Starting phenix.real_space_refine on Fri May 16 08:26:43 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8jif_36311/05_2025/8jif_36311.cif Found real_map, /net/cci-nas-00/data/ceres_data/8jif_36311/05_2025/8jif_36311.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.28 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8jif_36311/05_2025/8jif_36311.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8jif_36311/05_2025/8jif_36311.map" model { file = "/net/cci-nas-00/data/ceres_data/8jif_36311/05_2025/8jif_36311.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8jif_36311/05_2025/8jif_36311.cif" } resolution = 2.28 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= 0.003 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 Zn 1 6.06 5 S 54 5.16 5 C 9243 2.51 5 N 2537 2.21 5 O 2795 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 19 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 14630 Number of models: 1 Model: "" Number of chains: 5 Chain: "R" Number of atoms: 2056 Number of conformers: 1 Conformer: "" Number of residues, atoms: 256, 2056 Classifications: {'peptide': 256} Link IDs: {'PTRANS': 17, 'TRANS': 238} Chain: "A" Number of atoms: 4191 Number of conformers: 1 Conformer: "" Number of residues, atoms: 525, 4191 Classifications: {'peptide': 525} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 36, 'TRANS': 488} Chain: "B" Number of atoms: 4191 Number of conformers: 1 Conformer: "" Number of residues, atoms: 525, 4191 Classifications: {'peptide': 525} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 36, 'TRANS': 488} Chain: "C" Number of atoms: 4191 Number of conformers: 1 Conformer: "" Number of residues, atoms: 525, 4191 Classifications: {'peptide': 525} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 36, 'TRANS': 488} Chain: "R" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Residues with excluded nonbonded symmetry interactions: 2 residue: pdb=" N ARG A 312 " occ=0.31 ... (9 atoms not shown) pdb=" NH2 ARG A 312 " occ=0.31 residue: pdb=" N ARG B 312 " occ=0.76 ... (9 atoms not shown) pdb=" NH2 ARG B 312 " occ=0.76 Time building chain proxies: 8.79, per 1000 atoms: 0.60 Number of scatterers: 14630 At special positions: 0 Unit cell: (140.831, 125.652, 124.808, 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) Zn 1 29.99 S 54 16.00 O 2795 8.00 N 2537 7.00 C 9243 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS R 23 " - pdb=" SG CYS R 35 " distance=2.02 Simple disulfide: pdb=" SG CYS R 45 " - pdb=" SG CYS R 222 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.97 Conformation dependent library (CDL) restraints added in 2.0 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN R 301 " pdb="ZN ZN R 301 " - pdb=" NE2 HIS R 114 " pdb="ZN ZN R 301 " - pdb=" NE2 HIS R 116 " pdb="ZN ZN R 301 " - pdb=" ND1 HIS R 139 " 3646 Ramachandran restraints generated. 1823 Oldfield, 0 Emsley, 1823 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3386 Finding SS restraints... Secondary structure from input PDB file: 27 helices and 32 sheets defined 9.6% alpha, 13.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.69 Creating SS restraints... Processing helix chain 'R' and resid 37 through 41 Processing helix chain 'R' and resid 173 through 180 Processing helix chain 'R' and resid 181 through 184 Processing helix chain 'R' and resid 238 through 248 removed outlier: 3.534A pdb=" N SER R 246 " --> pdb=" O PHE R 242 " (cutoff:3.500A) Processing helix chain 'A' and resid 262 through 266 Processing helix chain 'A' and resid 269 through 273 Processing helix chain 'A' and resid 288 through 292 Processing helix chain 'A' and resid 294 through 305 Processing helix chain 'A' and resid 396 through 400 Processing helix chain 'A' and resid 467 through 474 removed outlier: 4.088A pdb=" N MET A 471 " --> pdb=" O PRO A 468 " (cutoff:3.500A) removed outlier: 6.137A pdb=" N ALA A 472 " --> pdb=" O SER A 469 " (cutoff:3.500A) Processing helix chain 'A' and resid 563 through 569 removed outlier: 3.801A pdb=" N THR A 568 " --> pdb=" O GLU A 565 " (cutoff:3.500A) Processing helix chain 'B' and resid 252 through 256 Processing helix chain 'B' and resid 262 through 266 Processing helix chain 'B' and resid 269 through 273 Processing helix chain 'B' and resid 288 through 292 Processing helix chain 'B' and resid 294 through 305 Processing helix chain 'B' and resid 396 through 400 Processing helix chain 'B' and resid 467 through 474 removed outlier: 3.858A pdb=" N MET B 471 " --> pdb=" O PRO B 468 " (cutoff:3.500A) removed outlier: 5.857A pdb=" N ALA B 472 " --> pdb=" O SER B 469 " (cutoff:3.500A) Processing helix chain 'B' and resid 554 through 556 No H-bonds generated for 'chain 'B' and resid 554 through 556' Processing helix chain 'B' and resid 563 through 569 removed outlier: 4.125A pdb=" N THR B 568 " --> pdb=" O GLU B 565 " (cutoff:3.500A) Processing helix chain 'C' and resid 262 through 266 Processing helix chain 'C' and resid 269 through 273 Processing helix chain 'C' and resid 288 through 292 Processing helix chain 'C' and resid 294 through 304 Processing helix chain 'C' and resid 396 through 400 Processing helix chain 'C' and resid 467 through 474 removed outlier: 3.590A pdb=" N MET C 471 " --> pdb=" O PRO C 468 " (cutoff:3.500A) removed outlier: 6.130A pdb=" N ALA C 472 " --> pdb=" O SER C 469 " (cutoff:3.500A) Processing helix chain 'C' and resid 563 through 569 removed outlier: 4.020A pdb=" N THR C 568 " --> pdb=" O GLU C 565 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'R' and resid 54 through 55 Processing sheet with id=AA2, first strand: chain 'R' and resid 61 through 62 WARNING: can't find start of bonding for strands! previous: chain 'R' and resid 61 through 62 current: chain 'R' and resid 89 through 92 WARNING: can't find start of bonding for strands! previous: chain 'R' and resid 89 through 92 current: chain 'R' and resid 108 through 116 removed outlier: 5.339A pdb=" N ALA R 110 " --> pdb=" O LYS R 143 " (cutoff:3.500A) removed outlier: 5.822A pdb=" N LYS R 143 " --> pdb=" O ALA R 110 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N GLN R 112 " --> pdb=" O VAL R 141 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'R' and resid 156 through 163 current: chain 'R' and resid 229 through 231 Processing sheet with id=AA3, first strand: chain 'A' and resid 233 through 235 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 238 through 246 current: chain 'A' and resid 331 through 336 Processing sheet with id=AA4, first strand: chain 'A' and resid 258 through 261 Processing sheet with id=AA5, first strand: chain 'A' and resid 426 through 428 Processing sheet with id=AA6, first strand: chain 'A' and resid 445 through 451 removed outlier: 6.392A pdb=" N LYS A 462 " --> pdb=" O SER A 448 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N THR A 450 " --> pdb=" O THR A 460 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 479 through 480 removed outlier: 6.278A pdb=" N ILE A 479 " --> pdb=" O VAL A 606 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 483 through 484 Processing sheet with id=AA9, first strand: chain 'A' and resid 488 through 490 Processing sheet with id=AB1, first strand: chain 'A' and resid 514 through 517 removed outlier: 3.903A pdb=" N GLY C 578 " --> pdb=" O VAL C 596 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 542 through 544 Processing sheet with id=AB3, first strand: chain 'A' and resid 553 through 554 removed outlier: 4.026A pdb=" N THR C 450 " --> pdb=" O THR C 460 " (cutoff:3.500A) removed outlier: 6.427A pdb=" N LYS C 462 " --> pdb=" O SER C 448 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 593 through 596 removed outlier: 3.965A pdb=" N GLY A 578 " --> pdb=" O VAL A 596 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 619 through 621 removed outlier: 5.999A pdb=" N ALA A 620 " --> pdb=" O MET A 640 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB5 Processing sheet with id=AB6, first strand: chain 'A' and resid 627 through 629 removed outlier: 4.021A pdb=" N MET C 605 " --> pdb=" O PHE A 629 " (cutoff:3.500A) removed outlier: 6.288A pdb=" N ILE C 479 " --> pdb=" O VAL C 606 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 232 through 234 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 238 through 249 current: chain 'B' and resid 334 through 336 Processing sheet with id=AB8, first strand: chain 'B' and resid 258 through 261 Processing sheet with id=AB9, first strand: chain 'B' and resid 426 through 428 Processing sheet with id=AC1, first strand: chain 'B' and resid 445 through 449 removed outlier: 6.636A pdb=" N LYS B 462 " --> pdb=" O SER B 448 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 479 through 480 removed outlier: 6.206A pdb=" N ILE B 479 " --> pdb=" O VAL B 606 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 483 through 484 Processing sheet with id=AC4, first strand: chain 'B' and resid 488 through 490 Processing sheet with id=AC5, first strand: chain 'B' and resid 542 through 544 Processing sheet with id=AC6, first strand: chain 'B' and resid 593 through 596 removed outlier: 4.044A pdb=" N GLY B 578 " --> pdb=" O VAL B 596 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 619 through 621 removed outlier: 6.057A pdb=" N ALA B 620 " --> pdb=" O MET B 640 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC7 Processing sheet with id=AC8, first strand: chain 'C' and resid 231 through 234 Processing sheet with id=AC9, first strand: chain 'C' and resid 258 through 261 Processing sheet with id=AD1, first strand: chain 'C' and resid 427 through 428 removed outlier: 6.269A pdb=" N ALA C 427 " --> pdb=" O ARG C 734 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD1 Processing sheet with id=AD2, first strand: chain 'C' and resid 483 through 484 Processing sheet with id=AD3, first strand: chain 'C' and resid 488 through 490 Processing sheet with id=AD4, first strand: chain 'C' and resid 542 through 544 Processing sheet with id=AD5, first strand: chain 'C' and resid 619 through 621 removed outlier: 6.104A pdb=" N ALA C 620 " --> pdb=" O MET C 640 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD5 184 hydrogen bonds defined for protein. 366 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: 4.22 Time building geometry restraints manager: 4.64 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 2968 1.33 - 1.45: 3951 1.45 - 1.57: 8059 1.57 - 1.69: 0 1.69 - 1.81: 91 Bond restraints: 15069 Sorted by residual: bond pdb=" C ASP A 665 " pdb=" N LYS A 666 " ideal model delta sigma weight residual 1.331 1.278 0.052 1.29e-02 6.01e+03 1.65e+01 bond pdb=" N ALA A 248 " pdb=" CA ALA A 248 " ideal model delta sigma weight residual 1.457 1.498 -0.040 1.29e-02 6.01e+03 9.70e+00 bond pdb=" N THR A 341 " pdb=" CA THR A 341 " ideal model delta sigma weight residual 1.455 1.491 -0.036 1.27e-02 6.20e+03 8.09e+00 bond pdb=" CA ARG A 300 " pdb=" C ARG A 300 " ideal model delta sigma weight residual 1.524 1.489 0.035 1.28e-02 6.10e+03 7.64e+00 bond pdb=" CA PRO A 658 " pdb=" C PRO A 658 " ideal model delta sigma weight residual 1.517 1.542 -0.025 9.30e-03 1.16e+04 7.34e+00 ... (remaining 15064 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.82: 19868 2.82 - 5.65: 577 5.65 - 8.47: 72 8.47 - 11.29: 9 11.29 - 14.11: 2 Bond angle restraints: 20528 Sorted by residual: angle pdb=" N TRP A 247 " pdb=" CA TRP A 247 " pdb=" C TRP A 247 " ideal model delta sigma weight residual 111.71 125.82 -14.11 1.34e+00 5.57e-01 1.11e+02 angle pdb=" N THR A 494 " pdb=" CA THR A 494 " pdb=" C THR A 494 " ideal model delta sigma weight residual 114.75 104.32 10.43 1.26e+00 6.30e-01 6.85e+01 angle pdb=" N THR C 494 " pdb=" CA THR C 494 " pdb=" C THR C 494 " ideal model delta sigma weight residual 114.56 104.31 10.25 1.27e+00 6.20e-01 6.52e+01 angle pdb=" N GLY B 226 " pdb=" CA GLY B 226 " pdb=" C GLY B 226 " ideal model delta sigma weight residual 110.63 121.14 -10.51 1.45e+00 4.76e-01 5.25e+01 angle pdb=" N THR A 341 " pdb=" CA THR A 341 " pdb=" C THR A 341 " ideal model delta sigma weight residual 109.07 119.67 -10.60 1.52e+00 4.33e-01 4.86e+01 ... (remaining 20523 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.00: 7752 18.00 - 35.99: 717 35.99 - 53.99: 258 53.99 - 71.99: 96 71.99 - 89.99: 34 Dihedral angle restraints: 8857 sinusoidal: 3554 harmonic: 5303 Sorted by residual: dihedral pdb=" CA LYS R 260 " pdb=" C LYS R 260 " pdb=" N ASP R 261 " pdb=" CA ASP R 261 " ideal model delta harmonic sigma weight residual -180.00 -160.18 -19.82 0 5.00e+00 4.00e-02 1.57e+01 dihedral pdb=" CA ASP R 223 " pdb=" CB ASP R 223 " pdb=" CG ASP R 223 " pdb=" OD1 ASP R 223 " ideal model delta sinusoidal sigma weight residual -30.00 -89.51 59.51 1 2.00e+01 2.50e-03 1.18e+01 dihedral pdb=" CA ASP C 657 " pdb=" CB ASP C 657 " pdb=" CG ASP C 657 " pdb=" OD1 ASP C 657 " ideal model delta sinusoidal sigma weight residual -30.00 -89.24 59.24 1 2.00e+01 2.50e-03 1.17e+01 ... (remaining 8854 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.039: 1400 0.039 - 0.078: 484 0.078 - 0.117: 170 0.117 - 0.156: 41 0.156 - 0.195: 12 Chirality restraints: 2107 Sorted by residual: chirality pdb=" CA VAL C 342 " pdb=" N VAL C 342 " pdb=" C VAL C 342 " pdb=" CB VAL C 342 " both_signs ideal model delta sigma weight residual False 2.44 2.64 -0.19 2.00e-01 2.50e+01 9.50e-01 chirality pdb=" CA ASN A 519 " pdb=" N ASN A 519 " pdb=" C ASN A 519 " pdb=" CB ASN A 519 " both_signs ideal model delta sigma weight residual False 2.51 2.33 0.18 2.00e-01 2.50e+01 8.42e-01 chirality pdb=" CA VAL B 342 " pdb=" N VAL B 342 " pdb=" C VAL B 342 " pdb=" CB VAL B 342 " both_signs ideal model delta sigma weight residual False 2.44 2.62 -0.18 2.00e-01 2.50e+01 8.31e-01 ... (remaining 2104 not shown) Planarity restraints: 2728 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASN B 668 " -0.022 2.00e-02 2.50e+03 4.30e-02 1.85e+01 pdb=" C ASN B 668 " 0.074 2.00e-02 2.50e+03 pdb=" O ASN B 668 " -0.027 2.00e-02 2.50e+03 pdb=" N SER B 669 " -0.025 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASN B 519 " 0.064 5.00e-02 4.00e+02 9.53e-02 1.45e+01 pdb=" N PRO B 520 " -0.165 5.00e-02 4.00e+02 pdb=" CA PRO B 520 " 0.048 5.00e-02 4.00e+02 pdb=" CD PRO B 520 " 0.053 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ARG A 312 " 0.018 2.00e-02 2.50e+03 3.69e-02 1.36e+01 pdb=" C ARG A 312 " -0.064 2.00e-02 2.50e+03 pdb=" O ARG A 312 " 0.024 2.00e-02 2.50e+03 pdb=" N LEU A 313 " 0.021 2.00e-02 2.50e+03 ... (remaining 2725 not shown) Histogram of nonbonded interaction distances: 1.68 - 2.32: 7 2.32 - 2.97: 8347 2.97 - 3.61: 23365 3.61 - 4.26: 39458 4.26 - 4.90: 61049 Nonbonded interactions: 132226 Sorted by model distance: nonbonded pdb=" O SER R 51 " pdb=" OH TYR R 213 " model vdw 1.676 3.040 nonbonded pdb=" C SER R 51 " pdb=" OH TYR R 213 " model vdw 2.117 3.270 nonbonded pdb=" O ASN B 262 " pdb=" N GLY B 267 " model vdw 2.134 3.120 nonbonded pdb=" OG1 THR B 717 " pdb=" OE1 GLU B 718 " model vdw 2.152 3.040 nonbonded pdb=" CA SER R 51 " pdb=" OH TYR R 213 " model vdw 2.215 3.470 ... (remaining 132221 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' selection = chain 'B' selection = chain 'C' } 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=0.31 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.100 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: 37.640 Find NCS groups from input model: 0.410 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.010 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:14.080 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 55.300 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7041 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 15074 Z= 0.363 Angle : 1.139 14.115 20532 Z= 0.738 Chirality : 0.047 0.195 2107 Planarity : 0.005 0.095 2728 Dihedral : 17.824 89.987 5465 Min Nonbonded Distance : 1.676 Molprobity Statistics. All-atom Clashscore : 18.52 Ramachandran Plot: Outliers : 2.85 % Allowed : 8.67 % Favored : 88.48 % Rotamer: Outliers : 12.43 % Allowed : 12.43 % Favored : 75.14 % 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: -2.44 (0.18), residues: 1823 helix: -2.74 (0.44), residues: 104 sheet: -1.56 (0.25), residues: 327 loop : -1.66 (0.15), residues: 1392 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 298 HIS 0.005 0.001 HIS A 255 PHE 0.014 0.001 PHE A 315 TYR 0.030 0.002 TYR B 588E ARG 0.003 0.000 ARG A 312 Details of bonding type rmsd hydrogen bonds : bond 0.21193 ( 184) hydrogen bonds : angle 8.86265 ( 366) metal coordination : bond 0.02721 ( 3) SS BOND : bond 0.00563 ( 2) SS BOND : angle 1.35133 ( 4) covalent geometry : bond 0.00501 (15069) covalent geometry : angle 1.13891 (20528) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3646 Ramachandran restraints generated. 1823 Oldfield, 0 Emsley, 1823 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3646 Ramachandran restraints generated. 1823 Oldfield, 0 Emsley, 1823 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 444 residues out of total 1609 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 200 poor density : 244 time to evaluate : 1.704 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 99 ILE cc_start: 0.8303 (mt) cc_final: 0.7957 (pt) REVERT: R 244 GLU cc_start: 0.8514 (mm-30) cc_final: 0.8301 (mm-30) REVERT: A 256 LEU cc_start: 0.8760 (OUTLIER) cc_final: 0.8556 (mt) REVERT: B 313 LEU cc_start: 0.1334 (OUTLIER) cc_final: 0.1012 (tt) REVERT: C 296 ARG cc_start: 0.8501 (tpt90) cc_final: 0.7853 (mmp-170) REVERT: C 730 ARG cc_start: 0.8986 (OUTLIER) cc_final: 0.8533 (mtt90) outliers start: 200 outliers final: 83 residues processed: 393 average time/residue: 1.2901 time to fit residues: 554.3796 Evaluate side-chains 212 residues out of total 1609 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 126 time to evaluate : 1.555 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 72 VAL Chi-restraints excluded: chain R residue 115 LEU Chi-restraints excluded: chain R residue 141 VAL Chi-restraints excluded: chain R residue 169 VAL Chi-restraints excluded: chain R residue 209 THR Chi-restraints excluded: chain R residue 229 THR Chi-restraints excluded: chain R residue 230 VAL Chi-restraints excluded: chain R residue 274 VAL Chi-restraints excluded: chain A residue 223 SER Chi-restraints excluded: chain A residue 225 SER Chi-restraints excluded: chain A residue 229 HIS Chi-restraints excluded: chain A residue 232 SER Chi-restraints excluded: chain A residue 235 LEU Chi-restraints excluded: chain A residue 246 THR Chi-restraints excluded: chain A residue 256 LEU Chi-restraints excluded: chain A residue 313 LEU Chi-restraints excluded: chain A residue 316 LYS Chi-restraints excluded: chain A residue 323 LYS Chi-restraints excluded: chain A residue 324 GLU Chi-restraints excluded: chain A residue 325 VAL Chi-restraints excluded: chain A residue 326 THR Chi-restraints excluded: chain A residue 328 ASN Chi-restraints excluded: chain A residue 332 LYS Chi-restraints excluded: chain A residue 333 THR Chi-restraints excluded: chain A residue 334 ILE Chi-restraints excluded: chain A residue 341 THR Chi-restraints excluded: chain A residue 405 LEU Chi-restraints excluded: chain A residue 406 ARG Chi-restraints excluded: chain A residue 412 GLN Chi-restraints excluded: chain A residue 465 VAL Chi-restraints excluded: chain A residue 588 ASP Chi-restraints excluded: chain A residue 649 ILE Chi-restraints excluded: chain A residue 657 ASP Chi-restraints excluded: chain A residue 671 ILE Chi-restraints excluded: chain A residue 673 GLN Chi-restraints excluded: chain B residue 225 SER Chi-restraints excluded: chain B residue 233 GLN Chi-restraints excluded: chain B residue 238 ARG Chi-restraints excluded: chain B residue 240 ILE Chi-restraints excluded: chain B residue 251 THR Chi-restraints excluded: chain B residue 312 ARG Chi-restraints excluded: chain B residue 313 LEU Chi-restraints excluded: chain B residue 321 GLN Chi-restraints excluded: chain B residue 323 LYS Chi-restraints excluded: chain B residue 326 THR Chi-restraints excluded: chain B residue 331 VAL Chi-restraints excluded: chain B residue 332 LYS Chi-restraints excluded: chain B residue 333 THR Chi-restraints excluded: chain B residue 339 THR Chi-restraints excluded: chain B residue 341 THR Chi-restraints excluded: chain B residue 343 GLN Chi-restraints excluded: chain B residue 451 ILE Chi-restraints excluded: chain B residue 532 ASP Chi-restraints excluded: chain B residue 657 ASP Chi-restraints excluded: chain B residue 664 LYS Chi-restraints excluded: chain B residue 665 ASP Chi-restraints excluded: chain B residue 666 LYS Chi-restraints excluded: chain B residue 668 ASN Chi-restraints excluded: chain B residue 671 ILE Chi-restraints excluded: chain B residue 676 THR Chi-restraints excluded: chain B residue 707 LYS Chi-restraints excluded: chain C residue 235 LEU Chi-restraints excluded: chain C residue 251 THR Chi-restraints excluded: chain C residue 313 LEU Chi-restraints excluded: chain C residue 317 LEU Chi-restraints excluded: chain C residue 321 GLN Chi-restraints excluded: chain C residue 326 THR Chi-restraints excluded: chain C residue 332 LYS Chi-restraints excluded: chain C residue 333 THR Chi-restraints excluded: chain C residue 338 LEU Chi-restraints excluded: chain C residue 341 THR Chi-restraints excluded: chain C residue 342 VAL Chi-restraints excluded: chain C residue 407 THR Chi-restraints excluded: chain C residue 410 ASN Chi-restraints excluded: chain C residue 412 GLN Chi-restraints excluded: chain C residue 532 ASP Chi-restraints excluded: chain C residue 588 GLN Chi-restraints excluded: chain C residue 657 ASP Chi-restraints excluded: chain C residue 660 THR Chi-restraints excluded: chain C residue 665 ASP Chi-restraints excluded: chain C residue 666 LYS Chi-restraints excluded: chain C residue 668 ASN Chi-restraints excluded: chain C residue 671 ILE Chi-restraints excluded: chain C residue 673 GLN Chi-restraints excluded: chain C residue 702 THR Chi-restraints excluded: chain C residue 730 ARG Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 181 random chunks: chunk 152 optimal weight: 5.9990 chunk 137 optimal weight: 10.0000 chunk 76 optimal weight: 8.9990 chunk 46 optimal weight: 10.0000 chunk 92 optimal weight: 5.9990 chunk 73 optimal weight: 9.9990 chunk 141 optimal weight: 50.0000 chunk 54 optimal weight: 10.0000 chunk 86 optimal weight: 8.9990 chunk 105 optimal weight: 10.0000 chunk 164 optimal weight: 10.0000 overall best weight: 7.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 127 HIS R 133 HIS A 229 HIS A 253 ASN A 314 ASN A 321 GLN A 376 GLN A 412 GLN A 470 ASN A 474 GLN A 497 ASN A 646 GLN A 678 GLN A 735 ASN B 229 HIS B 233 GLN B 336 ASN B 470 ASN B 678 GLN C 227 ASN C 329 ASN C 343 GLN C 403 GLN C 419 ASN C 430 GLN C 452 ASN C 457 ASN C 495 GLN C 663 ASN C 678 GLN C 735 ASN Total number of N/Q/H flips: 31 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3794 r_free = 0.3794 target = 0.134763 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3050 r_free = 0.3050 target = 0.085716 restraints weight = 27637.493| |-----------------------------------------------------------------------------| r_work (start): 0.2975 rms_B_bonded: 3.53 r_work: 0.2842 rms_B_bonded: 4.17 restraints_weight: 0.5000 r_work (final): 0.2842 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2830 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2830 r_free = 0.2830 target_work(ls_wunit_k1) = 0.073 | | occupancies: max = 1.00 min = 0.31 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2829 r_free = 0.2829 target_work(ls_wunit_k1) = 0.073 | | occupancies: max = 1.00 min = 0.24 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2829 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8742 moved from start: 0.3110 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.075 15074 Z= 0.270 Angle : 0.700 8.938 20532 Z= 0.372 Chirality : 0.048 0.191 2107 Planarity : 0.006 0.107 2728 Dihedral : 10.371 81.886 2170 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 6.29 Ramachandran Plot: Outliers : 0.71 % Allowed : 7.41 % Favored : 91.88 % Rotamer: Outliers : 5.66 % Allowed : 15.16 % Favored : 79.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.80 % 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: -1.59 (0.19), residues: 1823 helix: -1.35 (0.52), residues: 85 sheet: -1.22 (0.23), residues: 402 loop : -1.01 (0.17), residues: 1336 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP A 306 HIS 0.008 0.001 HIS R 187 PHE 0.013 0.002 PHE C 535 TYR 0.018 0.002 TYR A 701 ARG 0.027 0.001 ARG C 296 Details of bonding type rmsd hydrogen bonds : bond 0.04385 ( 184) hydrogen bonds : angle 6.27735 ( 366) metal coordination : bond 0.01042 ( 3) SS BOND : bond 0.00262 ( 2) SS BOND : angle 1.31049 ( 4) covalent geometry : bond 0.00630 (15069) covalent geometry : angle 0.70009 (20528) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3646 Ramachandran restraints generated. 1823 Oldfield, 0 Emsley, 1823 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3646 Ramachandran restraints generated. 1823 Oldfield, 0 Emsley, 1823 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 222 residues out of total 1609 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 131 time to evaluate : 1.565 Fit side-chains REVERT: A 238 ARG cc_start: 0.7088 (mtt180) cc_final: 0.6322 (mtt90) REVERT: A 300 ARG cc_start: 0.8084 (mmt180) cc_final: 0.7617 (mmt180) REVERT: A 588 ASP cc_start: 0.8557 (OUTLIER) cc_final: 0.8350 (m-30) REVERT: A 682 GLU cc_start: 0.8186 (tt0) cc_final: 0.7837 (pp20) REVERT: A 684 GLU cc_start: 0.8360 (tm-30) cc_final: 0.7724 (tm-30) REVERT: B 518 MET cc_start: 0.9299 (mmt) cc_final: 0.9041 (tpp) REVERT: C 233 GLN cc_start: 0.2803 (OUTLIER) cc_final: 0.2491 (pm20) REVERT: C 300 ARG cc_start: 0.8635 (mmt180) cc_final: 0.7838 (mmt180) outliers start: 91 outliers final: 57 residues processed: 212 average time/residue: 1.3239 time to fit residues: 309.5728 Evaluate side-chains 175 residues out of total 1609 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 116 time to evaluate : 1.747 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 72 VAL Chi-restraints excluded: chain R residue 115 LEU Chi-restraints excluded: chain R residue 141 VAL Chi-restraints excluded: chain R residue 145 LEU Chi-restraints excluded: chain R residue 169 VAL Chi-restraints excluded: chain R residue 209 THR Chi-restraints excluded: chain R residue 229 THR Chi-restraints excluded: chain R residue 230 VAL Chi-restraints excluded: chain R residue 274 VAL Chi-restraints excluded: chain A residue 229 HIS Chi-restraints excluded: chain A residue 235 LEU Chi-restraints excluded: chain A residue 313 LEU Chi-restraints excluded: chain A residue 324 GLU Chi-restraints excluded: chain A residue 326 THR Chi-restraints excluded: chain A residue 328 ASN Chi-restraints excluded: chain A residue 332 LYS Chi-restraints excluded: chain A residue 338 LEU Chi-restraints excluded: chain A residue 588 ASP Chi-restraints excluded: chain B residue 225 SER Chi-restraints excluded: chain B residue 235 LEU Chi-restraints excluded: chain B residue 238 ARG Chi-restraints excluded: chain B residue 240 ILE Chi-restraints excluded: chain B residue 312 ARG Chi-restraints excluded: chain B residue 320 ILE Chi-restraints excluded: chain B residue 321 GLN Chi-restraints excluded: chain B residue 323 LYS Chi-restraints excluded: chain B residue 326 THR Chi-restraints excluded: chain B residue 329 ASN Chi-restraints excluded: chain B residue 331 VAL Chi-restraints excluded: chain B residue 333 THR Chi-restraints excluded: chain B residue 339 THR Chi-restraints excluded: chain B residue 341 THR Chi-restraints excluded: chain B residue 343 GLN Chi-restraints excluded: chain B residue 606 VAL Chi-restraints excluded: chain B residue 657 ASP Chi-restraints excluded: chain B residue 664 LYS Chi-restraints excluded: chain B residue 666 LYS Chi-restraints excluded: chain B residue 668 ASN Chi-restraints excluded: chain B residue 671 ILE Chi-restraints excluded: chain B residue 676 THR Chi-restraints excluded: chain C residue 233 GLN Chi-restraints excluded: chain C residue 251 THR Chi-restraints excluded: chain C residue 317 LEU Chi-restraints excluded: chain C residue 328 ASN Chi-restraints excluded: chain C residue 329 ASN Chi-restraints excluded: chain C residue 331 VAL Chi-restraints excluded: chain C residue 332 LYS Chi-restraints excluded: chain C residue 333 THR Chi-restraints excluded: chain C residue 338 LEU Chi-restraints excluded: chain C residue 341 THR Chi-restraints excluded: chain C residue 342 VAL Chi-restraints excluded: chain C residue 407 THR Chi-restraints excluded: chain C residue 410 ASN Chi-restraints excluded: chain C residue 657 ASP Chi-restraints excluded: chain C residue 660 THR Chi-restraints excluded: chain C residue 663 ASN Chi-restraints excluded: chain C residue 666 LYS Chi-restraints excluded: chain C residue 668 ASN Chi-restraints excluded: chain C residue 671 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 181 random chunks: chunk 68 optimal weight: 10.0000 chunk 3 optimal weight: 7.9990 chunk 154 optimal weight: 7.9990 chunk 175 optimal weight: 50.0000 chunk 149 optimal weight: 3.9990 chunk 8 optimal weight: 0.4980 chunk 165 optimal weight: 9.9990 chunk 76 optimal weight: 1.9990 chunk 38 optimal weight: 6.9990 chunk 176 optimal weight: 10.0000 chunk 126 optimal weight: 8.9990 overall best weight: 4.2988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 86 GLN R 187 HIS R 248 ASN A 456 GLN B 321 GLN C 329 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3788 r_free = 0.3788 target = 0.134733 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3014 r_free = 0.3014 target = 0.083701 restraints weight = 26901.775| |-----------------------------------------------------------------------------| r_work (start): 0.2937 rms_B_bonded: 3.89 r_work: 0.2794 rms_B_bonded: 4.32 restraints_weight: 0.5000 r_work (final): 0.2794 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2794 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2794 r_free = 0.2794 target_work(ls_wunit_k1) = 0.072 | | occupancies: max = 1.00 min = 0.24 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2794 r_free = 0.2794 target_work(ls_wunit_k1) = 0.072 | | occupancies: max = 1.00 min = 0.15 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2794 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8735 moved from start: 0.3392 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 15074 Z= 0.158 Angle : 0.583 7.143 20532 Z= 0.308 Chirality : 0.043 0.157 2107 Planarity : 0.005 0.108 2728 Dihedral : 8.212 59.352 2086 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 4.96 Ramachandran Plot: Outliers : 0.66 % Allowed : 7.68 % Favored : 91.66 % Rotamer: Outliers : 4.23 % Allowed : 16.41 % Favored : 79.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.80 % 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: -1.21 (0.19), residues: 1823 helix: -0.75 (0.57), residues: 85 sheet: -0.93 (0.23), residues: 405 loop : -0.78 (0.17), residues: 1333 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 247 HIS 0.008 0.001 HIS R 187 PHE 0.015 0.001 PHE A 372 TYR 0.015 0.001 TYR R 213 ARG 0.005 0.001 ARG R 59 Details of bonding type rmsd hydrogen bonds : bond 0.03638 ( 184) hydrogen bonds : angle 5.90506 ( 366) metal coordination : bond 0.00456 ( 3) SS BOND : bond 0.00305 ( 2) SS BOND : angle 1.24285 ( 4) covalent geometry : bond 0.00370 (15069) covalent geometry : angle 0.58280 (20528) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3646 Ramachandran restraints generated. 1823 Oldfield, 0 Emsley, 1823 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3646 Ramachandran restraints generated. 1823 Oldfield, 0 Emsley, 1823 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 1609 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 118 time to evaluate : 1.782 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 132 ARG cc_start: 0.9145 (OUTLIER) cc_final: 0.8745 (ttt180) REVERT: A 238 ARG cc_start: 0.6997 (mtt180) cc_final: 0.6290 (mtt90) REVERT: A 296 ARG cc_start: 0.5855 (mmp-170) cc_final: 0.5281 (mmt180) REVERT: A 300 ARG cc_start: 0.8008 (mmt180) cc_final: 0.7499 (mmt180) REVERT: A 312 ARG cc_start: 0.8368 (ptp-110) cc_final: 0.7989 (ptp90) REVERT: A 684 GLU cc_start: 0.8449 (tm-30) cc_final: 0.7685 (tm-30) REVERT: C 300 ARG cc_start: 0.8657 (OUTLIER) cc_final: 0.7739 (mmt180) REVERT: C 707 LYS cc_start: 0.5596 (tptt) cc_final: 0.5291 (tptt) outliers start: 68 outliers final: 51 residues processed: 182 average time/residue: 1.3444 time to fit residues: 268.4297 Evaluate side-chains 165 residues out of total 1609 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 112 time to evaluate : 1.722 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 72 VAL Chi-restraints excluded: chain R residue 115 LEU Chi-restraints excluded: chain R residue 132 ARG Chi-restraints excluded: chain R residue 141 VAL Chi-restraints excluded: chain R residue 145 LEU Chi-restraints excluded: chain R residue 169 VAL Chi-restraints excluded: chain R residue 209 THR Chi-restraints excluded: chain R residue 229 THR Chi-restraints excluded: chain R residue 230 VAL Chi-restraints excluded: chain R residue 274 VAL Chi-restraints excluded: chain A residue 229 HIS Chi-restraints excluded: chain A residue 235 LEU Chi-restraints excluded: chain A residue 313 LEU Chi-restraints excluded: chain A residue 328 ASN Chi-restraints excluded: chain A residue 332 LYS Chi-restraints excluded: chain A residue 338 LEU Chi-restraints excluded: chain A residue 344 VAL Chi-restraints excluded: chain B residue 235 LEU Chi-restraints excluded: chain B residue 238 ARG Chi-restraints excluded: chain B residue 240 ILE Chi-restraints excluded: chain B residue 251 THR Chi-restraints excluded: chain B residue 320 ILE Chi-restraints excluded: chain B residue 321 GLN Chi-restraints excluded: chain B residue 323 LYS Chi-restraints excluded: chain B residue 326 THR Chi-restraints excluded: chain B residue 331 VAL Chi-restraints excluded: chain B residue 333 THR Chi-restraints excluded: chain B residue 339 THR Chi-restraints excluded: chain B residue 341 THR Chi-restraints excluded: chain B residue 343 GLN Chi-restraints excluded: chain B residue 413 PHE Chi-restraints excluded: chain B residue 494 THR Chi-restraints excluded: chain B residue 588 GLN Chi-restraints excluded: chain B residue 606 VAL Chi-restraints excluded: chain B residue 657 ASP Chi-restraints excluded: chain B residue 664 LYS Chi-restraints excluded: chain B residue 666 LYS Chi-restraints excluded: chain B residue 668 ASN Chi-restraints excluded: chain B residue 671 ILE Chi-restraints excluded: chain B residue 676 THR Chi-restraints excluded: chain C residue 300 ARG Chi-restraints excluded: chain C residue 329 ASN Chi-restraints excluded: chain C residue 332 LYS Chi-restraints excluded: chain C residue 333 THR Chi-restraints excluded: chain C residue 338 LEU Chi-restraints excluded: chain C residue 341 THR Chi-restraints excluded: chain C residue 407 THR Chi-restraints excluded: chain C residue 410 ASN Chi-restraints excluded: chain C residue 588 GLN Chi-restraints excluded: chain C residue 666 LYS Chi-restraints excluded: chain C residue 668 ASN Chi-restraints excluded: chain C residue 671 ILE Chi-restraints excluded: chain C residue 684 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 181 random chunks: chunk 176 optimal weight: 20.0000 chunk 175 optimal weight: 50.0000 chunk 63 optimal weight: 9.9990 chunk 88 optimal weight: 50.0000 chunk 160 optimal weight: 2.9990 chunk 86 optimal weight: 6.9990 chunk 11 optimal weight: 20.0000 chunk 56 optimal weight: 10.0000 chunk 80 optimal weight: 8.9990 chunk 26 optimal weight: 3.9990 chunk 23 optimal weight: 0.0170 overall best weight: 4.6026 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 430 GLN B 343 GLN C 329 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3783 r_free = 0.3783 target = 0.134186 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3009 r_free = 0.3009 target = 0.083903 restraints weight = 27083.266| |-----------------------------------------------------------------------------| r_work (start): 0.2930 rms_B_bonded: 3.69 r_work: 0.2787 rms_B_bonded: 4.32 restraints_weight: 0.5000 r_work (final): 0.2787 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2787 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2787 r_free = 0.2787 target_work(ls_wunit_k1) = 0.071 | | occupancies: max = 1.00 min = 0.15 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2787 r_free = 0.2787 target_work(ls_wunit_k1) = 0.071 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2787 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8758 moved from start: 0.3620 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 15074 Z= 0.165 Angle : 0.575 6.744 20532 Z= 0.301 Chirality : 0.043 0.156 2107 Planarity : 0.005 0.112 2728 Dihedral : 7.477 59.915 2068 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 4.50 Ramachandran Plot: Outliers : 0.60 % Allowed : 7.41 % Favored : 91.99 % Rotamer: Outliers : 4.04 % Allowed : 16.66 % Favored : 79.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.80 % 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: -1.06 (0.19), residues: 1823 helix: -0.67 (0.58), residues: 85 sheet: -0.74 (0.23), residues: 407 loop : -0.70 (0.18), residues: 1331 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 247 HIS 0.006 0.001 HIS A 229 PHE 0.016 0.001 PHE A 372 TYR 0.011 0.001 TYR C 701 ARG 0.004 0.000 ARG R 65 Details of bonding type rmsd hydrogen bonds : bond 0.03529 ( 184) hydrogen bonds : angle 5.80118 ( 366) metal coordination : bond 0.00506 ( 3) SS BOND : bond 0.00295 ( 2) SS BOND : angle 1.22502 ( 4) covalent geometry : bond 0.00390 (15069) covalent geometry : angle 0.57438 (20528) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3646 Ramachandran restraints generated. 1823 Oldfield, 0 Emsley, 1823 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3646 Ramachandran restraints generated. 1823 Oldfield, 0 Emsley, 1823 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 1609 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 116 time to evaluate : 1.737 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 132 ARG cc_start: 0.9164 (OUTLIER) cc_final: 0.8754 (ttt180) REVERT: R 208 TYR cc_start: 0.9038 (m-80) cc_final: 0.8771 (m-80) REVERT: A 238 ARG cc_start: 0.6972 (mtt180) cc_final: 0.6324 (mtt90) REVERT: A 296 ARG cc_start: 0.5903 (mmp-170) cc_final: 0.5678 (mmt180) REVERT: A 373 MET cc_start: 0.8121 (OUTLIER) cc_final: 0.7896 (tpp) REVERT: A 684 GLU cc_start: 0.8550 (tm-30) cc_final: 0.7729 (tm-30) REVERT: A 708 SER cc_start: 0.8517 (OUTLIER) cc_final: 0.8298 (p) REVERT: B 311 LYS cc_start: 0.9036 (mmtt) cc_final: 0.8658 (mmpt) REVERT: C 300 ARG cc_start: 0.8681 (mmt180) cc_final: 0.7789 (mmt180) outliers start: 65 outliers final: 50 residues processed: 174 average time/residue: 1.3458 time to fit residues: 257.3691 Evaluate side-chains 167 residues out of total 1609 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 114 time to evaluate : 1.681 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 72 VAL Chi-restraints excluded: chain R residue 115 LEU Chi-restraints excluded: chain R residue 132 ARG Chi-restraints excluded: chain R residue 141 VAL Chi-restraints excluded: chain R residue 145 LEU Chi-restraints excluded: chain R residue 169 VAL Chi-restraints excluded: chain R residue 209 THR Chi-restraints excluded: chain R residue 229 THR Chi-restraints excluded: chain R residue 230 VAL Chi-restraints excluded: chain R residue 274 VAL Chi-restraints excluded: chain A residue 229 HIS Chi-restraints excluded: chain A residue 235 LEU Chi-restraints excluded: chain A residue 263 SER Chi-restraints excluded: chain A residue 328 ASN Chi-restraints excluded: chain A residue 332 LYS Chi-restraints excluded: chain A residue 338 LEU Chi-restraints excluded: chain A residue 344 VAL Chi-restraints excluded: chain A residue 373 MET Chi-restraints excluded: chain A residue 404 MET Chi-restraints excluded: chain A residue 708 SER Chi-restraints excluded: chain B residue 238 ARG Chi-restraints excluded: chain B residue 240 ILE Chi-restraints excluded: chain B residue 251 THR Chi-restraints excluded: chain B residue 312 ARG Chi-restraints excluded: chain B residue 320 ILE Chi-restraints excluded: chain B residue 323 LYS Chi-restraints excluded: chain B residue 326 THR Chi-restraints excluded: chain B residue 333 THR Chi-restraints excluded: chain B residue 339 THR Chi-restraints excluded: chain B residue 341 THR Chi-restraints excluded: chain B residue 396 CYS Chi-restraints excluded: chain B residue 413 PHE Chi-restraints excluded: chain B residue 494 THR Chi-restraints excluded: chain B residue 588 GLN Chi-restraints excluded: chain B residue 606 VAL Chi-restraints excluded: chain B residue 657 ASP Chi-restraints excluded: chain B residue 666 LYS Chi-restraints excluded: chain B residue 668 ASN Chi-restraints excluded: chain B residue 671 ILE Chi-restraints excluded: chain C residue 264 THR Chi-restraints excluded: chain C residue 322 VAL Chi-restraints excluded: chain C residue 328 ASN Chi-restraints excluded: chain C residue 329 ASN Chi-restraints excluded: chain C residue 332 LYS Chi-restraints excluded: chain C residue 333 THR Chi-restraints excluded: chain C residue 338 LEU Chi-restraints excluded: chain C residue 341 THR Chi-restraints excluded: chain C residue 410 ASN Chi-restraints excluded: chain C residue 660 THR Chi-restraints excluded: chain C residue 666 LYS Chi-restraints excluded: chain C residue 668 ASN Chi-restraints excluded: chain C residue 671 ILE Chi-restraints excluded: chain C residue 684 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 181 random chunks: chunk 70 optimal weight: 30.0000 chunk 37 optimal weight: 40.0000 chunk 97 optimal weight: 20.0000 chunk 32 optimal weight: 6.9990 chunk 58 optimal weight: 7.9990 chunk 163 optimal weight: 2.9990 chunk 76 optimal weight: 8.9990 chunk 166 optimal weight: 20.0000 chunk 27 optimal weight: 30.0000 chunk 134 optimal weight: 9.9990 chunk 128 optimal weight: 9.9990 overall best weight: 7.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 691 ASN B 229 HIS C 329 ASN C 376 GLN C 410 ASN C 458 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3756 r_free = 0.3756 target = 0.132284 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2957 r_free = 0.2957 target = 0.080643 restraints weight = 26983.848| |-----------------------------------------------------------------------------| r_work (start): 0.2880 rms_B_bonded: 3.92 r_work: 0.2736 rms_B_bonded: 4.34 restraints_weight: 0.5000 r_work (final): 0.2736 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2737 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2737 r_free = 0.2737 target_work(ls_wunit_k1) = 0.068 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2737 r_free = 0.2737 target_work(ls_wunit_k1) = 0.068 | | occupancies: max = 1.00 min = 0.24 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2737 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8802 moved from start: 0.3792 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.063 15074 Z= 0.242 Angle : 0.614 7.008 20532 Z= 0.323 Chirality : 0.045 0.154 2107 Planarity : 0.005 0.119 2728 Dihedral : 7.115 59.882 2053 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 4.85 Ramachandran Plot: Outliers : 0.55 % Allowed : 7.95 % Favored : 91.50 % Rotamer: Outliers : 3.67 % Allowed : 16.90 % Favored : 79.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.80 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.05 (0.19), residues: 1823 helix: -0.90 (0.56), residues: 85 sheet: -0.62 (0.23), residues: 402 loop : -0.71 (0.18), residues: 1336 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 247 HIS 0.005 0.001 HIS A 229 PHE 0.017 0.001 PHE A 372 TYR 0.014 0.002 TYR C 701 ARG 0.006 0.001 ARG R 59 Details of bonding type rmsd hydrogen bonds : bond 0.03936 ( 184) hydrogen bonds : angle 5.98153 ( 366) metal coordination : bond 0.00824 ( 3) SS BOND : bond 0.00259 ( 2) SS BOND : angle 1.21002 ( 4) covalent geometry : bond 0.00570 (15069) covalent geometry : angle 0.61427 (20528) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3646 Ramachandran restraints generated. 1823 Oldfield, 0 Emsley, 1823 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3646 Ramachandran restraints generated. 1823 Oldfield, 0 Emsley, 1823 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 1609 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 116 time to evaluate : 1.571 Fit side-chains revert: symmetry clash REVERT: R 132 ARG cc_start: 0.9119 (OUTLIER) cc_final: 0.8676 (ttt180) REVERT: A 238 ARG cc_start: 0.6974 (mtt180) cc_final: 0.6238 (mtt90) REVERT: A 300 ARG cc_start: 0.7916 (mmt180) cc_final: 0.7449 (mmt180) REVERT: A 684 GLU cc_start: 0.8639 (tm-30) cc_final: 0.7659 (tm-30) REVERT: A 708 SER cc_start: 0.8592 (OUTLIER) cc_final: 0.8362 (p) REVERT: B 311 LYS cc_start: 0.9002 (mmtt) cc_final: 0.8632 (mtpt) REVERT: B 693 LYS cc_start: 0.9295 (mmmm) cc_final: 0.8762 (mmmm) REVERT: C 300 ARG cc_start: 0.8697 (OUTLIER) cc_final: 0.7773 (mmt180) outliers start: 59 outliers final: 46 residues processed: 168 average time/residue: 1.3521 time to fit residues: 249.1780 Evaluate side-chains 159 residues out of total 1609 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 110 time to evaluate : 1.732 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 72 VAL Chi-restraints excluded: chain R residue 115 LEU Chi-restraints excluded: chain R residue 132 ARG Chi-restraints excluded: chain R residue 141 VAL Chi-restraints excluded: chain R residue 145 LEU Chi-restraints excluded: chain R residue 158 VAL Chi-restraints excluded: chain R residue 169 VAL Chi-restraints excluded: chain R residue 229 THR Chi-restraints excluded: chain R residue 230 VAL Chi-restraints excluded: chain R residue 274 VAL Chi-restraints excluded: chain A residue 229 HIS Chi-restraints excluded: chain A residue 235 LEU Chi-restraints excluded: chain A residue 263 SER Chi-restraints excluded: chain A residue 264 THR Chi-restraints excluded: chain A residue 328 ASN Chi-restraints excluded: chain A residue 332 LYS Chi-restraints excluded: chain A residue 338 LEU Chi-restraints excluded: chain A residue 372 PHE Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 708 SER Chi-restraints excluded: chain B residue 238 ARG Chi-restraints excluded: chain B residue 240 ILE Chi-restraints excluded: chain B residue 251 THR Chi-restraints excluded: chain B residue 320 ILE Chi-restraints excluded: chain B residue 323 LYS Chi-restraints excluded: chain B residue 333 THR Chi-restraints excluded: chain B residue 339 THR Chi-restraints excluded: chain B residue 341 THR Chi-restraints excluded: chain B residue 396 CYS Chi-restraints excluded: chain B residue 413 PHE Chi-restraints excluded: chain B residue 494 THR Chi-restraints excluded: chain B residue 588 GLN Chi-restraints excluded: chain B residue 606 VAL Chi-restraints excluded: chain B residue 657 ASP Chi-restraints excluded: chain B residue 666 LYS Chi-restraints excluded: chain B residue 668 ASN Chi-restraints excluded: chain B residue 671 ILE Chi-restraints excluded: chain C residue 264 THR Chi-restraints excluded: chain C residue 300 ARG Chi-restraints excluded: chain C residue 328 ASN Chi-restraints excluded: chain C residue 329 ASN Chi-restraints excluded: chain C residue 332 LYS Chi-restraints excluded: chain C residue 338 LEU Chi-restraints excluded: chain C residue 341 THR Chi-restraints excluded: chain C residue 660 THR Chi-restraints excluded: chain C residue 666 LYS Chi-restraints excluded: chain C residue 668 ASN Chi-restraints excluded: chain C residue 671 ILE Chi-restraints excluded: chain C residue 684 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 181 random chunks: chunk 158 optimal weight: 10.0000 chunk 160 optimal weight: 6.9990 chunk 55 optimal weight: 9.9990 chunk 22 optimal weight: 2.9990 chunk 15 optimal weight: 0.9980 chunk 18 optimal weight: 2.9990 chunk 68 optimal weight: 10.0000 chunk 109 optimal weight: 10.0000 chunk 155 optimal weight: 6.9990 chunk 9 optimal weight: 0.9990 chunk 16 optimal weight: 4.9990 overall best weight: 2.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 651 ASN A 691 ASN B 579 GLN C 329 ASN C 663 ASN C 709 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3799 r_free = 0.3799 target = 0.135138 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3027 r_free = 0.3027 target = 0.083807 restraints weight = 27041.045| |-----------------------------------------------------------------------------| r_work (start): 0.2939 rms_B_bonded: 3.99 r_work: 0.2798 rms_B_bonded: 4.39 restraints_weight: 0.5000 r_work (final): 0.2798 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2799 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2799 r_free = 0.2799 target_work(ls_wunit_k1) = 0.070 | | occupancies: max = 1.00 min = 0.24 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2799 r_free = 0.2799 target_work(ls_wunit_k1) = 0.070 | | occupancies: max = 1.00 min = 0.24 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2799 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8769 moved from start: 0.3899 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.071 15074 Z= 0.116 Angle : 0.542 6.286 20532 Z= 0.281 Chirality : 0.042 0.155 2107 Planarity : 0.005 0.116 2728 Dihedral : 6.615 59.947 2048 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 4.53 Ramachandran Plot: Outliers : 0.55 % Allowed : 7.24 % Favored : 92.21 % Rotamer: Outliers : 3.17 % Allowed : 17.22 % Favored : 79.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.80 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.90 (0.19), residues: 1823 helix: -0.61 (0.58), residues: 85 sheet: -0.51 (0.23), residues: 407 loop : -0.62 (0.18), residues: 1331 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A 247 HIS 0.005 0.001 HIS A 229 PHE 0.015 0.001 PHE A 372 TYR 0.015 0.001 TYR R 213 ARG 0.006 0.000 ARG R 59 Details of bonding type rmsd hydrogen bonds : bond 0.03068 ( 184) hydrogen bonds : angle 5.58345 ( 366) metal coordination : bond 0.00295 ( 3) SS BOND : bond 0.00280 ( 2) SS BOND : angle 1.15475 ( 4) covalent geometry : bond 0.00274 (15069) covalent geometry : angle 0.54199 (20528) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3646 Ramachandran restraints generated. 1823 Oldfield, 0 Emsley, 1823 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3646 Ramachandran restraints generated. 1823 Oldfield, 0 Emsley, 1823 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 1609 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 120 time to evaluate : 1.723 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 208 TYR cc_start: 0.9012 (m-80) cc_final: 0.8729 (m-80) REVERT: A 296 ARG cc_start: 0.5775 (mmp-170) cc_final: 0.5205 (mmt180) REVERT: A 300 ARG cc_start: 0.8003 (mmt180) cc_final: 0.7511 (mmt180) REVERT: A 684 GLU cc_start: 0.8614 (tm-30) cc_final: 0.7760 (tm-30) REVERT: B 311 LYS cc_start: 0.8964 (mmtt) cc_final: 0.8623 (mtpt) REVERT: B 693 LYS cc_start: 0.9261 (mmmm) cc_final: 0.8747 (mmmm) REVERT: C 238 ARG cc_start: 0.8036 (mpt180) cc_final: 0.7636 (tpt170) REVERT: C 300 ARG cc_start: 0.8639 (OUTLIER) cc_final: 0.7758 (mmt180) outliers start: 51 outliers final: 43 residues processed: 165 average time/residue: 1.2751 time to fit residues: 232.2252 Evaluate side-chains 158 residues out of total 1609 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 114 time to evaluate : 1.556 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 72 VAL Chi-restraints excluded: chain R residue 115 LEU Chi-restraints excluded: chain R residue 141 VAL Chi-restraints excluded: chain R residue 145 LEU Chi-restraints excluded: chain R residue 169 VAL Chi-restraints excluded: chain R residue 229 THR Chi-restraints excluded: chain R residue 230 VAL Chi-restraints excluded: chain R residue 274 VAL Chi-restraints excluded: chain A residue 229 HIS Chi-restraints excluded: chain A residue 235 LEU Chi-restraints excluded: chain A residue 263 SER Chi-restraints excluded: chain A residue 328 ASN Chi-restraints excluded: chain A residue 332 LYS Chi-restraints excluded: chain A residue 338 LEU Chi-restraints excluded: chain A residue 404 MET Chi-restraints excluded: chain B residue 238 ARG Chi-restraints excluded: chain B residue 240 ILE Chi-restraints excluded: chain B residue 251 THR Chi-restraints excluded: chain B residue 320 ILE Chi-restraints excluded: chain B residue 322 VAL Chi-restraints excluded: chain B residue 332 LYS Chi-restraints excluded: chain B residue 334 ILE Chi-restraints excluded: chain B residue 339 THR Chi-restraints excluded: chain B residue 341 THR Chi-restraints excluded: chain B residue 396 CYS Chi-restraints excluded: chain B residue 413 PHE Chi-restraints excluded: chain B residue 494 THR Chi-restraints excluded: chain B residue 588 GLN Chi-restraints excluded: chain B residue 606 VAL Chi-restraints excluded: chain B residue 657 ASP Chi-restraints excluded: chain B residue 666 LYS Chi-restraints excluded: chain B residue 668 ASN Chi-restraints excluded: chain B residue 671 ILE Chi-restraints excluded: chain C residue 300 ARG Chi-restraints excluded: chain C residue 322 VAL Chi-restraints excluded: chain C residue 328 ASN Chi-restraints excluded: chain C residue 329 ASN Chi-restraints excluded: chain C residue 332 LYS Chi-restraints excluded: chain C residue 338 LEU Chi-restraints excluded: chain C residue 660 THR Chi-restraints excluded: chain C residue 666 LYS Chi-restraints excluded: chain C residue 668 ASN Chi-restraints excluded: chain C residue 671 ILE Chi-restraints excluded: chain C residue 684 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 181 random chunks: chunk 140 optimal weight: 50.0000 chunk 51 optimal weight: 3.9990 chunk 70 optimal weight: 7.9990 chunk 68 optimal weight: 8.9990 chunk 22 optimal weight: 1.9990 chunk 17 optimal weight: 7.9990 chunk 72 optimal weight: 7.9990 chunk 6 optimal weight: 5.9990 chunk 13 optimal weight: 5.9990 chunk 149 optimal weight: 8.9990 chunk 171 optimal weight: 5.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 691 ASN C 329 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3781 r_free = 0.3781 target = 0.133880 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2992 r_free = 0.2992 target = 0.082163 restraints weight = 27106.412| |-----------------------------------------------------------------------------| r_work (start): 0.2909 rms_B_bonded: 3.97 r_work: 0.2764 rms_B_bonded: 4.47 restraints_weight: 0.5000 r_work (final): 0.2764 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2764 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2764 r_free = 0.2764 target_work(ls_wunit_k1) = 0.068 | | occupancies: max = 1.00 min = 0.24 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2764 r_free = 0.2764 target_work(ls_wunit_k1) = 0.068 | | occupancies: max = 1.00 min = 0.26 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2764 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8797 moved from start: 0.3948 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 15074 Z= 0.169 Angle : 0.567 6.632 20532 Z= 0.295 Chirality : 0.043 0.153 2107 Planarity : 0.005 0.118 2728 Dihedral : 6.503 59.845 2042 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 4.29 Ramachandran Plot: Outliers : 0.55 % Allowed : 7.73 % Favored : 91.72 % Rotamer: Outliers : 3.23 % Allowed : 17.34 % Favored : 79.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.80 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.86 (0.20), residues: 1823 helix: -0.72 (0.56), residues: 85 sheet: -0.48 (0.23), residues: 410 loop : -0.58 (0.18), residues: 1328 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.001 TRP A 247 HIS 0.005 0.001 HIS B 255 PHE 0.018 0.001 PHE A 372 TYR 0.012 0.001 TYR R 213 ARG 0.005 0.000 ARG R 59 Details of bonding type rmsd hydrogen bonds : bond 0.03389 ( 184) hydrogen bonds : angle 5.69540 ( 366) metal coordination : bond 0.00548 ( 3) SS BOND : bond 0.00262 ( 2) SS BOND : angle 1.12276 ( 4) covalent geometry : bond 0.00403 (15069) covalent geometry : angle 0.56700 (20528) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3646 Ramachandran restraints generated. 1823 Oldfield, 0 Emsley, 1823 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3646 Ramachandran restraints generated. 1823 Oldfield, 0 Emsley, 1823 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 1609 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 115 time to evaluate : 1.566 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 132 ARG cc_start: 0.9152 (OUTLIER) cc_final: 0.8688 (ttt180) REVERT: A 296 ARG cc_start: 0.5829 (mmp-170) cc_final: 0.5614 (mmt180) REVERT: A 684 GLU cc_start: 0.8623 (tm-30) cc_final: 0.7771 (tm-30) REVERT: B 311 LYS cc_start: 0.8943 (mmtt) cc_final: 0.8606 (mmmt) REVERT: B 693 LYS cc_start: 0.9299 (mmmm) cc_final: 0.8792 (mmmm) REVERT: C 300 ARG cc_start: 0.8638 (mmt180) cc_final: 0.7750 (mmt180) outliers start: 52 outliers final: 47 residues processed: 161 average time/residue: 1.2925 time to fit residues: 228.9301 Evaluate side-chains 161 residues out of total 1609 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 113 time to evaluate : 1.604 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 72 VAL Chi-restraints excluded: chain R residue 115 LEU Chi-restraints excluded: chain R residue 132 ARG Chi-restraints excluded: chain R residue 141 VAL Chi-restraints excluded: chain R residue 145 LEU Chi-restraints excluded: chain R residue 169 VAL Chi-restraints excluded: chain R residue 229 THR Chi-restraints excluded: chain R residue 230 VAL Chi-restraints excluded: chain R residue 274 VAL Chi-restraints excluded: chain A residue 229 HIS Chi-restraints excluded: chain A residue 235 LEU Chi-restraints excluded: chain A residue 263 SER Chi-restraints excluded: chain A residue 328 ASN Chi-restraints excluded: chain A residue 332 LYS Chi-restraints excluded: chain A residue 338 LEU Chi-restraints excluded: chain A residue 372 PHE Chi-restraints excluded: chain A residue 404 MET Chi-restraints excluded: chain B residue 238 ARG Chi-restraints excluded: chain B residue 251 THR Chi-restraints excluded: chain B residue 312 ARG Chi-restraints excluded: chain B residue 320 ILE Chi-restraints excluded: chain B residue 322 VAL Chi-restraints excluded: chain B residue 332 LYS Chi-restraints excluded: chain B residue 334 ILE Chi-restraints excluded: chain B residue 339 THR Chi-restraints excluded: chain B residue 341 THR Chi-restraints excluded: chain B residue 396 CYS Chi-restraints excluded: chain B residue 413 PHE Chi-restraints excluded: chain B residue 494 THR Chi-restraints excluded: chain B residue 588 GLN Chi-restraints excluded: chain B residue 606 VAL Chi-restraints excluded: chain B residue 657 ASP Chi-restraints excluded: chain B residue 666 LYS Chi-restraints excluded: chain B residue 668 ASN Chi-restraints excluded: chain B residue 671 ILE Chi-restraints excluded: chain B residue 681 VAL Chi-restraints excluded: chain C residue 264 THR Chi-restraints excluded: chain C residue 322 VAL Chi-restraints excluded: chain C residue 328 ASN Chi-restraints excluded: chain C residue 329 ASN Chi-restraints excluded: chain C residue 332 LYS Chi-restraints excluded: chain C residue 338 LEU Chi-restraints excluded: chain C residue 396 CYS Chi-restraints excluded: chain C residue 660 THR Chi-restraints excluded: chain C residue 666 LYS Chi-restraints excluded: chain C residue 668 ASN Chi-restraints excluded: chain C residue 671 ILE Chi-restraints excluded: chain C residue 684 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 181 random chunks: chunk 173 optimal weight: 50.0000 chunk 118 optimal weight: 8.9990 chunk 110 optimal weight: 20.0000 chunk 174 optimal weight: 50.0000 chunk 5 optimal weight: 10.0000 chunk 149 optimal weight: 7.9990 chunk 98 optimal weight: 0.6980 chunk 175 optimal weight: 20.0000 chunk 55 optimal weight: 8.9990 chunk 78 optimal weight: 10.0000 chunk 159 optimal weight: 10.0000 overall best weight: 7.3390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 691 ASN B 704 ASN C 329 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3760 r_free = 0.3760 target = 0.132318 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2963 r_free = 0.2963 target = 0.080589 restraints weight = 26863.196| |-----------------------------------------------------------------------------| r_work (start): 0.2878 rms_B_bonded: 4.03 r_work: 0.2726 rms_B_bonded: 4.43 restraints_weight: 0.5000 r_work (final): 0.2726 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2727 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2727 r_free = 0.2727 target_work(ls_wunit_k1) = 0.067 | | occupancies: max = 1.00 min = 0.26 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2727 r_free = 0.2727 target_work(ls_wunit_k1) = 0.067 | | occupancies: max = 1.00 min = 0.29 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2727 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8818 moved from start: 0.4042 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.063 15074 Z= 0.238 Angle : 0.608 6.883 20532 Z= 0.319 Chirality : 0.045 0.151 2107 Planarity : 0.005 0.122 2728 Dihedral : 6.523 59.177 2040 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 4.50 Ramachandran Plot: Outliers : 0.60 % Allowed : 7.95 % Favored : 91.44 % Rotamer: Outliers : 3.23 % Allowed : 17.40 % Favored : 79.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.80 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.89 (0.19), residues: 1823 helix: -0.95 (0.55), residues: 85 sheet: -0.48 (0.23), residues: 408 loop : -0.60 (0.18), residues: 1330 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.001 TRP A 247 HIS 0.005 0.001 HIS B 255 PHE 0.019 0.001 PHE A 372 TYR 0.014 0.001 TYR C 701 ARG 0.010 0.001 ARG R 59 Details of bonding type rmsd hydrogen bonds : bond 0.03829 ( 184) hydrogen bonds : angle 5.87979 ( 366) metal coordination : bond 0.00773 ( 3) SS BOND : bond 0.00259 ( 2) SS BOND : angle 1.13993 ( 4) covalent geometry : bond 0.00562 (15069) covalent geometry : angle 0.60803 (20528) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3646 Ramachandran restraints generated. 1823 Oldfield, 0 Emsley, 1823 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3646 Ramachandran restraints generated. 1823 Oldfield, 0 Emsley, 1823 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 1609 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 115 time to evaluate : 1.552 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 132 ARG cc_start: 0.9114 (OUTLIER) cc_final: 0.8668 (ttt180) REVERT: A 300 ARG cc_start: 0.7915 (mmt180) cc_final: 0.7504 (mmt180) REVERT: A 684 GLU cc_start: 0.8630 (tm-30) cc_final: 0.7796 (tm-30) REVERT: B 311 LYS cc_start: 0.8863 (mmtt) cc_final: 0.8517 (mmmt) REVERT: B 693 LYS cc_start: 0.9299 (mmmm) cc_final: 0.8945 (mmmm) REVERT: C 300 ARG cc_start: 0.8672 (OUTLIER) cc_final: 0.7752 (mmt180) outliers start: 52 outliers final: 47 residues processed: 159 average time/residue: 1.2941 time to fit residues: 226.5730 Evaluate side-chains 161 residues out of total 1609 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 112 time to evaluate : 1.778 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 72 VAL Chi-restraints excluded: chain R residue 115 LEU Chi-restraints excluded: chain R residue 132 ARG Chi-restraints excluded: chain R residue 141 VAL Chi-restraints excluded: chain R residue 169 VAL Chi-restraints excluded: chain R residue 217 LEU Chi-restraints excluded: chain R residue 229 THR Chi-restraints excluded: chain R residue 230 VAL Chi-restraints excluded: chain R residue 274 VAL Chi-restraints excluded: chain A residue 229 HIS Chi-restraints excluded: chain A residue 263 SER Chi-restraints excluded: chain A residue 264 THR Chi-restraints excluded: chain A residue 328 ASN Chi-restraints excluded: chain A residue 332 LYS Chi-restraints excluded: chain A residue 338 LEU Chi-restraints excluded: chain A residue 372 PHE Chi-restraints excluded: chain A residue 404 MET Chi-restraints excluded: chain B residue 238 ARG Chi-restraints excluded: chain B residue 251 THR Chi-restraints excluded: chain B residue 312 ARG Chi-restraints excluded: chain B residue 320 ILE Chi-restraints excluded: chain B residue 322 VAL Chi-restraints excluded: chain B residue 332 LYS Chi-restraints excluded: chain B residue 334 ILE Chi-restraints excluded: chain B residue 339 THR Chi-restraints excluded: chain B residue 341 THR Chi-restraints excluded: chain B residue 396 CYS Chi-restraints excluded: chain B residue 413 PHE Chi-restraints excluded: chain B residue 494 THR Chi-restraints excluded: chain B residue 588 GLN Chi-restraints excluded: chain B residue 606 VAL Chi-restraints excluded: chain B residue 657 ASP Chi-restraints excluded: chain B residue 666 LYS Chi-restraints excluded: chain B residue 668 ASN Chi-restraints excluded: chain B residue 671 ILE Chi-restraints excluded: chain B residue 681 VAL Chi-restraints excluded: chain C residue 264 THR Chi-restraints excluded: chain C residue 300 ARG Chi-restraints excluded: chain C residue 322 VAL Chi-restraints excluded: chain C residue 328 ASN Chi-restraints excluded: chain C residue 329 ASN Chi-restraints excluded: chain C residue 332 LYS Chi-restraints excluded: chain C residue 338 LEU Chi-restraints excluded: chain C residue 396 CYS Chi-restraints excluded: chain C residue 660 THR Chi-restraints excluded: chain C residue 666 LYS Chi-restraints excluded: chain C residue 668 ASN Chi-restraints excluded: chain C residue 671 ILE Chi-restraints excluded: chain C residue 684 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 181 random chunks: chunk 53 optimal weight: 2.9990 chunk 161 optimal weight: 5.9990 chunk 151 optimal weight: 5.9990 chunk 174 optimal weight: 50.0000 chunk 124 optimal weight: 8.9990 chunk 32 optimal weight: 4.9990 chunk 129 optimal weight: 6.9990 chunk 104 optimal weight: 8.9990 chunk 37 optimal weight: 30.0000 chunk 55 optimal weight: 8.9990 chunk 25 optimal weight: 30.0000 overall best weight: 5.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 329 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3773 r_free = 0.3773 target = 0.133355 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2980 r_free = 0.2980 target = 0.081791 restraints weight = 26791.801| |-----------------------------------------------------------------------------| r_work (start): 0.2897 rms_B_bonded: 3.97 r_work: 0.2746 rms_B_bonded: 4.42 restraints_weight: 0.5000 r_work (final): 0.2746 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2748 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2748 r_free = 0.2748 target_work(ls_wunit_k1) = 0.068 | | occupancies: max = 1.00 min = 0.29 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2748 r_free = 0.2748 target_work(ls_wunit_k1) = 0.068 | | occupancies: max = 1.00 min = 0.29 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2748 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8805 moved from start: 0.4076 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 15074 Z= 0.185 Angle : 0.586 6.722 20532 Z= 0.305 Chirality : 0.044 0.152 2107 Planarity : 0.005 0.122 2728 Dihedral : 6.240 58.935 2038 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 4.57 Ramachandran Plot: Outliers : 0.60 % Allowed : 7.73 % Favored : 91.66 % Rotamer: Outliers : 2.98 % Allowed : 17.96 % Favored : 79.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.80 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.81 (0.20), residues: 1823 helix: -0.86 (0.55), residues: 85 sheet: -0.39 (0.24), residues: 402 loop : -0.56 (0.18), residues: 1336 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.001 TRP A 247 HIS 0.005 0.001 HIS B 255 PHE 0.018 0.001 PHE A 372 TYR 0.013 0.001 TYR R 213 ARG 0.010 0.001 ARG R 59 Details of bonding type rmsd hydrogen bonds : bond 0.03531 ( 184) hydrogen bonds : angle 5.78160 ( 366) metal coordination : bond 0.00574 ( 3) SS BOND : bond 0.00250 ( 2) SS BOND : angle 1.08638 ( 4) covalent geometry : bond 0.00439 (15069) covalent geometry : angle 0.58597 (20528) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3646 Ramachandran restraints generated. 1823 Oldfield, 0 Emsley, 1823 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3646 Ramachandran restraints generated. 1823 Oldfield, 0 Emsley, 1823 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 1609 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 113 time to evaluate : 1.770 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 132 ARG cc_start: 0.9129 (OUTLIER) cc_final: 0.8683 (ttt180) REVERT: R 208 TYR cc_start: 0.8990 (m-80) cc_final: 0.8706 (m-80) REVERT: A 296 ARG cc_start: 0.5942 (mmp-170) cc_final: 0.5371 (mmt180) REVERT: A 300 ARG cc_start: 0.7928 (mmt180) cc_final: 0.7478 (mmt180) REVERT: A 684 GLU cc_start: 0.8659 (tm-30) cc_final: 0.7802 (tm-30) REVERT: B 311 LYS cc_start: 0.8874 (mmtt) cc_final: 0.8531 (mmmt) REVERT: B 693 LYS cc_start: 0.9285 (mmmm) cc_final: 0.8947 (mmmm) REVERT: C 300 ARG cc_start: 0.8662 (OUTLIER) cc_final: 0.7743 (mmt180) outliers start: 48 outliers final: 46 residues processed: 155 average time/residue: 1.3468 time to fit residues: 229.0875 Evaluate side-chains 160 residues out of total 1609 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 112 time to evaluate : 1.525 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 72 VAL Chi-restraints excluded: chain R residue 115 LEU Chi-restraints excluded: chain R residue 132 ARG Chi-restraints excluded: chain R residue 141 VAL Chi-restraints excluded: chain R residue 169 VAL Chi-restraints excluded: chain R residue 229 THR Chi-restraints excluded: chain R residue 230 VAL Chi-restraints excluded: chain R residue 274 VAL Chi-restraints excluded: chain A residue 229 HIS Chi-restraints excluded: chain A residue 263 SER Chi-restraints excluded: chain A residue 264 THR Chi-restraints excluded: chain A residue 328 ASN Chi-restraints excluded: chain A residue 332 LYS Chi-restraints excluded: chain A residue 338 LEU Chi-restraints excluded: chain A residue 372 PHE Chi-restraints excluded: chain A residue 404 MET Chi-restraints excluded: chain B residue 238 ARG Chi-restraints excluded: chain B residue 251 THR Chi-restraints excluded: chain B residue 312 ARG Chi-restraints excluded: chain B residue 320 ILE Chi-restraints excluded: chain B residue 322 VAL Chi-restraints excluded: chain B residue 332 LYS Chi-restraints excluded: chain B residue 334 ILE Chi-restraints excluded: chain B residue 339 THR Chi-restraints excluded: chain B residue 341 THR Chi-restraints excluded: chain B residue 396 CYS Chi-restraints excluded: chain B residue 413 PHE Chi-restraints excluded: chain B residue 494 THR Chi-restraints excluded: chain B residue 588 GLN Chi-restraints excluded: chain B residue 606 VAL Chi-restraints excluded: chain B residue 666 LYS Chi-restraints excluded: chain B residue 668 ASN Chi-restraints excluded: chain B residue 671 ILE Chi-restraints excluded: chain B residue 681 VAL Chi-restraints excluded: chain C residue 264 THR Chi-restraints excluded: chain C residue 300 ARG Chi-restraints excluded: chain C residue 322 VAL Chi-restraints excluded: chain C residue 328 ASN Chi-restraints excluded: chain C residue 329 ASN Chi-restraints excluded: chain C residue 332 LYS Chi-restraints excluded: chain C residue 338 LEU Chi-restraints excluded: chain C residue 396 CYS Chi-restraints excluded: chain C residue 588 GLN Chi-restraints excluded: chain C residue 660 THR Chi-restraints excluded: chain C residue 666 LYS Chi-restraints excluded: chain C residue 668 ASN Chi-restraints excluded: chain C residue 671 ILE Chi-restraints excluded: chain C residue 684 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 181 random chunks: chunk 167 optimal weight: 7.9990 chunk 56 optimal weight: 4.9990 chunk 42 optimal weight: 5.9990 chunk 107 optimal weight: 8.9990 chunk 127 optimal weight: 3.9990 chunk 133 optimal weight: 10.0000 chunk 44 optimal weight: 6.9990 chunk 9 optimal weight: 10.0000 chunk 15 optimal weight: 0.9990 chunk 39 optimal weight: 1.9990 chunk 70 optimal weight: 5.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 691 ASN C 329 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3787 r_free = 0.3787 target = 0.134305 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3013 r_free = 0.3013 target = 0.083035 restraints weight = 26705.119| |-----------------------------------------------------------------------------| r_work (start): 0.2924 rms_B_bonded: 3.85 r_work: 0.2781 rms_B_bonded: 4.29 restraints_weight: 0.5000 r_work (final): 0.2781 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2782 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2782 r_free = 0.2782 target_work(ls_wunit_k1) = 0.069 | | occupancies: max = 1.00 min = 0.29 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2782 r_free = 0.2782 target_work(ls_wunit_k1) = 0.069 | | occupancies: max = 1.00 min = 0.26 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2782 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8782 moved from start: 0.4137 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 15074 Z= 0.140 Angle : 0.566 6.881 20532 Z= 0.293 Chirality : 0.043 0.212 2107 Planarity : 0.005 0.120 2728 Dihedral : 5.978 58.449 2036 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 4.53 Ramachandran Plot: Outliers : 0.55 % Allowed : 7.73 % Favored : 91.72 % Rotamer: Outliers : 2.67 % Allowed : 18.27 % Favored : 79.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.80 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.75 (0.20), residues: 1823 helix: -0.69 (0.57), residues: 85 sheet: -0.25 (0.24), residues: 398 loop : -0.56 (0.18), residues: 1340 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.001 TRP A 247 HIS 0.004 0.001 HIS B 255 PHE 0.017 0.001 PHE A 372 TYR 0.014 0.001 TYR R 213 ARG 0.012 0.001 ARG R 59 Details of bonding type rmsd hydrogen bonds : bond 0.03369 ( 184) hydrogen bonds : angle 5.60220 ( 366) metal coordination : bond 0.00397 ( 3) SS BOND : bond 0.00270 ( 2) SS BOND : angle 1.11913 ( 4) covalent geometry : bond 0.00334 (15069) covalent geometry : angle 0.56545 (20528) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3646 Ramachandran restraints generated. 1823 Oldfield, 0 Emsley, 1823 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3646 Ramachandran restraints generated. 1823 Oldfield, 0 Emsley, 1823 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 1609 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 118 time to evaluate : 1.542 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 132 ARG cc_start: 0.9139 (OUTLIER) cc_final: 0.8676 (ttt180) REVERT: R 208 TYR cc_start: 0.8933 (m-80) cc_final: 0.8674 (m-80) REVERT: A 296 ARG cc_start: 0.5908 (mmp-170) cc_final: 0.5663 (mmt180) REVERT: A 684 GLU cc_start: 0.8626 (tm-30) cc_final: 0.7820 (tm-30) REVERT: B 311 LYS cc_start: 0.8933 (mmtt) cc_final: 0.8625 (mmmt) REVERT: B 693 LYS cc_start: 0.9280 (mmmm) cc_final: 0.8964 (mmmm) REVERT: C 238 ARG cc_start: 0.8118 (mpt180) cc_final: 0.7710 (tpt170) REVERT: C 300 ARG cc_start: 0.8656 (OUTLIER) cc_final: 0.7767 (mmt180) outliers start: 43 outliers final: 42 residues processed: 156 average time/residue: 1.3944 time to fit residues: 238.6147 Evaluate side-chains 160 residues out of total 1609 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 116 time to evaluate : 1.676 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 72 VAL Chi-restraints excluded: chain R residue 115 LEU Chi-restraints excluded: chain R residue 132 ARG Chi-restraints excluded: chain R residue 141 VAL Chi-restraints excluded: chain R residue 169 VAL Chi-restraints excluded: chain R residue 229 THR Chi-restraints excluded: chain R residue 230 VAL Chi-restraints excluded: chain R residue 274 VAL Chi-restraints excluded: chain A residue 229 HIS Chi-restraints excluded: chain A residue 263 SER Chi-restraints excluded: chain A residue 328 ASN Chi-restraints excluded: chain A residue 332 LYS Chi-restraints excluded: chain A residue 338 LEU Chi-restraints excluded: chain A residue 372 PHE Chi-restraints excluded: chain A residue 404 MET Chi-restraints excluded: chain B residue 238 ARG Chi-restraints excluded: chain B residue 312 ARG Chi-restraints excluded: chain B residue 320 ILE Chi-restraints excluded: chain B residue 322 VAL Chi-restraints excluded: chain B residue 332 LYS Chi-restraints excluded: chain B residue 334 ILE Chi-restraints excluded: chain B residue 339 THR Chi-restraints excluded: chain B residue 341 THR Chi-restraints excluded: chain B residue 396 CYS Chi-restraints excluded: chain B residue 413 PHE Chi-restraints excluded: chain B residue 494 THR Chi-restraints excluded: chain B residue 588 GLN Chi-restraints excluded: chain B residue 606 VAL Chi-restraints excluded: chain B residue 666 LYS Chi-restraints excluded: chain B residue 668 ASN Chi-restraints excluded: chain B residue 671 ILE Chi-restraints excluded: chain B residue 681 VAL Chi-restraints excluded: chain C residue 264 THR Chi-restraints excluded: chain C residue 300 ARG Chi-restraints excluded: chain C residue 322 VAL Chi-restraints excluded: chain C residue 328 ASN Chi-restraints excluded: chain C residue 329 ASN Chi-restraints excluded: chain C residue 332 LYS Chi-restraints excluded: chain C residue 338 LEU Chi-restraints excluded: chain C residue 396 CYS Chi-restraints excluded: chain C residue 588 GLN Chi-restraints excluded: chain C residue 660 THR Chi-restraints excluded: chain C residue 666 LYS Chi-restraints excluded: chain C residue 684 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 181 random chunks: chunk 126 optimal weight: 7.9990 chunk 125 optimal weight: 6.9990 chunk 3 optimal weight: 20.0000 chunk 143 optimal weight: 10.0000 chunk 54 optimal weight: 7.9990 chunk 70 optimal weight: 30.0000 chunk 59 optimal weight: 5.9990 chunk 91 optimal weight: 8.9990 chunk 81 optimal weight: 0.6980 chunk 1 optimal weight: 9.9990 chunk 123 optimal weight: 50.0000 overall best weight: 5.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 329 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3768 r_free = 0.3768 target = 0.132881 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2984 r_free = 0.2984 target = 0.081434 restraints weight = 26945.941| |-----------------------------------------------------------------------------| r_work (start): 0.2892 rms_B_bonded: 3.90 r_work: 0.2749 rms_B_bonded: 4.35 restraints_weight: 0.5000 r_work (final): 0.2749 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2750 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2750 r_free = 0.2750 target_work(ls_wunit_k1) = 0.068 | | occupancies: max = 1.00 min = 0.26 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2750 r_free = 0.2750 target_work(ls_wunit_k1) = 0.068 | | occupancies: max = 1.00 min = 0.28 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2750 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8812 moved from start: 0.4160 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 15074 Z= 0.201 Angle : 0.595 6.726 20532 Z= 0.310 Chirality : 0.044 0.197 2107 Planarity : 0.005 0.122 2728 Dihedral : 6.021 58.065 2032 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 4.60 Ramachandran Plot: Outliers : 0.55 % Allowed : 7.95 % Favored : 91.50 % Rotamer: Outliers : 2.67 % Allowed : 18.46 % Favored : 78.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.80 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.78 (0.20), residues: 1823 helix: -0.87 (0.55), residues: 85 sheet: -0.28 (0.24), residues: 402 loop : -0.56 (0.18), residues: 1336 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.001 TRP A 247 HIS 0.004 0.001 HIS B 255 PHE 0.018 0.001 PHE A 372 TYR 0.012 0.001 TYR C 701 ARG 0.012 0.001 ARG R 59 Details of bonding type rmsd hydrogen bonds : bond 0.03714 ( 184) hydrogen bonds : angle 5.76483 ( 366) metal coordination : bond 0.00635 ( 3) SS BOND : bond 0.00248 ( 2) SS BOND : angle 1.11259 ( 4) covalent geometry : bond 0.00474 (15069) covalent geometry : angle 0.59485 (20528) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 14837.30 seconds wall clock time: 256 minutes 23.21 seconds (15383.21 seconds total)