Starting phenix.real_space_refine on Mon Mar 11 01:55:31 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7f46_31444/03_2024/7f46_31444.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7f46_31444/03_2024/7f46_31444.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.79 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7f46_31444/03_2024/7f46_31444.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7f46_31444/03_2024/7f46_31444.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7f46_31444/03_2024/7f46_31444.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7f46_31444/03_2024/7f46_31444.pdb" } resolution = 4.79 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= 0.015 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 25 5.16 5 C 4187 2.51 5 N 1091 2.21 5 O 1261 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "C TYR 38": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 58": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 92": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 140": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 186": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 265": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 275": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 342": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 346": "NH1" <-> "NH2" Residue "B PHE 347": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 364": "OD1" <-> "OD2" Residue "B PHE 377": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 398": "OD1" <-> "OD2" Residue "B ARG 403": "NH1" <-> "NH2" Residue "B TYR 449": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 456": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 466": "NH1" <-> "NH2" Residue "B TYR 473": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ARG 19": "NH1" <-> "NH2" Residue "H PHE 27": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 46": "OE1" <-> "OE2" Residue "H ASP 62": "OD1" <-> "OD2" Residue "H ARG 72": "NH1" <-> "NH2" Residue "H ARG 84": "NH1" <-> "NH2" Residue "H TYR 115": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ASP 1": "OD1" <-> "OD2" Residue "L TYR 35": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ASP 39": "OD1" <-> "OD2" Residue "L TYR 54": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L GLU 86": "OE1" <-> "OE2" Residue "L TYR 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 123": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 145": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L GLU 148": "OE1" <-> "OE2" Residue "L GLU 170": "OE1" <-> "OE2" Residue "L GLU 200": "OE1" <-> "OE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 6564 Number of models: 1 Model: "" Number of chains: 6 Chain: "C" Number of atoms: 1652 Number of conformers: 1 Conformer: "" Number of residues, atoms: 203, 1652 Classifications: {'peptide': 203} Link IDs: {'PTRANS': 10, 'TRANS': 192} Chain breaks: 4 Chain: "B" Number of atoms: 1543 Number of conformers: 1 Conformer: "" Number of residues, atoms: 195, 1543 Classifications: {'peptide': 195} Link IDs: {'PTRANS': 11, 'TRANS': 183} Chain: "H" Number of atoms: 1668 Number of conformers: 1 Conformer: "" Number of residues, atoms: 226, 1668 Classifications: {'peptide': 226} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PCIS': 2, 'PTRANS': 10, 'TRANS': 213} Chain breaks: 2 Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 16 Chain: "L" Number of atoms: 1673 Number of conformers: 1 Conformer: "" Number of residues, atoms: 218, 1673 Classifications: {'peptide': 218} Link IDs: {'PCIS': 3, 'PTRANS': 11, 'TRANS': 203} Chain: "C" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 3.98, per 1000 atoms: 0.61 Number of scatterers: 6564 At special positions: 0 Unit cell: (91.98, 82.125, 129.21, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 25 16.00 O 1261 8.00 N 1091 7.00 C 4187 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=8, symmetry=0 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.04 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.03 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.03 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.04 Simple disulfide: pdb=" SG CYS H 157 " - pdb=" SG CYS H 213 " distance=2.04 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 93 " distance=2.04 Simple disulfide: pdb=" SG CYS L 139 " - pdb=" SG CYS L 199 " distance=2.04 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 Links applied NAG-ASN " NAG B1301 " - " ASN B 343 " " NAG C1301 " - " ASN C 165 " Time building additional restraints: 2.24 Conformation dependent library (CDL) restraints added in 1.3 seconds 1644 Ramachandran restraints generated. 822 Oldfield, 0 Emsley, 822 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1556 Finding SS restraints... Secondary structure from input PDB file: 9 helices and 13 sheets defined 6.3% alpha, 32.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.70 Creating SS restraints... Processing helix chain 'B' and resid 338 through 343 removed outlier: 3.520A pdb=" N ASN B 343 " --> pdb=" O GLY B 339 " (cutoff:3.500A) Processing helix chain 'B' and resid 349 through 353 removed outlier: 3.520A pdb=" N ALA B 352 " --> pdb=" O SER B 349 " (cutoff:3.500A) Processing helix chain 'B' and resid 364 through 371 removed outlier: 4.529A pdb=" N LEU B 368 " --> pdb=" O ASP B 364 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N TYR B 369 " --> pdb=" O TYR B 365 " (cutoff:3.500A) Processing helix chain 'B' and resid 383 through 390 removed outlier: 5.674A pdb=" N ASN B 388 " --> pdb=" O THR B 385 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N ASP B 389 " --> pdb=" O LYS B 386 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N LEU B 390 " --> pdb=" O LEU B 387 " (cutoff:3.500A) Processing helix chain 'B' and resid 404 through 410 removed outlier: 3.761A pdb=" N VAL B 407 " --> pdb=" O GLY B 404 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N ARG B 408 " --> pdb=" O ASP B 405 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N ILE B 410 " --> pdb=" O VAL B 407 " (cutoff:3.500A) Processing helix chain 'B' and resid 417 through 422 Processing helix chain 'H' and resid 28 through 32 removed outlier: 3.905A pdb=" N TYR H 32 " --> pdb=" O PHE H 29 " (cutoff:3.500A) Processing helix chain 'H' and resid 173 through 175 No H-bonds generated for 'chain 'H' and resid 173 through 175' Processing helix chain 'L' and resid 126 through 130 Processing sheet with id=AA1, first strand: chain 'C' and resid 28 through 31 removed outlier: 3.726A pdb=" N SER C 60 " --> pdb=" O SER C 31 " (cutoff:3.500A) removed outlier: 8.430A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 6.672A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 4.798A pdb=" N ALA C 264 " --> pdb=" O THR C 95 " (cutoff:3.500A) removed outlier: 4.136A pdb=" N THR C 95 " --> pdb=" O ALA C 264 " (cutoff:3.500A) removed outlier: 6.214A pdb=" N SER C 205 " --> pdb=" O PRO C 225 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 47 through 55 removed outlier: 4.174A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 84 through 85 removed outlier: 3.723A pdb=" N GLY C 103 " --> pdb=" O LEU C 241 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 354 through 358 removed outlier: 3.603A pdb=" N VAL B 395 " --> pdb=" O ILE B 358 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 452 through 453 Processing sheet with id=AA6, first strand: chain 'H' and resid 3 through 7 Processing sheet with id=AA7, first strand: chain 'H' and resid 11 through 12 removed outlier: 3.668A pdb=" N THR H 124 " --> pdb=" O TYR H 94 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N TYR H 94 " --> pdb=" O THR H 124 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N VAL H 126 " --> pdb=" O ALA H 92 " (cutoff:3.500A) removed outlier: 5.755A pdb=" N ARG H 38 " --> pdb=" O TRP H 47 " (cutoff:3.500A) removed outlier: 5.522A pdb=" N TRP H 47 " --> pdb=" O ARG H 38 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'H' and resid 137 through 141 removed outlier: 6.009A pdb=" N TYR H 193 " --> pdb=" O ASP H 161 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'H' and resid 167 through 171 Processing sheet with id=AB1, first strand: chain 'L' and resid 5 through 7 Processing sheet with id=AB2, first strand: chain 'L' and resid 10 through 13 removed outlier: 3.563A pdb=" N LEU L 11 " --> pdb=" O LYS L 108 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N ASP L 110 " --> pdb=" O LEU L 11 " (cutoff:3.500A) removed outlier: 6.519A pdb=" N TRP L 40 " --> pdb=" O LEU L 52 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'L' and resid 119 through 123 removed outlier: 5.918A pdb=" N TYR L 178 " --> pdb=" O ASN L 143 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'L' and resid 158 through 159 removed outlier: 3.771A pdb=" N VAL L 155 " --> pdb=" O ALA L 158 " (cutoff:3.500A) 221 hydrogen bonds defined for protein. 546 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: 1.83 Time building geometry restraints manager: 2.47 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: 2075 1.34 - 1.46: 1637 1.46 - 1.58: 2986 1.58 - 1.71: 0 1.71 - 1.83: 31 Bond restraints: 6729 Sorted by residual: bond pdb=" N LEU H 206 " pdb=" CA LEU H 206 " ideal model delta sigma weight residual 1.458 1.503 -0.046 1.27e-02 6.20e+03 1.29e+01 bond pdb=" N VAL B 524 " pdb=" CA VAL B 524 " ideal model delta sigma weight residual 1.458 1.495 -0.037 1.18e-02 7.18e+03 9.96e+00 bond pdb=" N LYS H 76 " pdb=" CA LYS H 76 " ideal model delta sigma weight residual 1.457 1.493 -0.036 1.16e-02 7.43e+03 9.70e+00 bond pdb=" N VAL H 103 " pdb=" CA VAL H 103 " ideal model delta sigma weight residual 1.457 1.493 -0.036 1.19e-02 7.06e+03 8.96e+00 bond pdb=" N VAL B 483 " pdb=" CA VAL B 483 " ideal model delta sigma weight residual 1.458 1.495 -0.036 1.21e-02 6.83e+03 8.86e+00 ... (remaining 6724 not shown) Histogram of bond angle deviations from ideal: 99.70 - 106.61: 212 106.61 - 113.52: 3606 113.52 - 120.43: 2489 120.43 - 127.33: 2789 127.33 - 134.24: 60 Bond angle restraints: 9156 Sorted by residual: angle pdb=" N SER H 204 " pdb=" CA SER H 204 " pdb=" C SER H 204 " ideal model delta sigma weight residual 112.38 107.89 4.49 1.22e+00 6.72e-01 1.35e+01 angle pdb=" CA CYS C 166 " pdb=" C CYS C 166 " pdb=" O CYS C 166 " ideal model delta sigma weight residual 121.40 117.34 4.06 1.13e+00 7.83e-01 1.29e+01 angle pdb=" CA SER B 477 " pdb=" C SER B 477 " pdb=" O SER B 477 " ideal model delta sigma weight residual 122.13 118.24 3.89 1.13e+00 7.83e-01 1.18e+01 angle pdb=" N LYS C 187 " pdb=" CA LYS C 187 " pdb=" C LYS C 187 " ideal model delta sigma weight residual 113.89 108.54 5.35 1.58e+00 4.01e-01 1.14e+01 angle pdb=" N SER L 57 " pdb=" CA SER L 57 " pdb=" C SER L 57 " ideal model delta sigma weight residual 114.56 110.32 4.24 1.27e+00 6.20e-01 1.12e+01 ... (remaining 9151 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.08: 3578 17.08 - 34.15: 347 34.15 - 51.23: 54 51.23 - 68.31: 10 68.31 - 85.38: 3 Dihedral angle restraints: 3992 sinusoidal: 1559 harmonic: 2433 Sorted by residual: dihedral pdb=" CB CYS H 157 " pdb=" SG CYS H 157 " pdb=" SG CYS H 213 " pdb=" CB CYS H 213 " ideal model delta sinusoidal sigma weight residual 93.00 141.24 -48.24 1 1.00e+01 1.00e-02 3.21e+01 dihedral pdb=" CB CYS B 336 " pdb=" SG CYS B 336 " pdb=" SG CYS B 361 " pdb=" CB CYS B 361 " ideal model delta sinusoidal sigma weight residual 93.00 48.52 44.48 1 1.00e+01 1.00e-02 2.75e+01 dihedral pdb=" CA CYS B 361 " pdb=" C CYS B 361 " pdb=" N VAL B 362 " pdb=" CA VAL B 362 " ideal model delta harmonic sigma weight residual 180.00 157.16 22.84 0 5.00e+00 4.00e-02 2.09e+01 ... (remaining 3989 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.045: 677 0.045 - 0.089: 243 0.089 - 0.134: 77 0.134 - 0.178: 18 0.178 - 0.222: 4 Chirality restraints: 1019 Sorted by residual: chirality pdb=" C1 NAG B1301 " pdb=" ND2 ASN B 343 " pdb=" C2 NAG B1301 " pdb=" O5 NAG B1301 " both_signs ideal model delta sigma weight residual False -2.40 -2.18 -0.22 2.00e-01 2.50e+01 1.24e+00 chirality pdb=" CA ALA C 222 " pdb=" N ALA C 222 " pdb=" C ALA C 222 " pdb=" CB ALA C 222 " both_signs ideal model delta sigma weight residual False 2.48 2.68 -0.20 2.00e-01 2.50e+01 9.74e-01 chirality pdb=" CA LEU H 206 " pdb=" N LEU H 206 " pdb=" C LEU H 206 " pdb=" CB LEU H 206 " both_signs ideal model delta sigma weight residual False 2.51 2.70 -0.19 2.00e-01 2.50e+01 9.45e-01 ... (remaining 1016 not shown) Planarity restraints: 1180 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG B1301 " -0.287 2.00e-02 2.50e+03 2.46e-01 7.56e+02 pdb=" C7 NAG B1301 " 0.064 2.00e-02 2.50e+03 pdb=" C8 NAG B1301 " 0.017 2.00e-02 2.50e+03 pdb=" N2 NAG B1301 " 0.414 2.00e-02 2.50e+03 pdb=" O7 NAG B1301 " -0.208 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG C1301 " 0.257 2.00e-02 2.50e+03 2.14e-01 5.71e+02 pdb=" C7 NAG C1301 " -0.070 2.00e-02 2.50e+03 pdb=" C8 NAG C1301 " 0.176 2.00e-02 2.50e+03 pdb=" N2 NAG C1301 " -0.355 2.00e-02 2.50e+03 pdb=" O7 NAG C1301 " -0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLU C 224 " -0.065 5.00e-02 4.00e+02 1.00e-01 1.60e+01 pdb=" N PRO C 225 " 0.173 5.00e-02 4.00e+02 pdb=" CA PRO C 225 " -0.055 5.00e-02 4.00e+02 pdb=" CD PRO C 225 " -0.054 5.00e-02 4.00e+02 ... (remaining 1177 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.75: 908 2.75 - 3.29: 6132 3.29 - 3.83: 9898 3.83 - 4.36: 11286 4.36 - 4.90: 20294 Nonbonded interactions: 48518 Sorted by model distance: nonbonded pdb=" OD2 ASP B 398 " pdb=" OH TYR B 423 " model vdw 2.218 2.440 nonbonded pdb=" OG SER B 349 " pdb=" O LEU B 452 " model vdw 2.220 2.440 nonbonded pdb=" O PHE C 106 " pdb=" OG SER C 116 " model vdw 2.223 2.440 nonbonded pdb=" OG SER B 443 " pdb=" O PHE B 497 " model vdw 2.277 2.440 nonbonded pdb=" O ARG L 147 " pdb=" NH1 ARG L 147 " model vdw 2.304 2.520 ... (remaining 48513 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=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: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.240 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 7.310 Check model and map are aligned: 0.090 Set scattering table: 0.060 Process input model: 20.990 Find NCS groups from input model: 0.230 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: 33.830 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6012 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 : 0.006 0.054 6729 Z= 0.377 Angle : 0.840 6.643 9156 Z= 0.507 Chirality : 0.053 0.222 1019 Planarity : 0.011 0.246 1178 Dihedral : 13.319 85.382 2412 Min Nonbonded Distance : 2.218 Molprobity Statistics. All-atom Clashscore : 12.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.88 % Favored : 91.12 % Rotamer: Outliers : 0.00 % Allowed : 0.97 % Favored : 99.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.64 % 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: -2.90 (0.27), residues: 822 helix: -3.98 (0.66), residues: 25 sheet: -0.97 (0.27), residues: 327 loop : -2.62 (0.26), residues: 470 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 436 HIS 0.006 0.001 HIS H 35 PHE 0.020 0.002 PHE H 139 TYR 0.034 0.002 TYR B 473 ARG 0.005 0.001 ARG B 408 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1644 Ramachandran restraints generated. 822 Oldfield, 0 Emsley, 822 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1644 Ramachandran restraints generated. 822 Oldfield, 0 Emsley, 822 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 729 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 75 time to evaluate : 0.650 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: C 53 ASP cc_start: 0.8147 (m-30) cc_final: 0.7851 (m-30) REVERT: H 83 MET cc_start: 0.5586 (mtm) cc_final: 0.4143 (mtm) REVERT: H 102 MET cc_start: 0.0415 (ppp) cc_final: -0.0067 (mpp) REVERT: H 117 MET cc_start: 0.6580 (mtt) cc_final: 0.5373 (mmp) REVERT: H 198 VAL cc_start: 0.1912 (p) cc_final: 0.1363 (t) REVERT: L 41 TYR cc_start: 0.6811 (m-80) cc_final: 0.6403 (m-80) REVERT: L 91 TYR cc_start: 0.6202 (m-10) cc_final: 0.5704 (m-10) outliers start: 0 outliers final: 0 residues processed: 75 average time/residue: 0.1721 time to fit residues: 18.0146 Evaluate side-chains 40 residues out of total 729 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 40 time to evaluate : 0.769 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 69 optimal weight: 4.9990 chunk 62 optimal weight: 2.9990 chunk 34 optimal weight: 7.9990 chunk 21 optimal weight: 0.9980 chunk 41 optimal weight: 6.9990 chunk 33 optimal weight: 3.9990 chunk 64 optimal weight: 5.9990 chunk 24 optimal weight: 4.9990 chunk 39 optimal weight: 0.9980 chunk 47 optimal weight: 7.9990 chunk 74 optimal weight: 6.9990 overall best weight: 2.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 207 HIS C 218 GLN ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 50 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 58 ASN L 203 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6228 moved from start: 0.4778 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.079 6729 Z= 0.379 Angle : 0.880 10.678 9156 Z= 0.462 Chirality : 0.051 0.348 1019 Planarity : 0.007 0.092 1178 Dihedral : 7.183 48.725 950 Min Nonbonded Distance : 2.120 Molprobity Statistics. All-atom Clashscore : 24.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.18 % Favored : 92.82 % Rotamer: Outliers : 0.97 % Allowed : 11.03 % Favored : 88.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.64 % 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: -2.65 (0.27), residues: 822 helix: -4.30 (0.64), residues: 25 sheet: -0.71 (0.29), residues: 318 loop : -2.47 (0.25), residues: 479 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.003 TRP H 53 HIS 0.014 0.003 HIS H 82 PHE 0.025 0.003 PHE L 121 TYR 0.037 0.003 TYR L 145 ARG 0.013 0.001 ARG B 408 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1644 Ramachandran restraints generated. 822 Oldfield, 0 Emsley, 822 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1644 Ramachandran restraints generated. 822 Oldfield, 0 Emsley, 822 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 62 residues out of total 729 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 55 time to evaluate : 0.654 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 387 LEU cc_start: 0.8899 (OUTLIER) cc_final: 0.8564 (mm) REVERT: H 102 MET cc_start: 0.0568 (ppp) cc_final: 0.0276 (mpp) REVERT: H 155 LEU cc_start: -0.7120 (OUTLIER) cc_final: -0.8003 (mp) REVERT: L 53 ILE cc_start: 0.3261 (mt) cc_final: 0.2614 (mt) REVERT: L 77 THR cc_start: 0.4247 (p) cc_final: 0.4028 (p) outliers start: 7 outliers final: 2 residues processed: 62 average time/residue: 0.1502 time to fit residues: 13.6659 Evaluate side-chains 40 residues out of total 729 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 36 time to evaluate : 0.760 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 41 optimal weight: 6.9990 chunk 23 optimal weight: 3.9990 chunk 61 optimal weight: 8.9990 chunk 50 optimal weight: 9.9990 chunk 20 optimal weight: 0.0980 chunk 74 optimal weight: 3.9990 chunk 80 optimal weight: 9.9990 chunk 66 optimal weight: 0.0050 chunk 73 optimal weight: 0.8980 chunk 25 optimal weight: 1.9990 chunk 59 optimal weight: 5.9990 overall best weight: 1.3998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 481 ASN ** B 519 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 82 HIS L 31 HIS L 50 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6218 moved from start: 0.5209 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.068 6729 Z= 0.223 Angle : 0.670 11.438 9156 Z= 0.347 Chirality : 0.046 0.227 1019 Planarity : 0.005 0.092 1178 Dihedral : 6.075 45.319 950 Min Nonbonded Distance : 2.149 Molprobity Statistics. All-atom Clashscore : 17.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.33 % Favored : 93.67 % Rotamer: Outliers : 0.00 % Allowed : 4.14 % Favored : 95.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.64 % 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: -2.44 (0.28), residues: 822 helix: -3.98 (0.67), residues: 25 sheet: -0.73 (0.28), residues: 325 loop : -2.20 (0.26), residues: 472 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP H 53 HIS 0.005 0.001 HIS C 207 PHE 0.015 0.002 PHE L 144 TYR 0.026 0.002 TYR L 145 ARG 0.005 0.001 ARG C 214 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1644 Ramachandran restraints generated. 822 Oldfield, 0 Emsley, 822 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1644 Ramachandran restraints generated. 822 Oldfield, 0 Emsley, 822 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 46 residues out of total 729 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 46 time to evaluate : 0.736 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 102 MET cc_start: 0.1026 (ppp) cc_final: 0.0797 (mpp) REVERT: H 198 VAL cc_start: 0.3291 (p) cc_final: 0.3061 (t) REVERT: L 94 MET cc_start: 0.7442 (ptt) cc_final: 0.7052 (ppp) REVERT: L 178 TYR cc_start: -0.0256 (m-80) cc_final: -0.0733 (m-80) outliers start: 0 outliers final: 0 residues processed: 46 average time/residue: 0.1598 time to fit residues: 10.9462 Evaluate side-chains 38 residues out of total 729 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 38 time to evaluate : 0.741 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 73 optimal weight: 0.0050 chunk 56 optimal weight: 4.9990 chunk 38 optimal weight: 3.9990 chunk 8 optimal weight: 4.9990 chunk 35 optimal weight: 0.8980 chunk 50 optimal weight: 0.0170 chunk 74 optimal weight: 0.8980 chunk 79 optimal weight: 0.9990 chunk 39 optimal weight: 20.0000 chunk 70 optimal weight: 2.9990 chunk 21 optimal weight: 1.9990 overall best weight: 0.5634 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 519 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 50 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6197 moved from start: 0.5388 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 6729 Z= 0.143 Angle : 0.584 7.445 9156 Z= 0.300 Chirality : 0.045 0.213 1019 Planarity : 0.005 0.089 1178 Dihedral : 5.294 41.859 950 Min Nonbonded Distance : 2.202 Molprobity Statistics. All-atom Clashscore : 13.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.72 % Favored : 94.28 % Rotamer: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.64 % 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: -2.09 (0.28), residues: 822 helix: -3.84 (0.72), residues: 25 sheet: -0.59 (0.28), residues: 330 loop : -1.89 (0.28), residues: 467 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP H 171 HIS 0.006 0.001 HIS H 35 PHE 0.015 0.001 PHE L 144 TYR 0.013 0.001 TYR L 178 ARG 0.003 0.000 ARG C 214 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1644 Ramachandran restraints generated. 822 Oldfield, 0 Emsley, 822 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1644 Ramachandran restraints generated. 822 Oldfield, 0 Emsley, 822 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 48 residues out of total 729 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 48 time to evaluate : 0.694 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 456 PHE cc_start: 0.9563 (m-10) cc_final: 0.9361 (m-80) REVERT: H 102 MET cc_start: 0.1465 (ppp) cc_final: 0.1171 (mpp) REVERT: L 145 TYR cc_start: 0.3612 (t80) cc_final: 0.3083 (t80) outliers start: 0 outliers final: 0 residues processed: 48 average time/residue: 0.1668 time to fit residues: 12.2709 Evaluate side-chains 35 residues out of total 729 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 35 time to evaluate : 0.709 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 66 optimal weight: 10.0000 chunk 44 optimal weight: 7.9990 chunk 1 optimal weight: 0.8980 chunk 59 optimal weight: 0.0980 chunk 32 optimal weight: 6.9990 chunk 67 optimal weight: 7.9990 chunk 54 optimal weight: 6.9990 chunk 0 optimal weight: 5.9990 chunk 40 optimal weight: 0.0270 chunk 71 optimal weight: 10.0000 chunk 20 optimal weight: 0.0020 overall best weight: 1.4048 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 519 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 216 ASN L 50 GLN L 58 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6250 moved from start: 0.6404 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 6729 Z= 0.218 Angle : 0.650 9.014 9156 Z= 0.335 Chirality : 0.045 0.222 1019 Planarity : 0.005 0.089 1178 Dihedral : 5.529 35.505 950 Min Nonbonded Distance : 2.150 Molprobity Statistics. All-atom Clashscore : 19.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.33 % Favored : 93.67 % Rotamer: Outliers : 0.00 % Allowed : 4.28 % Favored : 95.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.64 % 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: -1.96 (0.28), residues: 822 helix: -3.70 (0.92), residues: 19 sheet: -0.50 (0.28), residues: 326 loop : -1.83 (0.27), residues: 477 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP C 64 HIS 0.011 0.002 HIS C 66 PHE 0.013 0.002 PHE L 144 TYR 0.042 0.002 TYR C 266 ARG 0.003 0.000 ARG C 214 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1644 Ramachandran restraints generated. 822 Oldfield, 0 Emsley, 822 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1644 Ramachandran restraints generated. 822 Oldfield, 0 Emsley, 822 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 42 residues out of total 729 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 42 time to evaluate : 0.825 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 102 MET cc_start: 0.1670 (ppp) cc_final: 0.1333 (mpp) outliers start: 0 outliers final: 0 residues processed: 42 average time/residue: 0.1361 time to fit residues: 9.2333 Evaluate side-chains 31 residues out of total 729 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 31 time to evaluate : 0.734 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 26 optimal weight: 1.9990 chunk 71 optimal weight: 3.9990 chunk 15 optimal weight: 5.9990 chunk 46 optimal weight: 10.0000 chunk 19 optimal weight: 0.4980 chunk 79 optimal weight: 0.9990 chunk 65 optimal weight: 10.0000 chunk 36 optimal weight: 7.9990 chunk 6 optimal weight: 0.7980 chunk 41 optimal weight: 9.9990 chunk 76 optimal weight: 0.9980 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 519 HIS L 50 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6233 moved from start: 0.6751 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 6729 Z= 0.174 Angle : 0.585 6.595 9156 Z= 0.302 Chirality : 0.044 0.172 1019 Planarity : 0.005 0.090 1178 Dihedral : 4.911 30.107 950 Min Nonbonded Distance : 2.145 Molprobity Statistics. All-atom Clashscore : 14.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.84 % Favored : 94.16 % Rotamer: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.64 % 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: -1.80 (0.28), residues: 822 helix: -3.60 (0.99), residues: 19 sheet: -0.29 (0.29), residues: 322 loop : -1.80 (0.27), residues: 481 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 64 HIS 0.014 0.002 HIS C 66 PHE 0.014 0.001 PHE L 144 TYR 0.021 0.001 TYR C 266 ARG 0.003 0.000 ARG B 408 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1644 Ramachandran restraints generated. 822 Oldfield, 0 Emsley, 822 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1644 Ramachandran restraints generated. 822 Oldfield, 0 Emsley, 822 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 37 residues out of total 729 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 37 time to evaluate : 0.786 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 102 MET cc_start: 0.1689 (ppp) cc_final: 0.1398 (mpp) REVERT: L 91 TYR cc_start: 0.5403 (m-10) cc_final: 0.5050 (m-10) REVERT: L 94 MET cc_start: 0.7682 (ptt) cc_final: 0.7347 (ppp) REVERT: L 178 TYR cc_start: 0.1512 (m-10) cc_final: 0.1277 (m-10) outliers start: 0 outliers final: 0 residues processed: 37 average time/residue: 0.1803 time to fit residues: 9.8567 Evaluate side-chains 29 residues out of total 729 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 29 time to evaluate : 0.751 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 8 optimal weight: 3.9990 chunk 45 optimal weight: 0.4980 chunk 57 optimal weight: 6.9990 chunk 44 optimal weight: 10.0000 chunk 66 optimal weight: 8.9990 chunk 79 optimal weight: 0.9990 chunk 49 optimal weight: 0.9980 chunk 48 optimal weight: 9.9990 chunk 36 optimal weight: 8.9990 chunk 31 optimal weight: 0.7980 chunk 47 optimal weight: 5.9990 overall best weight: 1.4584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 50 GLN L 58 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6261 moved from start: 0.7707 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.069 6729 Z= 0.224 Angle : 0.643 7.104 9156 Z= 0.334 Chirality : 0.045 0.257 1019 Planarity : 0.005 0.092 1178 Dihedral : 5.442 33.988 950 Min Nonbonded Distance : 2.083 Molprobity Statistics. All-atom Clashscore : 20.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.93 % Favored : 93.07 % Rotamer: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.64 % 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: -1.88 (0.28), residues: 822 helix: -3.62 (0.92), residues: 19 sheet: -0.35 (0.29), residues: 330 loop : -1.86 (0.27), residues: 473 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP H 171 HIS 0.011 0.002 HIS C 66 PHE 0.020 0.002 PHE C 135 TYR 0.026 0.002 TYR L 145 ARG 0.003 0.000 ARG B 509 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1644 Ramachandran restraints generated. 822 Oldfield, 0 Emsley, 822 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1644 Ramachandran restraints generated. 822 Oldfield, 0 Emsley, 822 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 43 residues out of total 729 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 43 time to evaluate : 0.724 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 102 MET cc_start: 0.1706 (ppp) cc_final: 0.1413 (mpp) REVERT: L 94 MET cc_start: 0.7742 (ptt) cc_final: 0.7438 (ppp) outliers start: 0 outliers final: 0 residues processed: 43 average time/residue: 0.1530 time to fit residues: 9.9117 Evaluate side-chains 28 residues out of total 729 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 28 time to evaluate : 0.721 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 23 optimal weight: 5.9990 chunk 15 optimal weight: 4.9990 chunk 50 optimal weight: 5.9990 chunk 53 optimal weight: 6.9990 chunk 39 optimal weight: 9.9990 chunk 7 optimal weight: 0.5980 chunk 62 optimal weight: 9.9990 chunk 71 optimal weight: 7.9990 chunk 75 optimal weight: 3.9990 chunk 69 optimal weight: 0.9980 chunk 73 optimal weight: 0.6980 overall best weight: 2.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 137 ASN ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 481 ASN ** L 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6272 moved from start: 0.8760 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.078 6729 Z= 0.296 Angle : 0.744 9.406 9156 Z= 0.389 Chirality : 0.048 0.300 1019 Planarity : 0.006 0.100 1178 Dihedral : 6.007 35.797 950 Min Nonbonded Distance : 2.071 Molprobity Statistics. All-atom Clashscore : 24.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.88 % Favored : 91.12 % Rotamer: Outliers : 0.00 % Allowed : 1.24 % Favored : 98.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.64 % 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: -2.04 (0.28), residues: 822 helix: -3.88 (0.71), residues: 18 sheet: -0.29 (0.29), residues: 326 loop : -2.12 (0.26), residues: 478 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP H 171 HIS 0.010 0.002 HIS C 66 PHE 0.019 0.002 PHE C 186 TYR 0.032 0.002 TYR L 145 ARG 0.004 0.001 ARG H 104 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1644 Ramachandran restraints generated. 822 Oldfield, 0 Emsley, 822 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1644 Ramachandran restraints generated. 822 Oldfield, 0 Emsley, 822 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 39 residues out of total 729 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 39 time to evaluate : 0.740 Fit side-chains revert: symmetry clash REVERT: H 102 MET cc_start: 0.1453 (ppp) cc_final: 0.1142 (mpp) REVERT: L 91 TYR cc_start: 0.5138 (m-80) cc_final: 0.4775 (m-10) REVERT: L 94 MET cc_start: 0.8143 (ptt) cc_final: 0.7772 (ppp) outliers start: 0 outliers final: 0 residues processed: 39 average time/residue: 0.1527 time to fit residues: 9.1817 Evaluate side-chains 27 residues out of total 729 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 27 time to evaluate : 0.728 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 75 optimal weight: 0.9990 chunk 44 optimal weight: 9.9990 chunk 32 optimal weight: 0.8980 chunk 57 optimal weight: 4.9990 chunk 22 optimal weight: 2.9990 chunk 66 optimal weight: 0.7980 chunk 69 optimal weight: 0.6980 chunk 73 optimal weight: 2.9990 chunk 48 optimal weight: 6.9990 chunk 77 optimal weight: 1.9990 chunk 47 optimal weight: 0.7980 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 31 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6245 moved from start: 0.8621 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 6729 Z= 0.174 Angle : 0.627 7.600 9156 Z= 0.321 Chirality : 0.045 0.199 1019 Planarity : 0.005 0.100 1178 Dihedral : 5.395 30.848 950 Min Nonbonded Distance : 2.117 Molprobity Statistics. All-atom Clashscore : 16.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.57 % Favored : 93.43 % Rotamer: Outliers : 0.00 % Allowed : 0.55 % Favored : 99.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.64 % 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: -1.78 (0.28), residues: 822 helix: -3.39 (0.81), residues: 24 sheet: -0.07 (0.30), residues: 315 loop : -1.92 (0.26), residues: 483 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP H 47 HIS 0.010 0.001 HIS C 66 PHE 0.015 0.001 PHE L 144 TYR 0.015 0.001 TYR C 266 ARG 0.002 0.000 ARG C 190 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1644 Ramachandran restraints generated. 822 Oldfield, 0 Emsley, 822 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1644 Ramachandran restraints generated. 822 Oldfield, 0 Emsley, 822 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 44 residues out of total 729 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 44 time to evaluate : 0.850 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 414 GLN cc_start: 0.8646 (tp-100) cc_final: 0.8355 (tp-100) REVERT: H 102 MET cc_start: 0.1596 (ppp) cc_final: 0.1303 (mpp) outliers start: 0 outliers final: 0 residues processed: 44 average time/residue: 0.1704 time to fit residues: 11.5434 Evaluate side-chains 34 residues out of total 729 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 34 time to evaluate : 0.757 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 36 optimal weight: 5.9990 chunk 54 optimal weight: 4.9990 chunk 81 optimal weight: 5.9990 chunk 75 optimal weight: 0.2980 chunk 65 optimal weight: 0.9990 chunk 6 optimal weight: 5.9990 chunk 50 optimal weight: 5.9990 chunk 39 optimal weight: 9.9990 chunk 51 optimal weight: 8.9990 chunk 69 optimal weight: 5.9990 chunk 19 optimal weight: 0.8980 overall best weight: 2.6386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 33 ASN ** L 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6280 moved from start: 0.9821 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.074 6729 Z= 0.346 Angle : 0.820 9.976 9156 Z= 0.426 Chirality : 0.050 0.357 1019 Planarity : 0.006 0.109 1178 Dihedral : 6.514 39.032 950 Min Nonbonded Distance : 2.032 Molprobity Statistics. All-atom Clashscore : 30.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.73 % Favored : 90.27 % Rotamer: Outliers : 0.00 % Allowed : 0.41 % Favored : 99.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.64 % 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: -2.24 (0.28), residues: 822 helix: -4.37 (0.44), residues: 24 sheet: -0.36 (0.29), residues: 334 loop : -2.27 (0.26), residues: 464 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.003 TRP H 171 HIS 0.006 0.002 HIS H 181 PHE 0.020 0.003 PHE C 32 TYR 0.041 0.003 TYR L 145 ARG 0.008 0.001 ARG H 104 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1644 Ramachandran restraints generated. 822 Oldfield, 0 Emsley, 822 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1644 Ramachandran restraints generated. 822 Oldfield, 0 Emsley, 822 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 46 residues out of total 729 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 46 time to evaluate : 0.571 Fit side-chains revert: symmetry clash REVERT: H 102 MET cc_start: 0.1794 (ppp) cc_final: 0.1430 (mpp) outliers start: 0 outliers final: 0 residues processed: 46 average time/residue: 0.1421 time to fit residues: 10.1017 Evaluate side-chains 30 residues out of total 729 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 30 time to evaluate : 0.732 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 59 optimal weight: 3.9990 chunk 9 optimal weight: 7.9990 chunk 18 optimal weight: 2.9990 chunk 65 optimal weight: 1.9990 chunk 27 optimal weight: 0.0980 chunk 66 optimal weight: 3.9990 chunk 8 optimal weight: 10.0000 chunk 12 optimal weight: 0.7980 chunk 57 optimal weight: 0.6980 chunk 3 optimal weight: 0.7980 chunk 47 optimal weight: 6.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 172 ASN ** 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 = 0.4266 r_free = 0.4266 target = 0.137225 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3869 r_free = 0.3869 target = 0.099965 restraints weight = 61879.298| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.3816 r_free = 0.3816 target = 0.097239 restraints weight = 61372.624| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3819 r_free = 0.3819 target = 0.095883 restraints weight = 50101.374| |-----------------------------------------------------------------------------| r_work (final): 0.3573 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6343 moved from start: 0.9663 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 6729 Z= 0.177 Angle : 0.658 7.921 9156 Z= 0.337 Chirality : 0.046 0.192 1019 Planarity : 0.005 0.102 1178 Dihedral : 5.557 26.006 950 Min Nonbonded Distance : 2.102 Molprobity Statistics. All-atom Clashscore : 17.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.93 % Favored : 93.07 % Rotamer: Outliers : 0.00 % Allowed : 0.69 % Favored : 99.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.64 % 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: -1.99 (0.28), residues: 822 helix: -3.76 (0.63), residues: 30 sheet: -0.09 (0.30), residues: 315 loop : -2.12 (0.26), residues: 477 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP H 120 HIS 0.007 0.001 HIS C 66 PHE 0.016 0.001 PHE L 144 TYR 0.014 0.001 TYR C 266 ARG 0.005 0.000 ARG B 408 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1808.85 seconds wall clock time: 33 minutes 41.64 seconds (2021.64 seconds total)