Starting phenix.real_space_refine on Mon May 12 08:49:21 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8wba_37418/05_2025/8wba_37418.cif Found real_map, /net/cci-nas-00/data/ceres_data/8wba_37418/05_2025/8wba_37418.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8wba_37418/05_2025/8wba_37418.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8wba_37418/05_2025/8wba_37418.map" model { file = "/net/cci-nas-00/data/ceres_data/8wba_37418/05_2025/8wba_37418.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8wba_37418/05_2025/8wba_37418.cif" } resolution = 3.1 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= -0.002 sd= 0.080 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 58 5.16 5 C 5646 2.51 5 N 1430 2.21 5 O 1512 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 20 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 8646 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 4288 Number of conformers: 1 Conformer: "" Number of residues, atoms: 553, 4288 Classifications: {'peptide': 553} Link IDs: {'PTRANS': 18, 'TRANS': 534} Chain breaks: 4 Chain: "B" Number of atoms: 4288 Number of conformers: 1 Conformer: "" Number of residues, atoms: 553, 4288 Classifications: {'peptide': 553} Link IDs: {'PTRANS': 18, 'TRANS': 534} Chain breaks: 4 Chain: "A" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 70 Unusual residues: {'Y01': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 5.89, per 1000 atoms: 0.68 Number of scatterers: 8646 At special positions: 0 Unit cell: (68.2, 105.6, 122.1, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 58 16.00 O 1512 8.00 N 1430 7.00 C 5646 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS A 606 " - pdb=" SG CYS A 622 " distance=2.03 Simple disulfide: pdb=" SG CYS B 606 " - pdb=" SG CYS B 622 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.49 Conformation dependent library (CDL) restraints added in 956.4 milliseconds 2172 Ramachandran restraints generated. 1086 Oldfield, 0 Emsley, 1086 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2028 Finding SS restraints... Secondary structure from input PDB file: 48 helices and 5 sheets defined 66.1% alpha, 6.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.79 Creating SS restraints... Processing helix chain 'A' and resid 106 through 115 Processing helix chain 'A' and resid 135 through 140 removed outlier: 3.538A pdb=" N LYS A 140 " --> pdb=" O LYS A 136 " (cutoff:3.500A) Processing helix chain 'A' and resid 156 through 169 Processing helix chain 'A' and resid 174 through 189 Processing helix chain 'A' and resid 190 through 194 removed outlier: 4.184A pdb=" N LYS A 193 " --> pdb=" O GLY A 190 " (cutoff:3.500A) Processing helix chain 'A' and resid 208 through 220 Processing helix chain 'A' and resid 238 through 255 Processing helix chain 'A' and resid 268 through 275 removed outlier: 3.596A pdb=" N PHE A 275 " --> pdb=" O VAL A 271 " (cutoff:3.500A) Processing helix chain 'A' and resid 294 through 303 Processing helix chain 'A' and resid 311 through 321 Processing helix chain 'A' and resid 338 through 357 removed outlier: 4.832A pdb=" N ALA A 350 " --> pdb=" O ASP A 346 " (cutoff:3.500A) Proline residue: A 351 - end of helix Processing helix chain 'A' and resid 379 through 406 removed outlier: 4.569A pdb=" N LYS A 399 " --> pdb=" O HIS A 395 " (cutoff:3.500A) removed outlier: 4.644A pdb=" N GLU A 400 " --> pdb=" O ARG A 396 " (cutoff:3.500A) Processing helix chain 'A' and resid 407 through 425 Processing helix chain 'A' and resid 432 through 456 Proline residue: A 451 - end of helix removed outlier: 3.683A pdb=" N VAL A 456 " --> pdb=" O SER A 452 " (cutoff:3.500A) Processing helix chain 'A' and resid 457 through 469 removed outlier: 3.620A pdb=" N GLU A 462 " --> pdb=" O THR A 458 " (cutoff:3.500A) removed outlier: 4.367A pdb=" N ALA A 464 " --> pdb=" O PRO A 460 " (cutoff:3.500A) removed outlier: 5.626A pdb=" N ILE A 465 " --> pdb=" O GLN A 461 " (cutoff:3.500A) Processing helix chain 'A' and resid 476 through 492 Processing helix chain 'A' and resid 493 through 508 removed outlier: 4.020A pdb=" N TRP A 505 " --> pdb=" O THR A 501 " (cutoff:3.500A) Processing helix chain 'A' and resid 513 through 541 removed outlier: 3.746A pdb=" N ILE A 541 " --> pdb=" O LEU A 537 " (cutoff:3.500A) Processing helix chain 'A' and resid 543 through 561 Processing helix chain 'A' and resid 575 through 579 Processing helix chain 'A' and resid 580 through 595 Processing helix chain 'A' and resid 597 through 605 Processing helix chain 'A' and resid 619 through 630 removed outlier: 3.635A pdb=" N VAL A 625 " --> pdb=" O GLY A 621 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N GLU A 628 " --> pdb=" O PHE A 624 " (cutoff:3.500A) Processing helix chain 'A' and resid 634 through 660 removed outlier: 3.753A pdb=" N ARG A 650 " --> pdb=" O PHE A 646 " (cutoff:3.500A) Processing helix chain 'B' and resid 106 through 115 Processing helix chain 'B' and resid 135 through 141 Processing helix chain 'B' and resid 156 through 169 Processing helix chain 'B' and resid 174 through 189 Processing helix chain 'B' and resid 190 through 194 removed outlier: 4.082A pdb=" N LYS B 193 " --> pdb=" O GLY B 190 " (cutoff:3.500A) Processing helix chain 'B' and resid 208 through 220 removed outlier: 3.514A pdb=" N GLU B 220 " --> pdb=" O SER B 216 " (cutoff:3.500A) Processing helix chain 'B' and resid 238 through 255 Processing helix chain 'B' and resid 268 through 275 removed outlier: 3.650A pdb=" N PHE B 275 " --> pdb=" O VAL B 271 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 303 Processing helix chain 'B' and resid 311 through 321 Processing helix chain 'B' and resid 338 through 357 removed outlier: 4.612A pdb=" N ALA B 350 " --> pdb=" O ASP B 346 " (cutoff:3.500A) Proline residue: B 351 - end of helix Processing helix chain 'B' and resid 379 through 405 removed outlier: 4.583A pdb=" N LYS B 399 " --> pdb=" O HIS B 395 " (cutoff:3.500A) removed outlier: 4.660A pdb=" N GLU B 400 " --> pdb=" O ARG B 396 " (cutoff:3.500A) Processing helix chain 'B' and resid 407 through 425 Processing helix chain 'B' and resid 432 through 456 Proline residue: B 451 - end of helix Processing helix chain 'B' and resid 457 through 472 removed outlier: 4.979A pdb=" N ALA B 464 " --> pdb=" O PRO B 460 " (cutoff:3.500A) removed outlier: 5.590A pdb=" N ILE B 465 " --> pdb=" O GLN B 461 " (cutoff:3.500A) Processing helix chain 'B' and resid 476 through 492 Processing helix chain 'B' and resid 493 through 508 removed outlier: 4.170A pdb=" N TRP B 505 " --> pdb=" O THR B 501 " (cutoff:3.500A) Processing helix chain 'B' and resid 513 through 541 removed outlier: 3.628A pdb=" N ILE B 541 " --> pdb=" O LEU B 537 " (cutoff:3.500A) Processing helix chain 'B' and resid 543 through 561 Processing helix chain 'B' and resid 573 through 578 removed outlier: 4.232A pdb=" N LYS B 577 " --> pdb=" O MET B 573 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N TYR B 578 " --> pdb=" O VAL B 574 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 573 through 578' Processing helix chain 'B' and resid 580 through 595 Processing helix chain 'B' and resid 597 through 605 Processing helix chain 'B' and resid 619 through 625 removed outlier: 3.539A pdb=" N VAL B 625 " --> pdb=" O GLY B 621 " (cutoff:3.500A) Processing helix chain 'B' and resid 634 through 660 removed outlier: 3.629A pdb=" N VAL B 639 " --> pdb=" O MET B 635 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N ARG B 650 " --> pdb=" O PHE B 646 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 89 through 91 removed outlier: 5.209A pdb=" N PHE A 42 " --> pdb=" O LEU A 128 " (cutoff:3.500A) removed outlier: 7.137A pdb=" N LEU A 128 " --> pdb=" O PHE A 42 " (cutoff:3.500A) removed outlier: 5.097A pdb=" N ASP A 44 " --> pdb=" O LYS A 126 " (cutoff:3.500A) removed outlier: 4.471A pdb=" N LYS A 126 " --> pdb=" O ASP A 44 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 227 through 230 removed outlier: 6.171A pdb=" N LEU A 228 " --> pdb=" O VAL A 261 " (cutoff:3.500A) removed outlier: 5.866A pdb=" N PHE A 96 " --> pdb=" O THR A 277 " (cutoff:3.500A) removed outlier: 7.848A pdb=" N LEU A 279 " --> pdb=" O PHE A 96 " (cutoff:3.500A) removed outlier: 6.189A pdb=" N ALA A 98 " --> pdb=" O LEU A 279 " (cutoff:3.500A) removed outlier: 7.588A pdb=" N LEU A 281 " --> pdb=" O ALA A 98 " (cutoff:3.500A) removed outlier: 6.936A pdb=" N LEU A 100 " --> pdb=" O LEU A 281 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N PHE A 288 " --> pdb=" O LEU A 280 " (cutoff:3.500A) removed outlier: 6.420A pdb=" N SER A 282 " --> pdb=" O CYS A 286 " (cutoff:3.500A) removed outlier: 5.422A pdb=" N CYS A 286 " --> pdb=" O SER A 282 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 87 through 91 removed outlier: 5.401A pdb=" N VAL B 87 " --> pdb=" O ASP B 44 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 99 through 100 removed outlier: 5.938A pdb=" N SER B 282 " --> pdb=" O CYS B 286 " (cutoff:3.500A) removed outlier: 5.486A pdb=" N CYS B 286 " --> pdb=" O SER B 282 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 142 through 145 removed outlier: 6.632A pdb=" N GLY B 143 " --> pdb=" O VAL B 229 " (cutoff:3.500A) removed outlier: 6.364A pdb=" N LEU B 228 " --> pdb=" O VAL B 261 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 529 hydrogen bonds defined for protein. 1560 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: 2.48 Time building geometry restraints manager: 2.87 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 1502 1.33 - 1.45: 2237 1.45 - 1.57: 4996 1.57 - 1.69: 1 1.69 - 1.81: 92 Bond restraints: 8828 Sorted by residual: bond pdb=" CBE Y01 A 702 " pdb=" CBI Y01 A 702 " ideal model delta sigma weight residual 1.550 1.570 -0.020 2.00e-02 2.50e+03 1.01e+00 bond pdb=" CB MET B 603 " pdb=" CG MET B 603 " ideal model delta sigma weight residual 1.520 1.548 -0.028 3.00e-02 1.11e+03 8.87e-01 bond pdb=" CB PHE A 516 " pdb=" CG PHE A 516 " ideal model delta sigma weight residual 1.502 1.522 -0.020 2.30e-02 1.89e+03 7.79e-01 bond pdb=" CB MET A 603 " pdb=" CG MET A 603 " ideal model delta sigma weight residual 1.520 1.545 -0.025 3.00e-02 1.11e+03 6.99e-01 bond pdb=" CB PHE B 516 " pdb=" CG PHE B 516 " ideal model delta sigma weight residual 1.502 1.520 -0.018 2.30e-02 1.89e+03 6.18e-01 ... (remaining 8823 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.80: 11787 1.80 - 3.59: 156 3.59 - 5.39: 28 5.39 - 7.19: 2 7.19 - 8.99: 5 Bond angle restraints: 11978 Sorted by residual: angle pdb=" CB MET B 603 " pdb=" CG MET B 603 " pdb=" SD MET B 603 " ideal model delta sigma weight residual 112.70 121.32 -8.62 3.00e+00 1.11e-01 8.26e+00 angle pdb=" CA PHE B 308 " pdb=" C PHE B 308 " pdb=" N PRO B 309 " ideal model delta sigma weight residual 117.82 120.00 -2.18 7.80e-01 1.64e+00 7.83e+00 angle pdb=" CB MET A 603 " pdb=" CG MET A 603 " pdb=" SD MET A 603 " ideal model delta sigma weight residual 112.70 120.70 -8.00 3.00e+00 1.11e-01 7.10e+00 angle pdb=" CA LEU A 161 " pdb=" CB LEU A 161 " pdb=" CG LEU A 161 " ideal model delta sigma weight residual 116.30 107.31 8.99 3.50e+00 8.16e-02 6.59e+00 angle pdb=" CA ILE A 541 " pdb=" CB ILE A 541 " pdb=" CG1 ILE A 541 " ideal model delta sigma weight residual 110.40 114.68 -4.28 1.70e+00 3.46e-01 6.33e+00 ... (remaining 11973 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.36: 4425 16.36 - 32.71: 648 32.71 - 49.07: 172 49.07 - 65.42: 30 65.42 - 81.78: 15 Dihedral angle restraints: 5290 sinusoidal: 2130 harmonic: 3160 Sorted by residual: dihedral pdb=" CB CYS A 606 " pdb=" SG CYS A 606 " pdb=" SG CYS A 622 " pdb=" CB CYS A 622 " ideal model delta sinusoidal sigma weight residual 93.00 142.65 -49.65 1 1.00e+01 1.00e-02 3.38e+01 dihedral pdb=" CA ASP A 148 " pdb=" CB ASP A 148 " pdb=" CG ASP A 148 " pdb=" OD1 ASP A 148 " ideal model delta sinusoidal sigma weight residual -30.00 -89.28 59.28 1 2.00e+01 2.50e-03 1.17e+01 dihedral pdb=" CA ASP A 607 " pdb=" CB ASP A 607 " pdb=" CG ASP A 607 " pdb=" OD1 ASP A 607 " ideal model delta sinusoidal sigma weight residual -30.00 -89.14 59.14 1 2.00e+01 2.50e-03 1.17e+01 ... (remaining 5287 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.055: 1223 0.055 - 0.110: 190 0.110 - 0.165: 18 0.165 - 0.220: 1 0.220 - 0.275: 2 Chirality restraints: 1434 Sorted by residual: chirality pdb=" CG LEU A 517 " pdb=" CB LEU A 517 " pdb=" CD1 LEU A 517 " pdb=" CD2 LEU A 517 " both_signs ideal model delta sigma weight residual False -2.59 -2.31 -0.27 2.00e-01 2.50e+01 1.89e+00 chirality pdb=" CBB Y01 A 702 " pdb=" CAC Y01 A 702 " pdb=" CAO Y01 A 702 " pdb=" CBE Y01 A 702 " both_signs ideal model delta sigma weight residual False 2.58 2.34 0.23 2.00e-01 2.50e+01 1.33e+00 chirality pdb=" CBE Y01 A 702 " pdb=" CAP Y01 A 702 " pdb=" CBB Y01 A 702 " pdb=" CBI Y01 A 702 " both_signs ideal model delta sigma weight residual False 2.57 2.40 0.17 2.00e-01 2.50e+01 7.42e-01 ... (remaining 1431 not shown) Planarity restraints: 1458 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL A 514 " 0.036 5.00e-02 4.00e+02 5.44e-02 4.73e+00 pdb=" N PRO A 515 " -0.094 5.00e-02 4.00e+02 pdb=" CA PRO A 515 " 0.027 5.00e-02 4.00e+02 pdb=" CD PRO A 515 " 0.031 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB PHE B 275 " 0.017 2.00e-02 2.50e+03 1.53e-02 4.11e+00 pdb=" CG PHE B 275 " -0.035 2.00e-02 2.50e+03 pdb=" CD1 PHE B 275 " 0.002 2.00e-02 2.50e+03 pdb=" CD2 PHE B 275 " 0.008 2.00e-02 2.50e+03 pdb=" CE1 PHE B 275 " 0.007 2.00e-02 2.50e+03 pdb=" CE2 PHE B 275 " 0.001 2.00e-02 2.50e+03 pdb=" CZ PHE B 275 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C VAL B 514 " 0.034 5.00e-02 4.00e+02 5.04e-02 4.06e+00 pdb=" N PRO B 515 " -0.087 5.00e-02 4.00e+02 pdb=" CA PRO B 515 " 0.025 5.00e-02 4.00e+02 pdb=" CD PRO B 515 " 0.029 5.00e-02 4.00e+02 ... (remaining 1455 not shown) Histogram of nonbonded interaction distances: 2.29 - 2.81: 2394 2.81 - 3.33: 8736 3.33 - 3.86: 15301 3.86 - 4.38: 17514 4.38 - 4.90: 30572 Nonbonded interactions: 74517 Sorted by model distance: nonbonded pdb=" NH1 ARG B 168 " pdb=" O HIS B 219 " model vdw 2.289 3.120 nonbonded pdb=" O ALA A 464 " pdb=" OG1 THR A 467 " model vdw 2.352 3.040 nonbonded pdb=" OG SER A 452 " pdb=" O SER A 530 " model vdw 2.357 3.040 nonbonded pdb=" N ILE B 129 " pdb=" O GLY B 132 " model vdw 2.393 3.120 nonbonded pdb=" OE1 GLU A 232 " pdb=" OG SER A 235 " model vdw 2.395 3.040 ... (remaining 74512 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and resid 35 through 660) 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: 5.400 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: 0.000 Check model and map are aligned: 0.000 Set scattering table: 0.000 Process input model: 20.940 Find NCS groups from input model: 0.320 Set up NCS constraints: 0.030 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:2.890 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.580 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7690 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 0.028 8830 Z= 0.107 Angle : 0.537 8.987 11982 Z= 0.267 Chirality : 0.040 0.275 1434 Planarity : 0.004 0.054 1458 Dihedral : 16.646 81.777 3256 Min Nonbonded Distance : 2.289 Molprobity Statistics. All-atom Clashscore : 9.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.57 % Favored : 98.43 % Rotamer: Outliers : 0.32 % Allowed : 25.85 % Favored : 73.82 % 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: 1.56 (0.27), residues: 1086 helix: 1.82 (0.20), residues: 676 sheet: -2.57 (0.55), residues: 68 loop : 0.39 (0.38), residues: 342 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP A 575 HIS 0.004 0.001 HIS B 154 PHE 0.035 0.002 PHE B 275 TYR 0.009 0.001 TYR B 584 ARG 0.002 0.000 ARG B 401 Details of bonding type rmsd hydrogen bonds : bond 0.12331 ( 529) hydrogen bonds : angle 5.47708 ( 1560) SS BOND : bond 0.00096 ( 2) SS BOND : angle 0.28483 ( 4) covalent geometry : bond 0.00224 ( 8828) covalent geometry : angle 0.53717 (11978) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2172 Ramachandran restraints generated. 1086 Oldfield, 0 Emsley, 1086 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2172 Ramachandran restraints generated. 1086 Oldfield, 0 Emsley, 1086 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 936 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 131 time to evaluate : 0.853 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 3 outliers final: 2 residues processed: 131 average time/residue: 0.1949 time to fit residues: 35.8854 Evaluate side-chains 128 residues out of total 936 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 126 time to evaluate : 0.848 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 517 LEU Chi-restraints excluded: chain A residue 601 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 92 optimal weight: 2.9990 chunk 83 optimal weight: 4.9990 chunk 46 optimal weight: 1.9990 chunk 28 optimal weight: 5.9990 chunk 56 optimal weight: 0.5980 chunk 44 optimal weight: 0.9980 chunk 86 optimal weight: 1.9990 chunk 33 optimal weight: 3.9990 chunk 52 optimal weight: 0.0870 chunk 64 optimal weight: 2.9990 chunk 99 optimal weight: 2.9990 overall best weight: 1.1362 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 413 GLN A 461 GLN B 531 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3909 r_free = 0.3909 target = 0.168385 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.124991 restraints weight = 9356.593| |-----------------------------------------------------------------------------| r_work (start): 0.3324 rms_B_bonded: 1.99 r_work: 0.3185 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.3036 rms_B_bonded: 4.55 restraints_weight: 0.2500 r_work (final): 0.3036 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7846 moved from start: 0.1079 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 8830 Z= 0.196 Angle : 0.582 9.269 11982 Z= 0.284 Chirality : 0.042 0.226 1434 Planarity : 0.005 0.045 1458 Dihedral : 6.060 59.613 1340 Min Nonbonded Distance : 2.581 Molprobity Statistics. All-atom Clashscore : 8.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.93 % Favored : 98.07 % Rotamer: Outliers : 4.49 % Allowed : 21.26 % Favored : 74.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.25 (0.26), residues: 1086 helix: 1.48 (0.19), residues: 698 sheet: -2.61 (0.66), residues: 44 loop : 0.12 (0.38), residues: 344 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 447 HIS 0.006 0.001 HIS B 154 PHE 0.029 0.002 PHE A 275 TYR 0.011 0.002 TYR B 526 ARG 0.002 0.000 ARG A 510 Details of bonding type rmsd hydrogen bonds : bond 0.03595 ( 529) hydrogen bonds : angle 4.69083 ( 1560) SS BOND : bond 0.00174 ( 2) SS BOND : angle 0.43381 ( 4) covalent geometry : bond 0.00460 ( 8828) covalent geometry : angle 0.58231 (11978) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2172 Ramachandran restraints generated. 1086 Oldfield, 0 Emsley, 1086 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2172 Ramachandran restraints generated. 1086 Oldfield, 0 Emsley, 1086 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 936 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 140 time to evaluate : 0.844 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 41 LYS cc_start: 0.7793 (mmmt) cc_final: 0.7374 (mmmt) REVERT: A 256 LYS cc_start: 0.8396 (mmtt) cc_final: 0.7977 (mmmm) REVERT: B 274 MET cc_start: 0.8044 (mmm) cc_final: 0.7417 (mmt) REVERT: B 291 LYS cc_start: 0.8351 (ttmm) cc_final: 0.7835 (ttpt) REVERT: B 517 LEU cc_start: 0.8474 (OUTLIER) cc_final: 0.8250 (mm) REVERT: B 630 ILE cc_start: 0.7797 (mp) cc_final: 0.7493 (mp) REVERT: B 636 TRP cc_start: 0.8403 (m100) cc_final: 0.8057 (m100) outliers start: 42 outliers final: 24 residues processed: 167 average time/residue: 0.1903 time to fit residues: 45.2149 Evaluate side-chains 159 residues out of total 936 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 134 time to evaluate : 0.925 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 91 ILE Chi-restraints excluded: chain A residue 114 VAL Chi-restraints excluded: chain A residue 148 ASP Chi-restraints excluded: chain A residue 174 THR Chi-restraints excluded: chain A residue 198 VAL Chi-restraints excluded: chain A residue 248 THR Chi-restraints excluded: chain A residue 280 LEU Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 408 LEU Chi-restraints excluded: chain A residue 517 LEU Chi-restraints excluded: chain A residue 566 VAL Chi-restraints excluded: chain A residue 574 VAL Chi-restraints excluded: chain A residue 655 LEU Chi-restraints excluded: chain A residue 660 ILE Chi-restraints excluded: chain B residue 38 ILE Chi-restraints excluded: chain B residue 114 VAL Chi-restraints excluded: chain B residue 148 ASP Chi-restraints excluded: chain B residue 198 VAL Chi-restraints excluded: chain B residue 289 VAL Chi-restraints excluded: chain B residue 461 GLN Chi-restraints excluded: chain B residue 517 LEU Chi-restraints excluded: chain B residue 552 THR Chi-restraints excluded: chain B residue 601 LEU Chi-restraints excluded: chain B residue 639 VAL Chi-restraints excluded: chain B residue 660 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 107 optimal weight: 4.9990 chunk 70 optimal weight: 2.9990 chunk 76 optimal weight: 0.7980 chunk 27 optimal weight: 10.0000 chunk 21 optimal weight: 4.9990 chunk 38 optimal weight: 1.9990 chunk 31 optimal weight: 1.9990 chunk 45 optimal weight: 1.9990 chunk 58 optimal weight: 0.9980 chunk 55 optimal weight: 5.9990 chunk 25 optimal weight: 0.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 413 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 = 0.3888 r_free = 0.3888 target = 0.166290 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.122481 restraints weight = 9486.030| |-----------------------------------------------------------------------------| r_work (start): 0.3288 rms_B_bonded: 2.04 r_work: 0.3146 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.2993 rms_B_bonded: 4.55 restraints_weight: 0.2500 r_work (final): 0.2993 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7810 moved from start: 0.1415 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 8830 Z= 0.222 Angle : 0.603 8.301 11982 Z= 0.296 Chirality : 0.042 0.222 1434 Planarity : 0.005 0.045 1458 Dihedral : 6.042 57.264 1338 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 9.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.93 % Favored : 98.07 % Rotamer: Outliers : 4.59 % Allowed : 21.79 % Favored : 73.61 % 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: 1.10 (0.26), residues: 1086 helix: 1.33 (0.19), residues: 694 sheet: -2.66 (0.64), residues: 44 loop : 0.15 (0.38), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP A 575 HIS 0.006 0.001 HIS B 154 PHE 0.043 0.002 PHE A 275 TYR 0.011 0.002 TYR A 526 ARG 0.003 0.000 ARG A 410 Details of bonding type rmsd hydrogen bonds : bond 0.03698 ( 529) hydrogen bonds : angle 4.71932 ( 1560) SS BOND : bond 0.00166 ( 2) SS BOND : angle 0.39579 ( 4) covalent geometry : bond 0.00526 ( 8828) covalent geometry : angle 0.60287 (11978) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2172 Ramachandran restraints generated. 1086 Oldfield, 0 Emsley, 1086 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2172 Ramachandran restraints generated. 1086 Oldfield, 0 Emsley, 1086 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 936 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 140 time to evaluate : 0.860 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 41 LYS cc_start: 0.7853 (mmmt) cc_final: 0.7595 (mmmt) REVERT: A 256 LYS cc_start: 0.8382 (mmtt) cc_final: 0.7903 (mmmm) REVERT: B 291 LYS cc_start: 0.8334 (ttmm) cc_final: 0.7821 (ttpt) REVERT: B 413 GLN cc_start: 0.8225 (OUTLIER) cc_final: 0.8019 (tt0) REVERT: B 517 LEU cc_start: 0.8582 (OUTLIER) cc_final: 0.8285 (mm) REVERT: B 630 ILE cc_start: 0.7997 (mp) cc_final: 0.7659 (mp) REVERT: B 636 TRP cc_start: 0.8422 (m100) cc_final: 0.8120 (m100) outliers start: 43 outliers final: 30 residues processed: 164 average time/residue: 0.1793 time to fit residues: 42.0634 Evaluate side-chains 163 residues out of total 936 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 131 time to evaluate : 0.897 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 91 ILE Chi-restraints excluded: chain A residue 114 VAL Chi-restraints excluded: chain A residue 148 ASP Chi-restraints excluded: chain A residue 198 VAL Chi-restraints excluded: chain A residue 204 ILE Chi-restraints excluded: chain A residue 248 THR Chi-restraints excluded: chain A residue 261 VAL Chi-restraints excluded: chain A residue 280 LEU Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 408 LEU Chi-restraints excluded: chain A residue 450 LEU Chi-restraints excluded: chain A residue 517 LEU Chi-restraints excluded: chain A residue 549 THR Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 566 VAL Chi-restraints excluded: chain A residue 574 VAL Chi-restraints excluded: chain A residue 601 LEU Chi-restraints excluded: chain A residue 655 LEU Chi-restraints excluded: chain B residue 38 ILE Chi-restraints excluded: chain B residue 114 VAL Chi-restraints excluded: chain B residue 148 ASP Chi-restraints excluded: chain B residue 198 VAL Chi-restraints excluded: chain B residue 279 LEU Chi-restraints excluded: chain B residue 289 VAL Chi-restraints excluded: chain B residue 413 GLN Chi-restraints excluded: chain B residue 517 LEU Chi-restraints excluded: chain B residue 552 THR Chi-restraints excluded: chain B residue 566 VAL Chi-restraints excluded: chain B residue 601 LEU Chi-restraints excluded: chain B residue 639 VAL Chi-restraints excluded: chain B residue 655 LEU Chi-restraints excluded: chain B residue 660 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 51 optimal weight: 9.9990 chunk 92 optimal weight: 0.8980 chunk 67 optimal weight: 0.5980 chunk 3 optimal weight: 1.9990 chunk 48 optimal weight: 0.9980 chunk 94 optimal weight: 0.0070 chunk 86 optimal weight: 0.7980 chunk 35 optimal weight: 0.8980 chunk 99 optimal weight: 0.5980 chunk 27 optimal weight: 10.0000 chunk 21 optimal weight: 0.8980 overall best weight: 0.5798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 413 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 = 0.3928 r_free = 0.3928 target = 0.170054 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.126626 restraints weight = 9310.586| |-----------------------------------------------------------------------------| r_work (start): 0.3349 rms_B_bonded: 2.05 r_work: 0.3212 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.3060 rms_B_bonded: 4.59 restraints_weight: 0.2500 r_work (final): 0.3060 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7745 moved from start: 0.1316 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 8830 Z= 0.129 Angle : 0.526 7.384 11982 Z= 0.258 Chirality : 0.040 0.220 1434 Planarity : 0.004 0.049 1458 Dihedral : 5.749 56.107 1338 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 9.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.21 % Favored : 97.79 % Rotamer: Outliers : 3.95 % Allowed : 23.82 % Favored : 72.22 % 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: 1.41 (0.26), residues: 1086 helix: 1.61 (0.19), residues: 700 sheet: -1.85 (0.69), residues: 48 loop : 0.07 (0.38), residues: 338 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 575 HIS 0.006 0.001 HIS B 154 PHE 0.041 0.001 PHE A 275 TYR 0.009 0.001 TYR B 584 ARG 0.001 0.000 ARG A 587 Details of bonding type rmsd hydrogen bonds : bond 0.03018 ( 529) hydrogen bonds : angle 4.36746 ( 1560) SS BOND : bond 0.00114 ( 2) SS BOND : angle 0.28947 ( 4) covalent geometry : bond 0.00304 ( 8828) covalent geometry : angle 0.52654 (11978) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2172 Ramachandran restraints generated. 1086 Oldfield, 0 Emsley, 1086 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2172 Ramachandran restraints generated. 1086 Oldfield, 0 Emsley, 1086 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 936 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 147 time to evaluate : 0.859 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 41 LYS cc_start: 0.7859 (mmmt) cc_final: 0.7520 (mmmt) REVERT: A 256 LYS cc_start: 0.8350 (mmtt) cc_final: 0.7876 (mmmm) REVERT: A 568 LYS cc_start: 0.8564 (mttp) cc_final: 0.8078 (mptt) REVERT: B 291 LYS cc_start: 0.8172 (ttmm) cc_final: 0.7615 (ttpt) REVERT: B 517 LEU cc_start: 0.8496 (OUTLIER) cc_final: 0.8234 (mm) REVERT: B 630 ILE cc_start: 0.7927 (mp) cc_final: 0.7618 (mp) REVERT: B 636 TRP cc_start: 0.8435 (m100) cc_final: 0.8119 (m100) outliers start: 37 outliers final: 27 residues processed: 169 average time/residue: 0.1783 time to fit residues: 43.2586 Evaluate side-chains 169 residues out of total 936 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 141 time to evaluate : 0.841 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 91 ILE Chi-restraints excluded: chain A residue 114 VAL Chi-restraints excluded: chain A residue 148 ASP Chi-restraints excluded: chain A residue 174 THR Chi-restraints excluded: chain A residue 248 THR Chi-restraints excluded: chain A residue 261 VAL Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 408 LEU Chi-restraints excluded: chain A residue 478 SER Chi-restraints excluded: chain A residue 517 LEU Chi-restraints excluded: chain A residue 566 VAL Chi-restraints excluded: chain A residue 574 VAL Chi-restraints excluded: chain A residue 601 LEU Chi-restraints excluded: chain A residue 655 LEU Chi-restraints excluded: chain B residue 38 ILE Chi-restraints excluded: chain B residue 114 VAL Chi-restraints excluded: chain B residue 148 ASP Chi-restraints excluded: chain B residue 174 THR Chi-restraints excluded: chain B residue 198 VAL Chi-restraints excluded: chain B residue 204 ILE Chi-restraints excluded: chain B residue 289 VAL Chi-restraints excluded: chain B residue 517 LEU Chi-restraints excluded: chain B residue 522 VAL Chi-restraints excluded: chain B residue 552 THR Chi-restraints excluded: chain B residue 566 VAL Chi-restraints excluded: chain B residue 639 VAL Chi-restraints excluded: chain B residue 655 LEU Chi-restraints excluded: chain B residue 660 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 97 optimal weight: 0.9990 chunk 71 optimal weight: 3.9990 chunk 87 optimal weight: 2.9990 chunk 50 optimal weight: 0.4980 chunk 80 optimal weight: 0.9990 chunk 7 optimal weight: 0.9990 chunk 98 optimal weight: 0.5980 chunk 88 optimal weight: 2.9990 chunk 26 optimal weight: 0.9990 chunk 84 optimal weight: 0.9980 chunk 106 optimal weight: 2.9990 overall best weight: 0.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 531 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3904 r_free = 0.3904 target = 0.167833 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.124567 restraints weight = 9451.811| |-----------------------------------------------------------------------------| r_work (start): 0.3331 rms_B_bonded: 2.01 r_work: 0.3193 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.3045 rms_B_bonded: 4.54 restraints_weight: 0.2500 r_work (final): 0.3045 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7826 moved from start: 0.1436 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 8830 Z= 0.155 Angle : 0.547 7.767 11982 Z= 0.267 Chirality : 0.040 0.213 1434 Planarity : 0.004 0.048 1458 Dihedral : 5.764 55.287 1338 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 8.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer: Outliers : 4.59 % Allowed : 23.72 % Favored : 71.69 % 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: 1.36 (0.26), residues: 1086 helix: 1.54 (0.19), residues: 702 sheet: -1.84 (0.69), residues: 48 loop : 0.11 (0.39), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 575 HIS 0.005 0.001 HIS B 154 PHE 0.039 0.002 PHE A 275 TYR 0.009 0.001 TYR B 584 ARG 0.002 0.000 ARG A 410 Details of bonding type rmsd hydrogen bonds : bond 0.03185 ( 529) hydrogen bonds : angle 4.36919 ( 1560) SS BOND : bond 0.00126 ( 2) SS BOND : angle 0.25280 ( 4) covalent geometry : bond 0.00367 ( 8828) covalent geometry : angle 0.54739 (11978) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2172 Ramachandran restraints generated. 1086 Oldfield, 0 Emsley, 1086 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2172 Ramachandran restraints generated. 1086 Oldfield, 0 Emsley, 1086 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 936 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 143 time to evaluate : 0.929 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 41 LYS cc_start: 0.7757 (mmmt) cc_final: 0.7357 (mmmt) REVERT: A 256 LYS cc_start: 0.8409 (mmtt) cc_final: 0.7951 (mmmm) REVERT: B 291 LYS cc_start: 0.8275 (ttmm) cc_final: 0.7740 (ttpt) REVERT: B 300 GLU cc_start: 0.7608 (pp20) cc_final: 0.7406 (pp20) REVERT: B 304 PHE cc_start: 0.7784 (m-80) cc_final: 0.7554 (m-80) REVERT: B 517 LEU cc_start: 0.8537 (OUTLIER) cc_final: 0.8302 (mm) REVERT: B 630 ILE cc_start: 0.7992 (mp) cc_final: 0.7654 (mp) REVERT: B 636 TRP cc_start: 0.8480 (m100) cc_final: 0.8176 (m100) outliers start: 43 outliers final: 31 residues processed: 166 average time/residue: 0.1921 time to fit residues: 45.3312 Evaluate side-chains 167 residues out of total 936 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 135 time to evaluate : 0.928 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 91 ILE Chi-restraints excluded: chain A residue 114 VAL Chi-restraints excluded: chain A residue 148 ASP Chi-restraints excluded: chain A residue 174 THR Chi-restraints excluded: chain A residue 198 VAL Chi-restraints excluded: chain A residue 248 THR Chi-restraints excluded: chain A residue 261 VAL Chi-restraints excluded: chain A residue 281 LEU Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 408 LEU Chi-restraints excluded: chain A residue 478 SER Chi-restraints excluded: chain A residue 517 LEU Chi-restraints excluded: chain A residue 522 VAL Chi-restraints excluded: chain A residue 549 THR Chi-restraints excluded: chain A residue 566 VAL Chi-restraints excluded: chain A residue 601 LEU Chi-restraints excluded: chain A residue 655 LEU Chi-restraints excluded: chain A residue 660 ILE Chi-restraints excluded: chain B residue 38 ILE Chi-restraints excluded: chain B residue 114 VAL Chi-restraints excluded: chain B residue 148 ASP Chi-restraints excluded: chain B residue 174 THR Chi-restraints excluded: chain B residue 198 VAL Chi-restraints excluded: chain B residue 204 ILE Chi-restraints excluded: chain B residue 279 LEU Chi-restraints excluded: chain B residue 289 VAL Chi-restraints excluded: chain B residue 517 LEU Chi-restraints excluded: chain B residue 552 THR Chi-restraints excluded: chain B residue 566 VAL Chi-restraints excluded: chain B residue 639 VAL Chi-restraints excluded: chain B residue 655 LEU Chi-restraints excluded: chain B residue 660 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 32 optimal weight: 1.9990 chunk 2 optimal weight: 0.0020 chunk 68 optimal weight: 0.0970 chunk 36 optimal weight: 0.4980 chunk 107 optimal weight: 0.8980 chunk 89 optimal weight: 0.5980 chunk 37 optimal weight: 0.9980 chunk 4 optimal weight: 0.6980 chunk 8 optimal weight: 1.9990 chunk 92 optimal weight: 0.6980 chunk 25 optimal weight: 0.6980 overall best weight: 0.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 413 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 484 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 531 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3941 r_free = 0.3941 target = 0.171407 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.128892 restraints weight = 9242.798| |-----------------------------------------------------------------------------| r_work (start): 0.3405 rms_B_bonded: 2.03 r_work: 0.3268 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.3118 rms_B_bonded: 4.66 restraints_weight: 0.2500 r_work (final): 0.3118 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7759 moved from start: 0.1385 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 8830 Z= 0.110 Angle : 0.518 7.704 11982 Z= 0.252 Chirality : 0.039 0.209 1434 Planarity : 0.004 0.049 1458 Dihedral : 5.551 54.672 1338 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 9.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.21 % Favored : 97.79 % Rotamer: Outliers : 4.17 % Allowed : 24.36 % Favored : 71.47 % 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: 1.63 (0.27), residues: 1086 helix: 1.82 (0.20), residues: 698 sheet: -1.86 (0.69), residues: 48 loop : 0.08 (0.38), residues: 340 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 575 HIS 0.006 0.001 HIS B 154 PHE 0.037 0.001 PHE B 275 TYR 0.009 0.001 TYR B 584 ARG 0.002 0.000 ARG A 436 Details of bonding type rmsd hydrogen bonds : bond 0.02846 ( 529) hydrogen bonds : angle 4.17357 ( 1560) SS BOND : bond 0.00095 ( 2) SS BOND : angle 0.26786 ( 4) covalent geometry : bond 0.00256 ( 8828) covalent geometry : angle 0.51778 (11978) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2172 Ramachandran restraints generated. 1086 Oldfield, 0 Emsley, 1086 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2172 Ramachandran restraints generated. 1086 Oldfield, 0 Emsley, 1086 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 936 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 145 time to evaluate : 0.942 Fit side-chains revert: symmetry clash REVERT: A 41 LYS cc_start: 0.7753 (mmmt) cc_final: 0.7307 (mmmt) REVERT: A 136 LYS cc_start: 0.7430 (OUTLIER) cc_final: 0.7036 (mmmt) REVERT: A 256 LYS cc_start: 0.8309 (mmtt) cc_final: 0.7875 (mmmm) REVERT: B 154 HIS cc_start: 0.8260 (m90) cc_final: 0.8024 (m-70) REVERT: B 291 LYS cc_start: 0.8206 (ttmm) cc_final: 0.7641 (ttpt) REVERT: B 300 GLU cc_start: 0.7570 (pp20) cc_final: 0.7311 (pp20) REVERT: B 508 TYR cc_start: 0.6285 (t80) cc_final: 0.5960 (t80) REVERT: B 517 LEU cc_start: 0.8458 (OUTLIER) cc_final: 0.8242 (mm) REVERT: B 630 ILE cc_start: 0.7982 (mp) cc_final: 0.7679 (mp) REVERT: B 636 TRP cc_start: 0.8424 (m100) cc_final: 0.8106 (m100) outliers start: 39 outliers final: 28 residues processed: 171 average time/residue: 0.1895 time to fit residues: 45.9042 Evaluate side-chains 167 residues out of total 936 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 137 time to evaluate : 0.931 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 91 ILE Chi-restraints excluded: chain A residue 114 VAL Chi-restraints excluded: chain A residue 136 LYS Chi-restraints excluded: chain A residue 174 THR Chi-restraints excluded: chain A residue 204 ILE Chi-restraints excluded: chain A residue 261 VAL Chi-restraints excluded: chain A residue 287 LEU Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 408 LEU Chi-restraints excluded: chain A residue 450 LEU Chi-restraints excluded: chain A residue 461 GLN Chi-restraints excluded: chain A residue 517 LEU Chi-restraints excluded: chain A residue 522 VAL Chi-restraints excluded: chain A residue 549 THR Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 566 VAL Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 601 LEU Chi-restraints excluded: chain A residue 655 LEU Chi-restraints excluded: chain B residue 38 ILE Chi-restraints excluded: chain B residue 114 VAL Chi-restraints excluded: chain B residue 148 ASP Chi-restraints excluded: chain B residue 204 ILE Chi-restraints excluded: chain B residue 289 VAL Chi-restraints excluded: chain B residue 517 LEU Chi-restraints excluded: chain B residue 522 VAL Chi-restraints excluded: chain B residue 552 THR Chi-restraints excluded: chain B residue 566 VAL Chi-restraints excluded: chain B residue 639 VAL Chi-restraints excluded: chain B residue 655 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 2 optimal weight: 4.9990 chunk 103 optimal weight: 0.5980 chunk 15 optimal weight: 0.7980 chunk 81 optimal weight: 3.9990 chunk 29 optimal weight: 0.6980 chunk 53 optimal weight: 0.0370 chunk 70 optimal weight: 3.9990 chunk 39 optimal weight: 0.5980 chunk 74 optimal weight: 0.6980 chunk 8 optimal weight: 0.7980 chunk 26 optimal weight: 0.9980 overall best weight: 0.5258 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 484 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 531 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3937 r_free = 0.3937 target = 0.170934 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.128129 restraints weight = 9412.214| |-----------------------------------------------------------------------------| r_work (start): 0.3377 rms_B_bonded: 2.06 r_work: 0.3239 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.3089 rms_B_bonded: 4.63 restraints_weight: 0.2500 r_work (final): 0.3089 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7732 moved from start: 0.1478 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 8830 Z= 0.122 Angle : 0.521 7.113 11982 Z= 0.255 Chirality : 0.039 0.210 1434 Planarity : 0.004 0.048 1458 Dihedral : 5.533 56.055 1338 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 9.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer: Outliers : 4.38 % Allowed : 23.93 % Favored : 71.69 % 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: 1.64 (0.27), residues: 1086 helix: 1.75 (0.19), residues: 708 sheet: -1.72 (0.71), residues: 48 loop : 0.23 (0.40), residues: 330 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 575 HIS 0.005 0.001 HIS B 154 PHE 0.035 0.001 PHE B 275 TYR 0.009 0.001 TYR A 584 ARG 0.005 0.000 ARG B 401 Details of bonding type rmsd hydrogen bonds : bond 0.02920 ( 529) hydrogen bonds : angle 4.14648 ( 1560) SS BOND : bond 0.00103 ( 2) SS BOND : angle 0.21838 ( 4) covalent geometry : bond 0.00286 ( 8828) covalent geometry : angle 0.52066 (11978) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2172 Ramachandran restraints generated. 1086 Oldfield, 0 Emsley, 1086 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2172 Ramachandran restraints generated. 1086 Oldfield, 0 Emsley, 1086 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 936 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 139 time to evaluate : 0.909 Fit side-chains revert: symmetry clash REVERT: A 41 LYS cc_start: 0.7711 (mmmt) cc_final: 0.7285 (mmmt) REVERT: A 256 LYS cc_start: 0.8292 (mmtt) cc_final: 0.7836 (mmmm) REVERT: A 517 LEU cc_start: 0.8376 (OUTLIER) cc_final: 0.7985 (mp) REVERT: B 154 HIS cc_start: 0.8070 (m90) cc_final: 0.7830 (m-70) REVERT: B 291 LYS cc_start: 0.8250 (ttmm) cc_final: 0.7679 (ttpt) REVERT: B 300 GLU cc_start: 0.7681 (pp20) cc_final: 0.7389 (pp20) REVERT: B 304 PHE cc_start: 0.7708 (m-80) cc_final: 0.7485 (m-80) REVERT: B 508 TYR cc_start: 0.6273 (t80) cc_final: 0.5932 (t80) REVERT: B 517 LEU cc_start: 0.8455 (OUTLIER) cc_final: 0.8226 (mm) REVERT: B 630 ILE cc_start: 0.7953 (mp) cc_final: 0.7624 (mp) REVERT: B 636 TRP cc_start: 0.8453 (m100) cc_final: 0.8133 (m100) outliers start: 41 outliers final: 33 residues processed: 165 average time/residue: 0.1884 time to fit residues: 44.1919 Evaluate side-chains 172 residues out of total 936 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 137 time to evaluate : 0.919 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 91 ILE Chi-restraints excluded: chain A residue 114 VAL Chi-restraints excluded: chain A residue 123 LEU Chi-restraints excluded: chain A residue 148 ASP Chi-restraints excluded: chain A residue 174 THR Chi-restraints excluded: chain A residue 204 ILE Chi-restraints excluded: chain A residue 248 THR Chi-restraints excluded: chain A residue 287 LEU Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 408 LEU Chi-restraints excluded: chain A residue 450 LEU Chi-restraints excluded: chain A residue 461 GLN Chi-restraints excluded: chain A residue 478 SER Chi-restraints excluded: chain A residue 517 LEU Chi-restraints excluded: chain A residue 522 VAL Chi-restraints excluded: chain A residue 549 THR Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 566 VAL Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 601 LEU Chi-restraints excluded: chain A residue 655 LEU Chi-restraints excluded: chain B residue 38 ILE Chi-restraints excluded: chain B residue 114 VAL Chi-restraints excluded: chain B residue 148 ASP Chi-restraints excluded: chain B residue 198 VAL Chi-restraints excluded: chain B residue 204 ILE Chi-restraints excluded: chain B residue 289 VAL Chi-restraints excluded: chain B residue 517 LEU Chi-restraints excluded: chain B residue 522 VAL Chi-restraints excluded: chain B residue 552 THR Chi-restraints excluded: chain B residue 566 VAL Chi-restraints excluded: chain B residue 601 LEU Chi-restraints excluded: chain B residue 639 VAL Chi-restraints excluded: chain B residue 655 LEU Chi-restraints excluded: chain B residue 660 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 20 optimal weight: 0.0970 chunk 81 optimal weight: 0.9980 chunk 36 optimal weight: 0.9990 chunk 62 optimal weight: 1.9990 chunk 25 optimal weight: 4.9990 chunk 21 optimal weight: 0.7980 chunk 29 optimal weight: 0.5980 chunk 24 optimal weight: 0.0980 chunk 41 optimal weight: 0.4980 chunk 48 optimal weight: 1.9990 chunk 71 optimal weight: 0.8980 overall best weight: 0.4178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 531 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3947 r_free = 0.3947 target = 0.171827 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.129592 restraints weight = 9460.379| |-----------------------------------------------------------------------------| r_work (start): 0.3398 rms_B_bonded: 2.05 r_work: 0.3257 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.3108 rms_B_bonded: 4.64 restraints_weight: 0.2500 r_work (final): 0.3108 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7713 moved from start: 0.1484 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 8830 Z= 0.111 Angle : 0.511 7.242 11982 Z= 0.249 Chirality : 0.039 0.209 1434 Planarity : 0.004 0.049 1458 Dihedral : 5.454 56.561 1338 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 8.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer: Outliers : 4.59 % Allowed : 23.29 % Favored : 72.12 % 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: 1.72 (0.27), residues: 1086 helix: 1.85 (0.19), residues: 706 sheet: -1.98 (0.57), residues: 70 loop : 0.42 (0.41), residues: 310 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 575 HIS 0.006 0.001 HIS B 154 PHE 0.036 0.001 PHE A 275 TYR 0.009 0.001 TYR A 584 ARG 0.002 0.000 ARG B 401 Details of bonding type rmsd hydrogen bonds : bond 0.02813 ( 529) hydrogen bonds : angle 4.08363 ( 1560) SS BOND : bond 0.00092 ( 2) SS BOND : angle 0.23078 ( 4) covalent geometry : bond 0.00260 ( 8828) covalent geometry : angle 0.51106 (11978) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2172 Ramachandran restraints generated. 1086 Oldfield, 0 Emsley, 1086 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2172 Ramachandran restraints generated. 1086 Oldfield, 0 Emsley, 1086 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 936 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 145 time to evaluate : 0.892 Fit side-chains revert: symmetry clash REVERT: A 41 LYS cc_start: 0.7672 (mmmt) cc_final: 0.7236 (mmmt) REVERT: A 136 LYS cc_start: 0.7436 (OUTLIER) cc_final: 0.7039 (mmmt) REVERT: A 256 LYS cc_start: 0.8282 (mmtt) cc_final: 0.7836 (mmmm) REVERT: A 517 LEU cc_start: 0.8349 (mp) cc_final: 0.7714 (mp) REVERT: A 568 LYS cc_start: 0.8533 (mptt) cc_final: 0.8237 (mptt) REVERT: B 154 HIS cc_start: 0.8051 (m90) cc_final: 0.7839 (m-70) REVERT: B 291 LYS cc_start: 0.8179 (ttmm) cc_final: 0.7595 (ttpt) REVERT: B 300 GLU cc_start: 0.7678 (pp20) cc_final: 0.7372 (pp20) REVERT: B 304 PHE cc_start: 0.7699 (m-80) cc_final: 0.7483 (m-80) REVERT: B 508 TYR cc_start: 0.6365 (t80) cc_final: 0.6042 (t80) REVERT: B 517 LEU cc_start: 0.8439 (OUTLIER) cc_final: 0.8216 (mm) REVERT: B 630 ILE cc_start: 0.7934 (mp) cc_final: 0.7611 (mp) REVERT: B 636 TRP cc_start: 0.8433 (m100) cc_final: 0.8130 (m100) outliers start: 43 outliers final: 35 residues processed: 172 average time/residue: 0.1748 time to fit residues: 43.3124 Evaluate side-chains 178 residues out of total 936 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 141 time to evaluate : 0.877 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 91 ILE Chi-restraints excluded: chain A residue 114 VAL Chi-restraints excluded: chain A residue 123 LEU Chi-restraints excluded: chain A residue 136 LYS Chi-restraints excluded: chain A residue 148 ASP Chi-restraints excluded: chain A residue 174 THR Chi-restraints excluded: chain A residue 198 VAL Chi-restraints excluded: chain A residue 204 ILE Chi-restraints excluded: chain A residue 261 VAL Chi-restraints excluded: chain A residue 281 LEU Chi-restraints excluded: chain A residue 287 LEU Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 319 LEU Chi-restraints excluded: chain A residue 408 LEU Chi-restraints excluded: chain A residue 450 LEU Chi-restraints excluded: chain A residue 461 GLN Chi-restraints excluded: chain A residue 478 SER Chi-restraints excluded: chain A residue 522 VAL Chi-restraints excluded: chain A residue 549 THR Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 566 VAL Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 601 LEU Chi-restraints excluded: chain A residue 655 LEU Chi-restraints excluded: chain B residue 38 ILE Chi-restraints excluded: chain B residue 114 VAL Chi-restraints excluded: chain B residue 148 ASP Chi-restraints excluded: chain B residue 198 VAL Chi-restraints excluded: chain B residue 204 ILE Chi-restraints excluded: chain B residue 289 VAL Chi-restraints excluded: chain B residue 517 LEU Chi-restraints excluded: chain B residue 522 VAL Chi-restraints excluded: chain B residue 552 THR Chi-restraints excluded: chain B residue 566 VAL Chi-restraints excluded: chain B residue 601 LEU Chi-restraints excluded: chain B residue 639 VAL Chi-restraints excluded: chain B residue 655 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 50 optimal weight: 1.9990 chunk 59 optimal weight: 2.9990 chunk 36 optimal weight: 0.9990 chunk 82 optimal weight: 0.9980 chunk 2 optimal weight: 5.9990 chunk 91 optimal weight: 2.9990 chunk 49 optimal weight: 0.5980 chunk 34 optimal weight: 0.9990 chunk 9 optimal weight: 0.7980 chunk 31 optimal weight: 2.9990 chunk 71 optimal weight: 1.9990 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 531 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3919 r_free = 0.3919 target = 0.169051 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.125817 restraints weight = 9477.574| |-----------------------------------------------------------------------------| r_work (start): 0.3367 rms_B_bonded: 2.07 r_work: 0.3225 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.3073 rms_B_bonded: 4.71 restraints_weight: 0.2500 r_work (final): 0.3073 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7804 moved from start: 0.1654 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 8830 Z= 0.163 Angle : 0.565 7.966 11982 Z= 0.273 Chirality : 0.041 0.214 1434 Planarity : 0.004 0.048 1458 Dihedral : 5.527 57.409 1336 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 9.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer: Outliers : 4.49 % Allowed : 23.29 % Favored : 72.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.54 (0.27), residues: 1086 helix: 1.66 (0.19), residues: 706 sheet: -2.01 (0.57), residues: 70 loop : 0.47 (0.41), residues: 310 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP A 575 HIS 0.005 0.001 HIS B 154 PHE 0.038 0.002 PHE A 275 TYR 0.015 0.001 TYR B 584 ARG 0.003 0.000 ARG B 401 Details of bonding type rmsd hydrogen bonds : bond 0.03182 ( 529) hydrogen bonds : angle 4.24546 ( 1560) SS BOND : bond 0.00110 ( 2) SS BOND : angle 0.19449 ( 4) covalent geometry : bond 0.00386 ( 8828) covalent geometry : angle 0.56466 (11978) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2172 Ramachandran restraints generated. 1086 Oldfield, 0 Emsley, 1086 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2172 Ramachandran restraints generated. 1086 Oldfield, 0 Emsley, 1086 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 936 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 138 time to evaluate : 0.975 Fit side-chains revert: symmetry clash REVERT: A 41 LYS cc_start: 0.7669 (mmmt) cc_final: 0.7178 (mmmt) REVERT: A 136 LYS cc_start: 0.7475 (OUTLIER) cc_final: 0.7073 (mmmt) REVERT: A 256 LYS cc_start: 0.8376 (mmtt) cc_final: 0.7913 (mmmm) REVERT: A 517 LEU cc_start: 0.8279 (mp) cc_final: 0.7667 (mp) REVERT: B 154 HIS cc_start: 0.8281 (m90) cc_final: 0.8005 (m-70) REVERT: B 291 LYS cc_start: 0.8403 (ttmm) cc_final: 0.7879 (ttpt) REVERT: B 300 GLU cc_start: 0.7719 (pp20) cc_final: 0.7413 (pp20) REVERT: B 304 PHE cc_start: 0.7751 (m-80) cc_final: 0.7493 (m-80) REVERT: B 508 TYR cc_start: 0.6147 (t80) cc_final: 0.5842 (t80) REVERT: B 517 LEU cc_start: 0.8490 (OUTLIER) cc_final: 0.8265 (mm) REVERT: B 548 SER cc_start: 0.8410 (OUTLIER) cc_final: 0.8094 (m) REVERT: B 630 ILE cc_start: 0.7992 (mp) cc_final: 0.7649 (mp) REVERT: B 636 TRP cc_start: 0.8559 (m100) cc_final: 0.8230 (m100) outliers start: 42 outliers final: 36 residues processed: 164 average time/residue: 0.1877 time to fit residues: 44.5181 Evaluate side-chains 176 residues out of total 936 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 137 time to evaluate : 0.870 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 91 ILE Chi-restraints excluded: chain A residue 114 VAL Chi-restraints excluded: chain A residue 136 LYS Chi-restraints excluded: chain A residue 148 ASP Chi-restraints excluded: chain A residue 174 THR Chi-restraints excluded: chain A residue 198 VAL Chi-restraints excluded: chain A residue 204 ILE Chi-restraints excluded: chain A residue 248 THR Chi-restraints excluded: chain A residue 281 LEU Chi-restraints excluded: chain A residue 287 LEU Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 319 LEU Chi-restraints excluded: chain A residue 408 LEU Chi-restraints excluded: chain A residue 450 LEU Chi-restraints excluded: chain A residue 461 GLN Chi-restraints excluded: chain A residue 478 SER Chi-restraints excluded: chain A residue 522 VAL Chi-restraints excluded: chain A residue 549 THR Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 566 VAL Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 601 LEU Chi-restraints excluded: chain A residue 655 LEU Chi-restraints excluded: chain B residue 38 ILE Chi-restraints excluded: chain B residue 114 VAL Chi-restraints excluded: chain B residue 148 ASP Chi-restraints excluded: chain B residue 198 VAL Chi-restraints excluded: chain B residue 204 ILE Chi-restraints excluded: chain B residue 289 VAL Chi-restraints excluded: chain B residue 310 MET Chi-restraints excluded: chain B residue 517 LEU Chi-restraints excluded: chain B residue 522 VAL Chi-restraints excluded: chain B residue 548 SER Chi-restraints excluded: chain B residue 552 THR Chi-restraints excluded: chain B residue 566 VAL Chi-restraints excluded: chain B residue 601 LEU Chi-restraints excluded: chain B residue 639 VAL Chi-restraints excluded: chain B residue 655 LEU Chi-restraints excluded: chain B residue 660 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 65 optimal weight: 2.9990 chunk 98 optimal weight: 0.8980 chunk 71 optimal weight: 2.9990 chunk 29 optimal weight: 0.5980 chunk 53 optimal weight: 0.9990 chunk 74 optimal weight: 1.9990 chunk 96 optimal weight: 0.7980 chunk 43 optimal weight: 0.6980 chunk 20 optimal weight: 0.4980 chunk 30 optimal weight: 0.7980 chunk 28 optimal weight: 0.2980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 531 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3926 r_free = 0.3926 target = 0.169618 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.126793 restraints weight = 9415.454| |-----------------------------------------------------------------------------| r_work (start): 0.3403 rms_B_bonded: 2.05 r_work: 0.3261 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.3109 rms_B_bonded: 4.71 restraints_weight: 0.2500 r_work (final): 0.3109 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7777 moved from start: 0.1627 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 8830 Z= 0.130 Angle : 0.541 7.843 11982 Z= 0.263 Chirality : 0.040 0.211 1434 Planarity : 0.004 0.049 1458 Dihedral : 5.458 57.387 1336 Min Nonbonded Distance : 2.563 Molprobity Statistics. All-atom Clashscore : 9.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer: Outliers : 4.06 % Allowed : 23.82 % Favored : 72.12 % 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: 1.67 (0.27), residues: 1086 helix: 1.80 (0.19), residues: 702 sheet: -2.00 (0.57), residues: 70 loop : 0.43 (0.41), residues: 314 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP A 575 HIS 0.005 0.001 HIS B 154 PHE 0.036 0.001 PHE A 275 TYR 0.015 0.001 TYR B 584 ARG 0.002 0.000 ARG B 401 Details of bonding type rmsd hydrogen bonds : bond 0.02978 ( 529) hydrogen bonds : angle 4.14522 ( 1560) SS BOND : bond 0.00097 ( 2) SS BOND : angle 0.20895 ( 4) covalent geometry : bond 0.00304 ( 8828) covalent geometry : angle 0.54100 (11978) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2172 Ramachandran restraints generated. 1086 Oldfield, 0 Emsley, 1086 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2172 Ramachandran restraints generated. 1086 Oldfield, 0 Emsley, 1086 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 936 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 136 time to evaluate : 0.886 Fit side-chains revert: symmetry clash REVERT: A 41 LYS cc_start: 0.7675 (mmmt) cc_final: 0.7230 (mmmt) REVERT: A 136 LYS cc_start: 0.7472 (OUTLIER) cc_final: 0.7095 (mmmt) REVERT: A 256 LYS cc_start: 0.8339 (mmtt) cc_final: 0.7887 (mmmm) REVERT: A 517 LEU cc_start: 0.8281 (mp) cc_final: 0.7667 (mp) REVERT: B 154 HIS cc_start: 0.8242 (m90) cc_final: 0.7970 (m-70) REVERT: B 291 LYS cc_start: 0.8409 (ttmm) cc_final: 0.7880 (ttpt) REVERT: B 300 GLU cc_start: 0.7710 (pp20) cc_final: 0.7389 (pp20) REVERT: B 304 PHE cc_start: 0.7726 (m-80) cc_final: 0.7504 (m-80) REVERT: B 508 TYR cc_start: 0.6214 (t80) cc_final: 0.5904 (t80) REVERT: B 517 LEU cc_start: 0.8468 (OUTLIER) cc_final: 0.8259 (mm) REVERT: B 630 ILE cc_start: 0.7967 (mp) cc_final: 0.7629 (mp) REVERT: B 636 TRP cc_start: 0.8569 (m100) cc_final: 0.8231 (m100) outliers start: 38 outliers final: 33 residues processed: 157 average time/residue: 0.1860 time to fit residues: 42.2171 Evaluate side-chains 171 residues out of total 936 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 136 time to evaluate : 0.938 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 91 ILE Chi-restraints excluded: chain A residue 114 VAL Chi-restraints excluded: chain A residue 136 LYS Chi-restraints excluded: chain A residue 148 ASP Chi-restraints excluded: chain A residue 174 THR Chi-restraints excluded: chain A residue 198 VAL Chi-restraints excluded: chain A residue 204 ILE Chi-restraints excluded: chain A residue 248 THR Chi-restraints excluded: chain A residue 281 LEU Chi-restraints excluded: chain A residue 287 LEU Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 319 LEU Chi-restraints excluded: chain A residue 408 LEU Chi-restraints excluded: chain A residue 450 LEU Chi-restraints excluded: chain A residue 461 GLN Chi-restraints excluded: chain A residue 478 SER Chi-restraints excluded: chain A residue 522 VAL Chi-restraints excluded: chain A residue 549 THR Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 566 VAL Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 601 LEU Chi-restraints excluded: chain A residue 655 LEU Chi-restraints excluded: chain B residue 38 ILE Chi-restraints excluded: chain B residue 114 VAL Chi-restraints excluded: chain B residue 148 ASP Chi-restraints excluded: chain B residue 198 VAL Chi-restraints excluded: chain B residue 204 ILE Chi-restraints excluded: chain B residue 289 VAL Chi-restraints excluded: chain B residue 517 LEU Chi-restraints excluded: chain B residue 522 VAL Chi-restraints excluded: chain B residue 552 THR Chi-restraints excluded: chain B residue 566 VAL Chi-restraints excluded: chain B residue 639 VAL Chi-restraints excluded: chain B residue 655 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 47 optimal weight: 1.9990 chunk 12 optimal weight: 0.9990 chunk 108 optimal weight: 0.0170 chunk 48 optimal weight: 1.9990 chunk 97 optimal weight: 0.5980 chunk 85 optimal weight: 2.9990 chunk 6 optimal weight: 2.9990 chunk 39 optimal weight: 0.2980 chunk 28 optimal weight: 0.9990 chunk 103 optimal weight: 0.5980 chunk 50 optimal weight: 0.8980 overall best weight: 0.4818 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 531 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3947 r_free = 0.3947 target = 0.171768 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.129171 restraints weight = 9362.568| |-----------------------------------------------------------------------------| r_work (start): 0.3382 rms_B_bonded: 2.05 r_work: 0.3241 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.3091 rms_B_bonded: 4.64 restraints_weight: 0.2500 r_work (final): 0.3091 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7714 moved from start: 0.1652 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 8830 Z= 0.119 Angle : 0.531 7.813 11982 Z= 0.258 Chirality : 0.039 0.209 1434 Planarity : 0.004 0.048 1458 Dihedral : 5.405 57.426 1336 Min Nonbonded Distance : 2.582 Molprobity Statistics. All-atom Clashscore : 9.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.21 % Favored : 97.79 % Rotamer: Outliers : 4.38 % Allowed : 23.50 % Favored : 72.12 % 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: 1.75 (0.27), residues: 1086 helix: 1.89 (0.19), residues: 700 sheet: -2.02 (0.54), residues: 82 loop : 0.57 (0.41), residues: 304 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP A 575 HIS 0.005 0.001 HIS B 154 PHE 0.035 0.001 PHE A 275 TYR 0.014 0.001 TYR B 584 ARG 0.002 0.000 ARG B 401 Details of bonding type rmsd hydrogen bonds : bond 0.02862 ( 529) hydrogen bonds : angle 4.07419 ( 1560) SS BOND : bond 0.00078 ( 2) SS BOND : angle 0.23627 ( 4) covalent geometry : bond 0.00279 ( 8828) covalent geometry : angle 0.53064 (11978) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4685.55 seconds wall clock time: 81 minutes 58.84 seconds (4918.84 seconds total)