Starting phenix.real_space_refine on Thu Dec 7 21:05:35 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6u2k_20621/12_2023/6u2k_20621_neut.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6u2k_20621/12_2023/6u2k_20621.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.93 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6u2k_20621/12_2023/6u2k_20621.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6u2k_20621/12_2023/6u2k_20621.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6u2k_20621/12_2023/6u2k_20621_neut.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6u2k_20621/12_2023/6u2k_20621_neut.pdb" } resolution = 2.93 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 ------------------------------------------------------------------------------- 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= 0.031 sd= 0.579 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 26 5.16 5 C 2979 2.51 5 N 802 2.21 5 O 912 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B ARG 118": "NH1" <-> "NH2" Residue "B ARG 136": "NH1" <-> "NH2" Residue "B ARG 205": "NH1" <-> "NH2" Residue "B ARG 257": "NH1" <-> "NH2" Residue "B PHE 433": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 434": "NH1" <-> "NH2" Residue "B TYR 474": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 529": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 560": "NH1" <-> "NH2" Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/chem_data/mon_lib" Total number of atoms: 4719 Number of models: 1 Model: "" Number of chains: 3 Chain: "B" Number of atoms: 4663 Number of conformers: 1 Conformer: "" Number of residues, atoms: 604, 4663 Classifications: {'peptide': 604} Incomplete info: {'truncation_to_alanine': 13} Link IDs: {'PCIS': 1, 'PTRANS': 33, 'TRANS': 569} Chain breaks: 2 Unresolved non-hydrogen bonds: 44 Unresolved non-hydrogen angles: 54 Unresolved non-hydrogen dihedrals: 36 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 3, 'ARG:plan': 2, 'ASN:plan1': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 34 Chain: "A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Time building chain proxies: 3.20, per 1000 atoms: 0.68 Number of scatterers: 4719 At special positions: 0 Unit cell: (96.46, 75.26, 104.94, 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 26 16.00 O 912 8.00 N 802 7.00 C 2979 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=8, symmetry=0 Simple disulfide: pdb=" SG CYS B 17 " - pdb=" SG CYS B 53 " distance=2.03 Simple disulfide: pdb=" SG CYS B 333 " - pdb=" SG CYS B 352 " distance=2.03 Simple disulfide: pdb=" SG CYS B 368 " - pdb=" SG CYS B 380 " distance=2.03 Simple disulfide: pdb=" SG CYS B 395 " - pdb=" SG CYS B 438 " distance=2.03 Simple disulfide: pdb=" SG CYS B 418 " - pdb=" SG CYS B 422 " distance=2.03 Simple disulfide: pdb=" SG CYS B 470 " - pdb=" SG CYS B 486 " distance=2.03 Simple disulfide: pdb=" SG CYS B 507 " - pdb=" SG CYS B 540 " distance=2.03 Simple disulfide: pdb=" SG CYS B 525 " - pdb=" SG CYS B 545 " distance=2.02 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG A 1 " - " NAG A 2 " " NAG C 1 " - " NAG C 2 " NAG-ASN " NAG A 1 " - " ASN B 168 " " NAG C 1 " - " ASN B 252 " Time building additional restraints: 1.72 Conformation dependent library (CDL) restraints added in 891.4 milliseconds 1196 Ramachandran restraints generated. 598 Oldfield, 0 Emsley, 598 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1126 Finding SS restraints... Secondary structure from input PDB file: 12 helices and 11 sheets defined 19.0% alpha, 19.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.56 Creating SS restraints... Processing helix chain 'B' and resid 13 through 22 removed outlier: 4.047A pdb=" N CYS B 17 " --> pdb=" O GLY B 13 " (cutoff:3.500A) Processing helix chain 'B' and resid 95 through 100 removed outlier: 3.619A pdb=" N THR B 100 " --> pdb=" O TYR B 96 " (cutoff:3.500A) Processing helix chain 'B' and resid 113 through 125 removed outlier: 3.583A pdb=" N THR B 121 " --> pdb=" O GLN B 117 " (cutoff:3.500A) Processing helix chain 'B' and resid 151 through 157 removed outlier: 3.656A pdb=" N LYS B 156 " --> pdb=" O SER B 152 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N GLU B 157 " --> pdb=" O GLY B 153 " (cutoff:3.500A) Processing helix chain 'B' and resid 160 through 165 Processing helix chain 'B' and resid 172 through 185 removed outlier: 3.726A pdb=" N VAL B 181 " --> pdb=" O ALA B 177 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N LEU B 182 " --> pdb=" O GLU B 178 " (cutoff:3.500A) Processing helix chain 'B' and resid 206 through 211 removed outlier: 3.994A pdb=" N GLN B 210 " --> pdb=" O ALA B 206 " (cutoff:3.500A) removed outlier: 4.154A pdb=" N ASP B 211 " --> pdb=" O SER B 207 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 206 through 211' Processing helix chain 'B' and resid 215 through 233 removed outlier: 3.719A pdb=" N ALA B 221 " --> pdb=" O SER B 217 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N GLN B 228 " --> pdb=" O GLY B 224 " (cutoff:3.500A) Processing helix chain 'B' and resid 248 through 252 Processing helix chain 'B' and resid 271 through 276 Processing helix chain 'B' and resid 294 through 297 removed outlier: 3.615A pdb=" N ILE B 297 " --> pdb=" O HIS B 294 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 294 through 297' Processing helix chain 'B' and resid 309 through 327 removed outlier: 3.795A pdb=" N LYS B 315 " --> pdb=" O LYS B 311 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N TYR B 324 " --> pdb=" O ALA B 320 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 33 through 35 removed outlier: 3.535A pdb=" N MET B 42 " --> pdb=" O GLY B 33 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N VAL B 40 " --> pdb=" O ASP B 35 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 67 through 71 removed outlier: 3.858A pdb=" N ALA B 194 " --> pdb=" O TYR B 140 " (cutoff:3.500A) removed outlier: 7.894A pdb=" N THR B 190 " --> pdb=" O ILE B 144 " (cutoff:3.500A) removed outlier: 5.432A pdb=" N THR B 189 " --> pdb=" O LEU B 291 " (cutoff:3.500A) removed outlier: 6.479A pdb=" N LEU B 291 " --> pdb=" O THR B 189 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N SER B 191 " --> pdb=" O SER B 289 " (cutoff:3.500A) removed outlier: 4.104A pdb=" N ASP B 287 " --> pdb=" O ASP B 193 " (cutoff:3.500A) removed outlier: 6.461A pdb=" N GLY B 195 " --> pdb=" O ALA B 285 " (cutoff:3.500A) removed outlier: 5.118A pdb=" N ALA B 285 " --> pdb=" O GLY B 195 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 82 through 84 removed outlier: 3.741A pdb=" N THR B 130 " --> pdb=" O LEU B 84 " (cutoff:3.500A) removed outlier: 6.689A pdb=" N ILE B 199 " --> pdb=" O VAL B 258 " (cutoff:3.500A) removed outlier: 4.539A pdb=" N VAL B 258 " --> pdb=" O ILE B 199 " (cutoff:3.500A) removed outlier: 6.981A pdb=" N GLU B 201 " --> pdb=" O SER B 256 " (cutoff:3.500A) removed outlier: 4.361A pdb=" N SER B 256 " --> pdb=" O GLU B 201 " (cutoff:3.500A) removed outlier: 6.515A pdb=" N HIS B 203 " --> pdb=" O THR B 254 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 331 through 332 Processing sheet with id=AA5, first strand: chain 'B' and resid 364 through 368 Processing sheet with id=AA6, first strand: chain 'B' and resid 364 through 368 Processing sheet with id=AA7, first strand: chain 'B' and resid 411 through 414 removed outlier: 3.897A pdb=" N TYR B 413 " --> pdb=" O GLN B 427 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N GLN B 427 " --> pdb=" O TYR B 413 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 417 through 418 Processing sheet with id=AA9, first strand: chain 'B' and resid 455 through 456 Processing sheet with id=AB1, first strand: chain 'B' and resid 501 through 505 removed outlier: 5.504A pdb=" N CYS B 545 " --> pdb=" O GLY B 502 " (cutoff:3.500A) removed outlier: 4.461A pdb=" N PHE B 504 " --> pdb=" O SER B 543 " (cutoff:3.500A) removed outlier: 6.713A pdb=" N SER B 543 " --> pdb=" O PHE B 504 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N VAL B 542 " --> pdb=" O ALA B 534 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 579 through 582 removed outlier: 3.561A pdb=" N ASN B 582 " --> pdb=" O ARG B 587 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N ARG B 587 " --> pdb=" O ASN B 582 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N ARG B 599 " --> pdb=" O ILE B 590 " (cutoff:3.500A) 110 hydrogen bonds defined for protein. 306 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: 1.24 Time building geometry restraints manager: 1.85 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 1497 1.34 - 1.46: 1046 1.46 - 1.58: 2244 1.58 - 1.70: 0 1.70 - 1.82: 36 Bond restraints: 4823 Sorted by residual: bond pdb=" C1 NAG A 2 " pdb=" O5 NAG A 2 " ideal model delta sigma weight residual 1.406 1.450 -0.044 2.00e-02 2.50e+03 4.74e+00 bond pdb=" CB ASN B 328 " pdb=" CG ASN B 328 " ideal model delta sigma weight residual 1.516 1.466 0.050 2.50e-02 1.60e+03 3.93e+00 bond pdb=" C1 NAG C 2 " pdb=" O5 NAG C 2 " ideal model delta sigma weight residual 1.406 1.445 -0.039 2.00e-02 2.50e+03 3.89e+00 bond pdb=" CB VAL B 310 " pdb=" CG1 VAL B 310 " ideal model delta sigma weight residual 1.521 1.458 0.063 3.30e-02 9.18e+02 3.63e+00 bond pdb=" CB VAL B 142 " pdb=" CG1 VAL B 142 " ideal model delta sigma weight residual 1.521 1.460 0.061 3.30e-02 9.18e+02 3.47e+00 ... (remaining 4818 not shown) Histogram of bond angle deviations from ideal: 97.03 - 104.45: 93 104.45 - 111.88: 2221 111.88 - 119.31: 1737 119.31 - 126.73: 2436 126.73 - 134.16: 69 Bond angle restraints: 6556 Sorted by residual: angle pdb=" CA TYR B 50 " pdb=" CB TYR B 50 " pdb=" CG TYR B 50 " ideal model delta sigma weight residual 113.90 122.23 -8.33 1.80e+00 3.09e-01 2.14e+01 angle pdb=" C HIS B 403 " pdb=" N LEU B 404 " pdb=" CA LEU B 404 " ideal model delta sigma weight residual 121.54 129.86 -8.32 1.91e+00 2.74e-01 1.90e+01 angle pdb=" C ARG B 375 " pdb=" N ASP B 376 " pdb=" CA ASP B 376 " ideal model delta sigma weight residual 121.54 128.77 -7.23 1.91e+00 2.74e-01 1.43e+01 angle pdb=" C PHE B 480 " pdb=" N GLU B 481 " pdb=" CA GLU B 481 " ideal model delta sigma weight residual 121.54 128.51 -6.97 1.91e+00 2.74e-01 1.33e+01 angle pdb=" N PHE B 327 " pdb=" CA PHE B 327 " pdb=" C PHE B 327 " ideal model delta sigma weight residual 110.53 105.83 4.70 1.32e+00 5.74e-01 1.27e+01 ... (remaining 6551 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.88: 2789 14.88 - 29.76: 126 29.76 - 44.64: 36 44.64 - 59.52: 9 59.52 - 74.40: 4 Dihedral angle restraints: 2964 sinusoidal: 1218 harmonic: 1746 Sorted by residual: dihedral pdb=" CA VAL B 402 " pdb=" C VAL B 402 " pdb=" N HIS B 403 " pdb=" CA HIS B 403 " ideal model delta harmonic sigma weight residual -180.00 -151.91 -28.09 0 5.00e+00 4.00e-02 3.16e+01 dihedral pdb=" CA VAL B 135 " pdb=" C VAL B 135 " pdb=" N ARG B 136 " pdb=" CA ARG B 136 " ideal model delta harmonic sigma weight residual -180.00 -156.48 -23.52 0 5.00e+00 4.00e-02 2.21e+01 dihedral pdb=" CA PRO B 396 " pdb=" C PRO B 396 " pdb=" N SER B 397 " pdb=" CA SER B 397 " ideal model delta harmonic sigma weight residual 180.00 -156.87 -23.13 0 5.00e+00 4.00e-02 2.14e+01 ... (remaining 2961 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.042: 379 0.042 - 0.083: 246 0.083 - 0.125: 87 0.125 - 0.166: 30 0.166 - 0.208: 7 Chirality restraints: 749 Sorted by residual: chirality pdb=" CB ILE B 579 " pdb=" CA ILE B 579 " pdb=" CG1 ILE B 579 " pdb=" CG2 ILE B 579 " both_signs ideal model delta sigma weight residual False 2.64 2.44 0.21 2.00e-01 2.50e+01 1.08e+00 chirality pdb=" CA ILE B 67 " pdb=" N ILE B 67 " pdb=" C ILE B 67 " pdb=" CB ILE B 67 " both_signs ideal model delta sigma weight residual False 2.43 2.62 -0.19 2.00e-01 2.50e+01 8.72e-01 chirality pdb=" CB THR B 552 " pdb=" CA THR B 552 " pdb=" OG1 THR B 552 " pdb=" CG2 THR B 552 " both_signs ideal model delta sigma weight residual False 2.55 2.37 0.18 2.00e-01 2.50e+01 8.14e-01 ... (remaining 746 not shown) Planarity restraints: 855 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LEU B 404 " 0.017 2.00e-02 2.50e+03 3.33e-02 1.11e+01 pdb=" C LEU B 404 " -0.058 2.00e-02 2.50e+03 pdb=" O LEU B 404 " 0.021 2.00e-02 2.50e+03 pdb=" N LEU B 405 " 0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C TYR B 330 " 0.051 5.00e-02 4.00e+02 7.77e-02 9.65e+00 pdb=" N PRO B 331 " -0.134 5.00e-02 4.00e+02 pdb=" CA PRO B 331 " 0.041 5.00e-02 4.00e+02 pdb=" CD PRO B 331 " 0.043 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA PHE B 480 " 0.012 2.00e-02 2.50e+03 2.34e-02 5.47e+00 pdb=" C PHE B 480 " -0.040 2.00e-02 2.50e+03 pdb=" O PHE B 480 " 0.015 2.00e-02 2.50e+03 pdb=" N GLU B 481 " 0.014 2.00e-02 2.50e+03 ... (remaining 852 not shown) Histogram of nonbonded interaction distances: 2.35 - 2.86: 1667 2.86 - 3.37: 3987 3.37 - 3.88: 7168 3.88 - 4.39: 8323 4.39 - 4.90: 14511 Nonbonded interactions: 35656 Sorted by model distance: nonbonded pdb=" OG SER B 248 " pdb=" OD1 ASN B 252 " model vdw 2.354 2.440 nonbonded pdb=" ND2 ASN B 387 " pdb=" O SER B 394 " model vdw 2.359 2.520 nonbonded pdb=" O TYR B 325 " pdb=" OG1 THR B 329 " model vdw 2.387 2.440 nonbonded pdb=" O CYS B 507 " pdb=" NZ LYS B 523 " model vdw 2.397 2.520 nonbonded pdb=" ND2 ASN B 414 " pdb=" O HIS B 415 " model vdw 2.428 2.520 ... (remaining 35651 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' } 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: 0.430 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: 1.490 Check model and map are aligned: 0.070 Set scattering table: 0.040 Process input model: 16.870 Find NCS groups from input model: 0.120 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:10.280 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.320 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7971 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 : 0.010 0.074 4823 Z= 0.658 Angle : 0.989 8.704 6556 Z= 0.542 Chirality : 0.061 0.208 749 Planarity : 0.008 0.078 853 Dihedral : 10.371 74.405 1814 Min Nonbonded Distance : 2.354 Molprobity Statistics. All-atom Clashscore : 3.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.70 % Favored : 90.30 % Rotamer: Outliers : 0.19 % Allowed : 4.44 % Favored : 95.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.70 (0.27), residues: 598 helix: -4.66 (0.16), residues: 119 sheet: -2.91 (0.40), residues: 113 loop : -2.72 (0.27), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.003 TRP B 437 HIS 0.009 0.002 HIS B 203 PHE 0.032 0.004 PHE B 551 TYR 0.031 0.004 TYR B 324 ARG 0.013 0.001 ARG B 132 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1196 Ramachandran restraints generated. 598 Oldfield, 0 Emsley, 598 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1196 Ramachandran restraints generated. 598 Oldfield, 0 Emsley, 598 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 531 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 139 time to evaluate : 0.561 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 140 average time/residue: 0.8775 time to fit residues: 129.0193 Evaluate side-chains 98 residues out of total 531 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 98 time to evaluate : 0.530 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.7458 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 50 optimal weight: 4.9990 chunk 45 optimal weight: 2.9990 chunk 25 optimal weight: 1.9990 chunk 15 optimal weight: 0.6980 chunk 30 optimal weight: 0.8980 chunk 24 optimal weight: 1.9990 chunk 47 optimal weight: 0.6980 chunk 18 optimal weight: 1.9990 chunk 28 optimal weight: 0.0970 chunk 35 optimal weight: 5.9990 chunk 54 optimal weight: 1.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 36 ASN B 52 ASN B 80 ASN B 109 ASN B 255 ASN B 370 GLN B 387 ASN B 414 ASN B 489 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7915 moved from start: 0.1865 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 4823 Z= 0.226 Angle : 0.607 6.058 6556 Z= 0.325 Chirality : 0.046 0.212 749 Planarity : 0.006 0.044 853 Dihedral : 7.285 54.448 727 Min Nonbonded Distance : 2.300 Molprobity Statistics. All-atom Clashscore : 6.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.53 % Favored : 91.47 % Rotamer: Outliers : 3.86 % Allowed : 11.78 % Favored : 84.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % 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: -3.93 (0.28), residues: 598 helix: -3.35 (0.32), residues: 124 sheet: -2.95 (0.38), residues: 110 loop : -2.26 (0.29), residues: 364 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 275 HIS 0.003 0.001 HIS B 203 PHE 0.014 0.002 PHE B 480 TYR 0.014 0.002 TYR B 50 ARG 0.005 0.000 ARG B 257 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1196 Ramachandran restraints generated. 598 Oldfield, 0 Emsley, 598 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1196 Ramachandran restraints generated. 598 Oldfield, 0 Emsley, 598 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 531 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 100 time to evaluate : 0.560 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 20 outliers final: 12 residues processed: 109 average time/residue: 0.8464 time to fit residues: 97.3454 Evaluate side-chains 105 residues out of total 531 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 93 time to evaluate : 0.551 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 5 residues processed: 7 average time/residue: 0.0936 time to fit residues: 1.6979 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 30 optimal weight: 1.9990 chunk 16 optimal weight: 1.9990 chunk 45 optimal weight: 4.9990 chunk 37 optimal weight: 5.9990 chunk 15 optimal weight: 0.5980 chunk 54 optimal weight: 3.9990 chunk 58 optimal weight: 7.9990 chunk 48 optimal weight: 4.9990 chunk 18 optimal weight: 4.9990 chunk 43 optimal weight: 7.9990 chunk 53 optimal weight: 0.5980 overall best weight: 1.8386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 482 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7964 moved from start: 0.2155 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.065 4823 Z= 0.382 Angle : 0.634 7.034 6556 Z= 0.338 Chirality : 0.047 0.176 749 Planarity : 0.005 0.036 853 Dihedral : 6.962 55.729 727 Min Nonbonded Distance : 2.255 Molprobity Statistics. All-atom Clashscore : 6.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.70 % Favored : 91.30 % Rotamer: Outliers : 5.02 % Allowed : 14.29 % Favored : 80.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % 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: -3.49 (0.30), residues: 598 helix: -2.45 (0.40), residues: 124 sheet: -2.90 (0.37), residues: 122 loop : -2.05 (0.30), residues: 352 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 437 HIS 0.004 0.001 HIS B 282 PHE 0.017 0.002 PHE B 480 TYR 0.016 0.002 TYR B 324 ARG 0.004 0.001 ARG B 132 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1196 Ramachandran restraints generated. 598 Oldfield, 0 Emsley, 598 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1196 Ramachandran restraints generated. 598 Oldfield, 0 Emsley, 598 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 531 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 95 time to evaluate : 0.581 Fit side-chains revert: symmetry clash outliers start: 26 outliers final: 17 residues processed: 106 average time/residue: 0.7749 time to fit residues: 87.1696 Evaluate side-chains 104 residues out of total 531 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 87 time to evaluate : 0.530 Switching outliers to nearest non-outliers outliers start: 17 outliers final: 10 residues processed: 7 average time/residue: 0.0839 time to fit residues: 1.5846 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 41 optimal weight: 4.9990 chunk 28 optimal weight: 0.9990 chunk 6 optimal weight: 0.4980 chunk 26 optimal weight: 1.9990 chunk 36 optimal weight: 2.9990 chunk 54 optimal weight: 0.5980 chunk 57 optimal weight: 3.9990 chunk 51 optimal weight: 0.0970 chunk 15 optimal weight: 0.9990 chunk 48 optimal weight: 0.9980 chunk 32 optimal weight: 4.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- 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: 0.7904 moved from start: 0.2483 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.098 4823 Z= 0.199 Angle : 0.576 9.318 6556 Z= 0.304 Chirality : 0.044 0.203 749 Planarity : 0.004 0.037 853 Dihedral : 6.368 54.573 727 Min Nonbonded Distance : 2.292 Molprobity Statistics. All-atom Clashscore : 6.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.36 % Favored : 91.64 % Rotamer: Outliers : 4.63 % Allowed : 16.41 % Favored : 78.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % 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: -3.13 (0.31), residues: 598 helix: -1.82 (0.44), residues: 124 sheet: -2.56 (0.39), residues: 126 loop : -1.99 (0.31), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 275 HIS 0.002 0.000 HIS B 203 PHE 0.018 0.001 PHE B 497 TYR 0.011 0.001 TYR B 267 ARG 0.007 0.000 ARG B 54 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1196 Ramachandran restraints generated. 598 Oldfield, 0 Emsley, 598 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1196 Ramachandran restraints generated. 598 Oldfield, 0 Emsley, 598 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 531 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 91 time to evaluate : 0.490 Fit side-chains revert: symmetry clash outliers start: 24 outliers final: 12 residues processed: 104 average time/residue: 0.8100 time to fit residues: 89.1489 Evaluate side-chains 98 residues out of total 531 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 86 time to evaluate : 0.532 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 6 residues processed: 6 average time/residue: 0.3330 time to fit residues: 2.9846 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 0 optimal weight: 0.9990 chunk 43 optimal weight: 0.3980 chunk 23 optimal weight: 5.9990 chunk 49 optimal weight: 0.0050 chunk 40 optimal weight: 2.9990 chunk 29 optimal weight: 0.0050 chunk 52 optimal weight: 0.9980 chunk 14 optimal weight: 0.9990 chunk 19 optimal weight: 3.9990 chunk 11 optimal weight: 0.7980 chunk 34 optimal weight: 0.0770 overall best weight: 0.2566 ------------------------------------------------------------------------------- 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: 0.7861 moved from start: 0.2810 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 4823 Z= 0.144 Angle : 0.543 7.812 6556 Z= 0.284 Chirality : 0.043 0.166 749 Planarity : 0.004 0.033 853 Dihedral : 5.937 54.027 727 Min Nonbonded Distance : 2.266 Molprobity Statistics. All-atom Clashscore : 6.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.03 % Favored : 91.97 % Rotamer: Outliers : 4.05 % Allowed : 18.34 % Favored : 77.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.88 (0.32), residues: 598 helix: -1.36 (0.45), residues: 130 sheet: -2.45 (0.38), residues: 122 loop : -1.94 (0.32), residues: 346 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 275 HIS 0.002 0.000 HIS B 203 PHE 0.012 0.001 PHE B 68 TYR 0.011 0.001 TYR B 50 ARG 0.003 0.000 ARG B 54 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1196 Ramachandran restraints generated. 598 Oldfield, 0 Emsley, 598 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1196 Ramachandran restraints generated. 598 Oldfield, 0 Emsley, 598 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 531 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 96 time to evaluate : 0.502 Fit side-chains revert: symmetry clash outliers start: 21 outliers final: 12 residues processed: 106 average time/residue: 0.7847 time to fit residues: 88.0230 Evaluate side-chains 101 residues out of total 531 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 89 time to evaluate : 0.534 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 6 residues processed: 6 average time/residue: 0.0936 time to fit residues: 1.5398 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 14 optimal weight: 1.9990 chunk 58 optimal weight: 0.1980 chunk 48 optimal weight: 7.9990 chunk 26 optimal weight: 0.0000 chunk 4 optimal weight: 4.9990 chunk 19 optimal weight: 2.9990 chunk 30 optimal weight: 0.9990 chunk 55 optimal weight: 0.9980 chunk 6 optimal weight: 1.9990 chunk 33 optimal weight: 2.9990 chunk 42 optimal weight: 1.9990 overall best weight: 0.8388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 203 HIS B 358 ASN B 387 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7889 moved from start: 0.2944 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 4823 Z= 0.212 Angle : 0.586 8.309 6556 Z= 0.301 Chirality : 0.044 0.155 749 Planarity : 0.004 0.032 853 Dihedral : 5.909 54.569 727 Min Nonbonded Distance : 2.259 Molprobity Statistics. All-atom Clashscore : 6.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.03 % Favored : 91.97 % Rotamer: Outliers : 3.28 % Allowed : 19.50 % Favored : 77.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.62 (0.32), residues: 598 helix: -1.07 (0.46), residues: 130 sheet: -2.15 (0.39), residues: 121 loop : -1.86 (0.32), residues: 347 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 87 HIS 0.003 0.001 HIS B 282 PHE 0.013 0.001 PHE B 68 TYR 0.013 0.001 TYR B 324 ARG 0.005 0.000 ARG B 205 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1196 Ramachandran restraints generated. 598 Oldfield, 0 Emsley, 598 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1196 Ramachandran restraints generated. 598 Oldfield, 0 Emsley, 598 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 531 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 87 time to evaluate : 0.567 Fit side-chains outliers start: 17 outliers final: 13 residues processed: 95 average time/residue: 0.8031 time to fit residues: 80.8033 Evaluate side-chains 97 residues out of total 531 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 84 time to evaluate : 0.534 Switching outliers to nearest non-outliers outliers start: 13 outliers final: 7 residues processed: 6 average time/residue: 0.0934 time to fit residues: 1.5239 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 32 optimal weight: 0.9990 chunk 48 optimal weight: 7.9990 chunk 57 optimal weight: 4.9990 chunk 36 optimal weight: 6.9990 chunk 35 optimal weight: 6.9990 chunk 26 optimal weight: 3.9990 chunk 23 optimal weight: 0.0060 chunk 34 optimal weight: 4.9990 chunk 17 optimal weight: 1.9990 chunk 11 optimal weight: 0.9980 chunk 39 optimal weight: 0.0670 overall best weight: 0.8138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 358 ASN B 489 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7885 moved from start: 0.3088 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.067 4823 Z= 0.223 Angle : 0.580 8.816 6556 Z= 0.299 Chirality : 0.044 0.156 749 Planarity : 0.004 0.034 853 Dihedral : 5.901 54.526 727 Min Nonbonded Distance : 2.199 Molprobity Statistics. All-atom Clashscore : 6.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.53 % Favored : 91.47 % Rotamer: Outliers : 4.05 % Allowed : 19.11 % Favored : 76.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.49 (0.32), residues: 598 helix: -0.84 (0.46), residues: 130 sheet: -2.22 (0.38), residues: 127 loop : -1.75 (0.33), residues: 341 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 87 HIS 0.002 0.001 HIS B 419 PHE 0.013 0.001 PHE B 68 TYR 0.012 0.001 TYR B 324 ARG 0.004 0.000 ARG B 205 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1196 Ramachandran restraints generated. 598 Oldfield, 0 Emsley, 598 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1196 Ramachandran restraints generated. 598 Oldfield, 0 Emsley, 598 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 531 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 86 time to evaluate : 0.486 Fit side-chains outliers start: 21 outliers final: 16 residues processed: 98 average time/residue: 0.7820 time to fit residues: 81.1239 Evaluate side-chains 97 residues out of total 531 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 81 time to evaluate : 0.497 Switching outliers to nearest non-outliers outliers start: 16 outliers final: 8 residues processed: 8 average time/residue: 0.0881 time to fit residues: 1.7632 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 28 optimal weight: 0.7980 chunk 5 optimal weight: 2.9990 chunk 45 optimal weight: 3.9990 chunk 52 optimal weight: 0.6980 chunk 55 optimal weight: 0.6980 chunk 50 optimal weight: 0.7980 chunk 53 optimal weight: 1.9990 chunk 32 optimal weight: 0.0870 chunk 23 optimal weight: 1.9990 chunk 42 optimal weight: 4.9990 chunk 16 optimal weight: 0.5980 overall best weight: 0.5758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 52 ASN B 358 ASN B 489 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7865 moved from start: 0.3256 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 4823 Z= 0.182 Angle : 0.570 8.960 6556 Z= 0.289 Chirality : 0.043 0.158 749 Planarity : 0.004 0.032 853 Dihedral : 5.773 53.893 727 Min Nonbonded Distance : 2.177 Molprobity Statistics. All-atom Clashscore : 7.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.19 % Favored : 91.81 % Rotamer: Outliers : 3.86 % Allowed : 19.31 % Favored : 76.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.34 (0.33), residues: 598 helix: -0.64 (0.47), residues: 130 sheet: -2.11 (0.38), residues: 127 loop : -1.69 (0.33), residues: 341 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 87 HIS 0.002 0.001 HIS B 415 PHE 0.012 0.001 PHE B 497 TYR 0.010 0.001 TYR B 324 ARG 0.004 0.000 ARG B 205 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1196 Ramachandran restraints generated. 598 Oldfield, 0 Emsley, 598 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1196 Ramachandran restraints generated. 598 Oldfield, 0 Emsley, 598 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 531 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 88 time to evaluate : 0.564 Fit side-chains outliers start: 20 outliers final: 17 residues processed: 99 average time/residue: 0.8806 time to fit residues: 91.9318 Evaluate side-chains 100 residues out of total 531 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 83 time to evaluate : 0.515 Switching outliers to nearest non-outliers outliers start: 17 outliers final: 10 residues processed: 8 average time/residue: 0.3710 time to fit residues: 3.9993 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 48 optimal weight: 0.9980 chunk 50 optimal weight: 1.9990 chunk 53 optimal weight: 3.9990 chunk 35 optimal weight: 6.9990 chunk 56 optimal weight: 4.9990 chunk 34 optimal weight: 0.0370 chunk 27 optimal weight: 0.3980 chunk 39 optimal weight: 0.9990 chunk 59 optimal weight: 0.1980 chunk 55 optimal weight: 0.6980 chunk 47 optimal weight: 0.9990 overall best weight: 0.4658 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 489 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7850 moved from start: 0.3406 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 4823 Z= 0.164 Angle : 0.542 7.781 6556 Z= 0.277 Chirality : 0.043 0.162 749 Planarity : 0.004 0.033 853 Dihedral : 5.613 53.951 727 Min Nonbonded Distance : 2.208 Molprobity Statistics. All-atom Clashscore : 6.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.36 % Favored : 91.64 % Rotamer: Outliers : 2.90 % Allowed : 20.85 % Favored : 76.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.14 (0.33), residues: 598 helix: -0.24 (0.48), residues: 127 sheet: -2.00 (0.38), residues: 127 loop : -1.65 (0.33), residues: 344 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 87 HIS 0.001 0.000 HIS B 203 PHE 0.012 0.001 PHE B 497 TYR 0.009 0.001 TYR B 324 ARG 0.004 0.000 ARG B 205 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1196 Ramachandran restraints generated. 598 Oldfield, 0 Emsley, 598 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1196 Ramachandran restraints generated. 598 Oldfield, 0 Emsley, 598 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 531 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 85 time to evaluate : 0.558 Fit side-chains outliers start: 15 outliers final: 13 residues processed: 95 average time/residue: 0.8290 time to fit residues: 83.3038 Evaluate side-chains 94 residues out of total 531 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 81 time to evaluate : 0.521 Switching outliers to nearest non-outliers outliers start: 13 outliers final: 8 residues processed: 5 average time/residue: 0.0727 time to fit residues: 1.2869 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 4 optimal weight: 0.0470 chunk 36 optimal weight: 0.1980 chunk 29 optimal weight: 0.8980 chunk 37 optimal weight: 5.9990 chunk 50 optimal weight: 0.8980 chunk 14 optimal weight: 0.9980 chunk 43 optimal weight: 4.9990 chunk 7 optimal weight: 5.9990 chunk 13 optimal weight: 0.7980 chunk 47 optimal weight: 0.8980 chunk 19 optimal weight: 6.9990 overall best weight: 0.5678 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 358 ASN B 489 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7852 moved from start: 0.3475 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 4823 Z= 0.174 Angle : 0.571 10.644 6556 Z= 0.286 Chirality : 0.043 0.158 749 Planarity : 0.004 0.033 853 Dihedral : 5.568 53.979 727 Min Nonbonded Distance : 2.221 Molprobity Statistics. All-atom Clashscore : 6.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.86 % Favored : 92.14 % Rotamer: Outliers : 2.51 % Allowed : 21.62 % Favored : 75.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % 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: -1.98 (0.33), residues: 598 helix: -0.16 (0.49), residues: 129 sheet: -2.00 (0.37), residues: 139 loop : -1.43 (0.34), residues: 330 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 87 HIS 0.002 0.001 HIS B 203 PHE 0.012 0.001 PHE B 497 TYR 0.010 0.001 TYR B 324 ARG 0.003 0.000 ARG B 205 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1196 Ramachandran restraints generated. 598 Oldfield, 0 Emsley, 598 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1196 Ramachandran restraints generated. 598 Oldfield, 0 Emsley, 598 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 531 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 83 time to evaluate : 0.526 Fit side-chains outliers start: 13 outliers final: 11 residues processed: 92 average time/residue: 0.8455 time to fit residues: 82.2171 Evaluate side-chains 90 residues out of total 531 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 79 time to evaluate : 0.526 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 9 residues processed: 2 average time/residue: 0.1746 time to fit residues: 1.1640 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 48 optimal weight: 0.8980 chunk 6 optimal weight: 1.9990 chunk 8 optimal weight: 0.9980 chunk 41 optimal weight: 3.9990 chunk 2 optimal weight: 0.7980 chunk 34 optimal weight: 0.8980 chunk 54 optimal weight: 0.4980 chunk 32 optimal weight: 0.6980 chunk 40 optimal weight: 2.9990 chunk 1 optimal weight: 0.0570 chunk 38 optimal weight: 0.0010 overall best weight: 0.4104 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 358 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3761 r_free = 0.3761 target = 0.148904 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.112922 restraints weight = 5825.094| |-----------------------------------------------------------------------------| r_work (start): 0.3325 rms_B_bonded: 2.79 r_work: 0.3194 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work (final): 0.3194 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7641 moved from start: 0.3580 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 4823 Z= 0.156 Angle : 0.544 7.030 6556 Z= 0.280 Chirality : 0.043 0.163 749 Planarity : 0.004 0.033 853 Dihedral : 5.471 53.755 727 Min Nonbonded Distance : 2.227 Molprobity Statistics. All-atom Clashscore : 6.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.86 % Favored : 92.14 % Rotamer: Outliers : 2.12 % Allowed : 21.24 % Favored : 76.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % 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: -1.90 (0.33), residues: 598 helix: 0.07 (0.49), residues: 127 sheet: -1.92 (0.38), residues: 139 loop : -1.48 (0.33), residues: 332 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP B 87 HIS 0.001 0.000 HIS B 203 PHE 0.012 0.001 PHE B 497 TYR 0.009 0.001 TYR B 50 ARG 0.003 0.000 ARG B 205 =============================================================================== Job complete usr+sys time: 2117.33 seconds wall clock time: 38 minutes 14.43 seconds (2294.43 seconds total)