Starting phenix.real_space_refine on Thu Feb 15 06:01:27 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cni_16758/02_2024/8cni_16758.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cni_16758/02_2024/8cni_16758.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.35 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cni_16758/02_2024/8cni_16758.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cni_16758/02_2024/8cni_16758.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cni_16758/02_2024/8cni_16758.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cni_16758/02_2024/8cni_16758.pdb" } resolution = 3.35 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= 0.001 sd= 0.028 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 S 31 5.16 5 C 3750 2.51 5 N 921 2.21 5 O 1016 1.98 5 H 5679 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped None Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 11397 Number of models: 1 Model: "" Number of chains: 3 Chain: "B" Number of atoms: 7677 Number of conformers: 1 Conformer: "" Number of residues, atoms: 494, 7677 Classifications: {'peptide': 494} Link IDs: {'PTRANS': 22, 'TRANS': 471} Chain breaks: 4 Chain: "A" Number of atoms: 1860 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 1860 Classifications: {'peptide': 124} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 3, 'TRANS': 120} Chain: "C" Number of atoms: 1860 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 1860 Classifications: {'peptide': 124} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 3, 'TRANS': 120} Time building chain proxies: 5.81, per 1000 atoms: 0.51 Number of scatterers: 11397 At special positions: 0 Unit cell: (94.35, 102, 114.75, 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) S 31 16.00 O 1016 8.00 N 921 7.00 C 3750 6.00 H 5679 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS B 129 " - pdb=" SG CYS B 161 " distance=2.03 Simple disulfide: pdb=" SG CYS A 22 " - pdb=" SG CYS A 96 " distance=2.03 Simple disulfide: pdb=" SG CYS C 22 " - pdb=" SG CYS C 96 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 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: 9.13 Conformation dependent library (CDL) restraints added in 1.4 seconds 1456 Ramachandran restraints generated. 728 Oldfield, 0 Emsley, 728 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1340 Finding SS restraints... Secondary structure from input PDB file: 32 helices and 5 sheets defined 52.7% alpha, 12.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.05 Creating SS restraints... Processing helix chain 'B' and resid 24 through 29 Processing helix chain 'B' and resid 33 through 39 Processing helix chain 'B' and resid 47 through 52 Processing helix chain 'B' and resid 54 through 59 Processing helix chain 'B' and resid 66 through 84 removed outlier: 3.549A pdb=" N SER B 71 " --> pdb=" O GLY B 67 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N LEU B 74 " --> pdb=" O ALA B 70 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N MET B 78 " --> pdb=" O LEU B 74 " (cutoff:3.500A) Processing helix chain 'B' and resid 84 through 95 removed outlier: 3.577A pdb=" N LEU B 91 " --> pdb=" O PHE B 87 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N ALA B 92 " --> pdb=" O GLY B 88 " (cutoff:3.500A) Processing helix chain 'B' and resid 97 through 114 Processing helix chain 'B' and resid 114 through 121 removed outlier: 3.952A pdb=" N VAL B 118 " --> pdb=" O LEU B 114 " (cutoff:3.500A) Processing helix chain 'B' and resid 121 through 130 removed outlier: 4.303A pdb=" N GLN B 126 " --> pdb=" O PRO B 122 " (cutoff:3.500A) removed outlier: 5.046A pdb=" N GLY B 127 " --> pdb=" O HIS B 123 " (cutoff:3.500A) Processing helix chain 'B' and resid 161 through 190 removed outlier: 3.541A pdb=" N LEU B 171 " --> pdb=" O VAL B 167 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N GLY B 177 " --> pdb=" O GLY B 173 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N LYS B 180 " --> pdb=" O VAL B 176 " (cutoff:3.500A) removed outlier: 4.153A pdb=" N ALA B 181 " --> pdb=" O GLY B 177 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ASN B 182 " --> pdb=" O SER B 178 " (cutoff:3.500A) removed outlier: 4.708A pdb=" N THR B 184 " --> pdb=" O LYS B 180 " (cutoff:3.500A) Proline residue: B 185 - end of helix removed outlier: 3.540A pdb=" N ALA B 188 " --> pdb=" O THR B 184 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N GLN B 190 " --> pdb=" O PHE B 186 " (cutoff:3.500A) Processing helix chain 'B' and resid 191 through 194 Processing helix chain 'B' and resid 195 through 208 removed outlier: 3.525A pdb=" N THR B 199 " --> pdb=" O GLY B 195 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N TRP B 205 " --> pdb=" O ARG B 201 " (cutoff:3.500A) Processing helix chain 'B' and resid 210 through 227 removed outlier: 3.558A pdb=" N ALA B 214 " --> pdb=" O ILE B 210 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N ILE B 215 " --> pdb=" O ASN B 211 " (cutoff:3.500A) removed outlier: 4.379A pdb=" N ALA B 222 " --> pdb=" O LEU B 218 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N TYR B 223 " --> pdb=" O GLY B 219 " (cutoff:3.500A) Processing helix chain 'B' and resid 234 through 251 removed outlier: 3.945A pdb=" N ALA B 238 " --> pdb=" O TYR B 234 " (cutoff:3.500A) Processing helix chain 'B' and resid 252 through 254 No H-bonds generated for 'chain 'B' and resid 252 through 254' Processing helix chain 'B' and resid 262 through 277 removed outlier: 3.587A pdb=" N THR B 266 " --> pdb=" O GLY B 262 " (cutoff:3.500A) Processing helix chain 'B' and resid 302 through 306 removed outlier: 3.891A pdb=" N MET B 306 " --> pdb=" O LEU B 303 " (cutoff:3.500A) Processing helix chain 'B' and resid 316 through 335 removed outlier: 4.016A pdb=" N VAL B 320 " --> pdb=" O ARG B 316 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N LYS B 328 " --> pdb=" O LYS B 324 " (cutoff:3.500A) Proline residue: B 331 - end of helix Processing helix chain 'B' and resid 336 through 356 removed outlier: 4.618A pdb=" N MET B 346 " --> pdb=" O VAL B 342 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N GLN B 347 " --> pdb=" O TYR B 343 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N THR B 348 " --> pdb=" O PHE B 344 " (cutoff:3.500A) removed outlier: 4.156A pdb=" N VAL B 351 " --> pdb=" O GLN B 347 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N LEU B 352 " --> pdb=" O THR B 348 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N HIS B 356 " --> pdb=" O LEU B 352 " (cutoff:3.500A) Processing helix chain 'B' and resid 384 through 393 removed outlier: 3.834A pdb=" N ILE B 389 " --> pdb=" O ILE B 385 " (cutoff:3.500A) Proline residue: B 390 - end of helix Processing helix chain 'B' and resid 396 through 403 removed outlier: 3.804A pdb=" N ASN B 403 " --> pdb=" O VAL B 399 " (cutoff:3.500A) Processing helix chain 'B' and resid 409 through 439 removed outlier: 3.723A pdb=" N ALA B 414 " --> pdb=" O LEU B 410 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N PHE B 418 " --> pdb=" O ALA B 414 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N PHE B 419 " --> pdb=" O VAL B 415 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N MET B 421 " --> pdb=" O MET B 417 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N LYS B 436 " --> pdb=" O SER B 432 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N LYS B 439 " --> pdb=" O LEU B 435 " (cutoff:3.500A) Processing helix chain 'B' and resid 458 through 462 Processing helix chain 'B' and resid 463 through 471 removed outlier: 3.676A pdb=" N LEU B 468 " --> pdb=" O PRO B 464 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N ILE B 469 " --> pdb=" O GLN B 465 " (cutoff:3.500A) Processing helix chain 'B' and resid 471 through 476 removed outlier: 3.869A pdb=" N PHE B 475 " --> pdb=" O PHE B 471 " (cutoff:3.500A) Processing helix chain 'B' and resid 476 through 487 removed outlier: 3.661A pdb=" N LEU B 481 " --> pdb=" O SER B 477 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N GLU B 482 " --> pdb=" O ILE B 478 " (cutoff:3.500A) Processing helix chain 'B' and resid 494 through 501 Processing helix chain 'B' and resid 504 through 519 removed outlier: 3.616A pdb=" N ALA B 516 " --> pdb=" O SER B 512 " (cutoff:3.500A) Processing helix chain 'B' and resid 539 through 568 removed outlier: 4.203A pdb=" N TYR B 543 " --> pdb=" O GLN B 539 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N PHE B 545 " --> pdb=" O ASN B 541 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N THR B 554 " --> pdb=" O ILE B 550 " (cutoff:3.500A) Processing helix chain 'A' and resid 87 through 91 Processing helix chain 'A' and resid 108 through 112 Processing helix chain 'C' and resid 87 through 91 Processing sheet with id=AA1, first strand: chain 'B' and resid 443 through 447 removed outlier: 3.521A pdb=" N VAL B 450 " --> pdb=" O ILE B 447 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 2 through 7 removed outlier: 3.943A pdb=" N GLN A 3 " --> pdb=" O SER A 25 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N VAL A 79 " --> pdb=" O CYS A 22 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 11 through 12 removed outlier: 3.769A pdb=" N LEU A 93 " --> pdb=" O GLN A 39 " (cutoff:3.500A) removed outlier: 6.817A pdb=" N LEU A 34 " --> pdb=" O ALA A 50 " (cutoff:3.500A) removed outlier: 4.628A pdb=" N ALA A 50 " --> pdb=" O LEU A 34 " (cutoff:3.500A) removed outlier: 6.665A pdb=" N TRP A 36 " --> pdb=" O VAL A 48 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ALA A 50 " --> pdb=" O TYR A 59 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 4 through 7 removed outlier: 3.540A pdb=" N VAL C 79 " --> pdb=" O CYS C 22 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 11 through 12 removed outlier: 3.804A pdb=" N TYR C 33 " --> pdb=" O ALA C 99 " (cutoff:3.500A) removed outlier: 5.538A pdb=" N ARG C 38 " --> pdb=" O GLY C 47 " (cutoff:3.500A) removed outlier: 4.894A pdb=" N GLY C 47 " --> pdb=" O ARG C 38 " (cutoff:3.500A) 275 hydrogen bonds defined for protein. 765 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: 4.10 Time building geometry restraints manager: 9.39 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 5672 1.03 - 1.23: 17 1.23 - 1.42: 2512 1.42 - 1.61: 3295 1.61 - 1.81: 49 Bond restraints: 11545 Sorted by residual: bond pdb=" CB ILE B 210 " pdb=" CG2 ILE B 210 " ideal model delta sigma weight residual 1.521 1.489 0.032 3.30e-02 9.18e+02 9.20e-01 bond pdb=" CB ARG B 44 " pdb=" CG ARG B 44 " ideal model delta sigma weight residual 1.520 1.494 0.026 3.00e-02 1.11e+03 7.68e-01 bond pdb=" CB ASN B 204 " pdb=" CG ASN B 204 " ideal model delta sigma weight residual 1.516 1.496 0.020 2.50e-02 1.60e+03 6.64e-01 bond pdb=" CG TYR B 109 " pdb=" CD1 TYR B 109 " ideal model delta sigma weight residual 1.389 1.372 0.017 2.10e-02 2.27e+03 6.55e-01 bond pdb=" CB THR B 101 " pdb=" CG2 THR B 101 " ideal model delta sigma weight residual 1.521 1.495 0.026 3.30e-02 9.18e+02 6.35e-01 ... (remaining 11540 not shown) Histogram of bond angle deviations from ideal: 99.87 - 106.71: 164 106.71 - 113.55: 13381 113.55 - 120.40: 4013 120.40 - 127.24: 3176 127.24 - 134.08: 76 Bond angle restraints: 20810 Sorted by residual: angle pdb=" N ILE A 28 " pdb=" CA ILE A 28 " pdb=" C ILE A 28 " ideal model delta sigma weight residual 111.91 109.73 2.18 8.90e-01 1.26e+00 5.97e+00 angle pdb=" N ILE A 28 " pdb=" CA ILE A 28 " pdb=" CB ILE A 28 " ideal model delta sigma weight residual 112.39 110.24 2.15 1.17e+00 7.31e-01 3.38e+00 angle pdb=" N MET B 497 " pdb=" CA MET B 497 " pdb=" C MET B 497 " ideal model delta sigma weight residual 112.89 110.92 1.97 1.24e+00 6.50e-01 2.51e+00 angle pdb=" N PHE B 502 " pdb=" CA PHE B 502 " pdb=" C PHE B 502 " ideal model delta sigma weight residual 113.41 111.54 1.87 1.22e+00 6.72e-01 2.34e+00 angle pdb=" N THR B 51 " pdb=" CA THR B 51 " pdb=" C THR B 51 " ideal model delta sigma weight residual 111.82 113.59 -1.77 1.16e+00 7.43e-01 2.32e+00 ... (remaining 20805 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.24: 5038 16.24 - 32.49: 275 32.49 - 48.73: 98 48.73 - 64.98: 53 64.98 - 81.22: 4 Dihedral angle restraints: 5468 sinusoidal: 2854 harmonic: 2614 Sorted by residual: dihedral pdb=" CA ILE B 496 " pdb=" C ILE B 496 " pdb=" N MET B 497 " pdb=" CA MET B 497 " ideal model delta harmonic sigma weight residual 180.00 162.80 17.20 0 5.00e+00 4.00e-02 1.18e+01 dihedral pdb=" CA ARG B 29 " pdb=" C ARG B 29 " pdb=" N ARG B 30 " pdb=" CA ARG B 30 " ideal model delta harmonic sigma weight residual 180.00 163.62 16.38 0 5.00e+00 4.00e-02 1.07e+01 dihedral pdb=" CA LEU B 95 " pdb=" C LEU B 95 " pdb=" N LEU B 96 " pdb=" CA LEU B 96 " ideal model delta harmonic sigma weight residual -180.00 -163.69 -16.31 0 5.00e+00 4.00e-02 1.06e+01 ... (remaining 5465 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.027: 502 0.027 - 0.053: 270 0.053 - 0.080: 79 0.080 - 0.106: 23 0.106 - 0.133: 20 Chirality restraints: 894 Sorted by residual: chirality pdb=" CA ILE B 132 " pdb=" N ILE B 132 " pdb=" C ILE B 132 " pdb=" CB ILE B 132 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.40e-01 chirality pdb=" CA ILE B 447 " pdb=" N ILE B 447 " pdb=" C ILE B 447 " pdb=" CB ILE B 447 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.04e-01 chirality pdb=" CA ILE B 359 " pdb=" N ILE B 359 " pdb=" C ILE B 359 " pdb=" CB ILE B 359 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.12 2.00e-01 2.50e+01 3.82e-01 ... (remaining 891 not shown) Planarity restraints: 1690 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PRO B 61 " 0.023 5.00e-02 4.00e+02 3.44e-02 1.89e+00 pdb=" N PRO B 62 " -0.059 5.00e-02 4.00e+02 pdb=" CA PRO B 62 " 0.017 5.00e-02 4.00e+02 pdb=" CD PRO B 62 " 0.019 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE B 337 " -0.022 5.00e-02 4.00e+02 3.28e-02 1.72e+00 pdb=" N PRO B 338 " 0.057 5.00e-02 4.00e+02 pdb=" CA PRO B 338 " -0.017 5.00e-02 4.00e+02 pdb=" CD PRO B 338 " -0.018 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE B 330 " -0.021 5.00e-02 4.00e+02 3.10e-02 1.53e+00 pdb=" N PRO B 331 " 0.054 5.00e-02 4.00e+02 pdb=" CA PRO B 331 " -0.016 5.00e-02 4.00e+02 pdb=" CD PRO B 331 " -0.017 5.00e-02 4.00e+02 ... (remaining 1687 not shown) Histogram of nonbonded interaction distances: 1.62 - 2.22: 863 2.22 - 2.81: 24290 2.81 - 3.41: 28917 3.41 - 4.00: 39375 4.00 - 4.60: 60807 Nonbonded interactions: 154252 Sorted by model distance: nonbonded pdb=" OD1 ASN B 534 " pdb=" H ASN B 536 " model vdw 1.624 1.850 nonbonded pdb=" OE1 GLU A 89 " pdb=" H GLU A 89 " model vdw 1.650 1.850 nonbonded pdb=" HZ3 LYS B 308 " pdb=" OE2 GLU B 321 " model vdw 1.656 1.850 nonbonded pdb=" OG1 THR C 91 " pdb=" H VAL C 123 " model vdw 1.656 1.850 nonbonded pdb=" OE1 GLN A 117 " pdb=" H GLN A 117 " model vdw 1.665 1.850 ... (remaining 154247 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' 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=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.210 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: 0.190 Extract box with map and model: 4.190 Check model and map are aligned: 0.180 Set scattering table: 0.120 Process input model: 40.130 Find NCS groups from input model: 0.290 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.870 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 49.230 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8234 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 0.035 5866 Z= 0.324 Angle : 0.481 4.860 7974 Z= 0.258 Chirality : 0.038 0.133 894 Planarity : 0.003 0.034 989 Dihedral : 9.349 54.018 2018 Min Nonbonded Distance : 2.126 Molprobity Statistics. All-atom Clashscore : 6.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer: Outliers : 0.34 % Allowed : 5.05 % Favored : 94.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.46 (0.33), residues: 728 helix: -1.66 (0.26), residues: 358 sheet: -0.25 (0.51), residues: 120 loop : 0.19 (0.44), residues: 250 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 208 HIS 0.001 0.001 HIS B 529 PHE 0.009 0.001 PHE B 372 TYR 0.011 0.001 TYR B 109 ARG 0.002 0.000 ARG B 125 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1456 Ramachandran restraints generated. 728 Oldfield, 0 Emsley, 728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1456 Ramachandran restraints generated. 728 Oldfield, 0 Emsley, 728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 594 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 139 time to evaluate : 0.939 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 44 ARG cc_start: 0.8578 (tpp-160) cc_final: 0.8319 (tpt170) REVERT: B 125 ARG cc_start: 0.8544 (ttp-170) cc_final: 0.6093 (ttt180) REVERT: B 232 ILE cc_start: 0.8889 (mm) cc_final: 0.8607 (mp) REVERT: B 263 SER cc_start: 0.8099 (t) cc_final: 0.7884 (t) REVERT: B 318 ASP cc_start: 0.7796 (p0) cc_final: 0.7538 (t0) REVERT: B 542 TYR cc_start: 0.7948 (m-80) cc_final: 0.7622 (m-80) REVERT: A 4 LEU cc_start: 0.9084 (mt) cc_final: 0.8579 (mt) REVERT: A 84 ASN cc_start: 0.7749 (m-40) cc_final: 0.7479 (m-40) REVERT: A 93 LEU cc_start: 0.9091 (tp) cc_final: 0.8876 (tp) REVERT: C 109 GLN cc_start: 0.8387 (pt0) cc_final: 0.7683 (mt0) REVERT: C 119 THR cc_start: 0.8226 (t) cc_final: 0.8015 (p) outliers start: 2 outliers final: 1 residues processed: 141 average time/residue: 0.3444 time to fit residues: 64.4048 Evaluate side-chains 125 residues out of total 594 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 124 time to evaluate : 0.962 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 178 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 61 optimal weight: 10.0000 chunk 55 optimal weight: 10.0000 chunk 30 optimal weight: 2.9990 chunk 18 optimal weight: 1.9990 chunk 37 optimal weight: 3.9990 chunk 29 optimal weight: 4.9990 chunk 57 optimal weight: 0.8980 chunk 22 optimal weight: 2.9990 chunk 34 optimal weight: 0.9980 chunk 42 optimal weight: 0.9990 chunk 66 optimal weight: 0.8980 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 53 ASN B 252 GLN B 444 ASN ** A 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 77 ASN C 117 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8177 moved from start: 0.2067 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.024 5866 Z= 0.242 Angle : 0.559 5.943 7974 Z= 0.304 Chirality : 0.039 0.133 894 Planarity : 0.004 0.035 989 Dihedral : 4.194 37.565 792 Min Nonbonded Distance : 1.940 Molprobity Statistics. All-atom Clashscore : 6.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer: Outliers : 0.51 % Allowed : 12.46 % Favored : 87.04 % 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: -0.57 (0.33), residues: 728 helix: -0.54 (0.28), residues: 356 sheet: 0.08 (0.53), residues: 120 loop : -0.01 (0.42), residues: 252 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 110 HIS 0.002 0.001 HIS B 453 PHE 0.018 0.002 PHE B 425 TYR 0.021 0.001 TYR B 109 ARG 0.002 0.000 ARG B 29 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1456 Ramachandran restraints generated. 728 Oldfield, 0 Emsley, 728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1456 Ramachandran restraints generated. 728 Oldfield, 0 Emsley, 728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 594 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 130 time to evaluate : 1.038 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 44 ARG cc_start: 0.8522 (tpp-160) cc_final: 0.8246 (tpt170) REVERT: B 125 ARG cc_start: 0.8484 (ttp-170) cc_final: 0.6059 (ttt180) REVERT: B 232 ILE cc_start: 0.8874 (mm) cc_final: 0.8597 (mp) REVERT: B 542 TYR cc_start: 0.7708 (m-80) cc_final: 0.7417 (m-80) REVERT: B 567 HIS cc_start: 0.7759 (t70) cc_final: 0.7480 (t-90) REVERT: C 109 GLN cc_start: 0.8371 (pt0) cc_final: 0.7676 (mt0) outliers start: 3 outliers final: 2 residues processed: 132 average time/residue: 0.3391 time to fit residues: 61.3105 Evaluate side-chains 120 residues out of total 594 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 118 time to evaluate : 0.875 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 178 SER Chi-restraints excluded: chain C residue 77 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 36 optimal weight: 3.9990 chunk 20 optimal weight: 2.9990 chunk 55 optimal weight: 9.9990 chunk 45 optimal weight: 7.9990 chunk 18 optimal weight: 1.9990 chunk 66 optimal weight: 5.9990 chunk 71 optimal weight: 6.9990 chunk 59 optimal weight: 4.9990 chunk 65 optimal weight: 5.9990 chunk 22 optimal weight: 1.9990 chunk 53 optimal weight: 4.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 53 ASN B 529 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8249 moved from start: 0.2582 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.057 5866 Z= 0.558 Angle : 0.618 5.336 7974 Z= 0.335 Chirality : 0.043 0.131 894 Planarity : 0.004 0.038 989 Dihedral : 4.573 37.882 792 Min Nonbonded Distance : 1.992 Molprobity Statistics. All-atom Clashscore : 7.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.67 % Favored : 95.33 % Rotamer: Outliers : 2.36 % Allowed : 12.12 % Favored : 85.52 % 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: -0.89 (0.32), residues: 728 helix: -0.73 (0.27), residues: 354 sheet: 0.02 (0.53), residues: 120 loop : -0.35 (0.41), residues: 254 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 208 HIS 0.001 0.000 HIS B 453 PHE 0.017 0.002 PHE B 77 TYR 0.019 0.002 TYR B 109 ARG 0.002 0.000 ARG B 201 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1456 Ramachandran restraints generated. 728 Oldfield, 0 Emsley, 728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1456 Ramachandran restraints generated. 728 Oldfield, 0 Emsley, 728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 594 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 119 time to evaluate : 0.868 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 44 ARG cc_start: 0.8600 (tpp-160) cc_final: 0.8362 (tpt170) REVERT: B 125 ARG cc_start: 0.8533 (ttp-170) cc_final: 0.6118 (ttt180) REVERT: B 267 ASP cc_start: 0.7921 (m-30) cc_final: 0.7522 (m-30) REVERT: C 109 GLN cc_start: 0.8383 (pt0) cc_final: 0.7673 (mt0) outliers start: 14 outliers final: 10 residues processed: 127 average time/residue: 0.3409 time to fit residues: 58.2084 Evaluate side-chains 128 residues out of total 594 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 118 time to evaluate : 0.824 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 178 SER Chi-restraints excluded: chain B residue 387 ILE Chi-restraints excluded: chain B residue 442 THR Chi-restraints excluded: chain B residue 451 THR Chi-restraints excluded: chain B residue 472 SER Chi-restraints excluded: chain B residue 563 VAL Chi-restraints excluded: chain A residue 30 THR Chi-restraints excluded: chain A residue 90 ASP Chi-restraints excluded: chain A residue 101 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 65 optimal weight: 6.9990 chunk 49 optimal weight: 6.9990 chunk 34 optimal weight: 0.9990 chunk 7 optimal weight: 0.9990 chunk 31 optimal weight: 0.9980 chunk 44 optimal weight: 0.1980 chunk 66 optimal weight: 4.9990 chunk 70 optimal weight: 6.9990 chunk 63 optimal weight: 3.9990 chunk 19 optimal weight: 0.9990 chunk 58 optimal weight: 5.9990 overall best weight: 0.8386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 74 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8169 moved from start: 0.2876 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 5866 Z= 0.187 Angle : 0.494 5.437 7974 Z= 0.260 Chirality : 0.037 0.135 894 Planarity : 0.004 0.035 989 Dihedral : 4.091 26.830 792 Min Nonbonded Distance : 2.006 Molprobity Statistics. All-atom Clashscore : 6.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Rotamer: Outliers : 1.18 % Allowed : 14.81 % Favored : 84.01 % 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: -0.42 (0.32), residues: 728 helix: -0.24 (0.28), residues: 354 sheet: 0.17 (0.53), residues: 120 loop : -0.26 (0.41), residues: 254 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 110 HIS 0.002 0.001 HIS B 453 PHE 0.013 0.001 PHE B 425 TYR 0.012 0.001 TYR B 109 ARG 0.003 0.000 ARG A 67 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1456 Ramachandran restraints generated. 728 Oldfield, 0 Emsley, 728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1456 Ramachandran restraints generated. 728 Oldfield, 0 Emsley, 728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 594 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 124 time to evaluate : 0.947 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 44 ARG cc_start: 0.8496 (tpp-160) cc_final: 0.8209 (tpt170) REVERT: B 232 ILE cc_start: 0.8906 (mm) cc_final: 0.8638 (mp) REVERT: C 109 GLN cc_start: 0.8368 (pt0) cc_final: 0.7663 (mt0) outliers start: 7 outliers final: 6 residues processed: 126 average time/residue: 0.3282 time to fit residues: 56.2817 Evaluate side-chains 128 residues out of total 594 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 122 time to evaluate : 0.936 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 387 ILE Chi-restraints excluded: chain B residue 442 THR Chi-restraints excluded: chain A residue 30 THR Chi-restraints excluded: chain A residue 101 THR Chi-restraints excluded: chain C residue 119 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 40 optimal weight: 1.9990 chunk 1 optimal weight: 0.9990 chunk 52 optimal weight: 2.9990 chunk 29 optimal weight: 0.0670 chunk 60 optimal weight: 0.9990 chunk 48 optimal weight: 1.9990 chunk 0 optimal weight: 2.9990 chunk 36 optimal weight: 4.9990 chunk 63 optimal weight: 5.9990 chunk 17 optimal weight: 0.0870 chunk 23 optimal weight: 0.8980 overall best weight: 0.6100 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8145 moved from start: 0.3178 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 5866 Z= 0.160 Angle : 0.474 5.118 7974 Z= 0.247 Chirality : 0.037 0.134 894 Planarity : 0.003 0.032 989 Dihedral : 3.814 15.860 791 Min Nonbonded Distance : 1.963 Molprobity Statistics. All-atom Clashscore : 6.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 1.68 % Allowed : 14.81 % Favored : 83.50 % 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: -0.15 (0.32), residues: 728 helix: 0.10 (0.28), residues: 356 sheet: 0.18 (0.52), residues: 120 loop : -0.26 (0.41), residues: 252 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 110 HIS 0.001 0.000 HIS B 356 PHE 0.008 0.001 PHE B 425 TYR 0.010 0.001 TYR A 100 ARG 0.002 0.000 ARG A 67 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1456 Ramachandran restraints generated. 728 Oldfield, 0 Emsley, 728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1456 Ramachandran restraints generated. 728 Oldfield, 0 Emsley, 728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 594 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 121 time to evaluate : 0.815 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 44 ARG cc_start: 0.8470 (tpp-160) cc_final: 0.8126 (tpt170) REVERT: B 125 ARG cc_start: 0.8471 (ttp-170) cc_final: 0.6126 (ttt180) REVERT: B 232 ILE cc_start: 0.8876 (mm) cc_final: 0.8611 (mp) outliers start: 10 outliers final: 8 residues processed: 125 average time/residue: 0.3107 time to fit residues: 53.2649 Evaluate side-chains 129 residues out of total 594 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 121 time to evaluate : 0.893 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 438 VAL Chi-restraints excluded: chain B residue 442 THR Chi-restraints excluded: chain B residue 451 THR Chi-restraints excluded: chain B residue 472 SER Chi-restraints excluded: chain A residue 30 THR Chi-restraints excluded: chain A residue 101 THR Chi-restraints excluded: chain C residue 119 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 63 optimal weight: 20.0000 chunk 13 optimal weight: 1.9990 chunk 41 optimal weight: 1.9990 chunk 17 optimal weight: 0.0170 chunk 70 optimal weight: 10.0000 chunk 58 optimal weight: 10.0000 chunk 32 optimal weight: 2.9990 chunk 5 optimal weight: 1.9990 chunk 23 optimal weight: 0.9990 chunk 37 optimal weight: 2.9990 chunk 68 optimal weight: 3.9990 overall best weight: 1.4026 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 74 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8172 moved from start: 0.3186 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 5866 Z= 0.259 Angle : 0.496 4.642 7974 Z= 0.259 Chirality : 0.038 0.133 894 Planarity : 0.004 0.033 989 Dihedral : 3.843 15.235 791 Min Nonbonded Distance : 2.002 Molprobity Statistics. All-atom Clashscore : 6.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Rotamer: Outliers : 1.68 % Allowed : 15.99 % Favored : 82.32 % 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: -0.19 (0.32), residues: 728 helix: 0.09 (0.28), residues: 354 sheet: 0.17 (0.51), residues: 120 loop : -0.33 (0.41), residues: 254 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 110 HIS 0.001 0.000 HIS B 356 PHE 0.011 0.001 PHE C 37 TYR 0.013 0.001 TYR B 109 ARG 0.002 0.000 ARG B 434 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1456 Ramachandran restraints generated. 728 Oldfield, 0 Emsley, 728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1456 Ramachandran restraints generated. 728 Oldfield, 0 Emsley, 728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 594 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 117 time to evaluate : 0.905 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 44 ARG cc_start: 0.8517 (tpp-160) cc_final: 0.8202 (tpt170) REVERT: B 232 ILE cc_start: 0.8895 (mm) cc_final: 0.8627 (mp) outliers start: 10 outliers final: 8 residues processed: 121 average time/residue: 0.3051 time to fit residues: 50.9613 Evaluate side-chains 125 residues out of total 594 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 117 time to evaluate : 0.894 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 378 THR Chi-restraints excluded: chain B residue 438 VAL Chi-restraints excluded: chain B residue 442 THR Chi-restraints excluded: chain B residue 451 THR Chi-restraints excluded: chain B residue 472 SER Chi-restraints excluded: chain A residue 30 THR Chi-restraints excluded: chain A residue 101 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 7 optimal weight: 1.9990 chunk 40 optimal weight: 1.9990 chunk 51 optimal weight: 6.9990 chunk 39 optimal weight: 1.9990 chunk 59 optimal weight: 0.9980 chunk 70 optimal weight: 7.9990 chunk 44 optimal weight: 2.9990 chunk 42 optimal weight: 0.9990 chunk 32 optimal weight: 0.3980 chunk 43 optimal weight: 0.9990 chunk 28 optimal weight: 0.5980 overall best weight: 0.7984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 74 ASN ** A 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8143 moved from start: 0.3297 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 5866 Z= 0.169 Angle : 0.474 5.610 7974 Z= 0.247 Chirality : 0.037 0.134 894 Planarity : 0.003 0.031 989 Dihedral : 3.736 14.789 791 Min Nonbonded Distance : 1.969 Molprobity Statistics. All-atom Clashscore : 6.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 1.68 % Allowed : 15.82 % Favored : 82.49 % 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: 0.01 (0.32), residues: 728 helix: 0.29 (0.29), residues: 351 sheet: 0.22 (0.51), residues: 120 loop : -0.27 (0.41), residues: 257 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 110 HIS 0.001 0.000 HIS B 356 PHE 0.008 0.001 PHE B 77 TYR 0.011 0.001 TYR B 109 ARG 0.001 0.000 ARG A 45 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1456 Ramachandran restraints generated. 728 Oldfield, 0 Emsley, 728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1456 Ramachandran restraints generated. 728 Oldfield, 0 Emsley, 728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 594 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 119 time to evaluate : 0.946 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 44 ARG cc_start: 0.8479 (tpp-160) cc_final: 0.8139 (tpt170) REVERT: B 232 ILE cc_start: 0.8873 (mm) cc_final: 0.8616 (mp) REVERT: A 39 GLN cc_start: 0.7389 (tp40) cc_final: 0.7115 (tp40) REVERT: A 83 MET cc_start: 0.7255 (mpp) cc_final: 0.6978 (mtm) outliers start: 10 outliers final: 10 residues processed: 123 average time/residue: 0.3053 time to fit residues: 51.9548 Evaluate side-chains 128 residues out of total 594 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 118 time to evaluate : 0.918 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 378 THR Chi-restraints excluded: chain B residue 403 ASN Chi-restraints excluded: chain B residue 438 VAL Chi-restraints excluded: chain B residue 442 THR Chi-restraints excluded: chain B residue 451 THR Chi-restraints excluded: chain B residue 472 SER Chi-restraints excluded: chain A residue 18 LEU Chi-restraints excluded: chain A residue 30 THR Chi-restraints excluded: chain A residue 101 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 42 optimal weight: 0.9990 chunk 21 optimal weight: 0.7980 chunk 13 optimal weight: 0.9990 chunk 44 optimal weight: 2.9990 chunk 47 optimal weight: 1.9990 chunk 34 optimal weight: 0.9980 chunk 6 optimal weight: 0.9990 chunk 55 optimal weight: 3.9990 chunk 64 optimal weight: 8.9990 chunk 67 optimal weight: 20.0000 chunk 61 optimal weight: 8.9990 overall best weight: 0.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 227 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8147 moved from start: 0.3434 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 5866 Z= 0.195 Angle : 0.475 4.544 7974 Z= 0.247 Chirality : 0.037 0.134 894 Planarity : 0.003 0.031 989 Dihedral : 3.702 14.578 791 Min Nonbonded Distance : 1.986 Molprobity Statistics. All-atom Clashscore : 6.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer: Outliers : 1.68 % Allowed : 15.82 % Favored : 82.49 % 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: 0.01 (0.32), residues: 728 helix: 0.28 (0.28), residues: 358 sheet: 0.22 (0.50), residues: 120 loop : -0.27 (0.41), residues: 250 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 110 HIS 0.001 0.000 HIS B 356 PHE 0.009 0.001 PHE B 77 TYR 0.011 0.001 TYR B 109 ARG 0.001 0.000 ARG B 29 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1456 Ramachandran restraints generated. 728 Oldfield, 0 Emsley, 728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1456 Ramachandran restraints generated. 728 Oldfield, 0 Emsley, 728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 594 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 117 time to evaluate : 0.841 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 44 ARG cc_start: 0.8488 (tpp-160) cc_final: 0.8153 (tpt170) REVERT: B 232 ILE cc_start: 0.8871 (mm) cc_final: 0.8615 (mp) REVERT: A 39 GLN cc_start: 0.7476 (tp40) cc_final: 0.7214 (tp40) REVERT: A 83 MET cc_start: 0.7302 (mpp) cc_final: 0.6854 (mtm) outliers start: 10 outliers final: 10 residues processed: 121 average time/residue: 0.2827 time to fit residues: 47.8285 Evaluate side-chains 127 residues out of total 594 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 117 time to evaluate : 1.114 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 378 THR Chi-restraints excluded: chain B residue 403 ASN Chi-restraints excluded: chain B residue 438 VAL Chi-restraints excluded: chain B residue 442 THR Chi-restraints excluded: chain B residue 451 THR Chi-restraints excluded: chain B residue 472 SER Chi-restraints excluded: chain A residue 18 LEU Chi-restraints excluded: chain A residue 30 THR Chi-restraints excluded: chain A residue 101 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 65 optimal weight: 6.9990 chunk 67 optimal weight: 20.0000 chunk 39 optimal weight: 1.9990 chunk 28 optimal weight: 0.0030 chunk 51 optimal weight: 0.5980 chunk 20 optimal weight: 1.9990 chunk 59 optimal weight: 0.8980 chunk 62 optimal weight: 20.0000 chunk 43 optimal weight: 0.9980 chunk 69 optimal weight: 0.5980 chunk 42 optimal weight: 0.9990 overall best weight: 0.6190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 74 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8122 moved from start: 0.3479 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 5866 Z= 0.147 Angle : 0.462 4.528 7974 Z= 0.240 Chirality : 0.037 0.135 894 Planarity : 0.003 0.031 989 Dihedral : 3.591 14.227 791 Min Nonbonded Distance : 1.970 Molprobity Statistics. All-atom Clashscore : 6.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 1.18 % Allowed : 16.33 % Favored : 82.49 % 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: 0.17 (0.33), residues: 728 helix: 0.44 (0.29), residues: 358 sheet: 0.28 (0.50), residues: 120 loop : -0.24 (0.41), residues: 250 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 110 HIS 0.001 0.000 HIS B 356 PHE 0.007 0.001 PHE B 425 TYR 0.009 0.001 TYR B 109 ARG 0.001 0.000 ARG B 29 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1456 Ramachandran restraints generated. 728 Oldfield, 0 Emsley, 728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1456 Ramachandran restraints generated. 728 Oldfield, 0 Emsley, 728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 594 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 117 time to evaluate : 0.948 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 44 ARG cc_start: 0.8471 (tpp-160) cc_final: 0.8132 (tpt170) REVERT: B 232 ILE cc_start: 0.8830 (mm) cc_final: 0.8583 (mp) REVERT: A 83 MET cc_start: 0.7236 (mpp) cc_final: 0.6761 (mtm) outliers start: 7 outliers final: 6 residues processed: 119 average time/residue: 0.3127 time to fit residues: 52.1328 Evaluate side-chains 122 residues out of total 594 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 116 time to evaluate : 0.757 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 378 THR Chi-restraints excluded: chain B residue 403 ASN Chi-restraints excluded: chain B residue 442 THR Chi-restraints excluded: chain B residue 472 SER Chi-restraints excluded: chain A residue 18 LEU Chi-restraints excluded: chain A residue 30 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 32 optimal weight: 0.1980 chunk 48 optimal weight: 0.5980 chunk 72 optimal weight: 1.9990 chunk 66 optimal weight: 5.9990 chunk 57 optimal weight: 10.0000 chunk 6 optimal weight: 0.1980 chunk 44 optimal weight: 2.9990 chunk 35 optimal weight: 0.9990 chunk 46 optimal weight: 0.5980 chunk 61 optimal weight: 4.9990 chunk 17 optimal weight: 1.9990 overall best weight: 0.5182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8112 moved from start: 0.3601 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 5866 Z= 0.140 Angle : 0.460 4.551 7974 Z= 0.238 Chirality : 0.037 0.137 894 Planarity : 0.003 0.031 989 Dihedral : 3.535 14.270 791 Min Nonbonded Distance : 1.973 Molprobity Statistics. All-atom Clashscore : 5.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 0.84 % Allowed : 16.67 % Favored : 82.49 % 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: 0.27 (0.32), residues: 728 helix: 0.56 (0.29), residues: 358 sheet: 0.34 (0.50), residues: 120 loop : -0.25 (0.41), residues: 250 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP A 110 HIS 0.001 0.000 HIS B 356 PHE 0.006 0.001 PHE B 425 TYR 0.011 0.001 TYR A 100 ARG 0.001 0.000 ARG B 29 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1456 Ramachandran restraints generated. 728 Oldfield, 0 Emsley, 728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1456 Ramachandran restraints generated. 728 Oldfield, 0 Emsley, 728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 594 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 117 time to evaluate : 0.792 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 44 ARG cc_start: 0.8438 (tpp-160) cc_final: 0.8112 (tpt170) REVERT: B 232 ILE cc_start: 0.8794 (mm) cc_final: 0.8548 (mp) REVERT: A 82 GLN cc_start: 0.7966 (tm-30) cc_final: 0.7201 (tm-30) REVERT: A 83 MET cc_start: 0.7260 (mpp) cc_final: 0.6494 (mtm) outliers start: 5 outliers final: 5 residues processed: 118 average time/residue: 0.2990 time to fit residues: 49.0194 Evaluate side-chains 120 residues out of total 594 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 115 time to evaluate : 0.794 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 378 THR Chi-restraints excluded: chain B residue 403 ASN Chi-restraints excluded: chain B residue 442 THR Chi-restraints excluded: chain B residue 472 SER Chi-restraints excluded: chain A residue 18 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 53 optimal weight: 0.9980 chunk 8 optimal weight: 0.9980 chunk 16 optimal weight: 0.7980 chunk 58 optimal weight: 5.9990 chunk 24 optimal weight: 2.9990 chunk 59 optimal weight: 0.8980 chunk 7 optimal weight: 0.4980 chunk 10 optimal weight: 2.9990 chunk 50 optimal weight: 7.9990 chunk 3 optimal weight: 1.9990 chunk 41 optimal weight: 1.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4192 r_free = 0.4192 target = 0.197355 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.121179 restraints weight = 18317.732| |-----------------------------------------------------------------------------| r_work (start): 0.3225 rms_B_bonded: 2.91 r_work: 0.2996 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.2855 rms_B_bonded: 4.59 restraints_weight: 0.2500 r_work (final): 0.2855 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8413 moved from start: 0.3555 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 5866 Z= 0.175 Angle : 0.465 4.532 7974 Z= 0.242 Chirality : 0.037 0.135 894 Planarity : 0.003 0.030 989 Dihedral : 3.553 14.787 791 Min Nonbonded Distance : 1.993 Molprobity Statistics. All-atom Clashscore : 6.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 0.84 % Allowed : 16.84 % Favored : 82.32 % 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: 0.28 (0.32), residues: 728 helix: 0.56 (0.29), residues: 358 sheet: 0.36 (0.50), residues: 120 loop : -0.24 (0.41), residues: 250 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP A 110 HIS 0.001 0.000 HIS B 356 PHE 0.007 0.001 PHE B 77 TYR 0.010 0.001 TYR B 109 ARG 0.001 0.000 ARG B 29 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3274.34 seconds wall clock time: 58 minutes 33.33 seconds (3513.33 seconds total)