Starting phenix.real_space_refine on Sun Mar 10 18:32:07 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8i6q_35203/03_2024/8i6q_35203.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8i6q_35203/03_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_35203/03_2024/8i6q_35203.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8i6q_35203/03_2024/8i6q_35203.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8i6q_35203/03_2024/8i6q_35203.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8i6q_35203/03_2024/8i6q_35203.pdb" } 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 Symmetric amino acids flipped None Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/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: 2.85, per 1000 atoms: 0.72 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 - 3.50 Amino acid : False - 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: 1.88 Conformation dependent library (CDL) restraints added in 1.1 seconds 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: 0.43 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: 1.13 Time building geometry restraints manager: 2.00 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: 102.17 - 107.12: 35 107.12 - 112.07: 2074 112.07 - 117.03: 649 117.03 - 121.98: 1858 121.98 - 126.93: 877 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 2.520 nonbonded pdb=" O ILE D 2 " pdb=" N VAL D 25 " model vdw 2.230 2.520 nonbonded pdb=" O LEU A 70 " pdb=" N MET A 74 " model vdw 2.261 2.520 nonbonded pdb=" N HIS B 19 " pdb=" O GLY B 213 " model vdw 2.318 2.520 nonbonded pdb=" N GLN D 6 " pdb=" O VAL D 21 " model vdw 2.332 2.520 ... (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 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: 1.360 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: 6.530 Check model and map are aligned: 0.060 Set scattering table: 0.040 Process input model: 16.600 Find NCS groups from input model: 0.270 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:2.880 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.760 ------------------------------------------------------------------------------- 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 : 0.380 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 18 average time/residue: 0.0380 time to fit residues: 1.7474 Evaluate side-chains 18 residues out of total 669 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 18 time to evaluate : 0.382 ------------------------------------------------------------------------------- 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: 2.9990 chunk 60 optimal weight: 0.2980 chunk 33 optimal weight: 7.9990 chunk 20 optimal weight: 50.0000 chunk 40 optimal weight: 20.0000 chunk 32 optimal weight: 0.9980 chunk 62 optimal weight: 4.9990 chunk 24 optimal weight: 50.0000 chunk 38 optimal weight: 20.0000 chunk 46 optimal weight: 5.9990 chunk 72 optimal weight: 5.9990 overall best weight: 3.0586 ------------------------------------------------------------------------------- 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: 0.8174 moved from start: 0.1560 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= 0.143 Angle : 0.469 6.525 5493 Z= 0.299 Chirality : 0.039 0.124 728 Planarity : 0.003 0.012 803 Dihedral : 5.114 25.786 803 Min Nonbonded Distance : 2.139 Molprobity Statistics. All-atom Clashscore : 4.46 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.53 % Favored : 95.34 % 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: -0.26 (0.30), residues: 794 helix: 1.05 (0.23), residues: 492 sheet: -2.64 (0.86), residues: 34 loop : -2.18 (0.36), residues: 268 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 0.002 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 : 0.445 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 18 average time/residue: 0.0385 time to fit residues: 1.8985 Evaluate side-chains 18 residues out of total 669 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 18 time to evaluate : 0.415 ------------------------------------------------------------------------------- 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: 7.9990 chunk 60 optimal weight: 8.9990 chunk 49 optimal weight: 20.0000 chunk 20 optimal weight: 50.0000 chunk 72 optimal weight: 0.9990 chunk 78 optimal weight: 40.0000 chunk 64 optimal weight: 50.0000 chunk 24 optimal weight: 40.0000 chunk 58 optimal weight: 7.9990 chunk 71 optimal weight: 7.9990 overall best weight: 6.7990 ------------------------------------------------------------------------------- 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: 0.8189 moved from start: 0.1734 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= 0.236 Angle : 0.506 6.528 5493 Z= 0.334 Chirality : 0.039 0.131 728 Planarity : 0.003 0.012 803 Dihedral : 4.933 25.159 803 Min Nonbonded Distance : 2.044 Molprobity Statistics. All-atom Clashscore : 6.35 Ramachandran Plot: Outliers : 0.13 % Allowed : 8.31 % Favored : 91.56 % 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: -0.38 (0.30), residues: 794 helix: 1.01 (0.23), residues: 488 sheet: -2.85 (0.87), residues: 34 loop : -2.28 (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 : 0.496 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 18 average time/residue: 0.0359 time to fit residues: 1.8738 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 54 optimal weight: 20.0000 chunk 37 optimal weight: 40.0000 chunk 8 optimal weight: 30.0000 chunk 34 optimal weight: 8.9990 chunk 48 optimal weight: 30.0000 chunk 73 optimal weight: 7.9990 chunk 77 optimal weight: 20.0000 chunk 38 optimal weight: 30.0000 chunk 69 optimal weight: 20.0000 chunk 20 optimal weight: 0.9980 chunk 64 optimal weight: 30.0000 overall best weight: 11.5992 ------------------------------------------------------------------------------- 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: 0.8236 moved from start: 0.1997 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.032 3968 Z= 0.381 Angle : 0.669 8.085 5493 Z= 0.452 Chirality : 0.040 0.141 728 Planarity : 0.004 0.018 803 Dihedral : 5.959 28.236 803 Min Nonbonded Distance : 1.982 Molprobity Statistics. All-atom Clashscore : 12.86 Ramachandran Plot: Outliers : 0.13 % Allowed : 10.71 % Favored : 89.17 % 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: -2.25 (0.27), residues: 794 helix: -0.66 (0.21), residues: 484 sheet: -3.03 (0.84), residues: 46 loop : -2.63 (0.35), 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 0.034 0.004 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 : 0.408 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 18 average time/residue: 0.0365 time to fit residues: 1.7877 Evaluate side-chains 18 residues out of total 669 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 18 time to evaluate : 0.412 ------------------------------------------------------------------------------- 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: 10.0000 chunk 1 optimal weight: 20.0000 chunk 57 optimal weight: 9.9990 chunk 31 optimal weight: 0.0570 chunk 65 optimal weight: 2.9990 chunk 53 optimal weight: 20.0000 chunk 0 optimal weight: 20.0000 chunk 39 optimal weight: 0.0770 chunk 69 optimal weight: 8.9990 chunk 19 optimal weight: 5.9990 chunk 26 optimal weight: 40.0000 overall best weight: 3.6262 ------------------------------------------------------------------------------- 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: 0.8158 moved from start: 0.2365 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.009 3968 Z= 0.129 Angle : 0.432 6.601 5493 Z= 0.275 Chirality : 0.039 0.130 728 Planarity : 0.002 0.010 803 Dihedral : 4.824 24.702 803 Min Nonbonded Distance : 2.113 Molprobity Statistics. All-atom Clashscore : 5.66 Ramachandran Plot: Outliers : 0.13 % Allowed : 5.79 % Favored : 94.08 % 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: -0.29 (0.30), residues: 794 helix: 1.16 (0.23), residues: 490 sheet: -2.87 (0.92), residues: 34 loop : -2.43 (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 0.021 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 : 0.453 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 18 average time/residue: 0.0385 time to fit residues: 1.9175 Evaluate side-chains 18 residues out of total 669 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 18 time to evaluate : 0.481 ------------------------------------------------------------------------------- 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: 50.0000 chunk 19 optimal weight: 3.9990 chunk 77 optimal weight: 30.0000 chunk 64 optimal weight: 30.0000 chunk 35 optimal weight: 10.0000 chunk 6 optimal weight: 5.9990 chunk 25 optimal weight: 20.0000 chunk 40 optimal weight: 30.0000 chunk 74 optimal weight: 3.9990 overall best weight: 6.7992 ------------------------------------------------------------------------------- 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: 0.8178 moved from start: 0.2478 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.020 3968 Z= 0.221 Angle : 0.488 7.053 5493 Z= 0.320 Chirality : 0.039 0.135 728 Planarity : 0.002 0.011 803 Dihedral : 4.822 24.733 803 Min Nonbonded Distance : 2.056 Molprobity Statistics. All-atom Clashscore : 7.20 Ramachandran Plot: Outliers : 0.13 % Allowed : 9.32 % Favored : 90.55 % 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: -0.40 (0.30), residues: 794 helix: 1.10 (0.23), residues: 490 sheet: -2.99 (0.91), residues: 34 loop : -2.52 (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 0.020 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 : 0.433 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 18 average time/residue: 0.0393 time to fit residues: 1.9453 Evaluate side-chains 18 residues out of total 669 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 18 time to evaluate : 0.522 ------------------------------------------------------------------------------- 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: 6.9990 chunk 43 optimal weight: 8.9990 chunk 65 optimal weight: 7.9990 chunk 77 optimal weight: 40.0000 chunk 48 optimal weight: 30.0000 chunk 47 optimal weight: 10.0000 chunk 35 optimal weight: 9.9990 chunk 30 optimal weight: 6.9990 chunk 46 optimal weight: 9.9990 overall best weight: 8.1990 ------------------------------------------------------------------------------- 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: 0.8190 moved from start: 0.2785 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.023 3968 Z= 0.271 Angle : 0.537 7.129 5493 Z= 0.359 Chirality : 0.040 0.132 728 Planarity : 0.003 0.012 803 Dihedral : 5.126 25.073 803 Min Nonbonded Distance : 2.030 Molprobity Statistics. All-atom Clashscore : 8.75 Ramachandran Plot: Outliers : 0.13 % Allowed : 9.19 % Favored : 90.68 % 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: -0.92 (0.29), residues: 794 helix: 0.62 (0.22), residues: 489 sheet: -3.14 (0.74), residues: 51 loop : -2.47 (0.37), residues: 254 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 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 : 0.480 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 18 average time/residue: 0.0393 time to fit residues: 1.9647 Evaluate side-chains 18 residues out of total 669 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 18 time to evaluate : 0.417 ------------------------------------------------------------------------------- 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: 40.0000 chunk 15 optimal weight: 9.9990 chunk 14 optimal weight: 0.2980 chunk 49 optimal weight: 7.9990 chunk 52 optimal weight: 2.9990 chunk 38 optimal weight: 20.0000 chunk 7 optimal weight: 20.0000 chunk 60 optimal weight: 30.0000 chunk 70 optimal weight: 0.0570 chunk 73 optimal weight: 10.0000 chunk 67 optimal weight: 5.9990 overall best weight: 3.4704 ------------------------------------------------------------------------------- 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: 0.8145 moved from start: 0.3081 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.011 3968 Z= 0.126 Angle : 0.415 6.414 5493 Z= 0.263 Chirality : 0.039 0.132 728 Planarity : 0.002 0.009 803 Dihedral : 4.509 24.508 803 Min Nonbonded Distance : 2.122 Molprobity Statistics. All-atom Clashscore : 5.32 Ramachandran Plot: Outliers : 0.13 % Allowed : 7.43 % Favored : 92.44 % 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: 0.33 (0.31), residues: 794 helix: 1.77 (0.23), residues: 490 sheet: -3.14 (0.87), residues: 34 loop : -2.38 (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 0.016 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 : 0.443 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 18 average time/residue: 0.0368 time to fit residues: 1.8571 Evaluate side-chains 18 residues out of total 669 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 18 time to evaluate : 0.438 ------------------------------------------------------------------------------- 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: 30.0000 chunk 73 optimal weight: 8.9990 chunk 43 optimal weight: 20.0000 chunk 31 optimal weight: 0.0170 chunk 56 optimal weight: 20.0000 chunk 22 optimal weight: 8.9990 chunk 64 optimal weight: 0.8980 chunk 67 optimal weight: 4.9990 chunk 47 optimal weight: 30.0000 chunk 75 optimal weight: 0.1980 chunk 46 optimal weight: 5.9990 overall best weight: 2.4222 ------------------------------------------------------------------------------- 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: 0.8110 moved from start: 0.3543 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.001 0.007 3968 Z= 0.093 Angle : 0.366 4.951 5493 Z= 0.231 Chirality : 0.039 0.132 728 Planarity : 0.002 0.008 803 Dihedral : 3.863 22.569 803 Min Nonbonded Distance : 2.188 Molprobity Statistics. All-atom Clashscore : 4.12 Ramachandran Plot: Outliers : 0.13 % Allowed : 5.79 % Favored : 94.08 % 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: 1.51 (0.33), residues: 794 helix: 2.90 (0.24), residues: 492 sheet: -2.79 (0.81), residues: 43 loop : -2.31 (0.39), residues: 259 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 0.002 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 : 0.446 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 18 average time/residue: 0.0376 time to fit residues: 1.8805 Evaluate side-chains 18 residues out of total 669 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 18 time to evaluate : 0.447 ------------------------------------------------------------------------------- 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: 0.7980 chunk 52 optimal weight: 3.9990 chunk 79 optimal weight: 30.0000 chunk 73 optimal weight: 7.9990 chunk 63 optimal weight: 50.0000 chunk 6 optimal weight: 7.9990 chunk 49 optimal weight: 6.9990 chunk 38 optimal weight: 20.0000 chunk 50 optimal weight: 9.9990 chunk 67 optimal weight: 0.9980 chunk 19 optimal weight: 0.7980 overall best weight: 2.7184 ------------------------------------------------------------------------------- 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: 0.8110 moved from start: 0.3652 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= 0.102 Angle : 0.369 5.391 5493 Z= 0.233 Chirality : 0.039 0.127 728 Planarity : 0.002 0.008 803 Dihedral : 3.741 22.185 803 Min Nonbonded Distance : 2.169 Molprobity Statistics. All-atom Clashscore : 4.12 Ramachandran Plot: Outliers : 0.13 % Allowed : 5.79 % Favored : 94.08 % 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: 1.87 (0.33), residues: 794 helix: 3.16 (0.24), residues: 494 sheet: -2.64 (0.81), residues: 43 loop : -2.15 (0.39), residues: 257 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 ********************** 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 : 0.432 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 18 average time/residue: 0.0380 time to fit residues: 1.8895 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=1.00 ------------------------------------------------------------------------------- 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: 0.7980 chunk 63 optimal weight: 40.0000 chunk 26 optimal weight: 30.0000 chunk 65 optimal weight: 30.0000 chunk 8 optimal weight: 20.0000 chunk 11 optimal weight: 6.9990 chunk 55 optimal weight: 50.0000 chunk 3 optimal weight: 20.0000 chunk 45 optimal weight: 30.0000 overall best weight: 13.5594 ------------------------------------------------------------------------------- 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 = 0.2701 r_free = 0.2701 target = 0.031598 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2477 r_free = 0.2477 target = 0.023867 restraints weight = 64664.973| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 22)----------------| | r_work = 0.2477 r_free = 0.2477 target = 0.023867 restraints weight = 64206.043| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 17)----------------| | r_work = 0.2477 r_free = 0.2477 target = 0.023867 restraints weight = 64208.388| |-----------------------------------------------------------------------------| r_work (final): 0.2465 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8334 moved from start: 0.3340 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.035 3968 Z= 0.446 Angle : 0.724 7.646 5493 Z= 0.495 Chirality : 0.041 0.149 728 Planarity : 0.005 0.023 803 Dihedral : 5.687 29.482 803 Min Nonbonded Distance : 1.976 Molprobity Statistics. All-atom Clashscore : 14.06 Ramachandran Plot: Outliers : 0.25 % Allowed : 12.34 % Favored : 87.41 % 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: -1.52 (0.28), residues: 794 helix: 0.05 (0.21), residues: 486 sheet: -3.42 (0.66), residues: 52 loop : -2.45 (0.38), residues: 256 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 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 838.49 seconds wall clock time: 15 minutes 45.21 seconds (945.21 seconds total)