Starting phenix.real_space_refine on Sat Oct 11 11:25:27 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8jif_36311/10_2025/8jif_36311.cif Found real_map, /net/cci-nas-00/data/ceres_data/8jif_36311/10_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 { model { file = "/net/cci-nas-00/data/ceres_data/8jif_36311/10_2025/8jif_36311.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8jif_36311/10_2025/8jif_36311.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8jif_36311/10_2025/8jif_36311.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8jif_36311/10_2025/8jif_36311.map" } resolution = 2.28 write_initial_geo_file = False refinement { macro_cycles = 10 } 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5842/lib/python3.9/site-packages/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: 3.78, per 1000 atoms: 0.26 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: 1.04 Conformation dependent library (CDL) restraints added in 590.4 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 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: 0.50 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: 2.40 Time building geometry restraints manager: 1.45 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: 0.210 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: 0.260 Check model and map are aligned: 0.050 Set scattering table: 0.050 Process input model: 16.290 Find NCS groups from input model: 0.200 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.800 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.890 ------------------------------------------------------------------------------- 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. 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 ARG 0.003 0.000 ARG A 312 TYR 0.030 0.002 TYR B 588E PHE 0.014 0.001 PHE A 315 TRP 0.010 0.001 TRP A 298 HIS 0.005 0.001 HIS A 255 Details of bonding type rmsd covalent geometry : bond 0.00501 (15069) covalent geometry : angle 1.13891 (20528) SS BOND : bond 0.00563 ( 2) SS BOND : angle 1.35133 ( 4) hydrogen bonds : bond 0.21193 ( 184) hydrogen bonds : angle 8.86265 ( 366) metal coordination : bond 0.02721 ( 3) *********************** 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 : 0.535 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: 0.6665 time to fit residues: 285.5834 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 : 0.562 ------------------------------------------------------------------------------- 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 98 optimal weight: 8.9990 chunk 107 optimal weight: 20.0000 chunk 10 optimal weight: 40.0000 chunk 66 optimal weight: 5.9990 chunk 130 optimal weight: 30.0000 chunk 124 optimal weight: 9.9990 chunk 103 optimal weight: 3.9990 chunk 77 optimal weight: 7.9990 chunk 122 optimal weight: 50.0000 chunk 91 optimal weight: 6.9990 chunk 149 optimal weight: 0.9990 overall best weight: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 127 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 403 GLN C 419 ASN C 430 GLN C 457 ASN C 495 GLN C 663 ASN ** C 678 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 735 ASN Total number of N/Q/H flips: 27 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3826 r_free = 0.3826 target = 0.137008 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3097 r_free = 0.3097 target = 0.088056 restraints weight = 27669.522| |-----------------------------------------------------------------------------| r_work (start): 0.3011 rms_B_bonded: 3.54 r_work: 0.2872 rms_B_bonded: 4.14 restraints_weight: 0.5000 r_work (final): 0.2872 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2874 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2874 r_free = 0.2874 target_work(ls_wunit_k1) = 0.076 | | occupancies: max = 1.00 min = 0.31 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2873 r_free = 0.2873 target_work(ls_wunit_k1) = 0.075 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2873 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8709 moved from start: 0.3011 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 15074 Z= 0.194 Angle : 0.656 8.829 20532 Z= 0.348 Chirality : 0.046 0.173 2107 Planarity : 0.006 0.103 2728 Dihedral : 10.151 81.549 2170 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 5.83 Ramachandran Plot: Outliers : 0.77 % Allowed : 7.19 % Favored : 92.05 % Rotamer: Outliers : 5.84 % Allowed : 15.23 % Favored : 78.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.80 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.51 (0.19), residues: 1823 helix: -1.12 (0.54), residues: 85 sheet: -1.21 (0.23), residues: 405 loop : -0.95 (0.17), residues: 1333 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C 296 TYR 0.016 0.002 TYR C 701 PHE 0.013 0.001 PHE C 535 TRP 0.021 0.002 TRP A 306 HIS 0.005 0.001 HIS B 255 Details of bonding type rmsd covalent geometry : bond 0.00449 (15069) covalent geometry : angle 0.65557 (20528) SS BOND : bond 0.00284 ( 2) SS BOND : angle 1.29104 ( 4) hydrogen bonds : bond 0.03983 ( 184) hydrogen bonds : angle 6.09350 ( 366) metal coordination : bond 0.00658 ( 3) *********************** 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 229 residues out of total 1609 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 135 time to evaluate : 0.582 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 238 ARG cc_start: 0.7017 (mtt180) cc_final: 0.6313 (mtt90) REVERT: A 300 ARG cc_start: 0.8037 (mmt180) cc_final: 0.7509 (mmt180) REVERT: A 312 ARG cc_start: 0.7781 (ptp-110) cc_final: 0.7396 (ptp90) REVERT: A 588 ASP cc_start: 0.8474 (OUTLIER) cc_final: 0.8272 (m-30) REVERT: A 684 GLU cc_start: 0.8307 (tm-30) cc_final: 0.7632 (tm-30) REVERT: B 518 MET cc_start: 0.9209 (mmt) cc_final: 0.8975 (tpp) REVERT: B 687 LEU cc_start: 0.9061 (OUTLIER) cc_final: 0.8770 (mp) REVERT: C 233 GLN cc_start: 0.2711 (OUTLIER) cc_final: 0.2382 (pm20) REVERT: C 300 ARG cc_start: 0.8631 (OUTLIER) cc_final: 0.7848 (mmt180) outliers start: 94 outliers final: 62 residues processed: 217 average time/residue: 0.6269 time to fit residues: 149.4211 Evaluate side-chains 182 residues out of total 1609 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 116 time to evaluate : 0.611 ------------------------------------------------------------------------------- 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 251 THR 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 413 PHE Chi-restraints excluded: chain B residue 517 LEU 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 B residue 687 LEU Chi-restraints excluded: chain C residue 233 GLN Chi-restraints excluded: chain C residue 251 THR Chi-restraints excluded: chain C residue 300 ARG 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 588 GLN 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 Chi-restraints excluded: chain C residue 684 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 181 random chunks: chunk 73 optimal weight: 7.9990 chunk 61 optimal weight: 9.9990 chunk 40 optimal weight: 6.9990 chunk 36 optimal weight: 40.0000 chunk 165 optimal weight: 8.9990 chunk 168 optimal weight: 6.9990 chunk 10 optimal weight: 9.9990 chunk 95 optimal weight: 0.0020 chunk 79 optimal weight: 20.0000 chunk 65 optimal weight: 20.0000 chunk 16 optimal weight: 0.9990 overall best weight: 4.5996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 86 GLN R 133 HIS R 187 HIS R 248 ASN A 456 GLN B 321 GLN B 343 GLN C 329 ASN C 452 ASN C 663 ASN C 678 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3789 r_free = 0.3789 target = 0.134925 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3012 r_free = 0.3012 target = 0.083674 restraints weight = 27114.901| |-----------------------------------------------------------------------------| r_work (start): 0.2940 rms_B_bonded: 3.96 r_work: 0.2799 rms_B_bonded: 4.32 restraints_weight: 0.5000 r_work (final): 0.2799 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2799 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2799 r_free = 0.2799 target_work(ls_wunit_k1) = 0.072 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2799 r_free = 0.2799 target_work(ls_wunit_k1) = 0.072 | | occupancies: max = 1.00 min = 0.16 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2799 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8734 moved from start: 0.3385 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= 0.170 Angle : 0.589 6.977 20532 Z= 0.310 Chirality : 0.044 0.197 2107 Planarity : 0.005 0.107 2728 Dihedral : 8.145 59.444 2090 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 5.10 Ramachandran Plot: Outliers : 0.66 % Allowed : 7.24 % Favored : 92.10 % Rotamer: Outliers : 4.04 % Allowed : 16.84 % Favored : 79.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.80 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.18 (0.19), residues: 1823 helix: -0.71 (0.58), residues: 85 sheet: -0.92 (0.23), residues: 410 loop : -0.74 (0.17), residues: 1328 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG R 59 TYR 0.013 0.001 TYR R 213 PHE 0.014 0.001 PHE A 372 TRP 0.012 0.001 TRP A 509 HIS 0.008 0.001 HIS R 187 Details of bonding type rmsd covalent geometry : bond 0.00390 (15069) covalent geometry : angle 0.58836 (20528) SS BOND : bond 0.00276 ( 2) SS BOND : angle 1.18916 ( 4) hydrogen bonds : bond 0.03729 ( 184) hydrogen bonds : angle 5.88574 ( 366) metal coordination : bond 0.00513 ( 3) *********************** 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 183 residues out of total 1609 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 118 time to evaluate : 0.576 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 238 ARG cc_start: 0.6931 (mtt180) cc_final: 0.6279 (mtt90) REVERT: A 296 ARG cc_start: 0.5872 (mmp-170) cc_final: 0.5580 (mmt180) REVERT: A 312 ARG cc_start: 0.8334 (ptp-110) cc_final: 0.7976 (ptp90) REVERT: A 684 GLU cc_start: 0.8450 (tm-30) cc_final: 0.7676 (tm-30) REVERT: C 300 ARG cc_start: 0.8556 (mmt180) cc_final: 0.7824 (mmt180) outliers start: 65 outliers final: 45 residues processed: 178 average time/residue: 0.6768 time to fit residues: 131.6475 Evaluate side-chains 155 residues out of total 1609 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 110 time to evaluate : 0.552 ------------------------------------------------------------------------------- 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 191 THR 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 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 238 ARG Chi-restraints excluded: chain B residue 240 ILE 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 333 THR Chi-restraints excluded: chain B residue 339 THR Chi-restraints excluded: chain B residue 341 THR Chi-restraints excluded: chain B residue 413 PHE Chi-restraints excluded: chain B residue 494 THR 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 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 Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 181 random chunks: chunk 23 optimal weight: 20.0000 chunk 166 optimal weight: 3.9990 chunk 106 optimal weight: 6.9990 chunk 153 optimal weight: 10.0000 chunk 154 optimal weight: 5.9990 chunk 104 optimal weight: 10.0000 chunk 134 optimal weight: 10.0000 chunk 84 optimal weight: 8.9990 chunk 127 optimal weight: 0.5980 chunk 175 optimal weight: 20.0000 chunk 78 optimal weight: 50.0000 overall best weight: 5.3188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 329 ASN C 376 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3779 r_free = 0.3779 target = 0.134141 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.2996 r_free = 0.2996 target = 0.082777 restraints weight = 26934.629| |-----------------------------------------------------------------------------| r_work (start): 0.2920 rms_B_bonded: 3.96 r_work: 0.2775 rms_B_bonded: 4.37 restraints_weight: 0.5000 r_work (final): 0.2775 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2775 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2775 r_free = 0.2775 target_work(ls_wunit_k1) = 0.070 | | occupancies: max = 1.00 min = 0.16 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2775 r_free = 0.2775 target_work(ls_wunit_k1) = 0.070 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2775 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8774 moved from start: 0.3619 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 15074 Z= 0.184 Angle : 0.590 7.467 20532 Z= 0.308 Chirality : 0.044 0.157 2107 Planarity : 0.005 0.112 2728 Dihedral : 7.355 59.694 2065 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 4.50 Ramachandran Plot: Outliers : 0.66 % Allowed : 7.30 % Favored : 92.05 % Rotamer: Outliers : 3.67 % Allowed : 17.03 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.07 (0.19), residues: 1823 helix: -0.72 (0.58), residues: 85 sheet: -0.78 (0.23), residues: 410 loop : -0.69 (0.18), residues: 1328 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG R 32 TYR 0.012 0.001 TYR C 701 PHE 0.016 0.001 PHE A 372 TRP 0.014 0.001 TRP A 247 HIS 0.006 0.001 HIS A 229 Details of bonding type rmsd covalent geometry : bond 0.00431 (15069) covalent geometry : angle 0.59009 (20528) SS BOND : bond 0.00282 ( 2) SS BOND : angle 1.19794 ( 4) hydrogen bonds : bond 0.03625 ( 184) hydrogen bonds : angle 5.84324 ( 366) metal coordination : bond 0.00571 ( 3) *********************** 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 176 residues out of total 1609 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 117 time to evaluate : 0.501 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 132 ARG cc_start: 0.9140 (OUTLIER) cc_final: 0.8718 (ttt180) REVERT: A 238 ARG cc_start: 0.6912 (mtt180) cc_final: 0.6276 (mtt90) REVERT: A 300 ARG cc_start: 0.7942 (mmt180) cc_final: 0.7677 (mmt180) REVERT: A 312 ARG cc_start: 0.8537 (ptp-110) cc_final: 0.8181 (ptp90) REVERT: A 684 GLU cc_start: 0.8563 (tm-30) cc_final: 0.7617 (tm-30) REVERT: B 311 LYS cc_start: 0.9020 (mmtt) cc_final: 0.8653 (mmpt) REVERT: C 300 ARG cc_start: 0.8540 (mmt180) cc_final: 0.7854 (mmt180) outliers start: 59 outliers final: 46 residues processed: 169 average time/residue: 0.6769 time to fit residues: 124.7701 Evaluate side-chains 160 residues out of total 1609 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 113 time to evaluate : 0.569 ------------------------------------------------------------------------------- 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 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 588 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 320 ILE Chi-restraints excluded: chain B residue 323 LYS 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 396 CYS Chi-restraints excluded: chain B residue 413 PHE Chi-restraints excluded: chain B residue 494 THR 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 338 LEU Chi-restraints excluded: chain C residue 341 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 Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 181 random chunks: chunk 29 optimal weight: 20.0000 chunk 36 optimal weight: 30.0000 chunk 106 optimal weight: 5.9990 chunk 33 optimal weight: 9.9990 chunk 17 optimal weight: 0.0470 chunk 76 optimal weight: 8.9990 chunk 180 optimal weight: 6.9990 chunk 158 optimal weight: 5.9990 chunk 120 optimal weight: 20.0000 chunk 118 optimal weight: 4.9990 chunk 35 optimal weight: 20.0000 overall best weight: 4.8086 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 430 GLN A 691 ASN B 229 HIS B 579 GLN C 329 ASN C 410 ASN C 458 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3783 r_free = 0.3783 target = 0.134246 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3004 r_free = 0.3004 target = 0.082657 restraints weight = 26851.444| |-----------------------------------------------------------------------------| r_work (start): 0.2917 rms_B_bonded: 4.00 r_work: 0.2773 rms_B_bonded: 4.43 restraints_weight: 0.5000 r_work (final): 0.2773 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2773 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2773 r_free = 0.2773 target_work(ls_wunit_k1) = 0.069 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2773 r_free = 0.2773 target_work(ls_wunit_k1) = 0.069 | | occupancies: max = 1.00 min = 0.24 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2773 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8785 moved from start: 0.3757 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= 0.168 Angle : 0.572 6.669 20532 Z= 0.299 Chirality : 0.043 0.155 2107 Planarity : 0.005 0.115 2728 Dihedral : 6.968 59.682 2053 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 4.29 Ramachandran Plot: Outliers : 0.55 % Allowed : 7.57 % Favored : 91.88 % Rotamer: Outliers : 3.36 % Allowed : 16.97 % Favored : 79.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.80 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.99 (0.19), residues: 1823 helix: -0.70 (0.58), residues: 85 sheet: -0.69 (0.23), residues: 410 loop : -0.64 (0.18), residues: 1328 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG R 59 TYR 0.014 0.001 TYR R 213 PHE 0.015 0.001 PHE A 372 TRP 0.016 0.001 TRP A 247 HIS 0.005 0.001 HIS A 229 Details of bonding type rmsd covalent geometry : bond 0.00397 (15069) covalent geometry : angle 0.57168 (20528) SS BOND : bond 0.00277 ( 2) SS BOND : angle 1.13332 ( 4) hydrogen bonds : bond 0.03492 ( 184) hydrogen bonds : angle 5.75185 ( 366) metal coordination : bond 0.00524 ( 3) *********************** 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 173 residues out of total 1609 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 119 time to evaluate : 0.578 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 132 ARG cc_start: 0.9152 (OUTLIER) cc_final: 0.8716 (ttt180) REVERT: R 208 TYR cc_start: 0.9045 (m-80) cc_final: 0.8773 (m-80) REVERT: A 238 ARG cc_start: 0.6893 (mtt180) cc_final: 0.6232 (mtt90) REVERT: A 296 ARG cc_start: 0.5821 (mmp-170) cc_final: 0.5154 (mmt180) REVERT: A 300 ARG cc_start: 0.7976 (mmt180) cc_final: 0.7476 (mmt180) REVERT: A 312 ARG cc_start: 0.8614 (ptp-110) cc_final: 0.8235 (ptp90) REVERT: A 684 GLU cc_start: 0.8584 (tm-30) cc_final: 0.7573 (tm-30) REVERT: B 311 LYS cc_start: 0.8989 (mmtt) cc_final: 0.8632 (mtpt) REVERT: C 300 ARG cc_start: 0.8532 (mmt180) cc_final: 0.7806 (mmt180) REVERT: C 707 LYS cc_start: 0.5592 (tptt) cc_final: 0.5289 (tptt) outliers start: 54 outliers final: 45 residues processed: 168 average time/residue: 0.6985 time to fit residues: 128.0830 Evaluate side-chains 162 residues out of total 1609 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 116 time to evaluate : 0.435 ------------------------------------------------------------------------------- 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 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 312 ARG Chi-restraints excluded: chain B residue 320 ILE Chi-restraints excluded: chain B residue 322 VAL 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 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 494 THR 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 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 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 181 random chunks: chunk 110 optimal weight: 10.0000 chunk 91 optimal weight: 20.0000 chunk 134 optimal weight: 10.0000 chunk 106 optimal weight: 10.0000 chunk 67 optimal weight: 2.9990 chunk 114 optimal weight: 7.9990 chunk 50 optimal weight: 10.0000 chunk 117 optimal weight: 8.9990 chunk 108 optimal weight: 6.9990 chunk 121 optimal weight: 50.0000 chunk 36 optimal weight: 0.9980 overall best weight: 5.5988 ------------------------------------------------------------------------------- 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 C 329 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3772 r_free = 0.3772 target = 0.133463 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2985 r_free = 0.2985 target = 0.081696 restraints weight = 26964.765| |-----------------------------------------------------------------------------| r_work (start): 0.2905 rms_B_bonded: 3.90 r_work: 0.2761 rms_B_bonded: 4.35 restraints_weight: 0.5000 r_work (final): 0.2761 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2762 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2762 r_free = 0.2762 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 = 0.2762 r_free = 0.2762 target_work(ls_wunit_k1) = 0.068 | | occupancies: max = 1.00 min = 0.24 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2762 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8793 moved from start: 0.3853 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 15074 Z= 0.190 Angle : 0.580 6.719 20532 Z= 0.303 Chirality : 0.044 0.156 2107 Planarity : 0.005 0.118 2728 Dihedral : 6.809 59.510 2046 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 4.29 Ramachandran Plot: Outliers : 0.55 % Allowed : 7.46 % Favored : 91.99 % Rotamer: Outliers : 3.67 % Allowed : 16.59 % Favored : 79.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.80 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.95 (0.19), residues: 1823 helix: -0.77 (0.57), residues: 85 sheet: -0.60 (0.23), residues: 410 loop : -0.63 (0.18), residues: 1328 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG R 59 TYR 0.012 0.001 TYR R 213 PHE 0.017 0.001 PHE A 372 TRP 0.022 0.001 TRP A 247 HIS 0.005 0.001 HIS R 142 Details of bonding type rmsd covalent geometry : bond 0.00448 (15069) covalent geometry : angle 0.57950 (20528) SS BOND : bond 0.00272 ( 2) SS BOND : angle 1.13950 ( 4) hydrogen bonds : bond 0.03560 ( 184) hydrogen bonds : angle 5.79677 ( 366) metal coordination : bond 0.00608 ( 3) *********************** 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 174 residues out of total 1609 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 115 time to evaluate : 0.557 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 132 ARG cc_start: 0.9147 (OUTLIER) cc_final: 0.8705 (ttt180) REVERT: A 296 ARG cc_start: 0.5838 (mmp-170) cc_final: 0.5540 (mmt180) REVERT: A 312 ARG cc_start: 0.8638 (ptp-110) cc_final: 0.8146 (ptp90) REVERT: A 684 GLU cc_start: 0.8632 (tm-30) cc_final: 0.7714 (tm-30) REVERT: B 311 LYS cc_start: 0.8961 (mmtt) cc_final: 0.8611 (mtpt) REVERT: B 693 LYS cc_start: 0.9398 (mmmm) cc_final: 0.8894 (mmmm) REVERT: C 300 ARG cc_start: 0.8476 (mmt180) cc_final: 0.7742 (mmt180) REVERT: C 707 LYS cc_start: 0.5377 (tptt) cc_final: 0.5158 (tptt) outliers start: 59 outliers final: 47 residues processed: 167 average time/residue: 0.6528 time to fit residues: 119.3919 Evaluate side-chains 162 residues out of total 1609 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 114 time to evaluate : 0.566 ------------------------------------------------------------------------------- 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 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 A residue 588 THR 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 326 THR Chi-restraints excluded: chain B residue 331 VAL Chi-restraints excluded: chain B residue 332 LYS 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 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 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 22 optimal weight: 4.9990 chunk 179 optimal weight: 0.9980 chunk 127 optimal weight: 7.9990 chunk 134 optimal weight: 10.0000 chunk 117 optimal weight: 6.9990 chunk 94 optimal weight: 6.9990 chunk 43 optimal weight: 8.9990 chunk 2 optimal weight: 4.9990 chunk 97 optimal weight: 20.0000 chunk 162 optimal weight: 10.0000 chunk 149 optimal weight: 7.9990 overall best weight: 4.9988 ------------------------------------------------------------------------------- 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 = 0.3776 r_free = 0.3776 target = 0.133638 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2989 r_free = 0.2989 target = 0.081865 restraints weight = 26763.705| |-----------------------------------------------------------------------------| r_work (start): 0.2908 rms_B_bonded: 3.89 r_work: 0.2768 rms_B_bonded: 4.23 restraints_weight: 0.5000 r_work (final): 0.2768 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2768 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2768 r_free = 0.2768 target_work(ls_wunit_k1) = 0.069 | | occupancies: max = 1.00 min = 0.24 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2768 r_free = 0.2768 target_work(ls_wunit_k1) = 0.069 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2768 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8777 moved from start: 0.3929 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= 0.174 Angle : 0.570 6.614 20532 Z= 0.298 Chirality : 0.043 0.153 2107 Planarity : 0.005 0.119 2728 Dihedral : 6.433 58.956 2040 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 4.29 Ramachandran Plot: Outliers : 0.55 % Allowed : 7.41 % Favored : 92.05 % Rotamer: Outliers : 3.36 % Allowed : 16.78 % Favored : 79.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.80 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.89 (0.19), residues: 1823 helix: -0.76 (0.56), residues: 85 sheet: -0.52 (0.23), residues: 410 loop : -0.60 (0.18), residues: 1328 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG R 59 TYR 0.012 0.001 TYR R 213 PHE 0.016 0.001 PHE A 372 TRP 0.022 0.001 TRP A 247 HIS 0.005 0.001 HIS B 255 Details of bonding type rmsd covalent geometry : bond 0.00410 (15069) covalent geometry : angle 0.56991 (20528) SS BOND : bond 0.00271 ( 2) SS BOND : angle 1.14123 ( 4) hydrogen bonds : bond 0.03481 ( 184) hydrogen bonds : angle 5.74524 ( 366) metal coordination : bond 0.00531 ( 3) *********************** 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 170 residues out of total 1609 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 116 time to evaluate : 0.572 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 132 ARG cc_start: 0.9139 (OUTLIER) cc_final: 0.8695 (ttt180) REVERT: R 208 TYR cc_start: 0.9006 (m-80) cc_final: 0.8710 (m-80) REVERT: A 300 ARG cc_start: 0.7901 (mmt180) cc_final: 0.7683 (mmt180) REVERT: A 312 ARG cc_start: 0.8588 (ptp-110) cc_final: 0.8114 (ptp90) REVERT: A 684 GLU cc_start: 0.8626 (tm-30) cc_final: 0.7715 (tm-30) REVERT: B 311 LYS cc_start: 0.9005 (mmtt) cc_final: 0.8693 (mmmt) REVERT: C 300 ARG cc_start: 0.8498 (mmt180) cc_final: 0.7787 (mmt180) outliers start: 54 outliers final: 50 residues processed: 162 average time/residue: 0.6677 time to fit residues: 118.3684 Evaluate side-chains 163 residues out of total 1609 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 112 time to evaluate : 0.480 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 72 VAL Chi-restraints excluded: chain R residue 86 GLN 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 235 LEU 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 A residue 588 THR 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 326 THR Chi-restraints excluded: chain B residue 331 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 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 333 THR 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 14 optimal weight: 5.9990 chunk 60 optimal weight: 7.9990 chunk 106 optimal weight: 6.9990 chunk 30 optimal weight: 10.0000 chunk 155 optimal weight: 4.9990 chunk 126 optimal weight: 20.0000 chunk 0 optimal weight: 10.0000 chunk 28 optimal weight: 30.0000 chunk 109 optimal weight: 9.9990 chunk 91 optimal weight: 20.0000 chunk 27 optimal weight: 9.9990 overall best weight: 7.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 253 ASN A 691 ASN B 704 ASN C 329 ASN C 709 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3758 r_free = 0.3758 target = 0.132390 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.2958 r_free = 0.2958 target = 0.080307 restraints weight = 26900.338| |-----------------------------------------------------------------------------| r_work (start): 0.2879 rms_B_bonded: 4.01 r_work: 0.2733 rms_B_bonded: 4.40 restraints_weight: 0.5000 r_work (final): 0.2733 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2733 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2733 r_free = 0.2733 target_work(ls_wunit_k1) = 0.067 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2733 r_free = 0.2733 target_work(ls_wunit_k1) = 0.067 | | occupancies: max = 1.00 min = 0.24 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2733 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8824 moved from start: 0.4003 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.062 15074 Z= 0.234 Angle : 0.607 6.880 20532 Z= 0.318 Chirality : 0.045 0.151 2107 Planarity : 0.005 0.122 2728 Dihedral : 6.505 59.362 2040 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 4.67 Ramachandran Plot: Outliers : 0.60 % Allowed : 7.95 % Favored : 91.44 % Rotamer: Outliers : 3.23 % Allowed : 17.22 % Favored : 79.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.80 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.91 (0.19), residues: 1823 helix: -0.95 (0.55), residues: 85 sheet: -0.51 (0.23), residues: 408 loop : -0.61 (0.18), residues: 1330 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG R 59 TYR 0.014 0.001 TYR C 701 PHE 0.017 0.001 PHE A 372 TRP 0.027 0.001 TRP A 247 HIS 0.005 0.001 HIS B 255 Details of bonding type rmsd covalent geometry : bond 0.00551 (15069) covalent geometry : angle 0.60660 (20528) SS BOND : bond 0.00253 ( 2) SS BOND : angle 1.14354 ( 4) hydrogen bonds : bond 0.03846 ( 184) hydrogen bonds : angle 5.91379 ( 366) metal coordination : bond 0.00762 ( 3) *********************** 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 164 residues out of total 1609 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 112 time to evaluate : 0.553 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 132 ARG cc_start: 0.9109 (OUTLIER) cc_final: 0.8678 (ttt180) REVERT: A 296 ARG cc_start: 0.5842 (mmp-170) cc_final: 0.5163 (mmt180) REVERT: A 300 ARG cc_start: 0.7981 (mmt180) cc_final: 0.7510 (mmt180) REVERT: A 312 ARG cc_start: 0.8658 (ptp-110) cc_final: 0.8160 (ptp90) REVERT: A 684 GLU cc_start: 0.8669 (tm-30) cc_final: 0.7742 (tm-30) REVERT: B 311 LYS cc_start: 0.8996 (mmtt) cc_final: 0.8669 (mmmt) REVERT: B 693 LYS cc_start: 0.9460 (mmmm) cc_final: 0.8966 (mmmm) REVERT: C 300 ARG cc_start: 0.8525 (mmt180) cc_final: 0.7752 (mmt180) outliers start: 52 outliers final: 48 residues processed: 159 average time/residue: 0.6776 time to fit residues: 117.6949 Evaluate side-chains 160 residues out of total 1609 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 111 time to evaluate : 0.577 ------------------------------------------------------------------------------- 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 235 LEU 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 A residue 588 THR 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 326 THR Chi-restraints excluded: chain B residue 331 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 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 333 THR 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 35 optimal weight: 50.0000 chunk 21 optimal weight: 5.9990 chunk 150 optimal weight: 8.9990 chunk 104 optimal weight: 10.0000 chunk 153 optimal weight: 6.9990 chunk 154 optimal weight: 4.9990 chunk 85 optimal weight: 20.0000 chunk 34 optimal weight: 8.9990 chunk 5 optimal weight: 5.9990 chunk 33 optimal weight: 0.9990 chunk 71 optimal weight: 9.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 329 ASN C 709 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3775 r_free = 0.3775 target = 0.133312 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.2991 r_free = 0.2991 target = 0.081821 restraints weight = 27004.050| |-----------------------------------------------------------------------------| r_work (start): 0.2902 rms_B_bonded: 3.90 r_work: 0.2758 rms_B_bonded: 4.38 restraints_weight: 0.5000 r_work (final): 0.2758 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2758 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2758 r_free = 0.2758 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 = 0.2758 r_free = 0.2758 target_work(ls_wunit_k1) = 0.068 | | occupancies: max = 1.00 min = 0.24 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2758 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8804 moved from start: 0.4052 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 15074 Z= 0.174 Angle : 0.576 6.720 20532 Z= 0.300 Chirality : 0.043 0.153 2107 Planarity : 0.005 0.121 2728 Dihedral : 6.148 58.617 2036 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 4.39 Ramachandran Plot: Outliers : 0.60 % Allowed : 7.41 % Favored : 91.99 % Rotamer: Outliers : 2.98 % Allowed : 17.46 % Favored : 79.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.80 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.81 (0.20), residues: 1823 helix: -0.82 (0.56), residues: 85 sheet: -0.44 (0.24), residues: 404 loop : -0.54 (0.18), residues: 1334 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG R 59 TYR 0.013 0.001 TYR R 213 PHE 0.016 0.001 PHE A 372 TRP 0.025 0.001 TRP A 247 HIS 0.005 0.001 HIS B 255 Details of bonding type rmsd covalent geometry : bond 0.00411 (15069) covalent geometry : angle 0.57575 (20528) SS BOND : bond 0.00270 ( 2) SS BOND : angle 1.12177 ( 4) hydrogen bonds : bond 0.03485 ( 184) hydrogen bonds : angle 5.74089 ( 366) metal coordination : bond 0.00564 ( 3) *********************** 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 : 0.563 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 132 ARG cc_start: 0.9131 (OUTLIER) cc_final: 0.8689 (ttt180) REVERT: R 208 TYR cc_start: 0.8911 (m-80) cc_final: 0.8630 (m-80) REVERT: A 296 ARG cc_start: 0.5851 (mmp-170) cc_final: 0.5179 (mmt180) REVERT: A 300 ARG cc_start: 0.7998 (mmt180) cc_final: 0.7501 (mmt180) REVERT: A 312 ARG cc_start: 0.8668 (ptp-110) cc_final: 0.8153 (ptp90) REVERT: A 684 GLU cc_start: 0.8678 (tm-30) cc_final: 0.7746 (tm-30) REVERT: B 311 LYS cc_start: 0.8972 (mmtt) cc_final: 0.8655 (mmmt) REVERT: B 693 LYS cc_start: 0.9451 (mmmm) cc_final: 0.9026 (mmmm) REVERT: C 300 ARG cc_start: 0.8530 (mmt180) cc_final: 0.7774 (mmt180) outliers start: 48 outliers final: 45 residues processed: 156 average time/residue: 0.6429 time to fit residues: 109.7683 Evaluate side-chains 157 residues out of total 1609 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 111 time to evaluate : 0.536 ------------------------------------------------------------------------------- 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 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 A residue 588 THR 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 331 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 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 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 181 random chunks: chunk 93 optimal weight: 9.9990 chunk 43 optimal weight: 10.0000 chunk 47 optimal weight: 5.9990 chunk 81 optimal weight: 10.0000 chunk 16 optimal weight: 4.9990 chunk 149 optimal weight: 10.0000 chunk 143 optimal weight: 5.9990 chunk 17 optimal weight: 9.9990 chunk 0 optimal weight: 10.0000 chunk 10 optimal weight: 8.9990 chunk 30 optimal weight: 10.0000 overall best weight: 7.1990 ------------------------------------------------------------------------------- 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 = 0.3760 r_free = 0.3760 target = 0.132291 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.2967 r_free = 0.2967 target = 0.080662 restraints weight = 26906.207| |-----------------------------------------------------------------------------| r_work (start): 0.2876 rms_B_bonded: 3.87 r_work: 0.2734 rms_B_bonded: 4.27 restraints_weight: 0.5000 r_work (final): 0.2734 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2735 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2735 r_free = 0.2735 target_work(ls_wunit_k1) = 0.067 | | occupancies: max = 1.00 min = 0.24 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2735 r_free = 0.2735 target_work(ls_wunit_k1) = 0.067 | | occupancies: max = 1.00 min = 0.24 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2735 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8819 moved from start: 0.4122 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.058 15074 Z= 0.235 Angle : 0.613 7.022 20532 Z= 0.320 Chirality : 0.045 0.196 2107 Planarity : 0.005 0.123 2728 Dihedral : 6.125 58.477 2032 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 4.50 Ramachandran Plot: Outliers : 0.55 % Allowed : 8.23 % Favored : 91.22 % Rotamer: Outliers : 2.80 % Allowed : 17.71 % Favored : 79.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.80 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.86 (0.19), residues: 1823 helix: -0.97 (0.55), residues: 85 sheet: -0.43 (0.24), residues: 404 loop : -0.58 (0.18), residues: 1334 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG R 59 TYR 0.013 0.001 TYR C 701 PHE 0.017 0.001 PHE A 372 TRP 0.025 0.001 TRP A 247 HIS 0.005 0.001 HIS B 255 Details of bonding type rmsd covalent geometry : bond 0.00552 (15069) covalent geometry : angle 0.61299 (20528) SS BOND : bond 0.00271 ( 2) SS BOND : angle 1.13018 ( 4) hydrogen bonds : bond 0.03997 ( 184) hydrogen bonds : angle 5.88635 ( 366) metal coordination : bond 0.00753 ( 3) ********************** 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 157 residues out of total 1609 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 112 time to evaluate : 0.579 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 132 ARG cc_start: 0.9112 (OUTLIER) cc_final: 0.8671 (ttt180) REVERT: A 296 ARG cc_start: 0.5817 (mmp-170) cc_final: 0.5182 (mmt180) REVERT: A 300 ARG cc_start: 0.7971 (mmt180) cc_final: 0.7556 (mmt180) REVERT: A 312 ARG cc_start: 0.8665 (ptp-110) cc_final: 0.8166 (ptp90) REVERT: A 684 GLU cc_start: 0.8690 (tm-30) cc_final: 0.7762 (tm-30) REVERT: B 311 LYS cc_start: 0.8991 (mmtt) cc_final: 0.8674 (mmmt) REVERT: B 693 LYS cc_start: 0.9442 (mmmm) cc_final: 0.8948 (mmmm) REVERT: C 300 ARG cc_start: 0.8576 (mmt180) cc_final: 0.7784 (mmt180) outliers start: 45 outliers final: 44 residues processed: 152 average time/residue: 0.6572 time to fit residues: 109.5879 Evaluate side-chains 154 residues out of total 1609 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 109 time to evaluate : 0.586 ------------------------------------------------------------------------------- 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 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 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 A residue 588 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 326 THR Chi-restraints excluded: chain B residue 331 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 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 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 396 CYS Chi-restraints excluded: chain C residue 660 THR Chi-restraints excluded: chain C residue 666 LYS 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 156 optimal weight: 3.9990 chunk 74 optimal weight: 5.9990 chunk 8 optimal weight: 0.9980 chunk 44 optimal weight: 5.9990 chunk 139 optimal weight: 40.0000 chunk 145 optimal weight: 9.9990 chunk 78 optimal weight: 30.0000 chunk 5 optimal weight: 6.9990 chunk 110 optimal weight: 9.9990 chunk 34 optimal weight: 7.9990 chunk 166 optimal weight: 0.2980 overall best weight: 3.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 579 GLN 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 = 0.134153 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3014 r_free = 0.3014 target = 0.083236 restraints weight = 26695.662| |-----------------------------------------------------------------------------| r_work (start): 0.2931 rms_B_bonded: 3.81 r_work: 0.2782 rms_B_bonded: 4.18 restraints_weight: 0.5000 r_work (final): 0.2782 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2784 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2784 r_free = 0.2784 target_work(ls_wunit_k1) = 0.069 | | occupancies: max = 1.00 min = 0.24 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2784 r_free = 0.2784 target_work(ls_wunit_k1) = 0.069 | | occupancies: max = 1.00 min = 0.26 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2784 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8779 moved from start: 0.4166 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.067 15074 Z= 0.137 Angle : 0.567 7.679 20532 Z= 0.294 Chirality : 0.043 0.208 2107 Planarity : 0.005 0.120 2728 Dihedral : 5.765 57.896 2030 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 4.25 Ramachandran Plot: Outliers : 0.55 % Allowed : 7.19 % Favored : 92.27 % Rotamer: Outliers : 2.55 % Allowed : 18.02 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.81 (0.20), residues: 1823 helix: -0.99 (0.54), residues: 91 sheet: -0.37 (0.24), residues: 402 loop : -0.55 (0.18), residues: 1330 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG R 59 TYR 0.014 0.001 TYR R 213 PHE 0.016 0.001 PHE A 372 TRP 0.025 0.001 TRP A 247 HIS 0.003 0.001 HIS B 255 Details of bonding type rmsd covalent geometry : bond 0.00327 (15069) covalent geometry : angle 0.56688 (20528) SS BOND : bond 0.00267 ( 2) SS BOND : angle 1.15297 ( 4) hydrogen bonds : bond 0.03337 ( 184) hydrogen bonds : angle 5.61283 ( 366) metal coordination : bond 0.00399 ( 3) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7714.75 seconds wall clock time: 131 minutes 49.50 seconds (7909.50 seconds total)