 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 8584 Z= 0.124 Angle : 0.636 14.635 11638 Z= 0.327 Chirality : 0.043 0.176 1331 Planarity : 0.004 0.055 1468 Dihedral : 5.338 38.809 1172 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 14.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.22 % Favored : 93.78 % Rotamer: Outliers : 2.77 % Allowed : 19.87 % Favored : 77.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.72 (0.26), residues: 1061 helix: 1.46 (0.27), residues: 356 sheet: -1.18 (0.33), residues: 234 loop : -1.62 (0.27), residues: 471 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 19 TYR 0.015 0.001 TYR H 178 PHE 0.019 0.002 PHE G 61 TRP 0.025 0.002 TRP B 82 HIS 0.010 0.002 HIS R 138 Details of bonding type rmsd covalent geometry : bond 0.00265 ( 8582) covalent geometry : angle 0.63560 (11634) SS BOND : bond 0.00367 ( 2) SS BOND : angle 0.93312 ( 4) hydrogen bonds : bond 0.03852 ( 380) hydrogen bonds : angle 4.97547 ( 1095) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2121.51 seconds wall clock time: 37 minutes 13.08 seconds (2233.08 seconds total)