Starting phenix.real_space_refine on Thu Feb 13 02:29:07 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8tpn_41478/02_2025/8tpn_41478.cif Found real_map, /net/cci-nas-00/data/ceres_data/8tpn_41478/02_2025/8tpn_41478.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.07 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8tpn_41478/02_2025/8tpn_41478.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8tpn_41478/02_2025/8tpn_41478.map" model { file = "/net/cci-nas-00/data/ceres_data/8tpn_41478/02_2025/8tpn_41478.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8tpn_41478/02_2025/8tpn_41478.cif" } resolution = 4.07 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= 0.001 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: 5 Type Number sf(0) Gaussians Ca 4 9.91 5 S 36 5.16 5 C 5662 2.51 5 N 1414 2.21 5 O 1496 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 10 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib" Total number of atoms: 8612 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 4304 Number of conformers: 1 Conformer: "" Number of residues, atoms: 551, 4304 Classifications: {'peptide': 551} Incomplete info: {'truncation_to_alanine': 35} Link IDs: {'PTRANS': 21, 'TRANS': 529} Chain breaks: 8 Unresolved non-hydrogen bonds: 159 Unresolved non-hydrogen angles: 196 Unresolved non-hydrogen dihedrals: 137 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLN:plan1': 2, 'ARG:plan': 4, 'TYR:plan': 1, 'ASN:plan1': 1, 'HIS:plan': 2, 'PHE:plan': 4, 'GLU:plan': 9, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 114 Chain: "A" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' CA': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Restraints were copied for chains: B Time building chain proxies: 7.78, per 1000 atoms: 0.90 Number of scatterers: 8612 At special positions: 0 Unit cell: (111.93, 115.57, 96.46, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Ca 4 19.99 S 36 16.00 O 1496 8.00 N 1414 7.00 C 5662 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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: 2.34 Conformation dependent library (CDL) restraints added in 994.0 milliseconds 2132 Ramachandran restraints generated. 1066 Oldfield, 0 Emsley, 1066 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2096 Finding SS restraints... Secondary structure from input PDB file: 48 helices and 2 sheets defined 74.4% alpha, 2.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.74 Creating SS restraints... Processing helix chain 'A' and resid 32 through 50 removed outlier: 3.511A pdb=" N VAL A 50 " --> pdb=" O ALA A 46 " (cutoff:3.500A) Processing helix chain 'A' and resid 72 through 90 Processing helix chain 'A' and resid 103 through 108 removed outlier: 4.438A pdb=" N ASP A 107 " --> pdb=" O GLN A 103 " (cutoff:3.500A) Processing helix chain 'A' and resid 111 through 125 Processing helix chain 'A' and resid 126 through 130 Processing helix chain 'A' and resid 152 through 164 Processing helix chain 'A' and resid 170 through 182 removed outlier: 3.775A pdb=" N ILE A 174 " --> pdb=" O GLU A 170 " (cutoff:3.500A) Processing helix chain 'A' and resid 183 through 199 Processing helix chain 'A' and resid 199 through 212 Processing helix chain 'A' and resid 217 through 246 Processing helix chain 'A' and resid 250 through 254 Processing helix chain 'A' and resid 280 through 289 removed outlier: 3.948A pdb=" N ARG A 284 " --> pdb=" O PRO A 280 " (cutoff:3.500A) Processing helix chain 'A' and resid 290 through 317 removed outlier: 3.640A pdb=" N PHE A 294 " --> pdb=" O LEU A 290 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N LEU A 305 " --> pdb=" O ALA A 301 " (cutoff:3.500A) Processing helix chain 'A' and resid 331 through 358 Proline residue: A 341 - end of helix removed outlier: 3.542A pdb=" N VAL A 346 " --> pdb=" O THR A 342 " (cutoff:3.500A) Processing helix chain 'A' and resid 362 through 392 removed outlier: 5.643A pdb=" N ALA A 385 " --> pdb=" O THR A 381 " (cutoff:3.500A) removed outlier: 5.537A pdb=" N LEU A 386 " --> pdb=" O SER A 382 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N VAL A 392 " --> pdb=" O PHE A 388 " (cutoff:3.500A) Processing helix chain 'A' and resid 403 through 411 removed outlier: 3.721A pdb=" N ALA A 411 " --> pdb=" O TRP A 407 " (cutoff:3.500A) Processing helix chain 'A' and resid 431 through 449 removed outlier: 3.607A pdb=" N TYR A 439 " --> pdb=" O ASN A 435 " (cutoff:3.500A) removed outlier: 4.500A pdb=" N ALA A 444 " --> pdb=" O PHE A 440 " (cutoff:3.500A) Processing helix chain 'A' and resid 453 through 465 Processing helix chain 'A' and resid 482 through 494 removed outlier: 3.873A pdb=" N THR A 494 " --> pdb=" O ARG A 490 " (cutoff:3.500A) Processing helix chain 'A' and resid 500 through 518 removed outlier: 3.614A pdb=" N SER A 518 " --> pdb=" O VAL A 514 " (cutoff:3.500A) Processing helix chain 'A' and resid 523 through 545 removed outlier: 3.856A pdb=" N CYS A 527 " --> pdb=" O LEU A 523 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N VAL A 530 " --> pdb=" O CYS A 526 " (cutoff:3.500A) removed outlier: 4.381A pdb=" N ARG A 537 " --> pdb=" O TRP A 533 " (cutoff:3.500A) removed outlier: 4.364A pdb=" N ALA A 540 " --> pdb=" O LEU A 536 " (cutoff:3.500A) Processing helix chain 'A' and resid 560 through 584 removed outlier: 3.670A pdb=" N ALA A 564 " --> pdb=" O PRO A 560 " (cutoff:3.500A) removed outlier: 4.205A pdb=" N SER A 577 " --> pdb=" O SER A 573 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N ALA A 578 " --> pdb=" O ILE A 574 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N SER A 584 " --> pdb=" O VAL A 580 " (cutoff:3.500A) Processing helix chain 'A' and resid 599 through 625 removed outlier: 3.590A pdb=" N SER A 625 " --> pdb=" O ARG A 621 " (cutoff:3.500A) Processing helix chain 'A' and resid 703 through 711 Processing helix chain 'B' and resid 32 through 50 removed outlier: 3.511A pdb=" N VAL B 50 " --> pdb=" O ALA B 46 " (cutoff:3.500A) Processing helix chain 'B' and resid 72 through 90 Processing helix chain 'B' and resid 103 through 108 removed outlier: 4.437A pdb=" N ASP B 107 " --> pdb=" O GLN B 103 " (cutoff:3.500A) Processing helix chain 'B' and resid 111 through 125 Processing helix chain 'B' and resid 126 through 130 Processing helix chain 'B' and resid 152 through 164 Processing helix chain 'B' and resid 170 through 182 removed outlier: 3.775A pdb=" N ILE B 174 " --> pdb=" O GLU B 170 " (cutoff:3.500A) Processing helix chain 'B' and resid 183 through 199 Processing helix chain 'B' and resid 199 through 212 Processing helix chain 'B' and resid 217 through 246 Processing helix chain 'B' and resid 250 through 254 Processing helix chain 'B' and resid 280 through 289 removed outlier: 3.948A pdb=" N ARG B 284 " --> pdb=" O PRO B 280 " (cutoff:3.500A) Processing helix chain 'B' and resid 290 through 317 removed outlier: 3.640A pdb=" N PHE B 294 " --> pdb=" O LEU B 290 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N LEU B 305 " --> pdb=" O ALA B 301 " (cutoff:3.500A) Processing helix chain 'B' and resid 331 through 358 Proline residue: B 341 - end of helix removed outlier: 3.542A pdb=" N VAL B 346 " --> pdb=" O THR B 342 " (cutoff:3.500A) Processing helix chain 'B' and resid 362 through 392 removed outlier: 5.644A pdb=" N ALA B 385 " --> pdb=" O THR B 381 " (cutoff:3.500A) removed outlier: 5.537A pdb=" N LEU B 386 " --> pdb=" O SER B 382 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N VAL B 392 " --> pdb=" O PHE B 388 " (cutoff:3.500A) Processing helix chain 'B' and resid 403 through 411 removed outlier: 3.721A pdb=" N ALA B 411 " --> pdb=" O TRP B 407 " (cutoff:3.500A) Processing helix chain 'B' and resid 431 through 449 removed outlier: 3.607A pdb=" N TYR B 439 " --> pdb=" O ASN B 435 " (cutoff:3.500A) removed outlier: 4.499A pdb=" N ALA B 444 " --> pdb=" O PHE B 440 " (cutoff:3.500A) Processing helix chain 'B' and resid 453 through 465 Processing helix chain 'B' and resid 482 through 494 removed outlier: 3.872A pdb=" N THR B 494 " --> pdb=" O ARG B 490 " (cutoff:3.500A) Processing helix chain 'B' and resid 500 through 518 removed outlier: 3.614A pdb=" N SER B 518 " --> pdb=" O VAL B 514 " (cutoff:3.500A) Processing helix chain 'B' and resid 523 through 545 removed outlier: 3.855A pdb=" N CYS B 527 " --> pdb=" O LEU B 523 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N VAL B 530 " --> pdb=" O CYS B 526 " (cutoff:3.500A) removed outlier: 4.380A pdb=" N ARG B 537 " --> pdb=" O TRP B 533 " (cutoff:3.500A) removed outlier: 4.365A pdb=" N ALA B 540 " --> pdb=" O LEU B 536 " (cutoff:3.500A) Processing helix chain 'B' and resid 560 through 584 removed outlier: 3.670A pdb=" N ALA B 564 " --> pdb=" O PRO B 560 " (cutoff:3.500A) removed outlier: 4.205A pdb=" N SER B 577 " --> pdb=" O SER B 573 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N ALA B 578 " --> pdb=" O ILE B 574 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N SER B 584 " --> pdb=" O VAL B 580 " (cutoff:3.500A) Processing helix chain 'B' and resid 599 through 625 removed outlier: 3.590A pdb=" N SER B 625 " --> pdb=" O ARG B 621 " (cutoff:3.500A) Processing helix chain 'B' and resid 703 through 711 Processing sheet with id=AA1, first strand: chain 'A' and resid 52 through 56 Processing sheet with id=AA2, first strand: chain 'B' and resid 52 through 56 598 hydrogen bonds defined for protein. 1758 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: 2.36 Time building geometry restraints manager: 2.64 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: 2670 1.34 - 1.46: 2218 1.46 - 1.58: 3886 1.58 - 1.69: 0 1.69 - 1.81: 58 Bond restraints: 8832 Sorted by residual: bond pdb=" C VAL B 455 " pdb=" N PRO B 456 " ideal model delta sigma weight residual 1.335 1.346 -0.011 1.36e-02 5.41e+03 6.47e-01 bond pdb=" C ILE B 394 " pdb=" N PRO B 395 " ideal model delta sigma weight residual 1.335 1.345 -0.010 1.28e-02 6.10e+03 6.40e-01 bond pdb=" C VAL A 455 " pdb=" N PRO A 456 " ideal model delta sigma weight residual 1.335 1.346 -0.011 1.36e-02 5.41e+03 6.38e-01 bond pdb=" C PHE A 181 " pdb=" N GLY A 182 " ideal model delta sigma weight residual 1.335 1.329 0.006 7.50e-03 1.78e+04 6.36e-01 bond pdb=" C ILE A 394 " pdb=" N PRO A 395 " ideal model delta sigma weight residual 1.335 1.345 -0.010 1.28e-02 6.10e+03 6.05e-01 ... (remaining 8827 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.37: 11797 1.37 - 2.74: 181 2.74 - 4.12: 32 4.12 - 5.49: 14 5.49 - 6.86: 4 Bond angle restraints: 12028 Sorted by residual: angle pdb=" N GLY A 182 " pdb=" CA GLY A 182 " pdb=" C GLY A 182 " ideal model delta sigma weight residual 111.21 114.35 -3.14 1.04e+00 9.25e-01 9.09e+00 angle pdb=" N GLY B 182 " pdb=" CA GLY B 182 " pdb=" C GLY B 182 " ideal model delta sigma weight residual 111.21 114.31 -3.10 1.04e+00 9.25e-01 8.89e+00 angle pdb=" CA VAL A 455 " pdb=" C VAL A 455 " pdb=" N PRO A 456 " ideal model delta sigma weight residual 118.88 122.02 -3.14 1.54e+00 4.22e-01 4.15e+00 angle pdb=" CA VAL B 455 " pdb=" C VAL B 455 " pdb=" N PRO B 456 " ideal model delta sigma weight residual 118.88 121.99 -3.11 1.54e+00 4.22e-01 4.07e+00 angle pdb=" C PHE B 181 " pdb=" N GLY B 182 " pdb=" CA GLY B 182 " ideal model delta sigma weight residual 122.63 120.64 1.99 1.03e+00 9.43e-01 3.73e+00 ... (remaining 12023 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.92: 4514 17.92 - 35.85: 480 35.85 - 53.77: 82 53.77 - 71.69: 12 71.69 - 89.62: 10 Dihedral angle restraints: 5098 sinusoidal: 1880 harmonic: 3218 Sorted by residual: dihedral pdb=" CA THR A 441 " pdb=" C THR A 441 " pdb=" N VAL A 442 " pdb=" CA VAL A 442 " ideal model delta harmonic sigma weight residual -180.00 -163.13 -16.87 0 5.00e+00 4.00e-02 1.14e+01 dihedral pdb=" CA THR B 441 " pdb=" C THR B 441 " pdb=" N VAL B 442 " pdb=" CA VAL B 442 " ideal model delta harmonic sigma weight residual -180.00 -163.13 -16.87 0 5.00e+00 4.00e-02 1.14e+01 dihedral pdb=" CB GLU A 452 " pdb=" CG GLU A 452 " pdb=" CD GLU A 452 " pdb=" OE1 GLU A 452 " ideal model delta sinusoidal sigma weight residual 0.00 89.62 -89.62 1 3.00e+01 1.11e-03 1.06e+01 ... (remaining 5095 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.030: 928 0.030 - 0.060: 289 0.060 - 0.091: 116 0.091 - 0.121: 35 0.121 - 0.151: 6 Chirality restraints: 1374 Sorted by residual: chirality pdb=" CA THR A 340 " pdb=" N THR A 340 " pdb=" C THR A 340 " pdb=" CB THR A 340 " both_signs ideal model delta sigma weight residual False 2.53 2.38 0.15 2.00e-01 2.50e+01 5.69e-01 chirality pdb=" CA THR B 340 " pdb=" N THR B 340 " pdb=" C THR B 340 " pdb=" CB THR B 340 " both_signs ideal model delta sigma weight residual False 2.53 2.38 0.15 2.00e-01 2.50e+01 5.64e-01 chirality pdb=" CA ILE A 147 " pdb=" N ILE A 147 " pdb=" C ILE A 147 " pdb=" CB ILE A 147 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.90e-01 ... (remaining 1371 not shown) Planarity restraints: 1496 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE A 292 " -0.051 5.00e-02 4.00e+02 7.61e-02 9.27e+00 pdb=" N PRO A 293 " 0.132 5.00e-02 4.00e+02 pdb=" CA PRO A 293 " -0.039 5.00e-02 4.00e+02 pdb=" CD PRO A 293 " -0.042 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE B 292 " -0.051 5.00e-02 4.00e+02 7.61e-02 9.26e+00 pdb=" N PRO B 293 " 0.132 5.00e-02 4.00e+02 pdb=" CA PRO B 293 " -0.039 5.00e-02 4.00e+02 pdb=" CD PRO B 293 " -0.042 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA TYR A 439 " -0.009 2.00e-02 2.50e+03 1.71e-02 2.91e+00 pdb=" C TYR A 439 " 0.029 2.00e-02 2.50e+03 pdb=" O TYR A 439 " -0.011 2.00e-02 2.50e+03 pdb=" N PHE A 440 " -0.010 2.00e-02 2.50e+03 ... (remaining 1493 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.76: 1291 2.76 - 3.29: 8532 3.29 - 3.83: 14341 3.83 - 4.36: 13948 4.36 - 4.90: 25865 Nonbonded interactions: 63977 Sorted by model distance: nonbonded pdb=" OG1 THR B 362 " pdb=" OD1 ASP B 364 " model vdw 2.220 3.040 nonbonded pdb=" OG1 THR A 362 " pdb=" OD1 ASP A 364 " model vdw 2.220 3.040 nonbonded pdb=" OH TYR A 26 " pdb=" O ALA A 36 " model vdw 2.229 3.040 nonbonded pdb=" OH TYR B 26 " pdb=" O ALA B 36 " model vdw 2.229 3.040 nonbonded pdb=" OH TYR A 188 " pdb=" OD2 ASP A 539 " model vdw 2.235 3.040 ... (remaining 63972 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: 0.04 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.830 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: 0.330 Check model and map are aligned: 0.060 Set scattering table: 0.090 Process input model: 23.930 Find NCS groups from input model: 0.140 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:2.840 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.250 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7957 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 : 0.002 0.034 8832 Z= 0.150 Angle : 0.464 6.861 12028 Z= 0.249 Chirality : 0.037 0.151 1374 Planarity : 0.004 0.076 1496 Dihedral : 15.102 89.616 3002 Min Nonbonded Distance : 2.220 Molprobity Statistics. All-atom Clashscore : 5.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer: Outliers : 0.00 % Allowed : 0.57 % Favored : 99.43 % 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: 2.66 (0.26), residues: 1066 helix: 2.61 (0.19), residues: 750 sheet: 0.63 (0.91), residues: 48 loop : -0.56 (0.37), residues: 268 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 163 HIS 0.002 0.000 HIS B 611 PHE 0.011 0.001 PHE A 187 TYR 0.009 0.001 TYR B 218 ARG 0.001 0.000 ARG B 45 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2132 Ramachandran restraints generated. 1066 Oldfield, 0 Emsley, 1066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2132 Ramachandran restraints generated. 1066 Oldfield, 0 Emsley, 1066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 946 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 116 time to evaluate : 0.908 Fit side-chains REVERT: A 456 PRO cc_start: 0.8284 (Cg_exo) cc_final: 0.8061 (Cg_endo) outliers start: 0 outliers final: 0 residues processed: 116 average time/residue: 0.1810 time to fit residues: 30.4962 Evaluate side-chains 87 residues out of total 946 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 87 time to evaluate : 0.910 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 92 optimal weight: 0.5980 chunk 83 optimal weight: 3.9990 chunk 46 optimal weight: 0.9990 chunk 28 optimal weight: 2.9990 chunk 56 optimal weight: 4.9990 chunk 44 optimal weight: 1.9990 chunk 86 optimal weight: 3.9990 chunk 33 optimal weight: 0.6980 chunk 52 optimal weight: 3.9990 chunk 64 optimal weight: 1.9990 chunk 99 optimal weight: 0.9980 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 79 GLN A 128 ASN A 374 GLN B 79 GLN B 128 ASN B 374 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.120951 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3195 r_free = 0.3195 target = 0.103205 restraints weight = 15213.562| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3172 r_free = 0.3172 target = 0.101830 restraints weight = 15640.402| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3183 r_free = 0.3183 target = 0.102602 restraints weight = 16852.813| |-----------------------------------------------------------------------------| r_work (final): 0.3182 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8007 moved from start: 0.0980 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 8832 Z= 0.214 Angle : 0.495 7.155 12028 Z= 0.267 Chirality : 0.039 0.148 1374 Planarity : 0.004 0.060 1496 Dihedral : 3.549 15.120 1166 Min Nonbonded Distance : 2.234 Molprobity Statistics. All-atom Clashscore : 3.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % Rotamer: Outliers : 0.00 % Allowed : 6.05 % Favored : 93.95 % 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: 2.65 (0.26), residues: 1066 helix: 2.55 (0.18), residues: 766 sheet: 0.62 (0.91), residues: 48 loop : -0.59 (0.37), residues: 252 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 521 HIS 0.003 0.001 HIS A 127 PHE 0.010 0.001 PHE A 198 TYR 0.008 0.001 TYR B 220 ARG 0.003 0.000 ARG A 432 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2132 Ramachandran restraints generated. 1066 Oldfield, 0 Emsley, 1066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2132 Ramachandran restraints generated. 1066 Oldfield, 0 Emsley, 1066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 946 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 118 time to evaluate : 1.010 Fit side-chains REVERT: A 286 LYS cc_start: 0.8314 (ttmt) cc_final: 0.7958 (tppt) REVERT: A 456 PRO cc_start: 0.8405 (Cg_exo) cc_final: 0.8153 (Cg_endo) REVERT: B 122 MET cc_start: 0.8518 (ttm) cc_final: 0.8301 (ttm) REVERT: B 286 LYS cc_start: 0.8445 (ttmt) cc_final: 0.8169 (tppt) outliers start: 0 outliers final: 0 residues processed: 118 average time/residue: 0.1813 time to fit residues: 31.0328 Evaluate side-chains 89 residues out of total 946 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 89 time to evaluate : 0.970 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 81 optimal weight: 1.9990 chunk 37 optimal weight: 2.9990 chunk 10 optimal weight: 0.0980 chunk 89 optimal weight: 2.9990 chunk 23 optimal weight: 0.0770 chunk 79 optimal weight: 0.0670 chunk 65 optimal weight: 0.9990 chunk 4 optimal weight: 0.9980 chunk 104 optimal weight: 0.9990 chunk 106 optimal weight: 2.9990 chunk 80 optimal weight: 3.9990 overall best weight: 0.4478 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 374 GLN A 445 GLN A 531 ASN B 445 GLN B 531 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3525 r_free = 0.3525 target = 0.129158 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.110138 restraints weight = 14670.920| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.111180 restraints weight = 11586.781| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 20)----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.111764 restraints weight = 9763.592| |-----------------------------------------------------------------------------| r_work (final): 0.3239 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7933 moved from start: 0.1158 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 8832 Z= 0.146 Angle : 0.458 7.007 12028 Z= 0.242 Chirality : 0.038 0.162 1374 Planarity : 0.004 0.054 1496 Dihedral : 3.485 16.236 1166 Min Nonbonded Distance : 2.317 Molprobity Statistics. All-atom Clashscore : 4.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % 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: 2.72 (0.26), residues: 1066 helix: 2.61 (0.18), residues: 766 sheet: 0.64 (0.92), residues: 48 loop : -0.57 (0.36), residues: 252 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 521 HIS 0.001 0.000 HIS B 611 PHE 0.011 0.001 PHE A 40 TYR 0.008 0.001 TYR B 234 ARG 0.005 0.000 ARG A 432 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2132 Ramachandran restraints generated. 1066 Oldfield, 0 Emsley, 1066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2132 Ramachandran restraints generated. 1066 Oldfield, 0 Emsley, 1066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 946 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 125 time to evaluate : 1.023 Fit side-chains REVERT: A 286 LYS cc_start: 0.8219 (ttmt) cc_final: 0.7907 (tppt) REVERT: B 41 VAL cc_start: 0.9077 (t) cc_final: 0.8785 (p) REVERT: B 286 LYS cc_start: 0.8302 (ttmt) cc_final: 0.8090 (tppt) outliers start: 0 outliers final: 0 residues processed: 125 average time/residue: 0.2101 time to fit residues: 39.2389 Evaluate side-chains 87 residues out of total 946 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 87 time to evaluate : 0.923 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 90 optimal weight: 8.9990 chunk 47 optimal weight: 2.9990 chunk 54 optimal weight: 8.9990 chunk 66 optimal weight: 6.9990 chunk 29 optimal weight: 5.9990 chunk 43 optimal weight: 0.6980 chunk 77 optimal weight: 2.9990 chunk 27 optimal weight: 0.8980 chunk 30 optimal weight: 5.9990 chunk 38 optimal weight: 2.9990 chunk 50 optimal weight: 2.9990 overall best weight: 2.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 374 GLN ** A 445 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 510 GLN ** A 531 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 445 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 531 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.115113 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 90)----------------| | r_work = 0.3057 r_free = 0.3057 target = 0.093883 restraints weight = 15671.138| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3067 r_free = 0.3067 target = 0.094579 restraints weight = 12911.405| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3079 r_free = 0.3079 target = 0.095331 restraints weight = 11303.848| |-----------------------------------------------------------------------------| r_work (final): 0.3066 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8161 moved from start: 0.1753 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.052 8832 Z= 0.387 Angle : 0.611 7.586 12028 Z= 0.331 Chirality : 0.043 0.162 1374 Planarity : 0.004 0.049 1496 Dihedral : 3.935 16.177 1166 Min Nonbonded Distance : 2.206 Molprobity Statistics. All-atom Clashscore : 5.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 0.11 % Allowed : 5.02 % Favored : 94.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.91 (0.25), residues: 1066 helix: 1.99 (0.18), residues: 766 sheet: 0.33 (0.92), residues: 48 loop : -0.82 (0.37), residues: 252 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 521 HIS 0.004 0.001 HIS B 401 PHE 0.020 0.002 PHE A 198 TYR 0.015 0.002 TYR B 220 ARG 0.005 0.001 ARG B 93 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2132 Ramachandran restraints generated. 1066 Oldfield, 0 Emsley, 1066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2132 Ramachandran restraints generated. 1066 Oldfield, 0 Emsley, 1066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 946 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 111 time to evaluate : 1.023 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 286 LYS cc_start: 0.8375 (ttmt) cc_final: 0.7934 (tppt) REVERT: B 286 LYS cc_start: 0.8422 (ttmt) cc_final: 0.7996 (tppt) outliers start: 1 outliers final: 0 residues processed: 112 average time/residue: 0.1801 time to fit residues: 29.7636 Evaluate side-chains 83 residues out of total 946 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 83 time to evaluate : 1.014 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 17 optimal weight: 0.9980 chunk 68 optimal weight: 2.9990 chunk 0 optimal weight: 4.9990 chunk 23 optimal weight: 0.6980 chunk 25 optimal weight: 0.0170 chunk 33 optimal weight: 0.9990 chunk 27 optimal weight: 0.7980 chunk 69 optimal weight: 0.9990 chunk 99 optimal weight: 0.9980 chunk 48 optimal weight: 0.9990 chunk 12 optimal weight: 2.9990 overall best weight: 0.7018 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 445 GLN A 531 ASN B 374 GLN B 445 GLN B 531 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.126277 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 80)----------------| | r_work = 0.3227 r_free = 0.3227 target = 0.106843 restraints weight = 14719.113| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3240 r_free = 0.3240 target = 0.107747 restraints weight = 11845.569| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3245 r_free = 0.3245 target = 0.108166 restraints weight = 10219.570| |-----------------------------------------------------------------------------| r_work (final): 0.3214 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8036 moved from start: 0.1695 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 8832 Z= 0.176 Angle : 0.494 7.102 12028 Z= 0.261 Chirality : 0.038 0.148 1374 Planarity : 0.004 0.044 1496 Dihedral : 3.719 16.424 1166 Min Nonbonded Distance : 2.305 Molprobity Statistics. All-atom Clashscore : 4.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % 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 (0.26), residues: 1066 helix: 2.22 (0.18), residues: 764 sheet: 0.44 (0.94), residues: 48 loop : -0.82 (0.36), residues: 254 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP B 521 HIS 0.001 0.001 HIS A 401 PHE 0.011 0.001 PHE A 40 TYR 0.011 0.001 TYR B 234 ARG 0.003 0.000 ARG A 432 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2132 Ramachandran restraints generated. 1066 Oldfield, 0 Emsley, 1066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2132 Ramachandran restraints generated. 1066 Oldfield, 0 Emsley, 1066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 946 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 123 time to evaluate : 0.806 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 286 LYS cc_start: 0.8234 (ttmt) cc_final: 0.7914 (tppt) REVERT: B 122 MET cc_start: 0.8790 (ttm) cc_final: 0.8565 (ttm) REVERT: B 286 LYS cc_start: 0.8261 (ttmt) cc_final: 0.7973 (tppt) outliers start: 0 outliers final: 0 residues processed: 123 average time/residue: 0.1767 time to fit residues: 31.5088 Evaluate side-chains 89 residues out of total 946 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 89 time to evaluate : 0.942 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 25 optimal weight: 5.9990 chunk 97 optimal weight: 2.9990 chunk 85 optimal weight: 2.9990 chunk 102 optimal weight: 0.0970 chunk 37 optimal weight: 2.9990 chunk 63 optimal weight: 0.9990 chunk 31 optimal weight: 2.9990 chunk 82 optimal weight: 0.5980 chunk 14 optimal weight: 2.9990 chunk 70 optimal weight: 0.9990 chunk 103 optimal weight: 0.4980 overall best weight: 0.6382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 531 ASN B 374 GLN ** B 531 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.126649 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.3241 r_free = 0.3241 target = 0.107414 restraints weight = 14474.133| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3252 r_free = 0.3252 target = 0.108252 restraints weight = 11613.264| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.108936 restraints weight = 9940.318| |-----------------------------------------------------------------------------| r_work (final): 0.3241 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8004 moved from start: 0.1759 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 8832 Z= 0.172 Angle : 0.491 7.376 12028 Z= 0.257 Chirality : 0.038 0.150 1374 Planarity : 0.004 0.042 1496 Dihedral : 3.622 15.081 1166 Min Nonbonded Distance : 2.299 Molprobity Statistics. All-atom Clashscore : 4.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % Rotamer: Outliers : 0.00 % Allowed : 1.26 % Favored : 98.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.26 (0.26), residues: 1066 helix: 2.29 (0.18), residues: 764 sheet: 0.58 (0.93), residues: 48 loop : -0.81 (0.37), residues: 254 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 88 HIS 0.002 0.001 HIS A 366 PHE 0.011 0.001 PHE B 187 TYR 0.011 0.001 TYR A 234 ARG 0.004 0.000 ARG A 93 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2132 Ramachandran restraints generated. 1066 Oldfield, 0 Emsley, 1066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2132 Ramachandran restraints generated. 1066 Oldfield, 0 Emsley, 1066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 946 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 117 time to evaluate : 0.915 Fit side-chains revert: symmetry clash REVERT: A 286 LYS cc_start: 0.8224 (ttmt) cc_final: 0.7922 (tppt) REVERT: B 286 LYS cc_start: 0.8269 (ttmt) cc_final: 0.7996 (tppt) outliers start: 0 outliers final: 0 residues processed: 117 average time/residue: 0.1825 time to fit residues: 30.8914 Evaluate side-chains 90 residues out of total 946 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 90 time to evaluate : 0.936 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 49 optimal weight: 0.9980 chunk 92 optimal weight: 2.9990 chunk 5 optimal weight: 3.9990 chunk 8 optimal weight: 4.9990 chunk 24 optimal weight: 4.9990 chunk 27 optimal weight: 0.8980 chunk 52 optimal weight: 0.6980 chunk 83 optimal weight: 5.9990 chunk 20 optimal weight: 1.9990 chunk 100 optimal weight: 1.9990 chunk 28 optimal weight: 0.8980 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 531 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 531 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.124154 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 87)----------------| | r_work = 0.3199 r_free = 0.3199 target = 0.104518 restraints weight = 14909.461| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3210 r_free = 0.3210 target = 0.105328 restraints weight = 12147.557| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3220 r_free = 0.3220 target = 0.106043 restraints weight = 10450.973| |-----------------------------------------------------------------------------| r_work (final): 0.3148 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8055 moved from start: 0.1884 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 8832 Z= 0.223 Angle : 0.511 6.957 12028 Z= 0.274 Chirality : 0.039 0.148 1374 Planarity : 0.004 0.039 1496 Dihedral : 3.724 15.856 1166 Min Nonbonded Distance : 2.249 Molprobity Statistics. All-atom Clashscore : 4.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 0.00 % Allowed : 0.80 % Favored : 99.20 % 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: 2.12 (0.26), residues: 1066 helix: 2.20 (0.18), residues: 764 sheet: 0.48 (0.93), residues: 48 loop : -0.90 (0.37), residues: 254 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 521 HIS 0.002 0.001 HIS B 401 PHE 0.014 0.001 PHE B 198 TYR 0.012 0.001 TYR B 513 ARG 0.002 0.000 ARG A 432 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2132 Ramachandran restraints generated. 1066 Oldfield, 0 Emsley, 1066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2132 Ramachandran restraints generated. 1066 Oldfield, 0 Emsley, 1066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 946 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 119 time to evaluate : 0.960 Fit side-chains revert: symmetry clash REVERT: A 286 LYS cc_start: 0.8311 (ttmt) cc_final: 0.7915 (tppt) REVERT: B 286 LYS cc_start: 0.8311 (ttmt) cc_final: 0.7988 (tppt) outliers start: 0 outliers final: 0 residues processed: 119 average time/residue: 0.1725 time to fit residues: 30.3119 Evaluate side-chains 83 residues out of total 946 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 83 time to evaluate : 0.907 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 45 optimal weight: 0.6980 chunk 33 optimal weight: 0.6980 chunk 63 optimal weight: 2.9990 chunk 48 optimal weight: 4.9990 chunk 65 optimal weight: 0.7980 chunk 24 optimal weight: 1.9990 chunk 11 optimal weight: 4.9990 chunk 6 optimal weight: 0.9980 chunk 50 optimal weight: 2.9990 chunk 89 optimal weight: 1.9990 chunk 30 optimal weight: 1.9990 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 531 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 531 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.124725 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 79)----------------| | r_work = 0.3210 r_free = 0.3210 target = 0.105423 restraints weight = 14938.042| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3218 r_free = 0.3218 target = 0.106005 restraints weight = 12298.389| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3220 r_free = 0.3220 target = 0.106207 restraints weight = 10644.761| |-----------------------------------------------------------------------------| r_work (final): 0.3144 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8060 moved from start: 0.1923 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 8832 Z= 0.218 Angle : 0.514 7.407 12028 Z= 0.273 Chirality : 0.039 0.148 1374 Planarity : 0.004 0.039 1496 Dihedral : 3.753 15.163 1166 Min Nonbonded Distance : 2.266 Molprobity Statistics. All-atom Clashscore : 4.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 0.00 % Allowed : 0.91 % Favored : 99.09 % 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: 2.05 (0.26), residues: 1066 helix: 2.16 (0.18), residues: 764 sheet: 0.35 (0.92), residues: 48 loop : -0.95 (0.37), residues: 254 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A 521 HIS 0.006 0.001 HIS A 151 PHE 0.017 0.001 PHE B 187 TYR 0.012 0.001 TYR A 234 ARG 0.002 0.000 ARG A 432 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2132 Ramachandran restraints generated. 1066 Oldfield, 0 Emsley, 1066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2132 Ramachandran restraints generated. 1066 Oldfield, 0 Emsley, 1066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 946 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 116 time to evaluate : 1.048 Fit side-chains REVERT: A 286 LYS cc_start: 0.8329 (ttmt) cc_final: 0.7905 (tppt) REVERT: B 286 LYS cc_start: 0.8305 (ttmt) cc_final: 0.7961 (tppt) outliers start: 0 outliers final: 0 residues processed: 116 average time/residue: 0.1730 time to fit residues: 29.6745 Evaluate side-chains 82 residues out of total 946 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 82 time to evaluate : 0.898 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 19 optimal weight: 2.9990 chunk 99 optimal weight: 0.9980 chunk 88 optimal weight: 2.9990 chunk 32 optimal weight: 5.9990 chunk 44 optimal weight: 1.9990 chunk 97 optimal weight: 0.8980 chunk 68 optimal weight: 3.9990 chunk 35 optimal weight: 3.9990 chunk 105 optimal weight: 2.9990 chunk 34 optimal weight: 2.9990 chunk 104 optimal weight: 0.7980 overall best weight: 1.5384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 531 ASN ** B 531 ASN ** 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 = 0.3419 r_free = 0.3419 target = 0.121462 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 86)----------------| | r_work = 0.3160 r_free = 0.3160 target = 0.101818 restraints weight = 14941.844| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3172 r_free = 0.3172 target = 0.102632 restraints weight = 12109.888| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3175 r_free = 0.3175 target = 0.102833 restraints weight = 10556.370| |-----------------------------------------------------------------------------| r_work (final): 0.3099 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8108 moved from start: 0.2106 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 8832 Z= 0.290 Angle : 0.567 6.791 12028 Z= 0.306 Chirality : 0.041 0.149 1374 Planarity : 0.004 0.038 1496 Dihedral : 3.934 15.342 1166 Min Nonbonded Distance : 2.206 Molprobity Statistics. All-atom Clashscore : 4.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 0.00 % Allowed : 1.37 % Favored : 98.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.84 (0.26), residues: 1066 helix: 2.03 (0.18), residues: 762 sheet: 0.24 (0.90), residues: 48 loop : -1.11 (0.36), residues: 256 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP A 521 HIS 0.007 0.001 HIS B 151 PHE 0.023 0.002 PHE A 198 TYR 0.010 0.002 TYR B 234 ARG 0.002 0.000 ARG A 432 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2132 Ramachandran restraints generated. 1066 Oldfield, 0 Emsley, 1066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2132 Ramachandran restraints generated. 1066 Oldfield, 0 Emsley, 1066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 946 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 108 time to evaluate : 1.054 Fit side-chains REVERT: A 122 MET cc_start: 0.8628 (ttm) cc_final: 0.8426 (ttm) REVERT: A 286 LYS cc_start: 0.8358 (ttmt) cc_final: 0.7915 (tppt) REVERT: B 122 MET cc_start: 0.8666 (ttm) cc_final: 0.8416 (ttm) REVERT: B 286 LYS cc_start: 0.8306 (ttmt) cc_final: 0.7942 (tppt) outliers start: 0 outliers final: 0 residues processed: 108 average time/residue: 0.1802 time to fit residues: 28.6121 Evaluate side-chains 81 residues out of total 946 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 81 time to evaluate : 0.861 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 65 optimal weight: 1.9990 chunk 45 optimal weight: 0.6980 chunk 101 optimal weight: 0.8980 chunk 88 optimal weight: 0.0770 chunk 0 optimal weight: 4.9990 chunk 56 optimal weight: 5.9990 chunk 73 optimal weight: 0.8980 chunk 26 optimal weight: 0.9990 chunk 103 optimal weight: 0.8980 chunk 41 optimal weight: 0.9990 chunk 105 optimal weight: 0.9990 overall best weight: 0.6938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 531 ASN ** B 531 ASN ** 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 = 0.3469 r_free = 0.3469 target = 0.125321 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 80)----------------| | r_work = 0.3220 r_free = 0.3220 target = 0.105985 restraints weight = 14697.678| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3233 r_free = 0.3233 target = 0.106935 restraints weight = 11719.880| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3240 r_free = 0.3240 target = 0.107456 restraints weight = 10049.474| |-----------------------------------------------------------------------------| r_work (final): 0.3229 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8034 moved from start: 0.2080 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 8832 Z= 0.182 Angle : 0.511 7.321 12028 Z= 0.268 Chirality : 0.039 0.170 1374 Planarity : 0.004 0.039 1496 Dihedral : 3.824 15.303 1166 Min Nonbonded Distance : 2.297 Molprobity Statistics. All-atom Clashscore : 4.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 0.00 % Allowed : 0.23 % Favored : 99.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.98 (0.26), residues: 1066 helix: 2.14 (0.18), residues: 764 sheet: 0.14 (0.89), residues: 48 loop : -1.05 (0.36), residues: 254 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP A 521 HIS 0.003 0.001 HIS B 151 PHE 0.016 0.001 PHE A 198 TYR 0.009 0.001 TYR A 613 ARG 0.002 0.000 ARG A 45 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2132 Ramachandran restraints generated. 1066 Oldfield, 0 Emsley, 1066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2132 Ramachandran restraints generated. 1066 Oldfield, 0 Emsley, 1066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 946 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 103 time to evaluate : 1.055 Fit side-chains REVERT: A 286 LYS cc_start: 0.8234 (ttmt) cc_final: 0.7899 (tppt) REVERT: B 286 LYS cc_start: 0.8218 (ttmt) cc_final: 0.7954 (tppt) outliers start: 0 outliers final: 0 residues processed: 103 average time/residue: 0.1896 time to fit residues: 28.7199 Evaluate side-chains 80 residues out of total 946 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 80 time to evaluate : 0.874 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 18 optimal weight: 0.9990 chunk 19 optimal weight: 0.3980 chunk 87 optimal weight: 5.9990 chunk 1 optimal weight: 4.9990 chunk 28 optimal weight: 0.8980 chunk 12 optimal weight: 0.9980 chunk 11 optimal weight: 0.6980 chunk 63 optimal weight: 3.9990 chunk 74 optimal weight: 1.9990 chunk 82 optimal weight: 4.9990 chunk 101 optimal weight: 0.9980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 445 GLN A 531 ASN ** B 531 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.125160 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.3220 r_free = 0.3220 target = 0.106047 restraints weight = 14820.487| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3231 r_free = 0.3231 target = 0.106881 restraints weight = 11898.351| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3235 r_free = 0.3235 target = 0.107182 restraints weight = 9767.003| |-----------------------------------------------------------------------------| r_work (final): 0.3215 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8043 moved from start: 0.2090 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 8832 Z= 0.190 Angle : 0.513 7.556 12028 Z= 0.268 Chirality : 0.039 0.166 1374 Planarity : 0.004 0.038 1496 Dihedral : 3.801 15.547 1166 Min Nonbonded Distance : 2.287 Molprobity Statistics. All-atom Clashscore : 5.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 0.11 % Allowed : 0.11 % Favored : 99.77 % 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: 2.02 (0.26), residues: 1066 helix: 2.17 (0.18), residues: 764 sheet: 0.17 (0.89), residues: 48 loop : -1.06 (0.36), residues: 254 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP A 521 HIS 0.003 0.001 HIS B 151 PHE 0.016 0.001 PHE A 198 TYR 0.008 0.001 TYR B 613 ARG 0.002 0.000 ARG A 432 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2414.54 seconds wall clock time: 44 minutes 11.93 seconds (2651.93 seconds total)