Starting phenix.real_space_refine on Tue Feb 11 13:34:40 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8yht_39300/02_2025/8yht_39300.cif Found real_map, /net/cci-nas-00/data/ceres_data/8yht_39300/02_2025/8yht_39300.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.88 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8yht_39300/02_2025/8yht_39300.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8yht_39300/02_2025/8yht_39300.map" model { file = "/net/cci-nas-00/data/ceres_data/8yht_39300/02_2025/8yht_39300.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8yht_39300/02_2025/8yht_39300.cif" } resolution = 2.88 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= -0.000 sd= 0.022 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 20 5.16 5 C 3724 2.51 5 N 972 2.21 5 O 1129 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 2 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib" Total number of atoms: 5845 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 5323 Number of conformers: 1 Conformer: "" Number of residues, atoms: 663, 5323 Classifications: {'peptide': 663} Link IDs: {'PTRANS': 26, 'TRANS': 636} Chain breaks: 1 Chain: "B" Number of atoms: 326 Number of conformers: 1 Conformer: "" Number of residues, atoms: 40, 326 Classifications: {'peptide': 40} Link IDs: {'PTRANS': 1, 'TRANS': 38} Chain: "C" 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: "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: "E" 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: "F" 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: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 84 Unusual residues: {'NAG': 6} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Time building chain proxies: 4.32, per 1000 atoms: 0.74 Number of scatterers: 5845 At special positions: 0 Unit cell: (52.456, 102.92, 111.552, 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 20 16.00 O 1129 8.00 N 972 7.00 C 3724 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS A 28 " - pdb=" SG CYS A 37 " distance=2.03 Simple disulfide: pdb=" SG CYS A 95 " - pdb=" SG CYS A 122 " distance=2.03 Simple disulfide: pdb=" SG CYS A 649 " - pdb=" SG CYS A 677 " distance=2.03 Simple disulfide: pdb=" SG CYS A 651 " - pdb=" SG CYS A 696 " distance=2.03 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 C 1 " - " NAG C 2 " " NAG D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " NAG-ASN " NAG A 801 " - " ASN A 52 " " NAG A 802 " - " ASN A 57 " " NAG A 803 " - " ASN A 124 " " NAG A 804 " - " ASN A 252 " " NAG A 805 " - " ASN A 275 " " NAG A 806 " - " ASN A 291 " " NAG C 1 " - " ASN A 247 " " NAG D 1 " - " ASN A 265 " " NAG E 1 " - " ASN A 398 " " NAG F 1 " - " ASN A 413 " Time building additional restraints: 1.48 Conformation dependent library (CDL) restraints added in 840.1 milliseconds 1394 Ramachandran restraints generated. 697 Oldfield, 0 Emsley, 697 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1354 Finding SS restraints... Secondary structure from input PDB file: 13 helices and 6 sheets defined 15.6% alpha, 5.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.54 Creating SS restraints... Processing helix chain 'A' and resid 69 through 73 removed outlier: 3.681A pdb=" N ARG A 73 " --> pdb=" O ASN A 70 " (cutoff:3.500A) Processing helix chain 'A' and resid 91 through 96 Processing helix chain 'A' and resid 188 through 195 removed outlier: 4.612A pdb=" N ILE A 193 " --> pdb=" O GLU A 190 " (cutoff:3.500A) Processing helix chain 'A' and resid 237 through 245 Processing helix chain 'A' and resid 269 through 273 removed outlier: 3.850A pdb=" N TRP A 273 " --> pdb=" O GLY A 270 " (cutoff:3.500A) Processing helix chain 'A' and resid 314 through 319 removed outlier: 4.166A pdb=" N LEU A 318 " --> pdb=" O SER A 315 " (cutoff:3.500A) removed outlier: 4.181A pdb=" N HIS A 319 " --> pdb=" O HIS A 316 " (cutoff:3.500A) Processing helix chain 'A' and resid 397 through 405 removed outlier: 3.591A pdb=" N THR A 400 " --> pdb=" O THR A 397 " (cutoff:3.500A) removed outlier: 4.159A pdb=" N PHE A 401 " --> pdb=" O ASN A 398 " (cutoff:3.500A) removed outlier: 5.386A pdb=" N VAL A 402 " --> pdb=" O GLU A 399 " (cutoff:3.500A) removed outlier: 4.858A pdb=" N SER A 403 " --> pdb=" O THR A 400 " (cutoff:3.500A) Processing helix chain 'A' and resid 542 through 546 removed outlier: 3.726A pdb=" N TRP A 546 " --> pdb=" O ALA A 543 " (cutoff:3.500A) Processing helix chain 'A' and resid 655 through 662 Processing helix chain 'A' and resid 680 through 684 removed outlier: 3.569A pdb=" N TYR A 683 " --> pdb=" O PRO A 680 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N HIS A 684 " --> pdb=" O PRO A 681 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 680 through 684' Processing helix chain 'A' and resid 687 through 691 Processing helix chain 'B' and resid 2 through 21 removed outlier: 3.713A pdb=" N LEU B 11 " --> pdb=" O VAL B 7 " (cutoff:3.500A) Processing helix chain 'B' and resid 22 through 40 Processing sheet with id=AA1, first strand: chain 'A' and resid 29 through 30 removed outlier: 4.413A pdb=" N THR A 29 " --> pdb=" O ASP A 36 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 79 through 81 removed outlier: 6.629A pdb=" N LEU A 104 " --> pdb=" O HIS A 129 " (cutoff:3.500A) removed outlier: 7.622A pdb=" N LEU A 128 " --> pdb=" O ASP A 153 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 333 through 335 removed outlier: 6.879A pdb=" N ILE A 310 " --> pdb=" O THR A 334 " (cutoff:3.500A) removed outlier: 4.167A pdb=" N LYS A 345 " --> pdb=" O GLN A 311 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N LEU A 313 " --> pdb=" O LYS A 345 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'A' and resid 395 through 396 Processing sheet with id=AA5, first strand: chain 'A' and resid 411 through 412 removed outlier: 3.699A pdb=" N MET A 486 " --> pdb=" O ILE A 461 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N SER A 514 " --> pdb=" O LEU A 487 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 444 through 446 removed outlier: 6.915A pdb=" N GLN A 445 " --> pdb=" O GLN A 470 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N LYS A 493 " --> pdb=" O LEU A 469 " (cutoff:3.500A) 69 hydrogen bonds defined for protein. 162 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: 1.32 Time building geometry restraints manager: 1.74 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 1874 1.34 - 1.46: 1285 1.46 - 1.58: 2773 1.58 - 1.70: 0 1.70 - 1.82: 29 Bond restraints: 5961 Sorted by residual: bond pdb=" N ASP A 292 " pdb=" CA ASP A 292 " ideal model delta sigma weight residual 1.457 1.487 -0.030 1.29e-02 6.01e+03 5.29e+00 bond pdb=" N PHE A 294 " pdb=" CA PHE A 294 " ideal model delta sigma weight residual 1.457 1.485 -0.028 1.29e-02 6.01e+03 4.62e+00 bond pdb=" N SER A 293 " pdb=" CA SER A 293 " ideal model delta sigma weight residual 1.454 1.480 -0.026 1.31e-02 5.83e+03 3.96e+00 bond pdb=" CA SER A 293 " pdb=" CB SER A 293 " ideal model delta sigma weight residual 1.534 1.503 0.031 1.60e-02 3.91e+03 3.88e+00 bond pdb=" C1 NAG A 805 " pdb=" O5 NAG A 805 " ideal model delta sigma weight residual 1.406 1.441 -0.035 2.00e-02 2.50e+03 3.06e+00 ... (remaining 5956 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.57: 7741 1.57 - 3.14: 291 3.14 - 4.71: 43 4.71 - 6.28: 9 6.28 - 7.85: 1 Bond angle restraints: 8085 Sorted by residual: angle pdb=" N ALA A 491 " pdb=" CA ALA A 491 " pdb=" C ALA A 491 " ideal model delta sigma weight residual 108.63 103.06 5.57 1.60e+00 3.91e-01 1.21e+01 angle pdb=" CA SER A 293 " pdb=" C SER A 293 " pdb=" O SER A 293 " ideal model delta sigma weight residual 121.68 117.84 3.84 1.18e+00 7.18e-01 1.06e+01 angle pdb=" N GLU B 15 " pdb=" CA GLU B 15 " pdb=" CB GLU B 15 " ideal model delta sigma weight residual 110.16 114.68 -4.52 1.48e+00 4.57e-01 9.32e+00 angle pdb=" CA VAL A 144 " pdb=" C VAL A 144 " pdb=" N LYS A 145 " ideal model delta sigma weight residual 116.60 120.92 -4.32 1.45e+00 4.76e-01 8.89e+00 angle pdb=" C PHE A 294 " pdb=" N ALA A 295 " pdb=" CA ALA A 295 " ideal model delta sigma weight residual 120.99 115.82 5.17 1.86e+00 2.89e-01 7.72e+00 ... (remaining 8080 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.41: 3453 21.41 - 42.83: 290 42.83 - 64.24: 32 64.24 - 85.66: 8 85.66 - 107.07: 8 Dihedral angle restraints: 3791 sinusoidal: 1721 harmonic: 2070 Sorted by residual: dihedral pdb=" CB CYS A 651 " pdb=" SG CYS A 651 " pdb=" SG CYS A 696 " pdb=" CB CYS A 696 " ideal model delta sinusoidal sigma weight residual 93.00 12.59 80.41 1 1.00e+01 1.00e-02 8.00e+01 dihedral pdb=" CB CYS A 649 " pdb=" SG CYS A 649 " pdb=" SG CYS A 677 " pdb=" CB CYS A 677 " ideal model delta sinusoidal sigma weight residual 93.00 34.69 58.31 1 1.00e+01 1.00e-02 4.56e+01 dihedral pdb=" CA ASN A 61 " pdb=" C ASN A 61 " pdb=" N GLN A 62 " pdb=" CA GLN A 62 " ideal model delta harmonic sigma weight residual 180.00 157.29 22.71 0 5.00e+00 4.00e-02 2.06e+01 ... (remaining 3788 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.044: 634 0.044 - 0.088: 275 0.088 - 0.131: 59 0.131 - 0.175: 6 0.175 - 0.219: 2 Chirality restraints: 976 Sorted by residual: chirality pdb=" C1 NAG A 806 " pdb=" ND2 ASN A 291 " pdb=" C2 NAG A 806 " pdb=" O5 NAG A 806 " both_signs ideal model delta sigma weight residual False -2.40 -2.18 -0.22 2.00e-01 2.50e+01 1.20e+00 chirality pdb=" C1 NAG F 1 " pdb=" ND2 ASN A 413 " pdb=" C2 NAG F 1 " pdb=" O5 NAG F 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.22 -0.18 2.00e-01 2.50e+01 8.50e-01 chirality pdb=" CB ILE A 591 " pdb=" CA ILE A 591 " pdb=" CG1 ILE A 591 " pdb=" CG2 ILE A 591 " both_signs ideal model delta sigma weight residual False 2.64 2.48 0.16 2.00e-01 2.50e+01 6.63e-01 ... (remaining 973 not shown) Planarity restraints: 1024 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE A 668 " -0.028 5.00e-02 4.00e+02 4.26e-02 2.91e+00 pdb=" N PRO A 669 " 0.074 5.00e-02 4.00e+02 pdb=" CA PRO A 669 " -0.022 5.00e-02 4.00e+02 pdb=" CD PRO A 669 " -0.024 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ASN A 291 " 0.008 2.00e-02 2.50e+03 1.68e-02 2.81e+00 pdb=" C ASN A 291 " -0.029 2.00e-02 2.50e+03 pdb=" O ASN A 291 " 0.011 2.00e-02 2.50e+03 pdb=" N ASP A 292 " 0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLY A 631 " 0.026 5.00e-02 4.00e+02 3.98e-02 2.53e+00 pdb=" N PRO A 632 " -0.069 5.00e-02 4.00e+02 pdb=" CA PRO A 632 " 0.021 5.00e-02 4.00e+02 pdb=" CD PRO A 632 " 0.022 5.00e-02 4.00e+02 ... (remaining 1021 not shown) Histogram of nonbonded interaction distances: 2.00 - 2.58: 52 2.58 - 3.16: 4839 3.16 - 3.74: 8712 3.74 - 4.32: 12137 4.32 - 4.90: 19597 Nonbonded interactions: 45337 Sorted by model distance: nonbonded pdb=" NZ LYS A 416 " pdb=" OE2 GLU B 19 " model vdw 1.995 3.120 nonbonded pdb=" O GLU A 363 " pdb=" OG SER A 389 " model vdw 2.211 3.040 nonbonded pdb=" OG SER A 387 " pdb=" OG1 THR A 415 " model vdw 2.270 3.040 nonbonded pdb=" O ASP A 648 " pdb=" OG SER A 653 " model vdw 2.275 3.040 nonbonded pdb=" NZ LYS A 201 " pdb=" OE2 GLU A 203 " model vdw 2.285 3.120 ... (remaining 45332 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 Found NCS groups: ncs_group { reference = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' } 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.480 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: 0.230 Check model and map are aligned: 0.040 Set scattering table: 0.050 Process input model: 17.160 Find NCS groups from input model: 0.210 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:13.820 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.020 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6217 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 : 0.004 0.036 5961 Z= 0.248 Angle : 0.700 7.848 8085 Z= 0.359 Chirality : 0.047 0.219 976 Planarity : 0.004 0.043 1014 Dihedral : 15.457 107.071 2425 Min Nonbonded Distance : 1.995 Molprobity Statistics. All-atom Clashscore : 11.47 Ramachandran Plot: Outliers : 0.14 % Allowed : 12.05 % Favored : 87.80 % Rotamer: Outliers : 0.46 % Allowed : 0.31 % Favored : 99.23 % 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: -3.01 (0.32), residues: 697 helix: -0.67 (0.62), residues: 75 sheet: -4.11 (0.49), residues: 74 loop : -2.04 (0.27), residues: 548 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP A 546 HIS 0.003 0.001 HIS A 108 PHE 0.009 0.001 PHE A 119 TYR 0.020 0.002 TYR B 6 ARG 0.002 0.000 ARG A 689 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1394 Ramachandran restraints generated. 697 Oldfield, 0 Emsley, 697 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1394 Ramachandran restraints generated. 697 Oldfield, 0 Emsley, 697 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 651 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 157 time to evaluate : 0.774 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 3 outliers final: 0 residues processed: 160 average time/residue: 0.9064 time to fit residues: 154.1697 Evaluate side-chains 68 residues out of total 651 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 68 time to evaluate : 0.696 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 59 optimal weight: 4.9990 chunk 53 optimal weight: 4.9990 chunk 29 optimal weight: 3.9990 chunk 18 optimal weight: 0.9980 chunk 35 optimal weight: 0.9990 chunk 28 optimal weight: 2.9990 chunk 54 optimal weight: 0.8980 chunk 21 optimal weight: 0.7980 chunk 33 optimal weight: 2.9990 chunk 40 optimal weight: 0.0870 chunk 63 optimal weight: 0.9980 overall best weight: 0.7558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 107 GLN A 109 ASN A 169 GLN ** A 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 232 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 361 ASN A 365 ASN A 538 GLN A 541 ASN A 550 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4784 r_free = 0.4784 target = 0.146540 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4420 r_free = 0.4420 target = 0.119051 restraints weight = 14192.777| |-----------------------------------------------------------------------------| r_work (start): 0.4379 rms_B_bonded: 5.55 r_work (final): 0.4379 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6577 moved from start: 0.2614 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 5961 Z= 0.231 Angle : 0.760 7.326 8085 Z= 0.368 Chirality : 0.050 0.493 976 Planarity : 0.004 0.047 1014 Dihedral : 10.292 86.353 1032 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 13.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.05 % Favored : 88.95 % Rotamer: Outliers : 3.53 % Allowed : 14.59 % Favored : 81.87 % 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: -2.90 (0.31), residues: 697 helix: -0.56 (0.60), residues: 69 sheet: -4.09 (0.45), residues: 80 loop : -1.91 (0.27), residues: 548 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 546 HIS 0.002 0.001 HIS A 108 PHE 0.014 0.001 PHE A 574 TYR 0.018 0.002 TYR A 307 ARG 0.005 0.001 ARG A 394 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1394 Ramachandran restraints generated. 697 Oldfield, 0 Emsley, 697 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1394 Ramachandran restraints generated. 697 Oldfield, 0 Emsley, 697 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 651 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 75 time to evaluate : 0.771 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 94 LEU cc_start: 0.8427 (OUTLIER) cc_final: 0.8074 (mm) REVERT: A 245 LEU cc_start: 0.8509 (OUTLIER) cc_final: 0.8259 (mm) REVERT: A 330 LYS cc_start: 0.7694 (tttm) cc_final: 0.7174 (tttp) REVERT: A 347 ASP cc_start: 0.5933 (m-30) cc_final: 0.5497 (m-30) REVERT: A 361 ASN cc_start: 0.7110 (OUTLIER) cc_final: 0.6217 (t0) REVERT: A 440 LEU cc_start: 0.8305 (OUTLIER) cc_final: 0.8010 (mp) REVERT: A 525 MET cc_start: 0.4616 (OUTLIER) cc_final: 0.3734 (mpt) REVERT: B 8 LYS cc_start: 0.9146 (mtmm) cc_final: 0.8943 (ptpt) REVERT: B 27 ARG cc_start: 0.9333 (mmp80) cc_final: 0.9034 (mmp80) outliers start: 23 outliers final: 8 residues processed: 90 average time/residue: 0.7491 time to fit residues: 72.9212 Evaluate side-chains 75 residues out of total 651 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 62 time to evaluate : 0.724 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 THR Chi-restraints excluded: chain A residue 94 LEU Chi-restraints excluded: chain A residue 154 LEU Chi-restraints excluded: chain A residue 245 LEU Chi-restraints excluded: chain A residue 361 ASN Chi-restraints excluded: chain A residue 370 ILE Chi-restraints excluded: chain A residue 389 SER Chi-restraints excluded: chain A residue 413 ASN Chi-restraints excluded: chain A residue 440 LEU Chi-restraints excluded: chain A residue 525 MET Chi-restraints excluded: chain A residue 555 ILE Chi-restraints excluded: chain A residue 667 ASN Chi-restraints excluded: chain B residue 30 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 39 optimal weight: 5.9990 chunk 61 optimal weight: 0.8980 chunk 60 optimal weight: 0.0870 chunk 1 optimal weight: 10.0000 chunk 47 optimal weight: 6.9990 chunk 28 optimal weight: 3.9990 chunk 14 optimal weight: 5.9990 chunk 30 optimal weight: 0.5980 chunk 3 optimal weight: 6.9990 chunk 50 optimal weight: 2.9990 chunk 34 optimal weight: 4.9990 overall best weight: 1.7162 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 61 ASN ** A 232 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 609 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4738 r_free = 0.4738 target = 0.142917 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4362 r_free = 0.4362 target = 0.115383 restraints weight = 14122.467| |-----------------------------------------------------------------------------| r_work (start): 0.4324 rms_B_bonded: 5.41 r_work (final): 0.4324 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6710 moved from start: 0.3120 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 5961 Z= 0.283 Angle : 0.766 8.252 8085 Z= 0.371 Chirality : 0.050 0.452 976 Planarity : 0.004 0.052 1014 Dihedral : 8.717 65.530 1032 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 12.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.34 % Favored : 87.66 % Rotamer: Outliers : 3.84 % Allowed : 18.13 % Favored : 78.03 % 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: -2.85 (0.31), residues: 697 helix: -0.47 (0.61), residues: 68 sheet: -4.19 (0.44), residues: 80 loop : -1.86 (0.27), residues: 549 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 452 HIS 0.004 0.001 HIS A 108 PHE 0.014 0.001 PHE A 119 TYR 0.017 0.002 TYR B 5 ARG 0.004 0.000 ARG A 394 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1394 Ramachandran restraints generated. 697 Oldfield, 0 Emsley, 697 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1394 Ramachandran restraints generated. 697 Oldfield, 0 Emsley, 697 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 651 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 65 time to evaluate : 0.712 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 201 LYS cc_start: 0.8287 (tmmt) cc_final: 0.7813 (tmmm) REVERT: A 330 LYS cc_start: 0.7780 (tttm) cc_final: 0.7391 (ttmp) REVERT: A 347 ASP cc_start: 0.6338 (m-30) cc_final: 0.5916 (m-30) REVERT: A 525 MET cc_start: 0.4926 (OUTLIER) cc_final: 0.3996 (mpt) REVERT: A 575 ASP cc_start: 0.7472 (m-30) cc_final: 0.7141 (m-30) REVERT: A 585 LEU cc_start: 0.8091 (mt) cc_final: 0.7839 (mm) REVERT: A 613 LYS cc_start: 0.8563 (mttt) cc_final: 0.8183 (mmmt) REVERT: B 27 ARG cc_start: 0.9320 (mmp80) cc_final: 0.9052 (mmp80) REVERT: B 31 GLU cc_start: 0.8919 (mm-30) cc_final: 0.8707 (mm-30) outliers start: 25 outliers final: 10 residues processed: 81 average time/residue: 0.8178 time to fit residues: 71.4656 Evaluate side-chains 72 residues out of total 651 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 61 time to evaluate : 0.671 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 THR Chi-restraints excluded: chain A residue 122 CYS Chi-restraints excluded: chain A residue 231 VAL Chi-restraints excluded: chain A residue 370 ILE Chi-restraints excluded: chain A residue 389 SER Chi-restraints excluded: chain A residue 413 ASN Chi-restraints excluded: chain A residue 510 ILE Chi-restraints excluded: chain A residue 525 MET Chi-restraints excluded: chain A residue 555 ILE Chi-restraints excluded: chain A residue 570 GLU Chi-restraints excluded: chain B residue 30 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 45 optimal weight: 0.9980 chunk 43 optimal weight: 1.9990 chunk 50 optimal weight: 2.9990 chunk 11 optimal weight: 9.9990 chunk 42 optimal weight: 0.1980 chunk 56 optimal weight: 7.9990 chunk 63 optimal weight: 2.9990 chunk 57 optimal weight: 0.0010 chunk 36 optimal weight: 2.9990 chunk 68 optimal weight: 0.9990 chunk 60 optimal weight: 0.8980 overall best weight: 0.6188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 96 GLN A 133 ASN ** A 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 361 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4778 r_free = 0.4778 target = 0.145474 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4430 r_free = 0.4430 target = 0.118881 restraints weight = 14276.254| |-----------------------------------------------------------------------------| r_work (start): 0.4384 rms_B_bonded: 5.45 r_work (final): 0.4384 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6649 moved from start: 0.3494 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 5961 Z= 0.183 Angle : 0.738 17.731 8085 Z= 0.342 Chirality : 0.047 0.418 976 Planarity : 0.004 0.050 1014 Dihedral : 7.402 53.970 1032 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 10.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.04 % Favored : 89.96 % Rotamer: Outliers : 3.38 % Allowed : 20.28 % Favored : 76.34 % 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: -2.82 (0.31), residues: 697 helix: -0.32 (0.62), residues: 68 sheet: -4.05 (0.47), residues: 75 loop : -1.90 (0.27), residues: 554 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 452 HIS 0.002 0.000 HIS A 108 PHE 0.012 0.001 PHE A 333 TYR 0.017 0.002 TYR B 5 ARG 0.004 0.000 ARG A 394 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1394 Ramachandran restraints generated. 697 Oldfield, 0 Emsley, 697 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1394 Ramachandran restraints generated. 697 Oldfield, 0 Emsley, 697 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 651 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 70 time to evaluate : 0.658 Fit side-chains revert: symmetry clash REVERT: A 201 LYS cc_start: 0.8279 (tmmt) cc_final: 0.7987 (tmmm) REVERT: A 330 LYS cc_start: 0.7745 (tttm) cc_final: 0.7235 (ttmp) REVERT: A 347 ASP cc_start: 0.6380 (m-30) cc_final: 0.5933 (m-30) REVERT: A 361 ASN cc_start: 0.6879 (OUTLIER) cc_final: 0.6257 (t0) REVERT: A 525 MET cc_start: 0.4873 (OUTLIER) cc_final: 0.3796 (mpt) REVERT: A 575 ASP cc_start: 0.7496 (m-30) cc_final: 0.7145 (m-30) REVERT: A 613 LYS cc_start: 0.8294 (mttt) cc_final: 0.7878 (mmmt) REVERT: B 5 TYR cc_start: 0.8371 (t80) cc_final: 0.8140 (t80) REVERT: B 8 LYS cc_start: 0.9240 (mttp) cc_final: 0.8967 (pttp) REVERT: B 27 ARG cc_start: 0.9306 (mmp80) cc_final: 0.9000 (mmp80) outliers start: 22 outliers final: 9 residues processed: 85 average time/residue: 0.7710 time to fit residues: 70.7558 Evaluate side-chains 70 residues out of total 651 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 59 time to evaluate : 0.692 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 95 CYS Chi-restraints excluded: chain A residue 104 LEU Chi-restraints excluded: chain A residue 231 VAL Chi-restraints excluded: chain A residue 361 ASN Chi-restraints excluded: chain A residue 370 ILE Chi-restraints excluded: chain A residue 389 SER Chi-restraints excluded: chain A residue 448 THR Chi-restraints excluded: chain A residue 521 ILE Chi-restraints excluded: chain A residue 525 MET Chi-restraints excluded: chain A residue 555 ILE Chi-restraints excluded: chain B residue 30 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 52 optimal weight: 4.9990 chunk 35 optimal weight: 1.9990 chunk 38 optimal weight: 0.7980 chunk 43 optimal weight: 0.7980 chunk 33 optimal weight: 0.2980 chunk 54 optimal weight: 3.9990 chunk 50 optimal weight: 2.9990 chunk 49 optimal weight: 5.9990 chunk 8 optimal weight: 7.9990 chunk 0 optimal weight: 10.0000 chunk 51 optimal weight: 0.9990 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 361 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4752 r_free = 0.4752 target = 0.143943 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4402 r_free = 0.4402 target = 0.117563 restraints weight = 14439.471| |-----------------------------------------------------------------------------| r_work (start): 0.4352 rms_B_bonded: 5.45 r_work (final): 0.4352 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6699 moved from start: 0.3691 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 5961 Z= 0.208 Angle : 0.715 8.370 8085 Z= 0.341 Chirality : 0.050 0.620 976 Planarity : 0.004 0.049 1014 Dihedral : 7.090 54.102 1032 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 10.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.90 % Favored : 89.10 % Rotamer: Outliers : 4.15 % Allowed : 20.58 % Favored : 75.27 % 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: -2.83 (0.31), residues: 697 helix: -0.25 (0.60), residues: 68 sheet: -4.07 (0.46), residues: 75 loop : -1.92 (0.27), residues: 554 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 452 HIS 0.002 0.000 HIS A 108 PHE 0.008 0.001 PHE A 647 TYR 0.019 0.002 TYR B 6 ARG 0.003 0.000 ARG A 394 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1394 Ramachandran restraints generated. 697 Oldfield, 0 Emsley, 697 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1394 Ramachandran restraints generated. 697 Oldfield, 0 Emsley, 697 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 651 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 63 time to evaluate : 0.785 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 201 LYS cc_start: 0.8294 (tmmt) cc_final: 0.8040 (tmmm) REVERT: A 330 LYS cc_start: 0.7662 (tttm) cc_final: 0.7328 (ttmp) REVERT: A 347 ASP cc_start: 0.6463 (m-30) cc_final: 0.6023 (m-30) REVERT: A 361 ASN cc_start: 0.7273 (OUTLIER) cc_final: 0.6539 (t0) REVERT: A 363 GLU cc_start: 0.6852 (tp30) cc_final: 0.5910 (tp30) REVERT: A 525 MET cc_start: 0.5044 (OUTLIER) cc_final: 0.4109 (mpt) REVERT: A 531 LYS cc_start: 0.8279 (OUTLIER) cc_final: 0.7768 (tmmm) REVERT: A 575 ASP cc_start: 0.7534 (m-30) cc_final: 0.7173 (m-30) REVERT: B 15 GLU cc_start: 0.8900 (mm-30) cc_final: 0.8653 (mm-30) outliers start: 27 outliers final: 12 residues processed: 84 average time/residue: 0.7665 time to fit residues: 69.4293 Evaluate side-chains 73 residues out of total 651 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 58 time to evaluate : 0.716 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 THR Chi-restraints excluded: chain A residue 94 LEU Chi-restraints excluded: chain A residue 95 CYS Chi-restraints excluded: chain A residue 231 VAL Chi-restraints excluded: chain A residue 361 ASN Chi-restraints excluded: chain A residue 370 ILE Chi-restraints excluded: chain A residue 389 SER Chi-restraints excluded: chain A residue 413 ASN Chi-restraints excluded: chain A residue 448 THR Chi-restraints excluded: chain A residue 510 ILE Chi-restraints excluded: chain A residue 525 MET Chi-restraints excluded: chain A residue 529 LEU Chi-restraints excluded: chain A residue 531 LYS Chi-restraints excluded: chain A residue 555 ILE Chi-restraints excluded: chain B residue 30 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 43 optimal weight: 1.9990 chunk 3 optimal weight: 5.9990 chunk 17 optimal weight: 3.9990 chunk 49 optimal weight: 8.9990 chunk 13 optimal weight: 9.9990 chunk 32 optimal weight: 1.9990 chunk 38 optimal weight: 0.8980 chunk 67 optimal weight: 5.9990 chunk 6 optimal weight: 8.9990 chunk 47 optimal weight: 0.7980 chunk 52 optimal weight: 5.9990 overall best weight: 1.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 207 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4707 r_free = 0.4707 target = 0.140079 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4340 r_free = 0.4340 target = 0.113225 restraints weight = 14336.506| |-----------------------------------------------------------------------------| r_work (start): 0.4292 rms_B_bonded: 5.34 r_work (final): 0.4292 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6797 moved from start: 0.4008 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 5961 Z= 0.310 Angle : 0.786 9.486 8085 Z= 0.373 Chirality : 0.051 0.572 976 Planarity : 0.004 0.050 1014 Dihedral : 6.973 53.983 1032 Min Nonbonded Distance : 2.410 Molprobity Statistics. All-atom Clashscore : 12.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.48 % Favored : 87.52 % Rotamer: Outliers : 4.15 % Allowed : 22.58 % Favored : 73.27 % 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: -2.88 (0.31), residues: 697 helix: -0.28 (0.60), residues: 68 sheet: -4.12 (0.46), residues: 77 loop : -1.94 (0.27), residues: 552 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 452 HIS 0.004 0.001 HIS A 359 PHE 0.014 0.001 PHE A 119 TYR 0.032 0.003 TYR B 6 ARG 0.003 0.000 ARG A 394 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1394 Ramachandran restraints generated. 697 Oldfield, 0 Emsley, 697 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1394 Ramachandran restraints generated. 697 Oldfield, 0 Emsley, 697 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 651 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 65 time to evaluate : 0.661 Fit side-chains revert: symmetry clash REVERT: A 330 LYS cc_start: 0.7670 (tttm) cc_final: 0.7386 (ttmp) REVERT: A 347 ASP cc_start: 0.6643 (m-30) cc_final: 0.6174 (m-30) REVERT: A 363 GLU cc_start: 0.6938 (tp30) cc_final: 0.6084 (tp30) REVERT: A 525 MET cc_start: 0.5250 (OUTLIER) cc_final: 0.4247 (mpt) REVERT: A 531 LYS cc_start: 0.8246 (OUTLIER) cc_final: 0.7762 (tmmm) REVERT: A 575 ASP cc_start: 0.7593 (m-30) cc_final: 0.7337 (m-30) REVERT: A 585 LEU cc_start: 0.8147 (mt) cc_final: 0.7944 (mm) REVERT: B 27 ARG cc_start: 0.9304 (mmp80) cc_final: 0.8971 (mmp80) REVERT: B 31 GLU cc_start: 0.8928 (mm-30) cc_final: 0.8726 (mm-30) outliers start: 27 outliers final: 15 residues processed: 84 average time/residue: 0.7780 time to fit residues: 70.7123 Evaluate side-chains 75 residues out of total 651 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 58 time to evaluate : 0.688 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 ASN Chi-restraints excluded: chain A residue 86 THR Chi-restraints excluded: chain A residue 94 LEU Chi-restraints excluded: chain A residue 103 VAL Chi-restraints excluded: chain A residue 231 VAL Chi-restraints excluded: chain A residue 370 ILE Chi-restraints excluded: chain A residue 389 SER Chi-restraints excluded: chain A residue 448 THR Chi-restraints excluded: chain A residue 510 ILE Chi-restraints excluded: chain A residue 525 MET Chi-restraints excluded: chain A residue 529 LEU Chi-restraints excluded: chain A residue 531 LYS Chi-restraints excluded: chain A residue 546 TRP Chi-restraints excluded: chain A residue 555 ILE Chi-restraints excluded: chain A residue 654 ILE Chi-restraints excluded: chain A residue 667 ASN Chi-restraints excluded: chain B residue 30 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 61 optimal weight: 5.9990 chunk 33 optimal weight: 4.9990 chunk 4 optimal weight: 4.9990 chunk 21 optimal weight: 3.9990 chunk 31 optimal weight: 2.9990 chunk 67 optimal weight: 0.8980 chunk 10 optimal weight: 5.9990 chunk 9 optimal weight: 7.9990 chunk 20 optimal weight: 0.2980 chunk 52 optimal weight: 0.8980 chunk 49 optimal weight: 2.9990 overall best weight: 1.6184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 61 ASN A 361 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4698 r_free = 0.4698 target = 0.139505 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4334 r_free = 0.4334 target = 0.112533 restraints weight = 14341.542| |-----------------------------------------------------------------------------| r_work (start): 0.4281 rms_B_bonded: 5.34 r_work (final): 0.4281 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6812 moved from start: 0.4251 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 5961 Z= 0.270 Angle : 0.797 10.699 8085 Z= 0.375 Chirality : 0.051 0.583 976 Planarity : 0.004 0.050 1014 Dihedral : 6.863 54.003 1032 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 13.01 Ramachandran Plot: Outliers : 0.14 % Allowed : 12.63 % Favored : 87.23 % Rotamer: Outliers : 4.30 % Allowed : 23.04 % Favored : 72.66 % 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: -3.03 (0.31), residues: 697 helix: -0.56 (0.58), residues: 74 sheet: -4.11 (0.48), residues: 75 loop : -2.07 (0.26), residues: 548 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 452 HIS 0.004 0.001 HIS A 108 PHE 0.010 0.001 PHE A 557 TYR 0.033 0.003 TYR B 6 ARG 0.003 0.000 ARG A 394 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1394 Ramachandran restraints generated. 697 Oldfield, 0 Emsley, 697 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1394 Ramachandran restraints generated. 697 Oldfield, 0 Emsley, 697 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 651 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 61 time to evaluate : 0.682 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 330 LYS cc_start: 0.7657 (tttm) cc_final: 0.7260 (ttmp) REVERT: A 347 ASP cc_start: 0.6741 (m-30) cc_final: 0.6276 (m-30) REVERT: A 361 ASN cc_start: 0.7451 (OUTLIER) cc_final: 0.6794 (t0) REVERT: A 525 MET cc_start: 0.5385 (OUTLIER) cc_final: 0.4399 (mpt) REVERT: A 531 LYS cc_start: 0.8245 (OUTLIER) cc_final: 0.7768 (tmmm) REVERT: A 575 ASP cc_start: 0.7621 (m-30) cc_final: 0.7360 (m-30) outliers start: 28 outliers final: 14 residues processed: 82 average time/residue: 0.7493 time to fit residues: 66.4387 Evaluate side-chains 72 residues out of total 651 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 55 time to evaluate : 0.679 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 THR Chi-restraints excluded: chain A residue 94 LEU Chi-restraints excluded: chain A residue 103 VAL Chi-restraints excluded: chain A residue 231 VAL Chi-restraints excluded: chain A residue 361 ASN Chi-restraints excluded: chain A residue 367 ILE Chi-restraints excluded: chain A residue 370 ILE Chi-restraints excluded: chain A residue 389 SER Chi-restraints excluded: chain A residue 448 THR Chi-restraints excluded: chain A residue 510 ILE Chi-restraints excluded: chain A residue 525 MET Chi-restraints excluded: chain A residue 529 LEU Chi-restraints excluded: chain A residue 531 LYS Chi-restraints excluded: chain A residue 546 TRP Chi-restraints excluded: chain A residue 555 ILE Chi-restraints excluded: chain A residue 667 ASN Chi-restraints excluded: chain B residue 30 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 58 optimal weight: 4.9990 chunk 10 optimal weight: 5.9990 chunk 6 optimal weight: 5.9990 chunk 26 optimal weight: 6.9990 chunk 44 optimal weight: 5.9990 chunk 22 optimal weight: 0.9980 chunk 68 optimal weight: 5.9990 chunk 48 optimal weight: 0.9990 chunk 60 optimal weight: 3.9990 chunk 1 optimal weight: 9.9990 chunk 25 optimal weight: 0.7980 overall best weight: 2.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4665 r_free = 0.4665 target = 0.136843 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4291 r_free = 0.4291 target = 0.109899 restraints weight = 14412.513| |-----------------------------------------------------------------------------| r_work (start): 0.4236 rms_B_bonded: 5.30 r_work (final): 0.4236 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6886 moved from start: 0.4559 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 5961 Z= 0.361 Angle : 0.871 12.248 8085 Z= 0.410 Chirality : 0.055 0.813 976 Planarity : 0.005 0.052 1014 Dihedral : 6.972 54.012 1032 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 15.92 Ramachandran Plot: Outliers : 0.14 % Allowed : 14.20 % Favored : 85.65 % Rotamer: Outliers : 4.45 % Allowed : 24.12 % Favored : 71.43 % 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: -3.15 (0.30), residues: 697 helix: -0.85 (0.56), residues: 74 sheet: -4.25 (0.50), residues: 66 loop : -2.18 (0.26), residues: 557 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 546 HIS 0.007 0.001 HIS A 359 PHE 0.019 0.002 PHE A 119 TYR 0.035 0.003 TYR B 6 ARG 0.003 0.000 ARG A 394 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1394 Ramachandran restraints generated. 697 Oldfield, 0 Emsley, 697 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1394 Ramachandran restraints generated. 697 Oldfield, 0 Emsley, 697 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 651 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 66 time to evaluate : 0.736 Fit side-chains REVERT: A 143 PHE cc_start: 0.8512 (p90) cc_final: 0.7781 (p90) REVERT: A 330 LYS cc_start: 0.7708 (tttm) cc_final: 0.7415 (ttmp) REVERT: A 347 ASP cc_start: 0.6853 (m-30) cc_final: 0.6414 (m-30) REVERT: A 525 MET cc_start: 0.5592 (OUTLIER) cc_final: 0.4594 (mpt) REVERT: A 531 LYS cc_start: 0.8249 (OUTLIER) cc_final: 0.7801 (tmmm) REVERT: A 575 ASP cc_start: 0.7693 (m-30) cc_final: 0.7428 (m-30) REVERT: A 589 LYS cc_start: 0.8252 (mttt) cc_final: 0.8051 (mmtm) REVERT: B 27 ARG cc_start: 0.9325 (mmp80) cc_final: 0.9030 (mmp80) outliers start: 29 outliers final: 17 residues processed: 86 average time/residue: 0.8039 time to fit residues: 74.4473 Evaluate side-chains 81 residues out of total 651 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 62 time to evaluate : 0.737 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 THR Chi-restraints excluded: chain A residue 61 ASN Chi-restraints excluded: chain A residue 86 THR Chi-restraints excluded: chain A residue 94 LEU Chi-restraints excluded: chain A residue 103 VAL Chi-restraints excluded: chain A residue 231 VAL Chi-restraints excluded: chain A residue 367 ILE Chi-restraints excluded: chain A residue 370 ILE Chi-restraints excluded: chain A residue 389 SER Chi-restraints excluded: chain A residue 448 THR Chi-restraints excluded: chain A residue 510 ILE Chi-restraints excluded: chain A residue 525 MET Chi-restraints excluded: chain A residue 529 LEU Chi-restraints excluded: chain A residue 531 LYS Chi-restraints excluded: chain A residue 546 TRP Chi-restraints excluded: chain A residue 555 ILE Chi-restraints excluded: chain A residue 605 VAL Chi-restraints excluded: chain A residue 667 ASN Chi-restraints excluded: chain B residue 30 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 57 optimal weight: 0.6980 chunk 64 optimal weight: 6.9990 chunk 6 optimal weight: 6.9990 chunk 15 optimal weight: 10.0000 chunk 54 optimal weight: 4.9990 chunk 44 optimal weight: 3.9990 chunk 62 optimal weight: 1.9990 chunk 61 optimal weight: 3.9990 chunk 37 optimal weight: 1.9990 chunk 24 optimal weight: 6.9990 chunk 55 optimal weight: 0.8980 overall best weight: 1.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4669 r_free = 0.4669 target = 0.137157 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4300 r_free = 0.4300 target = 0.110127 restraints weight = 14432.539| |-----------------------------------------------------------------------------| r_work (start): 0.4247 rms_B_bonded: 5.32 r_work (final): 0.4247 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6879 moved from start: 0.4779 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.060 5961 Z= 0.309 Angle : 0.861 12.200 8085 Z= 0.401 Chirality : 0.056 0.831 976 Planarity : 0.004 0.051 1014 Dihedral : 6.968 54.024 1032 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 16.09 Ramachandran Plot: Outliers : 0.14 % Allowed : 13.63 % Favored : 86.23 % Rotamer: Outliers : 3.99 % Allowed : 25.19 % Favored : 70.81 % 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 (0.30), residues: 697 helix: -0.94 (0.57), residues: 74 sheet: -3.95 (0.57), residues: 56 loop : -2.28 (0.26), residues: 567 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 452 HIS 0.004 0.001 HIS A 108 PHE 0.012 0.001 PHE A 294 TYR 0.035 0.003 TYR B 6 ARG 0.005 0.000 ARG B 12 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1394 Ramachandran restraints generated. 697 Oldfield, 0 Emsley, 697 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1394 Ramachandran restraints generated. 697 Oldfield, 0 Emsley, 697 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 651 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 63 time to evaluate : 0.652 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 143 PHE cc_start: 0.8547 (p90) cc_final: 0.7804 (p90) REVERT: A 330 LYS cc_start: 0.7633 (tttm) cc_final: 0.7172 (tppt) REVERT: A 347 ASP cc_start: 0.6848 (m-30) cc_final: 0.6366 (m-30) REVERT: A 363 GLU cc_start: 0.7464 (tm-30) cc_final: 0.7173 (tm-30) REVERT: A 525 MET cc_start: 0.5555 (OUTLIER) cc_final: 0.4615 (mpt) REVERT: A 531 LYS cc_start: 0.8270 (OUTLIER) cc_final: 0.7802 (tmmm) REVERT: A 569 LEU cc_start: 0.7832 (OUTLIER) cc_final: 0.7629 (tp) REVERT: A 575 ASP cc_start: 0.7763 (m-30) cc_final: 0.7498 (m-30) REVERT: B 19 GLU cc_start: 0.8921 (tm-30) cc_final: 0.8445 (pp20) outliers start: 26 outliers final: 19 residues processed: 81 average time/residue: 0.7713 time to fit residues: 67.3669 Evaluate side-chains 79 residues out of total 651 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 57 time to evaluate : 0.773 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 THR Chi-restraints excluded: chain A residue 61 ASN Chi-restraints excluded: chain A residue 86 THR Chi-restraints excluded: chain A residue 94 LEU Chi-restraints excluded: chain A residue 103 VAL Chi-restraints excluded: chain A residue 231 VAL Chi-restraints excluded: chain A residue 361 ASN Chi-restraints excluded: chain A residue 367 ILE Chi-restraints excluded: chain A residue 370 ILE Chi-restraints excluded: chain A residue 389 SER Chi-restraints excluded: chain A residue 448 THR Chi-restraints excluded: chain A residue 510 ILE Chi-restraints excluded: chain A residue 521 ILE Chi-restraints excluded: chain A residue 525 MET Chi-restraints excluded: chain A residue 529 LEU Chi-restraints excluded: chain A residue 531 LYS Chi-restraints excluded: chain A residue 546 TRP Chi-restraints excluded: chain A residue 555 ILE Chi-restraints excluded: chain A residue 569 LEU Chi-restraints excluded: chain A residue 605 VAL Chi-restraints excluded: chain A residue 667 ASN Chi-restraints excluded: chain B residue 30 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 63 optimal weight: 0.9990 chunk 4 optimal weight: 7.9990 chunk 69 optimal weight: 4.9990 chunk 1 optimal weight: 3.9990 chunk 56 optimal weight: 1.9990 chunk 59 optimal weight: 0.0030 chunk 27 optimal weight: 1.9990 chunk 11 optimal weight: 5.9990 chunk 54 optimal weight: 0.9980 chunk 31 optimal weight: 2.9990 chunk 50 optimal weight: 2.9990 overall best weight: 1.1996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4696 r_free = 0.4696 target = 0.139079 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4338 r_free = 0.4338 target = 0.112434 restraints weight = 14476.962| |-----------------------------------------------------------------------------| r_work (start): 0.4288 rms_B_bonded: 5.42 r_work (final): 0.4288 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6825 moved from start: 0.4924 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.067 5961 Z= 0.245 Angle : 0.846 13.101 8085 Z= 0.389 Chirality : 0.058 1.006 976 Planarity : 0.004 0.050 1014 Dihedral : 6.837 54.035 1032 Min Nonbonded Distance : 2.390 Molprobity Statistics. All-atom Clashscore : 14.38 Ramachandran Plot: Outliers : 0.14 % Allowed : 12.34 % Favored : 87.52 % Rotamer: Outliers : 3.84 % Allowed : 25.35 % Favored : 70.81 % 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: -3.11 (0.30), residues: 697 helix: -0.93 (0.57), residues: 74 sheet: -3.84 (0.60), residues: 54 loop : -2.25 (0.25), residues: 569 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 546 HIS 0.003 0.000 HIS A 108 PHE 0.019 0.001 PHE A 119 TYR 0.010 0.002 TYR A 462 ARG 0.003 0.000 ARG B 12 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1394 Ramachandran restraints generated. 697 Oldfield, 0 Emsley, 697 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1394 Ramachandran restraints generated. 697 Oldfield, 0 Emsley, 697 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 651 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 61 time to evaluate : 0.547 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 94 LEU cc_start: 0.7341 (OUTLIER) cc_final: 0.6876 (mm) REVERT: A 143 PHE cc_start: 0.8582 (p90) cc_final: 0.7831 (p90) REVERT: A 330 LYS cc_start: 0.7644 (tttm) cc_final: 0.7140 (tppt) REVERT: A 347 ASP cc_start: 0.6746 (m-30) cc_final: 0.6259 (m-30) REVERT: A 361 ASN cc_start: 0.7424 (OUTLIER) cc_final: 0.6691 (t0) REVERT: A 363 GLU cc_start: 0.7410 (tm-30) cc_final: 0.7039 (tm-30) REVERT: A 525 MET cc_start: 0.5575 (OUTLIER) cc_final: 0.4666 (mpt) REVERT: A 531 LYS cc_start: 0.8314 (OUTLIER) cc_final: 0.7844 (tmmm) REVERT: A 575 ASP cc_start: 0.7726 (m-30) cc_final: 0.7459 (m-30) REVERT: B 15 GLU cc_start: 0.9009 (mm-30) cc_final: 0.8748 (mm-30) REVERT: B 19 GLU cc_start: 0.8871 (tm-30) cc_final: 0.8409 (pp20) outliers start: 25 outliers final: 15 residues processed: 80 average time/residue: 0.8027 time to fit residues: 69.0164 Evaluate side-chains 78 residues out of total 651 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 59 time to evaluate : 0.684 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 THR Chi-restraints excluded: chain A residue 86 THR Chi-restraints excluded: chain A residue 94 LEU Chi-restraints excluded: chain A residue 103 VAL Chi-restraints excluded: chain A residue 231 VAL Chi-restraints excluded: chain A residue 361 ASN Chi-restraints excluded: chain A residue 367 ILE Chi-restraints excluded: chain A residue 370 ILE Chi-restraints excluded: chain A residue 389 SER Chi-restraints excluded: chain A residue 448 THR Chi-restraints excluded: chain A residue 510 ILE Chi-restraints excluded: chain A residue 521 ILE Chi-restraints excluded: chain A residue 525 MET Chi-restraints excluded: chain A residue 529 LEU Chi-restraints excluded: chain A residue 531 LYS Chi-restraints excluded: chain A residue 555 ILE Chi-restraints excluded: chain A residue 605 VAL Chi-restraints excluded: chain A residue 667 ASN Chi-restraints excluded: chain B residue 30 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 38 optimal weight: 0.8980 chunk 69 optimal weight: 4.9990 chunk 64 optimal weight: 0.4980 chunk 57 optimal weight: 0.0970 chunk 54 optimal weight: 0.0370 chunk 55 optimal weight: 1.9990 chunk 45 optimal weight: 0.9990 chunk 16 optimal weight: 1.9990 chunk 62 optimal weight: 2.9990 chunk 5 optimal weight: 0.0270 chunk 49 optimal weight: 0.4980 overall best weight: 0.2314 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4751 r_free = 0.4751 target = 0.142783 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4425 r_free = 0.4425 target = 0.117211 restraints weight = 14430.755| |-----------------------------------------------------------------------------| r_work (start): 0.4378 rms_B_bonded: 5.32 r_work (final): 0.4378 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6702 moved from start: 0.5094 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 5961 Z= 0.185 Angle : 0.821 10.739 8085 Z= 0.377 Chirality : 0.055 0.938 976 Planarity : 0.004 0.049 1014 Dihedral : 6.785 55.300 1032 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 11.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.33 % Favored : 89.67 % Rotamer: Outliers : 2.76 % Allowed : 26.88 % Favored : 70.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.15 % 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: -2.90 (0.31), residues: 697 helix: -0.73 (0.58), residues: 74 sheet: -3.57 (0.56), residues: 72 loop : -2.03 (0.26), residues: 551 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 546 HIS 0.003 0.001 HIS A 129 PHE 0.020 0.001 PHE A 294 TYR 0.013 0.001 TYR B 6 ARG 0.004 0.000 ARG B 12 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3976.03 seconds wall clock time: 71 minutes 18.74 seconds (4278.74 seconds total)