Starting phenix.real_space_refine on Tue Sep 24 08:19:32 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7y49_33604/09_2024/7y49_33604.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7y49_33604/09_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_33604/09_2024/7y49_33604.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7y49_33604/09_2024/7y49_33604.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7y49_33604/09_2024/7y49_33604.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7y49_33604/09_2024/7y49_33604.cif" } 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. Time to flip 1 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/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: 3.83, per 1000 atoms: 0.92 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 - 3.00 Amino acid : True - 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: 1.05 Conformation dependent library (CDL) restraints added in 544.4 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: 0.45 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: 1.10 Time building geometry restraints manager: 1.23 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: 0.00 - 1.22: 5505 1.22 - 2.44: 181 2.44 - 3.66: 46 3.66 - 4.88: 15 4.88 - 6.10: 7 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 3.040 nonbonded pdb=" O ALA A 296 " pdb=" OG SER A 444 " model vdw 2.328 3.040 nonbonded pdb=" O SER A 516 " pdb=" OH TYR A 712 " model vdw 2.392 3.040 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 3.040 ... (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: 4.340 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: 0.200 Check model and map are aligned: 0.030 Set scattering table: 0.050 Process input model: 15.140 Find NCS groups from input model: 0.050 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:2.820 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.710 ------------------------------------------------------------------------------- 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 : 0.454 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: 0.2296 time to fit residues: 13.3715 Evaluate side-chains 45 residues out of total 464 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 44 time to evaluate : 0.490 ------------------------------------------------------------------------------- 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: 3.9990 chunk 42 optimal weight: 0.6980 chunk 23 optimal weight: 0.3980 chunk 14 optimal weight: 0.6980 chunk 28 optimal weight: 0.3980 chunk 22 optimal weight: 0.0980 chunk 43 optimal weight: 0.8980 chunk 16 optimal weight: 0.0570 chunk 26 optimal weight: 0.3980 chunk 32 optimal weight: 0.9990 chunk 50 optimal weight: 50.0000 overall best weight: 0.2698 ------------------------------------------------------------------------------- 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: 0.6191 moved from start: 0.1279 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 4239 Z= 0.176 Angle : 0.517 7.425 5754 Z= 0.261 Chirality : 0.038 0.126 691 Planarity : 0.004 0.037 734 Dihedral : 4.217 49.102 608 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 4.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.40 % Favored : 96.60 % Rotamer: Outliers : 0.94 % Allowed : 7.76 % Favored : 91.29 % 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: 1.95 (0.29), residues: 330 sheet: -0.01 (2.87), residues: 5 loop : -1.80 (0.37), residues: 224 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 0.016 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 54 residues out of total 464 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 50 time to evaluate : 0.437 Fit side-chains REVERT: A 285 SER cc_start: 0.8187 (p) cc_final: 0.7938 (t) outliers start: 4 outliers final: 1 residues processed: 51 average time/residue: 0.2417 time to fit residues: 14.7617 Evaluate side-chains 46 residues out of total 464 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 45 time to evaluate : 0.383 ------------------------------------------------------------------------------- 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: 0.9990 chunk 15 optimal weight: 0.0980 chunk 42 optimal weight: 0.8980 chunk 34 optimal weight: 0.7980 chunk 14 optimal weight: 0.7980 chunk 50 optimal weight: 30.0000 chunk 55 optimal weight: 7.9990 chunk 45 optimal weight: 0.9990 chunk 17 optimal weight: 0.0570 chunk 40 optimal weight: 0.0000 chunk 38 optimal weight: 0.5980 overall best weight: 0.3102 ------------------------------------------------------------------------------- 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: 0.6201 moved from start: 0.1633 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 4239 Z= 0.181 Angle : 0.489 7.299 5754 Z= 0.247 Chirality : 0.038 0.129 691 Planarity : 0.003 0.037 734 Dihedral : 3.319 11.342 605 Min Nonbonded Distance : 2.592 Molprobity Statistics. All-atom Clashscore : 3.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.40 % Favored : 96.60 % Rotamer: Outliers : 0.94 % Allowed : 12.24 % Favored : 86.82 % 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: 0.90 (0.36), residues: 559 helix: 2.08 (0.29), residues: 329 sheet: -0.19 (2.63), residues: 5 loop : -1.75 (0.37), 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 0.023 0.001 PHE A 317 TYR 0.019 0.001 TYR A 207 ARG 0.003 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 49 residues out of total 464 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 45 time to evaluate : 0.412 Fit side-chains REVERT: A 285 SER cc_start: 0.8207 (p) cc_final: 0.7917 (t) outliers start: 4 outliers final: 3 residues processed: 47 average time/residue: 0.2089 time to fit residues: 12.0093 Evaluate side-chains 45 residues out of total 464 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 42 time to evaluate : 0.424 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 459 LEU 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: 1.9990 chunk 5 optimal weight: 0.9990 chunk 24 optimal weight: 0.5980 chunk 34 optimal weight: 0.9980 chunk 51 optimal weight: 0.0980 chunk 54 optimal weight: 1.9990 chunk 48 optimal weight: 0.9990 chunk 14 optimal weight: 0.9990 chunk 45 optimal weight: 0.8980 chunk 30 optimal weight: 1.9990 chunk 0 optimal weight: 2.9990 overall best weight: 0.7182 ------------------------------------------------------------------------------- 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: 0.6303 moved from start: 0.1844 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 4239 Z= 0.333 Angle : 0.563 7.835 5754 Z= 0.289 Chirality : 0.041 0.135 691 Planarity : 0.004 0.039 734 Dihedral : 3.647 16.452 605 Min Nonbonded Distance : 2.573 Molprobity Statistics. All-atom Clashscore : 5.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.29 % Favored : 95.71 % Rotamer: Outliers : 2.12 % Allowed : 14.12 % Favored : 83.76 % 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: 0.45 (0.35), residues: 559 helix: 1.69 (0.28), residues: 329 sheet: -4.24 (1.79), residues: 5 loop : -1.80 (0.38), residues: 225 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 0.013 0.002 PHE A 619 TYR 0.017 0.002 TYR A 207 ARG 0.003 0.000 ARG A 242 *********************** 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 52 residues out of total 464 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 43 time to evaluate : 0.409 Fit side-chains REVERT: A 285 SER cc_start: 0.8183 (p) cc_final: 0.7946 (t) outliers start: 9 outliers final: 4 residues processed: 49 average time/residue: 0.1967 time to fit residues: 11.9442 Evaluate side-chains 48 residues out of total 464 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 44 time to evaluate : 0.428 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 427 THR Chi-restraints excluded: chain A residue 499 PHE Chi-restraints excluded: chain A residue 648 LEU Chi-restraints excluded: chain A residue 687 VAL 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: 3.9990 chunk 37 optimal weight: 2.9990 chunk 0 optimal weight: 2.9990 chunk 27 optimal weight: 0.2980 chunk 48 optimal weight: 0.9980 chunk 13 optimal weight: 0.9980 chunk 18 optimal weight: 0.5980 chunk 10 optimal weight: 0.7980 chunk 31 optimal weight: 0.5980 overall best weight: 0.4180 ------------------------------------------------------------------------------- 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: 0.6243 moved from start: 0.1921 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= 0.219 Angle : 0.520 7.704 5754 Z= 0.265 Chirality : 0.038 0.128 691 Planarity : 0.003 0.037 734 Dihedral : 3.444 14.957 605 Min Nonbonded Distance : 2.586 Molprobity Statistics. All-atom Clashscore : 3.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.11 % Favored : 95.89 % Rotamer: Outliers : 0.94 % Allowed : 16.47 % Favored : 82.59 % 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 (0.36), residues: 559 helix: 1.91 (0.29), residues: 329 sheet: -4.09 (1.85), residues: 5 loop : -1.76 (0.38), residues: 225 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 0.010 0.001 PHE A 619 TYR 0.014 0.001 TYR A 207 ARG 0.002 0.000 ARG A 242 *********************** 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 50 residues out of total 464 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 46 time to evaluate : 0.467 Fit side-chains REVERT: A 285 SER cc_start: 0.8234 (p) cc_final: 0.7977 (t) REVERT: A 362 ARG cc_start: 0.5586 (mmt180) cc_final: 0.2659 (mtt180) outliers start: 4 outliers final: 3 residues processed: 49 average time/residue: 0.2355 time to fit residues: 13.9751 Evaluate side-chains 47 residues out of total 464 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 44 time to evaluate : 0.434 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 427 THR Chi-restraints excluded: chain A residue 648 LEU Chi-restraints excluded: chain A residue 687 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 13 optimal weight: 0.8980 chunk 54 optimal weight: 3.9990 chunk 44 optimal weight: 0.9980 chunk 25 optimal weight: 0.9980 chunk 4 optimal weight: 0.5980 chunk 17 optimal weight: 0.5980 chunk 28 optimal weight: 0.7980 chunk 52 optimal weight: 0.6980 chunk 6 optimal weight: 0.5980 chunk 30 optimal weight: 1.9990 chunk 39 optimal weight: 3.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6296 moved from start: 0.2091 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 4239 Z= 0.309 Angle : 0.552 7.803 5754 Z= 0.285 Chirality : 0.040 0.131 691 Planarity : 0.004 0.038 734 Dihedral : 3.616 17.461 605 Min Nonbonded Distance : 2.563 Molprobity Statistics. All-atom Clashscore : 4.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.65 % Favored : 95.35 % Rotamer: Outliers : 2.12 % Allowed : 16.24 % Favored : 81.65 % 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 (0.35), residues: 559 helix: 1.71 (0.28), residues: 328 sheet: -4.15 (1.89), residues: 5 loop : -1.84 (0.38), residues: 226 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 0.011 0.002 PHE A 439 TYR 0.013 0.002 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 50 residues out of total 464 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 41 time to evaluate : 0.450 Fit side-chains REVERT: A 285 SER cc_start: 0.8236 (p) cc_final: 0.7971 (t) REVERT: A 362 ARG cc_start: 0.5487 (mmt180) cc_final: 0.2282 (mtt180) outliers start: 9 outliers final: 7 residues processed: 46 average time/residue: 0.2345 time to fit residues: 13.1283 Evaluate side-chains 48 residues out of total 464 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 41 time to evaluate : 0.427 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 310 VAL 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: 0.5980 chunk 45 optimal weight: 2.9990 chunk 53 optimal weight: 8.9990 chunk 33 optimal weight: 1.9990 chunk 32 optimal weight: 0.6980 chunk 24 optimal weight: 0.5980 chunk 21 optimal weight: 0.2980 chunk 16 optimal weight: 0.0970 chunk 10 optimal weight: 0.6980 chunk 34 optimal weight: 0.8980 chunk 36 optimal weight: 2.9990 overall best weight: 0.4578 ------------------------------------------------------------------------------- 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: 0.6258 moved from start: 0.2122 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 4239 Z= 0.232 Angle : 0.514 7.933 5754 Z= 0.263 Chirality : 0.039 0.128 691 Planarity : 0.003 0.037 734 Dihedral : 3.473 16.178 605 Min Nonbonded Distance : 2.560 Molprobity Statistics. All-atom Clashscore : 3.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.47 % Favored : 95.53 % Rotamer: Outliers : 1.88 % Allowed : 16.71 % Favored : 81.41 % 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: 1.88 (0.29), residues: 329 sheet: -4.05 (1.96), residues: 5 loop : -1.81 (0.38), residues: 225 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 439 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 53 residues out of total 464 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 45 time to evaluate : 0.403 Fit side-chains REVERT: A 285 SER cc_start: 0.8233 (p) cc_final: 0.7953 (t) REVERT: A 362 ARG cc_start: 0.5421 (mmt180) cc_final: 0.2830 (mmt180) outliers start: 8 outliers final: 6 residues processed: 50 average time/residue: 0.2497 time to fit residues: 14.9368 Evaluate side-chains 50 residues out of total 464 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 44 time to evaluate : 0.395 ------------------------------------------------------------------------------- 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 539 LEU Chi-restraints excluded: chain A residue 648 LEU Chi-restraints excluded: chain A residue 687 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 26 optimal weight: 0.5980 chunk 5 optimal weight: 0.9980 chunk 42 optimal weight: 0.8980 chunk 49 optimal weight: 0.5980 chunk 51 optimal weight: 0.5980 chunk 47 optimal weight: 3.9990 chunk 50 optimal weight: 0.0050 chunk 30 optimal weight: 1.9990 chunk 21 optimal weight: 0.5980 chunk 39 optimal weight: 3.9990 chunk 15 optimal weight: 0.0470 overall best weight: 0.3692 ------------------------------------------------------------------------------- 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: 0.2182 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= 0.204 Angle : 0.499 7.802 5754 Z= 0.256 Chirality : 0.039 0.183 691 Planarity : 0.003 0.037 734 Dihedral : 3.355 15.015 605 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 4.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.11 % Favored : 95.89 % Rotamer: Outliers : 1.65 % Allowed : 16.71 % Favored : 81.65 % 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: 2.06 (0.29), residues: 328 sheet: -4.02 (1.97), residues: 5 loop : -1.83 (0.38), residues: 226 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 565 HIS 0.004 0.001 HIS A 498 PHE 0.012 0.001 PHE A 439 TYR 0.011 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 53 residues out of total 464 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 46 time to evaluate : 0.471 Fit side-chains REVERT: A 362 ARG cc_start: 0.5713 (mmt180) cc_final: 0.3130 (mmt180) outliers start: 7 outliers final: 6 residues processed: 51 average time/residue: 0.2463 time to fit residues: 15.0562 Evaluate side-chains 51 residues out of total 464 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 45 time to evaluate : 0.427 ------------------------------------------------------------------------------- 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 539 LEU Chi-restraints excluded: chain A residue 648 LEU Chi-restraints excluded: chain A residue 687 VAL 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: 0.0070 chunk 50 optimal weight: 5.9990 chunk 33 optimal weight: 1.9990 chunk 53 optimal weight: 0.9980 chunk 32 optimal weight: 0.8980 chunk 25 optimal weight: 0.9990 chunk 36 optimal weight: 0.8980 chunk 55 optimal weight: 0.0970 chunk 51 optimal weight: 0.3980 chunk 44 optimal weight: 2.9990 overall best weight: 0.4596 ------------------------------------------------------------------------------- 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: 0.6253 moved from start: 0.2220 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= 0.235 Angle : 0.517 8.002 5754 Z= 0.264 Chirality : 0.039 0.170 691 Planarity : 0.003 0.038 734 Dihedral : 3.394 16.008 605 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 4.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.11 % Favored : 95.89 % Rotamer: Outliers : 1.41 % Allowed : 16.94 % Favored : 81.65 % 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 (0.36), residues: 559 helix: 2.02 (0.29), residues: 328 sheet: -4.41 (1.77), residues: 5 loop : -1.88 (0.38), residues: 226 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 0.013 0.001 PHE A 439 TYR 0.010 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 49 residues out of total 464 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 43 time to evaluate : 0.434 Fit side-chains REVERT: A 286 VAL cc_start: 0.7981 (p) cc_final: 0.7757 (t) REVERT: A 362 ARG cc_start: 0.5765 (mmt180) cc_final: 0.3604 (mmt180) outliers start: 6 outliers final: 6 residues processed: 47 average time/residue: 0.2554 time to fit residues: 14.4173 Evaluate side-chains 49 residues out of total 464 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 43 time to evaluate : 0.458 ------------------------------------------------------------------------------- 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 539 LEU Chi-restraints excluded: chain A residue 648 LEU Chi-restraints excluded: chain A residue 687 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 4 optimal weight: 0.6980 chunk 34 optimal weight: 0.6980 chunk 27 optimal weight: 0.9990 chunk 35 optimal weight: 0.6980 chunk 47 optimal weight: 0.3980 chunk 13 optimal weight: 0.7980 chunk 40 optimal weight: 0.5980 chunk 6 optimal weight: 0.7980 chunk 12 optimal weight: 0.6980 chunk 44 optimal weight: 3.9990 chunk 18 optimal weight: 0.9980 overall best weight: 0.6180 ------------------------------------------------------------------------------- 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: 0.6289 moved from start: 0.2302 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 4239 Z= 0.296 Angle : 0.551 8.671 5754 Z= 0.283 Chirality : 0.041 0.175 691 Planarity : 0.003 0.039 734 Dihedral : 3.565 17.808 605 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 4.43 Ramachandran Plot: Outliers : 0.18 % Allowed : 4.47 % Favored : 95.35 % Rotamer: Outliers : 1.88 % Allowed : 17.18 % 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: 0.51 (0.35), residues: 559 helix: 1.87 (0.28), residues: 326 sheet: -4.47 (1.75), residues: 5 loop : -1.94 (0.37), residues: 228 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 0.013 0.001 PHE A 439 TYR 0.010 0.002 TYR A 590 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: 8 poor density : 48 time to evaluate : 0.474 Fit side-chains REVERT: A 282 LEU cc_start: 0.8049 (tp) cc_final: 0.7814 (tt) REVERT: A 285 SER cc_start: 0.8218 (p) cc_final: 0.7913 (t) REVERT: A 309 PHE cc_start: 0.7051 (t80) cc_final: 0.6726 (t80) REVERT: A 362 ARG cc_start: 0.5819 (mmt180) cc_final: 0.3605 (mmt180) outliers start: 8 outliers final: 8 residues processed: 53 average time/residue: 0.2252 time to fit residues: 14.5265 Evaluate side-chains 54 residues out of total 464 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 46 time to evaluate : 0.425 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 310 VAL 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 45 optimal weight: 3.9990 chunk 5 optimal weight: 0.7980 chunk 8 optimal weight: 0.5980 chunk 39 optimal weight: 3.9990 chunk 2 optimal weight: 0.7980 chunk 32 optimal weight: 0.9980 chunk 50 optimal weight: 20.0000 chunk 29 optimal weight: 0.9990 chunk 38 optimal weight: 0.0670 chunk 1 optimal weight: 0.7980 chunk 35 optimal weight: 0.6980 overall best weight: 0.5918 ------------------------------------------------------------------------------- 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 = 0.4131 r_free = 0.4131 target = 0.175717 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 74)----------------| | r_work = 0.3939 r_free = 0.3939 target = 0.158493 restraints weight = 5825.125| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.3912 r_free = 0.3912 target = 0.156347 restraints weight = 8323.302| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 54)----------------| | r_work = 0.3907 r_free = 0.3907 target = 0.155918 restraints weight = 7834.641| |-----------------------------------------------------------------------------| r_work (final): 0.3916 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6470 moved from start: 0.2349 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 4239 Z= 0.287 Angle : 0.551 8.249 5754 Z= 0.285 Chirality : 0.040 0.166 691 Planarity : 0.003 0.038 734 Dihedral : 3.572 17.737 605 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 4.31 Ramachandran Plot: Outliers : 0.18 % Allowed : 4.47 % Favored : 95.35 % Rotamer: Outliers : 2.12 % Allowed : 17.88 % 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: 0.39 (0.35), residues: 559 helix: 1.75 (0.28), residues: 333 sheet: -4.48 (1.74), residues: 5 loop : -2.09 (0.37), residues: 221 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 0.013 0.001 PHE A 439 TYR 0.010 0.002 TYR A 207 ARG 0.002 0.000 ARG A 242 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1325.43 seconds wall clock time: 23 minutes 57.84 seconds (1437.84 seconds total)