Starting phenix.real_space_refine (version: 1.21rc1) on Thu Apr 20 02:07:00 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rnn_24580/04_2023/7rnn_24580.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rnn_24580/04_2023/7rnn_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_24580/04_2023/7rnn_24580.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rnn_24580/04_2023/7rnn_24580.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rnn_24580/04_2023/7rnn_24580.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rnn_24580/04_2023/7rnn_24580.pdb" } resolution = 2.86 write_initial_geo_file = False refinement { macro_cycles = 10 } 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 ------------------------------------------------------------------------------- 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-1.21rc1-4938/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: 155 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: 2.72, per 1000 atoms: 0.68 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: 1.40 Conformation dependent library (CDL) restraints added in 789.7 milliseconds 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: 0.29 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: 1.18 Time building geometry restraints manager: 1.54 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 - 16.61: 2175 16.61 - 33.23: 181 33.23 - 49.84: 40 49.84 - 66.46: 8 66.46 - 83.07: 5 Dihedral angle restraints: 2409 sinusoidal: 837 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 2406 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: 1.160 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: 5.260 Check model and map are aligned: 0.060 Set scattering table: 0.040 Process input model: 15.300 Find NCS groups from input model: 0.100 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:11.610 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.550 ------------------------------------------------------------------------------- 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 : 13.562 83.073 1382 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 % 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 *********************** 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 : 0.529 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 2 outliers final: 1 residues processed: 66 average time/residue: 1.0390 time to fit residues: 71.4008 Evaluate side-chains 40 residues out of total 468 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 39 time to evaluate : 0.487 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 1 residues processed: 0 time to fit residues: 0.6400 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.9980 chunk 16 optimal weight: 0.6980 chunk 25 optimal weight: 0.8980 chunk 30 optimal weight: 4.9990 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: 0.7223 moved from start: 0.1607 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.035 4093 Z= 0.160 Angle : 0.619 11.678 5571 Z= 0.309 Chirality : 0.044 0.229 621 Planarity : 0.004 0.043 730 Dihedral : 4.520 20.481 588 Min Nonbonded Distance : 2.226 Molprobity Statistics. All-atom Clashscore : 6.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer Outliers : 1.64 % 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: -0.62 (0.44), residues: 139 loop : -0.28 (0.43), residues: 255 *********************** 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 : 0.474 Fit side-chains revert: symmetry clash outliers start: 6 outliers final: 3 residues processed: 53 average time/residue: 0.9160 time to fit residues: 50.9582 Evaluate side-chains 42 residues out of total 468 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 39 time to evaluate : 0.497 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 2 residues processed: 1 average time/residue: 0.0439 time to fit residues: 0.7501 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 1.9990 chunk 40 optimal weight: 0.3980 chunk 32 optimal weight: 3.9990 chunk 13 optimal weight: 0.9980 chunk 48 optimal weight: 3.9990 chunk 52 optimal weight: 10.0000 chunk 42 optimal weight: 10.0000 chunk 47 optimal weight: 3.9990 chunk 16 optimal weight: 0.5980 chunk 38 optimal weight: 0.7980 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 81 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7240 moved from start: 0.1936 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.019 4093 Z= 0.171 Angle : 0.572 10.550 5571 Z= 0.280 Chirality : 0.043 0.240 621 Planarity : 0.004 0.040 730 Dihedral : 4.256 19.421 588 Min Nonbonded Distance : 2.237 Molprobity Statistics. All-atom Clashscore : 4.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer Outliers : 1.91 % 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: 0.05 (0.39), residues: 536 helix: 0.83 (0.45), residues: 145 sheet: -0.44 (0.44), residues: 145 loop : 0.02 (0.45), residues: 246 *********************** 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 47 residues out of total 468 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 40 time to evaluate : 0.496 Fit side-chains revert: symmetry clash outliers start: 7 outliers final: 4 residues processed: 44 average time/residue: 0.9857 time to fit residues: 45.4766 Evaluate side-chains 42 residues out of total 468 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 38 time to evaluate : 0.469 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 2 residues processed: 2 average time/residue: 0.0399 time to fit residues: 0.7641 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 10.0000 chunk 25 optimal weight: 0.7980 chunk 5 optimal weight: 9.9990 chunk 23 optimal weight: 4.9990 chunk 32 optimal weight: 0.0670 chunk 48 optimal weight: 2.9990 chunk 51 optimal weight: 4.9990 chunk 45 optimal weight: 3.9990 chunk 13 optimal weight: 0.7980 chunk 42 optimal weight: 10.0000 overall best weight: 1.5322 ------------------------------------------------------------------------------- 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: 0.7273 moved from start: 0.2276 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.033 4093 Z= 0.243 Angle : 0.572 8.781 5571 Z= 0.285 Chirality : 0.044 0.303 621 Planarity : 0.004 0.038 730 Dihedral : 4.278 20.972 588 Min Nonbonded Distance : 2.190 Molprobity Statistics. All-atom Clashscore : 4.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer Outliers : 2.19 % 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: 0.16 (0.39), residues: 536 helix: 0.81 (0.45), residues: 151 sheet: -0.39 (0.45), residues: 139 loop : 0.15 (0.44), residues: 246 *********************** 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 46 residues out of total 468 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 38 time to evaluate : 0.361 Fit side-chains outliers start: 8 outliers final: 4 residues processed: 44 average time/residue: 0.7990 time to fit residues: 36.8408 Evaluate side-chains 39 residues out of total 468 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 35 time to evaluate : 0.472 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 3 residues processed: 1 average time/residue: 0.0393 time to fit residues: 0.7148 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 1.9990 chunk 21 optimal weight: 9.9990 chunk 43 optimal weight: 3.9990 chunk 35 optimal weight: 0.9980 chunk 26 optimal weight: 2.9990 chunk 45 optimal weight: 4.9990 chunk 12 optimal weight: 0.7980 chunk 17 optimal weight: 5.9990 chunk 46 optimal weight: 0.8980 overall best weight: 1.3384 ------------------------------------------------------------------------------- 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: 0.7263 moved from start: 0.2501 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.033 4093 Z= 0.213 Angle : 0.538 7.316 5571 Z= 0.270 Chirality : 0.044 0.258 621 Planarity : 0.003 0.041 730 Dihedral : 4.127 18.633 588 Min Nonbonded Distance : 2.279 Molprobity Statistics. All-atom Clashscore : 5.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Rotamer Outliers : 2.46 % 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: 0.19 (0.39), residues: 536 helix: 0.89 (0.45), residues: 151 sheet: -0.46 (0.45), residues: 140 loop : 0.18 (0.44), residues: 245 *********************** 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 48 residues out of total 468 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 39 time to evaluate : 0.481 Fit side-chains revert: symmetry clash outliers start: 9 outliers final: 5 residues processed: 46 average time/residue: 1.0168 time to fit residues: 48.9927 Evaluate side-chains 41 residues out of total 468 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 36 time to evaluate : 0.493 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 4 residues processed: 1 average time/residue: 0.0399 time to fit residues: 0.7295 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 10 optimal weight: 8.9990 chunk 30 optimal weight: 4.9990 chunk 12 optimal weight: 0.7980 chunk 51 optimal weight: 0.9990 chunk 42 optimal weight: 3.9990 chunk 23 optimal weight: 3.9990 chunk 4 optimal weight: 0.6980 chunk 16 optimal weight: 2.9990 chunk 26 optimal weight: 0.9980 chunk 49 optimal weight: 3.9990 chunk 5 optimal weight: 9.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- 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: 0.7264 moved from start: 0.2644 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= 0.208 Angle : 0.537 9.016 5571 Z= 0.268 Chirality : 0.043 0.249 621 Planarity : 0.003 0.040 730 Dihedral : 4.070 19.706 588 Min Nonbonded Distance : 2.284 Molprobity Statistics. All-atom Clashscore : 5.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer Outliers : 2.46 % 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 (0.39), residues: 536 helix: 1.08 (0.45), residues: 151 sheet: -0.42 (0.45), residues: 139 loop : 0.22 (0.44), residues: 246 *********************** 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 46 residues out of total 468 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 37 time to evaluate : 0.560 Fit side-chains revert: symmetry clash outliers start: 9 outliers final: 5 residues processed: 43 average time/residue: 0.8654 time to fit residues: 39.6296 Evaluate side-chains 38 residues out of total 468 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 33 time to evaluate : 0.698 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 4 residues processed: 1 average time/residue: 0.0642 time to fit residues: 1.0006 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 29 optimal weight: 1.9990 chunk 37 optimal weight: 4.9990 chunk 43 optimal weight: 0.8980 chunk 28 optimal weight: 0.0570 chunk 51 optimal weight: 4.9990 chunk 31 optimal weight: 0.9990 chunk 23 optimal weight: 2.9990 chunk 20 optimal weight: 6.9990 chunk 30 optimal weight: 2.9990 chunk 15 optimal weight: 2.9990 chunk 10 optimal weight: 5.9990 overall best weight: 1.3904 ------------------------------------------------------------------------------- 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: 0.7270 moved from start: 0.2750 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= 0.224 Angle : 0.546 11.490 5571 Z= 0.274 Chirality : 0.043 0.253 621 Planarity : 0.003 0.036 730 Dihedral : 4.066 19.645 588 Min Nonbonded Distance : 2.278 Molprobity Statistics. All-atom Clashscore : 5.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.24 % Favored : 97.76 % Rotamer Outliers : 2.46 % 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: 0.38 (0.39), residues: 536 helix: 1.16 (0.45), residues: 151 sheet: -0.36 (0.45), residues: 139 loop : 0.23 (0.44), residues: 246 *********************** 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 43 residues out of total 468 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 34 time to evaluate : 0.483 Fit side-chains revert: symmetry clash outliers start: 9 outliers final: 5 residues processed: 41 average time/residue: 0.9081 time to fit residues: 39.2975 Evaluate side-chains 39 residues out of total 468 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 34 time to evaluate : 0.486 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 4 residues processed: 1 average time/residue: 0.0400 time to fit residues: 0.7131 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 9 optimal weight: 10.0000 chunk 32 optimal weight: 4.9990 chunk 34 optimal weight: 4.9990 chunk 25 optimal weight: 0.2980 chunk 4 optimal weight: 8.9990 chunk 40 optimal weight: 0.0170 chunk 46 optimal weight: 2.9990 chunk 48 optimal weight: 2.9990 chunk 44 optimal weight: 3.9990 chunk 47 optimal weight: 0.9990 chunk 28 optimal weight: 0.2980 overall best weight: 0.9222 ------------------------------------------------------------------------------- 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: 0.7243 moved from start: 0.2850 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= 0.170 Angle : 0.552 13.584 5571 Z= 0.272 Chirality : 0.043 0.257 621 Planarity : 0.003 0.039 730 Dihedral : 3.910 19.060 588 Min Nonbonded Distance : 2.269 Molprobity Statistics. All-atom Clashscore : 5.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer Outliers : 1.91 % 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: 1.30 (0.45), residues: 151 sheet: -0.30 (0.47), residues: 133 loop : 0.24 (0.44), residues: 252 *********************** 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 47 residues out of total 468 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 40 time to evaluate : 0.483 Fit side-chains revert: symmetry clash outliers start: 7 outliers final: 5 residues processed: 45 average time/residue: 1.0593 time to fit residues: 49.9319 Evaluate side-chains 41 residues out of total 468 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 36 time to evaluate : 0.484 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 4 residues processed: 1 average time/residue: 0.0407 time to fit residues: 0.7084 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 20 optimal weight: 5.9990 chunk 37 optimal weight: 2.9990 chunk 14 optimal weight: 1.9990 chunk 43 optimal weight: 0.0070 chunk 45 optimal weight: 1.9990 chunk 47 optimal weight: 0.7980 chunk 31 optimal weight: 4.9990 chunk 50 optimal weight: 2.9990 chunk 30 optimal weight: 0.3980 chunk 23 optimal weight: 0.8980 chunk 34 optimal weight: 0.9980 overall best weight: 0.6198 ------------------------------------------------------------------------------- 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: 0.7224 moved from start: 0.2938 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.029 4093 Z= 0.146 Angle : 0.534 14.159 5571 Z= 0.264 Chirality : 0.042 0.260 621 Planarity : 0.003 0.043 730 Dihedral : 3.771 18.476 588 Min Nonbonded Distance : 2.260 Molprobity Statistics. All-atom Clashscore : 5.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Rotamer Outliers : 1.91 % 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: 0.61 (0.39), residues: 536 helix: 1.41 (0.45), residues: 151 sheet: -0.16 (0.48), residues: 131 loop : 0.25 (0.44), residues: 254 *********************** 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 45 residues out of total 468 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 38 time to evaluate : 0.504 Fit side-chains revert: symmetry clash outliers start: 7 outliers final: 4 residues processed: 43 average time/residue: 0.9287 time to fit residues: 42.0516 Evaluate side-chains 37 residues out of total 468 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 33 time to evaluate : 0.480 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 4 residues processed: 0 time to fit residues: 0.6300 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.9980 chunk 4 optimal weight: 0.7980 chunk 32 optimal weight: 0.9980 chunk 25 optimal weight: 1.9990 chunk 33 optimal weight: 2.9990 chunk 44 optimal weight: 0.9980 chunk 12 optimal weight: 0.6980 chunk 38 optimal weight: 0.9980 chunk 6 optimal weight: 0.0980 overall best weight: 0.7180 ------------------------------------------------------------------------------- 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: 0.7221 moved from start: 0.3030 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= 0.157 Angle : 0.552 13.792 5571 Z= 0.270 Chirality : 0.042 0.260 621 Planarity : 0.003 0.044 730 Dihedral : 3.748 18.399 588 Min Nonbonded Distance : 2.259 Molprobity Statistics. All-atom Clashscore : 4.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer Outliers : 1.91 % 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: 0.64 (0.39), residues: 536 helix: 1.48 (0.45), residues: 151 sheet: -0.23 (0.47), residues: 131 loop : 0.30 (0.44), residues: 254 ********************** 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 42 residues out of total 468 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 35 time to evaluate : 0.464 Fit side-chains revert: symmetry clash outliers start: 7 outliers final: 5 residues processed: 41 average time/residue: 0.9554 time to fit residues: 41.1911 Evaluate side-chains 40 residues out of total 468 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 35 time to evaluate : 0.440 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 4 residues processed: 1 average time/residue: 0.0366 time to fit residues: 0.6402 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 2.9990 chunk 17 optimal weight: 7.9990 chunk 43 optimal weight: 0.3980 chunk 5 optimal weight: 0.5980 chunk 7 optimal weight: 2.9990 chunk 36 optimal weight: 8.9990 chunk 2 optimal weight: 5.9990 chunk 30 optimal weight: 1.9990 chunk 48 optimal weight: 3.9990 chunk 28 optimal weight: 0.6980 overall best weight: 1.3384 ------------------------------------------------------------------------------- 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 = 0.3523 r_free = 0.3523 target = 0.094411 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3047 r_free = 0.3047 target = 0.067868 restraints weight = 8499.345| |-----------------------------------------------------------------------------| r_work (start): 0.3007 rms_B_bonded: 3.05 r_work: 0.2865 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.2865 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8441 moved from start: 0.3029 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.028 4093 Z= 0.227 Angle : 0.568 14.051 5571 Z= 0.282 Chirality : 0.043 0.257 621 Planarity : 0.004 0.047 730 Dihedral : 3.957 19.645 588 Min Nonbonded Distance : 2.212 Molprobity Statistics. All-atom Clashscore : 6.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Rotamer Outliers : 1.09 % 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: 0.60 (0.39), residues: 536 helix: 1.41 (0.45), residues: 151 sheet: -0.24 (0.47), residues: 131 loop : 0.30 (0.44), residues: 254 =============================================================================== Job complete usr+sys time: 1550.76 seconds wall clock time: 28 minutes 43.19 seconds (1723.19 seconds total)