Starting phenix.real_space_refine on Mon Sep 23 16:54:00 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8i6q_35203/09_2024/8i6q_35203.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8i6q_35203/09_2024/8i6q_35203.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.23 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8i6q_35203/09_2024/8i6q_35203.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8i6q_35203/09_2024/8i6q_35203.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8i6q_35203/09_2024/8i6q_35203.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8i6q_35203/09_2024/8i6q_35203.cif" } resolution = 4.23 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= -0.001 sd= 0.029 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: 3 Type Number sf(0) Gaussians C 2354 2.51 5 N 810 2.21 5 O 811 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 3975 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 884 Number of conformers: 1 Conformer: "" Number of residues, atoms: 181, 884 Classifications: {'peptide': 181} Incomplete info: {'truncation_to_alanine': 148} Link IDs: {'PTRANS': 4, 'TRANS': 176} Chain breaks: 2 Unresolved chain link angles: 4 Unresolved non-hydrogen bonds: 551 Unresolved non-hydrogen angles: 724 Unresolved non-hydrogen dihedrals: 456 Unresolved non-hydrogen chiralities: 73 Planarities with less than four sites: {'GLN:plan1': 1, 'HIS:plan': 4, 'TYR:plan': 5, 'ASN:plan1': 7, 'TRP:plan': 5, 'ASP:plan': 5, 'PHE:plan': 8, 'GLU:plan': 7, 'ARG:plan': 12} Unresolved non-hydrogen planarities: 276 Chain: "B" Number of atoms: 1090 Number of conformers: 1 Conformer: "" Number of residues, atoms: 222, 1090 Classifications: {'peptide': 222} Incomplete info: {'truncation_to_alanine': 184} Link IDs: {'PTRANS': 10, 'TRANS': 211} Unresolved chain link angles: 10 Unresolved non-hydrogen bonds: 659 Unresolved non-hydrogen angles: 837 Unresolved non-hydrogen dihedrals: 522 Unresolved non-hydrogen chiralities: 74 Planarities with less than four sites: {'GLN:plan1': 12, 'ASP:plan': 10, 'TYR:plan': 1, 'ASN:plan1': 6, 'HIS:plan': 8, 'PHE:plan': 6, 'GLU:plan': 13, 'ARG:plan': 22} Unresolved non-hydrogen planarities: 341 Chain: "C" Number of atoms: 904 Number of conformers: 1 Conformer: "" Number of residues, atoms: 185, 904 Classifications: {'peptide': 185} Incomplete info: {'truncation_to_alanine': 153} Link IDs: {'PTRANS': 4, 'TRANS': 180} Chain breaks: 2 Unresolved chain link angles: 4 Unresolved non-hydrogen bonds: 566 Unresolved non-hydrogen angles: 742 Unresolved non-hydrogen dihedrals: 468 Unresolved non-hydrogen chiralities: 74 Planarities with less than four sites: {'GLN:plan1': 1, 'ARG:plan': 13, 'TYR:plan': 5, 'ASN:plan1': 7, 'TRP:plan': 5, 'ASP:plan': 5, 'PHE:plan': 8, 'GLU:plan': 8, 'HIS:plan': 4} Unresolved non-hydrogen planarities: 285 Chain: "D" Number of atoms: 1097 Number of conformers: 1 Conformer: "" Number of residues, atoms: 222, 1097 Classifications: {'peptide': 222} Incomplete info: {'truncation_to_alanine': 183} Link IDs: {'PTRANS': 10, 'TRANS': 211} Unresolved chain link angles: 10 Unresolved non-hydrogen bonds: 651 Unresolved non-hydrogen angles: 826 Unresolved non-hydrogen dihedrals: 514 Unresolved non-hydrogen chiralities: 74 Planarities with less than four sites: {'GLN:plan1': 12, 'ASP:plan': 10, 'ASN:plan1': 6, 'HIS:plan': 8, 'PHE:plan': 6, 'GLU:plan': 13, 'ARG:plan': 22} Unresolved non-hydrogen planarities: 334 Time building chain proxies: 4.27, per 1000 atoms: 1.07 Number of scatterers: 3975 At special positions: 0 Unit cell: (81.51, 76.362, 120.978, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 3 Type Number sf(0) O 811 8.00 N 810 7.00 C 2354 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.30 Conformation dependent library (CDL) restraints added in 752.7 milliseconds 1588 Ramachandran restraints generated. 794 Oldfield, 0 Emsley, 794 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1456 Finding SS restraints... Secondary structure from input PDB file: 33 helices and 3 sheets defined 64.3% alpha, 3.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.45 Creating SS restraints... Processing helix chain 'A' and resid 35 through 54 Processing helix chain 'A' and resid 55 through 78 Proline residue: A 73 - end of helix Processing helix chain 'A' and resid 190 through 194 removed outlier: 3.509A pdb=" N TRP A 193 " --> pdb=" O ASP A 190 " (cutoff:3.500A) Processing helix chain 'A' and resid 195 through 196 No H-bonds generated for 'chain 'A' and resid 195 through 196' Processing helix chain 'A' and resid 197 through 206 removed outlier: 3.754A pdb=" N LEU A 201 " --> pdb=" O LEU A 197 " (cutoff:3.500A) removed outlier: 4.199A pdb=" N LYS A 202 " --> pdb=" O SER A 198 " (cutoff:3.500A) removed outlier: 4.174A pdb=" N ARG A 206 " --> pdb=" O LYS A 202 " (cutoff:3.500A) Processing helix chain 'A' and resid 208 through 233 removed outlier: 4.248A pdb=" N ILE A 213 " --> pdb=" O PHE A 209 " (cutoff:3.500A) Processing helix chain 'A' and resid 234 through 245 Processing helix chain 'A' and resid 247 through 283 Proline residue: A 254 - end of helix removed outlier: 3.649A pdb=" N MET A 258 " --> pdb=" O PRO A 254 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N TYR A 262 " --> pdb=" O MET A 258 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N ALA A 272 " --> pdb=" O ILE A 268 " (cutoff:3.500A) removed outlier: 4.189A pdb=" N ALA A 275 " --> pdb=" O TRP A 271 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N TRP A 280 " --> pdb=" O TYR A 276 " (cutoff:3.500A) Processing helix chain 'A' and resid 303 through 333 removed outlier: 4.128A pdb=" N THR A 310 " --> pdb=" O GLY A 306 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N GLY A 312 " --> pdb=" O SER A 308 " (cutoff:3.500A) removed outlier: 4.294A pdb=" N ALA A 313 " --> pdb=" O LEU A 309 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N GLY A 317 " --> pdb=" O ALA A 313 " (cutoff:3.500A) Processing helix chain 'B' and resid 40 through 49 Processing helix chain 'B' and resid 72 through 79 removed outlier: 4.011A pdb=" N PHE B 76 " --> pdb=" O ALA B 72 " (cutoff:3.500A) Processing helix chain 'B' and resid 95 through 101 Processing helix chain 'B' and resid 101 through 108 removed outlier: 3.514A pdb=" N GLN B 105 " --> pdb=" O ALA B 101 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N ILE B 106 " --> pdb=" O LEU B 102 " (cutoff:3.500A) Processing helix chain 'B' and resid 110 through 125 removed outlier: 4.231A pdb=" N ARG B 117 " --> pdb=" O GLU B 113 " (cutoff:3.500A) Processing helix chain 'B' and resid 139 through 153 Processing helix chain 'B' and resid 169 through 186 Processing helix chain 'B' and resid 197 through 203 removed outlier: 4.020A pdb=" N ARG B 202 " --> pdb=" O ALA B 198 " (cutoff:3.500A) Processing helix chain 'C' and resid 34 through 54 Processing helix chain 'C' and resid 57 through 87 Proline residue: C 73 - end of helix removed outlier: 4.532A pdb=" N LEU C 76 " --> pdb=" O LEU C 72 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N SER C 77 " --> pdb=" O PRO C 73 " (cutoff:3.500A) removed outlier: 4.206A pdb=" N ASN C 81 " --> pdb=" O SER C 77 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N GLY C 87 " --> pdb=" O VAL C 83 " (cutoff:3.500A) Processing helix chain 'C' and resid 193 through 200 Processing helix chain 'C' and resid 202 through 233 removed outlier: 4.312A pdb=" N ARG C 206 " --> pdb=" O LYS C 202 " (cutoff:3.500A) removed outlier: 4.403A pdb=" N PHE C 207 " --> pdb=" O LEU C 203 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N LEU C 211 " --> pdb=" O PHE C 207 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N ILE C 213 " --> pdb=" O PHE C 209 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N LEU C 215 " --> pdb=" O LEU C 211 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N LEU C 217 " --> pdb=" O ILE C 213 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N THR C 218 " --> pdb=" O LEU C 214 " (cutoff:3.500A) Processing helix chain 'C' and resid 234 through 245 Processing helix chain 'C' and resid 247 through 283 Proline residue: C 254 - end of helix removed outlier: 3.882A pdb=" N MET C 258 " --> pdb=" O PRO C 254 " (cutoff:3.500A) removed outlier: 4.274A pdb=" N ALA C 275 " --> pdb=" O TRP C 271 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N TYR C 276 " --> pdb=" O ALA C 272 " (cutoff:3.500A) Processing helix chain 'C' and resid 302 through 309 Processing helix chain 'C' and resid 310 through 330 removed outlier: 5.363A pdb=" N ALA C 321 " --> pdb=" O GLY C 317 " (cutoff:3.500A) removed outlier: 4.295A pdb=" N TRP C 322 " --> pdb=" O TRP C 318 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N ALA C 326 " --> pdb=" O TRP C 322 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N ARG C 327 " --> pdb=" O LEU C 323 " (cutoff:3.500A) Processing helix chain 'D' and resid 40 through 49 Processing helix chain 'D' and resid 72 through 81 removed outlier: 4.431A pdb=" N PHE D 76 " --> pdb=" O ALA D 72 " (cutoff:3.500A) Processing helix chain 'D' and resid 95 through 108 Proline residue: D 103 - end of helix Processing helix chain 'D' and resid 110 through 125 removed outlier: 4.097A pdb=" N ARG D 117 " --> pdb=" O GLU D 113 " (cutoff:3.500A) Processing helix chain 'D' and resid 134 through 138 Processing helix chain 'D' and resid 139 through 153 Processing helix chain 'D' and resid 169 through 186 Processing helix chain 'D' and resid 197 through 203 removed outlier: 3.518A pdb=" N MET D 203 " --> pdb=" O LEU D 199 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 23 through 25 removed outlier: 5.130A pdb=" N PHE B 4 " --> pdb=" O LEU B 60 " (cutoff:3.500A) removed outlier: 6.380A pdb=" N LEU B 60 " --> pdb=" O PHE B 4 " (cutoff:3.500A) removed outlier: 4.196A pdb=" N GLN B 6 " --> pdb=" O LYS B 58 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 158 through 159 removed outlier: 3.502A pdb=" N LEU B 191 " --> pdb=" O LEU B 159 " (cutoff:3.500A) removed outlier: 6.472A pdb=" N LEU B 31 " --> pdb=" O ILE B 192 " (cutoff:3.500A) removed outlier: 7.896A pdb=" N SER B 194 " --> pdb=" O LEU B 31 " (cutoff:3.500A) removed outlier: 6.317A pdb=" N VAL B 33 " --> pdb=" O SER B 194 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N LEU B 208 " --> pdb=" O PHE B 32 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'D' and resid 9 through 11 removed outlier: 5.823A pdb=" N LYS D 9 " --> pdb=" O GLY D 17 " (cutoff:3.500A) 352 hydrogen bonds defined for protein. 1032 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: 1.12 Time building geometry restraints manager: 1.46 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.29: 810 1.29 - 1.36: 802 1.36 - 1.42: 7 1.42 - 1.48: 810 1.48 - 1.55: 1539 Bond restraints: 3968 Sorted by residual: bond pdb=" N GLN B 142 " pdb=" CA GLN B 142 " ideal model delta sigma weight residual 1.459 1.433 0.026 1.21e-02 6.83e+03 4.53e+00 bond pdb=" CA GLN B 155 " pdb=" C GLN B 155 " ideal model delta sigma weight residual 1.531 1.517 0.014 7.40e-03 1.83e+04 3.68e+00 bond pdb=" CA GLY C 249 " pdb=" C GLY C 249 " ideal model delta sigma weight residual 1.516 1.500 0.016 1.12e-02 7.97e+03 2.12e+00 bond pdb=" C GLU D 163 " pdb=" N PRO D 164 " ideal model delta sigma weight residual 1.334 1.301 0.033 2.34e-02 1.83e+03 1.98e+00 bond pdb=" C GLN D 155 " pdb=" O GLN D 155 " ideal model delta sigma weight residual 1.235 1.228 0.006 4.70e-03 4.53e+04 1.91e+00 ... (remaining 3963 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.35: 5178 1.35 - 2.71: 266 2.71 - 4.06: 36 4.06 - 5.41: 9 5.41 - 6.76: 4 Bond angle restraints: 5493 Sorted by residual: angle pdb=" C THR B 55 " pdb=" CA THR B 55 " pdb=" CB THR B 55 " ideal model delta sigma weight residual 116.54 110.07 6.47 1.15e+00 7.56e-01 3.16e+01 angle pdb=" N GLY B 57 " pdb=" CA GLY B 57 " pdb=" C GLY B 57 " ideal model delta sigma weight residual 111.85 116.48 -4.63 1.06e+00 8.90e-01 1.91e+01 angle pdb=" CA TYR D 11 " pdb=" CB TYR D 11 " pdb=" CG TYR D 11 " ideal model delta sigma weight residual 113.90 119.62 -5.72 1.80e+00 3.09e-01 1.01e+01 angle pdb=" C GLY C 245 " pdb=" N GLY C 246 " pdb=" CA GLY C 246 " ideal model delta sigma weight residual 121.32 116.43 4.89 1.58e+00 4.01e-01 9.56e+00 angle pdb=" N GLU B 132 " pdb=" CA GLU B 132 " pdb=" C GLU B 132 " ideal model delta sigma weight residual 111.36 114.66 -3.30 1.09e+00 8.42e-01 9.15e+00 ... (remaining 5488 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 5.91: 2043 5.91 - 11.82: 172 11.82 - 17.73: 35 17.73 - 23.64: 8 23.64 - 29.55: 3 Dihedral angle restraints: 2261 sinusoidal: 2 harmonic: 2259 Sorted by residual: dihedral pdb=" CA ARG D 10 " pdb=" C ARG D 10 " pdb=" N TYR D 11 " pdb=" CA TYR D 11 " ideal model delta harmonic sigma weight residual 180.00 150.45 29.55 0 5.00e+00 4.00e-02 3.49e+01 dihedral pdb=" CA ARG D 185 " pdb=" C ARG D 185 " pdb=" N LEU D 186 " pdb=" CA LEU D 186 " ideal model delta harmonic sigma weight residual 180.00 152.06 27.94 0 5.00e+00 4.00e-02 3.12e+01 dihedral pdb=" CA ARG B 185 " pdb=" C ARG B 185 " pdb=" N LEU B 186 " pdb=" CA LEU B 186 " ideal model delta harmonic sigma weight residual 180.00 152.60 27.40 0 5.00e+00 4.00e-02 3.00e+01 ... (remaining 2258 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.026: 437 0.026 - 0.053: 143 0.053 - 0.079: 102 0.079 - 0.106: 39 0.106 - 0.132: 7 Chirality restraints: 728 Sorted by residual: chirality pdb=" CA PRO D 170 " pdb=" N PRO D 170 " pdb=" C PRO D 170 " pdb=" CB PRO D 170 " both_signs ideal model delta sigma weight residual False 2.72 2.59 0.13 2.00e-01 2.50e+01 4.35e-01 chirality pdb=" CA ILE D 30 " pdb=" N ILE D 30 " pdb=" C ILE D 30 " pdb=" CB ILE D 30 " both_signs ideal model delta sigma weight residual False 2.43 2.55 -0.12 2.00e-01 2.50e+01 3.35e-01 chirality pdb=" CA VAL C 301 " pdb=" N VAL C 301 " pdb=" C VAL C 301 " pdb=" CB VAL C 301 " both_signs ideal model delta sigma weight residual False 2.44 2.56 -0.11 2.00e-01 2.50e+01 3.30e-01 ... (remaining 725 not shown) Planarity restraints: 803 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR D 11 " 0.016 2.00e-02 2.50e+03 1.30e-02 3.39e+00 pdb=" CG TYR D 11 " -0.031 2.00e-02 2.50e+03 pdb=" CD1 TYR D 11 " 0.009 2.00e-02 2.50e+03 pdb=" CD2 TYR D 11 " 0.003 2.00e-02 2.50e+03 pdb=" CE1 TYR D 11 " -0.003 2.00e-02 2.50e+03 pdb=" CE2 TYR D 11 " 0.003 2.00e-02 2.50e+03 pdb=" CZ TYR D 11 " -0.000 2.00e-02 2.50e+03 pdb=" OH TYR D 11 " 0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL B 21 " 0.008 2.00e-02 2.50e+03 1.66e-02 2.76e+00 pdb=" C VAL B 21 " -0.029 2.00e-02 2.50e+03 pdb=" O VAL B 21 " 0.011 2.00e-02 2.50e+03 pdb=" N SER B 22 " 0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU D 122 " 0.008 2.00e-02 2.50e+03 1.58e-02 2.49e+00 pdb=" C LEU D 122 " -0.027 2.00e-02 2.50e+03 pdb=" O LEU D 122 " 0.010 2.00e-02 2.50e+03 pdb=" N GLU D 123 " 0.009 2.00e-02 2.50e+03 ... (remaining 800 not shown) Histogram of nonbonded interaction distances: 2.03 - 2.60: 44 2.60 - 3.18: 4580 3.18 - 3.75: 6332 3.75 - 4.33: 7457 4.33 - 4.90: 10306 Nonbonded interactions: 28719 Sorted by model distance: nonbonded pdb=" O HIS C 55 " pdb=" N SER C 59 " model vdw 2.031 3.120 nonbonded pdb=" O ILE D 2 " pdb=" N VAL D 25 " model vdw 2.230 3.120 nonbonded pdb=" O LEU A 70 " pdb=" N MET A 74 " model vdw 2.261 3.120 nonbonded pdb=" N HIS B 19 " pdb=" O GLY B 213 " model vdw 2.318 3.120 nonbonded pdb=" N GLN D 6 " pdb=" O VAL D 21 " model vdw 2.332 3.120 ... (remaining 28714 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 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 35 through 283 or resid 298 through 332)) selection = (chain 'C' and (resid 35 through 83 or resid 190 through 283 or resid 298 throug \ h 332)) } ncs_group { reference = chain 'B' selection = (chain 'D' and ((resid 1 through 13 and (name N or name CA or name C or name O o \ r name CB )) or resid 14 through 222)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue 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: 2.240 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: 0.000 Extract box with map and model: 0.180 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 16.220 Find NCS groups from input model: 0.160 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:2.860 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.750 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8248 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 : 0.005 0.033 3968 Z= 0.374 Angle : 0.734 6.764 5493 Z= 0.518 Chirality : 0.040 0.132 728 Planarity : 0.004 0.017 803 Dihedral : 6.123 29.547 805 Min Nonbonded Distance : 2.031 Molprobity Statistics. All-atom Clashscore : 15.78 Ramachandran Plot: Outliers : 0.13 % Allowed : 7.30 % Favored : 92.57 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % 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: -1.63 (0.28), residues: 794 helix: -0.21 (0.23), residues: 449 sheet: -2.80 (0.88), residues: 34 loop : -2.13 (0.34), residues: 311 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP A 193 PHE 0.000 0.000 PHE A 53 TYR 0.031 0.004 TYR D 11 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1588 Ramachandran restraints generated. 794 Oldfield, 0 Emsley, 794 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1588 Ramachandran restraints generated. 794 Oldfield, 0 Emsley, 794 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 18 residues out of total 669 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 18 time to evaluate : 0.388 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 18 average time/residue: 0.0582 time to fit residues: 2.6377 Evaluate side-chains 18 residues out of total 669 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 18 time to evaluate : 0.579 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 67 optimal weight: 4.9990 chunk 60 optimal weight: 0.0370 chunk 33 optimal weight: 20.0000 chunk 20 optimal weight: 50.0000 chunk 40 optimal weight: 20.0000 chunk 32 optimal weight: 0.8980 chunk 62 optimal weight: 5.9990 chunk 24 optimal weight: 50.0000 chunk 38 optimal weight: 10.0000 chunk 46 optimal weight: 5.9990 chunk 72 optimal weight: 5.9990 overall best weight: 3.5864 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8176 moved from start: 0.1660 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.010 3968 Z= 0.159 Angle : 0.478 6.568 5493 Z= 0.305 Chirality : 0.039 0.128 728 Planarity : 0.003 0.013 803 Dihedral : 5.064 25.824 803 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 3.60 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.16 % Favored : 95.72 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % 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: -0.32 (0.30), residues: 794 helix: 1.00 (0.23), residues: 490 sheet: -2.66 (0.86), residues: 34 loop : -2.18 (0.36), residues: 270 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP A 193 PHE 0.000 0.000 PHE A 53 TYR 0.012 0.001 TYR D 11 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1588 Ramachandran restraints generated. 794 Oldfield, 0 Emsley, 794 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1588 Ramachandran restraints generated. 794 Oldfield, 0 Emsley, 794 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 18 residues out of total 669 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 18 time to evaluate : 0.470 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 18 average time/residue: 0.0357 time to fit residues: 1.8246 Evaluate side-chains 18 residues out of total 669 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 18 time to evaluate : 0.440 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 40 optimal weight: 30.0000 chunk 22 optimal weight: 8.9990 chunk 60 optimal weight: 5.9990 chunk 49 optimal weight: 20.0000 chunk 20 optimal weight: 1.9990 chunk 72 optimal weight: 0.9990 chunk 78 optimal weight: 10.0000 chunk 64 optimal weight: 9.9990 chunk 24 optimal weight: 50.0000 chunk 58 optimal weight: 7.9990 chunk 71 optimal weight: 6.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8159 moved from start: 0.2119 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.018 3968 Z= 0.172 Angle : 0.440 5.955 5493 Z= 0.285 Chirality : 0.039 0.134 728 Planarity : 0.002 0.009 803 Dihedral : 4.447 24.146 803 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 3.43 Ramachandran Plot: Outliers : 0.13 % Allowed : 6.42 % Favored : 93.45 % Rotamer: Outliers : 0.00 % Allowed : 100.00 % Favored : 0.00 % 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: 0.25 (0.31), residues: 794 helix: 1.56 (0.23), residues: 488 sheet: -2.63 (0.89), residues: 34 loop : -2.13 (0.37), residues: 272 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP A 193 PHE 0.000 0.000 PHE A 53 TYR 0.013 0.001 TYR D 11 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1588 Ramachandran restraints generated. 794 Oldfield, 0 Emsley, 794 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1588 Ramachandran restraints generated. 794 Oldfield, 0 Emsley, 794 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 18 residues out of total 669 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 18 time to evaluate : 0.395 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 18 average time/residue: 0.0389 time to fit residues: 1.9013 Evaluate side-chains 18 residues out of total 669 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 18 time to evaluate : 0.419 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 54 optimal weight: 3.9990 chunk 37 optimal weight: 40.0000 chunk 8 optimal weight: 30.0000 chunk 34 optimal weight: 7.9990 chunk 48 optimal weight: 30.0000 chunk 73 optimal weight: 10.0000 chunk 77 optimal weight: 30.0000 chunk 38 optimal weight: 30.0000 chunk 69 optimal weight: 20.0000 chunk 20 optimal weight: 6.9990 chunk 64 optimal weight: 6.9990 overall best weight: 7.1992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8179 moved from start: 0.2165 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 3968 Z= 0.240 Angle : 0.498 7.160 5493 Z= 0.328 Chirality : 0.039 0.131 728 Planarity : 0.003 0.010 803 Dihedral : 4.657 24.622 803 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 4.46 Ramachandran Plot: Outliers : 0.13 % Allowed : 6.68 % Favored : 93.20 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % 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: -0.09 (0.30), residues: 794 helix: 1.24 (0.23), residues: 490 sheet: -2.70 (0.91), residues: 34 loop : -2.19 (0.37), residues: 270 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP A 193 PHE 0.000 0.000 PHE A 53 TYR 0.025 0.003 TYR D 11 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1588 Ramachandran restraints generated. 794 Oldfield, 0 Emsley, 794 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1588 Ramachandran restraints generated. 794 Oldfield, 0 Emsley, 794 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 18 residues out of total 669 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 18 time to evaluate : 0.353 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 18 average time/residue: 0.0314 time to fit residues: 1.5896 Evaluate side-chains 18 residues out of total 669 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 18 time to evaluate : 0.358 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 43 optimal weight: 5.9990 chunk 1 optimal weight: 20.0000 chunk 57 optimal weight: 8.9990 chunk 31 optimal weight: 0.0980 chunk 65 optimal weight: 30.0000 chunk 53 optimal weight: 8.9990 chunk 0 optimal weight: 10.0000 chunk 39 optimal weight: 0.0870 chunk 69 optimal weight: 20.0000 chunk 19 optimal weight: 30.0000 chunk 26 optimal weight: 50.0000 overall best weight: 4.8364 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8152 moved from start: 0.2494 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.015 3968 Z= 0.166 Angle : 0.427 6.515 5493 Z= 0.276 Chirality : 0.039 0.130 728 Planarity : 0.002 0.009 803 Dihedral : 4.306 24.106 803 Min Nonbonded Distance : 2.569 Molprobity Statistics. All-atom Clashscore : 3.77 Ramachandran Plot: Outliers : 0.13 % Allowed : 5.54 % Favored : 94.33 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % 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: 0.50 (0.31), residues: 794 helix: 1.80 (0.23), residues: 491 sheet: -2.23 (0.86), residues: 43 loop : -2.19 (0.38), residues: 260 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP A 193 PHE 0.000 0.000 PHE A 53 TYR 0.023 0.002 TYR D 11 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1588 Ramachandran restraints generated. 794 Oldfield, 0 Emsley, 794 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1588 Ramachandran restraints generated. 794 Oldfield, 0 Emsley, 794 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 18 residues out of total 669 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 18 time to evaluate : 0.485 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 18 average time/residue: 0.0423 time to fit residues: 2.0790 Evaluate side-chains 18 residues out of total 669 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 18 time to evaluate : 0.492 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 69 optimal weight: 20.0000 chunk 15 optimal weight: 9.9990 chunk 45 optimal weight: 40.0000 chunk 19 optimal weight: 20.0000 chunk 77 optimal weight: 40.0000 chunk 64 optimal weight: 0.4980 chunk 35 optimal weight: 9.9990 chunk 6 optimal weight: 5.9990 chunk 25 optimal weight: 20.0000 chunk 40 optimal weight: 20.0000 chunk 74 optimal weight: 8.9990 overall best weight: 7.0988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8176 moved from start: 0.2543 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 3968 Z= 0.240 Angle : 0.495 7.117 5493 Z= 0.326 Chirality : 0.039 0.132 728 Planarity : 0.003 0.010 803 Dihedral : 4.614 24.556 803 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 5.32 Ramachandran Plot: Outliers : 0.13 % Allowed : 7.93 % Favored : 91.94 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % 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: -0.05 (0.30), residues: 794 helix: 1.31 (0.22), residues: 491 sheet: -2.78 (0.92), residues: 34 loop : -2.26 (0.37), residues: 269 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP A 193 PHE 0.000 0.000 PHE A 53 TYR 0.021 0.002 TYR D 11 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1588 Ramachandran restraints generated. 794 Oldfield, 0 Emsley, 794 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1588 Ramachandran restraints generated. 794 Oldfield, 0 Emsley, 794 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 18 residues out of total 669 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 18 time to evaluate : 0.431 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 18 average time/residue: 0.0367 time to fit residues: 1.8316 Evaluate side-chains 18 residues out of total 669 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 18 time to evaluate : 0.454 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 8 optimal weight: 30.0000 chunk 44 optimal weight: 30.0000 chunk 56 optimal weight: 9.9990 chunk 43 optimal weight: 7.9990 chunk 65 optimal weight: 30.0000 chunk 77 optimal weight: 40.0000 chunk 48 optimal weight: 30.0000 chunk 47 optimal weight: 5.9990 chunk 35 optimal weight: 10.0000 chunk 30 optimal weight: 10.0000 chunk 46 optimal weight: 7.9990 overall best weight: 8.3992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8187 moved from start: 0.2801 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.025 3968 Z= 0.278 Angle : 0.538 7.503 5493 Z= 0.359 Chirality : 0.040 0.140 728 Planarity : 0.003 0.012 803 Dihedral : 4.968 24.854 803 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 6.35 Ramachandran Plot: Outliers : 0.13 % Allowed : 8.19 % Favored : 91.69 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % 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: -0.71 (0.29), residues: 794 helix: 0.71 (0.22), residues: 491 sheet: -2.93 (0.75), residues: 51 loop : -2.26 (0.38), residues: 252 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP A 193 PHE 0.000 0.000 PHE A 53 TYR 0.019 0.002 TYR D 11 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1588 Ramachandran restraints generated. 794 Oldfield, 0 Emsley, 794 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1588 Ramachandran restraints generated. 794 Oldfield, 0 Emsley, 794 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 18 residues out of total 669 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 18 time to evaluate : 0.462 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 18 average time/residue: 0.0378 time to fit residues: 1.9183 Evaluate side-chains 18 residues out of total 669 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 18 time to evaluate : 0.460 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 23 optimal weight: 4.9990 chunk 15 optimal weight: 0.9980 chunk 14 optimal weight: 0.9980 chunk 49 optimal weight: 20.0000 chunk 52 optimal weight: 10.0000 chunk 38 optimal weight: 20.0000 chunk 7 optimal weight: 0.9980 chunk 60 optimal weight: 0.7980 chunk 70 optimal weight: 20.0000 chunk 73 optimal weight: 20.0000 chunk 67 optimal weight: 2.9990 overall best weight: 1.3582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8107 moved from start: 0.3377 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.001 0.009 3968 Z= 0.083 Angle : 0.377 6.047 5493 Z= 0.233 Chirality : 0.039 0.130 728 Planarity : 0.002 0.008 803 Dihedral : 4.055 23.290 803 Min Nonbonded Distance : 2.601 Molprobity Statistics. All-atom Clashscore : 2.40 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.28 % Favored : 95.59 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % 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: 1.12 (0.32), residues: 794 helix: 2.42 (0.23), residues: 493 sheet: -2.31 (0.88), residues: 38 loop : -2.22 (0.38), residues: 263 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP A 193 PHE 0.000 0.000 PHE A 53 TYR 0.019 0.002 TYR D 11 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1588 Ramachandran restraints generated. 794 Oldfield, 0 Emsley, 794 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1588 Ramachandran restraints generated. 794 Oldfield, 0 Emsley, 794 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 18 residues out of total 669 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 18 time to evaluate : 0.465 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 18 average time/residue: 0.0386 time to fit residues: 1.9469 Evaluate side-chains 18 residues out of total 669 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 18 time to evaluate : 0.459 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 71 optimal weight: 4.9990 chunk 73 optimal weight: 20.0000 chunk 43 optimal weight: 5.9990 chunk 31 optimal weight: 9.9990 chunk 56 optimal weight: 5.9990 chunk 22 optimal weight: 8.9990 chunk 64 optimal weight: 30.0000 chunk 67 optimal weight: 0.8980 chunk 47 optimal weight: 20.0000 chunk 75 optimal weight: 0.7980 chunk 46 optimal weight: 0.9990 overall best weight: 2.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8117 moved from start: 0.3495 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.001 0.010 3968 Z= 0.103 Angle : 0.374 5.568 5493 Z= 0.235 Chirality : 0.039 0.124 728 Planarity : 0.002 0.008 803 Dihedral : 3.821 22.481 803 Min Nonbonded Distance : 2.590 Molprobity Statistics. All-atom Clashscore : 2.74 Ramachandran Plot: Outliers : 0.13 % Allowed : 5.92 % Favored : 93.95 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % 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: 1.55 (0.32), residues: 794 helix: 2.78 (0.23), residues: 493 sheet: -2.21 (0.89), residues: 38 loop : -2.09 (0.39), residues: 263 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP A 193 PHE 0.000 0.000 PHE A 53 TYR 0.014 0.001 TYR D 11 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1588 Ramachandran restraints generated. 794 Oldfield, 0 Emsley, 794 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1588 Ramachandran restraints generated. 794 Oldfield, 0 Emsley, 794 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 18 residues out of total 669 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 18 time to evaluate : 0.459 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 18 average time/residue: 0.0375 time to fit residues: 1.8996 Evaluate side-chains 18 residues out of total 669 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 18 time to evaluate : 0.428 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 36 optimal weight: 9.9990 chunk 52 optimal weight: 10.0000 chunk 79 optimal weight: 40.0000 chunk 73 optimal weight: 20.0000 chunk 63 optimal weight: 30.0000 chunk 6 optimal weight: 5.9990 chunk 49 optimal weight: 10.0000 chunk 38 optimal weight: 20.0000 chunk 50 optimal weight: 9.9990 chunk 67 optimal weight: 0.8980 chunk 19 optimal weight: 30.0000 overall best weight: 7.3790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8168 moved from start: 0.3312 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 3968 Z= 0.253 Angle : 0.500 6.536 5493 Z= 0.333 Chirality : 0.039 0.129 728 Planarity : 0.003 0.011 803 Dihedral : 4.318 23.692 803 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 4.63 Ramachandran Plot: Outliers : 0.13 % Allowed : 8.19 % Favored : 91.69 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % 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: 0.64 (0.30), residues: 794 helix: 1.96 (0.22), residues: 492 sheet: -2.39 (0.87), residues: 38 loop : -2.24 (0.38), residues: 264 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP A 193 PHE 0.000 0.000 PHE A 53 TYR 0.018 0.002 TYR D 11 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1588 Ramachandran restraints generated. 794 Oldfield, 0 Emsley, 794 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1588 Ramachandran restraints generated. 794 Oldfield, 0 Emsley, 794 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 18 residues out of total 669 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 18 time to evaluate : 0.490 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 18 average time/residue: 0.0372 time to fit residues: 1.8969 Evaluate side-chains 18 residues out of total 669 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 18 time to evaluate : 0.408 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 58 optimal weight: 50.0000 chunk 9 optimal weight: 20.0000 chunk 17 optimal weight: 0.2980 chunk 63 optimal weight: 20.0000 chunk 26 optimal weight: 30.0000 chunk 65 optimal weight: 30.0000 chunk 8 optimal weight: 20.0000 chunk 11 optimal weight: 5.9990 chunk 55 optimal weight: 50.0000 chunk 3 optimal weight: 20.0000 chunk 45 optimal weight: 0.2980 overall best weight: 9.3190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2725 r_free = 0.2725 target = 0.032016 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.2489 r_free = 0.2489 target = 0.024155 restraints weight = 70079.666| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.2489 r_free = 0.2489 target = 0.024162 restraints weight = 66579.595| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.2489 r_free = 0.2489 target = 0.024162 restraints weight = 66505.702| |-----------------------------------------------------------------------------| r_work (final): 0.2468 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8220 moved from start: 0.3348 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 3968 Z= 0.309 Angle : 0.562 7.520 5493 Z= 0.377 Chirality : 0.040 0.134 728 Planarity : 0.003 0.014 803 Dihedral : 4.975 24.606 803 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 6.00 Ramachandran Plot: Outliers : 0.13 % Allowed : 9.07 % Favored : 90.81 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % 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: -0.66 (0.29), residues: 794 helix: 0.77 (0.22), residues: 488 sheet: -3.25 (0.69), residues: 51 loop : -2.18 (0.39), residues: 255 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP A 193 PHE 0.000 0.000 PHE A 53 TYR 0.016 0.002 TYR D 11 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 829.10 seconds wall clock time: 19 minutes 0.00 seconds (1140.00 seconds total)