Starting phenix.real_space_refine on Tue Feb 11 06:33:04 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9bum_44912/02_2025/9bum_44912.cif Found real_map, /net/cci-nas-00/data/ceres_data/9bum_44912/02_2025/9bum_44912.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.63 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9bum_44912/02_2025/9bum_44912.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9bum_44912/02_2025/9bum_44912.map" model { file = "/net/cci-nas-00/data/ceres_data/9bum_44912/02_2025/9bum_44912.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9bum_44912/02_2025/9bum_44912.cif" } resolution = 3.63 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= 0.003 sd= 0.047 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 24 5.16 5 C 2883 2.51 5 N 736 2.21 5 O 772 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 45 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib" Total number of atoms: 4415 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 4359 Number of conformers: 1 Conformer: "" Number of residues, atoms: 538, 4359 Classifications: {'peptide': 538} Incomplete info: {'truncation_to_alanine': 17} Link IDs: {'PTRANS': 31, 'TRANS': 506} Chain breaks: 3 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 93 Unresolved non-hydrogen angles: 117 Unresolved non-hydrogen dihedrals: 87 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'PHE:plan': 4, 'GLU:plan': 1, 'ARG:plan': 5, 'TRP:plan': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 67 Chain: "d" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'CLR': 1} Classifications: {'undetermined': 1} Time building chain proxies: 3.47, per 1000 atoms: 0.79 Number of scatterers: 4415 At special positions: 0 Unit cell: (74.7, 85.49, 107.07, 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 24 16.00 O 772 8.00 N 736 7.00 C 2883 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS A 99 " - pdb=" SG CYS A 450 " distance=2.02 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 Links applied BETA1-4 " NAG d 1 " - " NAG d 2 " NAG-ASN " NAG d 1 " - " ASN A 570 " Time building additional restraints: 1.16 Conformation dependent library (CDL) restraints added in 530.9 milliseconds 1060 Ramachandran restraints generated. 530 Oldfield, 0 Emsley, 530 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1024 Finding SS restraints... Secondary structure from input PDB file: 26 helices and 4 sheets defined 47.0% alpha, 9.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.50 Creating SS restraints... Processing helix chain 'A' and resid 48 through 56 Processing helix chain 'A' and resid 61 through 73 removed outlier: 3.605A pdb=" N ALA A 65 " --> pdb=" O PRO A 61 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N PHE A 67 " --> pdb=" O SER A 63 " (cutoff:3.500A) Processing helix chain 'A' and resid 77 through 82 removed outlier: 3.744A pdb=" N GLN A 81 " --> pdb=" O LEU A 77 " (cutoff:3.500A) Processing helix chain 'A' and resid 84 through 88 removed outlier: 4.230A pdb=" N LEU A 88 " --> pdb=" O LEU A 85 " (cutoff:3.500A) Processing helix chain 'A' and resid 111 through 132 removed outlier: 4.336A pdb=" N LEU A 117 " --> pdb=" O ASP A 113 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N TYR A 119 " --> pdb=" O MET A 115 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N MET A 130 " --> pdb=" O ALA A 126 " (cutoff:3.500A) Processing helix chain 'A' and resid 134 through 139 Processing helix chain 'A' and resid 139 through 144 Processing helix chain 'A' and resid 149 through 157 removed outlier: 3.901A pdb=" N ASP A 153 " --> pdb=" O PHE A 150 " (cutoff:3.500A) removed outlier: 5.546A pdb=" N LYS A 154 " --> pdb=" O LEU A 151 " (cutoff:3.500A) removed outlier: 6.595A pdb=" N THR A 155 " --> pdb=" O LEU A 152 " (cutoff:3.500A) Processing helix chain 'A' and resid 162 through 174 removed outlier: 3.848A pdb=" N PHE A 169 " --> pdb=" O GLY A 165 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N THR A 172 " --> pdb=" O ALA A 168 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N PHE A 173 " --> pdb=" O PHE A 169 " (cutoff:3.500A) Processing helix chain 'A' and resid 175 through 179 removed outlier: 3.816A pdb=" N HIS A 178 " --> pdb=" O ASP A 175 " (cutoff:3.500A) removed outlier: 4.159A pdb=" N TYR A 179 " --> pdb=" O ALA A 176 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 175 through 179' Processing helix chain 'A' and resid 197 through 217 removed outlier: 3.524A pdb=" N VAL A 202 " --> pdb=" O TRP A 198 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N LEU A 203 " --> pdb=" O ASN A 199 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ILE A 207 " --> pdb=" O LEU A 203 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ILE A 209 " --> pdb=" O GLY A 205 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N ALA A 214 " --> pdb=" O VAL A 210 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N GLY A 215 " --> pdb=" O TYR A 211 " (cutoff:3.500A) Processing helix chain 'A' and resid 218 through 220 No H-bonds generated for 'chain 'A' and resid 218 through 220' Processing helix chain 'A' and resid 298 through 306 removed outlier: 3.513A pdb=" N MET A 303 " --> pdb=" O PHE A 299 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N LEU A 304 " --> pdb=" O SER A 300 " (cutoff:3.500A) Processing helix chain 'A' and resid 307 through 310 Processing helix chain 'A' and resid 314 through 318 Processing helix chain 'A' and resid 325 through 329 removed outlier: 3.777A pdb=" N GLN A 329 " --> pdb=" O ARG A 326 " (cutoff:3.500A) Processing helix chain 'A' and resid 357 through 362 removed outlier: 3.684A pdb=" N LEU A 362 " --> pdb=" O LEU A 358 " (cutoff:3.500A) Processing helix chain 'A' and resid 368 through 375 removed outlier: 4.067A pdb=" N GLU A 373 " --> pdb=" O LEU A 369 " (cutoff:3.500A) Processing helix chain 'A' and resid 376 through 380 Processing helix chain 'A' and resid 441 through 455 removed outlier: 4.054A pdb=" N ARG A 453 " --> pdb=" O THR A 449 " (cutoff:3.500A) Processing helix chain 'A' and resid 456 through 459 removed outlier: 3.614A pdb=" N ASN A 459 " --> pdb=" O PRO A 456 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 456 through 459' Processing helix chain 'A' and resid 506 through 510 Processing helix chain 'A' and resid 511 through 523 removed outlier: 4.915A pdb=" N GLN A 517 " --> pdb=" O ARG A 513 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N GLU A 518 " --> pdb=" O ALA A 514 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N SER A 522 " --> pdb=" O GLU A 518 " (cutoff:3.500A) Processing helix chain 'A' and resid 605 through 614 Processing helix chain 'A' and resid 677 through 708 removed outlier: 3.756A pdb=" N PHE A 681 " --> pdb=" O PHE A 677 " (cutoff:3.500A) removed outlier: 4.606A pdb=" N PHE A 682 " --> pdb=" O HIS A 678 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N CYS A 700 " --> pdb=" O PHE A 696 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N ASN A 705 " --> pdb=" O ILE A 701 " (cutoff:3.500A) removed outlier: 4.482A pdb=" N LEU A 706 " --> pdb=" O SER A 702 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N ILE A 707 " --> pdb=" O LEU A 703 " (cutoff:3.500A) Processing helix chain 'A' and resid 712 through 725 removed outlier: 3.850A pdb=" N GLN A 718 " --> pdb=" O GLU A 714 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N THR A 721 " --> pdb=" O ALA A 717 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N ALA A 723 " --> pdb=" O GLU A 719 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N LEU A 725 " --> pdb=" O THR A 721 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 58 through 59 Processing sheet with id=AA2, first strand: chain 'A' and resid 423 through 426 removed outlier: 4.241A pdb=" N ILE A 413 " --> pdb=" O LEU A 426 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 470 through 471 removed outlier: 3.576A pdb=" N GLN A 479 " --> pdb=" O VAL A 471 " (cutoff:3.500A) removed outlier: 4.486A pdb=" N ARG A 480 " --> pdb=" O ALA A 533 " (cutoff:3.500A) removed outlier: 7.107A pdb=" N MET A 600 " --> pdb=" O LEU A 555 " (cutoff:3.500A) removed outlier: 5.706A pdb=" N LEU A 555 " --> pdb=" O MET A 600 " (cutoff:3.500A) removed outlier: 6.708A pdb=" N VAL A 602 " --> pdb=" O ILE A 553 " (cutoff:3.500A) removed outlier: 5.351A pdb=" N ILE A 553 " --> pdb=" O VAL A 602 " (cutoff:3.500A) removed outlier: 4.283A pdb=" N THR A 551 " --> pdb=" O LEU A 581 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 539 through 543 removed outlier: 3.655A pdb=" N VAL A 589 " --> pdb=" O LEU A 540 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N LEU A 564 " --> pdb=" O LYS A 569 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N LYS A 569 " --> pdb=" O LEU A 564 " (cutoff:3.500A) 152 hydrogen bonds defined for protein. 405 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: 1.26 Time building geometry restraints manager: 1.35 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: 1362 1.34 - 1.46: 950 1.46 - 1.58: 2190 1.58 - 1.69: 0 1.69 - 1.81: 39 Bond restraints: 4541 Sorted by residual: bond pdb=" C LYS A 412 " pdb=" N ILE A 413 " ideal model delta sigma weight residual 1.329 1.275 0.054 1.17e-02 7.31e+03 2.14e+01 bond pdb=" C SER A 307 " pdb=" N PRO A 308 " ideal model delta sigma weight residual 1.334 1.365 -0.032 8.40e-03 1.42e+04 1.42e+01 bond pdb=" C1 NAG d 2 " pdb=" O5 NAG d 2 " ideal model delta sigma weight residual 1.406 1.444 -0.038 2.00e-02 2.50e+03 3.60e+00 bond pdb=" CB PRO A 145 " pdb=" CG PRO A 145 " ideal model delta sigma weight residual 1.492 1.408 0.084 5.00e-02 4.00e+02 2.85e+00 bond pdb=" C LEU A 144 " pdb=" N PRO A 145 " ideal model delta sigma weight residual 1.331 1.344 -0.013 7.90e-03 1.60e+04 2.55e+00 ... (remaining 4536 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.07: 5910 2.07 - 4.14: 224 4.14 - 6.21: 39 6.21 - 8.27: 12 8.27 - 10.34: 2 Bond angle restraints: 6187 Sorted by residual: angle pdb=" N PRO A 676 " pdb=" CA PRO A 676 " pdb=" CB PRO A 676 " ideal model delta sigma weight residual 103.00 110.07 -7.07 1.10e+00 8.26e-01 4.13e+01 angle pdb=" N HIS A 408 " pdb=" CA HIS A 408 " pdb=" C HIS A 408 " ideal model delta sigma weight residual 111.02 117.82 -6.80 1.25e+00 6.40e-01 2.96e+01 angle pdb=" C ASP A 78 " pdb=" N ILE A 79 " pdb=" CA ILE A 79 " ideal model delta sigma weight residual 120.24 123.55 -3.31 6.30e-01 2.52e+00 2.77e+01 angle pdb=" C LEU A 454 " pdb=" N LEU A 455 " pdb=" CA LEU A 455 " ideal model delta sigma weight residual 120.06 124.80 -4.74 1.19e+00 7.06e-01 1.59e+01 angle pdb=" N VAL A 430 " pdb=" CA VAL A 430 " pdb=" C VAL A 430 " ideal model delta sigma weight residual 110.30 114.09 -3.79 9.70e-01 1.06e+00 1.52e+01 ... (remaining 6182 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.01: 2403 16.01 - 32.01: 269 32.01 - 48.01: 64 48.01 - 64.02: 12 64.02 - 80.02: 4 Dihedral angle restraints: 2752 sinusoidal: 1163 harmonic: 1589 Sorted by residual: dihedral pdb=" CA SER A 407 " pdb=" C SER A 407 " pdb=" N HIS A 408 " pdb=" CA HIS A 408 " ideal model delta harmonic sigma weight residual 180.00 152.75 27.25 0 5.00e+00 4.00e-02 2.97e+01 dihedral pdb=" CA HIS A 410 " pdb=" C HIS A 410 " pdb=" N VAL A 411 " pdb=" CA VAL A 411 " ideal model delta harmonic sigma weight residual 180.00 153.53 26.47 0 5.00e+00 4.00e-02 2.80e+01 dihedral pdb=" CA CYS A 134 " pdb=" C CYS A 134 " pdb=" N TYR A 135 " pdb=" CA TYR A 135 " ideal model delta harmonic sigma weight residual -180.00 -153.68 -26.32 0 5.00e+00 4.00e-02 2.77e+01 ... (remaining 2749 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.053: 510 0.053 - 0.106: 134 0.106 - 0.159: 35 0.159 - 0.212: 7 0.212 - 0.264: 2 Chirality restraints: 688 Sorted by residual: chirality pdb=" CA TRP A 399 " pdb=" N TRP A 399 " pdb=" C TRP A 399 " pdb=" CB TRP A 399 " both_signs ideal model delta sigma weight residual False 2.51 2.25 0.26 2.00e-01 2.50e+01 1.75e+00 chirality pdb=" CA PRO A 676 " pdb=" N PRO A 676 " pdb=" C PRO A 676 " pdb=" CB PRO A 676 " both_signs ideal model delta sigma weight residual False 2.72 2.47 0.25 2.00e-01 2.50e+01 1.52e+00 chirality pdb=" C13 CLR A 801 " pdb=" C12 CLR A 801 " pdb=" C14 CLR A 801 " pdb=" C17 CLR A 801 " both_signs ideal model delta sigma weight residual False -2.93 -2.73 -0.21 2.00e-01 2.50e+01 1.05e+00 ... (remaining 685 not shown) Planarity restraints: 772 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C SER A 307 " -0.061 5.00e-02 4.00e+02 9.28e-02 1.38e+01 pdb=" N PRO A 308 " 0.160 5.00e-02 4.00e+02 pdb=" CA PRO A 308 " -0.048 5.00e-02 4.00e+02 pdb=" CD PRO A 308 " -0.052 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA GLY A 418 " -0.013 2.00e-02 2.50e+03 2.69e-02 7.25e+00 pdb=" C GLY A 418 " 0.047 2.00e-02 2.50e+03 pdb=" O GLY A 418 " -0.018 2.00e-02 2.50e+03 pdb=" N ARG A 419 " -0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU A 455 " -0.042 5.00e-02 4.00e+02 6.36e-02 6.47e+00 pdb=" N PRO A 456 " 0.110 5.00e-02 4.00e+02 pdb=" CA PRO A 456 " -0.032 5.00e-02 4.00e+02 pdb=" CD PRO A 456 " -0.036 5.00e-02 4.00e+02 ... (remaining 769 not shown) Histogram of nonbonded interaction distances: 2.28 - 2.80: 1271 2.80 - 3.33: 3772 3.33 - 3.85: 7334 3.85 - 4.38: 8707 4.38 - 4.90: 14309 Nonbonded interactions: 35393 Sorted by model distance: nonbonded pdb=" O GLY A 363 " pdb=" OG1 THR A 367 " model vdw 2.278 3.040 nonbonded pdb=" O SER A 695 " pdb=" OG1 THR A 699 " model vdw 2.316 3.040 nonbonded pdb=" OD1 ASP A 153 " pdb=" OG1 THR A 155 " model vdw 2.322 3.040 nonbonded pdb=" O LYS A 318 " pdb=" OG SER A 321 " model vdw 2.335 3.040 nonbonded pdb=" O TYR A 116 " pdb=" OG1 THR A 120 " model vdw 2.339 3.040 ... (remaining 35388 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== 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: 1.840 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.170 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 16.600 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:2.940 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.700 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7676 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.084 4541 Z= 0.322 Angle : 0.972 10.343 6187 Z= 0.544 Chirality : 0.055 0.264 688 Planarity : 0.009 0.093 771 Dihedral : 14.420 80.023 1725 Min Nonbonded Distance : 2.278 Molprobity Statistics. All-atom Clashscore : 5.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.34 % Favored : 95.66 % Rotamer: Outliers : 0.43 % Allowed : 5.33 % Favored : 94.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.76 (0.28), residues: 530 helix: -4.50 (0.14), residues: 233 sheet: -2.50 (0.51), residues: 75 loop : -1.51 (0.38), residues: 222 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 198 HIS 0.005 0.001 HIS A 160 PHE 0.013 0.002 PHE A 382 TYR 0.027 0.002 TYR A 164 ARG 0.009 0.000 ARG A 419 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1060 Ramachandran restraints generated. 530 Oldfield, 0 Emsley, 530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1060 Ramachandran restraints generated. 530 Oldfield, 0 Emsley, 530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 486 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 87 time to evaluate : 0.472 Fit side-chains revert: symmetry clash REVERT: A 115 MET cc_start: 0.8524 (mmm) cc_final: 0.8077 (tpt) REVERT: A 150 PHE cc_start: 0.8386 (t80) cc_final: 0.8178 (t80) REVERT: A 180 TRP cc_start: 0.8292 (t60) cc_final: 0.8073 (t60) REVERT: A 361 GLN cc_start: 0.7283 (pt0) cc_final: 0.6482 (tp40) REVERT: A 476 ARG cc_start: 0.8370 (mpt-90) cc_final: 0.8076 (mmt90) REVERT: A 507 MET cc_start: 0.4511 (pmm) cc_final: 0.4187 (pmm) REVERT: A 546 GLU cc_start: 0.7997 (mm-30) cc_final: 0.7729 (mm-30) outliers start: 2 outliers final: 0 residues processed: 89 average time/residue: 0.1954 time to fit residues: 21.4255 Evaluate side-chains 65 residues out of total 486 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 65 time to evaluate : 0.529 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 44 optimal weight: 9.9990 chunk 40 optimal weight: 0.5980 chunk 22 optimal weight: 5.9990 chunk 13 optimal weight: 2.9990 chunk 27 optimal weight: 7.9990 chunk 21 optimal weight: 5.9990 chunk 41 optimal weight: 0.8980 chunk 16 optimal weight: 0.6980 chunk 25 optimal weight: 2.9990 chunk 30 optimal weight: 0.4980 chunk 48 optimal weight: 0.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 81 GLN A 159 ASN A 170 GLN A 329 GLN A 381 HIS A 433 GLN A 446 GLN A 464 GLN A 478 GLN A 539 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4137 r_free = 0.4137 target = 0.163946 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3754 r_free = 0.3754 target = 0.128029 restraints weight = 6883.570| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3737 r_free = 0.3737 target = 0.128367 restraints weight = 4289.933| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3751 r_free = 0.3751 target = 0.130167 restraints weight = 3804.787| |-----------------------------------------------------------------------------| r_work (final): 0.3750 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7646 moved from start: 0.2128 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 4541 Z= 0.205 Angle : 0.679 8.965 6187 Z= 0.339 Chirality : 0.042 0.168 688 Planarity : 0.006 0.055 771 Dihedral : 7.051 56.558 703 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 9.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.34 % Favored : 95.66 % Rotamer: Outliers : 1.49 % Allowed : 11.09 % Favored : 87.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.17 (0.33), residues: 530 helix: -2.78 (0.26), residues: 240 sheet: -2.31 (0.50), residues: 75 loop : -0.84 (0.42), residues: 215 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 147 HIS 0.004 0.001 HIS A 160 PHE 0.018 0.002 PHE A 696 TYR 0.012 0.002 TYR A 586 ARG 0.010 0.001 ARG A 419 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1060 Ramachandran restraints generated. 530 Oldfield, 0 Emsley, 530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1060 Ramachandran restraints generated. 530 Oldfield, 0 Emsley, 530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 486 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 72 time to evaluate : 0.551 Fit side-chains revert: symmetry clash REVERT: A 361 GLN cc_start: 0.7228 (pt0) cc_final: 0.6559 (tp40) REVERT: A 507 MET cc_start: 0.4708 (pmm) cc_final: 0.4418 (pmm) REVERT: A 588 LYS cc_start: 0.8793 (mttt) cc_final: 0.8558 (mtmt) REVERT: A 689 LEU cc_start: 0.8472 (tt) cc_final: 0.7933 (mt) outliers start: 7 outliers final: 4 residues processed: 73 average time/residue: 0.1403 time to fit residues: 14.0491 Evaluate side-chains 66 residues out of total 486 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 62 time to evaluate : 0.475 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 319 LEU Chi-restraints excluded: chain A residue 368 LEU Chi-restraints excluded: chain A residue 530 VAL Chi-restraints excluded: chain A residue 573 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 34 optimal weight: 3.9990 chunk 35 optimal weight: 0.6980 chunk 49 optimal weight: 6.9990 chunk 30 optimal weight: 0.9980 chunk 37 optimal weight: 1.9990 chunk 24 optimal weight: 0.6980 chunk 3 optimal weight: 1.9990 chunk 5 optimal weight: 1.9990 chunk 33 optimal weight: 0.8980 chunk 20 optimal weight: 5.9990 chunk 9 optimal weight: 0.5980 overall best weight: 0.7780 ------------------------------------------------------------------------------- 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 = 0.4130 r_free = 0.4130 target = 0.163710 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3742 r_free = 0.3742 target = 0.127152 restraints weight = 6868.771| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3719 r_free = 0.3719 target = 0.127079 restraints weight = 4463.196| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3735 r_free = 0.3735 target = 0.129020 restraints weight = 3983.444| |-----------------------------------------------------------------------------| r_work (final): 0.3739 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7661 moved from start: 0.2445 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 4541 Z= 0.194 Angle : 0.632 8.112 6187 Z= 0.312 Chirality : 0.042 0.136 688 Planarity : 0.005 0.053 771 Dihedral : 6.466 59.148 703 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 9.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.15 % Favored : 95.85 % Rotamer: Outliers : 1.71 % Allowed : 13.65 % Favored : 84.65 % 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: -2.28 (0.34), residues: 530 helix: -1.82 (0.31), residues: 239 sheet: -2.21 (0.50), residues: 75 loop : -0.53 (0.42), residues: 216 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 147 HIS 0.004 0.001 HIS A 160 PHE 0.015 0.001 PHE A 431 TYR 0.017 0.002 TYR A 603 ARG 0.012 0.001 ARG A 694 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1060 Ramachandran restraints generated. 530 Oldfield, 0 Emsley, 530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1060 Ramachandran restraints generated. 530 Oldfield, 0 Emsley, 530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 486 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 65 time to evaluate : 0.512 Fit side-chains revert: symmetry clash REVERT: A 115 MET cc_start: 0.8263 (mmm) cc_final: 0.7745 (tpp) REVERT: A 361 GLN cc_start: 0.7292 (pt0) cc_final: 0.6606 (tp40) REVERT: A 507 MET cc_start: 0.4713 (pmm) cc_final: 0.4501 (pmm) REVERT: A 689 LEU cc_start: 0.8430 (tt) cc_final: 0.7814 (mt) outliers start: 8 outliers final: 6 residues processed: 67 average time/residue: 0.1166 time to fit residues: 11.1020 Evaluate side-chains 67 residues out of total 486 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 61 time to evaluate : 0.528 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 319 LEU Chi-restraints excluded: chain A residue 367 THR Chi-restraints excluded: chain A residue 368 LEU Chi-restraints excluded: chain A residue 401 MET Chi-restraints excluded: chain A residue 530 VAL Chi-restraints excluded: chain A residue 573 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 42 optimal weight: 1.9990 chunk 34 optimal weight: 1.9990 chunk 31 optimal weight: 0.6980 chunk 21 optimal weight: 6.9990 chunk 7 optimal weight: 0.6980 chunk 11 optimal weight: 0.6980 chunk 10 optimal weight: 0.8980 chunk 41 optimal weight: 7.9990 chunk 3 optimal weight: 0.0270 chunk 24 optimal weight: 0.5980 chunk 38 optimal weight: 0.6980 overall best weight: 0.5438 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 199 ASN A 410 HIS A 715 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4138 r_free = 0.4138 target = 0.164781 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3747 r_free = 0.3747 target = 0.127779 restraints weight = 6885.185| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3724 r_free = 0.3724 target = 0.127547 restraints weight = 4441.814| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3738 r_free = 0.3738 target = 0.129516 restraints weight = 3990.677| |-----------------------------------------------------------------------------| r_work (final): 0.3743 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7632 moved from start: 0.2715 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 4541 Z= 0.157 Angle : 0.585 9.175 6187 Z= 0.287 Chirality : 0.041 0.131 688 Planarity : 0.005 0.054 771 Dihedral : 5.944 54.383 703 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 9.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.53 % Favored : 95.47 % Rotamer: Outliers : 2.13 % Allowed : 15.57 % Favored : 82.30 % 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: -1.62 (0.36), residues: 530 helix: -1.20 (0.33), residues: 235 sheet: -1.98 (0.50), residues: 75 loop : -0.28 (0.43), residues: 220 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 198 HIS 0.004 0.001 HIS A 160 PHE 0.015 0.001 PHE A 431 TYR 0.017 0.001 TYR A 603 ARG 0.006 0.000 ARG A 694 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1060 Ramachandran restraints generated. 530 Oldfield, 0 Emsley, 530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1060 Ramachandran restraints generated. 530 Oldfield, 0 Emsley, 530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 486 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 69 time to evaluate : 0.495 Fit side-chains revert: symmetry clash REVERT: A 127 LEU cc_start: 0.7112 (OUTLIER) cc_final: 0.6860 (mp) REVERT: A 361 GLN cc_start: 0.7276 (pt0) cc_final: 0.6626 (tp40) REVERT: A 417 ASP cc_start: 0.7120 (t0) cc_final: 0.6900 (t0) REVERT: A 507 MET cc_start: 0.4737 (pmm) cc_final: 0.4527 (pmm) REVERT: A 600 MET cc_start: 0.6896 (ptt) cc_final: 0.6658 (ptt) outliers start: 10 outliers final: 7 residues processed: 72 average time/residue: 0.1129 time to fit residues: 11.5463 Evaluate side-chains 69 residues out of total 486 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 61 time to evaluate : 0.539 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 127 LEU Chi-restraints excluded: chain A residue 319 LEU Chi-restraints excluded: chain A residue 367 THR Chi-restraints excluded: chain A residue 368 LEU Chi-restraints excluded: chain A residue 401 MET Chi-restraints excluded: chain A residue 410 HIS Chi-restraints excluded: chain A residue 530 VAL Chi-restraints excluded: chain A residue 573 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 27 optimal weight: 0.0470 chunk 2 optimal weight: 2.9990 chunk 4 optimal weight: 2.9990 chunk 45 optimal weight: 1.9990 chunk 50 optimal weight: 3.9990 chunk 8 optimal weight: 2.9990 chunk 43 optimal weight: 8.9990 chunk 32 optimal weight: 0.0040 chunk 49 optimal weight: 7.9990 chunk 51 optimal weight: 4.9990 chunk 47 optimal weight: 1.9990 overall best weight: 1.4096 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 408 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 410 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4101 r_free = 0.4101 target = 0.161792 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3690 r_free = 0.3690 target = 0.123903 restraints weight = 7085.583| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3674 r_free = 0.3674 target = 0.124040 restraints weight = 4684.412| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3689 r_free = 0.3689 target = 0.125845 restraints weight = 4187.468| |-----------------------------------------------------------------------------| r_work (final): 0.3695 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7690 moved from start: 0.2847 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 4541 Z= 0.276 Angle : 0.636 8.158 6187 Z= 0.312 Chirality : 0.043 0.133 688 Planarity : 0.005 0.053 771 Dihedral : 5.996 54.656 703 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 10.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.09 % Favored : 94.91 % Rotamer: Outliers : 2.35 % Allowed : 17.48 % Favored : 80.17 % 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: -1.55 (0.36), residues: 530 helix: -1.05 (0.34), residues: 239 sheet: -1.75 (0.55), residues: 68 loop : -0.48 (0.41), residues: 223 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 147 HIS 0.011 0.002 HIS A 408 PHE 0.012 0.001 PHE A 69 TYR 0.017 0.002 TYR A 179 ARG 0.010 0.000 ARG A 694 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1060 Ramachandran restraints generated. 530 Oldfield, 0 Emsley, 530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1060 Ramachandran restraints generated. 530 Oldfield, 0 Emsley, 530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 486 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 66 time to evaluate : 0.495 Fit side-chains revert: symmetry clash REVERT: A 127 LEU cc_start: 0.7205 (OUTLIER) cc_final: 0.6989 (mp) REVERT: A 361 GLN cc_start: 0.7320 (pt0) cc_final: 0.6676 (tp40) REVERT: A 398 SER cc_start: 0.8426 (m) cc_final: 0.7938 (p) REVERT: A 507 MET cc_start: 0.4805 (pmm) cc_final: 0.4539 (pmm) REVERT: A 600 MET cc_start: 0.6888 (ptt) cc_final: 0.6662 (ptt) outliers start: 11 outliers final: 8 residues processed: 67 average time/residue: 0.1126 time to fit residues: 11.4308 Evaluate side-chains 71 residues out of total 486 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 62 time to evaluate : 0.545 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 127 LEU Chi-restraints excluded: chain A residue 319 LEU Chi-restraints excluded: chain A residue 367 THR Chi-restraints excluded: chain A residue 368 LEU Chi-restraints excluded: chain A residue 401 MET Chi-restraints excluded: chain A residue 410 HIS Chi-restraints excluded: chain A residue 530 VAL Chi-restraints excluded: chain A residue 573 LEU Chi-restraints excluded: chain A residue 698 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 8 optimal weight: 0.6980 chunk 28 optimal weight: 0.6980 chunk 44 optimal weight: 20.0000 chunk 27 optimal weight: 0.0770 chunk 11 optimal weight: 0.9990 chunk 39 optimal weight: 2.9990 chunk 12 optimal weight: 0.6980 chunk 10 optimal weight: 0.8980 chunk 35 optimal weight: 1.9990 chunk 50 optimal weight: 4.9990 chunk 51 optimal weight: 1.9990 overall best weight: 0.6138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 328 GLN A 410 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4134 r_free = 0.4134 target = 0.164853 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3748 r_free = 0.3748 target = 0.127955 restraints weight = 6966.434| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3704 r_free = 0.3704 target = 0.126825 restraints weight = 4801.847| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3724 r_free = 0.3724 target = 0.128943 restraints weight = 4250.443| |-----------------------------------------------------------------------------| r_work (final): 0.3733 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7646 moved from start: 0.3005 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 4541 Z= 0.166 Angle : 0.587 7.133 6187 Z= 0.289 Chirality : 0.041 0.134 688 Planarity : 0.005 0.054 771 Dihedral : 5.669 54.370 703 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 9.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.91 % Favored : 95.09 % Rotamer: Outliers : 2.56 % Allowed : 17.70 % Favored : 79.74 % 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: -1.25 (0.37), residues: 530 helix: -0.77 (0.35), residues: 235 sheet: -1.74 (0.51), residues: 75 loop : -0.27 (0.43), residues: 220 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 198 HIS 0.008 0.001 HIS A 410 PHE 0.015 0.001 PHE A 696 TYR 0.016 0.001 TYR A 179 ARG 0.007 0.000 ARG A 694 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1060 Ramachandran restraints generated. 530 Oldfield, 0 Emsley, 530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1060 Ramachandran restraints generated. 530 Oldfield, 0 Emsley, 530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 486 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 70 time to evaluate : 0.466 Fit side-chains revert: symmetry clash REVERT: A 75 MET cc_start: 0.8053 (mmp) cc_final: 0.7506 (mmp) REVERT: A 127 LEU cc_start: 0.7052 (OUTLIER) cc_final: 0.6815 (mp) REVERT: A 361 GLN cc_start: 0.7307 (pt0) cc_final: 0.6651 (tp40) REVERT: A 398 SER cc_start: 0.8344 (m) cc_final: 0.7871 (p) REVERT: A 507 MET cc_start: 0.4739 (pmm) cc_final: 0.4517 (pmm) REVERT: A 600 MET cc_start: 0.6834 (ptt) cc_final: 0.6581 (ptt) outliers start: 12 outliers final: 6 residues processed: 74 average time/residue: 0.1131 time to fit residues: 11.7544 Evaluate side-chains 76 residues out of total 486 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 69 time to evaluate : 0.471 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 127 LEU Chi-restraints excluded: chain A residue 319 LEU Chi-restraints excluded: chain A residue 367 THR Chi-restraints excluded: chain A residue 368 LEU Chi-restraints excluded: chain A residue 401 MET Chi-restraints excluded: chain A residue 530 VAL Chi-restraints excluded: chain A residue 573 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 15 optimal weight: 1.9990 chunk 51 optimal weight: 1.9990 chunk 48 optimal weight: 0.9990 chunk 39 optimal weight: 5.9990 chunk 21 optimal weight: 0.0470 chunk 23 optimal weight: 0.8980 chunk 29 optimal weight: 0.6980 chunk 20 optimal weight: 6.9990 chunk 44 optimal weight: 20.0000 chunk 32 optimal weight: 2.9990 chunk 27 optimal weight: 5.9990 overall best weight: 0.9282 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 410 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4120 r_free = 0.4120 target = 0.162955 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3734 r_free = 0.3734 target = 0.126492 restraints weight = 6971.678| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3691 r_free = 0.3691 target = 0.125544 restraints weight = 4677.886| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3708 r_free = 0.3708 target = 0.127604 restraints weight = 4081.025| |-----------------------------------------------------------------------------| r_work (final): 0.3718 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7663 moved from start: 0.3106 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 4541 Z= 0.209 Angle : 0.612 11.670 6187 Z= 0.295 Chirality : 0.042 0.129 688 Planarity : 0.005 0.053 771 Dihedral : 5.552 55.340 703 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 9.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.28 % Favored : 94.72 % Rotamer: Outliers : 1.92 % Allowed : 18.76 % Favored : 79.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.02 (0.37), residues: 530 helix: -0.57 (0.35), residues: 230 sheet: -1.76 (0.49), residues: 77 loop : -0.09 (0.43), residues: 223 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 147 HIS 0.004 0.001 HIS A 160 PHE 0.014 0.001 PHE A 69 TYR 0.014 0.001 TYR A 179 ARG 0.006 0.000 ARG A 694 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1060 Ramachandran restraints generated. 530 Oldfield, 0 Emsley, 530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1060 Ramachandran restraints generated. 530 Oldfield, 0 Emsley, 530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 486 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 71 time to evaluate : 0.494 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 127 LEU cc_start: 0.7060 (OUTLIER) cc_final: 0.6860 (mp) REVERT: A 398 SER cc_start: 0.8337 (m) cc_final: 0.7845 (p) REVERT: A 417 ASP cc_start: 0.7168 (t0) cc_final: 0.6965 (t0) REVERT: A 600 MET cc_start: 0.6868 (ptt) cc_final: 0.6662 (ptt) outliers start: 9 outliers final: 8 residues processed: 72 average time/residue: 0.1210 time to fit residues: 12.1419 Evaluate side-chains 77 residues out of total 486 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 68 time to evaluate : 0.630 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 127 LEU Chi-restraints excluded: chain A residue 319 LEU Chi-restraints excluded: chain A residue 367 THR Chi-restraints excluded: chain A residue 368 LEU Chi-restraints excluded: chain A residue 401 MET Chi-restraints excluded: chain A residue 410 HIS Chi-restraints excluded: chain A residue 530 VAL Chi-restraints excluded: chain A residue 573 LEU Chi-restraints excluded: chain A residue 698 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 26 optimal weight: 4.9990 chunk 46 optimal weight: 4.9990 chunk 50 optimal weight: 1.9990 chunk 18 optimal weight: 0.3980 chunk 38 optimal weight: 0.1980 chunk 32 optimal weight: 2.9990 chunk 27 optimal weight: 0.8980 chunk 51 optimal weight: 1.9990 chunk 47 optimal weight: 1.9990 chunk 40 optimal weight: 5.9990 chunk 8 optimal weight: 0.0470 overall best weight: 0.7080 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 440 HIS A 580 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4138 r_free = 0.4138 target = 0.164665 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3749 r_free = 0.3749 target = 0.128040 restraints weight = 6926.035| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3714 r_free = 0.3714 target = 0.127718 restraints weight = 4685.086| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3729 r_free = 0.3729 target = 0.129648 restraints weight = 4092.741| |-----------------------------------------------------------------------------| r_work (final): 0.3740 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7637 moved from start: 0.3264 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 4541 Z= 0.177 Angle : 0.607 10.833 6187 Z= 0.289 Chirality : 0.041 0.129 688 Planarity : 0.004 0.054 771 Dihedral : 5.410 56.341 703 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 9.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.09 % Favored : 94.91 % Rotamer: Outliers : 2.13 % Allowed : 19.19 % Favored : 78.68 % 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: -1.00 (0.37), residues: 530 helix: -0.48 (0.35), residues: 236 sheet: -1.71 (0.49), residues: 77 loop : -0.18 (0.44), residues: 217 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 198 HIS 0.011 0.001 HIS A 410 PHE 0.019 0.001 PHE A 696 TYR 0.015 0.002 TYR A 447 ARG 0.006 0.000 ARG A 694 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1060 Ramachandran restraints generated. 530 Oldfield, 0 Emsley, 530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1060 Ramachandran restraints generated. 530 Oldfield, 0 Emsley, 530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 486 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 69 time to evaluate : 0.459 Fit side-chains revert: symmetry clash REVERT: A 75 MET cc_start: 0.7935 (mmp) cc_final: 0.7454 (mmp) REVERT: A 127 LEU cc_start: 0.7144 (OUTLIER) cc_final: 0.6918 (mp) REVERT: A 213 ILE cc_start: 0.8361 (mm) cc_final: 0.7981 (mt) REVERT: A 398 SER cc_start: 0.8250 (m) cc_final: 0.7788 (p) REVERT: A 417 ASP cc_start: 0.7151 (t0) cc_final: 0.6926 (t0) REVERT: A 507 MET cc_start: 0.4721 (pmm) cc_final: 0.4489 (pmm) REVERT: A 600 MET cc_start: 0.6802 (ptt) cc_final: 0.6567 (ptt) REVERT: A 689 LEU cc_start: 0.8258 (OUTLIER) cc_final: 0.7626 (mt) outliers start: 10 outliers final: 6 residues processed: 72 average time/residue: 0.1184 time to fit residues: 11.9313 Evaluate side-chains 74 residues out of total 486 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 66 time to evaluate : 0.516 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 127 LEU Chi-restraints excluded: chain A residue 367 THR Chi-restraints excluded: chain A residue 368 LEU Chi-restraints excluded: chain A residue 401 MET Chi-restraints excluded: chain A residue 449 THR Chi-restraints excluded: chain A residue 530 VAL Chi-restraints excluded: chain A residue 573 LEU Chi-restraints excluded: chain A residue 689 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 18 optimal weight: 0.0970 chunk 29 optimal weight: 0.6980 chunk 7 optimal weight: 0.5980 chunk 17 optimal weight: 0.9990 chunk 37 optimal weight: 0.8980 chunk 11 optimal weight: 1.9990 chunk 44 optimal weight: 9.9990 chunk 51 optimal weight: 0.9980 chunk 14 optimal weight: 6.9990 chunk 2 optimal weight: 0.6980 chunk 28 optimal weight: 0.6980 overall best weight: 0.5578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 410 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4154 r_free = 0.4154 target = 0.166190 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3775 r_free = 0.3775 target = 0.129937 restraints weight = 6864.589| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3737 r_free = 0.3737 target = 0.129384 restraints weight = 4565.740| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3753 r_free = 0.3753 target = 0.131371 restraints weight = 4024.370| |-----------------------------------------------------------------------------| r_work (final): 0.3762 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7604 moved from start: 0.3376 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 4541 Z= 0.159 Angle : 0.590 10.582 6187 Z= 0.284 Chirality : 0.041 0.130 688 Planarity : 0.004 0.054 771 Dihedral : 5.154 55.950 703 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 8.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.53 % Favored : 95.47 % Rotamer: Outliers : 2.35 % Allowed : 19.40 % Favored : 78.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.72 (0.37), residues: 530 helix: -0.33 (0.35), residues: 240 sheet: -1.56 (0.51), residues: 75 loop : 0.06 (0.45), residues: 215 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 147 HIS 0.004 0.001 HIS A 160 PHE 0.008 0.001 PHE A 382 TYR 0.014 0.001 TYR A 447 ARG 0.005 0.000 ARG A 694 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1060 Ramachandran restraints generated. 530 Oldfield, 0 Emsley, 530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1060 Ramachandran restraints generated. 530 Oldfield, 0 Emsley, 530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 486 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 69 time to evaluate : 0.500 Fit side-chains revert: symmetry clash REVERT: A 75 MET cc_start: 0.7802 (mmp) cc_final: 0.7316 (mmp) REVERT: A 213 ILE cc_start: 0.8310 (mm) cc_final: 0.7918 (mt) REVERT: A 398 SER cc_start: 0.8157 (m) cc_final: 0.7941 (p) REVERT: A 462 GLU cc_start: 0.7164 (pm20) cc_final: 0.6734 (pm20) REVERT: A 600 MET cc_start: 0.6723 (ptt) cc_final: 0.6351 (ttp) REVERT: A 689 LEU cc_start: 0.8280 (OUTLIER) cc_final: 0.7630 (mt) outliers start: 11 outliers final: 8 residues processed: 71 average time/residue: 0.1421 time to fit residues: 13.7798 Evaluate side-chains 77 residues out of total 486 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 68 time to evaluate : 0.543 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 319 LEU Chi-restraints excluded: chain A residue 367 THR Chi-restraints excluded: chain A residue 368 LEU Chi-restraints excluded: chain A residue 401 MET Chi-restraints excluded: chain A residue 449 THR Chi-restraints excluded: chain A residue 530 VAL Chi-restraints excluded: chain A residue 573 LEU Chi-restraints excluded: chain A residue 689 LEU Chi-restraints excluded: chain A residue 698 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 25 optimal weight: 0.9980 chunk 12 optimal weight: 0.6980 chunk 49 optimal weight: 8.9990 chunk 27 optimal weight: 0.1980 chunk 47 optimal weight: 2.9990 chunk 41 optimal weight: 1.9990 chunk 32 optimal weight: 0.6980 chunk 7 optimal weight: 0.9980 chunk 43 optimal weight: 9.9990 chunk 45 optimal weight: 5.9990 chunk 26 optimal weight: 0.9980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 385 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4147 r_free = 0.4147 target = 0.165239 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3757 r_free = 0.3757 target = 0.128597 restraints weight = 6885.745| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3712 r_free = 0.3712 target = 0.127770 restraints weight = 4658.404| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3736 r_free = 0.3736 target = 0.130371 restraints weight = 4008.215| |-----------------------------------------------------------------------------| r_work (final): 0.3748 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7616 moved from start: 0.3512 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 4541 Z= 0.180 Angle : 0.606 10.482 6187 Z= 0.291 Chirality : 0.041 0.129 688 Planarity : 0.005 0.054 771 Dihedral : 5.088 56.354 703 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 9.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.09 % Favored : 94.91 % Rotamer: Outliers : 2.13 % Allowed : 19.62 % Favored : 78.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.53 (0.38), residues: 530 helix: -0.12 (0.36), residues: 241 sheet: -1.61 (0.55), residues: 71 loop : 0.10 (0.44), residues: 218 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 147 HIS 0.004 0.001 HIS A 160 PHE 0.026 0.001 PHE A 696 TYR 0.012 0.001 TYR A 447 ARG 0.006 0.000 ARG A 419 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1060 Ramachandran restraints generated. 530 Oldfield, 0 Emsley, 530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1060 Ramachandran restraints generated. 530 Oldfield, 0 Emsley, 530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 486 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 69 time to evaluate : 0.500 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 75 MET cc_start: 0.7756 (mmp) cc_final: 0.7200 (mmp) REVERT: A 213 ILE cc_start: 0.8346 (mm) cc_final: 0.7956 (mt) REVERT: A 398 SER cc_start: 0.8329 (m) cc_final: 0.7909 (p) REVERT: A 417 ASP cc_start: 0.7462 (m-30) cc_final: 0.6949 (m-30) REVERT: A 600 MET cc_start: 0.6762 (ptt) cc_final: 0.6377 (ttp) REVERT: A 689 LEU cc_start: 0.8267 (OUTLIER) cc_final: 0.7606 (mt) outliers start: 10 outliers final: 8 residues processed: 72 average time/residue: 0.1167 time to fit residues: 11.8398 Evaluate side-chains 77 residues out of total 486 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 68 time to evaluate : 0.510 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 319 LEU Chi-restraints excluded: chain A residue 367 THR Chi-restraints excluded: chain A residue 368 LEU Chi-restraints excluded: chain A residue 449 THR Chi-restraints excluded: chain A residue 530 VAL Chi-restraints excluded: chain A residue 561 THR Chi-restraints excluded: chain A residue 573 LEU Chi-restraints excluded: chain A residue 689 LEU Chi-restraints excluded: chain A residue 698 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 37 optimal weight: 0.9980 chunk 17 optimal weight: 0.7980 chunk 28 optimal weight: 3.9990 chunk 9 optimal weight: 0.9990 chunk 29 optimal weight: 0.9990 chunk 50 optimal weight: 4.9990 chunk 49 optimal weight: 7.9990 chunk 27 optimal weight: 0.8980 chunk 24 optimal weight: 0.8980 chunk 33 optimal weight: 0.9980 chunk 42 optimal weight: 10.0000 overall best weight: 0.9180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 199 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4141 r_free = 0.4141 target = 0.164731 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3743 r_free = 0.3743 target = 0.127374 restraints weight = 6962.334| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3695 r_free = 0.3695 target = 0.126519 restraints weight = 4954.632| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3723 r_free = 0.3723 target = 0.129289 restraints weight = 4065.574| |-----------------------------------------------------------------------------| r_work (final): 0.3731 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7635 moved from start: 0.3548 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 4541 Z= 0.211 Angle : 0.628 10.228 6187 Z= 0.300 Chirality : 0.042 0.128 688 Planarity : 0.005 0.054 771 Dihedral : 5.104 57.467 703 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 10.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.09 % Favored : 94.91 % Rotamer: Outliers : 1.92 % Allowed : 20.47 % Favored : 77.61 % 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: -0.52 (0.38), residues: 530 helix: -0.10 (0.36), residues: 241 sheet: -1.28 (0.57), residues: 68 loop : -0.05 (0.44), residues: 221 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 147 HIS 0.004 0.001 HIS A 160 PHE 0.015 0.001 PHE A 69 TYR 0.011 0.001 TYR A 447 ARG 0.006 0.000 ARG A 694 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1750.80 seconds wall clock time: 32 minutes 2.87 seconds (1922.87 seconds total)