Starting phenix.real_space_refine on Sun Mar 10 15:55:58 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6x2z_22014/03_2024/6x2z_22014.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6x2z_22014/03_2024/6x2z_22014.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.03 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6x2z_22014/03_2024/6x2z_22014.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6x2z_22014/03_2024/6x2z_22014.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6x2z_22014/03_2024/6x2z_22014.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6x2z_22014/03_2024/6x2z_22014.pdb" } resolution = 3.03 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.003 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: 5 Type Number sf(0) Gaussians S 23 5.16 5 Na 3 4.78 5 C 2094 2.51 5 N 511 2.21 5 O 574 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 39": "NH1" <-> "NH2" Residue "A PHE 50": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 83": "OD1" <-> "OD2" Residue "A TYR 97": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 152": "OE1" <-> "OE2" Residue "A GLU 231": "OE1" <-> "OE2" Residue "A PHE 239": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 277": "OE1" <-> "OE2" Residue "A PHE 279": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 280": "NH1" <-> "NH2" Residue "A PHE 306": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 316": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 346": "OE1" <-> "OE2" Residue "A ASP 351": "OD1" <-> "OD2" Residue "A ARG 353": "NH1" <-> "NH2" Residue "A ARG 356": "NH1" <-> "NH2" Residue "A ASP 368": "OD1" <-> "OD2" Residue "A ASP 386": "OD1" <-> "OD2" Residue "A ASP 444": "OD1" <-> "OD2" Residue "A ARG 447": "NH1" <-> "NH2" Residue "A GLU 469": "OE1" <-> "OE2" Residue "A ASP 600": "OD1" <-> "OD2" Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 3205 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 3205 Number of conformers: 1 Conformer: "" Number of residues, atoms: 423, 3205 Unusual residues: {' NA': 3} Inner-chain residues flagged as termini: ['pdbres="ASP A 600 "'] Classifications: {'peptide': 420, 'undetermined': 3} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 11, 'TRANS': 408, None: 3} Not linked: pdbres="ASP A 600 " pdbres=" NA A 601 " Not linked: pdbres=" NA A 601 " pdbres=" NA A 602 " Not linked: pdbres=" NA A 602 " pdbres=" NA A 603 " Chain breaks: 3 Time building chain proxies: 2.29, per 1000 atoms: 0.71 Number of scatterers: 3205 At special positions: 0 Unit cell: (67.392, 67.392, 82.368, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 23 16.00 Na 3 11.00 O 574 8.00 N 511 7.00 C 2094 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.37 Conformation dependent library (CDL) restraints added in 646.5 milliseconds 826 Ramachandran restraints generated. 413 Oldfield, 0 Emsley, 413 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 776 Finding SS restraints... Secondary structure from input PDB file: 23 helices and 1 sheets defined 79.3% alpha, 3.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.35 Creating SS restraints... Processing helix chain 'A' and resid 18 through 42 removed outlier: 3.778A pdb=" N LEU A 22 " --> pdb=" O ASN A 18 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N THR A 34 " --> pdb=" O LEU A 30 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N LEU A 37 " --> pdb=" O THR A 33 " (cutoff:3.500A) removed outlier: 4.842A pdb=" N ARG A 39 " --> pdb=" O GLY A 35 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N GLU A 40 " --> pdb=" O VAL A 36 " (cutoff:3.500A) Processing helix chain 'A' and resid 47 through 52 Processing helix chain 'A' and resid 53 through 81 removed outlier: 3.798A pdb=" N ILE A 66 " --> pdb=" O MET A 62 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N ILE A 67 " --> pdb=" O LEU A 63 " (cutoff:3.500A) removed outlier: 4.525A pdb=" N LEU A 68 " --> pdb=" O LYS A 64 " (cutoff:3.500A) Proline residue: A 69 - end of helix removed outlier: 3.887A pdb=" N VAL A 79 " --> pdb=" O MET A 75 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N ALA A 81 " --> pdb=" O THR A 77 " (cutoff:3.500A) Processing helix chain 'A' and resid 86 through 117 removed outlier: 3.525A pdb=" N LEU A 92 " --> pdb=" O GLY A 88 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N TYR A 97 " --> pdb=" O ARG A 93 " (cutoff:3.500A) removed outlier: 4.751A pdb=" N ILE A 104 " --> pdb=" O CYS A 100 " (cutoff:3.500A) Processing helix chain 'A' and resid 138 through 150 removed outlier: 3.694A pdb=" N ASP A 144 " --> pdb=" O ASP A 140 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N LEU A 145 " --> pdb=" O ALA A 141 " (cutoff:3.500A) removed outlier: 4.190A pdb=" N ILE A 146 " --> pdb=" O MET A 142 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N PHE A 150 " --> pdb=" O ILE A 146 " (cutoff:3.500A) Processing helix chain 'A' and resid 153 through 158 removed outlier: 3.572A pdb=" N CYS A 158 " --> pdb=" O LEU A 154 " (cutoff:3.500A) Processing helix chain 'A' and resid 211 through 228 Processing helix chain 'A' and resid 229 through 232 removed outlier: 3.621A pdb=" N LYS A 232 " --> pdb=" O MET A 229 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 229 through 232' Processing helix chain 'A' and resid 233 through 250 removed outlier: 3.584A pdb=" N MET A 248 " --> pdb=" O SER A 244 " (cutoff:3.500A) Processing helix chain 'A' and resid 250 through 266 removed outlier: 4.092A pdb=" N CYS A 256 " --> pdb=" O GLN A 252 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N TYR A 257 " --> pdb=" O ILE A 253 " (cutoff:3.500A) Proline residue: A 259 - end of helix removed outlier: 3.894A pdb=" N PHE A 264 " --> pdb=" O LEU A 260 " (cutoff:3.500A) Processing helix chain 'A' and resid 274 through 280 removed outlier: 4.679A pdb=" N ILE A 278 " --> pdb=" O GLU A 274 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N PHE A 279 " --> pdb=" O ASP A 275 " (cutoff:3.500A) Processing helix chain 'A' and resid 285 through 299 removed outlier: 4.204A pdb=" N THR A 291 " --> pdb=" O ALA A 287 " (cutoff:3.500A) Processing helix chain 'A' and resid 300 through 309 removed outlier: 3.503A pdb=" N TYR A 305 " --> pdb=" O LEU A 301 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N PHE A 306 " --> pdb=" O PRO A 302 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N VAL A 308 " --> pdb=" O ILE A 304 " (cutoff:3.500A) Processing helix chain 'A' and resid 312 through 320 removed outlier: 3.725A pdb=" N PHE A 316 " --> pdb=" O ASN A 312 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ALA A 317 " --> pdb=" O PRO A 313 " (cutoff:3.500A) Processing helix chain 'A' and resid 320 through 331 removed outlier: 3.560A pdb=" N MET A 329 " --> pdb=" O LEU A 325 " (cutoff:3.500A) Processing helix chain 'A' and resid 336 through 346 Processing helix chain 'A' and resid 351 through 365 removed outlier: 3.555A pdb=" N ARG A 356 " --> pdb=" O LYS A 352 " (cutoff:3.500A) removed outlier: 4.598A pdb=" N PHE A 357 " --> pdb=" O ARG A 353 " (cutoff:3.500A) Proline residue: A 360 - end of helix removed outlier: 3.889A pdb=" N THR A 364 " --> pdb=" O PRO A 360 " (cutoff:3.500A) Processing helix chain 'A' and resid 367 through 384 removed outlier: 4.054A pdb=" N VAL A 379 " --> pdb=" O ALA A 375 " (cutoff:3.500A) Processing helix chain 'A' and resid 390 through 408 removed outlier: 3.871A pdb=" N ILE A 395 " --> pdb=" O ILE A 391 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N THR A 396 " --> pdb=" O GLY A 392 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N THR A 402 " --> pdb=" O SER A 398 " (cutoff:3.500A) Processing helix chain 'A' and resid 418 through 427 removed outlier: 3.714A pdb=" N VAL A 422 " --> pdb=" O THR A 418 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N VAL A 426 " --> pdb=" O VAL A 422 " (cutoff:3.500A) Processing helix chain 'A' and resid 429 through 436 removed outlier: 3.519A pdb=" N ASP A 432 " --> pdb=" O PRO A 429 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N THR A 434 " --> pdb=" O GLU A 431 " (cutoff:3.500A) removed outlier: 4.101A pdb=" N LEU A 435 " --> pdb=" O ASP A 432 " (cutoff:3.500A) Processing helix chain 'A' and resid 442 through 466 removed outlier: 3.674A pdb=" N PHE A 446 " --> pdb=" O LEU A 442 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N ARG A 447 " --> pdb=" O LEU A 443 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N MET A 449 " --> pdb=" O ARG A 445 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N VAL A 450 " --> pdb=" O PHE A 446 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N ASN A 451 " --> pdb=" O ARG A 447 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N GLY A 460 " --> pdb=" O ALA A 456 " (cutoff:3.500A) Processing helix chain 'A' and resid 466 through 471 Processing sheet with id=AA1, first strand: chain 'A' and resid 160 through 167 192 hydrogen bonds defined for protein. 567 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: 0.91 Time building geometry restraints manager: 1.47 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 638 1.33 - 1.45: 651 1.45 - 1.57: 1917 1.57 - 1.69: 0 1.69 - 1.81: 41 Bond restraints: 3247 Sorted by residual: bond pdb=" N GLN A 122 " pdb=" CA GLN A 122 " ideal model delta sigma weight residual 1.458 1.485 -0.027 9.00e-03 1.23e+04 8.97e+00 bond pdb=" N VAL A 124 " pdb=" CA VAL A 124 " ideal model delta sigma weight residual 1.461 1.492 -0.032 1.19e-02 7.06e+03 7.10e+00 bond pdb=" C ASN A 451 " pdb=" O ASN A 451 " ideal model delta sigma weight residual 1.237 1.210 0.027 1.17e-02 7.31e+03 5.23e+00 bond pdb=" N VAL A 450 " pdb=" CA VAL A 450 " ideal model delta sigma weight residual 1.460 1.433 0.026 1.21e-02 6.83e+03 4.73e+00 bond pdb=" C LEU A 453 " pdb=" O LEU A 453 " ideal model delta sigma weight residual 1.237 1.211 0.025 1.17e-02 7.31e+03 4.67e+00 ... (remaining 3242 not shown) Histogram of bond angle deviations from ideal: 99.68 - 106.54: 69 106.54 - 113.39: 1868 113.39 - 120.24: 1232 120.24 - 127.10: 1215 127.10 - 133.95: 19 Bond angle restraints: 4403 Sorted by residual: angle pdb=" N ALA A 414 " pdb=" CA ALA A 414 " pdb=" C ALA A 414 " ideal model delta sigma weight residual 113.16 104.57 8.59 1.24e+00 6.50e-01 4.80e+01 angle pdb=" C GLY A 283 " pdb=" N LEU A 284 " pdb=" CA LEU A 284 " ideal model delta sigma weight residual 121.54 129.00 -7.46 1.91e+00 2.74e-01 1.53e+01 angle pdb=" N ILE A 271 " pdb=" CA ILE A 271 " pdb=" C ILE A 271 " ideal model delta sigma weight residual 112.29 108.77 3.52 9.40e-01 1.13e+00 1.40e+01 angle pdb=" N GLN A 122 " pdb=" CA GLN A 122 " pdb=" C GLN A 122 " ideal model delta sigma weight residual 113.50 107.77 5.73 1.65e+00 3.67e-01 1.21e+01 angle pdb=" C THR A 121 " pdb=" N GLN A 122 " pdb=" CA GLN A 122 " ideal model delta sigma weight residual 120.17 125.31 -5.14 1.54e+00 4.22e-01 1.11e+01 ... (remaining 4398 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.57: 1671 15.57 - 31.13: 198 31.13 - 46.69: 58 46.69 - 62.25: 12 62.25 - 77.82: 7 Dihedral angle restraints: 1946 sinusoidal: 744 harmonic: 1202 Sorted by residual: dihedral pdb=" CA GLU A 272 " pdb=" C GLU A 272 " pdb=" N VAL A 273 " pdb=" CA VAL A 273 " ideal model delta harmonic sigma weight residual -180.00 -157.92 -22.08 0 5.00e+00 4.00e-02 1.95e+01 dihedral pdb=" CA THR A 247 " pdb=" C THR A 247 " pdb=" N MET A 248 " pdb=" CA MET A 248 " ideal model delta harmonic sigma weight residual 180.00 162.07 17.93 0 5.00e+00 4.00e-02 1.29e+01 dihedral pdb=" CA ASP A 83 " pdb=" C ASP A 83 " pdb=" N SER A 84 " pdb=" CA SER A 84 " ideal model delta harmonic sigma weight residual 180.00 163.15 16.85 0 5.00e+00 4.00e-02 1.14e+01 ... (remaining 1943 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.067: 468 0.067 - 0.135: 79 0.135 - 0.202: 7 0.202 - 0.269: 3 0.269 - 0.336: 1 Chirality restraints: 558 Sorted by residual: chirality pdb=" CA ASP A 440 " pdb=" N ASP A 440 " pdb=" C ASP A 440 " pdb=" CB ASP A 440 " both_signs ideal model delta sigma weight residual False 2.51 2.17 0.34 2.00e-01 2.50e+01 2.83e+00 chirality pdb=" CA GLN A 413 " pdb=" N GLN A 413 " pdb=" C GLN A 413 " pdb=" CB GLN A 413 " both_signs ideal model delta sigma weight residual False 2.51 2.27 0.24 2.00e-01 2.50e+01 1.50e+00 chirality pdb=" CA ASP A 368 " pdb=" N ASP A 368 " pdb=" C ASP A 368 " pdb=" CB ASP A 368 " both_signs ideal model delta sigma weight residual False 2.51 2.27 0.24 2.00e-01 2.50e+01 1.41e+00 ... (remaining 555 not shown) Planarity restraints: 537 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU A 301 " -0.041 5.00e-02 4.00e+02 6.17e-02 6.08e+00 pdb=" N PRO A 302 " 0.107 5.00e-02 4.00e+02 pdb=" CA PRO A 302 " -0.031 5.00e-02 4.00e+02 pdb=" CD PRO A 302 " -0.034 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA THR A 121 " 0.012 2.00e-02 2.50e+03 2.42e-02 5.84e+00 pdb=" C THR A 121 " -0.042 2.00e-02 2.50e+03 pdb=" O THR A 121 " 0.016 2.00e-02 2.50e+03 pdb=" N GLN A 122 " 0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU A 337 " 0.037 5.00e-02 4.00e+02 5.51e-02 4.85e+00 pdb=" N PRO A 338 " -0.095 5.00e-02 4.00e+02 pdb=" CA PRO A 338 " 0.027 5.00e-02 4.00e+02 pdb=" CD PRO A 338 " 0.031 5.00e-02 4.00e+02 ... (remaining 534 not shown) Histogram of nonbonded interaction distances: 2.13 - 2.69: 78 2.69 - 3.24: 3006 3.24 - 3.79: 4910 3.79 - 4.35: 6687 4.35 - 4.90: 10760 Nonbonded interactions: 25441 Sorted by model distance: nonbonded pdb=" O ASN A 366 " pdb="NA NA A 601 " model vdw 2.131 2.470 nonbonded pdb=" O LYS A 16 " pdb=" OD1 ASN A 17 " model vdw 2.197 3.040 nonbonded pdb=" OG1 THR A 102 " pdb="NA NA A 603 " model vdw 2.242 2.470 nonbonded pdb=" O ASP A 444 " pdb=" OG1 THR A 448 " model vdw 2.282 2.440 nonbonded pdb=" OG1 THR A 370 " pdb=" OD2 ASP A 600 " model vdw 2.318 2.440 ... (remaining 25436 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: 1.000 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: 0.010 Extract box with map and model: 5.120 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 14.210 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.800 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.330 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8250 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 : 0.005 0.040 3247 Z= 0.294 Angle : 0.835 8.589 4403 Z= 0.502 Chirality : 0.054 0.336 558 Planarity : 0.006 0.062 537 Dihedral : 15.506 77.817 1170 Min Nonbonded Distance : 2.131 Molprobity Statistics. All-atom Clashscore : 6.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.63 % Favored : 96.37 % Rotamer: Outliers : 0.00 % Allowed : 20.68 % Favored : 79.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -5.65 (0.28), residues: 413 helix: -4.09 (0.16), residues: 296 sheet: -1.37 (1.46), residues: 18 loop : -1.95 (0.52), residues: 99 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP A 19 HIS 0.001 0.001 HIS A 296 PHE 0.011 0.001 PHE A 159 TYR 0.011 0.001 TYR A 257 ARG 0.002 0.000 ARG A 447 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 826 Ramachandran restraints generated. 413 Oldfield, 0 Emsley, 413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 826 Ramachandran restraints generated. 413 Oldfield, 0 Emsley, 413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 69 residues out of total 353 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 69 time to evaluate : 0.389 Fit side-chains REVERT: A 255 MET cc_start: 0.8606 (tpp) cc_final: 0.8163 (mmp) REVERT: A 352 LYS cc_start: 0.8222 (ttpt) cc_final: 0.7944 (ttpp) outliers start: 0 outliers final: 0 residues processed: 69 average time/residue: 0.1232 time to fit residues: 10.9983 Evaluate side-chains 55 residues out of total 353 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 55 time to evaluate : 0.388 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 35 optimal weight: 2.9990 chunk 31 optimal weight: 0.7980 chunk 17 optimal weight: 0.5980 chunk 10 optimal weight: 9.9990 chunk 21 optimal weight: 1.9990 chunk 32 optimal weight: 4.9990 chunk 12 optimal weight: 0.3980 chunk 20 optimal weight: 2.9990 chunk 24 optimal weight: 5.9990 chunk 38 optimal weight: 0.7980 chunk 11 optimal weight: 0.9980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 296 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8202 moved from start: 0.2073 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.018 3247 Z= 0.155 Angle : 0.574 7.589 4403 Z= 0.305 Chirality : 0.039 0.134 558 Planarity : 0.005 0.041 537 Dihedral : 5.157 22.310 440 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 8.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 1.98 % Allowed : 22.38 % Favored : 75.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -3.11 (0.36), residues: 413 helix: -1.93 (0.25), residues: 307 sheet: -0.72 (1.46), residues: 18 loop : -1.94 (0.59), residues: 88 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 276 HIS 0.010 0.003 HIS A 296 PHE 0.013 0.001 PHE A 218 TYR 0.008 0.001 TYR A 373 ARG 0.001 0.000 ARG A 61 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 826 Ramachandran restraints generated. 413 Oldfield, 0 Emsley, 413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 826 Ramachandran restraints generated. 413 Oldfield, 0 Emsley, 413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 70 residues out of total 353 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 63 time to evaluate : 0.398 Fit side-chains revert: symmetry clash REVERT: A 205 MET cc_start: 0.7497 (OUTLIER) cc_final: 0.7013 (pmm) REVERT: A 255 MET cc_start: 0.8631 (tpp) cc_final: 0.8108 (mmp) REVERT: A 277 GLU cc_start: 0.8260 (tp30) cc_final: 0.7979 (tp30) REVERT: A 455 ASP cc_start: 0.8129 (m-30) cc_final: 0.7889 (m-30) outliers start: 7 outliers final: 1 residues processed: 68 average time/residue: 0.0889 time to fit residues: 8.4880 Evaluate side-chains 56 residues out of total 353 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 54 time to evaluate : 0.399 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 205 MET Chi-restraints excluded: chain A residue 426 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 31 optimal weight: 3.9990 chunk 25 optimal weight: 3.9990 chunk 10 optimal weight: 9.9990 chunk 38 optimal weight: 0.7980 chunk 41 optimal weight: 0.9990 chunk 34 optimal weight: 5.9990 chunk 37 optimal weight: 1.9990 chunk 13 optimal weight: 0.0870 chunk 30 optimal weight: 0.7980 chunk 28 optimal weight: 0.8980 chunk 19 optimal weight: 1.9990 overall best weight: 0.7160 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 296 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8187 moved from start: 0.2490 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 3247 Z= 0.152 Angle : 0.534 6.250 4403 Z= 0.276 Chirality : 0.040 0.157 558 Planarity : 0.004 0.033 537 Dihedral : 4.721 19.758 440 Min Nonbonded Distance : 2.158 Molprobity Statistics. All-atom Clashscore : 9.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.12 % Favored : 95.88 % Rotamer: Outliers : 1.70 % Allowed : 25.21 % Favored : 73.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.43 (0.41), residues: 413 helix: -0.59 (0.30), residues: 307 sheet: -0.41 (1.46), residues: 18 loop : -1.80 (0.60), residues: 88 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 276 HIS 0.007 0.002 HIS A 296 PHE 0.011 0.001 PHE A 218 TYR 0.006 0.001 TYR A 285 ARG 0.001 0.000 ARG A 445 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 826 Ramachandran restraints generated. 413 Oldfield, 0 Emsley, 413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 826 Ramachandran restraints generated. 413 Oldfield, 0 Emsley, 413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 65 residues out of total 353 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 59 time to evaluate : 0.406 Fit side-chains revert: symmetry clash REVERT: A 205 MET cc_start: 0.7466 (OUTLIER) cc_final: 0.7038 (pmm) REVERT: A 255 MET cc_start: 0.8545 (tpp) cc_final: 0.8056 (mmp) outliers start: 6 outliers final: 5 residues processed: 61 average time/residue: 0.0901 time to fit residues: 7.8528 Evaluate side-chains 62 residues out of total 353 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 56 time to evaluate : 0.400 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 205 MET Chi-restraints excluded: chain A residue 229 MET Chi-restraints excluded: chain A residue 364 THR Chi-restraints excluded: chain A residue 405 SER Chi-restraints excluded: chain A residue 406 ILE Chi-restraints excluded: chain A residue 426 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 4 optimal weight: 0.8980 chunk 18 optimal weight: 0.5980 chunk 25 optimal weight: 0.1980 chunk 38 optimal weight: 0.7980 chunk 40 optimal weight: 2.9990 chunk 20 optimal weight: 2.9990 chunk 36 optimal weight: 5.9990 chunk 10 optimal weight: 8.9990 chunk 33 optimal weight: 0.0050 chunk 23 optimal weight: 0.9990 chunk 0 optimal weight: 6.9990 overall best weight: 0.4994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 296 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8156 moved from start: 0.2714 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 3247 Z= 0.125 Angle : 0.500 6.818 4403 Z= 0.257 Chirality : 0.039 0.170 558 Planarity : 0.003 0.030 537 Dihedral : 4.424 19.950 440 Min Nonbonded Distance : 2.190 Molprobity Statistics. All-atom Clashscore : 8.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Rotamer: Outliers : 3.12 % Allowed : 24.36 % Favored : 72.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.68 (0.42), residues: 413 helix: 0.03 (0.31), residues: 306 sheet: -0.28 (1.46), residues: 18 loop : -1.80 (0.60), residues: 89 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 276 HIS 0.005 0.002 HIS A 296 PHE 0.010 0.001 PHE A 218 TYR 0.006 0.001 TYR A 97 ARG 0.001 0.000 ARG A 61 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 826 Ramachandran restraints generated. 413 Oldfield, 0 Emsley, 413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 826 Ramachandran restraints generated. 413 Oldfield, 0 Emsley, 413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 69 residues out of total 353 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 58 time to evaluate : 0.404 Fit side-chains revert: symmetry clash REVERT: A 205 MET cc_start: 0.7307 (OUTLIER) cc_final: 0.7060 (pmm) REVERT: A 255 MET cc_start: 0.8462 (tpp) cc_final: 0.7996 (mmp) REVERT: A 284 LEU cc_start: 0.8340 (OUTLIER) cc_final: 0.8093 (tt) REVERT: A 419 MET cc_start: 0.8888 (tpt) cc_final: 0.8286 (tpt) REVERT: A 455 ASP cc_start: 0.8002 (m-30) cc_final: 0.7450 (m-30) outliers start: 11 outliers final: 7 residues processed: 64 average time/residue: 0.0898 time to fit residues: 8.1266 Evaluate side-chains 64 residues out of total 353 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 55 time to evaluate : 0.381 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 205 MET Chi-restraints excluded: chain A residue 229 MET Chi-restraints excluded: chain A residue 262 ILE Chi-restraints excluded: chain A residue 273 VAL Chi-restraints excluded: chain A residue 284 LEU Chi-restraints excluded: chain A residue 364 THR Chi-restraints excluded: chain A residue 405 SER Chi-restraints excluded: chain A residue 406 ILE Chi-restraints excluded: chain A residue 426 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 30 optimal weight: 0.6980 chunk 16 optimal weight: 0.7980 chunk 34 optimal weight: 5.9990 chunk 28 optimal weight: 0.8980 chunk 0 optimal weight: 7.9990 chunk 20 optimal weight: 0.9980 chunk 36 optimal weight: 0.9980 chunk 10 optimal weight: 6.9990 chunk 13 optimal weight: 1.9990 chunk 8 optimal weight: 0.8980 chunk 23 optimal weight: 1.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 296 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8179 moved from start: 0.2765 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 3247 Z= 0.157 Angle : 0.502 6.643 4403 Z= 0.258 Chirality : 0.040 0.162 558 Planarity : 0.003 0.027 537 Dihedral : 4.316 16.431 440 Min Nonbonded Distance : 2.188 Molprobity Statistics. All-atom Clashscore : 9.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.87 % Favored : 96.13 % Rotamer: Outliers : 2.83 % Allowed : 24.93 % Favored : 72.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.27 (0.43), residues: 413 helix: 0.34 (0.31), residues: 308 sheet: -0.14 (1.46), residues: 18 loop : -1.75 (0.61), residues: 87 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 276 HIS 0.004 0.002 HIS A 296 PHE 0.011 0.001 PHE A 218 TYR 0.006 0.001 TYR A 97 ARG 0.001 0.000 ARG A 445 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 826 Ramachandran restraints generated. 413 Oldfield, 0 Emsley, 413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 826 Ramachandran restraints generated. 413 Oldfield, 0 Emsley, 413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 65 residues out of total 353 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 55 time to evaluate : 0.399 Fit side-chains revert: symmetry clash REVERT: A 205 MET cc_start: 0.7374 (OUTLIER) cc_final: 0.7129 (pmm) REVERT: A 255 MET cc_start: 0.8461 (tpp) cc_final: 0.7986 (mmp) REVERT: A 284 LEU cc_start: 0.8349 (OUTLIER) cc_final: 0.8092 (tt) REVERT: A 329 MET cc_start: 0.7972 (mmt) cc_final: 0.7547 (mmt) REVERT: A 455 ASP cc_start: 0.8048 (m-30) cc_final: 0.7594 (m-30) outliers start: 10 outliers final: 6 residues processed: 61 average time/residue: 0.0908 time to fit residues: 7.7551 Evaluate side-chains 62 residues out of total 353 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 54 time to evaluate : 0.395 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 205 MET Chi-restraints excluded: chain A residue 229 MET Chi-restraints excluded: chain A residue 262 ILE Chi-restraints excluded: chain A residue 273 VAL Chi-restraints excluded: chain A residue 284 LEU Chi-restraints excluded: chain A residue 364 THR Chi-restraints excluded: chain A residue 406 ILE Chi-restraints excluded: chain A residue 426 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 10 optimal weight: 0.5980 chunk 40 optimal weight: 0.6980 chunk 33 optimal weight: 3.9990 chunk 18 optimal weight: 0.6980 chunk 3 optimal weight: 2.9990 chunk 13 optimal weight: 0.7980 chunk 21 optimal weight: 3.9990 chunk 39 optimal weight: 0.9990 chunk 4 optimal weight: 0.6980 chunk 23 optimal weight: 1.9990 chunk 29 optimal weight: 0.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 296 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8160 moved from start: 0.2872 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 3247 Z= 0.144 Angle : 0.516 9.605 4403 Z= 0.259 Chirality : 0.040 0.179 558 Planarity : 0.003 0.027 537 Dihedral : 4.242 16.904 440 Min Nonbonded Distance : 2.185 Molprobity Statistics. All-atom Clashscore : 9.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 3.12 % Allowed : 24.36 % Favored : 72.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.01 (0.43), residues: 413 helix: 0.58 (0.31), residues: 308 sheet: -0.10 (1.44), residues: 18 loop : -1.77 (0.60), residues: 87 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.000 TRP A 276 HIS 0.004 0.001 HIS A 296 PHE 0.010 0.001 PHE A 218 TYR 0.006 0.001 TYR A 97 ARG 0.001 0.000 ARG A 445 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 826 Ramachandran restraints generated. 413 Oldfield, 0 Emsley, 413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 826 Ramachandran restraints generated. 413 Oldfield, 0 Emsley, 413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 70 residues out of total 353 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 59 time to evaluate : 0.400 Fit side-chains REVERT: A 205 MET cc_start: 0.7342 (OUTLIER) cc_final: 0.7126 (pmm) REVERT: A 255 MET cc_start: 0.8380 (tpp) cc_final: 0.7921 (mmp) REVERT: A 284 LEU cc_start: 0.8312 (OUTLIER) cc_final: 0.8044 (tt) REVERT: A 384 LEU cc_start: 0.8119 (OUTLIER) cc_final: 0.7805 (mp) REVERT: A 419 MET cc_start: 0.9088 (tpt) cc_final: 0.8368 (tpt) REVERT: A 455 ASP cc_start: 0.8018 (m-30) cc_final: 0.7768 (m-30) outliers start: 11 outliers final: 6 residues processed: 66 average time/residue: 0.0838 time to fit residues: 7.8207 Evaluate side-chains 65 residues out of total 353 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 56 time to evaluate : 0.407 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 205 MET Chi-restraints excluded: chain A residue 229 MET Chi-restraints excluded: chain A residue 262 ILE Chi-restraints excluded: chain A residue 273 VAL Chi-restraints excluded: chain A residue 284 LEU Chi-restraints excluded: chain A residue 364 THR Chi-restraints excluded: chain A residue 384 LEU Chi-restraints excluded: chain A residue 406 ILE Chi-restraints excluded: chain A residue 426 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 22 optimal weight: 0.0670 chunk 34 optimal weight: 1.9990 chunk 40 optimal weight: 5.9990 chunk 25 optimal weight: 0.8980 chunk 24 optimal weight: 1.9990 chunk 18 optimal weight: 0.6980 chunk 16 optimal weight: 0.8980 chunk 12 optimal weight: 1.9990 chunk 7 optimal weight: 0.9990 chunk 27 optimal weight: 0.7980 chunk 20 optimal weight: 2.9990 overall best weight: 0.6718 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 296 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8149 moved from start: 0.2954 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 3247 Z= 0.146 Angle : 0.516 9.032 4403 Z= 0.261 Chirality : 0.039 0.126 558 Planarity : 0.003 0.026 537 Dihedral : 4.189 16.484 440 Min Nonbonded Distance : 2.180 Molprobity Statistics. All-atom Clashscore : 10.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Rotamer: Outliers : 3.68 % Allowed : 24.36 % Favored : 71.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.26 (0.43), residues: 413 helix: 0.77 (0.31), residues: 307 sheet: -0.12 (1.41), residues: 18 loop : -1.67 (0.60), residues: 88 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 276 HIS 0.003 0.001 HIS A 296 PHE 0.012 0.001 PHE A 316 TYR 0.007 0.001 TYR A 97 ARG 0.001 0.000 ARG A 445 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 826 Ramachandran restraints generated. 413 Oldfield, 0 Emsley, 413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 826 Ramachandran restraints generated. 413 Oldfield, 0 Emsley, 413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 69 residues out of total 353 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 56 time to evaluate : 0.359 Fit side-chains REVERT: A 205 MET cc_start: 0.7306 (OUTLIER) cc_final: 0.7105 (pmm) REVERT: A 255 MET cc_start: 0.8370 (tpp) cc_final: 0.7906 (mmp) REVERT: A 277 GLU cc_start: 0.8286 (tp30) cc_final: 0.7881 (tp30) REVERT: A 284 LEU cc_start: 0.8309 (OUTLIER) cc_final: 0.8022 (tt) REVERT: A 384 LEU cc_start: 0.8116 (OUTLIER) cc_final: 0.7795 (mp) REVERT: A 419 MET cc_start: 0.9067 (tpt) cc_final: 0.8327 (tpt) REVERT: A 455 ASP cc_start: 0.8002 (m-30) cc_final: 0.7542 (m-30) outliers start: 13 outliers final: 7 residues processed: 63 average time/residue: 0.0898 time to fit residues: 7.9692 Evaluate side-chains 66 residues out of total 353 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 56 time to evaluate : 0.359 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 205 MET Chi-restraints excluded: chain A residue 229 MET Chi-restraints excluded: chain A residue 262 ILE Chi-restraints excluded: chain A residue 284 LEU Chi-restraints excluded: chain A residue 364 THR Chi-restraints excluded: chain A residue 384 LEU Chi-restraints excluded: chain A residue 405 SER Chi-restraints excluded: chain A residue 406 ILE Chi-restraints excluded: chain A residue 426 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 3 optimal weight: 0.9990 chunk 31 optimal weight: 0.9980 chunk 36 optimal weight: 3.9990 chunk 38 optimal weight: 0.7980 chunk 35 optimal weight: 2.9990 chunk 37 optimal weight: 0.5980 chunk 22 optimal weight: 3.9990 chunk 16 optimal weight: 0.7980 chunk 29 optimal weight: 0.9980 chunk 11 optimal weight: 0.7980 chunk 34 optimal weight: 3.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 296 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8154 moved from start: 0.2993 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 3247 Z= 0.157 Angle : 0.529 8.537 4403 Z= 0.264 Chirality : 0.039 0.121 558 Planarity : 0.003 0.027 537 Dihedral : 4.173 16.470 440 Min Nonbonded Distance : 2.175 Molprobity Statistics. All-atom Clashscore : 10.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Rotamer: Outliers : 2.83 % Allowed : 25.50 % Favored : 71.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.41 (0.42), residues: 413 helix: 0.89 (0.31), residues: 307 sheet: -0.22 (1.36), residues: 18 loop : -1.62 (0.59), residues: 88 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 276 HIS 0.003 0.001 HIS A 296 PHE 0.012 0.001 PHE A 316 TYR 0.007 0.001 TYR A 97 ARG 0.001 0.000 ARG A 445 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 826 Ramachandran restraints generated. 413 Oldfield, 0 Emsley, 413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 826 Ramachandran restraints generated. 413 Oldfield, 0 Emsley, 413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 353 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 56 time to evaluate : 0.353 Fit side-chains REVERT: A 255 MET cc_start: 0.8324 (tpp) cc_final: 0.7873 (mmp) REVERT: A 277 GLU cc_start: 0.8236 (tp30) cc_final: 0.7835 (tp30) REVERT: A 284 LEU cc_start: 0.8283 (OUTLIER) cc_final: 0.7977 (tt) REVERT: A 384 LEU cc_start: 0.8102 (OUTLIER) cc_final: 0.7783 (mp) REVERT: A 455 ASP cc_start: 0.8017 (m-30) cc_final: 0.7792 (m-30) outliers start: 10 outliers final: 6 residues processed: 61 average time/residue: 0.0937 time to fit residues: 7.9351 Evaluate side-chains 64 residues out of total 353 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 56 time to evaluate : 0.357 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 229 MET Chi-restraints excluded: chain A residue 262 ILE Chi-restraints excluded: chain A residue 284 LEU Chi-restraints excluded: chain A residue 364 THR Chi-restraints excluded: chain A residue 384 LEU Chi-restraints excluded: chain A residue 405 SER Chi-restraints excluded: chain A residue 406 ILE Chi-restraints excluded: chain A residue 426 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 35 optimal weight: 1.9990 chunk 37 optimal weight: 10.0000 chunk 24 optimal weight: 0.9980 chunk 39 optimal weight: 0.7980 chunk 18 optimal weight: 0.7980 chunk 27 optimal weight: 3.9990 chunk 41 optimal weight: 0.9980 chunk 38 optimal weight: 0.8980 chunk 33 optimal weight: 8.9990 chunk 3 optimal weight: 0.6980 chunk 25 optimal weight: 0.8980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 296 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8156 moved from start: 0.3040 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 3247 Z= 0.159 Angle : 0.530 8.295 4403 Z= 0.265 Chirality : 0.039 0.127 558 Planarity : 0.003 0.026 537 Dihedral : 4.145 16.509 440 Min Nonbonded Distance : 2.172 Molprobity Statistics. All-atom Clashscore : 10.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 2.83 % Allowed : 25.21 % Favored : 71.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.53 (0.42), residues: 413 helix: 0.98 (0.31), residues: 308 sheet: -0.61 (1.30), residues: 18 loop : -1.51 (0.60), residues: 87 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.000 TRP A 276 HIS 0.003 0.001 HIS A 296 PHE 0.014 0.001 PHE A 316 TYR 0.009 0.001 TYR A 97 ARG 0.001 0.000 ARG A 445 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 826 Ramachandran restraints generated. 413 Oldfield, 0 Emsley, 413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 826 Ramachandran restraints generated. 413 Oldfield, 0 Emsley, 413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 64 residues out of total 353 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 54 time to evaluate : 0.402 Fit side-chains REVERT: A 255 MET cc_start: 0.8312 (tpp) cc_final: 0.7854 (mmp) REVERT: A 277 GLU cc_start: 0.8194 (tp30) cc_final: 0.7745 (tp30) REVERT: A 284 LEU cc_start: 0.8242 (OUTLIER) cc_final: 0.7957 (tt) REVERT: A 384 LEU cc_start: 0.8151 (OUTLIER) cc_final: 0.7848 (mp) REVERT: A 455 ASP cc_start: 0.8008 (m-30) cc_final: 0.7572 (m-30) outliers start: 10 outliers final: 6 residues processed: 61 average time/residue: 0.0927 time to fit residues: 7.8992 Evaluate side-chains 62 residues out of total 353 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 54 time to evaluate : 0.401 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 229 MET Chi-restraints excluded: chain A residue 262 ILE Chi-restraints excluded: chain A residue 284 LEU Chi-restraints excluded: chain A residue 364 THR Chi-restraints excluded: chain A residue 384 LEU Chi-restraints excluded: chain A residue 405 SER Chi-restraints excluded: chain A residue 426 VAL Chi-restraints excluded: chain A residue 475 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 20 optimal weight: 0.3980 chunk 26 optimal weight: 3.9990 chunk 35 optimal weight: 0.4980 chunk 10 optimal weight: 9.9990 chunk 30 optimal weight: 0.7980 chunk 4 optimal weight: 0.5980 chunk 9 optimal weight: 3.9990 chunk 33 optimal weight: 0.8980 chunk 13 optimal weight: 1.9990 chunk 34 optimal weight: 3.9990 chunk 6 optimal weight: 2.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 296 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8140 moved from start: 0.3128 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 3247 Z= 0.144 Angle : 0.525 8.062 4403 Z= 0.263 Chirality : 0.039 0.120 558 Planarity : 0.003 0.026 537 Dihedral : 4.101 16.364 440 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 9.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 2.83 % Allowed : 24.93 % Favored : 72.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.71 (0.43), residues: 413 helix: 1.13 (0.31), residues: 307 sheet: -0.66 (1.28), residues: 18 loop : -1.46 (0.60), residues: 88 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.000 TRP A 276 HIS 0.004 0.001 HIS A 296 PHE 0.017 0.001 PHE A 316 TYR 0.008 0.001 TYR A 97 ARG 0.001 0.000 ARG A 93 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 826 Ramachandran restraints generated. 413 Oldfield, 0 Emsley, 413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 826 Ramachandran restraints generated. 413 Oldfield, 0 Emsley, 413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 65 residues out of total 353 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 55 time to evaluate : 0.353 Fit side-chains REVERT: A 255 MET cc_start: 0.8267 (tpp) cc_final: 0.7810 (mmp) REVERT: A 284 LEU cc_start: 0.8263 (OUTLIER) cc_final: 0.7980 (tt) REVERT: A 384 LEU cc_start: 0.8152 (OUTLIER) cc_final: 0.7849 (mp) outliers start: 10 outliers final: 7 residues processed: 62 average time/residue: 0.0926 time to fit residues: 7.9281 Evaluate side-chains 64 residues out of total 353 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 55 time to evaluate : 0.396 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 229 MET Chi-restraints excluded: chain A residue 262 ILE Chi-restraints excluded: chain A residue 284 LEU Chi-restraints excluded: chain A residue 364 THR Chi-restraints excluded: chain A residue 384 LEU Chi-restraints excluded: chain A residue 405 SER Chi-restraints excluded: chain A residue 406 ILE Chi-restraints excluded: chain A residue 426 VAL Chi-restraints excluded: chain A residue 475 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 29 optimal weight: 5.9990 chunk 1 optimal weight: 0.9980 chunk 24 optimal weight: 5.9990 chunk 38 optimal weight: 0.9990 chunk 22 optimal weight: 0.9980 chunk 28 optimal weight: 0.6980 chunk 26 optimal weight: 0.9980 chunk 25 optimal weight: 7.9990 chunk 16 optimal weight: 0.7980 chunk 15 optimal weight: 1.9990 chunk 41 optimal weight: 0.1980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 296 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3814 r_free = 0.3814 target = 0.144957 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.108636 restraints weight = 4600.804| |-----------------------------------------------------------------------------| r_work (start): 0.3269 rms_B_bonded: 2.21 r_work: 0.3142 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.3027 rms_B_bonded: 4.60 restraints_weight: 0.2500 r_work (final): 0.3027 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8340 moved from start: 0.3148 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 3247 Z= 0.154 Angle : 0.538 8.524 4403 Z= 0.267 Chirality : 0.039 0.122 558 Planarity : 0.003 0.026 537 Dihedral : 4.100 16.396 440 Min Nonbonded Distance : 2.170 Molprobity Statistics. All-atom Clashscore : 8.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Rotamer: Outliers : 2.55 % Allowed : 25.21 % Favored : 72.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.82 (0.42), residues: 413 helix: 1.22 (0.31), residues: 305 sheet: -0.59 (1.28), residues: 18 loop : -1.41 (0.59), residues: 90 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.000 TRP A 276 HIS 0.004 0.001 HIS A 296 PHE 0.018 0.001 PHE A 316 TYR 0.008 0.001 TYR A 97 ARG 0.001 0.000 ARG A 93 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1148.41 seconds wall clock time: 21 minutes 31.80 seconds (1291.80 seconds total)