Starting phenix.real_space_refine on Sun May 11 04:50:10 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7y49_33604/05_2025/7y49_33604.cif Found real_map, /net/cci-nas-00/data/ceres_data/7y49_33604/05_2025/7y49_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/cci-nas-00/data/ceres_data/7y49_33604/05_2025/7y49_33604.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7y49_33604/05_2025/7y49_33604.map" model { file = "/net/cci-nas-00/data/ceres_data/7y49_33604/05_2025/7y49_33604.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7y49_33604/05_2025/7y49_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-5687/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: 4.26, per 1000 atoms: 1.02 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: 1.09 Conformation dependent library (CDL) restraints added in 616.8 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: 1.06 Time building geometry restraints manager: 1.25 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: 3.690 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.050 Construct map_model_manager: 0.010 Extract box with map and model: 0.180 Check model and map are aligned: 0.030 Set scattering table: 0.050 Process input model: 15.240 Find NCS groups from input model: 0.040 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:2.910 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.220 ------------------------------------------------------------------------------- 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= 0.177 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 Details of bonding type rmsd hydrogen bonds : bond 0.19557 ( 228) hydrogen bonds : angle 5.36755 ( 678) covalent geometry : bond 0.00346 ( 4239) covalent geometry : angle 0.59001 ( 5754) *********************** 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 to be fit. rotamer outliers: 2 poor density : 46 time to evaluate : 0.403 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: 0.2189 time to fit residues: 12.7752 Evaluate side-chains 45 residues out of total 464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 44 time to evaluate : 0.402 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4318 r_free = 0.4318 target = 0.189661 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4243 r_free = 0.4243 target = 0.183050 restraints weight = 5831.603| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 63)----------------| | r_work = 0.4143 r_free = 0.4143 target = 0.177871 restraints weight = 11696.351| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.4116 r_free = 0.4116 target = 0.174588 restraints weight = 8036.568| |-----------------------------------------------------------------------------| r_work (final): 0.4104 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6410 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= 0.138 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 Details of bonding type rmsd hydrogen bonds : bond 0.07113 ( 228) hydrogen bonds : angle 3.94470 ( 678) covalent geometry : bond 0.00267 ( 4239) covalent geometry : angle 0.51678 ( 5754) *********************** 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 to be fit. rotamer outliers: 4 poor density : 50 time to evaluate : 0.436 Fit side-chains REVERT: A 285 SER cc_start: 0.8198 (p) cc_final: 0.7952 (t) outliers start: 4 outliers final: 1 residues processed: 51 average time/residue: 0.2458 time to fit residues: 15.0626 Evaluate side-chains 46 residues out of total 464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 45 time to evaluate : 0.452 ------------------------------------------------------------------------------- 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 26 optimal weight: 0.5980 chunk 45 optimal weight: 0.1980 chunk 37 optimal weight: 3.9990 chunk 33 optimal weight: 2.9990 chunk 46 optimal weight: 3.9990 chunk 22 optimal weight: 0.0970 chunk 24 optimal weight: 0.5980 chunk 21 optimal weight: 0.4980 chunk 7 optimal weight: 0.4980 chunk 27 optimal weight: 0.1980 chunk 44 optimal weight: 1.9990 overall best weight: 0.2978 ------------------------------------------------------------------------------- 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 = 0.4315 r_free = 0.4315 target = 0.189256 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.4237 r_free = 0.4237 target = 0.182472 restraints weight = 5826.811| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 56)----------------| | r_work = 0.4130 r_free = 0.4130 target = 0.176827 restraints weight = 13279.017| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.4088 r_free = 0.4088 target = 0.172525 restraints weight = 10576.498| |-----------------------------------------------------------------------------| r_work (final): 0.4079 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6449 moved from start: 0.1636 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 4239 Z= 0.135 Angle : 0.488 7.292 5754 Z= 0.246 Chirality : 0.038 0.128 691 Planarity : 0.003 0.037 734 Dihedral : 3.311 11.230 605 Min Nonbonded Distance : 2.592 Molprobity Statistics. All-atom Clashscore : 3.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % Rotamer: Outliers : 0.94 % Allowed : 12.47 % Favored : 86.59 % 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: 0.93 (0.36), residues: 559 helix: 2.10 (0.29), residues: 329 sheet: -0.14 (2.66), 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 0.024 0.001 PHE A 317 TYR 0.018 0.001 TYR A 207 ARG 0.002 0.000 ARG A 542 Details of bonding type rmsd hydrogen bonds : bond 0.06855 ( 228) hydrogen bonds : angle 3.65506 ( 678) covalent geometry : bond 0.00264 ( 4239) covalent geometry : angle 0.48804 ( 5754) *********************** 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 46 residues out of total 464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 42 time to evaluate : 0.423 Fit side-chains REVERT: A 285 SER cc_start: 0.8202 (p) cc_final: 0.7903 (t) outliers start: 4 outliers final: 3 residues processed: 44 average time/residue: 0.2212 time to fit residues: 11.9617 Evaluate side-chains 43 residues out of total 464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 40 time to evaluate : 0.477 ------------------------------------------------------------------------------- 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 6 optimal weight: 0.1980 chunk 8 optimal weight: 0.5980 chunk 9 optimal weight: 0.0980 chunk 20 optimal weight: 0.2980 chunk 31 optimal weight: 0.9990 chunk 5 optimal weight: 0.5980 chunk 42 optimal weight: 0.5980 chunk 45 optimal weight: 0.0970 chunk 1 optimal weight: 0.4980 chunk 22 optimal weight: 0.0980 chunk 15 optimal weight: 0.1980 overall best weight: 0.1378 ------------------------------------------------------------------------------- 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 = 0.4213 r_free = 0.4213 target = 0.182751 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 128)---------------| | r_work = 0.3981 r_free = 0.3981 target = 0.161743 restraints weight = 6029.842| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 80)----------------| | r_work = 0.3933 r_free = 0.3933 target = 0.157883 restraints weight = 7448.251| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 55)----------------| | r_work = 0.3961 r_free = 0.3961 target = 0.160166 restraints weight = 5014.138| |-----------------------------------------------------------------------------| r_work (final): 0.3935 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6401 moved from start: 0.2097 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 4239 Z= 0.103 Angle : 0.450 6.973 5754 Z= 0.223 Chirality : 0.036 0.126 691 Planarity : 0.003 0.036 734 Dihedral : 3.087 11.329 605 Min Nonbonded Distance : 2.586 Molprobity Statistics. All-atom Clashscore : 3.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.40 % Favored : 96.60 % Rotamer: Outliers : 1.18 % Allowed : 13.65 % Favored : 85.18 % 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: 1.27 (0.37), residues: 559 helix: 2.35 (0.29), residues: 334 sheet: -1.04 (1.29), residues: 15 loop : -1.64 (0.39), residues: 210 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 565 HIS 0.002 0.000 HIS A 498 PHE 0.017 0.001 PHE A 317 TYR 0.014 0.001 TYR A 207 ARG 0.002 0.000 ARG A 242 Details of bonding type rmsd hydrogen bonds : bond 0.05268 ( 228) hydrogen bonds : angle 3.27500 ( 678) covalent geometry : bond 0.00189 ( 4239) covalent geometry : angle 0.44982 ( 5754) *********************** 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 44 residues out of total 464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 39 time to evaluate : 0.463 Fit side-chains REVERT: A 375 GLU cc_start: 0.3988 (OUTLIER) cc_final: 0.3787 (mt-10) outliers start: 5 outliers final: 3 residues processed: 43 average time/residue: 0.2336 time to fit residues: 12.2356 Evaluate side-chains 41 residues out of total 464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 37 time to evaluate : 0.576 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 375 GLU Chi-restraints excluded: chain A residue 459 LEU 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 7 optimal weight: 0.4980 chunk 21 optimal weight: 0.0870 chunk 24 optimal weight: 0.5980 chunk 1 optimal weight: 0.6980 chunk 42 optimal weight: 0.8980 chunk 45 optimal weight: 0.0980 chunk 11 optimal weight: 0.2980 chunk 33 optimal weight: 2.9990 chunk 16 optimal weight: 0.0970 chunk 52 optimal weight: 1.9990 chunk 19 optimal weight: 0.9990 overall best weight: 0.2156 ------------------------------------------------------------------------------- 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 = 0.4179 r_free = 0.4179 target = 0.179815 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3967 r_free = 0.3967 target = 0.160611 restraints weight = 6178.347| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 58)----------------| | r_work = 0.3939 r_free = 0.3939 target = 0.158274 restraints weight = 7988.550| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3916 r_free = 0.3916 target = 0.156390 restraints weight = 5365.672| |-----------------------------------------------------------------------------| r_work (final): 0.3903 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6436 moved from start: 0.2107 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 4239 Z= 0.115 Angle : 0.460 7.173 5754 Z= 0.228 Chirality : 0.037 0.126 691 Planarity : 0.003 0.037 734 Dihedral : 3.029 11.534 605 Min Nonbonded Distance : 2.583 Molprobity Statistics. All-atom Clashscore : 3.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.76 % Favored : 96.24 % Rotamer: Outliers : 1.88 % Allowed : 14.12 % Favored : 84.00 % 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: 1.31 (0.37), residues: 559 helix: 2.46 (0.29), residues: 330 sheet: -1.38 (1.64), residues: 10 loop : -1.67 (0.38), residues: 219 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 565 HIS 0.003 0.000 HIS A 498 PHE 0.012 0.001 PHE A 317 TYR 0.013 0.001 TYR A 207 ARG 0.002 0.000 ARG A 242 Details of bonding type rmsd hydrogen bonds : bond 0.05849 ( 228) hydrogen bonds : angle 3.29359 ( 678) covalent geometry : bond 0.00222 ( 4239) covalent geometry : angle 0.46026 ( 5754) *********************** 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 51 residues out of total 464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 43 time to evaluate : 0.417 Fit side-chains REVERT: A 375 GLU cc_start: 0.4156 (OUTLIER) cc_final: 0.3823 (mt-10) outliers start: 8 outliers final: 4 residues processed: 49 average time/residue: 0.2176 time to fit residues: 13.0427 Evaluate side-chains 47 residues out of total 464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 42 time to evaluate : 0.410 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 307 MET 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 687 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 3 optimal weight: 0.9990 chunk 6 optimal weight: 0.2980 chunk 41 optimal weight: 0.8980 chunk 2 optimal weight: 0.6980 chunk 5 optimal weight: 0.5980 chunk 10 optimal weight: 0.4980 chunk 31 optimal weight: 0.9990 chunk 43 optimal weight: 1.9990 chunk 14 optimal weight: 0.7980 chunk 45 optimal weight: 1.9990 chunk 7 optimal weight: 0.2980 overall best weight: 0.4780 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4152 r_free = 0.4152 target = 0.177327 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.4012 r_free = 0.4012 target = 0.164718 restraints weight = 5835.579| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3977 r_free = 0.3977 target = 0.161828 restraints weight = 9674.081| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 51)----------------| | r_work = 0.3959 r_free = 0.3959 target = 0.160297 restraints weight = 10322.798| |-----------------------------------------------------------------------------| r_work (final): 0.3966 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6369 moved from start: 0.1991 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= 0.167 Angle : 0.502 7.503 5754 Z= 0.256 Chirality : 0.039 0.131 691 Planarity : 0.003 0.038 734 Dihedral : 3.287 13.619 605 Min Nonbonded Distance : 2.568 Molprobity Statistics. All-atom Clashscore : 3.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.94 % Favored : 96.06 % Rotamer: Outliers : 2.35 % Allowed : 13.88 % 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: 1.02 (0.36), residues: 559 helix: 2.15 (0.29), residues: 331 sheet: -1.47 (1.66), residues: 10 loop : -1.66 (0.39), residues: 218 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 565 HIS 0.004 0.001 HIS A 498 PHE 0.009 0.001 PHE A 619 TYR 0.012 0.001 TYR A 207 ARG 0.002 0.000 ARG A 242 Details of bonding type rmsd hydrogen bonds : bond 0.07850 ( 228) hydrogen bonds : angle 3.68992 ( 678) covalent geometry : bond 0.00356 ( 4239) covalent geometry : angle 0.50213 ( 5754) *********************** 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 54 residues out of total 464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 44 time to evaluate : 0.458 Fit side-chains REVERT: A 187 SER cc_start: 0.7592 (m) cc_final: 0.7192 (p) REVERT: A 375 GLU cc_start: 0.4442 (OUTLIER) cc_final: 0.4214 (mt-10) REVERT: A 443 ILE cc_start: 0.8312 (mm) cc_final: 0.8045 (mt) outliers start: 10 outliers final: 5 residues processed: 51 average time/residue: 0.2027 time to fit residues: 12.8362 Evaluate side-chains 49 residues out of total 464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 43 time to evaluate : 0.455 ------------------------------------------------------------------------------- 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 499 PHE Chi-restraints excluded: chain A residue 648 LEU Chi-restraints excluded: chain A residue 687 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 26 optimal weight: 0.9980 chunk 8 optimal weight: 0.8980 chunk 40 optimal weight: 0.0040 chunk 16 optimal weight: 0.8980 chunk 24 optimal weight: 0.7980 chunk 1 optimal weight: 0.1980 chunk 30 optimal weight: 0.5980 chunk 0 optimal weight: 1.9990 chunk 2 optimal weight: 0.5980 chunk 14 optimal weight: 1.9990 chunk 55 optimal weight: 0.5980 overall best weight: 0.3992 ------------------------------------------------------------------------------- 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 = 0.4176 r_free = 0.4176 target = 0.179508 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.4122 r_free = 0.4122 target = 0.174616 restraints weight = 5829.443| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.4102 r_free = 0.4102 target = 0.172885 restraints weight = 8742.821| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.4095 r_free = 0.4095 target = 0.172252 restraints weight = 11994.926| |-----------------------------------------------------------------------------| r_work (final): 0.4095 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6144 moved from start: 0.2054 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= 0.150 Angle : 0.491 7.778 5754 Z= 0.248 Chirality : 0.038 0.127 691 Planarity : 0.003 0.038 734 Dihedral : 3.238 13.430 605 Min Nonbonded Distance : 2.576 Molprobity Statistics. All-atom Clashscore : 4.07 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: 0.98 (0.36), residues: 559 helix: 2.17 (0.29), residues: 330 sheet: None (None), residues: 0 loop : -1.78 (0.37), residues: 229 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 0.008 0.001 PHE A 619 TYR 0.011 0.001 TYR A 207 ARG 0.002 0.000 ARG A 295 Details of bonding type rmsd hydrogen bonds : bond 0.07260 ( 228) hydrogen bonds : angle 3.60547 ( 678) covalent geometry : bond 0.00314 ( 4239) covalent geometry : angle 0.49063 ( 5754) *********************** 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 54 residues out of total 464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 45 time to evaluate : 0.467 Fit side-chains REVERT: A 362 ARG cc_start: 0.5621 (mmt180) cc_final: 0.2614 (mtt180) REVERT: A 375 GLU cc_start: 0.4353 (OUTLIER) cc_final: 0.4120 (mt-10) REVERT: A 443 ILE cc_start: 0.8305 (mm) cc_final: 0.8059 (mt) outliers start: 9 outliers final: 5 residues processed: 51 average time/residue: 0.2338 time to fit residues: 14.4485 Evaluate side-chains 52 residues out of total 464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 46 time to evaluate : 0.424 ------------------------------------------------------------------------------- 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 499 PHE 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 19 optimal weight: 0.5980 chunk 54 optimal weight: 2.9990 chunk 24 optimal weight: 0.5980 chunk 11 optimal weight: 0.9980 chunk 38 optimal weight: 0.8980 chunk 53 optimal weight: 7.9990 chunk 48 optimal weight: 0.9980 chunk 28 optimal weight: 0.5980 chunk 29 optimal weight: 0.5980 chunk 2 optimal weight: 0.2980 chunk 31 optimal weight: 0.6980 overall best weight: 0.5380 ------------------------------------------------------------------------------- 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 = 0.4152 r_free = 0.4152 target = 0.177290 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.4005 r_free = 0.4005 target = 0.164164 restraints weight = 5809.768| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.3968 r_free = 0.3968 target = 0.161138 restraints weight = 9328.832| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 56)----------------| | r_work = 0.3963 r_free = 0.3963 target = 0.160751 restraints weight = 9139.962| |-----------------------------------------------------------------------------| r_work (final): 0.3962 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6370 moved from start: 0.2112 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= 0.180 Angle : 0.519 7.812 5754 Z= 0.266 Chirality : 0.040 0.204 691 Planarity : 0.003 0.038 734 Dihedral : 3.385 15.577 605 Min Nonbonded Distance : 2.569 Molprobity Statistics. All-atom Clashscore : 4.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.11 % Favored : 95.89 % Rotamer: Outliers : 1.88 % Allowed : 14.82 % Favored : 83.29 % 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: 0.83 (0.36), residues: 559 helix: 2.01 (0.29), residues: 331 sheet: None (None), residues: 0 loop : -1.78 (0.38), residues: 228 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 0.009 0.001 PHE A 619 TYR 0.012 0.002 TYR A 207 ARG 0.004 0.000 ARG A 542 Details of bonding type rmsd hydrogen bonds : bond 0.08051 ( 228) hydrogen bonds : angle 3.78039 ( 678) covalent geometry : bond 0.00395 ( 4239) covalent geometry : angle 0.51935 ( 5754) *********************** 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 51 residues out of total 464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 43 time to evaluate : 0.464 Fit side-chains REVERT: A 362 ARG cc_start: 0.5605 (mmt180) cc_final: 0.2418 (mtt180) REVERT: A 375 GLU cc_start: 0.4498 (OUTLIER) cc_final: 0.4273 (mt-10) REVERT: A 443 ILE cc_start: 0.8295 (mm) cc_final: 0.8030 (mt) outliers start: 8 outliers final: 5 residues processed: 49 average time/residue: 0.2412 time to fit residues: 14.3202 Evaluate side-chains 48 residues out of total 464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 42 time to evaluate : 0.441 ------------------------------------------------------------------------------- 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 499 PHE 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 55 optimal weight: 0.9980 chunk 3 optimal weight: 0.6980 chunk 32 optimal weight: 0.0070 chunk 53 optimal weight: 7.9990 chunk 34 optimal weight: 0.7980 chunk 15 optimal weight: 0.0870 chunk 40 optimal weight: 0.0670 chunk 41 optimal weight: 1.9990 chunk 45 optimal weight: 5.9990 chunk 6 optimal weight: 0.6980 chunk 30 optimal weight: 1.9990 overall best weight: 0.3114 ------------------------------------------------------------------------------- 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 = 0.4182 r_free = 0.4182 target = 0.180224 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.4041 r_free = 0.4041 target = 0.167344 restraints weight = 5883.560| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 62)----------------| | r_work = 0.4006 r_free = 0.4006 target = 0.164486 restraints weight = 8549.908| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.4006 r_free = 0.4006 target = 0.164486 restraints weight = 8670.719| |-----------------------------------------------------------------------------| r_work (final): 0.4009 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6305 moved from start: 0.2188 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= 0.137 Angle : 0.491 7.765 5754 Z= 0.248 Chirality : 0.038 0.162 691 Planarity : 0.003 0.037 734 Dihedral : 3.216 13.367 605 Min Nonbonded Distance : 2.565 Molprobity Statistics. All-atom Clashscore : 4.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.58 % Favored : 96.42 % Rotamer: Outliers : 1.65 % Allowed : 15.76 % 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: 0.97 (0.36), residues: 559 helix: 2.17 (0.29), residues: 334 sheet: None (None), residues: 0 loop : -1.87 (0.37), 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 0.008 0.001 PHE A 619 TYR 0.010 0.001 TYR A 207 ARG 0.004 0.000 ARG A 542 Details of bonding type rmsd hydrogen bonds : bond 0.06913 ( 228) hydrogen bonds : angle 3.57224 ( 678) covalent geometry : bond 0.00276 ( 4239) covalent geometry : angle 0.49069 ( 5754) *********************** 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 54 residues out of total 464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 47 time to evaluate : 0.455 Fit side-chains REVERT: A 362 ARG cc_start: 0.5670 (mmt180) cc_final: 0.3055 (mmt180) REVERT: A 375 GLU cc_start: 0.4401 (OUTLIER) cc_final: 0.4108 (mt-10) REVERT: A 443 ILE cc_start: 0.8223 (mm) cc_final: 0.7981 (mt) outliers start: 7 outliers final: 6 residues processed: 52 average time/residue: 0.2456 time to fit residues: 15.2708 Evaluate side-chains 54 residues out of total 464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 47 time to evaluate : 0.401 ------------------------------------------------------------------------------- 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 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 21 optimal weight: 0.6980 chunk 46 optimal weight: 2.9990 chunk 13 optimal weight: 0.8980 chunk 42 optimal weight: 0.0020 chunk 44 optimal weight: 0.4980 chunk 55 optimal weight: 0.3980 chunk 53 optimal weight: 0.6980 chunk 25 optimal weight: 0.9980 chunk 4 optimal weight: 0.3980 chunk 14 optimal weight: 1.9990 chunk 11 optimal weight: 0.3980 overall best weight: 0.3388 ------------------------------------------------------------------------------- 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 = 0.4181 r_free = 0.4181 target = 0.180078 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.4036 r_free = 0.4036 target = 0.166896 restraints weight = 5858.293| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 103)---------------| | r_work = 0.4003 r_free = 0.4003 target = 0.164116 restraints weight = 8400.667| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 97)----------------| | r_work = 0.3987 r_free = 0.3987 target = 0.162709 restraints weight = 9877.267| |-----------------------------------------------------------------------------| r_work (final): 0.3984 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6340 moved from start: 0.2235 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 4239 Z= 0.141 Angle : 0.498 7.759 5754 Z= 0.250 Chirality : 0.038 0.149 691 Planarity : 0.003 0.038 734 Dihedral : 3.205 13.443 605 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 4.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.11 % Favored : 95.89 % Rotamer: Outliers : 1.88 % Allowed : 15.76 % Favored : 82.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.02 (0.36), residues: 559 helix: 2.22 (0.29), residues: 334 sheet: None (None), residues: 0 loop : -1.86 (0.38), 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 0.008 0.001 PHE A 619 TYR 0.010 0.001 TYR A 207 ARG 0.004 0.000 ARG A 542 Details of bonding type rmsd hydrogen bonds : bond 0.07014 ( 228) hydrogen bonds : angle 3.56644 ( 678) covalent geometry : bond 0.00289 ( 4239) covalent geometry : angle 0.49836 ( 5754) ********************** 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 54 residues out of total 464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 46 time to evaluate : 0.421 Fit side-chains REVERT: A 362 ARG cc_start: 0.5776 (mmt180) cc_final: 0.3155 (mmt180) REVERT: A 375 GLU cc_start: 0.4391 (OUTLIER) cc_final: 0.4088 (mt-10) REVERT: A 443 ILE cc_start: 0.8225 (mm) cc_final: 0.7983 (mt) REVERT: A 501 TYR cc_start: 0.6717 (OUTLIER) cc_final: 0.6213 (m-80) outliers start: 8 outliers final: 6 residues processed: 52 average time/residue: 0.2360 time to fit residues: 14.6679 Evaluate side-chains 54 residues out of total 464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 46 time to evaluate : 0.417 ------------------------------------------------------------------------------- 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 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 1 optimal weight: 0.3980 chunk 22 optimal weight: 0.0980 chunk 10 optimal weight: 0.7980 chunk 31 optimal weight: 0.0770 chunk 42 optimal weight: 0.9990 chunk 25 optimal weight: 0.8980 chunk 16 optimal weight: 0.9980 chunk 51 optimal weight: 0.8980 chunk 37 optimal weight: 2.9990 chunk 50 optimal weight: 5.9990 chunk 41 optimal weight: 0.6980 overall best weight: 0.4138 ------------------------------------------------------------------------------- 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 = 0.4170 r_free = 0.4170 target = 0.179140 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.4024 r_free = 0.4024 target = 0.165852 restraints weight = 5799.302| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 63)----------------| | r_work = 0.3988 r_free = 0.3988 target = 0.162866 restraints weight = 8768.556| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 71)----------------| | r_work = 0.3981 r_free = 0.3981 target = 0.162295 restraints weight = 10257.875| |-----------------------------------------------------------------------------| r_work (final): 0.3973 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6348 moved from start: 0.2259 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= 0.156 Angle : 0.508 8.489 5754 Z= 0.257 Chirality : 0.039 0.153 691 Planarity : 0.003 0.038 734 Dihedral : 3.277 14.768 605 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 4.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.76 % Favored : 96.24 % Rotamer: Outliers : 2.59 % Allowed : 15.06 % Favored : 82.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.02 (0.36), residues: 559 helix: 2.20 (0.28), residues: 331 sheet: None (None), residues: 0 loop : -1.75 (0.38), residues: 228 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 0.009 0.001 PHE A 619 TYR 0.011 0.001 TYR A 207 ARG 0.004 0.000 ARG A 542 Details of bonding type rmsd hydrogen bonds : bond 0.07451 ( 228) hydrogen bonds : angle 3.64907 ( 678) covalent geometry : bond 0.00329 ( 4239) covalent geometry : angle 0.50816 ( 5754) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1886.71 seconds wall clock time: 33 minutes 30.69 seconds (2010.69 seconds total)