Starting phenix.real_space_refine on Sat Feb 17 20:45:19 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ul6_26593/02_2024/7ul6_26593.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ul6_26593/02_2024/7ul6_26593.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.73 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ul6_26593/02_2024/7ul6_26593.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ul6_26593/02_2024/7ul6_26593.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ul6_26593/02_2024/7ul6_26593.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ul6_26593/02_2024/7ul6_26593.pdb" } resolution = 3.73 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= 0.006 sd= 0.103 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 6628 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 S 24 5.16 5 C 4272 2.51 5 N 1146 2.21 5 O 1212 1.98 5 H 6614 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 72": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A GLU 111": "OE1" <-> "OE2" Residue "A ASP 192": "OD1" <-> "OD2" Residue "A TYR 239": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 243": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ASP 367": "OD1" <-> "OD2" Residue "A TYR 369": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B ASP 88": "OD1" <-> "OD2" Residue "B GLU 92": "OE1" <-> "OE2" Residue "B TYR 131": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B ASP 192": "OD1" <-> "OD2" Residue "B GLU 208": "OE1" <-> "OE2" Residue "B ASP 229": "OD1" <-> "OD2" Residue "B PHE 243": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B TYR 311": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B ASP 367": "OD1" <-> "OD2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 13268 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 6634 Number of conformers: 1 Conformer: "" Number of residues, atoms: 439, 6634 Classifications: {'peptide': 439} Link IDs: {'PCIS': 1, 'PTRANS': 20, 'TRANS': 417} Chain breaks: 2 Unresolved non-hydrogen bonds: 66 Unresolved non-hydrogen angles: 85 Unresolved non-hydrogen dihedrals: 55 Unresolved non-hydrogen chiralities: 9 Planarities with less than four sites: {'PHE:plan': 1, 'TYR:plan': 2, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 30 Chain: "B" Number of atoms: 6634 Number of conformers: 1 Conformer: "" Number of residues, atoms: 439, 6634 Classifications: {'peptide': 439} Link IDs: {'PCIS': 1, 'PTRANS': 20, 'TRANS': 417} Chain breaks: 2 Unresolved non-hydrogen bonds: 66 Unresolved non-hydrogen angles: 85 Unresolved non-hydrogen dihedrals: 55 Unresolved non-hydrogen chiralities: 9 Planarities with less than four sites: {'PHE:plan': 1, 'TYR:plan': 2, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 30 Time building chain proxies: 6.00, per 1000 atoms: 0.45 Number of scatterers: 13268 At special positions: 0 Unit cell: (89.925, 91.575, 103.95, 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 24 16.00 O 1212 8.00 N 1146 7.00 C 4272 6.00 H 6614 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS A 337 " - pdb=" SG CYS A 363 " distance=2.03 Simple disulfide: pdb=" SG CYS B 337 " - pdb=" SG CYS B 363 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 12.75 Conformation dependent library (CDL) restraints added in 1.5 seconds 1732 Ramachandran restraints generated. 866 Oldfield, 0 Emsley, 866 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1628 Finding SS restraints... Secondary structure from input PDB file: 38 helices and 10 sheets defined 52.1% alpha, 18.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.37 Creating SS restraints... Processing helix chain 'A' and resid 40 through 55 Processing helix chain 'A' and resid 96 through 111 removed outlier: 4.000A pdb=" N PHE A 100 " --> pdb=" O MET A 96 " (cutoff:3.500A) Processing helix chain 'A' and resid 119 through 123 Processing helix chain 'A' and resid 139 through 145 removed outlier: 3.680A pdb=" N PHE A 143 " --> pdb=" O THR A 139 " (cutoff:3.500A) Processing helix chain 'A' and resid 153 through 160 removed outlier: 3.693A pdb=" N ARG A 157 " --> pdb=" O SER A 153 " (cutoff:3.500A) Processing helix chain 'A' and resid 166 through 171 Processing helix chain 'A' and resid 189 through 203 removed outlier: 3.913A pdb=" N VAL A 193 " --> pdb=" O ALA A 189 " (cutoff:3.500A) Processing helix chain 'A' and resid 205 through 214 Processing helix chain 'A' and resid 254 through 261 Proline residue: A 259 - end of helix Processing helix chain 'A' and resid 267 through 278 Processing helix chain 'A' and resid 279 through 283 removed outlier: 4.384A pdb=" N ALA A 282 " --> pdb=" O HIS A 279 " (cutoff:3.500A) Processing helix chain 'A' and resid 284 through 295 removed outlier: 3.628A pdb=" N TRP A 295 " --> pdb=" O MET A 291 " (cutoff:3.500A) Processing helix chain 'A' and resid 342 through 344 No H-bonds generated for 'chain 'A' and resid 342 through 344' Processing helix chain 'A' and resid 361 through 373 removed outlier: 3.580A pdb=" N ILE A 366 " --> pdb=" O LEU A 362 " (cutoff:3.500A) removed outlier: 4.435A pdb=" N ASP A 367 " --> pdb=" O CYS A 363 " (cutoff:3.500A) Processing helix chain 'A' and resid 381 through 414 Processing helix chain 'A' and resid 434 through 455 removed outlier: 4.532A pdb=" N VAL A 439 " --> pdb=" O ILE A 435 " (cutoff:3.500A) Proline residue: A 440 - end of helix removed outlier: 3.906A pdb=" N ALA A 445 " --> pdb=" O GLY A 441 " (cutoff:3.500A) Proline residue: A 451 - end of helix Processing helix chain 'A' and resid 459 through 467 Processing helix chain 'A' and resid 468 through 471 Processing helix chain 'A' and resid 472 through 495 Processing helix chain 'B' and resid 40 through 55 Processing helix chain 'B' and resid 96 through 111 removed outlier: 3.820A pdb=" N PHE B 100 " --> pdb=" O MET B 96 " (cutoff:3.500A) Processing helix chain 'B' and resid 119 through 123 Processing helix chain 'B' and resid 139 through 145 removed outlier: 3.577A pdb=" N PHE B 143 " --> pdb=" O THR B 139 " (cutoff:3.500A) Processing helix chain 'B' and resid 153 through 159 removed outlier: 3.663A pdb=" N ARG B 157 " --> pdb=" O SER B 153 " (cutoff:3.500A) Processing helix chain 'B' and resid 166 through 172 Processing helix chain 'B' and resid 189 through 203 removed outlier: 3.896A pdb=" N VAL B 193 " --> pdb=" O ALA B 189 " (cutoff:3.500A) Processing helix chain 'B' and resid 205 through 214 Processing helix chain 'B' and resid 254 through 258 removed outlier: 3.581A pdb=" N VAL B 258 " --> pdb=" O ARG B 255 " (cutoff:3.500A) Processing helix chain 'B' and resid 267 through 279 Processing helix chain 'B' and resid 284 through 295 removed outlier: 3.613A pdb=" N TRP B 295 " --> pdb=" O MET B 291 " (cutoff:3.500A) Processing helix chain 'B' and resid 342 through 344 No H-bonds generated for 'chain 'B' and resid 342 through 344' Processing helix chain 'B' and resid 356 through 360 Processing helix chain 'B' and resid 361 through 372 Processing helix chain 'B' and resid 381 through 416 Processing helix chain 'B' and resid 434 through 455 removed outlier: 4.596A pdb=" N VAL B 439 " --> pdb=" O ILE B 435 " (cutoff:3.500A) Proline residue: B 440 - end of helix removed outlier: 4.054A pdb=" N ALA B 445 " --> pdb=" O GLY B 441 " (cutoff:3.500A) Proline residue: B 451 - end of helix Processing helix chain 'B' and resid 459 through 467 Processing helix chain 'B' and resid 468 through 471 Processing helix chain 'B' and resid 472 through 495 Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 84 removed outlier: 6.468A pdb=" N LYS A 83 " --> pdb=" O ALA A 77 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N SER A 335 " --> pdb=" O ALA A 352 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 83 through 84 removed outlier: 6.468A pdb=" N LYS A 83 " --> pdb=" O ALA A 77 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N SER A 335 " --> pdb=" O ALA A 352 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 90 through 92 Processing sheet with id=AA4, first strand: chain 'A' and resid 134 through 135 Processing sheet with id=AA5, first strand: chain 'A' and resid 239 through 242 Processing sheet with id=AA6, first strand: chain 'B' and resid 83 through 84 removed outlier: 6.426A pdb=" N LYS B 83 " --> pdb=" O ALA B 77 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N SER B 335 " --> pdb=" O ALA B 352 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 83 through 84 removed outlier: 6.426A pdb=" N LYS B 83 " --> pdb=" O ALA B 77 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N SER B 335 " --> pdb=" O ALA B 352 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 90 through 92 Processing sheet with id=AA9, first strand: chain 'B' and resid 134 through 135 Processing sheet with id=AB1, first strand: chain 'B' and resid 239 through 242 412 hydrogen bonds defined for protein. 1134 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: 5.69 Time building geometry restraints manager: 12.69 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 6612 1.03 - 1.23: 4 1.23 - 1.42: 2816 1.42 - 1.62: 3936 1.62 - 1.81: 42 Bond restraints: 13410 Sorted by residual: bond pdb=" CB PRO B 151 " pdb=" CG PRO B 151 " ideal model delta sigma weight residual 1.492 1.604 -0.112 5.00e-02 4.00e+02 4.99e+00 bond pdb=" CG PRO A 151 " pdb=" CD PRO A 151 " ideal model delta sigma weight residual 1.503 1.579 -0.076 3.40e-02 8.65e+02 4.94e+00 bond pdb=" CB PRO A 151 " pdb=" CG PRO A 151 " ideal model delta sigma weight residual 1.492 1.598 -0.106 5.00e-02 4.00e+02 4.47e+00 bond pdb=" N PRO A 151 " pdb=" CA PRO A 151 " ideal model delta sigma weight residual 1.469 1.454 0.015 1.28e-02 6.10e+03 1.33e+00 bond pdb=" CG PRO B 151 " pdb=" CD PRO B 151 " ideal model delta sigma weight residual 1.503 1.538 -0.035 3.40e-02 8.65e+02 1.04e+00 ... (remaining 13405 not shown) Histogram of bond angle deviations from ideal: 100.29 - 107.04: 305 107.04 - 113.78: 15875 113.78 - 120.53: 4418 120.53 - 127.27: 3567 127.27 - 134.02: 85 Bond angle restraints: 24250 Sorted by residual: angle pdb=" CA PRO B 151 " pdb=" N PRO B 151 " pdb=" CD PRO B 151 " ideal model delta sigma weight residual 112.00 104.62 7.38 1.40e+00 5.10e-01 2.78e+01 angle pdb=" CA PRO A 151 " pdb=" N PRO A 151 " pdb=" CD PRO A 151 " ideal model delta sigma weight residual 112.00 104.76 7.24 1.40e+00 5.10e-01 2.68e+01 angle pdb=" N ALA A 364 " pdb=" CA ALA A 364 " pdb=" C ALA A 364 " ideal model delta sigma weight residual 113.43 107.77 5.66 1.26e+00 6.30e-01 2.02e+01 angle pdb=" N ILE B 359 " pdb=" CA ILE B 359 " pdb=" C ILE B 359 " ideal model delta sigma weight residual 111.91 108.67 3.24 8.90e-01 1.26e+00 1.33e+01 angle pdb=" N ILE A 359 " pdb=" CA ILE A 359 " pdb=" C ILE A 359 " ideal model delta sigma weight residual 112.80 108.74 4.06 1.15e+00 7.56e-01 1.24e+01 ... (remaining 24245 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.96: 5780 17.96 - 35.91: 374 35.91 - 53.87: 141 53.87 - 71.83: 30 71.83 - 89.78: 9 Dihedral angle restraints: 6334 sinusoidal: 3392 harmonic: 2942 Sorted by residual: dihedral pdb=" CB CYS B 337 " pdb=" SG CYS B 337 " pdb=" SG CYS B 363 " pdb=" CB CYS B 363 " ideal model delta sinusoidal sigma weight residual -86.00 -144.88 58.88 1 1.00e+01 1.00e-02 4.64e+01 dihedral pdb=" CB CYS A 337 " pdb=" SG CYS A 337 " pdb=" SG CYS A 363 " pdb=" CB CYS A 363 " ideal model delta sinusoidal sigma weight residual -86.00 -143.45 57.45 1 1.00e+01 1.00e-02 4.44e+01 dihedral pdb=" CA TRP B 315 " pdb=" C TRP B 315 " pdb=" N PHE B 316 " pdb=" CA PHE B 316 " ideal model delta harmonic sigma weight residual 180.00 161.57 18.43 0 5.00e+00 4.00e-02 1.36e+01 ... (remaining 6331 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.029: 646 0.029 - 0.057: 275 0.057 - 0.086: 94 0.086 - 0.114: 49 0.114 - 0.143: 16 Chirality restraints: 1080 Sorted by residual: chirality pdb=" CA VAL B 73 " pdb=" N VAL B 73 " pdb=" C VAL B 73 " pdb=" CB VAL B 73 " both_signs ideal model delta sigma weight residual False 2.44 2.58 -0.14 2.00e-01 2.50e+01 5.11e-01 chirality pdb=" CA VAL A 73 " pdb=" N VAL A 73 " pdb=" C VAL A 73 " pdb=" CB VAL A 73 " both_signs ideal model delta sigma weight residual False 2.44 2.58 -0.14 2.00e-01 2.50e+01 5.01e-01 chirality pdb=" CA VAL A 301 " pdb=" N VAL A 301 " pdb=" C VAL A 301 " pdb=" CB VAL A 301 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 4.16e-01 ... (remaining 1077 not shown) Planarity restraints: 2020 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU B 150 " -0.058 5.00e-02 4.00e+02 8.45e-02 1.14e+01 pdb=" N PRO B 151 " 0.146 5.00e-02 4.00e+02 pdb=" CA PRO B 151 " -0.041 5.00e-02 4.00e+02 pdb=" CD PRO B 151 " -0.046 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE A 474 " -0.049 5.00e-02 4.00e+02 7.33e-02 8.60e+00 pdb=" N PRO A 475 " 0.127 5.00e-02 4.00e+02 pdb=" CA PRO A 475 " -0.037 5.00e-02 4.00e+02 pdb=" CD PRO A 475 " -0.041 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU A 150 " 0.051 5.00e-02 4.00e+02 7.29e-02 8.51e+00 pdb=" N PRO A 151 " -0.126 5.00e-02 4.00e+02 pdb=" CA PRO A 151 " 0.035 5.00e-02 4.00e+02 pdb=" CD PRO A 151 " 0.040 5.00e-02 4.00e+02 ... (remaining 2017 not shown) Histogram of nonbonded interaction distances: 1.61 - 2.20: 797 2.20 - 2.80: 27454 2.80 - 3.40: 37046 3.40 - 4.00: 48147 4.00 - 4.60: 74312 Nonbonded interactions: 187756 Sorted by model distance: nonbonded pdb=" O GLY A 314 " pdb=" HD1 HIS A 327 " model vdw 1.606 1.850 nonbonded pdb=" OD1 ASN B 85 " pdb=" HH TYR B 91 " model vdw 1.641 1.850 nonbonded pdb="HD21 ASN B 130 " pdb=" OD1 ASN B 173 " model vdw 1.654 1.850 nonbonded pdb=" HG1 THR A 101 " pdb=" O PRO A 259 " model vdw 1.662 1.850 nonbonded pdb=" OD1 ASN A 85 " pdb=" HH TYR A 91 " model vdw 1.668 1.850 ... (remaining 187751 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: 1.260 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.140 Construct map_model_manager: 0.220 Extract box with map and model: 4.290 Check model and map are aligned: 0.230 Set scattering table: 0.120 Process input model: 48.250 Find NCS groups from input model: 0.610 Set up NCS constraints: 0.080 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: 0.010 Load rotamer database and sin/cos tables:2.780 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 57.990 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7574 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 : 0.003 0.112 6796 Z= 0.169 Angle : 0.603 7.381 9266 Z= 0.354 Chirality : 0.041 0.143 1080 Planarity : 0.006 0.084 1190 Dihedral : 14.366 89.782 2398 Min Nonbonded Distance : 2.006 Molprobity Statistics. All-atom Clashscore : 5.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer: Outliers : 0.15 % Allowed : 12.28 % Favored : 87.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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: 1.33 (0.29), residues: 866 helix: 1.55 (0.27), residues: 382 sheet: -1.14 (0.60), residues: 62 loop : 0.76 (0.31), residues: 422 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP B 273 HIS 0.007 0.001 HIS B 327 PHE 0.007 0.001 PHE A 483 TYR 0.012 0.001 TYR B 131 ARG 0.004 0.000 ARG A 255 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1732 Ramachandran restraints generated. 866 Oldfield, 0 Emsley, 866 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1732 Ramachandran restraints generated. 866 Oldfield, 0 Emsley, 866 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 281 is missing expected H atoms. Skipping. Residue VAL 405 is missing expected H atoms. Skipping. Residue VAL 406 is missing expected H atoms. Skipping. Residue VAL 412 is missing expected H atoms. Skipping. Residue TYR 413 is missing expected H atoms. Skipping. Residue TYR 433 is missing expected H atoms. Skipping. Residue ILE 434 is missing expected H atoms. Skipping. Residue ILE 435 is missing expected H atoms. Skipping. Residue THR 486 is missing expected H atoms. Skipping. Residue ILE 491 is missing expected H atoms. Skipping. Residue LYS 492 is missing expected H atoms. Skipping. Residue ILE 494 is missing expected H atoms. Skipping. Residue LYS 281 is missing expected H atoms. Skipping. Residue VAL 405 is missing expected H atoms. Skipping. Residue VAL 406 is missing expected H atoms. Skipping. Residue VAL 412 is missing expected H atoms. Skipping. Residue TYR 413 is missing expected H atoms. Skipping. Residue TYR 433 is missing expected H atoms. Skipping. Residue ILE 434 is missing expected H atoms. Skipping. Residue ILE 435 is missing expected H atoms. Skipping. Residue THR 486 is missing expected H atoms. Skipping. Residue ILE 491 is missing expected H atoms. Skipping. Residue LYS 492 is missing expected H atoms. Skipping. Residue ILE 494 is missing expected H atoms. Skipping. Evaluate side-chains 135 residues out of total 716 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 134 time to evaluate : 1.312 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 227 LYS cc_start: 0.6960 (mptt) cc_final: 0.6650 (mptt) REVERT: A 367 ASP cc_start: 0.8655 (OUTLIER) cc_final: 0.8356 (m-30) outliers start: 1 outliers final: 0 residues processed: 135 average time/residue: 0.3586 time to fit residues: 67.8337 Evaluate side-chains 119 residues out of total 716 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 118 time to evaluate : 1.058 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 367 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 72 optimal weight: 2.9990 chunk 65 optimal weight: 2.9990 chunk 36 optimal weight: 2.9990 chunk 22 optimal weight: 2.9990 chunk 43 optimal weight: 3.9990 chunk 34 optimal weight: 1.9990 chunk 67 optimal weight: 6.9990 chunk 26 optimal weight: 2.9990 chunk 40 optimal weight: 2.9990 chunk 50 optimal weight: 3.9990 chunk 78 optimal weight: 0.9980 overall best weight: 2.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 110 GLN A 130 ASN B 116 GLN B 130 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7766 moved from start: 0.1352 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.051 6796 Z= 0.390 Angle : 0.655 6.830 9266 Z= 0.356 Chirality : 0.045 0.150 1080 Planarity : 0.005 0.054 1190 Dihedral : 5.185 52.352 944 Min Nonbonded Distance : 1.929 Molprobity Statistics. All-atom Clashscore : 6.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.39 % Favored : 95.61 % Rotamer: Outliers : 1.75 % Allowed : 12.57 % Favored : 85.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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: 0.86 (0.29), residues: 866 helix: 1.18 (0.26), residues: 418 sheet: -0.53 (0.62), residues: 74 loop : 0.27 (0.34), residues: 374 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.003 TRP A 400 HIS 0.004 0.001 HIS B 264 PHE 0.016 0.002 PHE B 316 TYR 0.014 0.002 TYR B 369 ARG 0.003 0.000 ARG B 213 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1732 Ramachandran restraints generated. 866 Oldfield, 0 Emsley, 866 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1732 Ramachandran restraints generated. 866 Oldfield, 0 Emsley, 866 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 281 is missing expected H atoms. Skipping. Residue VAL 405 is missing expected H atoms. Skipping. Residue VAL 406 is missing expected H atoms. Skipping. Residue VAL 412 is missing expected H atoms. Skipping. Residue TYR 413 is missing expected H atoms. Skipping. Residue TYR 433 is missing expected H atoms. Skipping. Residue ILE 434 is missing expected H atoms. Skipping. Residue ILE 435 is missing expected H atoms. Skipping. Residue THR 486 is missing expected H atoms. Skipping. Residue ILE 491 is missing expected H atoms. Skipping. Residue LYS 492 is missing expected H atoms. Skipping. Residue ILE 494 is missing expected H atoms. Skipping. Residue LYS 281 is missing expected H atoms. Skipping. Residue VAL 405 is missing expected H atoms. Skipping. Residue VAL 406 is missing expected H atoms. Skipping. Residue VAL 412 is missing expected H atoms. Skipping. Residue TYR 413 is missing expected H atoms. Skipping. Residue TYR 433 is missing expected H atoms. Skipping. Residue ILE 434 is missing expected H atoms. Skipping. Residue ILE 435 is missing expected H atoms. Skipping. Residue THR 486 is missing expected H atoms. Skipping. Residue ILE 491 is missing expected H atoms. Skipping. Residue LYS 492 is missing expected H atoms. Skipping. Residue ILE 494 is missing expected H atoms. Skipping. Evaluate side-chains 140 residues out of total 716 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 128 time to evaluate : 1.182 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 227 LYS cc_start: 0.7087 (mptt) cc_final: 0.6823 (mptt) REVERT: A 298 ASN cc_start: 0.8025 (t0) cc_final: 0.7753 (t0) REVERT: B 298 ASN cc_start: 0.8082 (t0) cc_final: 0.7819 (t0) REVERT: B 307 ASN cc_start: 0.7314 (t0) cc_final: 0.7051 (t0) outliers start: 12 outliers final: 10 residues processed: 135 average time/residue: 0.3529 time to fit residues: 65.6871 Evaluate side-chains 131 residues out of total 716 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 121 time to evaluate : 1.091 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 327 HIS Chi-restraints excluded: chain A residue 335 SER Chi-restraints excluded: chain A residue 336 SER Chi-restraints excluded: chain A residue 367 ASP Chi-restraints excluded: chain A residue 393 LEU Chi-restraints excluded: chain A residue 463 ILE Chi-restraints excluded: chain B residue 279 HIS Chi-restraints excluded: chain B residue 336 SER Chi-restraints excluded: chain B residue 393 LEU Chi-restraints excluded: chain B residue 463 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 43 optimal weight: 3.9990 chunk 24 optimal weight: 0.7980 chunk 64 optimal weight: 2.9990 chunk 53 optimal weight: 1.9990 chunk 21 optimal weight: 1.9990 chunk 78 optimal weight: 0.7980 chunk 84 optimal weight: 0.8980 chunk 69 optimal weight: 2.9990 chunk 77 optimal weight: 0.7980 chunk 26 optimal weight: 2.9990 chunk 62 optimal weight: 0.4980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 110 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7703 moved from start: 0.1532 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 6796 Z= 0.172 Angle : 0.533 5.738 9266 Z= 0.281 Chirality : 0.041 0.144 1080 Planarity : 0.005 0.048 1190 Dihedral : 4.812 48.435 944 Min Nonbonded Distance : 1.965 Molprobity Statistics. All-atom Clashscore : 5.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 1.17 % Allowed : 14.62 % Favored : 84.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.12 (0.29), residues: 866 helix: 1.49 (0.26), residues: 420 sheet: -0.27 (0.62), residues: 74 loop : 0.22 (0.34), residues: 372 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP B 273 HIS 0.004 0.001 HIS A 146 PHE 0.010 0.001 PHE B 316 TYR 0.011 0.001 TYR A 369 ARG 0.002 0.000 ARG A 42 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1732 Ramachandran restraints generated. 866 Oldfield, 0 Emsley, 866 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1732 Ramachandran restraints generated. 866 Oldfield, 0 Emsley, 866 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 281 is missing expected H atoms. Skipping. Residue VAL 405 is missing expected H atoms. Skipping. Residue VAL 406 is missing expected H atoms. Skipping. Residue VAL 412 is missing expected H atoms. Skipping. Residue TYR 413 is missing expected H atoms. Skipping. Residue TYR 433 is missing expected H atoms. Skipping. Residue ILE 434 is missing expected H atoms. Skipping. Residue ILE 435 is missing expected H atoms. Skipping. Residue THR 486 is missing expected H atoms. Skipping. Residue ILE 491 is missing expected H atoms. Skipping. Residue LYS 492 is missing expected H atoms. Skipping. Residue ILE 494 is missing expected H atoms. Skipping. Residue LYS 281 is missing expected H atoms. Skipping. Residue VAL 405 is missing expected H atoms. Skipping. Residue VAL 406 is missing expected H atoms. Skipping. Residue VAL 412 is missing expected H atoms. Skipping. Residue TYR 413 is missing expected H atoms. Skipping. Residue TYR 433 is missing expected H atoms. Skipping. Residue ILE 434 is missing expected H atoms. Skipping. Residue ILE 435 is missing expected H atoms. Skipping. Residue THR 486 is missing expected H atoms. Skipping. Residue ILE 491 is missing expected H atoms. Skipping. Residue LYS 492 is missing expected H atoms. Skipping. Residue ILE 494 is missing expected H atoms. Skipping. Evaluate side-chains 132 residues out of total 716 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 124 time to evaluate : 1.046 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 227 LYS cc_start: 0.7124 (mptt) cc_final: 0.6898 (mptt) REVERT: A 298 ASN cc_start: 0.7950 (t0) cc_final: 0.7646 (t0) REVERT: B 298 ASN cc_start: 0.7968 (t0) cc_final: 0.7675 (t0) outliers start: 8 outliers final: 5 residues processed: 129 average time/residue: 0.3436 time to fit residues: 62.2180 Evaluate side-chains 125 residues out of total 716 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 120 time to evaluate : 0.985 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 327 HIS Chi-restraints excluded: chain A residue 463 ILE Chi-restraints excluded: chain B residue 171 LEU Chi-restraints excluded: chain B residue 279 HIS Chi-restraints excluded: chain B residue 463 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 77 optimal weight: 1.9990 chunk 58 optimal weight: 2.9990 chunk 40 optimal weight: 2.9990 chunk 8 optimal weight: 2.9990 chunk 37 optimal weight: 8.9990 chunk 52 optimal weight: 0.7980 chunk 78 optimal weight: 1.9990 chunk 83 optimal weight: 2.9990 chunk 41 optimal weight: 0.9980 chunk 74 optimal weight: 1.9990 chunk 22 optimal weight: 2.9990 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 110 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7755 moved from start: 0.1916 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 6796 Z= 0.271 Angle : 0.556 5.777 9266 Z= 0.296 Chirality : 0.042 0.140 1080 Planarity : 0.005 0.047 1190 Dihedral : 4.428 18.442 942 Min Nonbonded Distance : 1.954 Molprobity Statistics. All-atom Clashscore : 6.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.93 % Favored : 96.07 % Rotamer: Outliers : 1.75 % Allowed : 15.35 % Favored : 82.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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: 1.10 (0.30), residues: 866 helix: 1.55 (0.26), residues: 422 sheet: -0.19 (0.61), residues: 74 loop : 0.07 (0.34), residues: 370 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 400 HIS 0.003 0.001 HIS B 327 PHE 0.013 0.002 PHE B 316 TYR 0.012 0.001 TYR A 369 ARG 0.002 0.000 ARG B 213 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1732 Ramachandran restraints generated. 866 Oldfield, 0 Emsley, 866 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1732 Ramachandran restraints generated. 866 Oldfield, 0 Emsley, 866 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 281 is missing expected H atoms. Skipping. Residue VAL 405 is missing expected H atoms. Skipping. Residue VAL 406 is missing expected H atoms. Skipping. Residue VAL 412 is missing expected H atoms. Skipping. Residue TYR 413 is missing expected H atoms. Skipping. Residue TYR 433 is missing expected H atoms. Skipping. Residue ILE 434 is missing expected H atoms. Skipping. Residue ILE 435 is missing expected H atoms. Skipping. Residue THR 486 is missing expected H atoms. Skipping. Residue ILE 491 is missing expected H atoms. Skipping. Residue LYS 492 is missing expected H atoms. Skipping. Residue ILE 494 is missing expected H atoms. Skipping. Residue LYS 281 is missing expected H atoms. Skipping. Residue VAL 405 is missing expected H atoms. Skipping. Residue VAL 406 is missing expected H atoms. Skipping. Residue VAL 412 is missing expected H atoms. Skipping. Residue TYR 413 is missing expected H atoms. Skipping. Residue TYR 433 is missing expected H atoms. Skipping. Residue ILE 434 is missing expected H atoms. Skipping. Residue ILE 435 is missing expected H atoms. Skipping. Residue THR 486 is missing expected H atoms. Skipping. Residue ILE 491 is missing expected H atoms. Skipping. Residue LYS 492 is missing expected H atoms. Skipping. Residue ILE 494 is missing expected H atoms. Skipping. Evaluate side-chains 138 residues out of total 716 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 126 time to evaluate : 1.045 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 298 ASN cc_start: 0.8083 (t0) cc_final: 0.7851 (t0) REVERT: A 393 LEU cc_start: 0.7577 (OUTLIER) cc_final: 0.7354 (tp) REVERT: B 298 ASN cc_start: 0.8049 (t0) cc_final: 0.7749 (t0) REVERT: B 307 ASN cc_start: 0.7277 (t0) cc_final: 0.7036 (t0) outliers start: 12 outliers final: 8 residues processed: 134 average time/residue: 0.3518 time to fit residues: 65.2731 Evaluate side-chains 129 residues out of total 716 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 120 time to evaluate : 1.032 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 327 HIS Chi-restraints excluded: chain A residue 335 SER Chi-restraints excluded: chain A residue 336 SER Chi-restraints excluded: chain A residue 367 ASP Chi-restraints excluded: chain A residue 393 LEU Chi-restraints excluded: chain A residue 463 ILE Chi-restraints excluded: chain B residue 279 HIS Chi-restraints excluded: chain B residue 336 SER Chi-restraints excluded: chain B residue 463 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 69 optimal weight: 2.9990 chunk 47 optimal weight: 4.9990 chunk 1 optimal weight: 0.7980 chunk 61 optimal weight: 3.9990 chunk 34 optimal weight: 1.9990 chunk 70 optimal weight: 0.9990 chunk 57 optimal weight: 0.8980 chunk 0 optimal weight: 3.9990 chunk 42 optimal weight: 3.9990 chunk 74 optimal weight: 1.9990 chunk 20 optimal weight: 0.8980 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 110 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7730 moved from start: 0.2113 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 6796 Z= 0.203 Angle : 0.520 5.902 9266 Z= 0.273 Chirality : 0.041 0.135 1080 Planarity : 0.004 0.044 1190 Dihedral : 4.262 17.920 942 Min Nonbonded Distance : 1.950 Molprobity Statistics. All-atom Clashscore : 6.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 2.05 % Allowed : 15.35 % Favored : 82.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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: 1.25 (0.30), residues: 866 helix: 1.74 (0.26), residues: 422 sheet: -0.08 (0.61), residues: 74 loop : 0.04 (0.34), residues: 370 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 273 HIS 0.003 0.001 HIS B 327 PHE 0.011 0.001 PHE A 476 TYR 0.011 0.001 TYR A 375 ARG 0.002 0.000 ARG B 213 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1732 Ramachandran restraints generated. 866 Oldfield, 0 Emsley, 866 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1732 Ramachandran restraints generated. 866 Oldfield, 0 Emsley, 866 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 281 is missing expected H atoms. Skipping. Residue VAL 405 is missing expected H atoms. Skipping. Residue VAL 406 is missing expected H atoms. Skipping. Residue VAL 412 is missing expected H atoms. Skipping. Residue TYR 413 is missing expected H atoms. Skipping. Residue TYR 433 is missing expected H atoms. Skipping. Residue ILE 434 is missing expected H atoms. Skipping. Residue ILE 435 is missing expected H atoms. Skipping. Residue THR 486 is missing expected H atoms. Skipping. Residue ILE 491 is missing expected H atoms. Skipping. Residue LYS 492 is missing expected H atoms. Skipping. Residue ILE 494 is missing expected H atoms. Skipping. Residue LYS 281 is missing expected H atoms. Skipping. Residue VAL 405 is missing expected H atoms. Skipping. Residue VAL 406 is missing expected H atoms. Skipping. Residue VAL 412 is missing expected H atoms. Skipping. Residue TYR 413 is missing expected H atoms. Skipping. Residue TYR 433 is missing expected H atoms. Skipping. Residue ILE 434 is missing expected H atoms. Skipping. Residue ILE 435 is missing expected H atoms. Skipping. Residue THR 486 is missing expected H atoms. Skipping. Residue ILE 491 is missing expected H atoms. Skipping. Residue LYS 492 is missing expected H atoms. Skipping. Residue ILE 494 is missing expected H atoms. Skipping. Evaluate side-chains 135 residues out of total 716 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 121 time to evaluate : 1.027 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 298 ASN cc_start: 0.8017 (t0) cc_final: 0.7781 (t0) REVERT: B 298 ASN cc_start: 0.8015 (t0) cc_final: 0.7693 (t0) outliers start: 14 outliers final: 11 residues processed: 129 average time/residue: 0.3920 time to fit residues: 68.4084 Evaluate side-chains 133 residues out of total 716 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 122 time to evaluate : 1.573 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 215 THR Chi-restraints excluded: chain A residue 327 HIS Chi-restraints excluded: chain A residue 335 SER Chi-restraints excluded: chain A residue 336 SER Chi-restraints excluded: chain A residue 463 ILE Chi-restraints excluded: chain B residue 171 LEU Chi-restraints excluded: chain B residue 194 LEU Chi-restraints excluded: chain B residue 215 THR Chi-restraints excluded: chain B residue 279 HIS Chi-restraints excluded: chain B residue 335 SER Chi-restraints excluded: chain B residue 463 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 27 optimal weight: 0.9980 chunk 74 optimal weight: 1.9990 chunk 16 optimal weight: 2.9990 chunk 48 optimal weight: 2.9990 chunk 20 optimal weight: 1.9990 chunk 83 optimal weight: 1.9990 chunk 69 optimal weight: 2.9990 chunk 38 optimal weight: 0.0970 chunk 6 optimal weight: 1.9990 chunk 43 optimal weight: 3.9990 chunk 80 optimal weight: 9.9990 overall best weight: 1.4184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 116 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7754 moved from start: 0.2302 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 6796 Z= 0.244 Angle : 0.535 5.534 9266 Z= 0.281 Chirality : 0.041 0.135 1080 Planarity : 0.005 0.067 1190 Dihedral : 4.254 18.007 942 Min Nonbonded Distance : 1.932 Molprobity Statistics. All-atom Clashscore : 6.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.93 % Favored : 96.07 % Rotamer: Outliers : 1.90 % Allowed : 15.94 % Favored : 82.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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: 1.24 (0.30), residues: 866 helix: 1.77 (0.26), residues: 422 sheet: -0.05 (0.62), residues: 74 loop : -0.02 (0.34), residues: 370 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 400 HIS 0.002 0.001 HIS A 327 PHE 0.012 0.002 PHE B 476 TYR 0.013 0.001 TYR A 369 ARG 0.007 0.000 ARG A 42 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1732 Ramachandran restraints generated. 866 Oldfield, 0 Emsley, 866 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1732 Ramachandran restraints generated. 866 Oldfield, 0 Emsley, 866 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 281 is missing expected H atoms. Skipping. Residue VAL 405 is missing expected H atoms. Skipping. Residue VAL 406 is missing expected H atoms. Skipping. Residue VAL 412 is missing expected H atoms. Skipping. Residue TYR 413 is missing expected H atoms. Skipping. Residue TYR 433 is missing expected H atoms. Skipping. Residue ILE 434 is missing expected H atoms. Skipping. Residue ILE 435 is missing expected H atoms. Skipping. Residue THR 486 is missing expected H atoms. Skipping. Residue ILE 491 is missing expected H atoms. Skipping. Residue LYS 492 is missing expected H atoms. Skipping. Residue ILE 494 is missing expected H atoms. Skipping. Residue LYS 281 is missing expected H atoms. Skipping. Residue VAL 405 is missing expected H atoms. Skipping. Residue VAL 406 is missing expected H atoms. Skipping. Residue VAL 412 is missing expected H atoms. Skipping. Residue TYR 413 is missing expected H atoms. Skipping. Residue TYR 433 is missing expected H atoms. Skipping. Residue ILE 434 is missing expected H atoms. Skipping. Residue ILE 435 is missing expected H atoms. Skipping. Residue THR 486 is missing expected H atoms. Skipping. Residue ILE 491 is missing expected H atoms. Skipping. Residue LYS 492 is missing expected H atoms. Skipping. Residue ILE 494 is missing expected H atoms. Skipping. Evaluate side-chains 137 residues out of total 716 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 124 time to evaluate : 1.168 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 162 MET cc_start: 0.8103 (tmm) cc_final: 0.7745 (tmm) REVERT: A 298 ASN cc_start: 0.8098 (t0) cc_final: 0.7865 (t0) REVERT: B 298 ASN cc_start: 0.8087 (t0) cc_final: 0.7774 (t0) REVERT: B 307 ASN cc_start: 0.7295 (t0) cc_final: 0.7065 (t0) outliers start: 13 outliers final: 11 residues processed: 131 average time/residue: 0.4663 time to fit residues: 79.2802 Evaluate side-chains 132 residues out of total 716 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 121 time to evaluate : 1.073 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 215 THR Chi-restraints excluded: chain A residue 327 HIS Chi-restraints excluded: chain A residue 335 SER Chi-restraints excluded: chain A residue 336 SER Chi-restraints excluded: chain A residue 463 ILE Chi-restraints excluded: chain B residue 171 LEU Chi-restraints excluded: chain B residue 194 LEU Chi-restraints excluded: chain B residue 279 HIS Chi-restraints excluded: chain B residue 335 SER Chi-restraints excluded: chain B residue 393 LEU Chi-restraints excluded: chain B residue 463 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 9 optimal weight: 2.9990 chunk 47 optimal weight: 4.9990 chunk 60 optimal weight: 1.9990 chunk 70 optimal weight: 0.9990 chunk 46 optimal weight: 2.9990 chunk 82 optimal weight: 0.7980 chunk 51 optimal weight: 2.9990 chunk 50 optimal weight: 0.9980 chunk 38 optimal weight: 1.9990 chunk 33 optimal weight: 2.9990 chunk 49 optimal weight: 0.8980 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7739 moved from start: 0.2457 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 6796 Z= 0.203 Angle : 0.516 6.230 9266 Z= 0.269 Chirality : 0.041 0.134 1080 Planarity : 0.005 0.055 1190 Dihedral : 4.127 17.758 942 Min Nonbonded Distance : 1.944 Molprobity Statistics. All-atom Clashscore : 6.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 1.75 % Allowed : 16.23 % Favored : 82.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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: 1.15 (0.30), residues: 866 helix: 1.72 (0.26), residues: 436 sheet: -0.01 (0.62), residues: 74 loop : -0.20 (0.35), residues: 356 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP B 273 HIS 0.002 0.001 HIS B 327 PHE 0.010 0.001 PHE A 483 TYR 0.011 0.001 TYR A 369 ARG 0.008 0.000 ARG A 42 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1732 Ramachandran restraints generated. 866 Oldfield, 0 Emsley, 866 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1732 Ramachandran restraints generated. 866 Oldfield, 0 Emsley, 866 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 281 is missing expected H atoms. Skipping. Residue VAL 405 is missing expected H atoms. Skipping. Residue VAL 406 is missing expected H atoms. Skipping. Residue VAL 412 is missing expected H atoms. Skipping. Residue TYR 413 is missing expected H atoms. Skipping. Residue TYR 433 is missing expected H atoms. Skipping. Residue ILE 434 is missing expected H atoms. Skipping. Residue ILE 435 is missing expected H atoms. Skipping. Residue THR 486 is missing expected H atoms. Skipping. Residue ILE 491 is missing expected H atoms. Skipping. Residue LYS 492 is missing expected H atoms. Skipping. Residue ILE 494 is missing expected H atoms. Skipping. Residue LYS 281 is missing expected H atoms. Skipping. Residue VAL 405 is missing expected H atoms. Skipping. Residue VAL 406 is missing expected H atoms. Skipping. Residue VAL 412 is missing expected H atoms. Skipping. Residue TYR 413 is missing expected H atoms. Skipping. Residue TYR 433 is missing expected H atoms. Skipping. Residue ILE 434 is missing expected H atoms. Skipping. Residue ILE 435 is missing expected H atoms. Skipping. Residue THR 486 is missing expected H atoms. Skipping. Residue ILE 491 is missing expected H atoms. Skipping. Residue LYS 492 is missing expected H atoms. Skipping. Residue ILE 494 is missing expected H atoms. Skipping. Evaluate side-chains 137 residues out of total 716 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 125 time to evaluate : 1.134 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 162 MET cc_start: 0.8084 (tmm) cc_final: 0.7751 (tmm) REVERT: A 298 ASN cc_start: 0.8056 (t0) cc_final: 0.7821 (t0) REVERT: B 298 ASN cc_start: 0.8082 (t0) cc_final: 0.7775 (t0) REVERT: B 461 ARG cc_start: 0.6637 (tpp-160) cc_final: 0.6123 (tpp-160) outliers start: 12 outliers final: 9 residues processed: 130 average time/residue: 0.4230 time to fit residues: 72.4777 Evaluate side-chains 127 residues out of total 716 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 118 time to evaluate : 1.059 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 215 THR Chi-restraints excluded: chain A residue 327 HIS Chi-restraints excluded: chain A residue 335 SER Chi-restraints excluded: chain A residue 336 SER Chi-restraints excluded: chain A residue 463 ILE Chi-restraints excluded: chain B residue 194 LEU Chi-restraints excluded: chain B residue 215 THR Chi-restraints excluded: chain B residue 279 HIS Chi-restraints excluded: chain B residue 463 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 24 optimal weight: 0.7980 chunk 16 optimal weight: 5.9990 chunk 52 optimal weight: 0.5980 chunk 56 optimal weight: 2.9990 chunk 40 optimal weight: 1.9990 chunk 7 optimal weight: 2.9990 chunk 65 optimal weight: 2.9990 chunk 75 optimal weight: 0.6980 chunk 79 optimal weight: 2.9990 chunk 72 optimal weight: 0.8980 chunk 77 optimal weight: 3.9990 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7735 moved from start: 0.2555 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 6796 Z= 0.189 Angle : 0.501 5.003 9266 Z= 0.261 Chirality : 0.041 0.137 1080 Planarity : 0.005 0.063 1190 Dihedral : 4.032 17.422 942 Min Nonbonded Distance : 1.962 Molprobity Statistics. All-atom Clashscore : 7.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 1.46 % Allowed : 16.67 % Favored : 81.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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: 1.25 (0.30), residues: 866 helix: 1.82 (0.26), residues: 436 sheet: -0.04 (0.61), residues: 74 loop : -0.17 (0.35), residues: 356 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 273 HIS 0.002 0.001 HIS B 327 PHE 0.010 0.001 PHE A 483 TYR 0.011 0.001 TYR A 369 ARG 0.007 0.000 ARG A 42 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1732 Ramachandran restraints generated. 866 Oldfield, 0 Emsley, 866 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1732 Ramachandran restraints generated. 866 Oldfield, 0 Emsley, 866 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 281 is missing expected H atoms. Skipping. Residue VAL 405 is missing expected H atoms. Skipping. Residue VAL 406 is missing expected H atoms. Skipping. Residue VAL 412 is missing expected H atoms. Skipping. Residue TYR 413 is missing expected H atoms. Skipping. Residue TYR 433 is missing expected H atoms. Skipping. Residue ILE 434 is missing expected H atoms. Skipping. Residue ILE 435 is missing expected H atoms. Skipping. Residue THR 486 is missing expected H atoms. Skipping. Residue ILE 491 is missing expected H atoms. Skipping. Residue LYS 492 is missing expected H atoms. Skipping. Residue ILE 494 is missing expected H atoms. Skipping. Residue LYS 281 is missing expected H atoms. Skipping. Residue VAL 405 is missing expected H atoms. Skipping. Residue VAL 406 is missing expected H atoms. Skipping. Residue VAL 412 is missing expected H atoms. Skipping. Residue TYR 413 is missing expected H atoms. Skipping. Residue TYR 433 is missing expected H atoms. Skipping. Residue ILE 434 is missing expected H atoms. Skipping. Residue ILE 435 is missing expected H atoms. Skipping. Residue THR 486 is missing expected H atoms. Skipping. Residue ILE 491 is missing expected H atoms. Skipping. Residue LYS 492 is missing expected H atoms. Skipping. Residue ILE 494 is missing expected H atoms. Skipping. Evaluate side-chains 131 residues out of total 716 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 121 time to evaluate : 1.004 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 162 MET cc_start: 0.8114 (tmm) cc_final: 0.7782 (tmm) REVERT: A 185 SER cc_start: 0.8517 (t) cc_final: 0.8253 (p) REVERT: A 298 ASN cc_start: 0.8062 (t0) cc_final: 0.7822 (t0) REVERT: B 298 ASN cc_start: 0.8096 (t0) cc_final: 0.7785 (t0) REVERT: B 307 ASN cc_start: 0.7321 (t0) cc_final: 0.7084 (t0) REVERT: B 461 ARG cc_start: 0.6640 (tpp-160) cc_final: 0.6116 (tpp-160) outliers start: 10 outliers final: 8 residues processed: 126 average time/residue: 0.4127 time to fit residues: 68.9732 Evaluate side-chains 129 residues out of total 716 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 121 time to evaluate : 1.054 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 327 HIS Chi-restraints excluded: chain A residue 335 SER Chi-restraints excluded: chain A residue 336 SER Chi-restraints excluded: chain A residue 463 ILE Chi-restraints excluded: chain B residue 194 LEU Chi-restraints excluded: chain B residue 215 THR Chi-restraints excluded: chain B residue 279 HIS Chi-restraints excluded: chain B residue 463 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 79 optimal weight: 2.9990 chunk 46 optimal weight: 4.9990 chunk 33 optimal weight: 1.9990 chunk 60 optimal weight: 2.9990 chunk 23 optimal weight: 1.9990 chunk 69 optimal weight: 0.3980 chunk 73 optimal weight: 1.9990 chunk 76 optimal weight: 2.9990 chunk 50 optimal weight: 0.8980 chunk 81 optimal weight: 0.9980 chunk 49 optimal weight: 0.5980 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7733 moved from start: 0.2626 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 6796 Z= 0.186 Angle : 0.500 5.186 9266 Z= 0.260 Chirality : 0.040 0.137 1080 Planarity : 0.005 0.063 1190 Dihedral : 3.994 17.289 942 Min Nonbonded Distance : 1.941 Molprobity Statistics. All-atom Clashscore : 7.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 1.32 % Allowed : 16.37 % Favored : 82.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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: 1.31 (0.30), residues: 866 helix: 1.90 (0.26), residues: 436 sheet: -0.03 (0.62), residues: 70 loop : -0.18 (0.35), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 273 HIS 0.002 0.001 HIS B 279 PHE 0.010 0.001 PHE A 483 TYR 0.010 0.001 TYR A 369 ARG 0.008 0.000 ARG A 42 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1732 Ramachandran restraints generated. 866 Oldfield, 0 Emsley, 866 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1732 Ramachandran restraints generated. 866 Oldfield, 0 Emsley, 866 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 281 is missing expected H atoms. Skipping. Residue VAL 405 is missing expected H atoms. Skipping. Residue VAL 406 is missing expected H atoms. Skipping. Residue VAL 412 is missing expected H atoms. Skipping. Residue TYR 413 is missing expected H atoms. Skipping. Residue TYR 433 is missing expected H atoms. Skipping. Residue ILE 434 is missing expected H atoms. Skipping. Residue ILE 435 is missing expected H atoms. Skipping. Residue THR 486 is missing expected H atoms. Skipping. Residue ILE 491 is missing expected H atoms. Skipping. Residue LYS 492 is missing expected H atoms. Skipping. Residue ILE 494 is missing expected H atoms. Skipping. Residue LYS 281 is missing expected H atoms. Skipping. Residue VAL 405 is missing expected H atoms. Skipping. Residue VAL 406 is missing expected H atoms. Skipping. Residue VAL 412 is missing expected H atoms. Skipping. Residue TYR 413 is missing expected H atoms. Skipping. Residue TYR 433 is missing expected H atoms. Skipping. Residue ILE 434 is missing expected H atoms. Skipping. Residue ILE 435 is missing expected H atoms. Skipping. Residue THR 486 is missing expected H atoms. Skipping. Residue ILE 491 is missing expected H atoms. Skipping. Residue LYS 492 is missing expected H atoms. Skipping. Residue ILE 494 is missing expected H atoms. Skipping. Evaluate side-chains 131 residues out of total 716 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 122 time to evaluate : 1.062 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 162 MET cc_start: 0.8107 (tmm) cc_final: 0.7780 (tmm) REVERT: A 185 SER cc_start: 0.8550 (t) cc_final: 0.8285 (p) REVERT: A 298 ASN cc_start: 0.8043 (t0) cc_final: 0.7804 (t0) REVERT: B 185 SER cc_start: 0.8467 (t) cc_final: 0.8212 (p) REVERT: B 298 ASN cc_start: 0.8076 (t0) cc_final: 0.7763 (t0) REVERT: B 461 ARG cc_start: 0.6602 (tpp-160) cc_final: 0.6078 (tpp-160) outliers start: 9 outliers final: 8 residues processed: 126 average time/residue: 0.4059 time to fit residues: 67.8263 Evaluate side-chains 126 residues out of total 716 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 118 time to evaluate : 0.926 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 335 SER Chi-restraints excluded: chain A residue 336 SER Chi-restraints excluded: chain A residue 463 ILE Chi-restraints excluded: chain B residue 194 LEU Chi-restraints excluded: chain B residue 215 THR Chi-restraints excluded: chain B residue 279 HIS Chi-restraints excluded: chain B residue 393 LEU Chi-restraints excluded: chain B residue 463 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 38 optimal weight: 0.0770 chunk 56 optimal weight: 3.9990 chunk 85 optimal weight: 0.9990 chunk 78 optimal weight: 0.6980 chunk 68 optimal weight: 5.9990 chunk 7 optimal weight: 2.9990 chunk 52 optimal weight: 0.2980 chunk 41 optimal weight: 0.6980 chunk 54 optimal weight: 0.6980 chunk 72 optimal weight: 0.4980 chunk 20 optimal weight: 0.7980 overall best weight: 0.4538 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7693 moved from start: 0.2695 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 6796 Z= 0.133 Angle : 0.480 5.078 9266 Z= 0.247 Chirality : 0.040 0.137 1080 Planarity : 0.005 0.065 1190 Dihedral : 3.828 16.669 942 Min Nonbonded Distance : 1.951 Molprobity Statistics. All-atom Clashscore : 7.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Rotamer: Outliers : 1.32 % Allowed : 16.23 % Favored : 82.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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: 1.50 (0.30), residues: 866 helix: 2.08 (0.26), residues: 436 sheet: -0.52 (0.60), residues: 78 loop : 0.04 (0.35), residues: 352 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 273 HIS 0.003 0.001 HIS B 279 PHE 0.009 0.001 PHE A 483 TYR 0.011 0.001 TYR B 191 ARG 0.008 0.000 ARG A 42 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1732 Ramachandran restraints generated. 866 Oldfield, 0 Emsley, 866 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1732 Ramachandran restraints generated. 866 Oldfield, 0 Emsley, 866 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 281 is missing expected H atoms. Skipping. Residue VAL 405 is missing expected H atoms. Skipping. Residue VAL 406 is missing expected H atoms. Skipping. Residue VAL 412 is missing expected H atoms. Skipping. Residue TYR 413 is missing expected H atoms. Skipping. Residue TYR 433 is missing expected H atoms. Skipping. Residue ILE 434 is missing expected H atoms. Skipping. Residue ILE 435 is missing expected H atoms. Skipping. Residue THR 486 is missing expected H atoms. Skipping. Residue ILE 491 is missing expected H atoms. Skipping. Residue LYS 492 is missing expected H atoms. Skipping. Residue ILE 494 is missing expected H atoms. Skipping. Residue LYS 281 is missing expected H atoms. Skipping. Residue VAL 405 is missing expected H atoms. Skipping. Residue VAL 406 is missing expected H atoms. Skipping. Residue VAL 412 is missing expected H atoms. Skipping. Residue TYR 413 is missing expected H atoms. Skipping. Residue TYR 433 is missing expected H atoms. Skipping. Residue ILE 434 is missing expected H atoms. Skipping. Residue ILE 435 is missing expected H atoms. Skipping. Residue THR 486 is missing expected H atoms. Skipping. Residue ILE 491 is missing expected H atoms. Skipping. Residue LYS 492 is missing expected H atoms. Skipping. Residue ILE 494 is missing expected H atoms. Skipping. Evaluate side-chains 131 residues out of total 716 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 122 time to evaluate : 1.161 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 162 MET cc_start: 0.8089 (tmm) cc_final: 0.7752 (tmm) REVERT: A 185 SER cc_start: 0.8497 (t) cc_final: 0.8273 (p) REVERT: A 298 ASN cc_start: 0.8007 (t0) cc_final: 0.7773 (t0) REVERT: B 185 SER cc_start: 0.8456 (t) cc_final: 0.8220 (p) REVERT: B 298 ASN cc_start: 0.7995 (t0) cc_final: 0.7679 (t0) outliers start: 9 outliers final: 7 residues processed: 126 average time/residue: 0.3927 time to fit residues: 66.9057 Evaluate side-chains 128 residues out of total 716 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 121 time to evaluate : 1.024 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 205 THR Chi-restraints excluded: chain A residue 335 SER Chi-restraints excluded: chain A residue 336 SER Chi-restraints excluded: chain A residue 463 ILE Chi-restraints excluded: chain B residue 194 LEU Chi-restraints excluded: chain B residue 279 HIS Chi-restraints excluded: chain B residue 463 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 62 optimal weight: 3.9990 chunk 10 optimal weight: 2.9990 chunk 18 optimal weight: 4.9990 chunk 68 optimal weight: 5.9990 chunk 28 optimal weight: 0.9990 chunk 70 optimal weight: 1.9990 chunk 8 optimal weight: 0.7980 chunk 12 optimal weight: 1.9990 chunk 59 optimal weight: 0.7980 chunk 3 optimal weight: 1.9990 chunk 49 optimal weight: 0.9990 overall best weight: 1.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3932 r_free = 0.3932 target = 0.176672 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3627 r_free = 0.3627 target = 0.147009 restraints weight = 23214.244| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3685 r_free = 0.3685 target = 0.153708 restraints weight = 15037.779| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3702 r_free = 0.3702 target = 0.155713 restraints weight = 10014.022| |-----------------------------------------------------------------------------| r_work (final): 0.3694 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7781 moved from start: 0.2759 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 6796 Z= 0.208 Angle : 0.503 4.974 9266 Z= 0.262 Chirality : 0.041 0.137 1080 Planarity : 0.005 0.066 1190 Dihedral : 3.888 16.758 942 Min Nonbonded Distance : 1.920 Molprobity Statistics. All-atom Clashscore : 7.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.58 % Favored : 96.42 % Rotamer: Outliers : 1.32 % Allowed : 16.23 % Favored : 82.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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: 1.47 (0.30), residues: 866 helix: 2.08 (0.26), residues: 436 sheet: -0.40 (0.59), residues: 76 loop : -0.04 (0.35), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 273 HIS 0.002 0.001 HIS B 279 PHE 0.010 0.001 PHE B 316 TYR 0.010 0.001 TYR A 369 ARG 0.009 0.000 ARG A 42 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3275.41 seconds wall clock time: 58 minutes 50.73 seconds (3530.73 seconds total)