Starting phenix.real_space_refine on Sun Nov 17 17:12:37 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jif_36311/11_2024/8jif_36311.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jif_36311/11_2024/8jif_36311.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.28 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jif_36311/11_2024/8jif_36311.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jif_36311/11_2024/8jif_36311.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jif_36311/11_2024/8jif_36311.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jif_36311/11_2024/8jif_36311.cif" } resolution = 2.28 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.003 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians Zn 1 6.06 5 S 54 5.16 5 C 9243 2.51 5 N 2537 2.21 5 O 2795 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 19 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/chem_data/mon_lib" Total number of atoms: 14630 Number of models: 1 Model: "" Number of chains: 5 Chain: "R" Number of atoms: 2056 Number of conformers: 1 Conformer: "" Number of residues, atoms: 256, 2056 Classifications: {'peptide': 256} Link IDs: {'PTRANS': 17, 'TRANS': 238} Chain: "A" Number of atoms: 4191 Number of conformers: 1 Conformer: "" Number of residues, atoms: 525, 4191 Classifications: {'peptide': 525} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 36, 'TRANS': 488} Chain: "B" Number of atoms: 4191 Number of conformers: 1 Conformer: "" Number of residues, atoms: 525, 4191 Classifications: {'peptide': 525} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 36, 'TRANS': 488} Chain: "C" Number of atoms: 4191 Number of conformers: 1 Conformer: "" Number of residues, atoms: 525, 4191 Classifications: {'peptide': 525} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 36, 'TRANS': 488} Chain: "R" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Residues with excluded nonbonded symmetry interactions: 2 residue: pdb=" N ARG A 312 " occ=0.31 ... (9 atoms not shown) pdb=" NH2 ARG A 312 " occ=0.31 residue: pdb=" N ARG B 312 " occ=0.76 ... (9 atoms not shown) pdb=" NH2 ARG B 312 " occ=0.76 Time building chain proxies: 8.60, per 1000 atoms: 0.59 Number of scatterers: 14630 At special positions: 0 Unit cell: (140.831, 125.652, 124.808, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Zn 1 29.99 S 54 16.00 O 2795 8.00 N 2537 7.00 C 9243 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS R 23 " - pdb=" SG CYS R 35 " distance=2.02 Simple disulfide: pdb=" SG CYS R 45 " - pdb=" SG CYS R 222 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.77 Conformation dependent library (CDL) restraints added in 2.1 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN R 301 " pdb="ZN ZN R 301 " - pdb=" NE2 HIS R 114 " pdb="ZN ZN R 301 " - pdb=" NE2 HIS R 116 " pdb="ZN ZN R 301 " - pdb=" ND1 HIS R 139 " 3646 Ramachandran restraints generated. 1823 Oldfield, 0 Emsley, 1823 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3386 Finding SS restraints... Secondary structure from input PDB file: 27 helices and 32 sheets defined 9.6% alpha, 13.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.43 Creating SS restraints... Processing helix chain 'R' and resid 37 through 41 Processing helix chain 'R' and resid 173 through 180 Processing helix chain 'R' and resid 181 through 184 Processing helix chain 'R' and resid 238 through 248 removed outlier: 3.534A pdb=" N SER R 246 " --> pdb=" O PHE R 242 " (cutoff:3.500A) Processing helix chain 'A' and resid 262 through 266 Processing helix chain 'A' and resid 269 through 273 Processing helix chain 'A' and resid 288 through 292 Processing helix chain 'A' and resid 294 through 305 Processing helix chain 'A' and resid 396 through 400 Processing helix chain 'A' and resid 467 through 474 removed outlier: 4.088A pdb=" N MET A 471 " --> pdb=" O PRO A 468 " (cutoff:3.500A) removed outlier: 6.137A pdb=" N ALA A 472 " --> pdb=" O SER A 469 " (cutoff:3.500A) Processing helix chain 'A' and resid 563 through 569 removed outlier: 3.801A pdb=" N THR A 568 " --> pdb=" O GLU A 565 " (cutoff:3.500A) Processing helix chain 'B' and resid 252 through 256 Processing helix chain 'B' and resid 262 through 266 Processing helix chain 'B' and resid 269 through 273 Processing helix chain 'B' and resid 288 through 292 Processing helix chain 'B' and resid 294 through 305 Processing helix chain 'B' and resid 396 through 400 Processing helix chain 'B' and resid 467 through 474 removed outlier: 3.858A pdb=" N MET B 471 " --> pdb=" O PRO B 468 " (cutoff:3.500A) removed outlier: 5.857A pdb=" N ALA B 472 " --> pdb=" O SER B 469 " (cutoff:3.500A) Processing helix chain 'B' and resid 554 through 556 No H-bonds generated for 'chain 'B' and resid 554 through 556' Processing helix chain 'B' and resid 563 through 569 removed outlier: 4.125A pdb=" N THR B 568 " --> pdb=" O GLU B 565 " (cutoff:3.500A) Processing helix chain 'C' and resid 262 through 266 Processing helix chain 'C' and resid 269 through 273 Processing helix chain 'C' and resid 288 through 292 Processing helix chain 'C' and resid 294 through 304 Processing helix chain 'C' and resid 396 through 400 Processing helix chain 'C' and resid 467 through 474 removed outlier: 3.590A pdb=" N MET C 471 " --> pdb=" O PRO C 468 " (cutoff:3.500A) removed outlier: 6.130A pdb=" N ALA C 472 " --> pdb=" O SER C 469 " (cutoff:3.500A) Processing helix chain 'C' and resid 563 through 569 removed outlier: 4.020A pdb=" N THR C 568 " --> pdb=" O GLU C 565 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'R' and resid 54 through 55 Processing sheet with id=AA2, first strand: chain 'R' and resid 61 through 62 WARNING: can't find start of bonding for strands! previous: chain 'R' and resid 61 through 62 current: chain 'R' and resid 89 through 92 WARNING: can't find start of bonding for strands! previous: chain 'R' and resid 89 through 92 current: chain 'R' and resid 108 through 116 removed outlier: 5.339A pdb=" N ALA R 110 " --> pdb=" O LYS R 143 " (cutoff:3.500A) removed outlier: 5.822A pdb=" N LYS R 143 " --> pdb=" O ALA R 110 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N GLN R 112 " --> pdb=" O VAL R 141 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'R' and resid 156 through 163 current: chain 'R' and resid 229 through 231 Processing sheet with id=AA3, first strand: chain 'A' and resid 233 through 235 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 238 through 246 current: chain 'A' and resid 331 through 336 Processing sheet with id=AA4, first strand: chain 'A' and resid 258 through 261 Processing sheet with id=AA5, first strand: chain 'A' and resid 426 through 428 Processing sheet with id=AA6, first strand: chain 'A' and resid 445 through 451 removed outlier: 6.392A pdb=" N LYS A 462 " --> pdb=" O SER A 448 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N THR A 450 " --> pdb=" O THR A 460 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 479 through 480 removed outlier: 6.278A pdb=" N ILE A 479 " --> pdb=" O VAL A 606 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 483 through 484 Processing sheet with id=AA9, first strand: chain 'A' and resid 488 through 490 Processing sheet with id=AB1, first strand: chain 'A' and resid 514 through 517 removed outlier: 3.903A pdb=" N GLY C 578 " --> pdb=" O VAL C 596 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 542 through 544 Processing sheet with id=AB3, first strand: chain 'A' and resid 553 through 554 removed outlier: 4.026A pdb=" N THR C 450 " --> pdb=" O THR C 460 " (cutoff:3.500A) removed outlier: 6.427A pdb=" N LYS C 462 " --> pdb=" O SER C 448 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 593 through 596 removed outlier: 3.965A pdb=" N GLY A 578 " --> pdb=" O VAL A 596 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 619 through 621 removed outlier: 5.999A pdb=" N ALA A 620 " --> pdb=" O MET A 640 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB5 Processing sheet with id=AB6, first strand: chain 'A' and resid 627 through 629 removed outlier: 4.021A pdb=" N MET C 605 " --> pdb=" O PHE A 629 " (cutoff:3.500A) removed outlier: 6.288A pdb=" N ILE C 479 " --> pdb=" O VAL C 606 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 232 through 234 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 238 through 249 current: chain 'B' and resid 334 through 336 Processing sheet with id=AB8, first strand: chain 'B' and resid 258 through 261 Processing sheet with id=AB9, first strand: chain 'B' and resid 426 through 428 Processing sheet with id=AC1, first strand: chain 'B' and resid 445 through 449 removed outlier: 6.636A pdb=" N LYS B 462 " --> pdb=" O SER B 448 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 479 through 480 removed outlier: 6.206A pdb=" N ILE B 479 " --> pdb=" O VAL B 606 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 483 through 484 Processing sheet with id=AC4, first strand: chain 'B' and resid 488 through 490 Processing sheet with id=AC5, first strand: chain 'B' and resid 542 through 544 Processing sheet with id=AC6, first strand: chain 'B' and resid 593 through 596 removed outlier: 4.044A pdb=" N GLY B 578 " --> pdb=" O VAL B 596 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 619 through 621 removed outlier: 6.057A pdb=" N ALA B 620 " --> pdb=" O MET B 640 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC7 Processing sheet with id=AC8, first strand: chain 'C' and resid 231 through 234 Processing sheet with id=AC9, first strand: chain 'C' and resid 258 through 261 Processing sheet with id=AD1, first strand: chain 'C' and resid 427 through 428 removed outlier: 6.269A pdb=" N ALA C 427 " --> pdb=" O ARG C 734 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD1 Processing sheet with id=AD2, first strand: chain 'C' and resid 483 through 484 Processing sheet with id=AD3, first strand: chain 'C' and resid 488 through 490 Processing sheet with id=AD4, first strand: chain 'C' and resid 542 through 544 Processing sheet with id=AD5, first strand: chain 'C' and resid 619 through 621 removed outlier: 6.104A pdb=" N ALA C 620 " --> pdb=" O MET C 640 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD5 184 hydrogen bonds defined for protein. 366 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 4.26 Time building geometry restraints manager: 4.44 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: 0.280 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: 0.020 Extract box with map and model: 0.700 Check model and map are aligned: 0.140 Set scattering table: 0.140 Process input model: 36.980 Find NCS groups from input model: 0.410 Set up NCS constraints: 0.070 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: 0.010 Load rotamer database and sin/cos tables:12.420 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 51.170 ------------------------------------------------------------------------------- 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 15069 Z= 0.329 Angle : 1.139 14.115 20528 Z= 0.738 Chirality : 0.047 0.195 2107 Planarity : 0.005 0.095 2728 Dihedral : 17.824 89.987 5465 Min Nonbonded Distance : 1.676 Molprobity Statistics. All-atom Clashscore : 18.52 Ramachandran Plot: Outliers : 2.85 % Allowed : 8.67 % Favored : 88.48 % Rotamer: Outliers : 12.43 % Allowed : 12.43 % Favored : 75.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.44 (0.18), residues: 1823 helix: -2.74 (0.44), residues: 104 sheet: -1.56 (0.25), residues: 327 loop : -1.66 (0.15), residues: 1392 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 298 HIS 0.005 0.001 HIS A 255 PHE 0.014 0.001 PHE A 315 TYR 0.030 0.002 TYR B 588E ARG 0.003 0.000 ARG A 312 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3646 Ramachandran restraints generated. 1823 Oldfield, 0 Emsley, 1823 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3646 Ramachandran restraints generated. 1823 Oldfield, 0 Emsley, 1823 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 444 residues out of total 1609 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 200 poor density : 244 time to evaluate : 1.670 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 99 ILE cc_start: 0.8303 (mt) cc_final: 0.7957 (pt) REVERT: R 244 GLU cc_start: 0.8514 (mm-30) cc_final: 0.8301 (mm-30) REVERT: A 256 LEU cc_start: 0.8760 (OUTLIER) cc_final: 0.8556 (mt) REVERT: B 313 LEU cc_start: 0.1334 (OUTLIER) cc_final: 0.1012 (tt) REVERT: C 296 ARG cc_start: 0.8501 (tpt90) cc_final: 0.7853 (mmp-170) REVERT: C 730 ARG cc_start: 0.8986 (OUTLIER) cc_final: 0.8533 (mtt90) outliers start: 200 outliers final: 83 residues processed: 393 average time/residue: 1.4132 time to fit residues: 606.8524 Evaluate side-chains 212 residues out of total 1609 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 126 time to evaluate : 1.868 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 72 VAL Chi-restraints excluded: chain R residue 115 LEU Chi-restraints excluded: chain R residue 141 VAL Chi-restraints excluded: chain R residue 169 VAL Chi-restraints excluded: chain R residue 209 THR Chi-restraints excluded: chain R residue 229 THR Chi-restraints excluded: chain R residue 230 VAL Chi-restraints excluded: chain R residue 274 VAL Chi-restraints excluded: chain A residue 223 SER Chi-restraints excluded: chain A residue 225 SER Chi-restraints excluded: chain A residue 229 HIS Chi-restraints excluded: chain A residue 232 SER Chi-restraints excluded: chain A residue 235 LEU Chi-restraints excluded: chain A residue 246 THR Chi-restraints excluded: chain A residue 256 LEU Chi-restraints excluded: chain A residue 313 LEU Chi-restraints excluded: chain A residue 316 LYS Chi-restraints excluded: chain A residue 323 LYS Chi-restraints excluded: chain A residue 324 GLU Chi-restraints excluded: chain A residue 325 VAL Chi-restraints excluded: chain A residue 326 THR Chi-restraints excluded: chain A residue 328 ASN Chi-restraints excluded: chain A residue 332 LYS Chi-restraints excluded: chain A residue 333 THR Chi-restraints excluded: chain A residue 334 ILE Chi-restraints excluded: chain A residue 341 THR Chi-restraints excluded: chain A residue 405 LEU Chi-restraints excluded: chain A residue 406 ARG Chi-restraints excluded: chain A residue 412 GLN Chi-restraints excluded: chain A residue 465 VAL Chi-restraints excluded: chain A residue 588 ASP Chi-restraints excluded: chain A residue 649 ILE Chi-restraints excluded: chain A residue 657 ASP Chi-restraints excluded: chain A residue 671 ILE Chi-restraints excluded: chain A residue 673 GLN Chi-restraints excluded: chain B residue 225 SER Chi-restraints excluded: chain B residue 233 GLN Chi-restraints excluded: chain B residue 238 ARG Chi-restraints excluded: chain B residue 240 ILE Chi-restraints excluded: chain B residue 251 THR Chi-restraints excluded: chain B residue 312 ARG Chi-restraints excluded: chain B residue 313 LEU Chi-restraints excluded: chain B residue 321 GLN Chi-restraints excluded: chain B residue 323 LYS Chi-restraints excluded: chain B residue 326 THR Chi-restraints excluded: chain B residue 331 VAL Chi-restraints excluded: chain B residue 332 LYS Chi-restraints excluded: chain B residue 333 THR Chi-restraints excluded: chain B residue 339 THR Chi-restraints excluded: chain B residue 341 THR Chi-restraints excluded: chain B residue 343 GLN Chi-restraints excluded: chain B residue 451 ILE Chi-restraints excluded: chain B residue 532 ASP Chi-restraints excluded: chain B residue 657 ASP Chi-restraints excluded: chain B residue 664 LYS Chi-restraints excluded: chain B residue 665 ASP Chi-restraints excluded: chain B residue 666 LYS Chi-restraints excluded: chain B residue 668 ASN Chi-restraints excluded: chain B residue 671 ILE Chi-restraints excluded: chain B residue 676 THR Chi-restraints excluded: chain B residue 707 LYS Chi-restraints excluded: chain C residue 235 LEU Chi-restraints excluded: chain C residue 251 THR Chi-restraints excluded: chain C residue 313 LEU Chi-restraints excluded: chain C residue 317 LEU Chi-restraints excluded: chain C residue 321 GLN Chi-restraints excluded: chain C residue 326 THR Chi-restraints excluded: chain C residue 332 LYS Chi-restraints excluded: chain C residue 333 THR Chi-restraints excluded: chain C residue 338 LEU Chi-restraints excluded: chain C residue 341 THR Chi-restraints excluded: chain C residue 342 VAL Chi-restraints excluded: chain C residue 407 THR Chi-restraints excluded: chain C residue 410 ASN Chi-restraints excluded: chain C residue 412 GLN Chi-restraints excluded: chain C residue 532 ASP Chi-restraints excluded: chain C residue 588 GLN Chi-restraints excluded: chain C residue 657 ASP Chi-restraints excluded: chain C residue 660 THR Chi-restraints excluded: chain C residue 665 ASP Chi-restraints excluded: chain C residue 666 LYS Chi-restraints excluded: chain C residue 668 ASN Chi-restraints excluded: chain C residue 671 ILE Chi-restraints excluded: chain C residue 673 GLN Chi-restraints excluded: chain C residue 702 THR Chi-restraints excluded: chain C residue 730 ARG Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 181 random chunks: chunk 152 optimal weight: 5.9990 chunk 137 optimal weight: 10.0000 chunk 76 optimal weight: 8.9990 chunk 46 optimal weight: 10.0000 chunk 92 optimal weight: 5.9990 chunk 73 optimal weight: 9.9990 chunk 141 optimal weight: 50.0000 chunk 54 optimal weight: 10.0000 chunk 86 optimal weight: 8.9990 chunk 105 optimal weight: 10.0000 chunk 164 optimal weight: 10.0000 overall best weight: 7.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 127 HIS R 133 HIS A 229 HIS A 253 ASN A 314 ASN A 321 GLN A 376 GLN A 412 GLN A 470 ASN A 474 GLN A 497 ASN A 646 GLN A 678 GLN A 735 ASN B 229 HIS B 233 GLN B 336 ASN B 470 ASN B 678 GLN C 227 ASN C 329 ASN C 343 GLN C 403 GLN C 419 ASN C 430 GLN C 452 ASN C 457 ASN C 495 GLN C 663 ASN C 678 GLN C 735 ASN Total number of N/Q/H flips: 31 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7316 moved from start: 0.3110 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.075 15069 Z= 0.418 Angle : 0.700 8.938 20528 Z= 0.372 Chirality : 0.048 0.191 2107 Planarity : 0.006 0.107 2728 Dihedral : 10.371 81.886 2170 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 6.26 Ramachandran Plot: Outliers : 0.71 % Allowed : 7.41 % Favored : 91.88 % Rotamer: Outliers : 5.66 % Allowed : 15.16 % Favored : 79.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.80 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.59 (0.19), residues: 1823 helix: -1.35 (0.52), residues: 85 sheet: -1.22 (0.23), residues: 402 loop : -1.01 (0.17), residues: 1336 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP A 306 HIS 0.008 0.001 HIS R 187 PHE 0.013 0.002 PHE C 535 TYR 0.018 0.002 TYR A 701 ARG 0.027 0.001 ARG C 296 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3646 Ramachandran restraints generated. 1823 Oldfield, 0 Emsley, 1823 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3646 Ramachandran restraints generated. 1823 Oldfield, 0 Emsley, 1823 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 222 residues out of total 1609 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 131 time to evaluate : 1.556 Fit side-chains REVERT: A 238 ARG cc_start: 0.7163 (mtt180) cc_final: 0.6808 (mtt90) REVERT: A 588 ASP cc_start: 0.8113 (OUTLIER) cc_final: 0.7904 (m-30) REVERT: B 229 HIS cc_start: 0.0470 (OUTLIER) cc_final: 0.0218 (m90) outliers start: 91 outliers final: 57 residues processed: 212 average time/residue: 1.1711 time to fit residues: 273.0949 Evaluate side-chains 175 residues out of total 1609 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 116 time to evaluate : 1.161 ------------------------------------------------------------------------------- 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 229 HIS Chi-restraints excluded: chain B residue 235 LEU Chi-restraints excluded: chain B residue 238 ARG Chi-restraints excluded: chain B residue 240 ILE Chi-restraints excluded: chain B residue 312 ARG Chi-restraints excluded: chain B residue 320 ILE Chi-restraints excluded: chain B residue 321 GLN Chi-restraints excluded: chain B residue 323 LYS Chi-restraints excluded: chain B residue 326 THR Chi-restraints excluded: chain B residue 329 ASN Chi-restraints excluded: chain B residue 331 VAL Chi-restraints excluded: chain B residue 333 THR Chi-restraints excluded: chain B residue 339 THR Chi-restraints excluded: chain B residue 341 THR Chi-restraints excluded: chain B residue 343 GLN Chi-restraints excluded: chain B residue 606 VAL Chi-restraints excluded: chain B residue 657 ASP Chi-restraints excluded: chain B residue 664 LYS Chi-restraints excluded: chain B residue 666 LYS Chi-restraints excluded: chain B residue 668 ASN Chi-restraints excluded: chain B residue 671 ILE Chi-restraints excluded: chain B residue 676 THR Chi-restraints excluded: chain C residue 251 THR Chi-restraints excluded: chain C residue 317 LEU Chi-restraints excluded: chain C residue 328 ASN Chi-restraints excluded: chain C residue 329 ASN Chi-restraints excluded: chain C residue 331 VAL Chi-restraints excluded: chain C residue 332 LYS Chi-restraints excluded: chain C residue 333 THR Chi-restraints excluded: chain C residue 338 LEU Chi-restraints excluded: chain C residue 341 THR Chi-restraints excluded: chain C residue 342 VAL Chi-restraints excluded: chain C residue 407 THR Chi-restraints excluded: chain C residue 410 ASN Chi-restraints excluded: chain C residue 657 ASP Chi-restraints excluded: chain C residue 660 THR Chi-restraints excluded: chain C residue 663 ASN Chi-restraints excluded: chain C residue 666 LYS Chi-restraints excluded: chain C residue 668 ASN Chi-restraints excluded: chain C residue 671 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 181 random chunks: chunk 91 optimal weight: 20.0000 chunk 51 optimal weight: 5.9990 chunk 136 optimal weight: 5.9990 chunk 111 optimal weight: 10.0000 chunk 45 optimal weight: 6.9990 chunk 164 optimal weight: 7.9990 chunk 177 optimal weight: 2.9990 chunk 146 optimal weight: 8.9990 chunk 163 optimal weight: 5.9990 chunk 56 optimal weight: 0.9990 chunk 132 optimal weight: 0.2980 overall best weight: 3.2588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 86 GLN R 248 ASN A 456 GLN B 229 HIS B 321 GLN C 233 GLN C 329 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7280 moved from start: 0.3363 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 15069 Z= 0.208 Angle : 0.576 7.054 20528 Z= 0.303 Chirality : 0.043 0.158 2107 Planarity : 0.005 0.106 2728 Dihedral : 8.252 59.511 2086 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 5.20 Ramachandran Plot: Outliers : 0.66 % Allowed : 7.57 % Favored : 91.77 % Rotamer: Outliers : 4.04 % Allowed : 16.72 % Favored : 79.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.80 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.17 (0.19), residues: 1823 helix: -0.66 (0.57), residues: 85 sheet: -0.91 (0.23), residues: 402 loop : -0.74 (0.18), residues: 1336 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 247 HIS 0.012 0.001 HIS B 229 PHE 0.015 0.001 PHE A 372 TYR 0.014 0.001 TYR R 213 ARG 0.004 0.000 ARG R 65 *********************** 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 182 residues out of total 1609 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 117 time to evaluate : 1.635 Fit side-chains REVERT: R 132 ARG cc_start: 0.9073 (OUTLIER) cc_final: 0.8693 (ttt180) REVERT: C 707 LYS cc_start: 0.6453 (tptt) cc_final: 0.6073 (tptt) outliers start: 65 outliers final: 50 residues processed: 179 average time/residue: 1.3742 time to fit residues: 269.6481 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 : 1.535 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 72 VAL Chi-restraints excluded: chain R residue 115 LEU Chi-restraints excluded: chain R residue 132 ARG Chi-restraints excluded: chain R residue 141 VAL Chi-restraints excluded: chain R residue 145 LEU Chi-restraints excluded: chain R residue 169 VAL Chi-restraints excluded: chain R residue 209 THR Chi-restraints excluded: chain R residue 229 THR Chi-restraints excluded: chain R residue 230 VAL Chi-restraints excluded: chain R residue 274 VAL Chi-restraints excluded: chain A residue 229 HIS Chi-restraints excluded: chain A residue 235 LEU Chi-restraints excluded: chain A residue 313 LEU Chi-restraints excluded: chain A residue 328 ASN Chi-restraints excluded: chain A residue 332 LYS Chi-restraints excluded: chain A residue 338 LEU Chi-restraints excluded: chain A residue 344 VAL Chi-restraints excluded: chain B residue 235 LEU Chi-restraints excluded: chain B residue 238 ARG Chi-restraints excluded: chain B residue 240 ILE Chi-restraints excluded: chain B residue 251 THR Chi-restraints excluded: chain B residue 320 ILE Chi-restraints excluded: chain B residue 321 GLN Chi-restraints excluded: chain B residue 323 LYS Chi-restraints excluded: chain B residue 326 THR Chi-restraints excluded: chain B residue 331 VAL Chi-restraints excluded: chain B residue 333 THR Chi-restraints excluded: chain B residue 339 THR Chi-restraints excluded: chain B residue 341 THR Chi-restraints excluded: chain B residue 343 GLN Chi-restraints excluded: chain B residue 413 PHE Chi-restraints excluded: chain B residue 494 THR Chi-restraints excluded: chain B residue 606 VAL Chi-restraints excluded: chain B residue 657 ASP Chi-restraints excluded: chain B residue 664 LYS Chi-restraints excluded: chain B residue 666 LYS Chi-restraints excluded: chain B residue 668 ASN Chi-restraints excluded: chain B residue 671 ILE Chi-restraints excluded: chain B residue 676 THR Chi-restraints excluded: chain C residue 233 GLN Chi-restraints excluded: chain C residue 317 LEU 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 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 162 optimal weight: 10.0000 chunk 123 optimal weight: 30.0000 chunk 85 optimal weight: 10.0000 chunk 18 optimal weight: 20.0000 chunk 78 optimal weight: 20.0000 chunk 110 optimal weight: 20.0000 chunk 165 optimal weight: 7.9990 chunk 174 optimal weight: 50.0000 chunk 86 optimal weight: 8.9990 chunk 156 optimal weight: 0.7980 chunk 47 optimal weight: 7.9990 overall best weight: 7.1590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 187 HIS B 343 GLN C 233 GLN C 329 ASN C 376 GLN C 663 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7339 moved from start: 0.3657 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.058 15069 Z= 0.365 Angle : 0.621 7.393 20528 Z= 0.328 Chirality : 0.045 0.152 2107 Planarity : 0.005 0.115 2728 Dihedral : 7.688 59.751 2070 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 4.99 Ramachandran Plot: Outliers : 0.66 % Allowed : 7.79 % Favored : 91.55 % Rotamer: Outliers : 4.23 % Allowed : 16.47 % Favored : 79.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.80 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.13 (0.19), residues: 1823 helix: -0.87 (0.56), residues: 85 sheet: -0.72 (0.23), residues: 402 loop : -0.76 (0.18), residues: 1336 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 247 HIS 0.007 0.001 HIS R 187 PHE 0.016 0.001 PHE A 372 TYR 0.014 0.001 TYR C 701 ARG 0.004 0.001 ARG R 65 *********************** 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 183 residues out of total 1609 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 115 time to evaluate : 1.528 Fit side-chains REVERT: R 132 ARG cc_start: 0.9016 (OUTLIER) cc_final: 0.8645 (ttt180) outliers start: 68 outliers final: 52 residues processed: 174 average time/residue: 1.3305 time to fit residues: 255.2521 Evaluate side-chains 165 residues out of total 1609 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 112 time to evaluate : 1.681 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 72 VAL Chi-restraints excluded: chain R residue 115 LEU Chi-restraints excluded: chain R residue 132 ARG Chi-restraints excluded: chain R residue 141 VAL Chi-restraints excluded: chain R residue 145 LEU Chi-restraints excluded: chain R residue 169 VAL Chi-restraints excluded: chain R residue 191 THR Chi-restraints excluded: chain R residue 229 THR Chi-restraints excluded: chain R residue 230 VAL Chi-restraints excluded: chain R residue 274 VAL Chi-restraints excluded: chain A residue 229 HIS Chi-restraints excluded: chain A residue 235 LEU Chi-restraints excluded: chain A residue 263 SER Chi-restraints excluded: chain A residue 264 THR Chi-restraints excluded: chain A residue 313 LEU Chi-restraints excluded: chain A residue 328 ASN Chi-restraints excluded: chain A residue 332 LYS Chi-restraints excluded: chain A residue 338 LEU Chi-restraints excluded: chain A residue 344 VAL Chi-restraints excluded: chain A residue 372 PHE Chi-restraints excluded: chain A residue 588 GLN Chi-restraints excluded: chain B residue 238 ARG Chi-restraints excluded: chain B residue 251 THR Chi-restraints excluded: chain B residue 320 ILE Chi-restraints excluded: chain B residue 323 LYS Chi-restraints excluded: chain B residue 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 373 MET 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 233 GLN Chi-restraints excluded: chain C residue 264 THR Chi-restraints excluded: chain C residue 322 VAL Chi-restraints excluded: chain C residue 328 ASN Chi-restraints excluded: chain C residue 329 ASN Chi-restraints excluded: chain C residue 332 LYS Chi-restraints excluded: chain C residue 333 THR Chi-restraints excluded: chain C residue 338 LEU Chi-restraints excluded: chain C residue 341 THR Chi-restraints excluded: chain C residue 410 ASN Chi-restraints excluded: chain C residue 660 THR Chi-restraints excluded: chain C residue 666 LYS Chi-restraints excluded: chain C residue 668 ASN Chi-restraints excluded: chain C residue 671 ILE Chi-restraints excluded: chain C residue 684 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 181 random chunks: chunk 145 optimal weight: 6.9990 chunk 99 optimal weight: 0.7980 chunk 2 optimal weight: 0.2980 chunk 130 optimal weight: 40.0000 chunk 72 optimal weight: 5.9990 chunk 149 optimal weight: 6.9990 chunk 120 optimal weight: 7.9990 chunk 0 optimal weight: 10.0000 chunk 89 optimal weight: 9.9990 chunk 157 optimal weight: 7.9990 chunk 44 optimal weight: 7.9990 overall best weight: 4.2186 ------------------------------------------------------------------------------- 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 579 GLN C 233 GLN C 329 ASN C 376 GLN C 410 ASN C 458 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7310 moved from start: 0.3766 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 15069 Z= 0.240 Angle : 0.570 6.692 20528 Z= 0.298 Chirality : 0.043 0.152 2107 Planarity : 0.005 0.114 2728 Dihedral : 6.912 59.763 2052 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 4.64 Ramachandran Plot: Outliers : 0.55 % Allowed : 7.35 % Favored : 92.10 % Rotamer: Outliers : 3.48 % Allowed : 17.28 % Favored : 79.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.80 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.01 (0.19), residues: 1823 helix: -0.69 (0.57), residues: 85 sheet: -0.63 (0.23), residues: 407 loop : -0.69 (0.18), residues: 1331 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 247 HIS 0.006 0.001 HIS A 229 PHE 0.016 0.001 PHE A 372 TYR 0.010 0.001 TYR C 701 ARG 0.007 0.000 ARG R 59 *********************** 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 172 residues out of total 1609 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 116 time to evaluate : 1.625 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 132 ARG cc_start: 0.9066 (OUTLIER) cc_final: 0.8674 (ttt180) REVERT: C 707 LYS cc_start: 0.6464 (tptt) cc_final: 0.6141 (tptt) outliers start: 56 outliers final: 45 residues processed: 165 average time/residue: 1.4324 time to fit residues: 259.0193 Evaluate side-chains 154 residues out of total 1609 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 108 time to evaluate : 1.740 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 72 VAL Chi-restraints excluded: chain R residue 115 LEU Chi-restraints excluded: chain R residue 132 ARG Chi-restraints excluded: chain R residue 141 VAL Chi-restraints excluded: chain R residue 145 LEU Chi-restraints excluded: chain R residue 169 VAL Chi-restraints excluded: chain R residue 229 THR Chi-restraints excluded: chain R residue 230 VAL Chi-restraints excluded: chain R residue 274 VAL Chi-restraints excluded: chain A residue 229 HIS Chi-restraints excluded: chain A residue 235 LEU Chi-restraints excluded: chain A residue 263 SER Chi-restraints excluded: chain A residue 313 LEU Chi-restraints excluded: chain A residue 328 ASN Chi-restraints excluded: chain A residue 332 LYS Chi-restraints excluded: chain A residue 338 LEU Chi-restraints excluded: chain A residue 404 MET Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain B residue 238 ARG Chi-restraints excluded: chain B residue 240 ILE Chi-restraints excluded: chain B residue 251 THR Chi-restraints excluded: chain B residue 320 ILE Chi-restraints excluded: chain B residue 323 LYS Chi-restraints excluded: chain B residue 333 THR Chi-restraints excluded: chain B residue 339 THR Chi-restraints excluded: chain B residue 341 THR Chi-restraints excluded: chain B residue 396 CYS Chi-restraints excluded: chain B residue 413 PHE Chi-restraints excluded: chain B residue 494 THR Chi-restraints excluded: chain B residue 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 233 GLN 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 396 CYS Chi-restraints excluded: chain C residue 588 GLN Chi-restraints excluded: chain C residue 660 THR Chi-restraints excluded: chain C residue 666 LYS Chi-restraints excluded: chain C residue 668 ASN Chi-restraints excluded: chain C residue 671 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 181 random chunks: chunk 58 optimal weight: 6.9990 chunk 157 optimal weight: 6.9990 chunk 34 optimal weight: 9.9990 chunk 102 optimal weight: 8.9990 chunk 43 optimal weight: 0.0470 chunk 175 optimal weight: 10.0000 chunk 145 optimal weight: 7.9990 chunk 81 optimal weight: 10.0000 chunk 14 optimal weight: 7.9990 chunk 57 optimal weight: 4.9990 chunk 91 optimal weight: 20.0000 overall best weight: 5.4086 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 651 ASN A 691 ASN B 704 ASN C 329 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7327 moved from start: 0.3870 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 15069 Z= 0.288 Angle : 0.581 6.771 20528 Z= 0.304 Chirality : 0.044 0.156 2107 Planarity : 0.005 0.117 2728 Dihedral : 6.787 59.717 2048 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 4.81 Ramachandran Plot: Outliers : 0.55 % Allowed : 7.57 % Favored : 91.88 % Rotamer: Outliers : 3.79 % Allowed : 16.72 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.97 (0.19), residues: 1823 helix: -0.73 (0.57), residues: 85 sheet: -0.52 (0.23), residues: 407 loop : -0.68 (0.18), residues: 1331 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 247 HIS 0.005 0.001 HIS A 229 PHE 0.017 0.001 PHE A 372 TYR 0.011 0.001 TYR C 701 ARG 0.005 0.000 ARG R 59 *********************** 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 175 residues out of total 1609 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 114 time to evaluate : 1.582 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 132 ARG cc_start: 0.9051 (OUTLIER) cc_final: 0.8661 (ttt180) REVERT: R 208 TYR cc_start: 0.8878 (m-80) cc_final: 0.8546 (m-80) outliers start: 61 outliers final: 50 residues processed: 165 average time/residue: 1.3637 time to fit residues: 247.7545 Evaluate side-chains 162 residues out of total 1609 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 111 time to evaluate : 1.672 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 72 VAL Chi-restraints excluded: chain R residue 115 LEU Chi-restraints excluded: chain R residue 132 ARG Chi-restraints excluded: chain R residue 141 VAL Chi-restraints excluded: chain R residue 145 LEU Chi-restraints excluded: chain R residue 158 VAL Chi-restraints excluded: chain R residue 169 VAL Chi-restraints excluded: chain R residue 229 THR Chi-restraints excluded: chain R residue 230 VAL Chi-restraints excluded: chain R residue 274 VAL Chi-restraints excluded: chain A residue 229 HIS Chi-restraints excluded: chain A residue 235 LEU Chi-restraints excluded: chain A residue 263 SER Chi-restraints excluded: chain A residue 264 THR Chi-restraints excluded: chain A residue 328 ASN Chi-restraints excluded: chain A residue 332 LYS Chi-restraints excluded: chain A residue 338 LEU Chi-restraints excluded: chain A residue 372 PHE Chi-restraints excluded: chain A residue 404 MET Chi-restraints excluded: chain A residue 588 THR 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 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 373 MET 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 396 CYS Chi-restraints excluded: chain C residue 588 GLN Chi-restraints excluded: chain C residue 660 THR Chi-restraints excluded: chain C residue 666 LYS Chi-restraints excluded: chain C residue 668 ASN Chi-restraints excluded: chain C residue 671 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 181 random chunks: chunk 168 optimal weight: 2.9990 chunk 19 optimal weight: 1.9990 chunk 99 optimal weight: 8.9990 chunk 127 optimal weight: 9.9990 chunk 147 optimal weight: 0.0870 chunk 97 optimal weight: 9.9990 chunk 174 optimal weight: 50.0000 chunk 109 optimal weight: 10.0000 chunk 106 optimal weight: 4.9990 chunk 80 optimal weight: 20.0000 chunk 107 optimal weight: 0.0970 overall best weight: 2.0362 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7281 moved from start: 0.3961 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.072 15069 Z= 0.166 Angle : 0.547 7.796 20528 Z= 0.283 Chirality : 0.042 0.153 2107 Planarity : 0.005 0.114 2728 Dihedral : 6.280 59.335 2040 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 4.36 Ramachandran Plot: Outliers : 0.55 % Allowed : 7.24 % Favored : 92.21 % Rotamer: Outliers : 3.05 % Allowed : 17.84 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.84 (0.20), residues: 1823 helix: -0.61 (0.58), residues: 88 sheet: -0.36 (0.24), residues: 404 loop : -0.61 (0.18), residues: 1331 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP A 247 HIS 0.004 0.001 HIS B 255 PHE 0.015 0.001 PHE A 372 TYR 0.009 0.001 TYR R 213 ARG 0.009 0.000 ARG R 59 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3646 Ramachandran restraints generated. 1823 Oldfield, 0 Emsley, 1823 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3646 Ramachandran restraints generated. 1823 Oldfield, 0 Emsley, 1823 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 1609 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 118 time to evaluate : 1.748 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 49 outliers final: 44 residues processed: 162 average time/residue: 1.3074 time to fit residues: 233.3889 Evaluate side-chains 157 residues out of total 1609 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 113 time to evaluate : 1.842 ------------------------------------------------------------------------------- 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 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 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 338 LEU Chi-restraints excluded: chain C residue 396 CYS Chi-restraints excluded: chain C residue 588 GLN Chi-restraints excluded: chain C residue 660 THR Chi-restraints excluded: chain C residue 666 LYS Chi-restraints excluded: chain C residue 668 ASN Chi-restraints excluded: chain C residue 671 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 181 random chunks: chunk 69 optimal weight: 0.8980 chunk 104 optimal weight: 9.9990 chunk 52 optimal weight: 9.9990 chunk 34 optimal weight: 6.9990 chunk 33 optimal weight: 6.9990 chunk 110 optimal weight: 10.0000 chunk 118 optimal weight: 10.0000 chunk 86 optimal weight: 10.0000 chunk 16 optimal weight: 0.3980 chunk 137 optimal weight: 6.9990 chunk 158 optimal weight: 4.9990 overall best weight: 4.0586 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7309 moved from start: 0.4013 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 15069 Z= 0.237 Angle : 0.570 6.880 20528 Z= 0.295 Chirality : 0.043 0.150 2107 Planarity : 0.005 0.116 2728 Dihedral : 6.213 58.887 2040 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 4.50 Ramachandran Plot: Outliers : 0.55 % Allowed : 7.79 % Favored : 91.66 % Rotamer: Outliers : 2.98 % Allowed : 17.84 % Favored : 79.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.80 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.81 (0.20), residues: 1823 helix: -0.77 (0.56), residues: 88 sheet: -0.42 (0.23), residues: 415 loop : -0.55 (0.18), residues: 1320 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.001 TRP A 247 HIS 0.005 0.001 HIS B 255 PHE 0.016 0.001 PHE A 372 TYR 0.009 0.001 TYR C 701 ARG 0.010 0.000 ARG R 59 *********************** 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 166 residues out of total 1609 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 118 time to evaluate : 1.657 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 132 ARG cc_start: 0.9074 (OUTLIER) cc_final: 0.8665 (ttt180) REVERT: R 208 TYR cc_start: 0.8840 (m-80) cc_final: 0.8499 (m-80) outliers start: 48 outliers final: 43 residues processed: 164 average time/residue: 1.3630 time to fit residues: 246.1342 Evaluate side-chains 155 residues out of total 1609 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 111 time to evaluate : 1.626 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 72 VAL Chi-restraints excluded: chain R residue 115 LEU Chi-restraints excluded: chain R residue 132 ARG Chi-restraints excluded: chain R residue 141 VAL Chi-restraints excluded: chain R residue 169 VAL Chi-restraints excluded: chain R residue 229 THR Chi-restraints excluded: chain R residue 230 VAL Chi-restraints excluded: chain R residue 274 VAL Chi-restraints excluded: chain A residue 229 HIS Chi-restraints excluded: chain A residue 263 SER Chi-restraints excluded: chain A residue 328 ASN Chi-restraints excluded: chain A residue 332 LYS Chi-restraints excluded: chain A residue 338 LEU Chi-restraints excluded: chain A residue 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 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 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 Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 181 random chunks: chunk 167 optimal weight: 9.9990 chunk 152 optimal weight: 6.9990 chunk 162 optimal weight: 9.9990 chunk 97 optimal weight: 20.0000 chunk 70 optimal weight: 20.0000 chunk 127 optimal weight: 7.9990 chunk 49 optimal weight: 10.0000 chunk 146 optimal weight: 9.9990 chunk 153 optimal weight: 5.9990 chunk 106 optimal weight: 4.9990 chunk 171 optimal weight: 0.0870 overall best weight: 5.2166 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7323 moved from start: 0.4055 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 15069 Z= 0.280 Angle : 0.587 6.770 20528 Z= 0.305 Chirality : 0.043 0.149 2107 Planarity : 0.005 0.118 2728 Dihedral : 6.150 58.590 2038 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 4.53 Ramachandran Plot: Outliers : 0.55 % Allowed : 7.68 % Favored : 91.77 % Rotamer: Outliers : 2.92 % Allowed : 18.15 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.79 (0.20), residues: 1823 helix: -0.72 (0.57), residues: 85 sheet: -0.40 (0.24), residues: 415 loop : -0.54 (0.18), residues: 1323 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.001 TRP A 247 HIS 0.005 0.001 HIS B 255 PHE 0.017 0.001 PHE A 372 TYR 0.011 0.001 TYR C 701 ARG 0.010 0.001 ARG R 59 *********************** 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: 47 poor density : 114 time to evaluate : 1.498 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 132 ARG cc_start: 0.9052 (OUTLIER) cc_final: 0.8632 (ttt180) REVERT: R 208 TYR cc_start: 0.8841 (m-80) cc_final: 0.8486 (m-80) outliers start: 47 outliers final: 44 residues processed: 156 average time/residue: 1.3809 time to fit residues: 236.6239 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 : 1.794 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 72 VAL Chi-restraints excluded: chain R residue 115 LEU Chi-restraints excluded: chain R residue 132 ARG Chi-restraints excluded: chain R residue 141 VAL Chi-restraints excluded: chain R residue 169 VAL Chi-restraints excluded: chain R residue 229 THR Chi-restraints excluded: chain R residue 230 VAL Chi-restraints excluded: chain R residue 274 VAL Chi-restraints excluded: chain A residue 229 HIS Chi-restraints excluded: chain A residue 263 SER Chi-restraints excluded: chain A residue 328 ASN Chi-restraints excluded: chain A residue 332 LYS Chi-restraints excluded: chain A residue 338 LEU Chi-restraints excluded: chain A residue 372 PHE Chi-restraints excluded: chain A residue 404 MET Chi-restraints excluded: chain B residue 238 ARG Chi-restraints excluded: chain B residue 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 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 329 ASN Chi-restraints excluded: chain C residue 332 LYS Chi-restraints excluded: chain C residue 338 LEU Chi-restraints excluded: chain C residue 396 CYS Chi-restraints excluded: chain C residue 588 GLN Chi-restraints excluded: chain C residue 660 THR Chi-restraints excluded: chain C residue 666 LYS Chi-restraints excluded: chain C residue 668 ASN Chi-restraints excluded: chain C residue 671 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 181 random chunks: chunk 104 optimal weight: 5.9990 chunk 81 optimal weight: 10.0000 chunk 119 optimal weight: 9.9990 chunk 180 optimal weight: 9.9990 chunk 165 optimal weight: 20.0000 chunk 143 optimal weight: 10.0000 chunk 14 optimal weight: 0.7980 chunk 110 optimal weight: 9.9990 chunk 88 optimal weight: 50.0000 chunk 114 optimal weight: 8.9990 chunk 152 optimal weight: 6.9990 overall best weight: 6.5588 ------------------------------------------------------------------------------- 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 C 376 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7341 moved from start: 0.4091 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 15069 Z= 0.338 Angle : 0.612 6.796 20528 Z= 0.319 Chirality : 0.044 0.150 2107 Planarity : 0.005 0.121 2728 Dihedral : 6.181 57.997 2036 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 4.50 Ramachandran Plot: Outliers : 0.60 % Allowed : 7.84 % Favored : 91.55 % Rotamer: Outliers : 2.80 % Allowed : 18.09 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.84 (0.20), residues: 1823 helix: -0.88 (0.56), residues: 85 sheet: -0.43 (0.24), residues: 413 loop : -0.57 (0.18), residues: 1325 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.001 TRP A 247 HIS 0.005 0.001 HIS B 255 PHE 0.018 0.001 PHE A 372 TYR 0.013 0.001 TYR C 701 ARG 0.011 0.001 ARG R 59 ********************** 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 159 residues out of total 1609 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 114 time to evaluate : 1.761 Fit side-chains revert: symmetry clash REVERT: R 132 ARG cc_start: 0.9035 (OUTLIER) cc_final: 0.8621 (ttt180) outliers start: 45 outliers final: 44 residues processed: 154 average time/residue: 1.3855 time to fit residues: 234.3189 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 : 1.673 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 72 VAL Chi-restraints excluded: chain R residue 115 LEU Chi-restraints excluded: chain R residue 132 ARG Chi-restraints excluded: chain R residue 141 VAL Chi-restraints excluded: chain R residue 169 VAL Chi-restraints excluded: chain R residue 229 THR Chi-restraints excluded: chain R residue 230 VAL Chi-restraints excluded: chain R residue 274 VAL Chi-restraints excluded: chain A residue 229 HIS Chi-restraints excluded: chain A residue 263 SER Chi-restraints excluded: chain A residue 328 ASN Chi-restraints excluded: chain A residue 332 LYS Chi-restraints excluded: chain A residue 338 LEU Chi-restraints excluded: chain A residue 372 PHE Chi-restraints excluded: chain A residue 404 MET Chi-restraints excluded: chain A residue 588 THR 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 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 329 ASN Chi-restraints excluded: chain C residue 332 LYS Chi-restraints excluded: chain C residue 338 LEU Chi-restraints excluded: chain C residue 396 CYS Chi-restraints excluded: chain C residue 660 THR Chi-restraints excluded: chain C residue 666 LYS Chi-restraints excluded: chain C residue 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 43 optimal weight: 8.9990 chunk 132 optimal weight: 10.0000 chunk 21 optimal weight: 6.9990 chunk 39 optimal weight: 1.9990 chunk 143 optimal weight: 8.9990 chunk 60 optimal weight: 0.1980 chunk 147 optimal weight: 7.9990 chunk 18 optimal weight: 5.9990 chunk 26 optimal weight: 4.9990 chunk 126 optimal weight: 0.0470 chunk 8 optimal weight: 3.9990 overall best weight: 2.2484 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 579 GLN C 253 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 = 0.3803 r_free = 0.3803 target = 0.135705 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3036 r_free = 0.3036 target = 0.084190 restraints weight = 26655.351| |-----------------------------------------------------------------------------| r_work (start): 0.2947 rms_B_bonded: 3.96 r_work: 0.2803 rms_B_bonded: 4.34 restraints_weight: 0.5000 r_work (final): 0.2803 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2807 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2807 r_free = 0.2807 target_work(ls_wunit_k1) = 0.071 | | occupancies: max = 1.00 min = 0.31 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2806 r_free = 0.2806 target_work(ls_wunit_k1) = 0.070 | | occupancies: max = 1.00 min = 0.28 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2806 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8768 moved from start: 0.4167 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.072 15069 Z= 0.172 Angle : 0.558 6.922 20528 Z= 0.288 Chirality : 0.042 0.215 2107 Planarity : 0.005 0.117 2728 Dihedral : 5.793 57.449 2034 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 4.46 Ramachandran Plot: Outliers : 0.49 % Allowed : 7.62 % Favored : 91.88 % Rotamer: Outliers : 2.42 % Allowed : 18.83 % Favored : 78.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.80 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.70 (0.20), residues: 1823 helix: -0.73 (0.57), residues: 88 sheet: -0.27 (0.24), residues: 404 loop : -0.50 (0.18), residues: 1331 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.001 TRP A 247 HIS 0.005 0.001 HIS B 255 PHE 0.014 0.001 PHE A 372 TYR 0.010 0.001 TYR R 213 ARG 0.012 0.001 ARG R 59 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5673.02 seconds wall clock time: 108 minutes 5.30 seconds (6485.30 seconds total)