Starting phenix.real_space_refine on Wed Mar 12 01:39:20 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8fht_29103/03_2025/8fht_29103.cif Found real_map, /net/cci-nas-00/data/ceres_data/8fht_29103/03_2025/8fht_29103.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.02 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8fht_29103/03_2025/8fht_29103.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8fht_29103/03_2025/8fht_29103.map" model { file = "/net/cci-nas-00/data/ceres_data/8fht_29103/03_2025/8fht_29103.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8fht_29103/03_2025/8fht_29103.cif" } resolution = 3.02 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.045 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: 6 Type Number sf(0) Gaussians S 42 5.16 5 Cl 2 4.86 5 Na 2 4.78 5 C 4618 2.51 5 N 1106 2.21 5 O 1236 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 14 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib" Total number of atoms: 7006 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 3501 Number of conformers: 1 Conformer: "" Number of residues, atoms: 468, 3501 Classifications: {'peptide': 468} Incomplete info: {'truncation_to_alanine': 15} Link IDs: {'PTRANS': 18, 'TRANS': 449} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 73 Unresolved non-hydrogen angles: 95 Unresolved non-hydrogen dihedrals: 69 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'TYR:plan': 2, 'PHE:plan': 2, 'ASN:plan1': 1, 'TRP:plan': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 42 Chain: "B" Number of atoms: 3501 Number of conformers: 1 Conformer: "" Number of residues, atoms: 468, 3501 Classifications: {'peptide': 468} Incomplete info: {'truncation_to_alanine': 15} Link IDs: {'PTRANS': 18, 'TRANS': 449} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 73 Unresolved non-hydrogen angles: 95 Unresolved non-hydrogen dihedrals: 69 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'TYR:plan': 2, 'PHE:plan': 2, 'ASN:plan1': 1, 'TRP:plan': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 42 Chain: "A" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' CL': 1, ' NA': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' CL': 1, ' NA': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 4.53, per 1000 atoms: 0.65 Number of scatterers: 7006 At special positions: 0 Unit cell: (105.78, 81.7, 94.6, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Cl 2 17.00 S 42 16.00 Na 2 11.00 O 1236 8.00 N 1106 7.00 C 4618 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS A 416 " - pdb=" SG CYS A 421 " distance=2.06 Simple disulfide: pdb=" SG CYS A 430 " - pdb=" SG CYS A 436 " distance=2.03 Simple disulfide: pdb=" SG CYS B 416 " - pdb=" SG CYS B 421 " distance=2.03 Simple disulfide: pdb=" SG CYS B 430 " - pdb=" SG CYS B 436 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.63 Conformation dependent library (CDL) restraints added in 911.2 milliseconds 1864 Ramachandran restraints generated. 932 Oldfield, 0 Emsley, 932 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1700 Finding SS restraints... Secondary structure from input PDB file: 45 helices and 0 sheets defined 80.3% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.58 Creating SS restraints... Processing helix chain 'A' and resid 142 through 151 Processing helix chain 'A' and resid 152 through 158 removed outlier: 4.145A pdb=" N TYR A 156 " --> pdb=" O GLY A 152 " (cutoff:3.500A) Processing helix chain 'A' and resid 158 through 195 removed outlier: 6.748A pdb=" N ILE A 168 " --> pdb=" O ALA A 164 " (cutoff:3.500A) removed outlier: 9.266A pdb=" N VAL A 169 " --> pdb=" O GLN A 165 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N LEU A 170 " --> pdb=" O ALA A 166 " (cutoff:3.500A) Processing helix chain 'A' and resid 201 through 212 removed outlier: 4.175A pdb=" N PHE A 205 " --> pdb=" O GLY A 201 " (cutoff:3.500A) Processing helix chain 'A' and resid 212 through 250 removed outlier: 4.418A pdb=" N SER A 218 " --> pdb=" O GLU A 214 " (cutoff:3.500A) Processing helix chain 'A' and resid 255 through 278 Processing helix chain 'A' and resid 279 through 306 removed outlier: 4.734A pdb=" N VAL A 287 " --> pdb=" O SER A 283 " (cutoff:3.500A) removed outlier: 4.103A pdb=" N LEU A 288 " --> pdb=" O LYS A 284 " (cutoff:3.500A) Processing helix chain 'A' and resid 309 through 315 Processing helix chain 'A' and resid 321 through 329 Processing helix chain 'A' and resid 339 through 348 Processing helix chain 'A' and resid 349 through 352 removed outlier: 3.573A pdb=" N THR A 352 " --> pdb=" O PRO A 349 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 349 through 352' Processing helix chain 'A' and resid 355 through 360 removed outlier: 4.345A pdb=" N ILE A 360 " --> pdb=" O ALA A 356 " (cutoff:3.500A) Processing helix chain 'A' and resid 361 through 364 removed outlier: 3.547A pdb=" N LEU A 364 " --> pdb=" O SER A 361 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 361 through 364' Processing helix chain 'A' and resid 366 through 395 Proline residue: A 372 - end of helix Processing helix chain 'A' and resid 419 through 424 Processing helix chain 'A' and resid 427 through 434 Processing helix chain 'A' and resid 445 through 451 removed outlier: 3.509A pdb=" N MET A 449 " --> pdb=" O GLN A 445 " (cutoff:3.500A) Processing helix chain 'A' and resid 453 through 486 removed outlier: 3.872A pdb=" N ILE A 457 " --> pdb=" O PHE A 453 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N ASP A 486 " --> pdb=" O CYS A 482 " (cutoff:3.500A) Processing helix chain 'A' and resid 491 through 496 removed outlier: 3.504A pdb=" N PHE A 494 " --> pdb=" O LEU A 491 " (cutoff:3.500A) Processing helix chain 'A' and resid 505 through 521 Processing helix chain 'A' and resid 524 through 554 Proline residue: A 530 - end of helix Processing helix chain 'A' and resid 566 through 585 Processing helix chain 'A' and resid 585 through 606 Processing helix chain 'B' and resid 142 through 151 Processing helix chain 'B' and resid 152 through 158 removed outlier: 4.132A pdb=" N TYR B 156 " --> pdb=" O GLY B 152 " (cutoff:3.500A) Processing helix chain 'B' and resid 158 through 195 removed outlier: 6.942A pdb=" N ILE B 168 " --> pdb=" O ALA B 164 " (cutoff:3.500A) removed outlier: 9.217A pdb=" N VAL B 169 " --> pdb=" O GLN B 165 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N LEU B 170 " --> pdb=" O ALA B 166 " (cutoff:3.500A) Processing helix chain 'B' and resid 201 through 212 removed outlier: 4.164A pdb=" N PHE B 205 " --> pdb=" O GLY B 201 " (cutoff:3.500A) Processing helix chain 'B' and resid 212 through 250 removed outlier: 4.430A pdb=" N SER B 218 " --> pdb=" O GLU B 214 " (cutoff:3.500A) Processing helix chain 'B' and resid 255 through 278 Processing helix chain 'B' and resid 279 through 306 removed outlier: 4.740A pdb=" N VAL B 287 " --> pdb=" O SER B 283 " (cutoff:3.500A) removed outlier: 4.113A pdb=" N LEU B 288 " --> pdb=" O LYS B 284 " (cutoff:3.500A) Processing helix chain 'B' and resid 309 through 315 Processing helix chain 'B' and resid 321 through 329 Processing helix chain 'B' and resid 339 through 348 Processing helix chain 'B' and resid 349 through 352 removed outlier: 3.559A pdb=" N THR B 352 " --> pdb=" O PRO B 349 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 349 through 352' Processing helix chain 'B' and resid 355 through 360 removed outlier: 4.315A pdb=" N ILE B 360 " --> pdb=" O ALA B 356 " (cutoff:3.500A) Processing helix chain 'B' and resid 361 through 364 removed outlier: 3.536A pdb=" N LEU B 364 " --> pdb=" O SER B 361 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 361 through 364' Processing helix chain 'B' and resid 366 through 395 Proline residue: B 372 - end of helix Processing helix chain 'B' and resid 427 through 434 removed outlier: 3.600A pdb=" N THR B 431 " --> pdb=" O PHE B 427 " (cutoff:3.500A) Processing helix chain 'B' and resid 445 through 451 removed outlier: 3.608A pdb=" N MET B 449 " --> pdb=" O GLN B 445 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N SER B 451 " --> pdb=" O MET B 447 " (cutoff:3.500A) Processing helix chain 'B' and resid 453 through 486 removed outlier: 3.858A pdb=" N ILE B 457 " --> pdb=" O PHE B 453 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ASP B 486 " --> pdb=" O CYS B 482 " (cutoff:3.500A) Processing helix chain 'B' and resid 491 through 496 removed outlier: 3.510A pdb=" N PHE B 494 " --> pdb=" O LEU B 491 " (cutoff:3.500A) Processing helix chain 'B' and resid 505 through 521 Processing helix chain 'B' and resid 524 through 554 Proline residue: B 530 - end of helix Processing helix chain 'B' and resid 566 through 585 Processing helix chain 'B' and resid 585 through 606 535 hydrogen bonds defined for protein. 1584 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: 1.80 Time building geometry restraints manager: 1.96 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 1078 1.31 - 1.44: 2024 1.44 - 1.57: 4014 1.57 - 1.71: 0 1.71 - 1.84: 62 Bond restraints: 7178 Sorted by residual: bond pdb=" C LEU A 601 " pdb=" O LEU A 601 " ideal model delta sigma weight residual 1.236 1.182 0.054 1.18e-02 7.18e+03 2.10e+01 bond pdb=" CA TYR A 602 " pdb=" C TYR A 602 " ideal model delta sigma weight residual 1.524 1.475 0.049 1.27e-02 6.20e+03 1.49e+01 bond pdb=" CA TYR B 602 " pdb=" C TYR B 602 " ideal model delta sigma weight residual 1.524 1.475 0.049 1.32e-02 5.74e+03 1.36e+01 bond pdb=" N LEU A 601 " pdb=" CA LEU A 601 " ideal model delta sigma weight residual 1.459 1.419 0.040 1.23e-02 6.61e+03 1.05e+01 bond pdb=" CA TYR A 602 " pdb=" CB TYR A 602 " ideal model delta sigma weight residual 1.529 1.480 0.049 1.55e-02 4.16e+03 9.81e+00 ... (remaining 7173 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.46: 9678 2.46 - 4.92: 110 4.92 - 7.38: 16 7.38 - 9.83: 1 9.83 - 12.29: 1 Bond angle restraints: 9806 Sorted by residual: angle pdb=" N CYS B 416 " pdb=" CA CYS B 416 " pdb=" C CYS B 416 " ideal model delta sigma weight residual 108.90 121.19 -12.29 1.63e+00 3.76e-01 5.69e+01 angle pdb=" N LEU A 419 " pdb=" CA LEU A 419 " pdb=" C LEU A 419 " ideal model delta sigma weight residual 111.36 115.92 -4.56 1.09e+00 8.42e-01 1.75e+01 angle pdb=" N CYS A 416 " pdb=" CA CYS A 416 " pdb=" C CYS A 416 " ideal model delta sigma weight residual 108.52 115.27 -6.75 1.63e+00 3.76e-01 1.72e+01 angle pdb=" N ALA A 420 " pdb=" CA ALA A 420 " pdb=" C ALA A 420 " ideal model delta sigma weight residual 111.37 117.81 -6.44 1.65e+00 3.67e-01 1.52e+01 angle pdb=" CA GLY A 414 " pdb=" C GLY A 414 " pdb=" N ALA A 415 " ideal model delta sigma weight residual 114.67 118.78 -4.11 1.11e+00 8.12e-01 1.37e+01 ... (remaining 9801 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.26: 3734 16.26 - 32.51: 278 32.51 - 48.77: 73 48.77 - 65.02: 17 65.02 - 81.28: 6 Dihedral angle restraints: 4108 sinusoidal: 1440 harmonic: 2668 Sorted by residual: dihedral pdb=" CB CYS A 430 " pdb=" SG CYS A 430 " pdb=" SG CYS A 436 " pdb=" CB CYS A 436 " ideal model delta sinusoidal sigma weight residual 93.00 172.85 -79.85 1 1.00e+01 1.00e-02 7.91e+01 dihedral pdb=" CB CYS A 416 " pdb=" SG CYS A 416 " pdb=" SG CYS A 421 " pdb=" CB CYS A 421 " ideal model delta sinusoidal sigma weight residual -86.00 -32.42 -53.58 1 1.00e+01 1.00e-02 3.90e+01 dihedral pdb=" C VAL B 603 " pdb=" N VAL B 603 " pdb=" CA VAL B 603 " pdb=" CB VAL B 603 " ideal model delta harmonic sigma weight residual -122.00 -131.87 9.87 0 2.50e+00 1.60e-01 1.56e+01 ... (remaining 4105 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.063: 1017 0.063 - 0.126: 131 0.126 - 0.188: 12 0.188 - 0.251: 4 0.251 - 0.314: 4 Chirality restraints: 1168 Sorted by residual: chirality pdb=" CA VAL B 603 " pdb=" N VAL B 603 " pdb=" C VAL B 603 " pdb=" CB VAL B 603 " both_signs ideal model delta sigma weight residual False 2.44 2.13 0.31 2.00e-01 2.50e+01 2.46e+00 chirality pdb=" CA CYS B 416 " pdb=" N CYS B 416 " pdb=" C CYS B 416 " pdb=" CB CYS B 416 " both_signs ideal model delta sigma weight residual False 2.51 2.20 0.31 2.00e-01 2.50e+01 2.45e+00 chirality pdb=" CA VAL A 603 " pdb=" N VAL A 603 " pdb=" C VAL A 603 " pdb=" CB VAL A 603 " both_signs ideal model delta sigma weight residual False 2.44 2.16 0.28 2.00e-01 2.50e+01 1.93e+00 ... (remaining 1165 not shown) Planarity restraints: 1206 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA TYR B 602 " -0.019 2.00e-02 2.50e+03 3.74e-02 1.40e+01 pdb=" C TYR B 602 " 0.065 2.00e-02 2.50e+03 pdb=" O TYR B 602 " -0.024 2.00e-02 2.50e+03 pdb=" N VAL B 603 " -0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA TYR A 602 " 0.019 2.00e-02 2.50e+03 3.65e-02 1.34e+01 pdb=" C TYR A 602 " -0.063 2.00e-02 2.50e+03 pdb=" O TYR A 602 " 0.023 2.00e-02 2.50e+03 pdb=" N VAL A 603 " 0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU A 601 " 0.011 2.00e-02 2.50e+03 2.24e-02 5.00e+00 pdb=" C LEU A 601 " -0.039 2.00e-02 2.50e+03 pdb=" O LEU A 601 " 0.014 2.00e-02 2.50e+03 pdb=" N TYR A 602 " 0.013 2.00e-02 2.50e+03 ... (remaining 1203 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.76: 1166 2.76 - 3.29: 7025 3.29 - 3.83: 12038 3.83 - 4.36: 12922 4.36 - 4.90: 23686 Nonbonded interactions: 56837 Sorted by model distance: nonbonded pdb=" O TRP B 151 " pdb="NA NA B1101 " model vdw 2.220 2.470 nonbonded pdb=" O TRP A 151 " pdb="NA NA A1101 " model vdw 2.228 2.470 nonbonded pdb=" O SER B 345 " pdb=" OG SER B 533 " model vdw 2.297 3.040 nonbonded pdb=" OG SER A 468 " pdb="NA NA A1101 " model vdw 2.299 2.470 nonbonded pdb=" O SER A 345 " pdb=" OG SER A 533 " model vdw 2.309 3.040 ... (remaining 56832 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: 0.03 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } 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: 1.310 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: 0.000 Extract box with map and model: 0.250 Check model and map are aligned: 0.050 Set scattering table: 0.060 Process input model: 18.500 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:2.690 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.090 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7617 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 0.054 7178 Z= 0.237 Angle : 0.633 12.293 9806 Z= 0.365 Chirality : 0.047 0.314 1168 Planarity : 0.004 0.037 1206 Dihedral : 12.982 81.279 2396 Min Nonbonded Distance : 2.220 Molprobity Statistics. All-atom Clashscore : 6.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.82 % Favored : 98.18 % Rotamer: Outliers : 0.96 % Allowed : 0.96 % Favored : 98.07 % Cbeta Deviations : 0.35 % 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: 2.06 (0.28), residues: 932 helix: 2.22 (0.20), residues: 670 sheet: None (None), residues: 0 loop : -0.94 (0.40), residues: 262 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP B 586 HIS 0.002 0.001 HIS B 234 PHE 0.025 0.002 PHE B 238 TYR 0.018 0.001 TYR A 602 ARG 0.002 0.000 ARG B 243 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1864 Ramachandran restraints generated. 932 Oldfield, 0 Emsley, 932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1864 Ramachandran restraints generated. 932 Oldfield, 0 Emsley, 932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 756 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 113 time to evaluate : 0.815 Fit side-chains REVERT: B 417 GLU cc_start: 0.7431 (OUTLIER) cc_final: 0.7170 (mt-10) outliers start: 7 outliers final: 0 residues processed: 117 average time/residue: 0.1873 time to fit residues: 29.7293 Evaluate side-chains 101 residues out of total 756 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 100 time to evaluate : 0.683 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 417 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 77 optimal weight: 0.9990 chunk 69 optimal weight: 1.9990 chunk 38 optimal weight: 0.0470 chunk 23 optimal weight: 3.9990 chunk 47 optimal weight: 0.9990 chunk 37 optimal weight: 0.8980 chunk 72 optimal weight: 0.0000 chunk 27 optimal weight: 5.9990 chunk 43 optimal weight: 1.9990 chunk 53 optimal weight: 5.9990 chunk 83 optimal weight: 0.6980 overall best weight: 0.5284 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 327 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4287 r_free = 0.4287 target = 0.200631 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3845 r_free = 0.3845 target = 0.155752 restraints weight = 7348.163| |-----------------------------------------------------------------------------| r_work (start): 0.3848 rms_B_bonded: 2.29 r_work: 0.3699 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.3699 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7639 moved from start: 0.0812 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 7178 Z= 0.169 Angle : 0.488 4.783 9806 Z= 0.267 Chirality : 0.039 0.165 1168 Planarity : 0.004 0.036 1206 Dihedral : 4.152 50.921 991 Min Nonbonded Distance : 2.312 Molprobity Statistics. All-atom Clashscore : 5.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.93 % Favored : 98.07 % Rotamer: Outliers : 1.24 % Allowed : 6.89 % Favored : 91.87 % 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: 2.29 (0.28), residues: 932 helix: 2.44 (0.20), residues: 660 sheet: None (None), residues: 0 loop : -0.88 (0.38), residues: 272 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 586 HIS 0.002 0.001 HIS A 549 PHE 0.017 0.002 PHE A 598 TYR 0.011 0.001 TYR A 602 ARG 0.001 0.000 ARG B 399 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1864 Ramachandran restraints generated. 932 Oldfield, 0 Emsley, 932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1864 Ramachandran restraints generated. 932 Oldfield, 0 Emsley, 932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 756 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 110 time to evaluate : 0.660 Fit side-chains revert: symmetry clash REVERT: A 309 SER cc_start: 0.7963 (t) cc_final: 0.7618 (p) REVERT: B 309 SER cc_start: 0.7948 (t) cc_final: 0.7628 (p) REVERT: B 416 CYS cc_start: 0.3665 (OUTLIER) cc_final: 0.2911 (t) outliers start: 9 outliers final: 5 residues processed: 117 average time/residue: 0.1773 time to fit residues: 28.4426 Evaluate side-chains 106 residues out of total 756 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 100 time to evaluate : 0.693 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 208 SER Chi-restraints excluded: chain A residue 245 LEU Chi-restraints excluded: chain A residue 539 SER Chi-restraints excluded: chain A residue 542 LEU Chi-restraints excluded: chain B residue 416 CYS Chi-restraints excluded: chain B residue 539 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 42 optimal weight: 0.1980 chunk 29 optimal weight: 4.9990 chunk 77 optimal weight: 1.9990 chunk 35 optimal weight: 0.1980 chunk 10 optimal weight: 2.9990 chunk 63 optimal weight: 0.8980 chunk 16 optimal weight: 0.9980 chunk 83 optimal weight: 0.9980 chunk 66 optimal weight: 1.9990 chunk 68 optimal weight: 0.7980 chunk 28 optimal weight: 0.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 327 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4280 r_free = 0.4280 target = 0.199790 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3833 r_free = 0.3833 target = 0.154556 restraints weight = 7378.500| |-----------------------------------------------------------------------------| r_work (start): 0.3833 rms_B_bonded: 2.29 r_work: 0.3682 rms_B_bonded: 3.41 restraints_weight: 0.5000 r_work (final): 0.3682 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7661 moved from start: 0.1080 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 7178 Z= 0.171 Angle : 0.477 4.692 9806 Z= 0.260 Chirality : 0.039 0.172 1168 Planarity : 0.004 0.036 1206 Dihedral : 3.468 14.993 988 Min Nonbonded Distance : 2.296 Molprobity Statistics. All-atom Clashscore : 5.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.72 % Favored : 98.28 % Rotamer: Outliers : 1.52 % Allowed : 8.95 % Favored : 89.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 2.29 (0.28), residues: 932 helix: 2.42 (0.20), residues: 660 sheet: None (None), residues: 0 loop : -0.83 (0.38), residues: 272 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 586 HIS 0.002 0.001 HIS A 549 PHE 0.027 0.002 PHE A 238 TYR 0.008 0.001 TYR B 605 ARG 0.001 0.000 ARG A 243 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1864 Ramachandran restraints generated. 932 Oldfield, 0 Emsley, 932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1864 Ramachandran restraints generated. 932 Oldfield, 0 Emsley, 932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 756 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 104 time to evaluate : 0.652 Fit side-chains revert: symmetry clash REVERT: A 309 SER cc_start: 0.7892 (t) cc_final: 0.7522 (p) REVERT: B 309 SER cc_start: 0.7951 (t) cc_final: 0.7618 (p) outliers start: 11 outliers final: 9 residues processed: 110 average time/residue: 0.1699 time to fit residues: 25.7286 Evaluate side-chains 106 residues out of total 756 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 97 time to evaluate : 0.654 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 165 GLN Chi-restraints excluded: chain A residue 208 SER Chi-restraints excluded: chain A residue 245 LEU Chi-restraints excluded: chain A residue 395 SER Chi-restraints excluded: chain A residue 539 SER Chi-restraints excluded: chain B residue 180 THR Chi-restraints excluded: chain B residue 395 SER Chi-restraints excluded: chain B residue 428 THR Chi-restraints excluded: chain B residue 539 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 76 optimal weight: 2.9990 chunk 31 optimal weight: 1.9990 chunk 70 optimal weight: 0.9990 chunk 91 optimal weight: 0.6980 chunk 62 optimal weight: 0.7980 chunk 37 optimal weight: 3.9990 chunk 82 optimal weight: 3.9990 chunk 25 optimal weight: 1.9990 chunk 20 optimal weight: 1.9990 chunk 43 optimal weight: 0.9980 chunk 83 optimal weight: 0.9980 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 442 ASN B 327 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4146 r_free = 0.4146 target = 0.192071 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3655 r_free = 0.3655 target = 0.143096 restraints weight = 7288.529| |-----------------------------------------------------------------------------| r_work (start): 0.3648 rms_B_bonded: 2.34 r_work: 0.3497 rms_B_bonded: 3.47 restraints_weight: 0.5000 r_work (final): 0.3497 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7629 moved from start: 0.1309 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 7178 Z= 0.216 Angle : 0.499 4.803 9806 Z= 0.273 Chirality : 0.039 0.181 1168 Planarity : 0.004 0.037 1206 Dihedral : 3.577 15.659 988 Min Nonbonded Distance : 2.265 Molprobity Statistics. All-atom Clashscore : 5.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.93 % Favored : 98.07 % Rotamer: Outliers : 2.62 % Allowed : 10.19 % Favored : 87.19 % 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: 2.17 (0.27), residues: 932 helix: 2.32 (0.19), residues: 660 sheet: None (None), residues: 0 loop : -0.85 (0.37), residues: 272 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 586 HIS 0.003 0.001 HIS A 549 PHE 0.018 0.002 PHE A 238 TYR 0.017 0.001 TYR B 602 ARG 0.001 0.000 ARG B 158 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1864 Ramachandran restraints generated. 932 Oldfield, 0 Emsley, 932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1864 Ramachandran restraints generated. 932 Oldfield, 0 Emsley, 932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 756 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 95 time to evaluate : 0.642 Fit side-chains revert: symmetry clash REVERT: A 309 SER cc_start: 0.7797 (t) cc_final: 0.7309 (p) REVERT: B 309 SER cc_start: 0.7859 (t) cc_final: 0.7466 (p) outliers start: 19 outliers final: 13 residues processed: 106 average time/residue: 0.1877 time to fit residues: 26.5730 Evaluate side-chains 106 residues out of total 756 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 93 time to evaluate : 0.635 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 165 GLN Chi-restraints excluded: chain A residue 194 THR Chi-restraints excluded: chain A residue 208 SER Chi-restraints excluded: chain A residue 245 LEU Chi-restraints excluded: chain A residue 395 SER Chi-restraints excluded: chain A residue 539 SER Chi-restraints excluded: chain A residue 542 LEU Chi-restraints excluded: chain B residue 180 THR Chi-restraints excluded: chain B residue 194 THR Chi-restraints excluded: chain B residue 395 SER Chi-restraints excluded: chain B residue 428 THR Chi-restraints excluded: chain B residue 441 ILE Chi-restraints excluded: chain B residue 539 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 74 optimal weight: 0.8980 chunk 61 optimal weight: 0.8980 chunk 37 optimal weight: 4.9990 chunk 0 optimal weight: 4.9990 chunk 85 optimal weight: 0.9990 chunk 78 optimal weight: 0.7980 chunk 5 optimal weight: 0.8980 chunk 77 optimal weight: 2.9990 chunk 60 optimal weight: 2.9990 chunk 21 optimal weight: 0.9980 chunk 22 optimal weight: 3.9990 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 327 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4140 r_free = 0.4140 target = 0.191250 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3645 r_free = 0.3645 target = 0.142119 restraints weight = 7221.436| |-----------------------------------------------------------------------------| r_work (start): 0.3636 rms_B_bonded: 2.35 r_work: 0.3488 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work (final): 0.3488 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7640 moved from start: 0.1542 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 7178 Z= 0.218 Angle : 0.490 4.714 9806 Z= 0.270 Chirality : 0.039 0.190 1168 Planarity : 0.004 0.037 1206 Dihedral : 3.571 16.053 988 Min Nonbonded Distance : 2.276 Molprobity Statistics. All-atom Clashscore : 4.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.93 % Favored : 98.07 % Rotamer: Outliers : 2.20 % Allowed : 11.57 % Favored : 86.23 % 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: 2.18 (0.27), residues: 932 helix: 2.31 (0.20), residues: 660 sheet: None (None), residues: 0 loop : -0.78 (0.38), residues: 272 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 586 HIS 0.002 0.001 HIS A 549 PHE 0.018 0.002 PHE A 238 TYR 0.014 0.001 TYR B 602 ARG 0.002 0.000 ARG B 261 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1864 Ramachandran restraints generated. 932 Oldfield, 0 Emsley, 932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1864 Ramachandran restraints generated. 932 Oldfield, 0 Emsley, 932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 756 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 96 time to evaluate : 0.656 Fit side-chains revert: symmetry clash REVERT: A 309 SER cc_start: 0.7651 (t) cc_final: 0.7190 (p) REVERT: B 309 SER cc_start: 0.7773 (t) cc_final: 0.7367 (p) REVERT: B 431 THR cc_start: 0.7556 (m) cc_final: 0.6988 (p) outliers start: 16 outliers final: 13 residues processed: 107 average time/residue: 0.1882 time to fit residues: 27.2150 Evaluate side-chains 102 residues out of total 756 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 89 time to evaluate : 0.673 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 165 GLN Chi-restraints excluded: chain A residue 194 THR Chi-restraints excluded: chain A residue 208 SER Chi-restraints excluded: chain A residue 245 LEU Chi-restraints excluded: chain A residue 395 SER Chi-restraints excluded: chain A residue 405 LEU Chi-restraints excluded: chain A residue 539 SER Chi-restraints excluded: chain A residue 542 LEU Chi-restraints excluded: chain B residue 165 GLN Chi-restraints excluded: chain B residue 194 THR Chi-restraints excluded: chain B residue 395 SER Chi-restraints excluded: chain B residue 428 THR Chi-restraints excluded: chain B residue 539 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 53 optimal weight: 5.9990 chunk 44 optimal weight: 0.5980 chunk 8 optimal weight: 0.9990 chunk 71 optimal weight: 0.8980 chunk 67 optimal weight: 0.5980 chunk 76 optimal weight: 0.7980 chunk 58 optimal weight: 0.6980 chunk 64 optimal weight: 0.9990 chunk 14 optimal weight: 2.9990 chunk 75 optimal weight: 0.7980 chunk 54 optimal weight: 0.8980 overall best weight: 0.6980 ------------------------------------------------------------------------------- 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 = 0.4147 r_free = 0.4147 target = 0.191802 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3657 r_free = 0.3657 target = 0.143023 restraints weight = 7229.696| |-----------------------------------------------------------------------------| r_work (start): 0.3649 rms_B_bonded: 2.33 r_work: 0.3502 rms_B_bonded: 3.45 restraints_weight: 0.5000 r_work (final): 0.3502 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7626 moved from start: 0.1617 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 7178 Z= 0.185 Angle : 0.477 4.664 9806 Z= 0.263 Chirality : 0.039 0.185 1168 Planarity : 0.004 0.037 1206 Dihedral : 3.520 15.342 988 Min Nonbonded Distance : 2.296 Molprobity Statistics. All-atom Clashscore : 4.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.82 % Favored : 98.18 % Rotamer: Outliers : 2.34 % Allowed : 11.85 % Favored : 85.81 % 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: 2.29 (0.28), residues: 932 helix: 2.41 (0.20), residues: 660 sheet: None (None), residues: 0 loop : -0.80 (0.38), residues: 272 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 586 HIS 0.002 0.000 HIS A 549 PHE 0.016 0.001 PHE A 238 TYR 0.016 0.001 TYR B 602 ARG 0.001 0.000 ARG A 209 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1864 Ramachandran restraints generated. 932 Oldfield, 0 Emsley, 932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1864 Ramachandran restraints generated. 932 Oldfield, 0 Emsley, 932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 756 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 89 time to evaluate : 0.668 Fit side-chains revert: symmetry clash REVERT: A 309 SER cc_start: 0.7635 (t) cc_final: 0.7154 (p) REVERT: A 343 MET cc_start: 0.8052 (mmt) cc_final: 0.7554 (mmt) REVERT: B 309 SER cc_start: 0.7795 (t) cc_final: 0.7378 (p) REVERT: B 431 THR cc_start: 0.7572 (m) cc_final: 0.7012 (p) outliers start: 17 outliers final: 13 residues processed: 99 average time/residue: 0.1888 time to fit residues: 25.1317 Evaluate side-chains 98 residues out of total 756 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 85 time to evaluate : 0.657 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 194 THR Chi-restraints excluded: chain A residue 208 SER Chi-restraints excluded: chain A residue 245 LEU Chi-restraints excluded: chain A residue 395 SER Chi-restraints excluded: chain A residue 405 LEU Chi-restraints excluded: chain A residue 539 SER Chi-restraints excluded: chain A residue 542 LEU Chi-restraints excluded: chain B residue 165 GLN Chi-restraints excluded: chain B residue 180 THR Chi-restraints excluded: chain B residue 194 THR Chi-restraints excluded: chain B residue 395 SER Chi-restraints excluded: chain B residue 428 THR Chi-restraints excluded: chain B residue 539 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 91 optimal weight: 0.9990 chunk 24 optimal weight: 0.7980 chunk 63 optimal weight: 0.7980 chunk 46 optimal weight: 4.9990 chunk 60 optimal weight: 5.9990 chunk 51 optimal weight: 0.5980 chunk 65 optimal weight: 2.9990 chunk 86 optimal weight: 0.6980 chunk 56 optimal weight: 3.9990 chunk 41 optimal weight: 3.9990 chunk 49 optimal weight: 0.5980 overall best weight: 0.6980 ------------------------------------------------------------------------------- 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 = 0.4148 r_free = 0.4148 target = 0.191932 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3656 r_free = 0.3656 target = 0.143018 restraints weight = 7250.620| |-----------------------------------------------------------------------------| r_work (start): 0.3649 rms_B_bonded: 2.35 r_work: 0.3500 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work (final): 0.3500 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7623 moved from start: 0.1731 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 7178 Z= 0.187 Angle : 0.475 4.674 9806 Z= 0.262 Chirality : 0.039 0.188 1168 Planarity : 0.004 0.037 1206 Dihedral : 3.492 15.708 988 Min Nonbonded Distance : 2.287 Molprobity Statistics. All-atom Clashscore : 4.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 2.48 % Allowed : 11.43 % Favored : 86.09 % 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: 2.35 (0.28), residues: 932 helix: 2.45 (0.20), residues: 660 sheet: None (None), residues: 0 loop : -0.76 (0.38), residues: 272 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 586 HIS 0.002 0.000 HIS A 549 PHE 0.014 0.001 PHE A 238 TYR 0.005 0.001 TYR A 249 ARG 0.001 0.000 ARG A 243 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1864 Ramachandran restraints generated. 932 Oldfield, 0 Emsley, 932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1864 Ramachandran restraints generated. 932 Oldfield, 0 Emsley, 932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 756 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 90 time to evaluate : 0.710 Fit side-chains revert: symmetry clash REVERT: A 309 SER cc_start: 0.7586 (t) cc_final: 0.7089 (p) REVERT: A 343 MET cc_start: 0.8073 (mmt) cc_final: 0.7575 (mmt) REVERT: B 165 GLN cc_start: 0.8137 (OUTLIER) cc_final: 0.7904 (mm-40) REVERT: B 309 SER cc_start: 0.7753 (t) cc_final: 0.7353 (p) REVERT: B 431 THR cc_start: 0.7621 (m) cc_final: 0.7068 (p) outliers start: 18 outliers final: 12 residues processed: 102 average time/residue: 0.1866 time to fit residues: 25.7313 Evaluate side-chains 102 residues out of total 756 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 89 time to evaluate : 0.646 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 194 THR Chi-restraints excluded: chain A residue 208 SER Chi-restraints excluded: chain A residue 245 LEU Chi-restraints excluded: chain A residue 395 SER Chi-restraints excluded: chain A residue 405 LEU Chi-restraints excluded: chain A residue 539 SER Chi-restraints excluded: chain A residue 542 LEU Chi-restraints excluded: chain B residue 165 GLN Chi-restraints excluded: chain B residue 180 THR Chi-restraints excluded: chain B residue 194 THR Chi-restraints excluded: chain B residue 395 SER Chi-restraints excluded: chain B residue 430 CYS Chi-restraints excluded: chain B residue 539 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 23 optimal weight: 0.8980 chunk 32 optimal weight: 0.5980 chunk 62 optimal weight: 1.9990 chunk 24 optimal weight: 0.5980 chunk 54 optimal weight: 0.9980 chunk 65 optimal weight: 0.8980 chunk 9 optimal weight: 2.9990 chunk 10 optimal weight: 0.8980 chunk 5 optimal weight: 1.9990 chunk 0 optimal weight: 4.9990 chunk 16 optimal weight: 0.9980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4140 r_free = 0.4140 target = 0.191143 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3644 r_free = 0.3644 target = 0.141997 restraints weight = 7341.998| |-----------------------------------------------------------------------------| r_work (start): 0.3643 rms_B_bonded: 2.37 r_work: 0.3494 rms_B_bonded: 3.49 restraints_weight: 0.5000 r_work (final): 0.3494 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7637 moved from start: 0.1833 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 7178 Z= 0.199 Angle : 0.486 4.727 9806 Z= 0.266 Chirality : 0.039 0.188 1168 Planarity : 0.004 0.037 1206 Dihedral : 3.505 15.446 988 Min Nonbonded Distance : 2.282 Molprobity Statistics. All-atom Clashscore : 4.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer: Outliers : 2.75 % Allowed : 11.57 % Favored : 85.67 % 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: 2.32 (0.28), residues: 932 helix: 2.43 (0.19), residues: 660 sheet: None (None), residues: 0 loop : -0.76 (0.38), residues: 272 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 586 HIS 0.002 0.001 HIS A 549 PHE 0.014 0.001 PHE A 238 TYR 0.006 0.001 TYR A 602 ARG 0.001 0.000 ARG A 158 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1864 Ramachandran restraints generated. 932 Oldfield, 0 Emsley, 932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1864 Ramachandran restraints generated. 932 Oldfield, 0 Emsley, 932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 756 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 91 time to evaluate : 0.722 Fit side-chains revert: symmetry clash REVERT: A 309 SER cc_start: 0.7478 (t) cc_final: 0.6964 (p) REVERT: B 309 SER cc_start: 0.7644 (t) cc_final: 0.7186 (p) outliers start: 20 outliers final: 14 residues processed: 104 average time/residue: 0.1888 time to fit residues: 26.7962 Evaluate side-chains 101 residues out of total 756 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 87 time to evaluate : 0.673 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 194 THR Chi-restraints excluded: chain A residue 208 SER Chi-restraints excluded: chain A residue 245 LEU Chi-restraints excluded: chain A residue 395 SER Chi-restraints excluded: chain A residue 539 SER Chi-restraints excluded: chain A residue 542 LEU Chi-restraints excluded: chain B residue 180 THR Chi-restraints excluded: chain B residue 194 THR Chi-restraints excluded: chain B residue 259 ASP Chi-restraints excluded: chain B residue 395 SER Chi-restraints excluded: chain B residue 428 THR Chi-restraints excluded: chain B residue 430 CYS Chi-restraints excluded: chain B residue 539 SER Chi-restraints excluded: chain B residue 567 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 32 optimal weight: 0.5980 chunk 91 optimal weight: 0.6980 chunk 46 optimal weight: 5.9990 chunk 61 optimal weight: 1.9990 chunk 29 optimal weight: 9.9990 chunk 31 optimal weight: 1.9990 chunk 15 optimal weight: 0.9990 chunk 4 optimal weight: 1.9990 chunk 37 optimal weight: 3.9990 chunk 66 optimal weight: 0.7980 chunk 63 optimal weight: 0.8980 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 165 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 = 0.4131 r_free = 0.4131 target = 0.190175 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3635 r_free = 0.3635 target = 0.141400 restraints weight = 7343.286| |-----------------------------------------------------------------------------| r_work (start): 0.3629 rms_B_bonded: 2.35 r_work: 0.3481 rms_B_bonded: 3.44 restraints_weight: 0.5000 r_work (final): 0.3481 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7651 moved from start: 0.1913 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 7178 Z= 0.203 Angle : 0.486 5.230 9806 Z= 0.269 Chirality : 0.039 0.193 1168 Planarity : 0.004 0.037 1206 Dihedral : 3.502 15.556 988 Min Nonbonded Distance : 2.284 Molprobity Statistics. All-atom Clashscore : 5.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer: Outliers : 2.62 % Allowed : 11.98 % Favored : 85.40 % 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: 2.35 (0.28), residues: 932 helix: 2.43 (0.19), residues: 660 sheet: None (None), residues: 0 loop : -0.72 (0.38), residues: 272 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 586 HIS 0.002 0.001 HIS A 549 PHE 0.014 0.001 PHE A 238 TYR 0.006 0.001 TYR A 602 ARG 0.001 0.000 ARG B 158 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1864 Ramachandran restraints generated. 932 Oldfield, 0 Emsley, 932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1864 Ramachandran restraints generated. 932 Oldfield, 0 Emsley, 932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 756 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 92 time to evaluate : 0.650 Fit side-chains revert: symmetry clash REVERT: A 309 SER cc_start: 0.7450 (t) cc_final: 0.6906 (p) REVERT: A 343 MET cc_start: 0.8092 (mmt) cc_final: 0.7609 (mmt) REVERT: B 165 GLN cc_start: 0.7884 (mm-40) cc_final: 0.7451 (mt0) REVERT: B 309 SER cc_start: 0.7575 (t) cc_final: 0.7105 (p) outliers start: 19 outliers final: 16 residues processed: 104 average time/residue: 0.1905 time to fit residues: 26.8130 Evaluate side-chains 105 residues out of total 756 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 89 time to evaluate : 0.728 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 194 THR Chi-restraints excluded: chain A residue 208 SER Chi-restraints excluded: chain A residue 245 LEU Chi-restraints excluded: chain A residue 395 SER Chi-restraints excluded: chain A residue 405 LEU Chi-restraints excluded: chain A residue 539 SER Chi-restraints excluded: chain A residue 542 LEU Chi-restraints excluded: chain B residue 180 THR Chi-restraints excluded: chain B residue 194 THR Chi-restraints excluded: chain B residue 259 ASP Chi-restraints excluded: chain B residue 395 SER Chi-restraints excluded: chain B residue 419 LEU Chi-restraints excluded: chain B residue 428 THR Chi-restraints excluded: chain B residue 430 CYS Chi-restraints excluded: chain B residue 539 SER Chi-restraints excluded: chain B residue 567 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 88 optimal weight: 0.2980 chunk 8 optimal weight: 0.5980 chunk 2 optimal weight: 0.8980 chunk 35 optimal weight: 8.9990 chunk 87 optimal weight: 0.7980 chunk 43 optimal weight: 0.5980 chunk 41 optimal weight: 0.8980 chunk 21 optimal weight: 0.9990 chunk 12 optimal weight: 0.7980 chunk 17 optimal weight: 0.8980 chunk 53 optimal weight: 3.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 165 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 = 0.4145 r_free = 0.4145 target = 0.191632 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3651 r_free = 0.3651 target = 0.142761 restraints weight = 7415.020| |-----------------------------------------------------------------------------| r_work (start): 0.3652 rms_B_bonded: 2.37 r_work: 0.3503 rms_B_bonded: 3.49 restraints_weight: 0.5000 r_work (final): 0.3503 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7623 moved from start: 0.1961 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 7178 Z= 0.178 Angle : 0.471 5.156 9806 Z= 0.261 Chirality : 0.038 0.191 1168 Planarity : 0.004 0.037 1206 Dihedral : 3.450 15.145 988 Min Nonbonded Distance : 2.313 Molprobity Statistics. All-atom Clashscore : 5.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.82 % Favored : 98.18 % Rotamer: Outliers : 1.79 % Allowed : 12.81 % Favored : 85.40 % 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: 2.52 (0.28), residues: 932 helix: 2.57 (0.19), residues: 660 sheet: None (None), residues: 0 loop : -0.68 (0.38), residues: 272 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 586 HIS 0.002 0.000 HIS A 549 PHE 0.014 0.001 PHE A 238 TYR 0.013 0.001 TYR B 602 ARG 0.001 0.000 ARG B 261 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1864 Ramachandran restraints generated. 932 Oldfield, 0 Emsley, 932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1864 Ramachandran restraints generated. 932 Oldfield, 0 Emsley, 932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 756 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 90 time to evaluate : 0.725 Fit side-chains revert: symmetry clash REVERT: B 165 GLN cc_start: 0.7868 (mm-40) cc_final: 0.7467 (mt0) REVERT: B 431 THR cc_start: 0.7671 (m) cc_final: 0.7105 (p) outliers start: 13 outliers final: 12 residues processed: 97 average time/residue: 0.1916 time to fit residues: 25.1495 Evaluate side-chains 101 residues out of total 756 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 89 time to evaluate : 0.722 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 194 THR Chi-restraints excluded: chain A residue 245 LEU Chi-restraints excluded: chain A residue 395 SER Chi-restraints excluded: chain A residue 405 LEU Chi-restraints excluded: chain A residue 539 SER Chi-restraints excluded: chain A residue 542 LEU Chi-restraints excluded: chain B residue 180 THR Chi-restraints excluded: chain B residue 194 THR Chi-restraints excluded: chain B residue 259 ASP Chi-restraints excluded: chain B residue 395 SER Chi-restraints excluded: chain B residue 430 CYS Chi-restraints excluded: chain B residue 539 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 32 optimal weight: 0.5980 chunk 25 optimal weight: 0.5980 chunk 0 optimal weight: 4.9990 chunk 68 optimal weight: 0.0040 chunk 47 optimal weight: 0.5980 chunk 41 optimal weight: 0.1980 chunk 50 optimal weight: 3.9990 chunk 24 optimal weight: 0.7980 chunk 39 optimal weight: 0.8980 chunk 22 optimal weight: 7.9990 chunk 13 optimal weight: 0.9990 overall best weight: 0.3992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 165 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 = 0.4159 r_free = 0.4159 target = 0.193307 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3674 r_free = 0.3674 target = 0.144735 restraints weight = 7355.869| |-----------------------------------------------------------------------------| r_work (start): 0.3668 rms_B_bonded: 2.37 r_work: 0.3519 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work (final): 0.3519 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7590 moved from start: 0.2050 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.052 7178 Z= 0.149 Angle : 0.451 4.939 9806 Z= 0.251 Chirality : 0.038 0.184 1168 Planarity : 0.004 0.038 1206 Dihedral : 3.325 14.231 988 Min Nonbonded Distance : 2.329 Molprobity Statistics. All-atom Clashscore : 5.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.50 % Favored : 98.50 % Rotamer: Outliers : 1.52 % Allowed : 13.36 % Favored : 85.12 % 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: 2.66 (0.28), residues: 932 helix: 2.68 (0.19), residues: 670 sheet: None (None), residues: 0 loop : -0.79 (0.40), residues: 262 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 586 HIS 0.001 0.000 HIS A 549 PHE 0.014 0.001 PHE A 238 TYR 0.005 0.001 TYR B 602 ARG 0.001 0.000 ARG B 261 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3322.51 seconds wall clock time: 57 minutes 51.34 seconds (3471.34 seconds total)