Starting phenix.real_space_refine on Fri Aug 22 14:52:01 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9bum_44912/08_2025/9bum_44912.cif Found real_map, /net/cci-nas-00/data/ceres_data/9bum_44912/08_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 { model { file = "/net/cci-nas-00/data/ceres_data/9bum_44912/08_2025/9bum_44912.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9bum_44912/08_2025/9bum_44912.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9bum_44912/08_2025/9bum_44912.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9bum_44912/08_2025/9bum_44912.map" } resolution = 3.63 write_initial_geo_file = False refinement { macro_cycles = 10 } 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/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: {'TRP:plan': 1, 'ARG:plan': 5, 'PHE:plan': 4, 'HIS:plan': 1, 'GLU: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: 1.37, per 1000 atoms: 0.31 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: 0.43 Conformation dependent library (CDL) restraints added in 166.0 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 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: 0.10 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: 0.43 Time building geometry restraints manager: 0.53 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: 1.220 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: 0.050 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 5.690 Find NCS groups from input model: 0.010 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.060 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 8.070 ------------------------------------------------------------------------------- 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 4544 Z= 0.252 Angle : 0.978 10.343 6195 Z= 0.545 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. 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 ARG 0.009 0.000 ARG A 419 TYR 0.027 0.002 TYR A 164 PHE 0.013 0.002 PHE A 382 TRP 0.012 0.002 TRP A 198 HIS 0.005 0.001 HIS A 160 Details of bonding type rmsd covalent geometry : bond 0.00512 ( 4541) covalent geometry : angle 0.97163 ( 6187) SS BOND : bond 0.00651 ( 1) SS BOND : angle 1.41376 ( 2) hydrogen bonds : bond 0.30417 ( 152) hydrogen bonds : angle 10.63127 ( 405) link_BETA1-4 : bond 0.00583 ( 1) link_BETA1-4 : angle 2.90600 ( 3) link_NAG-ASN : bond 0.00816 ( 1) link_NAG-ASN : angle 4.47125 ( 3) *********************** 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 : 0.138 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: 0.0836 time to fit residues: 9.2268 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 : 0.129 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 24 optimal weight: 0.0670 chunk 48 optimal weight: 0.9990 chunk 26 optimal weight: 3.9990 chunk 2 optimal weight: 2.9990 chunk 16 optimal weight: 0.9990 chunk 32 optimal weight: 0.1980 chunk 31 optimal weight: 0.6980 chunk 25 optimal weight: 0.7980 chunk 50 optimal weight: 2.9990 chunk 19 optimal weight: 0.9980 chunk 30 optimal weight: 0.5980 overall best weight: 0.4718 ------------------------------------------------------------------------------- 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 464 GLN A 478 GLN A 539 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4156 r_free = 0.4156 target = 0.165552 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3777 r_free = 0.3777 target = 0.129900 restraints weight = 6945.907| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3762 r_free = 0.3762 target = 0.130373 restraints weight = 4265.387| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3776 r_free = 0.3776 target = 0.132197 restraints weight = 3756.066| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3781 r_free = 0.3781 target = 0.132646 restraints weight = 2761.820| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3791 r_free = 0.3791 target = 0.133910 restraints weight = 2629.176| |-----------------------------------------------------------------------------| r_work (final): 0.3800 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7591 moved from start: 0.2133 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 4544 Z= 0.133 Angle : 0.673 9.048 6195 Z= 0.333 Chirality : 0.041 0.161 688 Planarity : 0.006 0.056 771 Dihedral : 6.961 58.235 703 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 8.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.34 % Favored : 95.66 % Rotamer: Outliers : 1.49 % Allowed : 10.66 % Favored : 87.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.22 (0.33), residues: 530 helix: -2.84 (0.26), residues: 245 sheet: -2.28 (0.51), residues: 75 loop : -0.80 (0.43), residues: 210 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 419 TYR 0.013 0.002 TYR A 586 PHE 0.017 0.001 PHE A 696 TRP 0.011 0.001 TRP A 147 HIS 0.008 0.001 HIS A 160 Details of bonding type rmsd covalent geometry : bond 0.00281 ( 4541) covalent geometry : angle 0.66841 ( 6187) SS BOND : bond 0.00250 ( 1) SS BOND : angle 0.25761 ( 2) hydrogen bonds : bond 0.04234 ( 152) hydrogen bonds : angle 5.74379 ( 405) link_BETA1-4 : bond 0.00278 ( 1) link_BETA1-4 : angle 1.36231 ( 3) link_NAG-ASN : bond 0.00051 ( 1) link_NAG-ASN : angle 3.34074 ( 3) *********************** 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 81 residues out of total 486 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 74 time to evaluate : 0.102 Fit side-chains revert: symmetry clash REVERT: A 361 GLN cc_start: 0.7175 (pt0) cc_final: 0.6559 (tp40) REVERT: A 507 MET cc_start: 0.4771 (pmm) cc_final: 0.4506 (pmm) REVERT: A 588 LYS cc_start: 0.8790 (mttt) cc_final: 0.8566 (mtmt) REVERT: A 689 LEU cc_start: 0.8467 (tt) cc_final: 0.7894 (mt) outliers start: 7 outliers final: 4 residues processed: 75 average time/residue: 0.0471 time to fit residues: 4.8379 Evaluate side-chains 67 residues out of total 486 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 63 time to evaluate : 0.144 ------------------------------------------------------------------------------- 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 36 optimal weight: 0.4980 chunk 0 optimal weight: 5.9990 chunk 19 optimal weight: 0.9990 chunk 47 optimal weight: 0.6980 chunk 11 optimal weight: 0.7980 chunk 6 optimal weight: 0.9990 chunk 9 optimal weight: 0.5980 chunk 16 optimal weight: 0.9990 chunk 25 optimal weight: 0.9980 chunk 33 optimal weight: 0.3980 chunk 41 optimal weight: 8.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 446 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4148 r_free = 0.4148 target = 0.165231 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3765 r_free = 0.3765 target = 0.128820 restraints weight = 6874.195| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3742 r_free = 0.3742 target = 0.128929 restraints weight = 4391.949| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3758 r_free = 0.3758 target = 0.130871 restraints weight = 3930.012| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3762 r_free = 0.3762 target = 0.131087 restraints weight = 2845.396| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3764 r_free = 0.3764 target = 0.131474 restraints weight = 3060.157| |-----------------------------------------------------------------------------| r_work (final): 0.3773 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7618 moved from start: 0.2485 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 4544 Z= 0.122 Angle : 0.631 8.332 6195 Z= 0.308 Chirality : 0.042 0.149 688 Planarity : 0.005 0.053 771 Dihedral : 6.288 55.962 703 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 9.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.58 % Favored : 96.42 % Rotamer: Outliers : 1.71 % Allowed : 13.01 % Favored : 85.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.25 (0.34), residues: 530 helix: -1.84 (0.31), residues: 239 sheet: -2.19 (0.50), residues: 75 loop : -0.46 (0.43), residues: 216 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG A 694 TYR 0.011 0.002 TYR A 179 PHE 0.016 0.001 PHE A 431 TRP 0.013 0.001 TRP A 198 HIS 0.004 0.001 HIS A 160 Details of bonding type rmsd covalent geometry : bond 0.00275 ( 4541) covalent geometry : angle 0.62932 ( 6187) SS BOND : bond 0.00222 ( 1) SS BOND : angle 0.33097 ( 2) hydrogen bonds : bond 0.03207 ( 152) hydrogen bonds : angle 5.08831 ( 405) link_BETA1-4 : bond 0.00440 ( 1) link_BETA1-4 : angle 1.10649 ( 3) link_NAG-ASN : bond 0.00294 ( 1) link_NAG-ASN : angle 2.00527 ( 3) *********************** 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 72 residues out of total 486 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 64 time to evaluate : 0.175 Fit side-chains revert: symmetry clash REVERT: A 115 MET cc_start: 0.8224 (mmm) cc_final: 0.7704 (tpp) REVERT: A 361 GLN cc_start: 0.7273 (pt0) cc_final: 0.6573 (tp40) REVERT: A 689 LEU cc_start: 0.8435 (tt) cc_final: 0.7807 (mt) outliers start: 8 outliers final: 6 residues processed: 66 average time/residue: 0.0343 time to fit residues: 3.2831 Evaluate side-chains 68 residues out of total 486 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 62 time to evaluate : 0.101 ------------------------------------------------------------------------------- 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 26 optimal weight: 4.9990 chunk 47 optimal weight: 0.9980 chunk 48 optimal weight: 7.9990 chunk 23 optimal weight: 3.9990 chunk 46 optimal weight: 6.9990 chunk 24 optimal weight: 0.9980 chunk 38 optimal weight: 0.9990 chunk 13 optimal weight: 2.9990 chunk 20 optimal weight: 7.9990 chunk 0 optimal weight: 5.9990 chunk 3 optimal weight: 1.9990 overall best weight: 1.5986 ------------------------------------------------------------------------------- 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 = 0.4085 r_free = 0.4085 target = 0.159567 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3675 r_free = 0.3675 target = 0.122226 restraints weight = 6921.540| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3653 r_free = 0.3653 target = 0.122239 restraints weight = 4531.641| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3669 r_free = 0.3669 target = 0.124122 restraints weight = 4083.157| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3670 r_free = 0.3670 target = 0.124267 restraints weight = 3018.413| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3673 r_free = 0.3673 target = 0.124505 restraints weight = 2873.626| |-----------------------------------------------------------------------------| r_work (final): 0.3676 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7733 moved from start: 0.2717 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.067 4544 Z= 0.217 Angle : 0.665 8.620 6195 Z= 0.326 Chirality : 0.044 0.128 688 Planarity : 0.005 0.052 771 Dihedral : 6.414 59.485 703 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 10.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.28 % Favored : 94.72 % Rotamer: Outliers : 2.56 % Allowed : 15.57 % Favored : 81.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.93 (0.35), residues: 530 helix: -1.44 (0.32), residues: 240 sheet: -1.94 (0.51), residues: 70 loop : -0.56 (0.41), residues: 220 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 419 TYR 0.015 0.002 TYR A 415 PHE 0.013 0.002 PHE A 123 TRP 0.013 0.002 TRP A 198 HIS 0.004 0.001 HIS A 160 Details of bonding type rmsd covalent geometry : bond 0.00506 ( 4541) covalent geometry : angle 0.66394 ( 6187) SS BOND : bond 0.00563 ( 1) SS BOND : angle 0.52922 ( 2) hydrogen bonds : bond 0.03225 ( 152) hydrogen bonds : angle 5.05297 ( 405) link_BETA1-4 : bond 0.00055 ( 1) link_BETA1-4 : angle 1.09939 ( 3) link_NAG-ASN : bond 0.00051 ( 1) link_NAG-ASN : angle 1.38677 ( 3) *********************** 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 78 residues out of total 486 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 66 time to evaluate : 0.110 Fit side-chains revert: symmetry clash REVERT: A 127 LEU cc_start: 0.7284 (OUTLIER) cc_final: 0.7024 (mp) REVERT: A 361 GLN cc_start: 0.7313 (pt0) cc_final: 0.6644 (tp40) REVERT: A 600 MET cc_start: 0.6917 (ptt) cc_final: 0.6698 (ptt) REVERT: A 689 LEU cc_start: 0.8432 (OUTLIER) cc_final: 0.7767 (mt) outliers start: 12 outliers final: 8 residues processed: 69 average time/residue: 0.0399 time to fit residues: 3.9751 Evaluate side-chains 70 residues out of total 486 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 60 time to evaluate : 0.115 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 THR 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 689 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 27 optimal weight: 3.9990 chunk 50 optimal weight: 0.8980 chunk 35 optimal weight: 0.7980 chunk 29 optimal weight: 0.8980 chunk 6 optimal weight: 2.9990 chunk 46 optimal weight: 9.9990 chunk 21 optimal weight: 2.9990 chunk 2 optimal weight: 2.9990 chunk 40 optimal weight: 1.9990 chunk 18 optimal weight: 0.3980 chunk 39 optimal weight: 5.9990 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 328 GLN ** A 408 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 410 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4107 r_free = 0.4107 target = 0.162016 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3700 r_free = 0.3700 target = 0.124344 restraints weight = 7016.649| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3676 r_free = 0.3676 target = 0.124065 restraints weight = 4703.883| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3693 r_free = 0.3693 target = 0.125966 restraints weight = 4248.619| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3696 r_free = 0.3696 target = 0.126204 restraints weight = 3124.289| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3698 r_free = 0.3698 target = 0.126442 restraints weight = 2992.757| |-----------------------------------------------------------------------------| r_work (final): 0.3699 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7682 moved from start: 0.2916 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 4544 Z= 0.152 Angle : 0.616 8.277 6195 Z= 0.302 Chirality : 0.042 0.133 688 Planarity : 0.005 0.054 771 Dihedral : 6.125 59.515 703 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 10.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.47 % Favored : 94.53 % Rotamer: Outliers : 2.13 % Allowed : 16.42 % Favored : 81.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.58 (0.35), residues: 530 helix: -1.11 (0.34), residues: 235 sheet: -1.77 (0.52), residues: 70 loop : -0.45 (0.41), residues: 225 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 694 TYR 0.015 0.001 TYR A 179 PHE 0.011 0.001 PHE A 69 TRP 0.014 0.001 TRP A 198 HIS 0.009 0.001 HIS A 408 Details of bonding type rmsd covalent geometry : bond 0.00353 ( 4541) covalent geometry : angle 0.61517 ( 6187) SS BOND : bond 0.00372 ( 1) SS BOND : angle 0.46392 ( 2) hydrogen bonds : bond 0.02913 ( 152) hydrogen bonds : angle 4.84880 ( 405) link_BETA1-4 : bond 0.00235 ( 1) link_BETA1-4 : angle 1.05017 ( 3) link_NAG-ASN : bond 0.00137 ( 1) link_NAG-ASN : angle 1.10170 ( 3) *********************** 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 76 residues out of total 486 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 66 time to evaluate : 0.122 Fit side-chains revert: symmetry clash REVERT: A 127 LEU cc_start: 0.7224 (OUTLIER) cc_final: 0.6987 (mp) REVERT: A 361 GLN cc_start: 0.7293 (pt0) cc_final: 0.6584 (tp40) REVERT: A 398 SER cc_start: 0.8464 (m) cc_final: 0.7980 (p) REVERT: A 546 GLU cc_start: 0.7700 (mm-30) cc_final: 0.7424 (mm-30) REVERT: A 600 MET cc_start: 0.6933 (ptt) cc_final: 0.6690 (ptt) REVERT: A 689 LEU cc_start: 0.8358 (OUTLIER) cc_final: 0.7750 (mt) outliers start: 10 outliers final: 7 residues processed: 67 average time/residue: 0.0398 time to fit residues: 3.9701 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 : 0.209 ------------------------------------------------------------------------------- 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 689 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 41 optimal weight: 9.9990 chunk 40 optimal weight: 5.9990 chunk 8 optimal weight: 2.9990 chunk 35 optimal weight: 0.7980 chunk 48 optimal weight: 0.8980 chunk 6 optimal weight: 3.9990 chunk 31 optimal weight: 0.8980 chunk 13 optimal weight: 0.6980 chunk 42 optimal weight: 9.9990 chunk 23 optimal weight: 0.4980 chunk 18 optimal weight: 0.7980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 410 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4117 r_free = 0.4117 target = 0.162952 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3727 r_free = 0.3727 target = 0.126034 restraints weight = 7047.372| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3681 r_free = 0.3681 target = 0.124741 restraints weight = 4987.924| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3700 r_free = 0.3700 target = 0.126809 restraints weight = 4346.607| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3708 r_free = 0.3708 target = 0.127279 restraints weight = 3039.783| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3708 r_free = 0.3708 target = 0.127514 restraints weight = 3177.888| |-----------------------------------------------------------------------------| r_work (final): 0.3713 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7668 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 0.047 4544 Z= 0.125 Angle : 0.589 7.778 6195 Z= 0.288 Chirality : 0.041 0.131 688 Planarity : 0.004 0.054 771 Dihedral : 5.816 58.161 703 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 9.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.28 % Favored : 94.72 % Rotamer: Outliers : 2.77 % Allowed : 16.20 % Favored : 81.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.18 (0.36), residues: 530 helix: -0.81 (0.35), residues: 229 sheet: -1.56 (0.53), residues: 70 loop : -0.23 (0.42), residues: 231 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 694 TYR 0.018 0.002 TYR A 179 PHE 0.017 0.001 PHE A 696 TRP 0.013 0.001 TRP A 198 HIS 0.005 0.001 HIS A 410 Details of bonding type rmsd covalent geometry : bond 0.00289 ( 4541) covalent geometry : angle 0.58827 ( 6187) SS BOND : bond 0.00293 ( 1) SS BOND : angle 0.41369 ( 2) hydrogen bonds : bond 0.02746 ( 152) hydrogen bonds : angle 4.68426 ( 405) link_BETA1-4 : bond 0.00293 ( 1) link_BETA1-4 : angle 1.05199 ( 3) link_NAG-ASN : bond 0.00216 ( 1) link_NAG-ASN : angle 1.00084 ( 3) *********************** 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 84 residues out of total 486 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 71 time to evaluate : 0.149 Fit side-chains revert: symmetry clash REVERT: A 361 GLN cc_start: 0.7234 (pt0) cc_final: 0.6605 (tp40) REVERT: A 398 SER cc_start: 0.8417 (m) cc_final: 0.7951 (p) REVERT: A 417 ASP cc_start: 0.7177 (t0) cc_final: 0.6935 (t0) REVERT: A 546 GLU cc_start: 0.7759 (mm-30) cc_final: 0.7526 (mm-30) REVERT: A 600 MET cc_start: 0.6895 (ptt) cc_final: 0.6623 (ptt) REVERT: A 689 LEU cc_start: 0.8309 (OUTLIER) cc_final: 0.7714 (mt) outliers start: 13 outliers final: 7 residues processed: 75 average time/residue: 0.0457 time to fit residues: 4.8474 Evaluate side-chains 75 residues out of total 486 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 67 time to evaluate : 0.166 ------------------------------------------------------------------------------- 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 Chi-restraints excluded: chain A residue 689 LEU Chi-restraints excluded: chain A residue 698 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 24 optimal weight: 0.6980 chunk 30 optimal weight: 0.4980 chunk 11 optimal weight: 0.6980 chunk 2 optimal weight: 1.9990 chunk 6 optimal weight: 0.9980 chunk 10 optimal weight: 0.8980 chunk 17 optimal weight: 7.9990 chunk 32 optimal weight: 0.0030 chunk 23 optimal weight: 1.9990 chunk 1 optimal weight: 0.3980 chunk 45 optimal weight: 10.0000 overall best weight: 0.4590 ------------------------------------------------------------------------------- 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 = 0.4143 r_free = 0.4143 target = 0.165168 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3761 r_free = 0.3761 target = 0.128569 restraints weight = 6878.337| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3712 r_free = 0.3712 target = 0.127392 restraints weight = 4626.198| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3730 r_free = 0.3730 target = 0.129518 restraints weight = 4080.008| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3739 r_free = 0.3739 target = 0.130006 restraints weight = 2874.183| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3738 r_free = 0.3738 target = 0.130212 restraints weight = 2968.061| |-----------------------------------------------------------------------------| r_work (final): 0.3746 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7613 moved from start: 0.3162 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 4544 Z= 0.105 Angle : 0.599 11.756 6195 Z= 0.285 Chirality : 0.041 0.130 688 Planarity : 0.004 0.054 771 Dihedral : 5.428 55.310 703 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 8.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.34 % Favored : 95.66 % Rotamer: Outliers : 1.92 % Allowed : 18.12 % Favored : 79.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.05 (0.37), residues: 530 helix: -0.64 (0.35), residues: 232 sheet: -1.79 (0.52), residues: 73 loop : -0.07 (0.43), residues: 225 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 694 TYR 0.015 0.001 TYR A 148 PHE 0.010 0.001 PHE A 431 TRP 0.011 0.001 TRP A 198 HIS 0.004 0.001 HIS A 160 Details of bonding type rmsd covalent geometry : bond 0.00238 ( 4541) covalent geometry : angle 0.59812 ( 6187) SS BOND : bond 0.00180 ( 1) SS BOND : angle 0.28144 ( 2) hydrogen bonds : bond 0.02606 ( 152) hydrogen bonds : angle 4.59832 ( 405) link_BETA1-4 : bond 0.00422 ( 1) link_BETA1-4 : angle 1.05574 ( 3) link_NAG-ASN : bond 0.00296 ( 1) link_NAG-ASN : angle 1.02653 ( 3) *********************** 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 77 residues out of total 486 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 68 time to evaluate : 0.120 Fit side-chains revert: symmetry clash REVERT: A 75 MET cc_start: 0.7934 (mmp) cc_final: 0.7496 (mmp) REVERT: A 115 MET cc_start: 0.8073 (mmm) cc_final: 0.7773 (tpp) REVERT: A 398 SER cc_start: 0.8305 (m) cc_final: 0.7817 (p) REVERT: A 417 ASP cc_start: 0.7173 (t0) cc_final: 0.6959 (t0) REVERT: A 600 MET cc_start: 0.6778 (ptt) cc_final: 0.6560 (ptt) REVERT: A 689 LEU cc_start: 0.8285 (OUTLIER) cc_final: 0.7670 (mt) outliers start: 9 outliers final: 6 residues processed: 71 average time/residue: 0.0376 time to fit residues: 3.9216 Evaluate side-chains 73 residues out of total 486 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 66 time to evaluate : 0.141 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 507 MET 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 2 optimal weight: 2.9990 chunk 30 optimal weight: 3.9990 chunk 40 optimal weight: 0.9980 chunk 17 optimal weight: 7.9990 chunk 34 optimal weight: 0.7980 chunk 31 optimal weight: 0.6980 chunk 27 optimal weight: 4.9990 chunk 14 optimal weight: 6.9990 chunk 26 optimal weight: 0.8980 chunk 37 optimal weight: 1.9990 chunk 50 optimal weight: 1.9990 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 440 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4121 r_free = 0.4121 target = 0.162828 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3726 r_free = 0.3726 target = 0.125871 restraints weight = 6923.651| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3689 r_free = 0.3689 target = 0.125361 restraints weight = 4693.535| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3710 r_free = 0.3710 target = 0.127797 restraints weight = 4072.228| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3711 r_free = 0.3711 target = 0.127579 restraints weight = 2845.285| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3712 r_free = 0.3712 target = 0.127924 restraints weight = 3123.374| |-----------------------------------------------------------------------------| r_work (final): 0.3721 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7665 moved from start: 0.3262 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 4544 Z= 0.157 Angle : 0.622 10.690 6195 Z= 0.299 Chirality : 0.042 0.131 688 Planarity : 0.005 0.054 771 Dihedral : 5.513 58.110 703 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 10.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.91 % Favored : 95.09 % Rotamer: Outliers : 2.35 % Allowed : 18.12 % Favored : 79.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.99 (0.37), residues: 530 helix: -0.53 (0.35), residues: 237 sheet: -1.55 (0.52), residues: 70 loop : -0.22 (0.42), residues: 223 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 694 TYR 0.015 0.002 TYR A 148 PHE 0.018 0.001 PHE A 696 TRP 0.013 0.001 TRP A 147 HIS 0.004 0.001 HIS A 160 Details of bonding type rmsd covalent geometry : bond 0.00370 ( 4541) covalent geometry : angle 0.62178 ( 6187) SS BOND : bond 0.00406 ( 1) SS BOND : angle 0.38240 ( 2) hydrogen bonds : bond 0.02742 ( 152) hydrogen bonds : angle 4.72464 ( 405) link_BETA1-4 : bond 0.00377 ( 1) link_BETA1-4 : angle 1.12641 ( 3) link_NAG-ASN : bond 0.00082 ( 1) link_NAG-ASN : angle 1.06297 ( 3) *********************** 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 77 residues out of total 486 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 66 time to evaluate : 0.139 Fit side-chains revert: symmetry clash REVERT: A 115 MET cc_start: 0.8178 (mmm) cc_final: 0.7802 (tpp) REVERT: A 127 LEU cc_start: 0.7226 (OUTLIER) cc_final: 0.6893 (mp) REVERT: A 398 SER cc_start: 0.8331 (m) cc_final: 0.8049 (p) REVERT: A 689 LEU cc_start: 0.8313 (OUTLIER) cc_final: 0.7678 (mt) outliers start: 11 outliers final: 9 residues processed: 68 average time/residue: 0.0380 time to fit residues: 3.8364 Evaluate side-chains 75 residues out of total 486 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 64 time to evaluate : 0.158 ------------------------------------------------------------------------------- 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 449 THR Chi-restraints excluded: chain A residue 507 MET 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 43 optimal weight: 9.9990 chunk 16 optimal weight: 1.9990 chunk 30 optimal weight: 2.9990 chunk 4 optimal weight: 1.9990 chunk 8 optimal weight: 0.0020 chunk 7 optimal weight: 0.7980 chunk 34 optimal weight: 0.0470 chunk 0 optimal weight: 5.9990 chunk 48 optimal weight: 2.9990 chunk 15 optimal weight: 0.9990 chunk 18 optimal weight: 0.0470 overall best weight: 0.3786 ------------------------------------------------------------------------------- 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 = 0.4165 r_free = 0.4165 target = 0.166931 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3775 r_free = 0.3775 target = 0.130043 restraints weight = 6948.154| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3759 r_free = 0.3759 target = 0.130643 restraints weight = 4177.753| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3774 r_free = 0.3774 target = 0.132484 restraints weight = 3739.341| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3778 r_free = 0.3778 target = 0.132850 restraints weight = 2721.577| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3780 r_free = 0.3780 target = 0.133093 restraints weight = 2612.007| |-----------------------------------------------------------------------------| r_work (final): 0.3770 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7562 moved from start: 0.3419 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 4544 Z= 0.101 Angle : 0.602 10.686 6195 Z= 0.285 Chirality : 0.041 0.130 688 Planarity : 0.004 0.054 771 Dihedral : 5.131 56.210 703 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 9.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.96 % Favored : 96.04 % Rotamer: Outliers : 1.92 % Allowed : 18.55 % Favored : 79.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.70 (0.38), residues: 530 helix: -0.31 (0.35), residues: 240 sheet: -1.66 (0.55), residues: 71 loop : 0.06 (0.44), residues: 219 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 694 TYR 0.013 0.001 TYR A 148 PHE 0.016 0.001 PHE A 69 TRP 0.011 0.001 TRP A 198 HIS 0.004 0.001 HIS A 160 Details of bonding type rmsd covalent geometry : bond 0.00230 ( 4541) covalent geometry : angle 0.60146 ( 6187) SS BOND : bond 0.00128 ( 1) SS BOND : angle 0.28857 ( 2) hydrogen bonds : bond 0.02444 ( 152) hydrogen bonds : angle 4.52328 ( 405) link_BETA1-4 : bond 0.00362 ( 1) link_BETA1-4 : angle 0.91406 ( 3) link_NAG-ASN : bond 0.00292 ( 1) link_NAG-ASN : angle 0.92213 ( 3) *********************** 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 79 residues out of total 486 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 70 time to evaluate : 0.131 Fit side-chains revert: symmetry clash REVERT: A 75 MET cc_start: 0.7700 (mmp) cc_final: 0.7400 (mmp) REVERT: A 115 MET cc_start: 0.7989 (mmm) cc_final: 0.7735 (tpp) REVERT: A 398 SER cc_start: 0.8300 (m) cc_final: 0.7884 (p) REVERT: A 417 ASP cc_start: 0.7281 (m-30) cc_final: 0.6747 (m-30) REVERT: A 462 GLU cc_start: 0.7249 (pm20) cc_final: 0.6999 (pm20) REVERT: A 600 MET cc_start: 0.6581 (ptt) cc_final: 0.6205 (ttp) REVERT: A 689 LEU cc_start: 0.8253 (OUTLIER) cc_final: 0.7639 (mt) outliers start: 9 outliers final: 5 residues processed: 72 average time/residue: 0.0318 time to fit residues: 3.4878 Evaluate side-chains 74 residues out of total 486 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 68 time to evaluate : 0.110 ------------------------------------------------------------------------------- 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 573 LEU Chi-restraints excluded: chain A residue 689 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 26 optimal weight: 0.0770 chunk 27 optimal weight: 2.9990 chunk 45 optimal weight: 0.5980 chunk 33 optimal weight: 2.9990 chunk 47 optimal weight: 6.9990 chunk 14 optimal weight: 0.9990 chunk 39 optimal weight: 0.0970 chunk 13 optimal weight: 0.9980 chunk 22 optimal weight: 0.7980 chunk 38 optimal weight: 5.9990 chunk 34 optimal weight: 1.9990 overall best weight: 0.5136 ------------------------------------------------------------------------------- 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 = 0.4157 r_free = 0.4157 target = 0.166386 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3773 r_free = 0.3773 target = 0.129363 restraints weight = 6909.480| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3719 r_free = 0.3719 target = 0.128274 restraints weight = 4552.369| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3739 r_free = 0.3739 target = 0.130498 restraints weight = 3799.319| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3742 r_free = 0.3742 target = 0.130616 restraints weight = 2866.050| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3744 r_free = 0.3744 target = 0.130860 restraints weight = 2707.967| |-----------------------------------------------------------------------------| r_work (final): 0.3763 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7600 moved from start: 0.3522 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.046 4544 Z= 0.107 Angle : 0.599 10.510 6195 Z= 0.284 Chirality : 0.041 0.123 688 Planarity : 0.004 0.054 771 Dihedral : 4.978 55.301 703 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 9.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.96 % Favored : 96.04 % Rotamer: Outliers : 1.92 % Allowed : 19.83 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.51 (0.38), residues: 530 helix: -0.14 (0.36), residues: 238 sheet: -1.50 (0.55), residues: 71 loop : 0.12 (0.44), residues: 221 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 694 TYR 0.014 0.001 TYR A 148 PHE 0.023 0.001 PHE A 696 TRP 0.011 0.001 TRP A 147 HIS 0.004 0.001 HIS A 160 Details of bonding type rmsd covalent geometry : bond 0.00249 ( 4541) covalent geometry : angle 0.59857 ( 6187) SS BOND : bond 0.00215 ( 1) SS BOND : angle 0.26909 ( 2) hydrogen bonds : bond 0.02399 ( 152) hydrogen bonds : angle 4.43184 ( 405) link_BETA1-4 : bond 0.00343 ( 1) link_BETA1-4 : angle 0.97233 ( 3) link_NAG-ASN : bond 0.00190 ( 1) link_NAG-ASN : angle 1.02418 ( 3) ********************** 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 80 residues out of total 486 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 71 time to evaluate : 0.113 Fit side-chains revert: symmetry clash REVERT: A 75 MET cc_start: 0.7650 (mmp) cc_final: 0.7247 (mmp) REVERT: A 115 MET cc_start: 0.8087 (mmm) cc_final: 0.7812 (tpp) REVERT: A 122 MET cc_start: 0.7418 (ttm) cc_final: 0.6718 (ttm) REVERT: A 213 ILE cc_start: 0.8334 (mm) cc_final: 0.8019 (mt) REVERT: A 398 SER cc_start: 0.8313 (m) cc_final: 0.7882 (p) REVERT: A 417 ASP cc_start: 0.7392 (m-30) cc_final: 0.6769 (m-30) REVERT: A 600 MET cc_start: 0.6696 (ptt) cc_final: 0.6324 (ttp) REVERT: A 689 LEU cc_start: 0.8219 (OUTLIER) cc_final: 0.7573 (mt) outliers start: 9 outliers final: 7 residues processed: 74 average time/residue: 0.0381 time to fit residues: 4.0759 Evaluate side-chains 77 residues out of total 486 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 69 time to evaluate : 0.100 ------------------------------------------------------------------------------- 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 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 10 optimal weight: 0.5980 chunk 6 optimal weight: 0.8980 chunk 14 optimal weight: 4.9990 chunk 13 optimal weight: 0.7980 chunk 2 optimal weight: 1.9990 chunk 27 optimal weight: 0.6980 chunk 1 optimal weight: 0.1980 chunk 8 optimal weight: 0.0770 chunk 7 optimal weight: 0.6980 chunk 46 optimal weight: 2.9990 chunk 42 optimal weight: 7.9990 overall best weight: 0.4538 ------------------------------------------------------------------------------- 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 = 0.4165 r_free = 0.4165 target = 0.167192 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3775 r_free = 0.3775 target = 0.130287 restraints weight = 6984.939| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3762 r_free = 0.3762 target = 0.131121 restraints weight = 4288.054| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3777 r_free = 0.3777 target = 0.133024 restraints weight = 3788.833| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3778 r_free = 0.3778 target = 0.133147 restraints weight = 2780.093| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3787 r_free = 0.3787 target = 0.134097 restraints weight = 2685.324| |-----------------------------------------------------------------------------| r_work (final): 0.3790 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7552 moved from start: 0.3584 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 4544 Z= 0.102 Angle : 0.594 10.423 6195 Z= 0.282 Chirality : 0.040 0.127 688 Planarity : 0.005 0.054 771 Dihedral : 4.834 54.577 703 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 9.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.15 % Favored : 95.85 % Rotamer: Outliers : 1.49 % Allowed : 20.47 % Favored : 78.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.36 (0.38), residues: 530 helix: -0.02 (0.36), residues: 238 sheet: -1.40 (0.56), residues: 71 loop : 0.19 (0.44), residues: 221 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 694 TYR 0.013 0.001 TYR A 148 PHE 0.022 0.001 PHE A 69 TRP 0.010 0.001 TRP A 147 HIS 0.004 0.001 HIS A 160 Details of bonding type rmsd covalent geometry : bond 0.00236 ( 4541) covalent geometry : angle 0.59382 ( 6187) SS BOND : bond 0.00221 ( 1) SS BOND : angle 0.22886 ( 2) hydrogen bonds : bond 0.02358 ( 152) hydrogen bonds : angle 4.36618 ( 405) link_BETA1-4 : bond 0.00358 ( 1) link_BETA1-4 : angle 0.93395 ( 3) link_NAG-ASN : bond 0.00205 ( 1) link_NAG-ASN : angle 1.02633 ( 3) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 842.63 seconds wall clock time: 15 minutes 7.20 seconds (907.20 seconds total)