Starting phenix.real_space_refine on Sun Apr 27 04:11:38 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9bum_44912/04_2025/9bum_44912.cif Found real_map, /net/cci-nas-00/data/ceres_data/9bum_44912/04_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_44912/04_2025/9bum_44912.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9bum_44912/04_2025/9bum_44912.map" model { file = "/net/cci-nas-00/data/ceres_data/9bum_44912/04_2025/9bum_44912.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9bum_44912/04_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-5669/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: 3.41, per 1000 atoms: 0.77 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: 1.06 Conformation dependent library (CDL) restraints added in 493.4 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: 0.53 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: 1.19 Time building geometry restraints manager: 1.28 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: 1.900 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: 0.190 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 15.060 Find NCS groups from input model: 0.040 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:2.960 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.250 ------------------------------------------------------------------------------- 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 (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 Details of bonding type rmsd link_NAG-ASN : bond 0.00816 ( 1) link_NAG-ASN : angle 4.47125 ( 3) link_BETA1-4 : bond 0.00583 ( 1) link_BETA1-4 : angle 2.90600 ( 3) hydrogen bonds : bond 0.30417 ( 152) hydrogen bonds : angle 10.63127 ( 405) SS BOND : bond 0.00651 ( 1) SS BOND : angle 1.41376 ( 2) covalent geometry : bond 0.00512 ( 4541) covalent geometry : angle 0.97163 ( 6187) *********************** 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 : 0.498 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: 0.2000 time to fit residues: 21.9547 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 : 0.503 ------------------------------------------------------------------------------- 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 = 0.128025 restraints weight = 6883.570| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3736 r_free = 0.3736 target = 0.128241 restraints weight = 4287.876| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3750 r_free = 0.3750 target = 0.130060 restraints weight = 3810.064| |-----------------------------------------------------------------------------| r_work (final): 0.3749 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7648 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 4544 Z= 0.146 Angle : 0.683 8.965 6195 Z= 0.340 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 Details of bonding type rmsd link_NAG-ASN : bond 0.00084 ( 1) link_NAG-ASN : angle 3.28489 ( 3) link_BETA1-4 : bond 0.00417 ( 1) link_BETA1-4 : angle 1.29157 ( 3) hydrogen bonds : bond 0.04040 ( 152) hydrogen bonds : angle 5.71055 ( 405) SS BOND : bond 0.00351 ( 1) SS BOND : angle 0.26311 ( 2) covalent geometry : bond 0.00323 ( 4541) covalent geometry : angle 0.67940 ( 6187) *********************** 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 : 0.512 Fit side-chains revert: symmetry clash REVERT: A 361 GLN cc_start: 0.7230 (pt0) cc_final: 0.6559 (tp40) REVERT: A 507 MET cc_start: 0.4708 (pmm) cc_final: 0.4417 (pmm) REVERT: A 588 LYS cc_start: 0.8794 (mttt) cc_final: 0.8558 (mtmt) REVERT: A 689 LEU cc_start: 0.8472 (tt) cc_final: 0.7932 (mt) outliers start: 7 outliers final: 4 residues processed: 73 average time/residue: 0.1536 time to fit residues: 15.3037 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 : 0.884 ------------------------------------------------------------------------------- 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: 0.9990 chunk 35 optimal weight: 0.9980 chunk 49 optimal weight: 5.9990 chunk 30 optimal weight: 0.9980 chunk 37 optimal weight: 0.8980 chunk 24 optimal weight: 0.7980 chunk 3 optimal weight: 1.9990 chunk 5 optimal weight: 0.8980 chunk 33 optimal weight: 0.6980 chunk 20 optimal weight: 0.6980 chunk 9 optimal weight: 0.5980 overall best weight: 0.7380 ------------------------------------------------------------------------------- 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 = 0.163684 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3744 r_free = 0.3744 target = 0.127186 restraints weight = 6867.706| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3721 r_free = 0.3721 target = 0.127136 restraints weight = 4497.962| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3737 r_free = 0.3737 target = 0.129099 restraints weight = 3975.850| |-----------------------------------------------------------------------------| r_work (final): 0.3746 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7654 moved from start: 0.2460 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 4544 Z= 0.133 Angle : 0.630 7.880 6195 Z= 0.310 Chirality : 0.043 0.152 688 Planarity : 0.005 0.053 771 Dihedral : 6.416 58.626 703 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 9.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.96 % Favored : 96.04 % Rotamer: Outliers : 1.71 % Allowed : 13.43 % Favored : 84.86 % 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: -2.26 (0.34), residues: 530 helix: -1.81 (0.31), residues: 239 sheet: -2.20 (0.50), residues: 75 loop : -0.51 (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 0.016 0.001 PHE A 431 TYR 0.017 0.002 TYR A 603 ARG 0.010 0.000 ARG A 694 Details of bonding type rmsd link_NAG-ASN : bond 0.00271 ( 1) link_NAG-ASN : angle 1.86433 ( 3) link_BETA1-4 : bond 0.00278 ( 1) link_BETA1-4 : angle 1.02995 ( 3) hydrogen bonds : bond 0.03234 ( 152) hydrogen bonds : angle 5.11026 ( 405) SS BOND : bond 0.00271 ( 1) SS BOND : angle 0.37327 ( 2) covalent geometry : bond 0.00302 ( 4541) covalent geometry : angle 0.62855 ( 6187) *********************** 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 : 1.417 Fit side-chains revert: symmetry clash REVERT: A 115 MET cc_start: 0.8238 (mmm) cc_final: 0.7733 (tpp) REVERT: A 361 GLN cc_start: 0.7296 (pt0) cc_final: 0.6603 (tp40) REVERT: A 507 MET cc_start: 0.4704 (pmm) cc_final: 0.4496 (pmm) REVERT: A 689 LEU cc_start: 0.8412 (tt) cc_final: 0.7781 (mt) outliers start: 8 outliers final: 6 residues processed: 67 average time/residue: 0.1899 time to fit residues: 19.1424 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 : 1.452 ------------------------------------------------------------------------------- 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: 9.9990 chunk 34 optimal weight: 3.9990 chunk 31 optimal weight: 1.9990 chunk 21 optimal weight: 5.9990 chunk 7 optimal weight: 0.6980 chunk 11 optimal weight: 1.9990 chunk 10 optimal weight: 0.9980 chunk 41 optimal weight: 6.9990 chunk 3 optimal weight: 0.5980 chunk 24 optimal weight: 0.7980 chunk 38 optimal weight: 0.1980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 410 HIS A 715 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4141 r_free = 0.4141 target = 0.165525 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3742 r_free = 0.3742 target = 0.127830 restraints weight = 6939.016| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3719 r_free = 0.3719 target = 0.127307 restraints weight = 4685.988| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3734 r_free = 0.3734 target = 0.129256 restraints weight = 4199.314| |-----------------------------------------------------------------------------| r_work (final): 0.3730 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7652 moved from start: 0.2726 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 4544 Z= 0.121 Angle : 0.590 9.388 6195 Z= 0.289 Chirality : 0.041 0.129 688 Planarity : 0.005 0.053 771 Dihedral : 5.915 54.231 703 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 9.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.72 % Favored : 95.28 % Rotamer: Outliers : 2.13 % Allowed : 15.78 % Favored : 82.09 % 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: -1.60 (0.36), residues: 530 helix: -1.17 (0.34), residues: 235 sheet: -1.95 (0.51), residues: 75 loop : -0.29 (0.42), residues: 220 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 0.015 0.001 PHE A 431 TYR 0.017 0.001 TYR A 603 ARG 0.005 0.000 ARG A 694 Details of bonding type rmsd link_NAG-ASN : bond 0.00184 ( 1) link_NAG-ASN : angle 1.34344 ( 3) link_BETA1-4 : bond 0.00184 ( 1) link_BETA1-4 : angle 0.89133 ( 3) hydrogen bonds : bond 0.02861 ( 152) hydrogen bonds : angle 4.79585 ( 405) SS BOND : bond 0.00247 ( 1) SS BOND : angle 0.38787 ( 2) covalent geometry : bond 0.00278 ( 4541) covalent geometry : angle 0.58881 ( 6187) *********************** 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 80 residues out of total 486 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 70 time to evaluate : 1.561 Fit side-chains revert: symmetry clash REVERT: A 115 MET cc_start: 0.8227 (mmm) cc_final: 0.7747 (tpp) REVERT: A 127 LEU cc_start: 0.7117 (OUTLIER) cc_final: 0.6861 (mp) REVERT: A 361 GLN cc_start: 0.7281 (pt0) cc_final: 0.6642 (tp40) REVERT: A 507 MET cc_start: 0.4749 (pmm) cc_final: 0.4534 (pmm) REVERT: A 600 MET cc_start: 0.6929 (ptt) cc_final: 0.6693 (ptt) REVERT: A 689 LEU cc_start: 0.8381 (OUTLIER) cc_final: 0.7722 (mt) outliers start: 10 outliers final: 7 residues processed: 73 average time/residue: 0.1986 time to fit residues: 20.6435 Evaluate side-chains 69 residues out of total 486 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 60 time to evaluate : 0.675 ------------------------------------------------------------------------------- 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 27 optimal weight: 0.6980 chunk 2 optimal weight: 2.9990 chunk 4 optimal weight: 0.0770 chunk 45 optimal weight: 4.9990 chunk 50 optimal weight: 2.9990 chunk 8 optimal weight: 2.9990 chunk 43 optimal weight: 7.9990 chunk 32 optimal weight: 1.9990 chunk 49 optimal weight: 9.9990 chunk 51 optimal weight: 1.9990 chunk 47 optimal weight: 2.9990 overall best weight: 1.5544 ------------------------------------------------------------------------------- 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 440 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4093 r_free = 0.4093 target = 0.160821 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3687 r_free = 0.3687 target = 0.123018 restraints weight = 7100.336| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3636 r_free = 0.3636 target = 0.121679 restraints weight = 5099.186| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3659 r_free = 0.3659 target = 0.123924 restraints weight = 4323.710| |-----------------------------------------------------------------------------| r_work (final): 0.3662 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7725 moved from start: 0.2855 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= 0.207 Angle : 0.641 8.520 6195 Z= 0.315 Chirality : 0.043 0.132 688 Planarity : 0.005 0.052 771 Dihedral : 6.055 55.975 703 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 10.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.28 % Favored : 94.72 % Rotamer: Outliers : 2.13 % Allowed : 17.70 % 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: -1.54 (0.36), residues: 530 helix: -1.03 (0.34), residues: 240 sheet: -1.75 (0.55), residues: 68 loop : -0.49 (0.41), residues: 222 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 147 HIS 0.009 0.002 HIS A 408 PHE 0.013 0.002 PHE A 123 TYR 0.017 0.002 TYR A 179 ARG 0.004 0.000 ARG A 694 Details of bonding type rmsd link_NAG-ASN : bond 0.00018 ( 1) link_NAG-ASN : angle 1.14734 ( 3) link_BETA1-4 : bond 0.00160 ( 1) link_BETA1-4 : angle 1.15030 ( 3) hydrogen bonds : bond 0.02994 ( 152) hydrogen bonds : angle 4.88363 ( 405) SS BOND : bond 0.00534 ( 1) SS BOND : angle 0.42185 ( 2) covalent geometry : bond 0.00483 ( 4541) covalent geometry : angle 0.64070 ( 6187) *********************** 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 75 residues out of total 486 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 65 time to evaluate : 0.498 Fit side-chains revert: symmetry clash REVERT: A 361 GLN cc_start: 0.7305 (pt0) cc_final: 0.6641 (tp40) REVERT: A 398 SER cc_start: 0.8442 (m) cc_final: 0.7942 (p) REVERT: A 600 MET cc_start: 0.6953 (ptt) cc_final: 0.6709 (ptt) REVERT: A 689 LEU cc_start: 0.8399 (OUTLIER) cc_final: 0.7708 (mt) outliers start: 10 outliers final: 7 residues processed: 66 average time/residue: 0.1083 time to fit residues: 10.4926 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 : 0.566 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 THR 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 Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 8 optimal weight: 0.7980 chunk 28 optimal weight: 0.7980 chunk 44 optimal weight: 20.0000 chunk 27 optimal weight: 0.2980 chunk 11 optimal weight: 0.5980 chunk 39 optimal weight: 0.0980 chunk 12 optimal weight: 0.0470 chunk 10 optimal weight: 0.5980 chunk 35 optimal weight: 0.0970 chunk 50 optimal weight: 1.9990 chunk 51 optimal weight: 0.6980 overall best weight: 0.2276 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 328 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4167 r_free = 0.4167 target = 0.167492 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3794 r_free = 0.3794 target = 0.131075 restraints weight = 6920.808| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3747 r_free = 0.3747 target = 0.130003 restraints weight = 4671.534| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3766 r_free = 0.3766 target = 0.132081 restraints weight = 4116.251| |-----------------------------------------------------------------------------| r_work (final): 0.3764 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7576 moved from start: 0.3095 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 4544 Z= 0.097 Angle : 0.574 7.599 6195 Z= 0.282 Chirality : 0.040 0.131 688 Planarity : 0.004 0.053 771 Dihedral : 5.340 51.475 703 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 8.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.77 % Favored : 96.23 % Rotamer: Outliers : 1.49 % Allowed : 18.12 % Favored : 80.38 % 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: -1.05 (0.37), residues: 530 helix: -0.66 (0.35), residues: 232 sheet: -1.72 (0.51), residues: 75 loop : -0.06 (0.43), residues: 223 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 198 HIS 0.003 0.001 HIS A 160 PHE 0.018 0.001 PHE A 696 TYR 0.013 0.001 TYR A 603 ARG 0.005 0.000 ARG A 694 Details of bonding type rmsd link_NAG-ASN : bond 0.00355 ( 1) link_NAG-ASN : angle 0.97280 ( 3) link_BETA1-4 : bond 0.00231 ( 1) link_BETA1-4 : angle 0.95639 ( 3) hydrogen bonds : bond 0.02493 ( 152) hydrogen bonds : angle 4.53916 ( 405) SS BOND : bond 0.00122 ( 1) SS BOND : angle 0.34969 ( 2) covalent geometry : bond 0.00210 ( 4541) covalent geometry : angle 0.57357 ( 6187) *********************** 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 78 residues out of total 486 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 71 time to evaluate : 0.653 Fit side-chains revert: symmetry clash REVERT: A 75 MET cc_start: 0.7883 (mmp) cc_final: 0.7503 (mmp) REVERT: A 115 MET cc_start: 0.8034 (mmm) cc_final: 0.7725 (tpp) REVERT: A 213 ILE cc_start: 0.8263 (mm) cc_final: 0.7892 (mt) REVERT: A 398 SER cc_start: 0.8326 (m) cc_final: 0.7831 (p) REVERT: A 600 MET cc_start: 0.6820 (ptt) cc_final: 0.6577 (ptt) REVERT: A 689 LEU cc_start: 0.8308 (OUTLIER) cc_final: 0.7698 (mt) outliers start: 7 outliers final: 4 residues processed: 71 average time/residue: 0.1510 time to fit residues: 15.4939 Evaluate side-chains 71 residues out of total 486 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 66 time to evaluate : 0.583 ------------------------------------------------------------------------------- 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 401 MET Chi-restraints excluded: chain A residue 573 LEU Chi-restraints excluded: chain A residue 689 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: 0.9990 chunk 48 optimal weight: 0.9980 chunk 39 optimal weight: 7.9990 chunk 21 optimal weight: 0.6980 chunk 23 optimal weight: 2.9990 chunk 29 optimal weight: 0.7980 chunk 20 optimal weight: 2.9990 chunk 44 optimal weight: 10.0000 chunk 32 optimal weight: 0.5980 chunk 27 optimal weight: 6.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- 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 = 0.4141 r_free = 0.4141 target = 0.164706 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3751 r_free = 0.3751 target = 0.127532 restraints weight = 7003.591| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3701 r_free = 0.3701 target = 0.126185 restraints weight = 4926.080| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3722 r_free = 0.3722 target = 0.128438 restraints weight = 4296.502| |-----------------------------------------------------------------------------| r_work (final): 0.3724 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7651 moved from start: 0.3190 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 4544 Z= 0.129 Angle : 0.578 6.784 6195 Z= 0.283 Chirality : 0.041 0.129 688 Planarity : 0.004 0.053 771 Dihedral : 5.301 51.447 703 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 8.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.09 % Favored : 94.91 % Rotamer: Outliers : 2.99 % Allowed : 17.27 % 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: -0.78 (0.37), residues: 530 helix: -0.40 (0.36), residues: 230 sheet: -1.71 (0.50), residues: 75 loop : 0.08 (0.44), residues: 225 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 0.010 0.001 PHE A 69 TYR 0.014 0.001 TYR A 415 ARG 0.004 0.000 ARG A 694 Details of bonding type rmsd link_NAG-ASN : bond 0.00125 ( 1) link_NAG-ASN : angle 1.00931 ( 3) link_BETA1-4 : bond 0.00289 ( 1) link_BETA1-4 : angle 1.10062 ( 3) hydrogen bonds : bond 0.02581 ( 152) hydrogen bonds : angle 4.53480 ( 405) SS BOND : bond 0.00310 ( 1) SS BOND : angle 0.32647 ( 2) covalent geometry : bond 0.00302 ( 4541) covalent geometry : angle 0.57719 ( 6187) *********************** 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 84 residues out of total 486 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 70 time to evaluate : 0.482 Fit side-chains revert: symmetry clash REVERT: A 75 MET cc_start: 0.7956 (mmp) cc_final: 0.7439 (mmp) REVERT: A 115 MET cc_start: 0.8111 (mmm) cc_final: 0.7787 (tpp) REVERT: A 127 LEU cc_start: 0.7189 (OUTLIER) cc_final: 0.6888 (mp) REVERT: A 213 ILE cc_start: 0.8340 (mm) cc_final: 0.7964 (mt) REVERT: A 398 SER cc_start: 0.8274 (m) cc_final: 0.7773 (p) REVERT: A 689 LEU cc_start: 0.8317 (OUTLIER) cc_final: 0.7678 (mt) outliers start: 14 outliers final: 7 residues processed: 74 average time/residue: 0.1048 time to fit residues: 11.2366 Evaluate side-chains 76 residues out of total 486 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 67 time to evaluate : 0.523 ------------------------------------------------------------------------------- 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 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 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: 5.9990 chunk 50 optimal weight: 0.9990 chunk 18 optimal weight: 0.2980 chunk 38 optimal weight: 2.9990 chunk 32 optimal weight: 2.9990 chunk 27 optimal weight: 1.9990 chunk 51 optimal weight: 1.9990 chunk 47 optimal weight: 0.9990 chunk 40 optimal weight: 6.9990 chunk 8 optimal weight: 0.0970 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 554 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4131 r_free = 0.4131 target = 0.164133 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3730 r_free = 0.3730 target = 0.126656 restraints weight = 6937.394| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3714 r_free = 0.3714 target = 0.127256 restraints weight = 4499.012| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3730 r_free = 0.3730 target = 0.129180 restraints weight = 3999.839| |-----------------------------------------------------------------------------| r_work (final): 0.3738 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7628 moved from start: 0.3318 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 4544 Z= 0.138 Angle : 0.609 12.464 6195 Z= 0.290 Chirality : 0.041 0.130 688 Planarity : 0.004 0.053 771 Dihedral : 5.245 52.338 703 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 9.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.72 % Favored : 95.28 % Rotamer: Outliers : 2.35 % Allowed : 18.34 % 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: -0.87 (0.37), residues: 530 helix: -0.39 (0.35), residues: 234 sheet: -1.73 (0.49), residues: 77 loop : -0.06 (0.44), residues: 219 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 198 HIS 0.011 0.001 HIS A 410 PHE 0.020 0.001 PHE A 696 TYR 0.016 0.002 TYR A 447 ARG 0.005 0.000 ARG A 694 Details of bonding type rmsd link_NAG-ASN : bond 0.00144 ( 1) link_NAG-ASN : angle 0.96652 ( 3) link_BETA1-4 : bond 0.00234 ( 1) link_BETA1-4 : angle 1.01237 ( 3) hydrogen bonds : bond 0.02579 ( 152) hydrogen bonds : angle 4.54813 ( 405) SS BOND : bond 0.00351 ( 1) SS BOND : angle 0.31015 ( 2) covalent geometry : bond 0.00324 ( 4541) covalent geometry : angle 0.60828 ( 6187) *********************** 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: 11 poor density : 68 time to evaluate : 0.736 Fit side-chains revert: symmetry clash REVERT: A 75 MET cc_start: 0.7970 (mmp) cc_final: 0.7445 (mmp) REVERT: A 115 MET cc_start: 0.8122 (mmm) cc_final: 0.7809 (tpp) REVERT: A 127 LEU cc_start: 0.7143 (OUTLIER) cc_final: 0.6790 (mp) REVERT: A 213 ILE cc_start: 0.8335 (mm) cc_final: 0.7942 (mt) REVERT: A 398 SER cc_start: 0.8223 (m) cc_final: 0.7737 (p) REVERT: A 462 GLU cc_start: 0.7175 (pm20) cc_final: 0.6776 (pm20) REVERT: A 689 LEU cc_start: 0.8277 (OUTLIER) cc_final: 0.7654 (mt) outliers start: 11 outliers final: 8 residues processed: 70 average time/residue: 0.1279 time to fit residues: 12.6521 Evaluate side-chains 77 residues out of total 486 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 67 time to evaluate : 0.481 ------------------------------------------------------------------------------- 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 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 18 optimal weight: 2.9990 chunk 29 optimal weight: 0.9990 chunk 7 optimal weight: 0.6980 chunk 17 optimal weight: 1.9990 chunk 37 optimal weight: 0.0370 chunk 11 optimal weight: 0.7980 chunk 44 optimal weight: 9.9990 chunk 51 optimal weight: 2.9990 chunk 14 optimal weight: 6.9990 chunk 2 optimal weight: 0.9990 chunk 28 optimal weight: 0.8980 overall best weight: 0.6860 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 410 HIS A 554 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4141 r_free = 0.4141 target = 0.165310 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3743 r_free = 0.3743 target = 0.127799 restraints weight = 6867.311| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3720 r_free = 0.3720 target = 0.127686 restraints weight = 4476.360| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3736 r_free = 0.3736 target = 0.129615 restraints weight = 4150.568| |-----------------------------------------------------------------------------| r_work (final): 0.3740 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7617 moved from start: 0.3392 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 4544 Z= 0.121 Angle : 0.614 12.092 6195 Z= 0.289 Chirality : 0.041 0.129 688 Planarity : 0.004 0.053 771 Dihedral : 5.156 53.077 703 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 9.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.53 % Favored : 95.47 % Rotamer: Outliers : 2.77 % Allowed : 18.55 % 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: -0.71 (0.37), residues: 530 helix: -0.23 (0.36), residues: 234 sheet: -1.67 (0.50), residues: 75 loop : -0.01 (0.44), residues: 221 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 198 HIS 0.004 0.001 HIS A 160 PHE 0.009 0.001 PHE A 382 TYR 0.014 0.001 TYR A 447 ARG 0.004 0.000 ARG A 694 Details of bonding type rmsd link_NAG-ASN : bond 0.00198 ( 1) link_NAG-ASN : angle 1.00073 ( 3) link_BETA1-4 : bond 0.00310 ( 1) link_BETA1-4 : angle 0.97695 ( 3) hydrogen bonds : bond 0.02478 ( 152) hydrogen bonds : angle 4.48341 ( 405) SS BOND : bond 0.00273 ( 1) SS BOND : angle 0.34298 ( 2) covalent geometry : bond 0.00284 ( 4541) covalent geometry : angle 0.61343 ( 6187) *********************** 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 84 residues out of total 486 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 71 time to evaluate : 0.507 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 75 MET cc_start: 0.7905 (mmp) cc_final: 0.7411 (mmp) REVERT: A 115 MET cc_start: 0.8070 (mmm) cc_final: 0.7784 (tpp) REVERT: A 127 LEU cc_start: 0.7119 (OUTLIER) cc_final: 0.6849 (mp) REVERT: A 213 ILE cc_start: 0.8316 (mm) cc_final: 0.7924 (mt) REVERT: A 398 SER cc_start: 0.8201 (m) cc_final: 0.7948 (p) REVERT: A 462 GLU cc_start: 0.7137 (pm20) cc_final: 0.6760 (pm20) REVERT: A 689 LEU cc_start: 0.8244 (OUTLIER) cc_final: 0.7631 (mt) outliers start: 13 outliers final: 9 residues processed: 74 average time/residue: 0.1291 time to fit residues: 13.0710 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 : 0.528 ------------------------------------------------------------------------------- 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 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: 0.8980 chunk 12 optimal weight: 0.5980 chunk 49 optimal weight: 9.9990 chunk 27 optimal weight: 0.6980 chunk 47 optimal weight: 0.9990 chunk 41 optimal weight: 0.1980 chunk 32 optimal weight: 0.7980 chunk 7 optimal weight: 0.6980 chunk 43 optimal weight: 10.0000 chunk 45 optimal weight: 0.0020 chunk 26 optimal weight: 0.8980 overall best weight: 0.4388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 554 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4161 r_free = 0.4161 target = 0.166664 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3769 r_free = 0.3769 target = 0.129451 restraints weight = 6820.346| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3755 r_free = 0.3755 target = 0.130251 restraints weight = 4091.706| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3769 r_free = 0.3769 target = 0.132051 restraints weight = 3695.630| |-----------------------------------------------------------------------------| r_work (final): 0.3773 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7582 moved from start: 0.3540 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= 0.104 Angle : 0.620 12.092 6195 Z= 0.294 Chirality : 0.041 0.135 688 Planarity : 0.004 0.054 771 Dihedral : 5.069 52.804 703 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 8.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.53 % Favored : 95.47 % Rotamer: Outliers : 2.13 % Allowed : 18.98 % Favored : 78.89 % 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: -0.54 (0.38), residues: 530 helix: -0.10 (0.36), residues: 240 sheet: -1.66 (0.52), residues: 75 loop : 0.12 (0.45), residues: 215 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 198 HIS 0.008 0.001 HIS A 410 PHE 0.026 0.001 PHE A 696 TYR 0.031 0.001 TYR A 447 ARG 0.005 0.000 ARG A 694 Details of bonding type rmsd link_NAG-ASN : bond 0.00248 ( 1) link_NAG-ASN : angle 0.95884 ( 3) link_BETA1-4 : bond 0.00376 ( 1) link_BETA1-4 : angle 0.95470 ( 3) hydrogen bonds : bond 0.02413 ( 152) hydrogen bonds : angle 4.45631 ( 405) SS BOND : bond 0.00196 ( 1) SS BOND : angle 0.25762 ( 2) covalent geometry : bond 0.00237 ( 4541) covalent geometry : angle 0.62014 ( 6187) ********************** 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 84 residues out of total 486 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 74 time to evaluate : 0.481 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 75 MET cc_start: 0.7847 (mmp) cc_final: 0.7392 (mmp) REVERT: A 115 MET cc_start: 0.8081 (mmm) cc_final: 0.7793 (tpp) REVERT: A 213 ILE cc_start: 0.8300 (mm) cc_final: 0.7894 (mt) REVERT: A 398 SER cc_start: 0.8302 (m) cc_final: 0.7902 (p) REVERT: A 462 GLU cc_start: 0.7191 (pm20) cc_final: 0.6824 (pm20) REVERT: A 689 LEU cc_start: 0.8230 (OUTLIER) cc_final: 0.7598 (mt) outliers start: 10 outliers final: 7 residues processed: 77 average time/residue: 0.1102 time to fit residues: 12.0428 Evaluate side-chains 82 residues out of total 486 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 74 time to evaluate : 0.471 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.0670 chunk 17 optimal weight: 0.0170 chunk 28 optimal weight: 3.9990 chunk 9 optimal weight: 0.9990 chunk 29 optimal weight: 3.9990 chunk 50 optimal weight: 1.9990 chunk 49 optimal weight: 9.9990 chunk 27 optimal weight: 0.8980 chunk 24 optimal weight: 0.6980 chunk 33 optimal weight: 0.6980 chunk 42 optimal weight: 6.9990 overall best weight: 0.4756 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 385 GLN A 410 HIS A 554 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4163 r_free = 0.4163 target = 0.167338 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3781 r_free = 0.3781 target = 0.130744 restraints weight = 6913.376| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3741 r_free = 0.3741 target = 0.129983 restraints weight = 4819.316| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3758 r_free = 0.3758 target = 0.131993 restraints weight = 4231.263| |-----------------------------------------------------------------------------| r_work (final): 0.3761 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7573 moved from start: 0.3617 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 4544 Z= 0.105 Angle : 0.613 11.949 6195 Z= 0.291 Chirality : 0.040 0.129 688 Planarity : 0.004 0.054 771 Dihedral : 5.010 51.861 703 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 8.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.96 % Favored : 96.04 % Rotamer: Outliers : 1.92 % Allowed : 20.26 % Favored : 77.83 % 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: -0.40 (0.38), residues: 530 helix: -0.00 (0.36), residues: 240 sheet: -1.63 (0.55), residues: 73 loop : 0.21 (0.45), residues: 217 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 0.027 0.001 TYR A 447 ARG 0.005 0.000 ARG A 694 Details of bonding type rmsd link_NAG-ASN : bond 0.00211 ( 1) link_NAG-ASN : angle 1.01438 ( 3) link_BETA1-4 : bond 0.00368 ( 1) link_BETA1-4 : angle 0.95623 ( 3) hydrogen bonds : bond 0.02324 ( 152) hydrogen bonds : angle 4.45244 ( 405) SS BOND : bond 0.00191 ( 1) SS BOND : angle 0.27680 ( 2) covalent geometry : bond 0.00243 ( 4541) covalent geometry : angle 0.61306 ( 6187) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2310.16 seconds wall clock time: 42 minutes 13.61 seconds (2533.61 seconds total)