Starting phenix.real_space_refine on Sun Mar 10 18:36:30 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rnn_24580/03_2024/7rnn_24580.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rnn_24580/03_2024/7rnn_24580.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.86 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rnn_24580/03_2024/7rnn_24580.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rnn_24580/03_2024/7rnn_24580.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rnn_24580/03_2024/7rnn_24580.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rnn_24580/03_2024/7rnn_24580.pdb" } resolution = 2.86 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.001 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 30 5.16 5 C 2551 2.51 5 N 678 2.21 5 O 741 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "C PHE 31": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 41": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 64": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 72": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 77": "OD1" <-> "OD2" Residue "C ARG 105": "NH1" <-> "NH2" Residue "D GLU 63": "OE1" <-> "OE2" Residue "D ARG 64": "NH1" <-> "NH2" Residue "D ASP 78": "OD1" <-> "OD2" Residue "D PHE 92": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 98": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 113": "OE1" <-> "OE2" Residue "D ARG 155": "NH1" <-> "NH2" Residue "D ARG 175": "NH1" <-> "NH2" Residue "D ARG 311": "NH1" <-> "NH2" Residue "D GLU 375": "OE1" <-> "OE2" Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 4000 Number of models: 1 Model: "" Number of chains: 2 Chain: "C" Number of atoms: 754 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 754 Classifications: {'peptide': 116} Incomplete info: {'truncation_to_alanine': 50} Link IDs: {'PTRANS': 4, 'TRANS': 111} Unresolved non-hydrogen bonds: 144 Unresolved non-hydrogen angles: 181 Unresolved non-hydrogen dihedrals: 116 Unresolved non-hydrogen chiralities: 15 Planarities with less than four sites: {'GLN:plan1': 6, 'ASP:plan': 2, 'ASN:plan1': 1, 'TRP:plan': 1, 'HIS:plan': 1, 'GLU:plan': 4, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 73 Chain: "D" Number of atoms: 3246 Number of conformers: 1 Conformer: "" Number of residues, atoms: 426, 3246 Unusual residues: {'NAG': 2} Classifications: {'peptide': 424, 'undetermined': 2} Incomplete info: {'truncation_to_alanine': 51} Link IDs: {'PCIS': 2, 'PTRANS': 16, 'TRANS': 405, None: 2} Not linked: pdbres="LYS D 462 " pdbres="NAG D 601 " Not linked: pdbres="NAG D 601 " pdbres="NAG D 602 " Unresolved non-hydrogen bonds: 193 Unresolved non-hydrogen angles: 239 Unresolved non-hydrogen dihedrals: 161 Unresolved non-hydrogen chiralities: 13 Planarities with less than four sites: {'GLN:plan1': 2, 'TYR:plan': 2, 'ASN:plan1': 2, 'ASP:plan': 5, 'PHE:plan': 1, 'GLU:plan': 13, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 116 Time building chain proxies: 2.65, per 1000 atoms: 0.66 Number of scatterers: 4000 At special positions: 0 Unit cell: (95.45, 60.59, 126.16, 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 30 16.00 O 741 8.00 N 678 7.00 C 2551 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=7, symmetry=0 Simple disulfide: pdb=" SG CYS D 93 " - pdb=" SG CYS D 194 " distance=2.04 Simple disulfide: pdb=" SG CYS D 172 " - pdb=" SG CYS D 179 " distance=2.05 Simple disulfide: pdb=" SG CYS D 290 " - pdb=" SG CYS D 367 " distance=2.02 Simple disulfide: pdb=" SG CYS D 310 " - pdb=" SG CYS D 363 " distance=2.03 Simple disulfide: pdb=" SG CYS D 314 " - pdb=" SG CYS D 361 " distance=2.03 Simple disulfide: pdb=" SG CYS D 323 " - pdb=" SG CYS D 345 " distance=2.03 Simple disulfide: pdb=" SG CYS D 325 " - pdb=" SG CYS D 337 " 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 Atom "HETATM 3984 O5 NAG D 601 .*. O " rejected from bonding due to valence issues. Number of custom bonds: simple=0, symmetry=0 Links applied NAG-ASN " NAG D 601 " - " ASN D 368 " " NAG D 602 " - " ASN D 395 " Time building additional restraints: 1.67 Conformation dependent library (CDL) restraints added in 1.2 seconds 1072 Ramachandran restraints generated. 536 Oldfield, 0 Emsley, 536 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1006 Finding SS restraints... Secondary structure from input PDB file: 17 helices and 7 sheets defined 32.6% alpha, 27.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.48 Creating SS restraints... Processing helix chain 'C' and resid 32 through 36 Processing helix chain 'C' and resid 91 through 95 Processing helix chain 'D' and resid 40 through 71 removed outlier: 3.813A pdb=" N ALA D 55 " --> pdb=" O LEU D 51 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N VAL D 56 " --> pdb=" O GLY D 52 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N GLU D 63 " --> pdb=" O CYS D 59 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N TYR D 71 " --> pdb=" O TYR D 67 " (cutoff:3.500A) Processing helix chain 'D' and resid 104 through 111 Processing helix chain 'D' and resid 131 through 140 Processing helix chain 'D' and resid 153 through 162 Processing helix chain 'D' and resid 164 through 168 Processing helix chain 'D' and resid 180 through 182 No H-bonds generated for 'chain 'D' and resid 180 through 182' Processing helix chain 'D' and resid 225 through 229 removed outlier: 3.625A pdb=" N TYR D 229 " --> pdb=" O GLN D 226 " (cutoff:3.500A) Processing helix chain 'D' and resid 257 through 262 Processing helix chain 'D' and resid 306 through 324 removed outlier: 3.734A pdb=" N ARG D 311 " --> pdb=" O ILE D 307 " (cutoff:3.500A) Processing helix chain 'D' and resid 338 through 343 removed outlier: 3.814A pdb=" N LYS D 343 " --> pdb=" O GLU D 340 " (cutoff:3.500A) Processing helix chain 'D' and resid 346 through 356 removed outlier: 3.669A pdb=" N LYS D 356 " --> pdb=" O PHE D 352 " (cutoff:3.500A) Processing helix chain 'D' and resid 386 through 394 Processing helix chain 'D' and resid 397 through 404 Processing helix chain 'D' and resid 427 through 443 removed outlier: 3.765A pdb=" N GLN D 438 " --> pdb=" O ASP D 434 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N LEU D 441 " --> pdb=" O GLY D 437 " (cutoff:3.500A) Processing helix chain 'D' and resid 446 through 462 Processing sheet with id=AA1, first strand: chain 'C' and resid 9 through 11 removed outlier: 3.673A pdb=" N THR C 82 " --> pdb=" O ASP C 77 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 62 through 64 removed outlier: 6.405A pdb=" N TRP C 40 " --> pdb=" O VAL C 52 " (cutoff:3.500A) removed outlier: 4.509A pdb=" N THR C 54 " --> pdb=" O MET C 38 " (cutoff:3.500A) removed outlier: 6.796A pdb=" N MET C 38 " --> pdb=" O THR C 54 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N VAL C 97 " --> pdb=" O GLN C 43 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N VAL C 116 " --> pdb=" O ALA C 96 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'D' and resid 73 through 81 removed outlier: 13.085A pdb=" N ASN D 416 " --> pdb=" O VAL D 273 " (cutoff:3.500A) removed outlier: 9.158A pdb=" N CYS D 275 " --> pdb=" O ASN D 416 " (cutoff:3.500A) removed outlier: 8.858A pdb=" N GLU D 418 " --> pdb=" O CYS D 275 " (cutoff:3.500A) removed outlier: 6.436A pdb=" N GLU D 277 " --> pdb=" O GLU D 418 " (cutoff:3.500A) removed outlier: 7.790A pdb=" N ILE D 420 " --> pdb=" O GLU D 277 " (cutoff:3.500A) removed outlier: 6.327A pdb=" N ARG D 279 " --> pdb=" O ILE D 420 " (cutoff:3.500A) removed outlier: 7.855A pdb=" N GLN D 422 " --> pdb=" O ARG D 279 " (cutoff:3.500A) removed outlier: 6.943A pdb=" N ILE D 281 " --> pdb=" O GLN D 422 " (cutoff:3.500A) removed outlier: 8.917A pdb=" N LYS D 424 " --> pdb=" O ILE D 281 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N PHE D 269 " --> pdb=" O ILE D 405 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N VAL D 407 " --> pdb=" O PHE D 269 " (cutoff:3.500A) removed outlier: 6.572A pdb=" N MET D 221 " --> pdb=" O LEU D 170 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 73 through 81 removed outlier: 13.085A pdb=" N ASN D 416 " --> pdb=" O VAL D 273 " (cutoff:3.500A) removed outlier: 9.158A pdb=" N CYS D 275 " --> pdb=" O ASN D 416 " (cutoff:3.500A) removed outlier: 8.858A pdb=" N GLU D 418 " --> pdb=" O CYS D 275 " (cutoff:3.500A) removed outlier: 6.436A pdb=" N GLU D 277 " --> pdb=" O GLU D 418 " (cutoff:3.500A) removed outlier: 7.790A pdb=" N ILE D 420 " --> pdb=" O GLU D 277 " (cutoff:3.500A) removed outlier: 6.327A pdb=" N ARG D 279 " --> pdb=" O ILE D 420 " (cutoff:3.500A) removed outlier: 7.855A pdb=" N GLN D 422 " --> pdb=" O ARG D 279 " (cutoff:3.500A) removed outlier: 6.943A pdb=" N ILE D 281 " --> pdb=" O GLN D 422 " (cutoff:3.500A) removed outlier: 8.917A pdb=" N LYS D 424 " --> pdb=" O ILE D 281 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'D' and resid 85 through 86 Processing sheet with id=AA6, first strand: chain 'D' and resid 184 through 189 removed outlier: 6.941A pdb=" N LYS D 193 " --> pdb=" O ASN D 94 " (cutoff:3.500A) removed outlier: 5.385A pdb=" N ASN D 94 " --> pdb=" O LYS D 193 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 173 through 174 195 hydrogen bonds defined for protein. 531 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: 1.23 Time building geometry restraints manager: 1.81 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: 1313 1.34 - 1.46: 1034 1.46 - 1.59: 1704 1.59 - 1.71: 0 1.71 - 1.83: 42 Bond restraints: 4093 Sorted by residual: bond pdb=" CG ASN D 368 " pdb=" ND2 ASN D 368 " ideal model delta sigma weight residual 1.328 1.394 -0.066 2.10e-02 2.27e+03 9.93e+00 bond pdb=" N CYS D 179 " pdb=" CA CYS D 179 " ideal model delta sigma weight residual 1.452 1.487 -0.035 1.22e-02 6.72e+03 8.11e+00 bond pdb=" N ASP D 296 " pdb=" CA ASP D 296 " ideal model delta sigma weight residual 1.454 1.487 -0.032 1.16e-02 7.43e+03 7.83e+00 bond pdb=" N LEU D 299 " pdb=" CA LEU D 299 " ideal model delta sigma weight residual 1.455 1.488 -0.033 1.23e-02 6.61e+03 7.03e+00 bond pdb=" N SER D 297 " pdb=" CA SER D 297 " ideal model delta sigma weight residual 1.454 1.484 -0.030 1.18e-02 7.18e+03 6.37e+00 ... (remaining 4088 not shown) Histogram of bond angle deviations from ideal: 96.18 - 103.74: 60 103.74 - 111.30: 1652 111.30 - 118.86: 1505 118.86 - 126.42: 2313 126.42 - 133.99: 41 Bond angle restraints: 5571 Sorted by residual: angle pdb=" C CYS D 345 " pdb=" N ALA D 346 " pdb=" CA ALA D 346 " ideal model delta sigma weight residual 122.56 114.80 7.76 1.50e+00 4.44e-01 2.68e+01 angle pdb=" N SER C 106 " pdb=" CA SER C 106 " pdb=" C SER C 106 " ideal model delta sigma weight residual 112.54 117.59 -5.05 1.22e+00 6.72e-01 1.71e+01 angle pdb=" C CYS D 345 " pdb=" CA CYS D 345 " pdb=" CB CYS D 345 " ideal model delta sigma weight residual 110.42 102.58 7.84 1.99e+00 2.53e-01 1.55e+01 angle pdb=" N ASP D 298 " pdb=" CA ASP D 298 " pdb=" C ASP D 298 " ideal model delta sigma weight residual 112.72 107.98 4.74 1.36e+00 5.41e-01 1.21e+01 angle pdb=" N SER C 107 " pdb=" CA SER C 107 " pdb=" C SER C 107 " ideal model delta sigma weight residual 109.39 114.88 -5.49 1.59e+00 3.96e-01 1.19e+01 ... (remaining 5566 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.58: 2324 24.58 - 49.16: 104 49.16 - 73.74: 15 73.74 - 98.32: 5 98.32 - 122.91: 3 Dihedral angle restraints: 2451 sinusoidal: 879 harmonic: 1572 Sorted by residual: dihedral pdb=" CB CYS D 323 " pdb=" SG CYS D 323 " pdb=" SG CYS D 345 " pdb=" CB CYS D 345 " ideal model delta sinusoidal sigma weight residual 93.00 169.27 -76.27 1 1.00e+01 1.00e-02 7.32e+01 dihedral pdb=" CB CYS D 93 " pdb=" SG CYS D 93 " pdb=" SG CYS D 194 " pdb=" CB CYS D 194 " ideal model delta sinusoidal sigma weight residual 93.00 37.25 55.75 1 1.00e+01 1.00e-02 4.20e+01 dihedral pdb=" CA CYS D 323 " pdb=" C CYS D 323 " pdb=" N ASN D 324 " pdb=" CA ASN D 324 " ideal model delta harmonic sigma weight residual 180.00 157.93 22.07 0 5.00e+00 4.00e-02 1.95e+01 ... (remaining 2448 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.627: 619 0.627 - 1.255: 1 1.255 - 1.882: 0 1.882 - 2.510: 0 2.510 - 3.137: 1 Chirality restraints: 621 Sorted by residual: chirality pdb=" C1 NAG D 602 " pdb=" ND2 ASN D 395 " pdb=" C2 NAG D 602 " pdb=" O5 NAG D 602 " both_signs ideal model delta sigma weight residual False -2.40 0.74 -3.14 2.00e-01 2.50e+01 2.46e+02 chirality pdb=" C1 NAG D 601 " pdb=" ND2 ASN D 368 " pdb=" C2 NAG D 601 " pdb=" O5 NAG D 601 " both_signs ideal model delta sigma weight residual False -2.40 -1.23 -1.17 2.00e-01 2.50e+01 3.42e+01 chirality pdb=" CA TYR C 108 " pdb=" N TYR C 108 " pdb=" C TYR C 108 " pdb=" CB TYR C 108 " both_signs ideal model delta sigma weight residual False 2.51 2.25 0.26 2.00e-01 2.50e+01 1.70e+00 ... (remaining 618 not shown) Planarity restraints: 732 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN D 395 " 0.073 2.00e-02 2.50e+03 2.02e-01 5.11e+02 pdb=" CG ASN D 395 " -0.032 2.00e-02 2.50e+03 pdb=" OD1 ASN D 395 " -0.011 2.00e-02 2.50e+03 pdb=" ND2 ASN D 395 " -0.329 2.00e-02 2.50e+03 pdb=" C1 NAG D 602 " 0.299 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN D 368 " 0.141 2.00e-02 2.50e+03 1.45e-01 2.62e+02 pdb=" CG ASN D 368 " -0.039 2.00e-02 2.50e+03 pdb=" OD1 ASN D 368 " -0.128 2.00e-02 2.50e+03 pdb=" ND2 ASN D 368 " -0.169 2.00e-02 2.50e+03 pdb=" C1 NAG D 601 " 0.196 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN D 395 " -0.013 2.00e-02 2.50e+03 2.62e-02 6.88e+00 pdb=" CG ASN D 395 " 0.045 2.00e-02 2.50e+03 pdb=" OD1 ASN D 395 " -0.018 2.00e-02 2.50e+03 pdb=" ND2 ASN D 395 " -0.015 2.00e-02 2.50e+03 ... (remaining 729 not shown) Histogram of nonbonded interaction distances: 1.93 - 2.52: 20 2.52 - 3.12: 2985 3.12 - 3.71: 5730 3.71 - 4.31: 8216 4.31 - 4.90: 14059 Nonbonded interactions: 31010 Sorted by model distance: nonbonded pdb=" ND2 ASN D 395 " pdb=" N2 NAG D 602 " model vdw 1.929 2.560 nonbonded pdb=" OD1 ASN D 368 " pdb=" C1 NAG D 601 " model vdw 2.033 2.776 nonbonded pdb=" NE ARG C 35 " pdb=" OD2 ASP D 298 " model vdw 2.171 2.520 nonbonded pdb=" OH TYR D 305 " pdb=" O GLU D 364 " model vdw 2.194 2.440 nonbonded pdb=" OG1 THR C 32 " pdb=" OD2 ASP D 298 " model vdw 2.270 2.440 ... (remaining 31005 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 individual isotropic 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: 1.270 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: 5.080 Check model and map are aligned: 0.060 Set scattering table: 0.060 Process input model: 15.530 Find NCS groups from input model: 0.120 Set up NCS constraints: 0.010 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:10.700 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.830 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7286 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 : 0.008 0.066 4093 Z= 0.516 Angle : 0.804 8.621 5571 Z= 0.458 Chirality : 0.143 3.137 621 Planarity : 0.004 0.050 730 Dihedral : 14.961 122.906 1424 Min Nonbonded Distance : 1.929 Molprobity Statistics. All-atom Clashscore : 6.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Rotamer: Outliers : 0.55 % Allowed : 0.00 % Favored : 99.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % 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: -1.11 (0.37), residues: 536 helix: -0.34 (0.44), residues: 136 sheet: -0.74 (0.43), residues: 140 loop : -0.82 (0.41), residues: 260 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP C 40 HIS 0.002 0.001 HIS D 163 PHE 0.023 0.002 PHE D 257 TYR 0.034 0.002 TYR D 426 ARG 0.010 0.001 ARG C 105 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1072 Ramachandran restraints generated. 536 Oldfield, 0 Emsley, 536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1072 Ramachandran restraints generated. 536 Oldfield, 0 Emsley, 536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 67 residues out of total 468 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 65 time to evaluate : 0.479 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 129 MET cc_start: 0.1470 (mmm) cc_final: 0.0955 (ptm) outliers start: 2 outliers final: 1 residues processed: 66 average time/residue: 1.0314 time to fit residues: 70.8383 Evaluate side-chains 40 residues out of total 468 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 39 time to evaluate : 0.474 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 345 CYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 44 optimal weight: 0.6980 chunk 40 optimal weight: 0.0670 chunk 22 optimal weight: 0.9980 chunk 13 optimal weight: 2.9990 chunk 27 optimal weight: 0.9980 chunk 21 optimal weight: 2.9990 chunk 41 optimal weight: 1.9990 chunk 16 optimal weight: 0.6980 chunk 25 optimal weight: 0.8980 chunk 30 optimal weight: 2.9990 chunk 48 optimal weight: 1.9990 overall best weight: 0.6718 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 110 HIS D 173 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7227 moved from start: 0.1579 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 4093 Z= 0.160 Angle : 0.633 10.870 5571 Z= 0.312 Chirality : 0.041 0.198 621 Planarity : 0.004 0.043 730 Dihedral : 8.040 57.302 631 Min Nonbonded Distance : 2.226 Molprobity Statistics. All-atom Clashscore : 5.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 1.64 % Allowed : 9.56 % Favored : 88.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.32 (0.38), residues: 536 helix: 0.58 (0.44), residues: 142 sheet: -0.63 (0.44), residues: 139 loop : -0.27 (0.43), residues: 255 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 233 HIS 0.003 0.001 HIS D 250 PHE 0.013 0.001 PHE D 100 TYR 0.019 0.001 TYR D 360 ARG 0.009 0.001 ARG D 204 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1072 Ramachandran restraints generated. 536 Oldfield, 0 Emsley, 536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1072 Ramachandran restraints generated. 536 Oldfield, 0 Emsley, 536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 56 residues out of total 468 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 50 time to evaluate : 0.483 Fit side-chains revert: symmetry clash REVERT: D 129 MET cc_start: 0.1812 (mmm) cc_final: 0.1214 (ptm) outliers start: 6 outliers final: 3 residues processed: 53 average time/residue: 0.9501 time to fit residues: 52.9309 Evaluate side-chains 42 residues out of total 468 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 39 time to evaluate : 0.485 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 6 VAL Chi-restraints excluded: chain D residue 345 CYS Chi-restraints excluded: chain D residue 379 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 26 optimal weight: 2.9990 chunk 14 optimal weight: 0.4980 chunk 40 optimal weight: 0.0980 chunk 32 optimal weight: 0.0050 chunk 13 optimal weight: 0.9990 chunk 48 optimal weight: 3.9990 chunk 52 optimal weight: 10.0000 chunk 42 optimal weight: 9.9990 chunk 47 optimal weight: 3.9990 chunk 16 optimal weight: 0.7980 chunk 38 optimal weight: 2.9990 overall best weight: 0.4796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 81 ASN D 399 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7209 moved from start: 0.2026 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 4093 Z= 0.129 Angle : 0.536 7.237 5571 Z= 0.267 Chirality : 0.040 0.151 621 Planarity : 0.004 0.041 730 Dihedral : 5.797 59.645 631 Min Nonbonded Distance : 2.223 Molprobity Statistics. All-atom Clashscore : 4.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.24 % Favored : 97.76 % Rotamer: Outliers : 1.91 % Allowed : 12.84 % Favored : 85.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % 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: -0.01 (0.39), residues: 536 helix: 0.68 (0.44), residues: 150 sheet: -0.40 (0.46), residues: 139 loop : -0.03 (0.45), residues: 247 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP D 233 HIS 0.002 0.001 HIS D 173 PHE 0.006 0.001 PHE C 33 TYR 0.013 0.001 TYR D 360 ARG 0.009 0.001 ARG D 201 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1072 Ramachandran restraints generated. 536 Oldfield, 0 Emsley, 536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1072 Ramachandran restraints generated. 536 Oldfield, 0 Emsley, 536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 51 residues out of total 468 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 44 time to evaluate : 0.499 Fit side-chains REVERT: D 98 PHE cc_start: 0.7812 (OUTLIER) cc_final: 0.7514 (p90) REVERT: D 129 MET cc_start: 0.1850 (mmm) cc_final: 0.1142 (ptm) outliers start: 7 outliers final: 3 residues processed: 47 average time/residue: 0.9907 time to fit residues: 48.8570 Evaluate side-chains 42 residues out of total 468 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 38 time to evaluate : 0.475 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 6 VAL Chi-restraints excluded: chain C residue 32 THR Chi-restraints excluded: chain D residue 98 PHE Chi-restraints excluded: chain D residue 379 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 47 optimal weight: 2.9990 chunk 36 optimal weight: 9.9990 chunk 25 optimal weight: 0.1980 chunk 5 optimal weight: 9.9990 chunk 23 optimal weight: 4.9990 chunk 32 optimal weight: 0.7980 chunk 48 optimal weight: 3.9990 chunk 51 optimal weight: 4.9990 chunk 45 optimal weight: 4.9990 chunk 13 optimal weight: 0.8980 chunk 42 optimal weight: 8.9990 overall best weight: 1.7784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 438 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7283 moved from start: 0.2265 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 4093 Z= 0.276 Angle : 0.566 7.814 5571 Z= 0.288 Chirality : 0.041 0.145 621 Planarity : 0.004 0.038 730 Dihedral : 5.205 36.638 630 Min Nonbonded Distance : 2.192 Molprobity Statistics. All-atom Clashscore : 5.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 2.19 % Allowed : 15.57 % Favored : 82.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % 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: 0.17 (0.39), residues: 536 helix: 0.83 (0.45), residues: 151 sheet: -0.33 (0.45), residues: 139 loop : 0.10 (0.45), residues: 246 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP D 233 HIS 0.004 0.001 HIS D 250 PHE 0.014 0.001 PHE C 72 TYR 0.012 0.001 TYR D 426 ARG 0.008 0.001 ARG D 201 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1072 Ramachandran restraints generated. 536 Oldfield, 0 Emsley, 536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1072 Ramachandran restraints generated. 536 Oldfield, 0 Emsley, 536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 48 residues out of total 468 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 40 time to evaluate : 0.500 Fit side-chains revert: symmetry clash REVERT: D 98 PHE cc_start: 0.7977 (OUTLIER) cc_final: 0.7657 (p90) REVERT: D 129 MET cc_start: 0.2375 (mmm) cc_final: 0.2019 (mmt) outliers start: 8 outliers final: 5 residues processed: 46 average time/residue: 0.9661 time to fit residues: 46.6120 Evaluate side-chains 41 residues out of total 468 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 35 time to evaluate : 0.487 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 6 VAL Chi-restraints excluded: chain C residue 32 THR Chi-restraints excluded: chain D residue 75 THR Chi-restraints excluded: chain D residue 98 PHE Chi-restraints excluded: chain D residue 345 CYS Chi-restraints excluded: chain D residue 379 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 29 optimal weight: 1.9990 chunk 0 optimal weight: 20.0000 chunk 38 optimal weight: 0.9980 chunk 21 optimal weight: 10.0000 chunk 43 optimal weight: 0.7980 chunk 35 optimal weight: 0.8980 chunk 26 optimal weight: 1.9990 chunk 45 optimal weight: 5.9990 chunk 12 optimal weight: 0.7980 chunk 17 optimal weight: 4.9990 chunk 46 optimal weight: 3.9990 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 270 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7257 moved from start: 0.2481 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 4093 Z= 0.184 Angle : 0.526 9.220 5571 Z= 0.264 Chirality : 0.040 0.142 621 Planarity : 0.003 0.042 730 Dihedral : 4.835 35.549 630 Min Nonbonded Distance : 2.255 Molprobity Statistics. All-atom Clashscore : 4.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 1.91 % Allowed : 16.39 % Favored : 81.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % 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: 0.27 (0.39), residues: 536 helix: 0.97 (0.45), residues: 151 sheet: -0.34 (0.45), residues: 137 loop : 0.16 (0.44), residues: 248 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP D 233 HIS 0.002 0.001 HIS D 250 PHE 0.006 0.001 PHE D 100 TYR 0.008 0.001 TYR D 360 ARG 0.009 0.001 ARG D 201 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1072 Ramachandran restraints generated. 536 Oldfield, 0 Emsley, 536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1072 Ramachandran restraints generated. 536 Oldfield, 0 Emsley, 536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 43 residues out of total 468 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 36 time to evaluate : 0.482 Fit side-chains revert: symmetry clash REVERT: D 98 PHE cc_start: 0.7949 (OUTLIER) cc_final: 0.7663 (p90) REVERT: D 129 MET cc_start: 0.2424 (mmm) cc_final: 0.2075 (mmt) outliers start: 7 outliers final: 4 residues processed: 42 average time/residue: 0.9726 time to fit residues: 42.8544 Evaluate side-chains 41 residues out of total 468 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 36 time to evaluate : 0.455 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 6 VAL Chi-restraints excluded: chain C residue 32 THR Chi-restraints excluded: chain D residue 98 PHE Chi-restraints excluded: chain D residue 345 CYS Chi-restraints excluded: chain D residue 379 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 10 optimal weight: 9.9990 chunk 30 optimal weight: 6.9990 chunk 12 optimal weight: 0.9990 chunk 51 optimal weight: 0.7980 chunk 42 optimal weight: 10.0000 chunk 23 optimal weight: 4.9990 chunk 4 optimal weight: 9.9990 chunk 16 optimal weight: 2.9990 chunk 26 optimal weight: 0.5980 chunk 49 optimal weight: 3.9990 chunk 5 optimal weight: 8.9990 overall best weight: 1.8786 ------------------------------------------------------------------------------- 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: 0.7298 moved from start: 0.2590 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 4093 Z= 0.283 Angle : 0.565 9.581 5571 Z= 0.284 Chirality : 0.041 0.143 621 Planarity : 0.003 0.041 730 Dihedral : 5.108 38.138 630 Min Nonbonded Distance : 2.262 Molprobity Statistics. All-atom Clashscore : 4.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.24 % Favored : 97.76 % Rotamer: Outliers : 2.46 % Allowed : 15.57 % Favored : 81.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % 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: 0.35 (0.39), residues: 536 helix: 1.26 (0.45), residues: 145 sheet: -0.43 (0.44), residues: 143 loop : 0.20 (0.44), residues: 248 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP D 233 HIS 0.004 0.001 HIS D 250 PHE 0.007 0.001 PHE D 69 TYR 0.012 0.001 TYR C 99 ARG 0.008 0.001 ARG D 201 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1072 Ramachandran restraints generated. 536 Oldfield, 0 Emsley, 536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1072 Ramachandran restraints generated. 536 Oldfield, 0 Emsley, 536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 45 residues out of total 468 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 36 time to evaluate : 0.486 Fit side-chains revert: symmetry clash REVERT: D 98 PHE cc_start: 0.7977 (OUTLIER) cc_final: 0.7670 (p90) REVERT: D 129 MET cc_start: 0.2223 (mmm) cc_final: 0.1962 (mmt) outliers start: 9 outliers final: 4 residues processed: 43 average time/residue: 0.9046 time to fit residues: 41.0139 Evaluate side-chains 39 residues out of total 468 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 34 time to evaluate : 0.484 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 6 VAL Chi-restraints excluded: chain C residue 32 THR Chi-restraints excluded: chain D residue 98 PHE Chi-restraints excluded: chain D residue 345 CYS Chi-restraints excluded: chain D residue 379 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 29 optimal weight: 0.9980 chunk 37 optimal weight: 3.9990 chunk 43 optimal weight: 10.0000 chunk 28 optimal weight: 3.9990 chunk 51 optimal weight: 4.9990 chunk 31 optimal weight: 3.9990 chunk 23 optimal weight: 3.9990 chunk 20 optimal weight: 5.9990 chunk 30 optimal weight: 0.8980 chunk 15 optimal weight: 2.9990 chunk 10 optimal weight: 1.9990 overall best weight: 2.1786 ------------------------------------------------------------------------------- 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: 0.7316 moved from start: 0.2786 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 4093 Z= 0.326 Angle : 0.598 12.094 5571 Z= 0.300 Chirality : 0.042 0.145 621 Planarity : 0.004 0.040 730 Dihedral : 5.294 38.069 630 Min Nonbonded Distance : 2.283 Molprobity Statistics. All-atom Clashscore : 5.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer: Outliers : 3.28 % Allowed : 16.94 % Favored : 79.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % 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: 0.31 (0.39), residues: 536 helix: 1.33 (0.46), residues: 144 sheet: -0.57 (0.42), residues: 146 loop : 0.19 (0.45), residues: 246 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 233 HIS 0.004 0.001 HIS D 250 PHE 0.007 0.001 PHE C 58 TYR 0.011 0.001 TYR D 360 ARG 0.009 0.001 ARG D 201 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1072 Ramachandran restraints generated. 536 Oldfield, 0 Emsley, 536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1072 Ramachandran restraints generated. 536 Oldfield, 0 Emsley, 536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 48 residues out of total 468 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 36 time to evaluate : 0.455 Fit side-chains revert: symmetry clash REVERT: C 33 PHE cc_start: 0.6157 (OUTLIER) cc_final: 0.5784 (p90) REVERT: C 35 ARG cc_start: 0.8156 (OUTLIER) cc_final: 0.7509 (ptp-170) REVERT: D 98 PHE cc_start: 0.7982 (OUTLIER) cc_final: 0.7656 (p90) REVERT: D 129 MET cc_start: 0.2320 (mmm) cc_final: 0.2064 (mmt) outliers start: 12 outliers final: 6 residues processed: 44 average time/residue: 1.0200 time to fit residues: 47.0128 Evaluate side-chains 43 residues out of total 468 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 34 time to evaluate : 0.474 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 6 VAL Chi-restraints excluded: chain C residue 32 THR Chi-restraints excluded: chain C residue 33 PHE Chi-restraints excluded: chain C residue 35 ARG Chi-restraints excluded: chain D residue 75 THR Chi-restraints excluded: chain D residue 98 PHE Chi-restraints excluded: chain D residue 345 CYS Chi-restraints excluded: chain D residue 379 VAL Chi-restraints excluded: chain D residue 447 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 9 optimal weight: 9.9990 chunk 32 optimal weight: 0.9980 chunk 34 optimal weight: 3.9990 chunk 25 optimal weight: 2.9990 chunk 4 optimal weight: 0.9990 chunk 40 optimal weight: 3.9990 chunk 46 optimal weight: 2.9990 chunk 48 optimal weight: 0.9980 chunk 44 optimal weight: 3.9990 chunk 47 optimal weight: 0.9990 chunk 28 optimal weight: 0.8980 overall best weight: 0.9784 ------------------------------------------------------------------------------- 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: 0.7274 moved from start: 0.2888 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 4093 Z= 0.178 Angle : 0.546 12.607 5571 Z= 0.271 Chirality : 0.040 0.139 621 Planarity : 0.003 0.046 730 Dihedral : 4.977 37.807 630 Min Nonbonded Distance : 2.231 Molprobity Statistics. All-atom Clashscore : 5.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % Rotamer: Outliers : 2.19 % Allowed : 19.13 % Favored : 78.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % 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: 0.31 (0.39), residues: 536 helix: 1.17 (0.45), residues: 151 sheet: -0.50 (0.45), residues: 133 loop : 0.17 (0.44), residues: 252 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 233 HIS 0.002 0.001 HIS D 250 PHE 0.005 0.001 PHE D 50 TYR 0.008 0.001 TYR D 360 ARG 0.010 0.001 ARG D 201 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1072 Ramachandran restraints generated. 536 Oldfield, 0 Emsley, 536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1072 Ramachandran restraints generated. 536 Oldfield, 0 Emsley, 536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 44 residues out of total 468 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 36 time to evaluate : 0.457 Fit side-chains revert: symmetry clash REVERT: C 35 ARG cc_start: 0.8117 (OUTLIER) cc_final: 0.7454 (ptp-170) REVERT: D 98 PHE cc_start: 0.7952 (OUTLIER) cc_final: 0.7708 (p90) REVERT: D 129 MET cc_start: 0.2286 (mmm) cc_final: 0.1938 (mmt) outliers start: 8 outliers final: 5 residues processed: 43 average time/residue: 1.0099 time to fit residues: 45.5587 Evaluate side-chains 41 residues out of total 468 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 34 time to evaluate : 0.487 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 6 VAL Chi-restraints excluded: chain C residue 32 THR Chi-restraints excluded: chain C residue 35 ARG Chi-restraints excluded: chain D residue 75 THR Chi-restraints excluded: chain D residue 98 PHE Chi-restraints excluded: chain D residue 345 CYS Chi-restraints excluded: chain D residue 379 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 20 optimal weight: 0.4980 chunk 37 optimal weight: 3.9990 chunk 14 optimal weight: 0.5980 chunk 43 optimal weight: 8.9990 chunk 45 optimal weight: 1.9990 chunk 47 optimal weight: 0.6980 chunk 31 optimal weight: 0.6980 chunk 50 optimal weight: 0.7980 chunk 30 optimal weight: 6.9990 chunk 23 optimal weight: 4.9990 chunk 34 optimal weight: 0.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- 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: 0.7245 moved from start: 0.2994 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 4093 Z= 0.144 Angle : 0.536 14.200 5571 Z= 0.262 Chirality : 0.040 0.140 621 Planarity : 0.003 0.044 730 Dihedral : 4.639 37.359 630 Min Nonbonded Distance : 2.224 Molprobity Statistics. All-atom Clashscore : 5.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Rotamer: Outliers : 1.91 % Allowed : 19.95 % Favored : 78.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.40 (0.39), residues: 536 helix: 1.27 (0.45), residues: 151 sheet: -0.43 (0.46), residues: 132 loop : 0.19 (0.44), residues: 253 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 40 HIS 0.002 0.001 HIS D 250 PHE 0.006 0.001 PHE D 50 TYR 0.013 0.001 TYR C 99 ARG 0.009 0.001 ARG D 201 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1072 Ramachandran restraints generated. 536 Oldfield, 0 Emsley, 536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1072 Ramachandran restraints generated. 536 Oldfield, 0 Emsley, 536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 42 residues out of total 468 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 35 time to evaluate : 0.400 Fit side-chains revert: symmetry clash REVERT: D 98 PHE cc_start: 0.7986 (OUTLIER) cc_final: 0.7718 (p90) REVERT: D 129 MET cc_start: 0.2340 (mmm) cc_final: 0.2015 (mmt) outliers start: 7 outliers final: 4 residues processed: 40 average time/residue: 0.9007 time to fit residues: 38.1155 Evaluate side-chains 39 residues out of total 468 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 34 time to evaluate : 0.558 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 6 VAL Chi-restraints excluded: chain C residue 32 THR Chi-restraints excluded: chain D residue 98 PHE Chi-restraints excluded: chain D residue 345 CYS Chi-restraints excluded: chain D residue 379 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 52 optimal weight: 10.0000 chunk 48 optimal weight: 3.9990 chunk 42 optimal weight: 1.9990 chunk 4 optimal weight: 0.6980 chunk 32 optimal weight: 2.9990 chunk 25 optimal weight: 0.0270 chunk 33 optimal weight: 0.8980 chunk 44 optimal weight: 1.9990 chunk 12 optimal weight: 0.9980 chunk 38 optimal weight: 0.9980 chunk 6 optimal weight: 8.9990 overall best weight: 0.7238 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7241 moved from start: 0.3076 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 4093 Z= 0.148 Angle : 0.525 13.857 5571 Z= 0.259 Chirality : 0.040 0.139 621 Planarity : 0.003 0.043 730 Dihedral : 4.557 37.391 630 Min Nonbonded Distance : 2.234 Molprobity Statistics. All-atom Clashscore : 5.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % Rotamer: Outliers : 1.64 % Allowed : 19.95 % Favored : 78.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % 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: 0.49 (0.39), residues: 536 helix: 1.37 (0.45), residues: 151 sheet: -0.38 (0.46), residues: 133 loop : 0.23 (0.44), residues: 252 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 233 HIS 0.002 0.000 HIS D 250 PHE 0.006 0.001 PHE D 50 TYR 0.008 0.001 TYR D 360 ARG 0.009 0.001 ARG D 201 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1072 Ramachandran restraints generated. 536 Oldfield, 0 Emsley, 536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1072 Ramachandran restraints generated. 536 Oldfield, 0 Emsley, 536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 41 residues out of total 468 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 35 time to evaluate : 0.511 Fit side-chains revert: symmetry clash REVERT: C 33 PHE cc_start: 0.6036 (OUTLIER) cc_final: 0.5612 (p90) REVERT: D 98 PHE cc_start: 0.7970 (OUTLIER) cc_final: 0.7732 (p90) REVERT: D 129 MET cc_start: 0.2358 (mmm) cc_final: 0.2026 (mmt) outliers start: 6 outliers final: 4 residues processed: 39 average time/residue: 0.8177 time to fit residues: 33.9180 Evaluate side-chains 39 residues out of total 468 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 33 time to evaluate : 0.483 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 6 VAL Chi-restraints excluded: chain C residue 32 THR Chi-restraints excluded: chain C residue 33 PHE Chi-restraints excluded: chain D residue 98 PHE Chi-restraints excluded: chain D residue 345 CYS Chi-restraints excluded: chain D residue 379 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 11 optimal weight: 7.9990 chunk 42 optimal weight: 1.9990 chunk 17 optimal weight: 7.9990 chunk 43 optimal weight: 5.9990 chunk 5 optimal weight: 10.0000 chunk 7 optimal weight: 0.7980 chunk 36 optimal weight: 3.9990 chunk 2 optimal weight: 7.9990 chunk 30 optimal weight: 0.8980 chunk 48 optimal weight: 3.9990 chunk 28 optimal weight: 1.9990 overall best weight: 1.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 84 GLN ** 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 = 0.3493 r_free = 0.3493 target = 0.092815 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3009 r_free = 0.3009 target = 0.065801 restraints weight = 8548.915| |-----------------------------------------------------------------------------| r_work (start): 0.2971 rms_B_bonded: 3.15 r_work: 0.2830 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work (final): 0.2830 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8458 moved from start: 0.3050 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 4093 Z= 0.291 Angle : 0.583 13.875 5571 Z= 0.290 Chirality : 0.042 0.148 621 Planarity : 0.004 0.048 730 Dihedral : 4.979 37.689 630 Min Nonbonded Distance : 2.242 Molprobity Statistics. All-atom Clashscore : 6.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Rotamer: Outliers : 1.91 % Allowed : 20.49 % Favored : 77.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % 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: 0.44 (0.39), residues: 536 helix: 1.31 (0.46), residues: 149 sheet: -0.37 (0.46), residues: 132 loop : 0.20 (0.44), residues: 255 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 233 HIS 0.003 0.001 HIS D 250 PHE 0.007 0.001 PHE D 69 TYR 0.011 0.001 TYR C 99 ARG 0.009 0.001 ARG D 201 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1596.03 seconds wall clock time: 30 minutes 13.31 seconds (1813.31 seconds total)