Starting phenix.real_space_refine on Mon Mar 11 12:23:40 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7y49_33604/03_2024/7y49_33604.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7y49_33604/03_2024/7y49_33604.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.67 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7y49_33604/03_2024/7y49_33604.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7y49_33604/03_2024/7y49_33604.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7y49_33604/03_2024/7y49_33604.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7y49_33604/03_2024/7y49_33604.pdb" } resolution = 3.67 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= 0.001 sd= 0.016 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 4095 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 16 5.16 5 C 2670 2.51 5 N 722 2.21 5 O 761 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 586": "OE1" <-> "OE2" Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 4169 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 4169 Number of conformers: 1 Conformer: "" Number of residues, atoms: 565, 4169 Classifications: {'peptide': 565} Incomplete info: {'truncation_to_alanine': 37} Link IDs: {'PTRANS': 20, 'TRANS': 544} Chain breaks: 2 Unresolved non-hydrogen bonds: 153 Unresolved non-hydrogen angles: 185 Unresolved non-hydrogen dihedrals: 124 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 3, 'GLU:plan': 13, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 98 Time building chain proxies: 2.76, per 1000 atoms: 0.66 Number of scatterers: 4169 At special positions: 0 Unit cell: (67.15, 98.6, 143.65, 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 16 16.00 O 761 8.00 N 722 7.00 C 2670 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: 1.84 Conformation dependent library (CDL) restraints added in 895.8 milliseconds 1118 Ramachandran restraints generated. 559 Oldfield, 0 Emsley, 559 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1036 Finding SS restraints... Secondary structure from input PDB file: 24 helices and 3 sheets defined 65.5% alpha, 2.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.41 Creating SS restraints... Processing helix chain 'A' and resid 156 through 164 removed outlier: 3.747A pdb=" N LEU A 161 " --> pdb=" O ALA A 157 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N GLY A 162 " --> pdb=" O ARG A 158 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N ALA A 164 " --> pdb=" O LEU A 160 " (cutoff:3.500A) Processing helix chain 'A' and resid 168 through 184 removed outlier: 3.829A pdb=" N ALA A 172 " --> pdb=" O ARG A 168 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N ALA A 173 " --> pdb=" O ARG A 169 " (cutoff:3.500A) Processing helix chain 'A' and resid 187 through 200 removed outlier: 3.875A pdb=" N PHE A 191 " --> pdb=" O SER A 187 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N LYS A 194 " --> pdb=" O PHE A 190 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N ILE A 199 " --> pdb=" O ILE A 195 " (cutoff:3.500A) Processing helix chain 'A' and resid 211 through 257 removed outlier: 3.953A pdb=" N ALA A 220 " --> pdb=" O LEU A 216 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N VAL A 221 " --> pdb=" O GLY A 217 " (cutoff:3.500A) removed outlier: 4.149A pdb=" N ARG A 246 " --> pdb=" O ARG A 242 " (cutoff:3.500A) Processing helix chain 'A' and resid 261 through 266 removed outlier: 4.131A pdb=" N LYS A 265 " --> pdb=" O ALA A 261 " (cutoff:3.500A) Processing helix chain 'A' and resid 267 through 285 removed outlier: 3.707A pdb=" N LEU A 271 " --> pdb=" O ARG A 267 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N ASP A 278 " --> pdb=" O ARG A 274 " (cutoff:3.500A) removed outlier: 5.255A pdb=" N THR A 279 " --> pdb=" O LEU A 275 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N ALA A 280 " --> pdb=" O SER A 276 " (cutoff:3.500A) Processing helix chain 'A' and resid 289 through 311 removed outlier: 3.613A pdb=" N PHE A 308 " --> pdb=" O ILE A 304 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N PHE A 309 " --> pdb=" O SER A 305 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N VAL A 310 " --> pdb=" O MET A 306 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N SER A 311 " --> pdb=" O MET A 307 " (cutoff:3.500A) Processing helix chain 'A' and resid 311 through 360 removed outlier: 3.659A pdb=" N PHE A 317 " --> pdb=" O ASN A 313 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N SER A 320 " --> pdb=" O THR A 316 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N VAL A 321 " --> pdb=" O PHE A 317 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N VAL A 322 " --> pdb=" O VAL A 318 " (cutoff:3.500A) Proline residue: A 323 - end of helix removed outlier: 3.668A pdb=" N ILE A 328 " --> pdb=" O PRO A 324 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N ARG A 334 " --> pdb=" O VAL A 330 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N TYR A 335 " --> pdb=" O ILE A 331 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N LEU A 336 " --> pdb=" O TYR A 332 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N ARG A 337 " --> pdb=" O GLY A 333 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N LEU A 353 " --> pdb=" O GLN A 349 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N ALA A 354 " --> pdb=" O ALA A 350 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N GLU A 356 " --> pdb=" O GLN A 352 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N ARG A 357 " --> pdb=" O LEU A 353 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N ILE A 358 " --> pdb=" O ALA A 354 " (cutoff:3.500A) Processing helix chain 'A' and resid 360 through 367 removed outlier: 3.569A pdb=" N ALA A 366 " --> pdb=" O ARG A 362 " (cutoff:3.500A) removed outlier: 4.320A pdb=" N PHE A 367 " --> pdb=" O THR A 363 " (cutoff:3.500A) Processing helix chain 'A' and resid 370 through 417 removed outlier: 3.551A pdb=" N ILE A 374 " --> pdb=" O GLU A 370 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N LYS A 390 " --> pdb=" O GLN A 386 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N GLU A 391 " --> pdb=" O LEU A 387 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N ALA A 392 " --> pdb=" O ALA A 388 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N ALA A 394 " --> pdb=" O LYS A 390 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N GLY A 417 " --> pdb=" O VAL A 413 " (cutoff:3.500A) Processing helix chain 'A' and resid 427 through 466 removed outlier: 3.573A pdb=" N LEU A 431 " --> pdb=" O THR A 427 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N GLY A 446 " --> pdb=" O GLY A 442 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N ARG A 464 " --> pdb=" O GLY A 460 " (cutoff:3.500A) Processing helix chain 'A' and resid 467 through 471 removed outlier: 3.503A pdb=" N ARG A 471 " --> pdb=" O LEU A 468 " (cutoff:3.500A) Processing helix chain 'A' and resid 532 through 534 No H-bonds generated for 'chain 'A' and resid 532 through 534' Processing helix chain 'A' and resid 535 through 541 removed outlier: 3.632A pdb=" N LEU A 541 " --> pdb=" O LEU A 537 " (cutoff:3.500A) Processing helix chain 'A' and resid 562 through 569 Processing helix chain 'A' and resid 583 through 588 Processing helix chain 'A' and resid 589 through 591 No H-bonds generated for 'chain 'A' and resid 589 through 591' Processing helix chain 'A' and resid 599 through 610 removed outlier: 3.936A pdb=" N ILE A 603 " --> pdb=" O THR A 599 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N GLN A 604 " --> pdb=" O ALA A 600 " (cutoff:3.500A) Processing helix chain 'A' and resid 612 through 617 Processing helix chain 'A' and resid 621 through 625 removed outlier: 3.789A pdb=" N ASN A 624 " --> pdb=" O GLN A 621 " (cutoff:3.500A) Processing helix chain 'A' and resid 635 through 647 removed outlier: 3.850A pdb=" N ALA A 643 " --> pdb=" O LYS A 639 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N ALA A 647 " --> pdb=" O ALA A 643 " (cutoff:3.500A) Processing helix chain 'A' and resid 668 through 674 removed outlier: 3.612A pdb=" N VAL A 672 " --> pdb=" O ASN A 668 " (cutoff:3.500A) Processing helix chain 'A' and resid 691 through 697 removed outlier: 3.614A pdb=" N ILE A 695 " --> pdb=" O ARG A 691 " (cutoff:3.500A) Processing helix chain 'A' and resid 714 through 720 removed outlier: 3.946A pdb=" N SER A 720 " --> pdb=" O GLU A 716 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 516 through 517 removed outlier: 3.669A pdb=" N LEU A 492 " --> pdb=" O ILE A 517 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N HIS A 556 " --> pdb=" O LEU A 553 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 570 through 572 Processing sheet with id=AA3, first strand: chain 'A' and resid 703 through 704 removed outlier: 6.749A pdb=" N VAL A 703 " --> pdb=" O THR A 710 " (cutoff:3.500A) 228 hydrogen bonds defined for protein. 678 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: 1.95 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 1364 1.34 - 1.46: 546 1.46 - 1.57: 2300 1.57 - 1.69: 0 1.69 - 1.81: 29 Bond restraints: 4239 Sorted by residual: bond pdb=" C VAL A 286 " pdb=" O VAL A 286 " ideal model delta sigma weight residual 1.242 1.228 0.014 1.17e-02 7.31e+03 1.42e+00 bond pdb=" C ALA A 438 " pdb=" N PHE A 439 " ideal model delta sigma weight residual 1.334 1.320 0.015 1.27e-02 6.20e+03 1.37e+00 bond pdb=" N PHE A 439 " pdb=" CA PHE A 439 " ideal model delta sigma weight residual 1.459 1.447 0.013 1.19e-02 7.06e+03 1.12e+00 bond pdb=" N THR A 402 " pdb=" CA THR A 402 " ideal model delta sigma weight residual 1.459 1.472 -0.013 1.23e-02 6.61e+03 1.08e+00 bond pdb=" C SER A 285 " pdb=" O SER A 285 " ideal model delta sigma weight residual 1.235 1.222 0.013 1.33e-02 5.65e+03 1.02e+00 ... (remaining 4234 not shown) Histogram of bond angle deviations from ideal: 99.74 - 106.58: 100 106.58 - 113.41: 2372 113.41 - 120.25: 1523 120.25 - 127.09: 1729 127.09 - 133.93: 30 Bond angle restraints: 5754 Sorted by residual: angle pdb=" N GLN A 659 " pdb=" CA GLN A 659 " pdb=" C GLN A 659 " ideal model delta sigma weight residual 108.90 113.97 -5.07 1.63e+00 3.76e-01 9.66e+00 angle pdb=" N ASN A 202 " pdb=" CA ASN A 202 " pdb=" C ASN A 202 " ideal model delta sigma weight residual 109.81 104.00 5.81 2.21e+00 2.05e-01 6.91e+00 angle pdb=" N PRO A 505 " pdb=" CA PRO A 505 " pdb=" C PRO A 505 " ideal model delta sigma weight residual 114.80 111.09 3.71 1.42e+00 4.96e-01 6.82e+00 angle pdb=" N VAL A 286 " pdb=" CA VAL A 286 " pdb=" C VAL A 286 " ideal model delta sigma weight residual 113.53 111.01 2.52 9.80e-01 1.04e+00 6.61e+00 angle pdb=" CA LYS A 369 " pdb=" CB LYS A 369 " pdb=" CG LYS A 369 " ideal model delta sigma weight residual 114.10 119.22 -5.12 2.00e+00 2.50e-01 6.55e+00 ... (remaining 5749 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.26: 2213 15.26 - 30.52: 226 30.52 - 45.78: 78 45.78 - 61.04: 9 61.04 - 76.31: 5 Dihedral angle restraints: 2531 sinusoidal: 919 harmonic: 1612 Sorted by residual: dihedral pdb=" CA ARG A 337 " pdb=" CB ARG A 337 " pdb=" CG ARG A 337 " pdb=" CD ARG A 337 " ideal model delta sinusoidal sigma weight residual 180.00 120.18 59.82 3 1.50e+01 4.44e-03 9.48e+00 dihedral pdb=" CA GLN A 659 " pdb=" CB GLN A 659 " pdb=" CG GLN A 659 " pdb=" CD GLN A 659 " ideal model delta sinusoidal sigma weight residual -180.00 -130.84 -49.16 3 1.50e+01 4.44e-03 8.74e+00 dihedral pdb=" N ARG A 357 " pdb=" CA ARG A 357 " pdb=" CB ARG A 357 " pdb=" CG ARG A 357 " ideal model delta sinusoidal sigma weight residual -60.00 -107.15 47.15 3 1.50e+01 4.44e-03 8.45e+00 ... (remaining 2528 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.029: 414 0.029 - 0.059: 197 0.059 - 0.088: 48 0.088 - 0.117: 20 0.117 - 0.147: 12 Chirality restraints: 691 Sorted by residual: chirality pdb=" CB VAL A 364 " pdb=" CA VAL A 364 " pdb=" CG1 VAL A 364 " pdb=" CG2 VAL A 364 " both_signs ideal model delta sigma weight residual False -2.63 -2.48 -0.15 2.00e-01 2.50e+01 5.39e-01 chirality pdb=" CA TYR A 200 " pdb=" N TYR A 200 " pdb=" C TYR A 200 " pdb=" CB TYR A 200 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.15 2.00e-01 2.50e+01 5.29e-01 chirality pdb=" CB THR A 204 " pdb=" CA THR A 204 " pdb=" OG1 THR A 204 " pdb=" CG2 THR A 204 " both_signs ideal model delta sigma weight residual False 2.55 2.69 -0.14 2.00e-01 2.50e+01 4.83e-01 ... (remaining 688 not shown) Planarity restraints: 734 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL A 322 " -0.025 5.00e-02 4.00e+02 3.76e-02 2.27e+00 pdb=" N PRO A 323 " 0.065 5.00e-02 4.00e+02 pdb=" CA PRO A 323 " -0.019 5.00e-02 4.00e+02 pdb=" CD PRO A 323 " -0.021 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA LYS A 369 " -0.006 2.00e-02 2.50e+03 1.28e-02 1.63e+00 pdb=" C LYS A 369 " 0.022 2.00e-02 2.50e+03 pdb=" O LYS A 369 " -0.008 2.00e-02 2.50e+03 pdb=" N GLU A 370 " -0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C TYR A 165 " -0.020 5.00e-02 4.00e+02 3.06e-02 1.50e+00 pdb=" N PRO A 166 " 0.053 5.00e-02 4.00e+02 pdb=" CA PRO A 166 " -0.015 5.00e-02 4.00e+02 pdb=" CD PRO A 166 " -0.017 5.00e-02 4.00e+02 ... (remaining 731 not shown) Histogram of nonbonded interaction distances: 2.32 - 2.83: 1295 2.83 - 3.35: 4043 3.35 - 3.87: 6370 3.87 - 4.38: 6579 4.38 - 4.90: 11724 Nonbonded interactions: 30011 Sorted by model distance: nonbonded pdb=" O SER A 311 " pdb=" OG SER A 311 " model vdw 2.317 2.440 nonbonded pdb=" O ALA A 296 " pdb=" OG SER A 444 " model vdw 2.328 2.440 nonbonded pdb=" O SER A 516 " pdb=" OH TYR A 712 " model vdw 2.392 2.440 nonbonded pdb=" O MET A 371 " pdb=" OE1 GLU A 375 " model vdw 2.468 3.040 nonbonded pdb=" O GLY A 622 " pdb=" OG1 THR A 625 " model vdw 2.519 2.440 ... (remaining 30006 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.070 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.060 Construct map_model_manager: 0.000 Extract box with map and model: 11.170 Check model and map are aligned: 0.060 Set scattering table: 0.040 Process input model: 16.150 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:2.600 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.290 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6209 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 4239 Z= 0.228 Angle : 0.590 6.099 5754 Z= 0.325 Chirality : 0.040 0.147 691 Planarity : 0.003 0.038 734 Dihedral : 14.272 76.306 1495 Min Nonbonded Distance : 2.317 Molprobity Statistics. All-atom Clashscore : 5.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.76 % Favored : 96.24 % Rotamer: Outliers : 0.47 % Allowed : 0.71 % Favored : 98.82 % 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: 0.44 (0.36), residues: 559 helix: 1.79 (0.30), residues: 302 sheet: None (None), residues: 0 loop : -1.65 (0.35), residues: 257 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 565 HIS 0.005 0.001 HIS A 498 PHE 0.018 0.001 PHE A 619 TYR 0.010 0.001 TYR A 501 ARG 0.004 0.000 ARG A 295 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1118 Ramachandran restraints generated. 559 Oldfield, 0 Emsley, 559 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1118 Ramachandran restraints generated. 559 Oldfield, 0 Emsley, 559 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 48 residues out of total 464 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 46 time to evaluate : 0.447 Fit side-chains REVERT: A 187 SER cc_start: 0.8089 (m) cc_final: 0.7652 (p) outliers start: 2 outliers final: 1 residues processed: 48 average time/residue: 0.2379 time to fit residues: 13.7724 Evaluate side-chains 45 residues out of total 464 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 44 time to evaluate : 0.749 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 586 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 47 optimal weight: 0.9990 chunk 42 optimal weight: 0.9980 chunk 23 optimal weight: 0.4980 chunk 14 optimal weight: 0.9990 chunk 28 optimal weight: 0.3980 chunk 22 optimal weight: 0.0980 chunk 43 optimal weight: 0.8980 chunk 16 optimal weight: 0.3980 chunk 26 optimal weight: 0.9980 chunk 32 optimal weight: 0.0670 chunk 50 optimal weight: 50.0000 overall best weight: 0.2918 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 556 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6197 moved from start: 0.1278 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 4239 Z= 0.181 Angle : 0.513 7.488 5754 Z= 0.260 Chirality : 0.038 0.125 691 Planarity : 0.004 0.037 734 Dihedral : 4.199 48.424 608 Min Nonbonded Distance : 2.311 Molprobity Statistics. All-atom Clashscore : 4.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.40 % Favored : 96.60 % Rotamer: Outliers : 0.94 % Allowed : 8.24 % Favored : 90.82 % 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 (0.36), residues: 559 helix: 1.98 (0.29), residues: 329 sheet: -0.04 (2.84), residues: 5 loop : -1.73 (0.38), residues: 225 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 565 HIS 0.004 0.001 HIS A 498 PHE 0.017 0.001 PHE A 619 TYR 0.022 0.001 TYR A 207 ARG 0.002 0.000 ARG A 295 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1118 Ramachandran restraints generated. 559 Oldfield, 0 Emsley, 559 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1118 Ramachandran restraints generated. 559 Oldfield, 0 Emsley, 559 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 50 residues out of total 464 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 46 time to evaluate : 0.401 Fit side-chains REVERT: A 285 SER cc_start: 0.8152 (p) cc_final: 0.7920 (t) outliers start: 4 outliers final: 1 residues processed: 47 average time/residue: 0.2369 time to fit residues: 13.5129 Evaluate side-chains 42 residues out of total 464 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 41 time to evaluate : 0.460 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 459 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 28 optimal weight: 0.2980 chunk 15 optimal weight: 0.5980 chunk 42 optimal weight: 0.5980 chunk 34 optimal weight: 2.9990 chunk 14 optimal weight: 0.5980 chunk 50 optimal weight: 6.9990 chunk 55 optimal weight: 7.9990 chunk 45 optimal weight: 0.9990 chunk 17 optimal weight: 0.9990 chunk 40 optimal weight: 0.5980 chunk 38 optimal weight: 0.6980 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 556 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6269 moved from start: 0.1569 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 4239 Z= 0.264 Angle : 0.526 7.409 5754 Z= 0.270 Chirality : 0.039 0.130 691 Planarity : 0.003 0.038 734 Dihedral : 3.521 14.158 605 Min Nonbonded Distance : 2.232 Molprobity Statistics. All-atom Clashscore : 4.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.29 % Favored : 95.71 % Rotamer: Outliers : 0.94 % Allowed : 13.65 % Favored : 85.41 % 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: 0.63 (0.36), residues: 559 helix: 1.84 (0.29), residues: 328 sheet: None (None), residues: 0 loop : -1.80 (0.37), residues: 231 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 565 HIS 0.005 0.001 HIS A 498 PHE 0.014 0.001 PHE A 619 TYR 0.019 0.002 TYR A 207 ARG 0.002 0.000 ARG A 284 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1118 Ramachandran restraints generated. 559 Oldfield, 0 Emsley, 559 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1118 Ramachandran restraints generated. 559 Oldfield, 0 Emsley, 559 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 50 residues out of total 464 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 46 time to evaluate : 0.429 Fit side-chains REVERT: A 187 SER cc_start: 0.7793 (m) cc_final: 0.7324 (p) REVERT: A 443 ILE cc_start: 0.8308 (mm) cc_final: 0.8021 (mt) outliers start: 4 outliers final: 2 residues processed: 47 average time/residue: 0.2336 time to fit residues: 13.3328 Evaluate side-chains 48 residues out of total 464 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 46 time to evaluate : 0.514 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 499 PHE Chi-restraints excluded: chain A residue 648 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 26 optimal weight: 0.1980 chunk 5 optimal weight: 0.9980 chunk 24 optimal weight: 0.5980 chunk 34 optimal weight: 0.9990 chunk 51 optimal weight: 0.4980 chunk 54 optimal weight: 5.9990 chunk 48 optimal weight: 0.9990 chunk 14 optimal weight: 0.5980 chunk 45 optimal weight: 0.2980 chunk 30 optimal weight: 0.9990 chunk 0 optimal weight: 2.9990 overall best weight: 0.4380 ------------------------------------------------------------------------------- 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: 0.6247 moved from start: 0.1761 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 4239 Z= 0.223 Angle : 0.500 7.568 5754 Z= 0.254 Chirality : 0.038 0.127 691 Planarity : 0.003 0.038 734 Dihedral : 3.437 13.701 605 Min Nonbonded Distance : 2.225 Molprobity Statistics. All-atom Clashscore : 4.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.94 % Favored : 96.06 % Rotamer: Outliers : 2.12 % Allowed : 14.82 % Favored : 83.06 % 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: 0.75 (0.36), residues: 559 helix: 1.93 (0.29), residues: 328 sheet: None (None), residues: 0 loop : -1.74 (0.38), residues: 231 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 565 HIS 0.004 0.001 HIS A 498 PHE 0.012 0.001 PHE A 619 TYR 0.016 0.002 TYR A 207 ARG 0.002 0.000 ARG A 295 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1118 Ramachandran restraints generated. 559 Oldfield, 0 Emsley, 559 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1118 Ramachandran restraints generated. 559 Oldfield, 0 Emsley, 559 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 56 residues out of total 464 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 47 time to evaluate : 0.466 Fit side-chains REVERT: A 285 SER cc_start: 0.8154 (OUTLIER) cc_final: 0.7913 (t) REVERT: A 375 GLU cc_start: 0.4389 (OUTLIER) cc_final: 0.4187 (mt-10) REVERT: A 443 ILE cc_start: 0.8286 (mm) cc_final: 0.8008 (mt) REVERT: A 680 MET cc_start: 0.4774 (OUTLIER) cc_final: 0.4534 (mmm) outliers start: 9 outliers final: 4 residues processed: 52 average time/residue: 0.2372 time to fit residues: 14.9009 Evaluate side-chains 52 residues out of total 464 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 45 time to evaluate : 0.446 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 285 SER Chi-restraints excluded: chain A residue 375 GLU Chi-restraints excluded: chain A residue 427 THR Chi-restraints excluded: chain A residue 648 LEU Chi-restraints excluded: chain A residue 680 MET Chi-restraints excluded: chain A residue 687 VAL Chi-restraints excluded: chain A residue 700 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 40 optimal weight: 0.3980 chunk 22 optimal weight: 0.1980 chunk 46 optimal weight: 2.9990 chunk 37 optimal weight: 1.9990 chunk 0 optimal weight: 2.9990 chunk 27 optimal weight: 0.2980 chunk 48 optimal weight: 0.9990 chunk 13 optimal weight: 0.6980 chunk 18 optimal weight: 0.7980 chunk 10 optimal weight: 0.6980 chunk 31 optimal weight: 0.8980 overall best weight: 0.4580 ------------------------------------------------------------------------------- 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: 0.6255 moved from start: 0.1945 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 4239 Z= 0.231 Angle : 0.504 7.593 5754 Z= 0.258 Chirality : 0.039 0.128 691 Planarity : 0.003 0.038 734 Dihedral : 3.439 14.643 605 Min Nonbonded Distance : 2.209 Molprobity Statistics. All-atom Clashscore : 4.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.47 % Favored : 95.53 % Rotamer: Outliers : 2.35 % Allowed : 15.53 % Favored : 82.12 % 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: 0.72 (0.36), residues: 559 helix: 1.91 (0.29), residues: 329 sheet: -3.97 (1.90), residues: 5 loop : -1.68 (0.39), residues: 225 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 565 HIS 0.004 0.001 HIS A 498 PHE 0.021 0.001 PHE A 317 TYR 0.012 0.001 TYR A 207 ARG 0.004 0.000 ARG A 542 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1118 Ramachandran restraints generated. 559 Oldfield, 0 Emsley, 559 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1118 Ramachandran restraints generated. 559 Oldfield, 0 Emsley, 559 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 56 residues out of total 464 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 46 time to evaluate : 0.437 Fit side-chains REVERT: A 285 SER cc_start: 0.8162 (p) cc_final: 0.7924 (t) REVERT: A 362 ARG cc_start: 0.5584 (mmt180) cc_final: 0.2591 (mtt180) REVERT: A 375 GLU cc_start: 0.4432 (OUTLIER) cc_final: 0.4202 (mt-10) REVERT: A 443 ILE cc_start: 0.8297 (mm) cc_final: 0.8014 (mt) REVERT: A 680 MET cc_start: 0.4887 (OUTLIER) cc_final: 0.4608 (mmm) outliers start: 10 outliers final: 6 residues processed: 52 average time/residue: 0.2375 time to fit residues: 14.9739 Evaluate side-chains 54 residues out of total 464 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 46 time to evaluate : 0.466 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 375 GLU Chi-restraints excluded: chain A residue 427 THR Chi-restraints excluded: chain A residue 499 PHE Chi-restraints excluded: chain A residue 539 LEU Chi-restraints excluded: chain A residue 648 LEU Chi-restraints excluded: chain A residue 680 MET Chi-restraints excluded: chain A residue 687 VAL Chi-restraints excluded: chain A residue 700 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 13 optimal weight: 0.9980 chunk 54 optimal weight: 1.9990 chunk 44 optimal weight: 0.9990 chunk 25 optimal weight: 0.9980 chunk 4 optimal weight: 0.4980 chunk 17 optimal weight: 0.5980 chunk 28 optimal weight: 0.6980 chunk 52 optimal weight: 0.0770 chunk 6 optimal weight: 0.9990 chunk 30 optimal weight: 1.9990 chunk 39 optimal weight: 0.8980 overall best weight: 0.5538 ------------------------------------------------------------------------------- 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: 0.6276 moved from start: 0.2078 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 4239 Z= 0.267 Angle : 0.518 7.891 5754 Z= 0.266 Chirality : 0.039 0.130 691 Planarity : 0.003 0.039 734 Dihedral : 3.537 16.717 605 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 5.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.47 % Favored : 95.53 % Rotamer: Outliers : 2.82 % Allowed : 15.29 % Favored : 81.88 % 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: 0.63 (0.36), residues: 559 helix: 1.83 (0.29), residues: 329 sheet: -4.02 (1.90), residues: 5 loop : -1.72 (0.39), residues: 225 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 565 HIS 0.004 0.001 HIS A 498 PHE 0.015 0.001 PHE A 317 TYR 0.011 0.001 TYR A 207 ARG 0.004 0.000 ARG A 542 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1118 Ramachandran restraints generated. 559 Oldfield, 0 Emsley, 559 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1118 Ramachandran restraints generated. 559 Oldfield, 0 Emsley, 559 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 56 residues out of total 464 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 44 time to evaluate : 0.491 Fit side-chains REVERT: A 285 SER cc_start: 0.8136 (OUTLIER) cc_final: 0.7897 (t) REVERT: A 362 ARG cc_start: 0.5518 (mmt180) cc_final: 0.2287 (mtt180) REVERT: A 443 ILE cc_start: 0.8272 (mm) cc_final: 0.7973 (mt) REVERT: A 654 ILE cc_start: 0.7554 (mp) cc_final: 0.7137 (mt) outliers start: 12 outliers final: 7 residues processed: 50 average time/residue: 0.2338 time to fit residues: 14.1436 Evaluate side-chains 52 residues out of total 464 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 44 time to evaluate : 0.437 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 285 SER Chi-restraints excluded: chain A residue 358 ILE Chi-restraints excluded: chain A residue 427 THR Chi-restraints excluded: chain A residue 499 PHE Chi-restraints excluded: chain A residue 539 LEU Chi-restraints excluded: chain A residue 648 LEU Chi-restraints excluded: chain A residue 687 VAL Chi-restraints excluded: chain A residue 700 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 30 optimal weight: 0.6980 chunk 45 optimal weight: 3.9990 chunk 53 optimal weight: 0.1980 chunk 33 optimal weight: 1.9990 chunk 32 optimal weight: 0.9980 chunk 24 optimal weight: 0.5980 chunk 21 optimal weight: 0.2980 chunk 16 optimal weight: 0.6980 chunk 10 optimal weight: 0.8980 chunk 34 optimal weight: 0.0980 chunk 36 optimal weight: 0.7980 overall best weight: 0.3780 ------------------------------------------------------------------------------- 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: 0.6234 moved from start: 0.2127 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 4239 Z= 0.201 Angle : 0.487 7.795 5754 Z= 0.248 Chirality : 0.038 0.128 691 Planarity : 0.003 0.038 734 Dihedral : 3.381 15.249 605 Min Nonbonded Distance : 2.200 Molprobity Statistics. All-atom Clashscore : 4.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.94 % Favored : 96.06 % Rotamer: Outliers : 2.82 % Allowed : 15.06 % Favored : 82.12 % 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: 0.83 (0.36), residues: 559 helix: 2.02 (0.29), residues: 329 sheet: -4.00 (1.86), residues: 5 loop : -1.69 (0.39), residues: 225 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 565 HIS 0.003 0.001 HIS A 498 PHE 0.014 0.001 PHE A 317 TYR 0.011 0.001 TYR A 207 ARG 0.004 0.000 ARG A 542 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1118 Ramachandran restraints generated. 559 Oldfield, 0 Emsley, 559 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1118 Ramachandran restraints generated. 559 Oldfield, 0 Emsley, 559 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 58 residues out of total 464 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 46 time to evaluate : 0.440 Fit side-chains REVERT: A 285 SER cc_start: 0.8183 (p) cc_final: 0.7951 (t) REVERT: A 286 VAL cc_start: 0.7978 (p) cc_final: 0.7716 (t) REVERT: A 362 ARG cc_start: 0.5439 (mmt180) cc_final: 0.3275 (mmt180) REVERT: A 443 ILE cc_start: 0.8297 (mm) cc_final: 0.8019 (mt) REVERT: A 501 TYR cc_start: 0.6824 (OUTLIER) cc_final: 0.6360 (m-80) outliers start: 12 outliers final: 7 residues processed: 54 average time/residue: 0.2289 time to fit residues: 14.8926 Evaluate side-chains 53 residues out of total 464 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 45 time to evaluate : 0.913 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 358 ILE Chi-restraints excluded: chain A residue 427 THR Chi-restraints excluded: chain A residue 499 PHE Chi-restraints excluded: chain A residue 501 TYR Chi-restraints excluded: chain A residue 539 LEU Chi-restraints excluded: chain A residue 648 LEU Chi-restraints excluded: chain A residue 687 VAL Chi-restraints excluded: chain A residue 700 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 26 optimal weight: 0.9980 chunk 5 optimal weight: 0.0170 chunk 42 optimal weight: 0.8980 chunk 49 optimal weight: 1.9990 chunk 51 optimal weight: 2.9990 chunk 47 optimal weight: 6.9990 chunk 50 optimal weight: 6.9990 chunk 30 optimal weight: 0.6980 chunk 21 optimal weight: 0.1980 chunk 39 optimal weight: 2.9990 chunk 15 optimal weight: 0.0070 overall best weight: 0.3636 ------------------------------------------------------------------------------- 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: 0.6227 moved from start: 0.2175 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 4239 Z= 0.200 Angle : 0.506 10.251 5754 Z= 0.253 Chirality : 0.039 0.187 691 Planarity : 0.003 0.038 734 Dihedral : 3.319 14.568 605 Min Nonbonded Distance : 2.194 Molprobity Statistics. All-atom Clashscore : 5.15 Ramachandran Plot: Outliers : 0.18 % Allowed : 4.11 % Favored : 95.71 % Rotamer: Outliers : 1.88 % Allowed : 16.94 % Favored : 81.18 % 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: 0.91 (0.36), residues: 559 helix: 2.11 (0.29), residues: 329 sheet: None (None), residues: 0 loop : -1.77 (0.39), residues: 230 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 565 HIS 0.003 0.001 HIS A 498 PHE 0.013 0.001 PHE A 317 TYR 0.009 0.001 TYR A 207 ARG 0.004 0.000 ARG A 542 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1118 Ramachandran restraints generated. 559 Oldfield, 0 Emsley, 559 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1118 Ramachandran restraints generated. 559 Oldfield, 0 Emsley, 559 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 54 residues out of total 464 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 46 time to evaluate : 0.396 Fit side-chains REVERT: A 285 SER cc_start: 0.8193 (p) cc_final: 0.7970 (t) REVERT: A 286 VAL cc_start: 0.7975 (p) cc_final: 0.7719 (t) REVERT: A 362 ARG cc_start: 0.5727 (mmt180) cc_final: 0.3150 (mmt180) REVERT: A 443 ILE cc_start: 0.8301 (mm) cc_final: 0.8028 (mt) REVERT: A 501 TYR cc_start: 0.6806 (OUTLIER) cc_final: 0.6378 (m-10) outliers start: 8 outliers final: 7 residues processed: 51 average time/residue: 0.2534 time to fit residues: 15.3301 Evaluate side-chains 54 residues out of total 464 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 46 time to evaluate : 0.478 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 358 ILE Chi-restraints excluded: chain A residue 427 THR Chi-restraints excluded: chain A residue 499 PHE Chi-restraints excluded: chain A residue 501 TYR Chi-restraints excluded: chain A residue 539 LEU Chi-restraints excluded: chain A residue 648 LEU Chi-restraints excluded: chain A residue 687 VAL Chi-restraints excluded: chain A residue 700 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 45 optimal weight: 5.9990 chunk 47 optimal weight: 0.0270 chunk 50 optimal weight: 4.9990 chunk 33 optimal weight: 1.9990 chunk 53 optimal weight: 1.9990 chunk 32 optimal weight: 0.9990 chunk 25 optimal weight: 0.9980 chunk 36 optimal weight: 0.0570 chunk 55 optimal weight: 0.9990 chunk 51 optimal weight: 0.8980 chunk 44 optimal weight: 0.5980 overall best weight: 0.5156 ------------------------------------------------------------------------------- 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: 0.6262 moved from start: 0.2243 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 4239 Z= 0.256 Angle : 0.527 11.845 5754 Z= 0.267 Chirality : 0.039 0.182 691 Planarity : 0.003 0.038 734 Dihedral : 3.443 16.264 605 Min Nonbonded Distance : 2.187 Molprobity Statistics. All-atom Clashscore : 5.39 Ramachandran Plot: Outliers : 0.18 % Allowed : 4.11 % Favored : 95.71 % Rotamer: Outliers : 2.82 % Allowed : 16.24 % Favored : 80.94 % 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: 0.77 (0.36), residues: 559 helix: 1.97 (0.29), residues: 329 sheet: None (None), residues: 0 loop : -1.78 (0.38), residues: 230 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 565 HIS 0.004 0.001 HIS A 498 PHE 0.011 0.001 PHE A 317 TYR 0.009 0.001 TYR A 207 ARG 0.004 0.000 ARG A 542 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1118 Ramachandran restraints generated. 559 Oldfield, 0 Emsley, 559 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1118 Ramachandran restraints generated. 559 Oldfield, 0 Emsley, 559 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 58 residues out of total 464 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 46 time to evaluate : 0.423 Fit side-chains REVERT: A 285 SER cc_start: 0.8193 (OUTLIER) cc_final: 0.7982 (t) REVERT: A 286 VAL cc_start: 0.7969 (p) cc_final: 0.7721 (t) REVERT: A 362 ARG cc_start: 0.5644 (mmt180) cc_final: 0.3522 (mmt180) REVERT: A 443 ILE cc_start: 0.8323 (mm) cc_final: 0.8041 (mt) REVERT: A 501 TYR cc_start: 0.6851 (OUTLIER) cc_final: 0.6423 (m-80) REVERT: A 654 ILE cc_start: 0.7515 (mp) cc_final: 0.7134 (mt) outliers start: 12 outliers final: 8 residues processed: 53 average time/residue: 0.2261 time to fit residues: 14.4701 Evaluate side-chains 56 residues out of total 464 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 46 time to evaluate : 0.443 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 285 SER Chi-restraints excluded: chain A residue 358 ILE Chi-restraints excluded: chain A residue 427 THR Chi-restraints excluded: chain A residue 499 PHE Chi-restraints excluded: chain A residue 501 TYR Chi-restraints excluded: chain A residue 515 LEU Chi-restraints excluded: chain A residue 539 LEU Chi-restraints excluded: chain A residue 648 LEU Chi-restraints excluded: chain A residue 687 VAL Chi-restraints excluded: chain A residue 700 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 4 optimal weight: 0.5980 chunk 34 optimal weight: 0.9980 chunk 27 optimal weight: 0.4980 chunk 35 optimal weight: 0.0470 chunk 47 optimal weight: 0.9980 chunk 13 optimal weight: 0.9980 chunk 40 optimal weight: 0.2980 chunk 6 optimal weight: 0.7980 chunk 12 optimal weight: 0.8980 chunk 44 optimal weight: 0.6980 chunk 18 optimal weight: 0.8980 overall best weight: 0.4278 ------------------------------------------------------------------------------- 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: 0.6244 moved from start: 0.2283 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 4239 Z= 0.222 Angle : 0.520 11.554 5754 Z= 0.260 Chirality : 0.039 0.159 691 Planarity : 0.003 0.038 734 Dihedral : 3.388 15.392 605 Min Nonbonded Distance : 2.189 Molprobity Statistics. All-atom Clashscore : 4.91 Ramachandran Plot: Outliers : 0.18 % Allowed : 3.94 % Favored : 95.89 % Rotamer: Outliers : 2.35 % Allowed : 17.65 % Favored : 80.00 % 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: 0.78 (0.36), residues: 559 helix: 1.96 (0.29), residues: 332 sheet: None (None), residues: 0 loop : -1.80 (0.38), residues: 227 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 565 HIS 0.003 0.001 HIS A 498 PHE 0.011 0.001 PHE A 317 TYR 0.009 0.001 TYR A 207 ARG 0.004 0.000 ARG A 542 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1118 Ramachandran restraints generated. 559 Oldfield, 0 Emsley, 559 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1118 Ramachandran restraints generated. 559 Oldfield, 0 Emsley, 559 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 56 residues out of total 464 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 46 time to evaluate : 0.476 Fit side-chains REVERT: A 285 SER cc_start: 0.8223 (OUTLIER) cc_final: 0.7995 (t) REVERT: A 286 VAL cc_start: 0.7968 (p) cc_final: 0.7719 (t) REVERT: A 362 ARG cc_start: 0.5744 (mmt180) cc_final: 0.3551 (mmt180) REVERT: A 443 ILE cc_start: 0.8309 (mm) cc_final: 0.8033 (mt) REVERT: A 501 TYR cc_start: 0.6839 (OUTLIER) cc_final: 0.6422 (m-80) outliers start: 10 outliers final: 8 residues processed: 52 average time/residue: 0.2380 time to fit residues: 14.8986 Evaluate side-chains 56 residues out of total 464 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 46 time to evaluate : 0.450 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 285 SER Chi-restraints excluded: chain A residue 358 ILE Chi-restraints excluded: chain A residue 427 THR Chi-restraints excluded: chain A residue 499 PHE Chi-restraints excluded: chain A residue 501 TYR Chi-restraints excluded: chain A residue 515 LEU Chi-restraints excluded: chain A residue 539 LEU Chi-restraints excluded: chain A residue 648 LEU Chi-restraints excluded: chain A residue 687 VAL Chi-restraints excluded: chain A residue 700 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 45 optimal weight: 4.9990 chunk 5 optimal weight: 0.9980 chunk 8 optimal weight: 0.0980 chunk 39 optimal weight: 3.9990 chunk 2 optimal weight: 0.0980 chunk 32 optimal weight: 0.9980 chunk 50 optimal weight: 8.9990 chunk 29 optimal weight: 0.5980 chunk 38 optimal weight: 0.3980 chunk 1 optimal weight: 0.6980 chunk 35 optimal weight: 0.9990 overall best weight: 0.3780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4322 r_free = 0.4322 target = 0.190345 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.4234 r_free = 0.4234 target = 0.182736 restraints weight = 5855.473| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.4142 r_free = 0.4142 target = 0.177808 restraints weight = 11313.069| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.4120 r_free = 0.4120 target = 0.175439 restraints weight = 9845.752| |-----------------------------------------------------------------------------| r_work (final): 0.4114 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6422 moved from start: 0.2327 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 4239 Z= 0.205 Angle : 0.504 11.326 5754 Z= 0.255 Chirality : 0.038 0.150 691 Planarity : 0.003 0.038 734 Dihedral : 3.318 14.452 605 Min Nonbonded Distance : 2.188 Molprobity Statistics. All-atom Clashscore : 4.67 Ramachandran Plot: Outliers : 0.18 % Allowed : 3.94 % Favored : 95.89 % Rotamer: Outliers : 2.82 % Allowed : 17.41 % Favored : 79.76 % 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: 0.83 (0.36), residues: 559 helix: 2.00 (0.29), residues: 333 sheet: None (None), residues: 0 loop : -1.79 (0.38), residues: 226 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 565 HIS 0.003 0.001 HIS A 498 PHE 0.011 0.001 PHE A 317 TYR 0.009 0.001 TYR A 207 ARG 0.004 0.000 ARG A 542 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1374.74 seconds wall clock time: 25 minutes 15.16 seconds (1515.16 seconds total)