Starting phenix.real_space_refine on Sat Dec 9 23:12:08 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5k10_8192/12_2023/5k10_8192_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5k10_8192/12_2023/5k10_8192.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5k10_8192/12_2023/5k10_8192.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5k10_8192/12_2023/5k10_8192.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5k10_8192/12_2023/5k10_8192_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5k10_8192/12_2023/5k10_8192_updated.pdb" } resolution = 3.8 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= 0.000 sd= 0.003 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 6334 atoms to isotropic. 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: 5 Type Number sf(0) Gaussians P 6 5.49 5 S 38 5.16 5 C 4016 2.51 5 N 1074 2.21 5 O 1204 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 34": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 42": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 144": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 183": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 265": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 314": "NH1" <-> "NH2" Residue "A PHE 371": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 34": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 42": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 144": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 183": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 265": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 314": "NH1" <-> "NH2" Residue "B PHE 371": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/chem_data/mon_lib" Total number of atoms: 6338 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 3121 Number of conformers: 1 Conformer: "" Number of residues, atoms: 397, 3121 Classifications: {'peptide': 397} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 12, 'TRANS': 384} Chain breaks: 2 Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 17 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 16 Chain: "B" Number of atoms: 3121 Number of conformers: 1 Conformer: "" Number of residues, atoms: 397, 3121 Classifications: {'peptide': 397} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 12, 'TRANS': 384} Chain breaks: 2 Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 17 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 16 Chain: "A" Number of atoms: 48 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 48 Unusual residues: {'NDP': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 48 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 48 Unusual residues: {'NDP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 3.95, per 1000 atoms: 0.62 Number of scatterers: 6338 At special positions: 0 Unit cell: (99.495, 76.725, 82.665, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 38 16.00 P 6 15.00 O 1204 8.00 N 1074 7.00 C 4016 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=2, symmetry=0 Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 2.38 Conformation dependent library (CDL) restraints added in 1.2 seconds 1564 Ramachandran restraints generated. 782 Oldfield, 0 Emsley, 782 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1464 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 28 helices and 8 sheets defined 40.1% alpha, 8.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.33 Creating SS restraints... Processing helix chain 'A' and resid 17 through 30 removed outlier: 4.085A pdb=" N ILE A 21 " --> pdb=" O GLU A 17 " (cutoff:3.500A) Processing helix chain 'A' and resid 55 through 67 Processing helix chain 'A' and resid 80 through 85 removed outlier: 3.754A pdb=" N GLU A 84 " --> pdb=" O GLU A 80 " (cutoff:3.500A) Processing helix chain 'A' and resid 95 through 103 removed outlier: 3.922A pdb=" N ILE A 102 " --> pdb=" O THR A 98 " (cutoff:3.500A) Processing helix chain 'A' and resid 186 through 203 Processing helix chain 'A' and resid 217 through 233 removed outlier: 3.883A pdb=" N PHE A 223 " --> pdb=" O TYR A 219 " (cutoff:3.500A) Processing helix chain 'A' and resid 236 through 243 removed outlier: 4.524A pdb=" N GLN A 242 " --> pdb=" O GLN A 238 " (cutoff:3.500A) Processing helix chain 'A' and resid 251 through 260 removed outlier: 4.414A pdb=" N GLN A 257 " --> pdb=" O ASP A 253 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N MET A 259 " --> pdb=" O VAL A 255 " (cutoff:3.500A) Processing helix chain 'A' and resid 288 through 290 No H-bonds generated for 'chain 'A' and resid 288 through 290' Processing helix chain 'A' and resid 330 through 347 removed outlier: 3.574A pdb=" N TRP A 336 " --> pdb=" O SER A 332 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N LEU A 346 " --> pdb=" O HIS A 342 " (cutoff:3.500A) Processing helix chain 'A' and resid 350 through 368 removed outlier: 3.791A pdb=" N GLU A 361 " --> pdb=" O ASN A 357 " (cutoff:3.500A) removed outlier: 4.306A pdb=" N ILE A 367 " --> pdb=" O SER A 363 " (cutoff:3.500A) Processing helix chain 'A' and resid 374 through 380 Processing helix chain 'A' and resid 388 through 390 No H-bonds generated for 'chain 'A' and resid 388 through 390' Processing helix chain 'A' and resid 397 through 410 removed outlier: 3.635A pdb=" N LEU A 401 " --> pdb=" O PHE A 397 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N GLY A 402 " --> pdb=" O MET A 398 " (cutoff:3.500A) Processing helix chain 'B' and resid 17 through 30 removed outlier: 4.086A pdb=" N ILE B 21 " --> pdb=" O GLU B 17 " (cutoff:3.500A) Processing helix chain 'B' and resid 55 through 67 Processing helix chain 'B' and resid 80 through 85 removed outlier: 3.754A pdb=" N GLU B 84 " --> pdb=" O GLU B 80 " (cutoff:3.500A) Processing helix chain 'B' and resid 95 through 103 removed outlier: 3.922A pdb=" N ILE B 102 " --> pdb=" O THR B 98 " (cutoff:3.500A) Processing helix chain 'B' and resid 186 through 203 Processing helix chain 'B' and resid 217 through 233 removed outlier: 3.883A pdb=" N PHE B 223 " --> pdb=" O TYR B 219 " (cutoff:3.500A) Processing helix chain 'B' and resid 236 through 243 removed outlier: 4.524A pdb=" N GLN B 242 " --> pdb=" O GLN B 238 " (cutoff:3.500A) Processing helix chain 'B' and resid 251 through 260 removed outlier: 4.414A pdb=" N GLN B 257 " --> pdb=" O ASP B 253 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N MET B 259 " --> pdb=" O VAL B 255 " (cutoff:3.500A) Processing helix chain 'B' and resid 288 through 290 No H-bonds generated for 'chain 'B' and resid 288 through 290' Processing helix chain 'B' and resid 330 through 347 removed outlier: 3.574A pdb=" N TRP B 336 " --> pdb=" O SER B 332 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N LEU B 346 " --> pdb=" O HIS B 342 " (cutoff:3.500A) Processing helix chain 'B' and resid 350 through 368 removed outlier: 3.791A pdb=" N GLU B 361 " --> pdb=" O ASN B 357 " (cutoff:3.500A) removed outlier: 4.305A pdb=" N ILE B 367 " --> pdb=" O SER B 363 " (cutoff:3.500A) Processing helix chain 'B' and resid 374 through 380 Processing helix chain 'B' and resid 388 through 390 No H-bonds generated for 'chain 'B' and resid 388 through 390' Processing helix chain 'B' and resid 397 through 410 removed outlier: 3.635A pdb=" N LEU B 401 " --> pdb=" O PHE B 397 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N GLY B 402 " --> pdb=" O MET B 398 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 12 through 14 Processing sheet with id= B, first strand: chain 'A' and resid 69 through 72 removed outlier: 6.078A pdb=" N VAL A 303 " --> pdb=" O GLY A 70 " (cutoff:3.500A) removed outlier: 7.653A pdb=" N LYS A 72 " --> pdb=" O VAL A 303 " (cutoff:3.500A) removed outlier: 6.624A pdb=" N ALA A 305 " --> pdb=" O LYS A 72 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 107 through 109 removed outlier: 4.761A pdb=" N VAL A 107 " --> pdb=" O CYS A 132 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N CYS A 132 " --> pdb=" O VAL A 107 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N PHE A 265 " --> pdb=" O ILE A 129 " (cutoff:3.500A) removed outlier: 7.388A pdb=" N GLY A 131 " --> pdb=" O PHE A 265 " (cutoff:3.500A) removed outlier: 6.154A pdb=" N TRP A 267 " --> pdb=" O GLY A 131 " (cutoff:3.500A) removed outlier: 7.792A pdb=" N ALA A 268 " --> pdb=" O PRO A 206 " (cutoff:3.500A) removed outlier: 7.109A pdb=" N TYR A 208 " --> pdb=" O ALA A 268 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 141 through 144 Processing sheet with id= E, first strand: chain 'B' and resid 12 through 14 Processing sheet with id= F, first strand: chain 'B' and resid 69 through 72 removed outlier: 6.079A pdb=" N VAL B 303 " --> pdb=" O GLY B 70 " (cutoff:3.500A) removed outlier: 7.652A pdb=" N LYS B 72 " --> pdb=" O VAL B 303 " (cutoff:3.500A) removed outlier: 6.624A pdb=" N ALA B 305 " --> pdb=" O LYS B 72 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 107 through 109 removed outlier: 4.760A pdb=" N VAL B 107 " --> pdb=" O CYS B 132 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N CYS B 132 " --> pdb=" O VAL B 107 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N PHE B 265 " --> pdb=" O ILE B 129 " (cutoff:3.500A) removed outlier: 7.389A pdb=" N GLY B 131 " --> pdb=" O PHE B 265 " (cutoff:3.500A) removed outlier: 6.154A pdb=" N TRP B 267 " --> pdb=" O GLY B 131 " (cutoff:3.500A) removed outlier: 7.792A pdb=" N ALA B 268 " --> pdb=" O PRO B 206 " (cutoff:3.500A) removed outlier: 7.109A pdb=" N TYR B 208 " --> pdb=" O ALA B 268 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 141 through 144 208 hydrogen bonds defined for protein. 618 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: 1.64 Time building geometry restraints manager: 2.53 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2032 1.34 - 1.46: 1468 1.46 - 1.58: 2896 1.58 - 1.70: 6 1.70 - 1.82: 68 Bond restraints: 6470 Sorted by residual: bond pdb=" CB PHE B 334 " pdb=" CG PHE B 334 " ideal model delta sigma weight residual 1.502 1.462 0.040 2.30e-02 1.89e+03 3.03e+00 bond pdb=" CB PHE A 334 " pdb=" CG PHE A 334 " ideal model delta sigma weight residual 1.502 1.462 0.040 2.30e-02 1.89e+03 2.98e+00 bond pdb=" CB TRP A 267 " pdb=" CG TRP A 267 " ideal model delta sigma weight residual 1.498 1.445 0.053 3.10e-02 1.04e+03 2.96e+00 bond pdb=" CB TRP B 267 " pdb=" CG TRP B 267 " ideal model delta sigma weight residual 1.498 1.445 0.053 3.10e-02 1.04e+03 2.91e+00 bond pdb=" CE3 TRP A 267 " pdb=" CZ3 TRP A 267 " ideal model delta sigma weight residual 1.382 1.334 0.048 3.00e-02 1.11e+03 2.54e+00 ... (remaining 6465 not shown) Histogram of bond angle deviations from ideal: 97.05 - 104.44: 128 104.44 - 111.84: 2991 111.84 - 119.23: 2354 119.23 - 126.63: 3168 126.63 - 134.02: 95 Bond angle restraints: 8736 Sorted by residual: angle pdb=" N ARG A 314 " pdb=" CA ARG A 314 " pdb=" C ARG A 314 " ideal model delta sigma weight residual 110.53 104.79 5.74 1.32e+00 5.74e-01 1.89e+01 angle pdb=" N ARG B 314 " pdb=" CA ARG B 314 " pdb=" C ARG B 314 " ideal model delta sigma weight residual 110.53 104.81 5.72 1.32e+00 5.74e-01 1.87e+01 angle pdb=" N VAL B 296 " pdb=" CA VAL B 296 " pdb=" C VAL B 296 " ideal model delta sigma weight residual 108.86 114.58 -5.72 1.63e+00 3.76e-01 1.23e+01 angle pdb=" N VAL A 296 " pdb=" CA VAL A 296 " pdb=" C VAL A 296 " ideal model delta sigma weight residual 108.86 114.54 -5.68 1.63e+00 3.76e-01 1.21e+01 angle pdb=" CA THR B 313 " pdb=" C THR B 313 " pdb=" N ARG B 314 " ideal model delta sigma weight residual 117.30 113.64 3.66 1.16e+00 7.43e-01 9.97e+00 ... (remaining 8731 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.77: 3750 24.77 - 49.55: 70 49.55 - 74.32: 14 74.32 - 99.09: 6 99.09 - 123.87: 2 Dihedral angle restraints: 3842 sinusoidal: 1564 harmonic: 2278 Sorted by residual: dihedral pdb=" CD ARG A 314 " pdb=" NE ARG A 314 " pdb=" CZ ARG A 314 " pdb=" NH1 ARG A 314 " ideal model delta sinusoidal sigma weight residual 0.00 -62.90 62.90 1 1.00e+01 1.00e-02 5.23e+01 dihedral pdb=" CD ARG B 314 " pdb=" NE ARG B 314 " pdb=" CZ ARG B 314 " pdb=" NH1 ARG B 314 " ideal model delta sinusoidal sigma weight residual 0.00 -62.88 62.88 1 1.00e+01 1.00e-02 5.22e+01 dihedral pdb=" CA GLN A 242 " pdb=" C GLN A 242 " pdb=" N LYS A 243 " pdb=" CA LYS A 243 " ideal model delta harmonic sigma weight residual 180.00 156.14 23.86 0 5.00e+00 4.00e-02 2.28e+01 ... (remaining 3839 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.053: 634 0.053 - 0.105: 263 0.105 - 0.158: 49 0.158 - 0.211: 6 0.211 - 0.263: 2 Chirality restraints: 954 Sorted by residual: chirality pdb=" CB ILE A 244 " pdb=" CA ILE A 244 " pdb=" CG1 ILE A 244 " pdb=" CG2 ILE A 244 " both_signs ideal model delta sigma weight residual False 2.64 2.38 0.26 2.00e-01 2.50e+01 1.73e+00 chirality pdb=" CB ILE B 244 " pdb=" CA ILE B 244 " pdb=" CG1 ILE B 244 " pdb=" CG2 ILE B 244 " both_signs ideal model delta sigma weight residual False 2.64 2.38 0.26 2.00e-01 2.50e+01 1.72e+00 chirality pdb=" CB ILE A 5 " pdb=" CA ILE A 5 " pdb=" CG1 ILE A 5 " pdb=" CG2 ILE A 5 " both_signs ideal model delta sigma weight residual False 2.64 2.81 -0.17 2.00e-01 2.50e+01 6.98e-01 ... (remaining 951 not shown) Planarity restraints: 1104 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG A 314 " 0.979 9.50e-02 1.11e+02 4.39e-01 1.17e+02 pdb=" NE ARG A 314 " -0.059 2.00e-02 2.50e+03 pdb=" CZ ARG A 314 " -0.010 2.00e-02 2.50e+03 pdb=" NH1 ARG A 314 " 0.002 2.00e-02 2.50e+03 pdb=" NH2 ARG A 314 " 0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG B 314 " 0.979 9.50e-02 1.11e+02 4.39e-01 1.16e+02 pdb=" NE ARG B 314 " -0.059 2.00e-02 2.50e+03 pdb=" CZ ARG B 314 " -0.010 2.00e-02 2.50e+03 pdb=" NH1 ARG B 314 " 0.002 2.00e-02 2.50e+03 pdb=" NH2 ARG B 314 " 0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE B 227 " -0.017 2.00e-02 2.50e+03 2.36e-02 9.73e+00 pdb=" CG PHE B 227 " 0.051 2.00e-02 2.50e+03 pdb=" CD1 PHE B 227 " -0.027 2.00e-02 2.50e+03 pdb=" CD2 PHE B 227 " -0.007 2.00e-02 2.50e+03 pdb=" CE1 PHE B 227 " 0.013 2.00e-02 2.50e+03 pdb=" CE2 PHE B 227 " -0.007 2.00e-02 2.50e+03 pdb=" CZ PHE B 227 " -0.005 2.00e-02 2.50e+03 ... (remaining 1101 not shown) Histogram of nonbonded interaction distances: 2.14 - 2.69: 289 2.69 - 3.24: 7111 3.24 - 3.80: 10611 3.80 - 4.35: 14331 4.35 - 4.90: 22370 Nonbonded interactions: 54712 Sorted by model distance: nonbonded pdb=" O GLY A 148 " pdb=" OH TYR B 156 " model vdw 2.138 2.440 nonbonded pdb=" OH TYR A 156 " pdb=" O GLY B 148 " model vdw 2.173 2.440 nonbonded pdb=" OD2 ASP B 347 " pdb=" ND2 ASN B 349 " model vdw 2.174 2.520 nonbonded pdb=" OD2 ASP A 347 " pdb=" ND2 ASN A 349 " model vdw 2.175 2.520 nonbonded pdb=" OE2 GLU B 12 " pdb=" NE1 TRP B 23 " model vdw 2.187 2.520 ... (remaining 54707 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' selection = chain 'B' } 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: 0.440 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.080 Construct map_model_manager: 0.010 Extract box with map and model: 2.110 Check model and map are aligned: 0.090 Set scattering table: 0.070 Process input model: 21.150 Find NCS groups from input model: 0.340 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.760 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.080 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6031 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 : 0.009 0.053 6470 Z= 0.556 Angle : 0.928 9.219 8736 Z= 0.515 Chirality : 0.056 0.263 954 Planarity : 0.020 0.439 1104 Dihedral : 12.219 123.867 2378 Min Nonbonded Distance : 2.138 Molprobity Statistics. All-atom Clashscore : 33.42 Ramachandran Plot: Outliers : 0.51 % Allowed : 6.91 % Favored : 92.58 % Rotamer: Outliers : 0.30 % Allowed : 2.42 % Favored : 97.28 % 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: -4.07 (0.25), residues: 782 helix: -3.57 (0.22), residues: 242 sheet: -2.83 (0.29), residues: 174 loop : -1.80 (0.30), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.004 TRP A 267 HIS 0.008 0.002 HIS B 133 PHE 0.051 0.004 PHE B 227 TYR 0.036 0.004 TYR A 156 ARG 0.009 0.001 ARG A 49 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1564 Ramachandran restraints generated. 782 Oldfield, 0 Emsley, 782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1564 Ramachandran restraints generated. 782 Oldfield, 0 Emsley, 782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 670 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 184 time to evaluate : 0.737 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 2 outliers final: 2 residues processed: 186 average time/residue: 0.3024 time to fit residues: 66.7556 Evaluate side-chains 91 residues out of total 670 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 89 time to evaluate : 0.715 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.5064 time to fit residues: 2.1162 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 65 optimal weight: 0.9980 chunk 59 optimal weight: 10.0000 chunk 32 optimal weight: 5.9990 chunk 20 optimal weight: 20.0000 chunk 39 optimal weight: 20.0000 chunk 31 optimal weight: 1.9990 chunk 61 optimal weight: 4.9990 chunk 23 optimal weight: 20.0000 chunk 37 optimal weight: 4.9990 chunk 45 optimal weight: 8.9990 chunk 70 optimal weight: 4.9990 overall best weight: 3.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 96 ASN ** A 170 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 185 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 198 GLN A 271 ASN A 349 ASN A 385 ASN B 96 ASN ** B 185 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 198 GLN B 271 ASN B 349 ASN B 385 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6046 moved from start: 0.4309 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 6470 Z= 0.227 Angle : 0.727 7.770 8736 Z= 0.378 Chirality : 0.045 0.144 954 Planarity : 0.005 0.038 1104 Dihedral : 9.410 122.167 860 Min Nonbonded Distance : 2.208 Molprobity Statistics. All-atom Clashscore : 24.14 Ramachandran Plot: Outliers : 0.26 % Allowed : 2.81 % Favored : 96.93 % Rotamer: Outliers : 2.57 % Allowed : 11.78 % Favored : 85.65 % 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: -2.30 (0.27), residues: 782 helix: -1.18 (0.27), residues: 318 sheet: -2.03 (0.34), residues: 164 loop : -1.32 (0.33), residues: 300 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.003 TRP B 124 HIS 0.009 0.002 HIS B 40 PHE 0.019 0.002 PHE A 197 TYR 0.012 0.001 TYR B 235 ARG 0.007 0.001 ARG A 109 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1564 Ramachandran restraints generated. 782 Oldfield, 0 Emsley, 782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1564 Ramachandran restraints generated. 782 Oldfield, 0 Emsley, 782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 670 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 115 time to evaluate : 0.760 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 17 outliers final: 5 residues processed: 127 average time/residue: 0.2015 time to fit residues: 33.1693 Evaluate side-chains 92 residues out of total 670 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 87 time to evaluate : 0.739 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.2362 time to fit residues: 2.4208 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 39 optimal weight: 40.0000 chunk 21 optimal weight: 20.0000 chunk 58 optimal weight: 20.0000 chunk 48 optimal weight: 4.9990 chunk 19 optimal weight: 10.0000 chunk 70 optimal weight: 5.9990 chunk 76 optimal weight: 20.0000 chunk 63 optimal weight: 10.0000 chunk 24 optimal weight: 20.0000 chunk 56 optimal weight: 30.0000 chunk 53 optimal weight: 8.9990 overall best weight: 7.9994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 185 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 228 GLN ** A 248 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 271 ASN ** A 309 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 185 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 228 GLN ** B 248 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 271 ASN ** B 309 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6211 moved from start: 0.5214 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 6470 Z= 0.278 Angle : 0.672 6.338 8736 Z= 0.346 Chirality : 0.043 0.244 954 Planarity : 0.004 0.038 1104 Dihedral : 9.199 123.148 860 Min Nonbonded Distance : 2.199 Molprobity Statistics. All-atom Clashscore : 26.60 Ramachandran Plot: Outliers : 0.26 % Allowed : 3.84 % Favored : 95.91 % Rotamer: Outliers : 2.11 % Allowed : 16.01 % Favored : 81.87 % 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: -1.56 (0.28), residues: 782 helix: -0.36 (0.28), residues: 326 sheet: -1.67 (0.37), residues: 138 loop : -1.28 (0.33), residues: 318 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.003 TRP A 124 HIS 0.007 0.001 HIS A 40 PHE 0.021 0.002 PHE A 227 TYR 0.012 0.001 TYR B 316 ARG 0.004 0.001 ARG B 222 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1564 Ramachandran restraints generated. 782 Oldfield, 0 Emsley, 782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1564 Ramachandran restraints generated. 782 Oldfield, 0 Emsley, 782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 670 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 85 time to evaluate : 0.735 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 14 outliers final: 9 residues processed: 93 average time/residue: 0.1889 time to fit residues: 23.5002 Evaluate side-chains 78 residues out of total 670 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 69 time to evaluate : 0.747 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 0.0668 time to fit residues: 1.9860 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 36 optimal weight: 10.0000 chunk 7 optimal weight: 8.9990 chunk 33 optimal weight: 5.9990 chunk 47 optimal weight: 50.0000 chunk 71 optimal weight: 6.9990 chunk 75 optimal weight: 6.9990 chunk 37 optimal weight: 30.0000 chunk 67 optimal weight: 2.9990 chunk 20 optimal weight: 10.0000 chunk 62 optimal weight: 20.0000 chunk 42 optimal weight: 20.0000 overall best weight: 6.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 185 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 185 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 271 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6190 moved from start: 0.5797 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 6470 Z= 0.229 Angle : 0.633 12.219 8736 Z= 0.321 Chirality : 0.042 0.140 954 Planarity : 0.003 0.029 1104 Dihedral : 9.124 125.171 860 Min Nonbonded Distance : 2.203 Molprobity Statistics. All-atom Clashscore : 24.30 Ramachandran Plot: Outliers : 0.26 % Allowed : 4.48 % Favored : 95.27 % Rotamer: Outliers : 1.51 % Allowed : 17.07 % Favored : 81.42 % 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: -1.02 (0.29), residues: 782 helix: 0.09 (0.28), residues: 328 sheet: -1.24 (0.41), residues: 138 loop : -1.08 (0.35), residues: 316 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP B 23 HIS 0.006 0.001 HIS A 40 PHE 0.014 0.002 PHE B 227 TYR 0.021 0.001 TYR B 231 ARG 0.004 0.001 ARG B 109 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1564 Ramachandran restraints generated. 782 Oldfield, 0 Emsley, 782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1564 Ramachandran restraints generated. 782 Oldfield, 0 Emsley, 782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 670 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 76 time to evaluate : 0.737 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 10 outliers final: 1 residues processed: 83 average time/residue: 0.1517 time to fit residues: 17.9037 Evaluate side-chains 67 residues out of total 670 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 66 time to evaluate : 0.722 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0614 time to fit residues: 1.1134 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 1 optimal weight: 40.0000 chunk 56 optimal weight: 20.0000 chunk 31 optimal weight: 5.9990 chunk 64 optimal weight: 5.9990 chunk 52 optimal weight: 6.9990 chunk 0 optimal weight: 30.0000 chunk 38 optimal weight: 9.9990 chunk 67 optimal weight: 20.0000 chunk 19 optimal weight: 6.9990 chunk 25 optimal weight: 8.9990 chunk 14 optimal weight: 50.0000 overall best weight: 6.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 185 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 248 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 309 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 185 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 248 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 271 ASN ** B 309 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6232 moved from start: 0.6124 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 6470 Z= 0.239 Angle : 0.628 9.355 8736 Z= 0.316 Chirality : 0.041 0.125 954 Planarity : 0.003 0.033 1104 Dihedral : 9.163 127.772 860 Min Nonbonded Distance : 2.221 Molprobity Statistics. All-atom Clashscore : 24.69 Ramachandran Plot: Outliers : 0.26 % Allowed : 4.35 % Favored : 95.40 % Rotamer: Outliers : 2.57 % Allowed : 18.43 % Favored : 79.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % 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: -0.57 (0.30), residues: 782 helix: 0.51 (0.29), residues: 314 sheet: -1.16 (0.45), residues: 122 loop : -0.80 (0.34), residues: 346 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.002 TRP A 23 HIS 0.004 0.001 HIS A 248 PHE 0.014 0.002 PHE B 227 TYR 0.018 0.001 TYR A 231 ARG 0.006 0.001 ARG B 317 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1564 Ramachandran restraints generated. 782 Oldfield, 0 Emsley, 782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1564 Ramachandran restraints generated. 782 Oldfield, 0 Emsley, 782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 670 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 74 time to evaluate : 0.776 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 17 outliers final: 3 residues processed: 89 average time/residue: 0.1946 time to fit residues: 23.2232 Evaluate side-chains 71 residues out of total 670 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 68 time to evaluate : 0.771 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.0627 time to fit residues: 1.3747 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 44 optimal weight: 10.0000 chunk 18 optimal weight: 10.0000 chunk 75 optimal weight: 2.9990 chunk 62 optimal weight: 7.9990 chunk 34 optimal weight: 10.0000 chunk 6 optimal weight: 1.9990 chunk 24 optimal weight: 4.9990 chunk 39 optimal weight: 40.0000 chunk 72 optimal weight: 20.0000 chunk 8 optimal weight: 7.9990 chunk 42 optimal weight: 2.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 185 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 248 HIS ** A 309 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 342 HIS B 14 GLN ** B 170 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 185 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 248 HIS ** B 309 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 342 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6178 moved from start: 0.6545 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 6470 Z= 0.187 Angle : 0.636 9.869 8736 Z= 0.314 Chirality : 0.042 0.133 954 Planarity : 0.003 0.029 1104 Dihedral : 9.064 128.539 860 Min Nonbonded Distance : 2.215 Molprobity Statistics. All-atom Clashscore : 21.59 Ramachandran Plot: Outliers : 0.26 % Allowed : 4.22 % Favored : 95.52 % Rotamer: Outliers : 1.66 % Allowed : 19.79 % Favored : 78.55 % 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 (0.31), residues: 782 helix: 0.70 (0.30), residues: 314 sheet: -0.97 (0.46), residues: 132 loop : -0.66 (0.36), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.046 0.002 TRP A 23 HIS 0.006 0.001 HIS B 342 PHE 0.012 0.001 PHE B 223 TYR 0.015 0.001 TYR B 231 ARG 0.003 0.001 ARG B 82 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1564 Ramachandran restraints generated. 782 Oldfield, 0 Emsley, 782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1564 Ramachandran restraints generated. 782 Oldfield, 0 Emsley, 782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 670 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 75 time to evaluate : 0.868 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 11 outliers final: 4 residues processed: 80 average time/residue: 0.1967 time to fit residues: 21.5615 Evaluate side-chains 75 residues out of total 670 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 71 time to evaluate : 0.843 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.0796 time to fit residues: 1.5060 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 55 optimal weight: 3.9990 chunk 42 optimal weight: 8.9990 chunk 63 optimal weight: 8.9990 chunk 75 optimal weight: 0.4980 chunk 47 optimal weight: 40.0000 chunk 45 optimal weight: 6.9990 chunk 34 optimal weight: 3.9990 chunk 46 optimal weight: 10.0000 chunk 30 optimal weight: 4.9990 chunk 44 optimal weight: 9.9990 chunk 22 optimal weight: 7.9990 overall best weight: 4.0988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 185 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 309 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 170 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 185 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6173 moved from start: 0.6900 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 6470 Z= 0.191 Angle : 0.670 11.396 8736 Z= 0.324 Chirality : 0.042 0.145 954 Planarity : 0.004 0.031 1104 Dihedral : 9.047 128.680 860 Min Nonbonded Distance : 2.156 Molprobity Statistics. All-atom Clashscore : 21.91 Ramachandran Plot: Outliers : 0.26 % Allowed : 3.84 % Favored : 95.91 % Rotamer: Outliers : 1.51 % Allowed : 19.94 % Favored : 78.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % 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: -0.18 (0.31), residues: 782 helix: 0.82 (0.30), residues: 316 sheet: -0.43 (0.45), residues: 136 loop : -0.82 (0.36), residues: 330 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP A 23 HIS 0.008 0.001 HIS B 342 PHE 0.012 0.001 PHE A 371 TYR 0.014 0.001 TYR B 231 ARG 0.006 0.001 ARG B 249 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1564 Ramachandran restraints generated. 782 Oldfield, 0 Emsley, 782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1564 Ramachandran restraints generated. 782 Oldfield, 0 Emsley, 782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 670 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 81 time to evaluate : 0.750 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 10 outliers final: 5 residues processed: 88 average time/residue: 0.1872 time to fit residues: 22.1542 Evaluate side-chains 69 residues out of total 670 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 64 time to evaluate : 0.694 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.2183 time to fit residues: 2.1356 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 14 optimal weight: 10.0000 chunk 47 optimal weight: 5.9990 chunk 51 optimal weight: 20.0000 chunk 37 optimal weight: 8.9990 chunk 7 optimal weight: 40.0000 chunk 59 optimal weight: 40.0000 chunk 68 optimal weight: 20.0000 chunk 72 optimal weight: 20.0000 chunk 65 optimal weight: 30.0000 chunk 70 optimal weight: 8.9990 chunk 42 optimal weight: 8.9990 overall best weight: 8.5992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 185 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 309 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 170 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 185 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 320 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6314 moved from start: 0.7149 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 6470 Z= 0.279 Angle : 0.750 12.112 8736 Z= 0.367 Chirality : 0.043 0.138 954 Planarity : 0.004 0.079 1104 Dihedral : 9.232 131.086 860 Min Nonbonded Distance : 2.130 Molprobity Statistics. All-atom Clashscore : 30.88 Ramachandran Plot: Outliers : 0.26 % Allowed : 4.22 % Favored : 95.52 % Rotamer: Outliers : 1.21 % Allowed : 21.75 % Favored : 77.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % 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: -0.30 (0.31), residues: 782 helix: 0.63 (0.30), residues: 316 sheet: -0.31 (0.45), residues: 128 loop : -0.86 (0.35), residues: 338 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.047 0.003 TRP B 23 HIS 0.007 0.002 HIS B 342 PHE 0.012 0.002 PHE B 223 TYR 0.032 0.002 TYR B 316 ARG 0.011 0.001 ARG B 109 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1564 Ramachandran restraints generated. 782 Oldfield, 0 Emsley, 782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1564 Ramachandran restraints generated. 782 Oldfield, 0 Emsley, 782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 670 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 68 time to evaluate : 0.746 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 8 outliers final: 6 residues processed: 72 average time/residue: 0.1879 time to fit residues: 18.4479 Evaluate side-chains 65 residues out of total 670 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 59 time to evaluate : 0.722 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.0750 time to fit residues: 1.7778 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 30 optimal weight: 10.0000 chunk 55 optimal weight: 20.0000 chunk 21 optimal weight: 8.9990 chunk 63 optimal weight: 8.9990 chunk 66 optimal weight: 40.0000 chunk 69 optimal weight: 0.0970 chunk 46 optimal weight: 30.0000 chunk 74 optimal weight: 30.0000 chunk 45 optimal weight: 50.0000 chunk 35 optimal weight: 6.9990 chunk 51 optimal weight: 20.0000 overall best weight: 7.0188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 185 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 170 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 185 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 320 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6295 moved from start: 0.7299 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 6470 Z= 0.252 Angle : 0.707 10.843 8736 Z= 0.352 Chirality : 0.043 0.141 954 Planarity : 0.004 0.069 1104 Dihedral : 9.279 133.429 860 Min Nonbonded Distance : 2.160 Molprobity Statistics. All-atom Clashscore : 27.15 Ramachandran Plot: Outliers : 0.26 % Allowed : 3.84 % Favored : 95.91 % Rotamer: Outliers : 0.60 % Allowed : 20.24 % Favored : 79.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % 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: -0.28 (0.30), residues: 782 helix: 0.58 (0.29), residues: 320 sheet: -0.05 (0.46), residues: 126 loop : -0.91 (0.35), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.084 0.003 TRP B 23 HIS 0.006 0.002 HIS B 342 PHE 0.016 0.002 PHE A 223 TYR 0.023 0.002 TYR B 316 ARG 0.010 0.001 ARG B 109 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1564 Ramachandran restraints generated. 782 Oldfield, 0 Emsley, 782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1564 Ramachandran restraints generated. 782 Oldfield, 0 Emsley, 782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 670 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 68 time to evaluate : 0.740 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 4 outliers final: 2 residues processed: 70 average time/residue: 0.1591 time to fit residues: 16.1657 Evaluate side-chains 68 residues out of total 670 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 66 time to evaluate : 0.778 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0603 time to fit residues: 1.2270 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 77 optimal weight: 9.9990 chunk 71 optimal weight: 20.0000 chunk 61 optimal weight: 9.9990 chunk 6 optimal weight: 1.9990 chunk 47 optimal weight: 7.9990 chunk 37 optimal weight: 4.9990 chunk 49 optimal weight: 20.0000 chunk 65 optimal weight: 20.0000 chunk 18 optimal weight: 6.9990 chunk 57 optimal weight: 6.9990 chunk 9 optimal weight: 4.9990 overall best weight: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 185 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 170 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 185 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 320 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6247 moved from start: 0.7486 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 6470 Z= 0.239 Angle : 0.730 10.063 8736 Z= 0.363 Chirality : 0.043 0.174 954 Planarity : 0.004 0.062 1104 Dihedral : 9.415 134.477 860 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 26.99 Ramachandran Plot: Outliers : 0.26 % Allowed : 4.22 % Favored : 95.52 % Rotamer: Outliers : 0.45 % Allowed : 20.69 % Favored : 78.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.26 % 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: -0.20 (0.30), residues: 782 helix: 0.58 (0.30), residues: 318 sheet: 0.29 (0.47), residues: 122 loop : -0.91 (0.35), residues: 342 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.091 0.003 TRP B 23 HIS 0.005 0.001 HIS B 342 PHE 0.016 0.002 PHE B 223 TYR 0.018 0.001 TYR B 316 ARG 0.010 0.001 ARG B 109 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1564 Ramachandran restraints generated. 782 Oldfield, 0 Emsley, 782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1564 Ramachandran restraints generated. 782 Oldfield, 0 Emsley, 782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 670 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 73 time to evaluate : 0.732 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 3 outliers final: 2 residues processed: 73 average time/residue: 0.1538 time to fit residues: 16.0651 Evaluate side-chains 66 residues out of total 670 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 64 time to evaluate : 0.736 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0892 time to fit residues: 1.3528 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 17 optimal weight: 20.0000 chunk 61 optimal weight: 0.9980 chunk 25 optimal weight: 10.0000 chunk 63 optimal weight: 0.9990 chunk 7 optimal weight: 40.0000 chunk 11 optimal weight: 0.6980 chunk 54 optimal weight: 8.9990 chunk 3 optimal weight: 5.9990 chunk 44 optimal weight: 30.0000 chunk 70 optimal weight: 8.9990 chunk 41 optimal weight: 7.9990 overall best weight: 3.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 185 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 170 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.054415 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3081 r_free = 0.3081 target = 0.042760 restraints weight = 35646.400| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3116 r_free = 0.3116 target = 0.044255 restraints weight = 23800.707| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3142 r_free = 0.3142 target = 0.045406 restraints weight = 17546.307| |-----------------------------------------------------------------------------| r_work (final): 0.3120 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8670 moved from start: 0.7690 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 6470 Z= 0.216 Angle : 0.748 12.279 8736 Z= 0.368 Chirality : 0.044 0.189 954 Planarity : 0.004 0.058 1104 Dihedral : 9.452 135.235 860 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 24.77 Ramachandran Plot: Outliers : 0.26 % Allowed : 3.71 % Favored : 96.04 % Rotamer: Outliers : 0.15 % Allowed : 21.60 % Favored : 78.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.26 % 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: -0.14 (0.31), residues: 782 helix: 0.57 (0.30), residues: 318 sheet: 0.47 (0.52), residues: 98 loop : -0.79 (0.33), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A 23 HIS 0.005 0.001 HIS B 67 PHE 0.014 0.002 PHE A 223 TYR 0.016 0.001 TYR B 231 ARG 0.009 0.001 ARG B 109 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1522.52 seconds wall clock time: 28 minutes 47.14 seconds (1727.14 seconds total)