Starting phenix.real_space_refine on Tue Feb 13 17:06:13 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6p2j_20238/02_2024/6p2j_20238_neut_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6p2j_20238/02_2024/6p2j_20238.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6p2j_20238/02_2024/6p2j_20238_neut_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6p2j_20238/02_2024/6p2j_20238_neut_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6p2j_20238/02_2024/6p2j_20238_neut_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6p2j_20238/02_2024/6p2j_20238.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6p2j_20238/02_2024/6p2j_20238.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6p2j_20238/02_2024/6p2j_20238_neut_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6p2j_20238/02_2024/6p2j_20238_neut_updated.pdb" } resolution = 3.0 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 P 6 5.49 5 S 38 5.16 5 C 4759 2.51 5 N 1091 2.21 5 O 1121 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 126": "NH1" <-> "NH2" Residue "A ARG 139": "NH1" <-> "NH2" Residue "A GLU 164": "OE1" <-> "OE2" Residue "A ARG 262": "NH1" <-> "NH2" Residue "A GLU 273": "OE1" <-> "OE2" Residue "A ARG 277": "NH1" <-> "NH2" Residue "A ARG 319": "NH1" <-> "NH2" Residue "A GLU 394": "OE1" <-> "OE2" Residue "A ARG 397": "NH1" <-> "NH2" Residue "A ARG 401": "NH1" <-> "NH2" Residue "A ARG 418": "NH1" <-> "NH2" Residue "A ARG 443": "NH1" <-> "NH2" Residue "A ARG 525": "NH1" <-> "NH2" Residue "B ARG 126": "NH1" <-> "NH2" Residue "B ARG 139": "NH1" <-> "NH2" Residue "B ARG 262": "NH1" <-> "NH2" Residue "B ARG 277": "NH1" <-> "NH2" Residue "B ARG 343": "NH1" <-> "NH2" Residue "B ARG 350": "NH1" <-> "NH2" Residue "B GLU 394": "OE1" <-> "OE2" Residue "B ARG 397": "NH1" <-> "NH2" Residue "B ARG 401": "NH1" <-> "NH2" Residue "B ARG 418": "NH1" <-> "NH2" Residue "B ARG 443": "NH1" <-> "NH2" Residue "B ARG 494": "NH1" <-> "NH2" Residue "B ARG 525": "NH1" <-> "NH2" 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: 7015 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 3448 Number of conformers: 1 Conformer: "" Number of residues, atoms: 408, 3448 Classifications: {'peptide': 408} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 18, 'TRANS': 389} Chain breaks: 1 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 3433 Number of conformers: 1 Conformer: "" Number of residues, atoms: 408, 3433 Classifications: {'peptide': 408} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 18, 'TRANS': 389} Chain breaks: 1 Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 19 Unresolved non-hydrogen dihedrals: 11 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "A" Number of atoms: 67 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 67 Unusual residues: {'3VV': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 67 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 67 Unusual residues: {'3VV': 1} Classifications: {'undetermined': 1} Time building chain proxies: 3.83, per 1000 atoms: 0.55 Number of scatterers: 7015 At special positions: 0 Unit cell: (134.794, 94.69, 79.094, 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 38 16.00 P 6 15.00 O 1121 8.00 N 1091 7.00 C 4759 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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: 2.81 Conformation dependent library (CDL) restraints added in 1.2 seconds 1616 Ramachandran restraints generated. 808 Oldfield, 0 Emsley, 808 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1572 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 37 helices and 0 sheets defined 70.8% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.51 Creating SS restraints... Processing helix chain 'A' and resid 128 through 132 removed outlier: 3.827A pdb=" N LEU A 132 " --> pdb=" O LEU A 128 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 128 through 132' Processing helix chain 'A' and resid 136 through 164 removed outlier: 3.816A pdb=" N ASP A 163 " --> pdb=" O VAL A 159 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N GLU A 164 " --> pdb=" O ASP A 160 " (cutoff:3.500A) Processing helix chain 'A' and resid 172 through 177 removed outlier: 3.532A pdb=" N TYR A 176 " --> pdb=" O SER A 172 " (cutoff:3.500A) Processing helix chain 'A' and resid 181 through 209 Proline residue: A 199 - end of helix removed outlier: 3.569A pdb=" N THR A 208 " --> pdb=" O GLN A 204 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N GLY A 209 " --> pdb=" O HIS A 205 " (cutoff:3.500A) Processing helix chain 'A' and resid 218 through 245 removed outlier: 3.613A pdb=" N LEU A 235 " --> pdb=" O GLN A 231 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N GLY A 236 " --> pdb=" O ILE A 232 " (cutoff:3.500A) Proline residue: A 239 - end of helix Processing helix chain 'A' and resid 250 through 272 Processing helix chain 'A' and resid 275 through 279 removed outlier: 3.793A pdb=" N LEU A 279 " --> pdb=" O VAL A 275 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 275 through 279' Processing helix chain 'A' and resid 294 through 302 removed outlier: 3.966A pdb=" N TYR A 299 " --> pdb=" O ASN A 295 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N PHE A 302 " --> pdb=" O LEU A 298 " (cutoff:3.500A) Processing helix chain 'A' and resid 320 through 344 Processing helix chain 'A' and resid 346 through 354 Processing helix chain 'A' and resid 362 through 366 Processing helix chain 'A' and resid 370 through 385 Processing helix chain 'A' and resid 387 through 396 Processing helix chain 'A' and resid 407 through 409 No H-bonds generated for 'chain 'A' and resid 407 through 409' Processing helix chain 'A' and resid 422 through 431 Processing helix chain 'A' and resid 433 through 439 removed outlier: 3.504A pdb=" N PHE A 439 " --> pdb=" O ASP A 435 " (cutoff:3.500A) Processing helix chain 'A' and resid 445 through 468 Processing helix chain 'A' and resid 474 through 491 removed outlier: 3.578A pdb=" N VAL A 490 " --> pdb=" O PHE A 486 " (cutoff:3.500A) Processing helix chain 'A' and resid 497 through 523 Processing helix chain 'B' and resid 129 through 132 No H-bonds generated for 'chain 'B' and resid 129 through 132' Processing helix chain 'B' and resid 136 through 163 removed outlier: 3.719A pdb=" N ILE B 162 " --> pdb=" O VAL B 158 " (cutoff:3.500A) Processing helix chain 'B' and resid 172 through 178 removed outlier: 3.873A pdb=" N TYR B 176 " --> pdb=" O SER B 172 " (cutoff:3.500A) Processing helix chain 'B' and resid 181 through 208 Proline residue: B 199 - end of helix removed outlier: 3.753A pdb=" N THR B 208 " --> pdb=" O GLN B 204 " (cutoff:3.500A) Processing helix chain 'B' and resid 218 through 245 removed outlier: 4.257A pdb=" N LEU B 235 " --> pdb=" O GLN B 231 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N GLY B 236 " --> pdb=" O ILE B 232 " (cutoff:3.500A) Proline residue: B 239 - end of helix Processing helix chain 'B' and resid 252 through 272 Processing helix chain 'B' and resid 275 through 279 Processing helix chain 'B' and resid 294 through 302 removed outlier: 3.805A pdb=" N TYR B 299 " --> pdb=" O ASN B 295 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N PHE B 302 " --> pdb=" O LEU B 298 " (cutoff:3.500A) Processing helix chain 'B' and resid 320 through 354 Proline residue: B 347 - end of helix Processing helix chain 'B' and resid 359 through 366 Processing helix chain 'B' and resid 370 through 385 Processing helix chain 'B' and resid 387 through 395 Processing helix chain 'B' and resid 407 through 409 No H-bonds generated for 'chain 'B' and resid 407 through 409' Processing helix chain 'B' and resid 422 through 430 Processing helix chain 'B' and resid 433 through 439 Processing helix chain 'B' and resid 442 through 468 removed outlier: 5.711A pdb=" N SER B 446 " --> pdb=" O ARG B 443 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N LEU B 450 " --> pdb=" O ALA B 447 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N PHE B 453 " --> pdb=" O LEU B 450 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N SER B 456 " --> pdb=" O PHE B 453 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N VAL B 458 " --> pdb=" O VAL B 455 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N VAL B 459 " --> pdb=" O SER B 456 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N GLU B 461 " --> pdb=" O VAL B 458 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N TYR B 462 " --> pdb=" O VAL B 459 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N LEU B 464 " --> pdb=" O GLU B 461 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ALA B 465 " --> pdb=" O TYR B 462 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N VAL B 466 " --> pdb=" O ALA B 463 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N LEU B 468 " --> pdb=" O ALA B 465 " (cutoff:3.500A) Processing helix chain 'B' and resid 474 through 490 Processing helix chain 'B' and resid 497 through 525 386 hydrogen bonds defined for protein. 1122 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: 1.69 Time building geometry restraints manager: 2.94 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 1041 1.33 - 1.46: 2442 1.46 - 1.58: 3728 1.58 - 1.71: 7 1.71 - 1.83: 65 Bond restraints: 7283 Sorted by residual: bond pdb=" C49 3VV B 700 " pdb=" C50 3VV B 700 " ideal model delta sigma weight residual 1.291 1.524 -0.233 2.00e-02 2.50e+03 1.36e+02 bond pdb=" C49 3VV A 700 " pdb=" C50 3VV A 700 " ideal model delta sigma weight residual 1.291 1.524 -0.233 2.00e-02 2.50e+03 1.36e+02 bond pdb=" C49 3VV B 700 " pdb=" O48 3VV B 700 " ideal model delta sigma weight residual 1.621 1.402 0.219 2.00e-02 2.50e+03 1.19e+02 bond pdb=" C49 3VV A 700 " pdb=" O48 3VV A 700 " ideal model delta sigma weight residual 1.621 1.409 0.212 2.00e-02 2.50e+03 1.12e+02 bond pdb=" C47 3VV A 700 " pdb=" O48 3VV A 700 " ideal model delta sigma weight residual 1.286 1.452 -0.166 2.00e-02 2.50e+03 6.89e+01 ... (remaining 7278 not shown) Histogram of bond angle deviations from ideal: 78.53 - 90.76: 3 90.76 - 102.99: 69 102.99 - 115.21: 3970 115.21 - 127.44: 5753 127.44 - 139.67: 128 Bond angle restraints: 9923 Sorted by residual: angle pdb=" O37 3VV A 700 " pdb=" P38 3VV A 700 " pdb=" O40 3VV A 700 " ideal model delta sigma weight residual 109.48 78.53 30.95 3.00e+00 1.11e-01 1.06e+02 angle pdb=" C09 3VV A 700 " pdb=" C10 3VV A 700 " pdb=" C11 3VV A 700 " ideal model delta sigma weight residual 152.65 125.82 26.83 3.00e+00 1.11e-01 8.00e+01 angle pdb=" C09 3VV B 700 " pdb=" C10 3VV B 700 " pdb=" C11 3VV B 700 " ideal model delta sigma weight residual 152.65 127.97 24.68 3.00e+00 1.11e-01 6.77e+01 angle pdb=" O41 3VV A 700 " pdb=" P42 3VV A 700 " pdb=" O44 3VV A 700 " ideal model delta sigma weight residual 109.47 86.77 22.70 3.00e+00 1.11e-01 5.72e+01 angle pdb=" CA PHE B 258 " pdb=" CB PHE B 258 " pdb=" CG PHE B 258 " ideal model delta sigma weight residual 113.80 121.35 -7.55 1.00e+00 1.00e+00 5.70e+01 ... (remaining 9918 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.27: 3795 23.27 - 46.54: 215 46.54 - 69.81: 49 69.81 - 93.08: 8 93.08 - 116.35: 2 Dihedral angle restraints: 4069 sinusoidal: 1631 harmonic: 2438 Sorted by residual: dihedral pdb=" CA ASN B 491 " pdb=" C ASN B 491 " pdb=" N ASP B 492 " pdb=" CA ASP B 492 " ideal model delta harmonic sigma weight residual -180.00 -151.04 -28.96 0 5.00e+00 4.00e-02 3.36e+01 dihedral pdb=" C VAL A 198 " pdb=" N VAL A 198 " pdb=" CA VAL A 198 " pdb=" CB VAL A 198 " ideal model delta harmonic sigma weight residual -122.00 -135.29 13.29 0 2.50e+00 1.60e-01 2.83e+01 dihedral pdb=" CA VAL A 361 " pdb=" C VAL A 361 " pdb=" N LEU A 362 " pdb=" CA LEU A 362 " ideal model delta harmonic sigma weight residual 180.00 153.87 26.13 0 5.00e+00 4.00e-02 2.73e+01 ... (remaining 4066 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.092: 612 0.092 - 0.183: 314 0.183 - 0.275: 82 0.275 - 0.366: 27 0.366 - 0.458: 8 Chirality restraints: 1043 Sorted by residual: chirality pdb=" CA PRO B 529 " pdb=" N PRO B 529 " pdb=" C PRO B 529 " pdb=" CB PRO B 529 " both_signs ideal model delta sigma weight residual False 2.72 2.26 0.46 2.00e-01 2.50e+01 5.23e+00 chirality pdb=" CA CYS B 345 " pdb=" N CYS B 345 " pdb=" C CYS B 345 " pdb=" CB CYS B 345 " both_signs ideal model delta sigma weight residual False 2.51 2.07 0.44 2.00e-01 2.50e+01 4.90e+00 chirality pdb=" CA ARG A 126 " pdb=" N ARG A 126 " pdb=" C ARG A 126 " pdb=" CB ARG A 126 " both_signs ideal model delta sigma weight residual False 2.51 2.07 0.44 2.00e-01 2.50e+01 4.78e+00 ... (remaining 1040 not shown) Planarity restraints: 1191 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C27 3VV A 700 " -0.346 2.00e-02 2.50e+03 2.94e-01 1.08e+03 pdb=" C29 3VV A 700 " 0.091 2.00e-02 2.50e+03 pdb=" C31 3VV A 700 " -0.163 2.00e-02 2.50e+03 pdb=" N28 3VV A 700 " 0.518 2.00e-02 2.50e+03 pdb=" O30 3VV A 700 " -0.101 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C08 3VV A 700 " 0.101 2.00e-02 2.50e+03 2.49e-01 6.20e+02 pdb=" C09 3VV A 700 " -0.335 2.00e-02 2.50e+03 pdb=" C10 3VV A 700 " 0.339 2.00e-02 2.50e+03 pdb=" C11 3VV A 700 " -0.105 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 230 " 0.115 2.00e-02 2.50e+03 7.03e-02 8.65e+01 pdb=" CG PHE A 230 " -0.099 2.00e-02 2.50e+03 pdb=" CD1 PHE A 230 " -0.064 2.00e-02 2.50e+03 pdb=" CD2 PHE A 230 " -0.054 2.00e-02 2.50e+03 pdb=" CE1 PHE A 230 " 0.024 2.00e-02 2.50e+03 pdb=" CE2 PHE A 230 " 0.015 2.00e-02 2.50e+03 pdb=" CZ PHE A 230 " 0.063 2.00e-02 2.50e+03 ... (remaining 1188 not shown) Histogram of nonbonded interaction distances: 2.51 - 2.99: 2812 2.99 - 3.47: 7278 3.47 - 3.94: 11372 3.94 - 4.42: 12182 4.42 - 4.90: 20369 Nonbonded interactions: 54013 Sorted by model distance: nonbonded pdb=" O51 3VV A 700 " pdb=" O57 3VV A 700 " model vdw 2.508 2.440 nonbonded pdb=" O GLU A 170 " pdb=" OH TYR A 338 " model vdw 2.528 2.440 nonbonded pdb=" O25 3VV A 700 " pdb=" O30 3VV A 700 " model vdw 2.552 3.040 nonbonded pdb=" O43 3VV A 700 " pdb=" O48 3VV A 700 " model vdw 2.553 3.040 nonbonded pdb=" O TRP A 407 " pdb=" N SER A 410 " model vdw 2.601 2.520 ... (remaining 54008 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' and (resid 118 through 165 or (resid 166 and (name N or name CA or na \ me C or name O or name CB )) or resid 167 through 168 or (resid 169 through 170 \ and (name N or name CA or name C or name O or name CB )) or resid 171 through 28 \ 8 or (resid 289 and (name N or name CA or name C or name O or name CB )) or resi \ d 290 through 529 or resid 700)) selection = (chain 'B' and (resid 118 through 286 or resid 288 through 290 or (resid 291 and \ (name N or name CA or name C or name O or name CB )) or resid 292 through 529 o \ r resid 700)) } 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: 0.890 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: 0.010 Extract box with map and model: 4.960 Check model and map are aligned: 0.110 Set scattering table: 0.070 Process input model: 21.490 Find NCS groups from input model: 0.380 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:12.120 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 40.060 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7014 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 : 0.017 0.233 7283 Z= 1.095 Angle : 2.200 30.953 9923 Z= 1.436 Chirality : 0.119 0.458 1043 Planarity : 0.018 0.294 1191 Dihedral : 16.097 116.352 2497 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 3.45 Ramachandran Plot: Outliers : 0.87 % Allowed : 6.06 % Favored : 93.07 % Rotamer: Outliers : 2.05 % Allowed : 6.43 % Favored : 91.52 % Cbeta Deviations : 0.89 % 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: -3.61 (0.24), residues: 808 helix: -1.98 (0.17), residues: 582 sheet: None (None), residues: 0 loop : -3.07 (0.35), residues: 226 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.086 0.016 TRP A 188 HIS 0.016 0.005 HIS A 143 PHE 0.115 0.021 PHE A 230 TYR 0.108 0.017 TYR A 518 ARG 0.008 0.001 ARG B 418 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1616 Ramachandran restraints generated. 808 Oldfield, 0 Emsley, 808 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1616 Ramachandran restraints generated. 808 Oldfield, 0 Emsley, 808 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 736 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 184 time to evaluate : 0.800 Fit side-chains REVERT: A 228 MET cc_start: 0.7676 (OUTLIER) cc_final: 0.5802 (mmt) REVERT: A 252 SER cc_start: 0.8556 (OUTLIER) cc_final: 0.8335 (m) REVERT: A 422 VAL cc_start: 0.6824 (OUTLIER) cc_final: 0.6560 (p) REVERT: A 449 MET cc_start: 0.6857 (ptm) cc_final: 0.6438 (ttm) REVERT: A 514 LEU cc_start: 0.7887 (pp) cc_final: 0.7590 (mt) REVERT: B 228 MET cc_start: 0.6689 (ptp) cc_final: 0.5519 (mmt) REVERT: B 354 GLN cc_start: 0.7818 (tm-30) cc_final: 0.5395 (mp10) REVERT: B 446 SER cc_start: 0.7123 (p) cc_final: 0.6750 (m) REVERT: B 498 ILE cc_start: 0.8497 (mp) cc_final: 0.8219 (tp) REVERT: B 514 LEU cc_start: 0.8258 (mt) cc_final: 0.7745 (tp) outliers start: 15 outliers final: 6 residues processed: 193 average time/residue: 0.7044 time to fit residues: 147.6786 Evaluate side-chains 134 residues out of total 736 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 125 time to evaluate : 0.789 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 228 MET Chi-restraints excluded: chain A residue 243 VAL Chi-restraints excluded: chain A residue 252 SER Chi-restraints excluded: chain A residue 362 LEU Chi-restraints excluded: chain A residue 422 VAL Chi-restraints excluded: chain A residue 523 TYR Chi-restraints excluded: chain B residue 243 VAL Chi-restraints excluded: chain B residue 261 ILE Chi-restraints excluded: chain B residue 426 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 67 optimal weight: 0.5980 chunk 60 optimal weight: 0.7980 chunk 33 optimal weight: 1.9990 chunk 20 optimal weight: 0.7980 chunk 40 optimal weight: 0.8980 chunk 32 optimal weight: 2.9990 chunk 62 optimal weight: 1.9990 chunk 24 optimal weight: 0.8980 chunk 38 optimal weight: 0.7980 chunk 46 optimal weight: 1.9990 chunk 72 optimal weight: 0.9980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 205 HIS A 223 HIS A 260 GLN A 329 GLN ** A 460 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 487 ASN A 500 ASN B 118 GLN B 280 ASN B 295 ASN B 351 ASN B 368 ASN B 487 ASN B 491 ASN B 526 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7138 moved from start: 0.2464 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 7283 Z= 0.218 Angle : 0.770 12.440 9923 Z= 0.385 Chirality : 0.046 0.206 1043 Planarity : 0.007 0.137 1191 Dihedral : 11.861 92.923 996 Min Nonbonded Distance : 2.225 Molprobity Statistics. All-atom Clashscore : 8.84 Ramachandran Plot: Outliers : 0.12 % Allowed : 5.32 % Favored : 94.55 % Rotamer: Outliers : 5.47 % Allowed : 13.82 % Favored : 80.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.78 % 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: -1.43 (0.27), residues: 808 helix: -0.27 (0.20), residues: 583 sheet: None (None), residues: 0 loop : -2.58 (0.39), residues: 225 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP B 186 HIS 0.003 0.001 HIS A 460 PHE 0.018 0.002 PHE B 453 TYR 0.020 0.002 TYR A 308 ARG 0.008 0.001 ARG A 139 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1616 Ramachandran restraints generated. 808 Oldfield, 0 Emsley, 808 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1616 Ramachandran restraints generated. 808 Oldfield, 0 Emsley, 808 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 736 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 132 time to evaluate : 0.767 Fit side-chains REVERT: A 154 LEU cc_start: 0.8513 (OUTLIER) cc_final: 0.8236 (mp) REVERT: A 228 MET cc_start: 0.8192 (OUTLIER) cc_final: 0.5905 (tpp) REVERT: A 384 PHE cc_start: 0.7952 (m-80) cc_final: 0.7321 (t80) REVERT: A 406 ASP cc_start: 0.7577 (p0) cc_final: 0.7311 (p0) REVERT: A 415 ASN cc_start: 0.6063 (OUTLIER) cc_final: 0.5742 (m110) REVERT: A 503 MET cc_start: 0.7836 (tmt) cc_final: 0.7554 (tmt) REVERT: B 228 MET cc_start: 0.6882 (ptp) cc_final: 0.5438 (mmt) REVERT: B 446 SER cc_start: 0.7445 (p) cc_final: 0.6792 (m) REVERT: B 456 SER cc_start: 0.8761 (t) cc_final: 0.8446 (t) outliers start: 40 outliers final: 15 residues processed: 160 average time/residue: 0.6677 time to fit residues: 116.7039 Evaluate side-chains 135 residues out of total 736 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 117 time to evaluate : 0.775 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 141 ILE Chi-restraints excluded: chain A residue 154 LEU Chi-restraints excluded: chain A residue 190 ILE Chi-restraints excluded: chain A residue 228 MET Chi-restraints excluded: chain A residue 376 ILE Chi-restraints excluded: chain A residue 415 ASN Chi-restraints excluded: chain A residue 496 LYS Chi-restraints excluded: chain A residue 502 LEU Chi-restraints excluded: chain A residue 523 TYR Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 183 THR Chi-restraints excluded: chain B residue 198 VAL Chi-restraints excluded: chain B residue 243 VAL Chi-restraints excluded: chain B residue 342 GLU Chi-restraints excluded: chain B residue 364 LEU Chi-restraints excluded: chain B residue 426 ASP Chi-restraints excluded: chain B residue 478 LEU Chi-restraints excluded: chain B residue 523 TYR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 40 optimal weight: 4.9990 chunk 22 optimal weight: 0.7980 chunk 60 optimal weight: 0.0980 chunk 49 optimal weight: 0.5980 chunk 20 optimal weight: 0.9980 chunk 72 optimal weight: 1.9990 chunk 78 optimal weight: 3.9990 chunk 64 optimal weight: 4.9990 chunk 24 optimal weight: 3.9990 chunk 58 optimal weight: 0.9980 chunk 71 optimal weight: 0.8980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 315 ASN ** A 460 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 118 GLN B 260 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7141 moved from start: 0.2954 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 7283 Z= 0.187 Angle : 0.677 8.862 9923 Z= 0.341 Chirality : 0.043 0.188 1043 Planarity : 0.006 0.110 1191 Dihedral : 11.303 94.155 989 Min Nonbonded Distance : 2.254 Molprobity Statistics. All-atom Clashscore : 8.12 Ramachandran Plot: Outliers : 0.12 % Allowed : 5.45 % Favored : 94.43 % Rotamer: Outliers : 5.34 % Allowed : 17.78 % Favored : 76.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.78 % 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: -0.52 (0.29), residues: 808 helix: 0.44 (0.21), residues: 586 sheet: None (None), residues: 0 loop : -2.39 (0.42), residues: 222 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP B 186 HIS 0.004 0.001 HIS B 223 PHE 0.017 0.001 PHE B 341 TYR 0.017 0.002 TYR B 142 ARG 0.004 0.001 ARG A 443 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1616 Ramachandran restraints generated. 808 Oldfield, 0 Emsley, 808 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1616 Ramachandran restraints generated. 808 Oldfield, 0 Emsley, 808 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 736 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 116 time to evaluate : 0.813 Fit side-chains REVERT: A 125 ARG cc_start: 0.7245 (ttm-80) cc_final: 0.6858 (ttp80) REVERT: A 154 LEU cc_start: 0.8544 (OUTLIER) cc_final: 0.8329 (mp) REVERT: A 228 MET cc_start: 0.8051 (OUTLIER) cc_final: 0.5825 (tpp) REVERT: A 372 PRO cc_start: 0.7823 (Cg_exo) cc_final: 0.7519 (Cg_endo) REVERT: A 384 PHE cc_start: 0.8002 (m-80) cc_final: 0.7468 (t80) REVERT: A 406 ASP cc_start: 0.7577 (p0) cc_final: 0.7259 (p0) REVERT: A 503 MET cc_start: 0.7850 (tmt) cc_final: 0.7590 (tmt) REVERT: B 229 ILE cc_start: 0.8340 (tt) cc_final: 0.8051 (pp) REVERT: B 456 SER cc_start: 0.8763 (t) cc_final: 0.8445 (t) REVERT: B 472 TYR cc_start: 0.5807 (OUTLIER) cc_final: 0.5068 (t80) REVERT: B 495 LYS cc_start: 0.6962 (mmpt) cc_final: 0.6662 (tptt) outliers start: 39 outliers final: 18 residues processed: 145 average time/residue: 0.6708 time to fit residues: 106.5639 Evaluate side-chains 131 residues out of total 736 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 110 time to evaluate : 0.708 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 141 ILE Chi-restraints excluded: chain A residue 154 LEU Chi-restraints excluded: chain A residue 228 MET Chi-restraints excluded: chain A residue 269 SER Chi-restraints excluded: chain A residue 278 VAL Chi-restraints excluded: chain A residue 376 ILE Chi-restraints excluded: chain A residue 450 LEU Chi-restraints excluded: chain A residue 461 GLU Chi-restraints excluded: chain A residue 502 LEU Chi-restraints excluded: chain A residue 523 TYR Chi-restraints excluded: chain B residue 198 VAL Chi-restraints excluded: chain B residue 223 HIS Chi-restraints excluded: chain B residue 243 VAL Chi-restraints excluded: chain B residue 318 VAL Chi-restraints excluded: chain B residue 338 TYR Chi-restraints excluded: chain B residue 364 LEU Chi-restraints excluded: chain B residue 459 VAL Chi-restraints excluded: chain B residue 472 TYR Chi-restraints excluded: chain B residue 478 LEU Chi-restraints excluded: chain B residue 514 LEU Chi-restraints excluded: chain B residue 523 TYR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 54 optimal weight: 2.9990 chunk 37 optimal weight: 5.9990 chunk 8 optimal weight: 0.9990 chunk 34 optimal weight: 3.9990 chunk 48 optimal weight: 1.9990 chunk 73 optimal weight: 2.9990 chunk 77 optimal weight: 5.9990 chunk 38 optimal weight: 0.7980 chunk 69 optimal weight: 0.0570 chunk 20 optimal weight: 2.9990 chunk 64 optimal weight: 4.9990 overall best weight: 1.3704 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 295 ASN ** A 460 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 118 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7213 moved from start: 0.3228 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 7283 Z= 0.284 Angle : 0.704 9.026 9923 Z= 0.358 Chirality : 0.045 0.178 1043 Planarity : 0.006 0.111 1191 Dihedral : 11.250 95.461 987 Min Nonbonded Distance : 2.223 Molprobity Statistics. All-atom Clashscore : 10.06 Ramachandran Plot: Outliers : 0.12 % Allowed : 6.06 % Favored : 93.81 % Rotamer: Outliers : 5.88 % Allowed : 18.88 % Favored : 75.24 % 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: -0.36 (0.30), residues: 808 helix: 0.54 (0.21), residues: 581 sheet: None (None), residues: 0 loop : -2.21 (0.43), residues: 227 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP B 186 HIS 0.003 0.001 HIS A 223 PHE 0.026 0.001 PHE B 392 TYR 0.020 0.002 TYR A 200 ARG 0.006 0.001 ARG A 319 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1616 Ramachandran restraints generated. 808 Oldfield, 0 Emsley, 808 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1616 Ramachandran restraints generated. 808 Oldfield, 0 Emsley, 808 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 736 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 120 time to evaluate : 0.873 Fit side-chains REVERT: A 154 LEU cc_start: 0.8612 (OUTLIER) cc_final: 0.8403 (mp) REVERT: A 228 MET cc_start: 0.8204 (ttt) cc_final: 0.5952 (tpp) REVERT: A 343 ARG cc_start: 0.6522 (tpt170) cc_final: 0.6242 (tpt90) REVERT: A 384 PHE cc_start: 0.8041 (m-80) cc_final: 0.7493 (t80) REVERT: A 402 MET cc_start: 0.6752 (OUTLIER) cc_final: 0.6477 (tmm) REVERT: A 406 ASP cc_start: 0.7689 (p0) cc_final: 0.7311 (p0) REVERT: A 415 ASN cc_start: 0.6374 (OUTLIER) cc_final: 0.6081 (m110) REVERT: A 472 TYR cc_start: 0.7613 (OUTLIER) cc_final: 0.7128 (t80) REVERT: B 357 PHE cc_start: 0.6658 (OUTLIER) cc_final: 0.5731 (t80) REVERT: B 456 SER cc_start: 0.8749 (t) cc_final: 0.8424 (t) REVERT: B 472 TYR cc_start: 0.5735 (OUTLIER) cc_final: 0.4942 (t80) REVERT: B 495 LYS cc_start: 0.6958 (mmpt) cc_final: 0.6616 (tptt) outliers start: 43 outliers final: 24 residues processed: 151 average time/residue: 0.6833 time to fit residues: 112.7739 Evaluate side-chains 141 residues out of total 736 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 111 time to evaluate : 0.803 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 141 ILE Chi-restraints excluded: chain A residue 154 LEU Chi-restraints excluded: chain A residue 190 ILE Chi-restraints excluded: chain A residue 217 LEU Chi-restraints excluded: chain A residue 269 SER Chi-restraints excluded: chain A residue 278 VAL Chi-restraints excluded: chain A residue 330 VAL Chi-restraints excluded: chain A residue 376 ILE Chi-restraints excluded: chain A residue 395 MET Chi-restraints excluded: chain A residue 402 MET Chi-restraints excluded: chain A residue 415 ASN Chi-restraints excluded: chain A residue 450 LEU Chi-restraints excluded: chain A residue 461 GLU Chi-restraints excluded: chain A residue 472 TYR Chi-restraints excluded: chain A residue 502 LEU Chi-restraints excluded: chain A residue 523 TYR Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 183 THR Chi-restraints excluded: chain B residue 198 VAL Chi-restraints excluded: chain B residue 223 HIS Chi-restraints excluded: chain B residue 243 VAL Chi-restraints excluded: chain B residue 318 VAL Chi-restraints excluded: chain B residue 338 TYR Chi-restraints excluded: chain B residue 357 PHE Chi-restraints excluded: chain B residue 446 SER Chi-restraints excluded: chain B residue 459 VAL Chi-restraints excluded: chain B residue 472 TYR Chi-restraints excluded: chain B residue 478 LEU Chi-restraints excluded: chain B residue 514 LEU Chi-restraints excluded: chain B residue 523 TYR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 43 optimal weight: 1.9990 chunk 1 optimal weight: 0.5980 chunk 57 optimal weight: 0.9990 chunk 31 optimal weight: 0.8980 chunk 65 optimal weight: 0.5980 chunk 53 optimal weight: 0.0170 chunk 0 optimal weight: 3.9990 chunk 39 optimal weight: 0.6980 chunk 69 optimal weight: 0.4980 chunk 19 optimal weight: 0.0570 chunk 26 optimal weight: 1.9990 overall best weight: 0.3536 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 460 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 260 GLN ** B 500 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7127 moved from start: 0.3502 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 7283 Z= 0.157 Angle : 0.658 12.667 9923 Z= 0.320 Chirality : 0.041 0.267 1043 Planarity : 0.005 0.103 1191 Dihedral : 10.705 93.797 984 Min Nonbonded Distance : 2.224 Molprobity Statistics. All-atom Clashscore : 7.90 Ramachandran Plot: Outliers : 0.12 % Allowed : 4.58 % Favored : 95.30 % Rotamer: Outliers : 4.38 % Allowed : 20.79 % Favored : 74.83 % 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 (0.30), residues: 808 helix: 0.86 (0.21), residues: 587 sheet: None (None), residues: 0 loop : -2.36 (0.42), residues: 221 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 186 HIS 0.004 0.001 HIS B 223 PHE 0.011 0.001 PHE B 203 TYR 0.016 0.001 TYR B 142 ARG 0.006 0.000 ARG A 319 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1616 Ramachandran restraints generated. 808 Oldfield, 0 Emsley, 808 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1616 Ramachandran restraints generated. 808 Oldfield, 0 Emsley, 808 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 736 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 121 time to evaluate : 0.872 Fit side-chains REVERT: A 125 ARG cc_start: 0.7252 (ttm-80) cc_final: 0.6879 (mtp85) REVERT: A 228 MET cc_start: 0.8200 (ttt) cc_final: 0.5852 (tpp) REVERT: A 343 ARG cc_start: 0.6540 (tpt170) cc_final: 0.6254 (tpt90) REVERT: A 372 PRO cc_start: 0.7983 (Cg_exo) cc_final: 0.7763 (Cg_endo) REVERT: A 406 ASP cc_start: 0.7484 (p0) cc_final: 0.7173 (p0) REVERT: A 449 MET cc_start: 0.7848 (ttm) cc_final: 0.7295 (ttm) REVERT: B 186 TRP cc_start: 0.6934 (p-90) cc_final: 0.6586 (m100) REVERT: B 229 ILE cc_start: 0.8254 (tt) cc_final: 0.8049 (pp) REVERT: B 331 PHE cc_start: 0.7901 (t80) cc_final: 0.7638 (t80) REVERT: B 357 PHE cc_start: 0.6666 (OUTLIER) cc_final: 0.5804 (t80) REVERT: B 472 TYR cc_start: 0.5627 (OUTLIER) cc_final: 0.5009 (t80) REVERT: B 495 LYS cc_start: 0.6858 (mmpt) cc_final: 0.6537 (tptt) REVERT: B 499 TRP cc_start: 0.8055 (m100) cc_final: 0.7847 (m100) outliers start: 32 outliers final: 13 residues processed: 144 average time/residue: 0.7632 time to fit residues: 118.8901 Evaluate side-chains 125 residues out of total 736 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 110 time to evaluate : 0.693 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 133 LEU Chi-restraints excluded: chain A residue 141 ILE Chi-restraints excluded: chain A residue 450 LEU Chi-restraints excluded: chain A residue 461 GLU Chi-restraints excluded: chain A residue 472 TYR Chi-restraints excluded: chain A residue 502 LEU Chi-restraints excluded: chain A residue 523 TYR Chi-restraints excluded: chain B residue 198 VAL Chi-restraints excluded: chain B residue 231 GLN Chi-restraints excluded: chain B residue 243 VAL Chi-restraints excluded: chain B residue 318 VAL Chi-restraints excluded: chain B residue 357 PHE Chi-restraints excluded: chain B residue 472 TYR Chi-restraints excluded: chain B residue 514 LEU Chi-restraints excluded: chain B residue 523 TYR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 69 optimal weight: 0.5980 chunk 15 optimal weight: 1.9990 chunk 45 optimal weight: 0.0070 chunk 19 optimal weight: 0.8980 chunk 77 optimal weight: 9.9990 chunk 64 optimal weight: 0.5980 chunk 35 optimal weight: 2.9990 chunk 6 optimal weight: 0.4980 chunk 25 optimal weight: 0.7980 chunk 40 optimal weight: 3.9990 chunk 74 optimal weight: 3.9990 overall best weight: 0.4998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 315 ASN A 351 ASN ** A 460 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7135 moved from start: 0.3670 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 7283 Z= 0.172 Angle : 0.669 16.233 9923 Z= 0.321 Chirality : 0.042 0.279 1043 Planarity : 0.005 0.101 1191 Dihedral : 10.619 94.194 984 Min Nonbonded Distance : 2.206 Molprobity Statistics. All-atom Clashscore : 9.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.57 % Favored : 94.43 % Rotamer: Outliers : 3.97 % Allowed : 22.16 % Favored : 73.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.78 % 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: 0.11 (0.30), residues: 808 helix: 0.97 (0.21), residues: 586 sheet: None (None), residues: 0 loop : -2.38 (0.41), residues: 222 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 186 HIS 0.003 0.001 HIS A 215 PHE 0.013 0.001 PHE A 225 TYR 0.015 0.001 TYR B 142 ARG 0.007 0.000 ARG A 319 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1616 Ramachandran restraints generated. 808 Oldfield, 0 Emsley, 808 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1616 Ramachandran restraints generated. 808 Oldfield, 0 Emsley, 808 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 736 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 119 time to evaluate : 0.749 Fit side-chains REVERT: A 125 ARG cc_start: 0.7280 (ttm-80) cc_final: 0.6890 (mtp85) REVERT: A 228 MET cc_start: 0.8217 (ttt) cc_final: 0.5911 (tpp) REVERT: A 343 ARG cc_start: 0.6546 (tpt170) cc_final: 0.6246 (tpt90) REVERT: A 372 PRO cc_start: 0.7966 (Cg_exo) cc_final: 0.7726 (Cg_endo) REVERT: A 406 ASP cc_start: 0.7543 (p0) cc_final: 0.7218 (p0) REVERT: B 229 ILE cc_start: 0.8175 (tt) cc_final: 0.7890 (pp) REVERT: B 331 PHE cc_start: 0.7933 (t80) cc_final: 0.7725 (t80) REVERT: B 357 PHE cc_start: 0.6679 (OUTLIER) cc_final: 0.5853 (t80) REVERT: B 446 SER cc_start: 0.7878 (m) cc_final: 0.7488 (p) REVERT: B 472 TYR cc_start: 0.5742 (OUTLIER) cc_final: 0.5021 (t80) REVERT: B 495 LYS cc_start: 0.7078 (mmpt) cc_final: 0.6692 (tptt) outliers start: 29 outliers final: 17 residues processed: 138 average time/residue: 0.7592 time to fit residues: 113.4075 Evaluate side-chains 130 residues out of total 736 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 111 time to evaluate : 0.759 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 141 ILE Chi-restraints excluded: chain A residue 278 VAL Chi-restraints excluded: chain A residue 450 LEU Chi-restraints excluded: chain A residue 461 GLU Chi-restraints excluded: chain A residue 472 TYR Chi-restraints excluded: chain A residue 502 LEU Chi-restraints excluded: chain A residue 523 TYR Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 198 VAL Chi-restraints excluded: chain B residue 243 VAL Chi-restraints excluded: chain B residue 269 SER Chi-restraints excluded: chain B residue 318 VAL Chi-restraints excluded: chain B residue 338 TYR Chi-restraints excluded: chain B residue 357 PHE Chi-restraints excluded: chain B residue 395 MET Chi-restraints excluded: chain B residue 459 VAL Chi-restraints excluded: chain B residue 472 TYR Chi-restraints excluded: chain B residue 514 LEU Chi-restraints excluded: chain B residue 523 TYR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 8 optimal weight: 0.4980 chunk 44 optimal weight: 4.9990 chunk 56 optimal weight: 0.4980 chunk 43 optimal weight: 0.5980 chunk 65 optimal weight: 2.9990 chunk 77 optimal weight: 6.9990 chunk 48 optimal weight: 1.9990 chunk 47 optimal weight: 1.9990 chunk 35 optimal weight: 0.9990 chunk 30 optimal weight: 1.9990 chunk 46 optimal weight: 1.9990 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 351 ASN ** A 460 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7172 moved from start: 0.3791 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 7283 Z= 0.209 Angle : 0.664 11.797 9923 Z= 0.329 Chirality : 0.044 0.294 1043 Planarity : 0.005 0.080 1191 Dihedral : 10.696 93.797 984 Min Nonbonded Distance : 2.149 Molprobity Statistics. All-atom Clashscore : 8.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.06 % Favored : 93.94 % Rotamer: Outliers : 4.65 % Allowed : 22.16 % Favored : 73.19 % 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: 0.13 (0.30), residues: 808 helix: 0.94 (0.21), residues: 585 sheet: None (None), residues: 0 loop : -2.18 (0.41), residues: 223 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 186 HIS 0.004 0.001 HIS A 215 PHE 0.016 0.001 PHE B 392 TYR 0.020 0.002 TYR A 161 ARG 0.007 0.000 ARG A 319 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1616 Ramachandran restraints generated. 808 Oldfield, 0 Emsley, 808 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1616 Ramachandran restraints generated. 808 Oldfield, 0 Emsley, 808 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 736 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 115 time to evaluate : 0.801 Fit side-chains REVERT: A 125 ARG cc_start: 0.7269 (ttm-80) cc_final: 0.6890 (mtp85) REVERT: A 228 MET cc_start: 0.8235 (ttt) cc_final: 0.5819 (tpp) REVERT: A 372 PRO cc_start: 0.7719 (Cg_exo) cc_final: 0.7444 (Cg_endo) REVERT: A 384 PHE cc_start: 0.8081 (m-80) cc_final: 0.7496 (t80) REVERT: A 406 ASP cc_start: 0.7506 (p0) cc_final: 0.7175 (p0) REVERT: A 415 ASN cc_start: 0.6424 (OUTLIER) cc_final: 0.6132 (m110) REVERT: A 449 MET cc_start: 0.8023 (ttm) cc_final: 0.7654 (ttm) REVERT: B 229 ILE cc_start: 0.8136 (tt) cc_final: 0.7866 (pp) REVERT: B 357 PHE cc_start: 0.6780 (OUTLIER) cc_final: 0.5898 (t80) REVERT: B 446 SER cc_start: 0.7818 (m) cc_final: 0.7462 (p) REVERT: B 472 TYR cc_start: 0.5700 (OUTLIER) cc_final: 0.4936 (t80) REVERT: B 495 LYS cc_start: 0.7064 (mmpt) cc_final: 0.6674 (tptt) outliers start: 34 outliers final: 18 residues processed: 138 average time/residue: 0.7302 time to fit residues: 109.3690 Evaluate side-chains 134 residues out of total 736 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 113 time to evaluate : 0.766 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 133 LEU Chi-restraints excluded: chain A residue 217 LEU Chi-restraints excluded: chain A residue 269 SER Chi-restraints excluded: chain A residue 278 VAL Chi-restraints excluded: chain A residue 415 ASN Chi-restraints excluded: chain A residue 461 GLU Chi-restraints excluded: chain A residue 472 TYR Chi-restraints excluded: chain A residue 502 LEU Chi-restraints excluded: chain A residue 523 TYR Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 183 THR Chi-restraints excluded: chain B residue 198 VAL Chi-restraints excluded: chain B residue 243 VAL Chi-restraints excluded: chain B residue 269 SER Chi-restraints excluded: chain B residue 318 VAL Chi-restraints excluded: chain B residue 338 TYR Chi-restraints excluded: chain B residue 357 PHE Chi-restraints excluded: chain B residue 395 MET Chi-restraints excluded: chain B residue 459 VAL Chi-restraints excluded: chain B residue 472 TYR Chi-restraints excluded: chain B residue 523 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 23 optimal weight: 4.9990 chunk 15 optimal weight: 2.9990 chunk 14 optimal weight: 0.5980 chunk 49 optimal weight: 7.9990 chunk 52 optimal weight: 0.8980 chunk 38 optimal weight: 0.7980 chunk 7 optimal weight: 0.6980 chunk 60 optimal weight: 0.1980 chunk 70 optimal weight: 0.0060 chunk 73 optimal weight: 0.0870 chunk 67 optimal weight: 2.9990 overall best weight: 0.3174 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 351 ASN ** A 460 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 386 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7108 moved from start: 0.4030 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 7283 Z= 0.152 Angle : 0.635 10.802 9923 Z= 0.312 Chirality : 0.041 0.281 1043 Planarity : 0.004 0.043 1191 Dihedral : 10.329 93.431 984 Min Nonbonded Distance : 2.183 Molprobity Statistics. All-atom Clashscore : 8.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.07 % Favored : 94.93 % Rotamer: Outliers : 2.74 % Allowed : 23.94 % Favored : 73.32 % 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: 0.20 (0.30), residues: 808 helix: 1.02 (0.21), residues: 589 sheet: None (None), residues: 0 loop : -2.32 (0.41), residues: 219 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 186 HIS 0.004 0.001 HIS A 215 PHE 0.015 0.001 PHE A 225 TYR 0.015 0.001 TYR B 142 ARG 0.005 0.000 ARG A 319 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1616 Ramachandran restraints generated. 808 Oldfield, 0 Emsley, 808 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1616 Ramachandran restraints generated. 808 Oldfield, 0 Emsley, 808 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 736 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 127 time to evaluate : 0.738 Fit side-chains REVERT: A 125 ARG cc_start: 0.7300 (ttm-80) cc_final: 0.6907 (mtp85) REVERT: A 228 MET cc_start: 0.8177 (ttt) cc_final: 0.5785 (tpp) REVERT: A 449 MET cc_start: 0.7966 (ttm) cc_final: 0.7523 (ttm) REVERT: B 229 ILE cc_start: 0.8170 (tt) cc_final: 0.7862 (pp) REVERT: B 331 PHE cc_start: 0.7815 (t80) cc_final: 0.7539 (t80) REVERT: B 357 PHE cc_start: 0.6705 (OUTLIER) cc_final: 0.5877 (t80) REVERT: B 446 SER cc_start: 0.7785 (m) cc_final: 0.7381 (p) REVERT: B 472 TYR cc_start: 0.5742 (OUTLIER) cc_final: 0.5063 (t80) REVERT: B 495 LYS cc_start: 0.7026 (mmpt) cc_final: 0.6666 (tptt) outliers start: 20 outliers final: 13 residues processed: 142 average time/residue: 0.7308 time to fit residues: 112.5963 Evaluate side-chains 130 residues out of total 736 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 115 time to evaluate : 0.667 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 141 ILE Chi-restraints excluded: chain A residue 269 SER Chi-restraints excluded: chain A residue 278 VAL Chi-restraints excluded: chain A residue 472 TYR Chi-restraints excluded: chain A residue 502 LEU Chi-restraints excluded: chain A residue 523 TYR Chi-restraints excluded: chain B residue 153 ILE Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 198 VAL Chi-restraints excluded: chain B residue 243 VAL Chi-restraints excluded: chain B residue 318 VAL Chi-restraints excluded: chain B residue 338 TYR Chi-restraints excluded: chain B residue 357 PHE Chi-restraints excluded: chain B residue 472 TYR Chi-restraints excluded: chain B residue 523 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 71 optimal weight: 3.9990 chunk 73 optimal weight: 4.9990 chunk 43 optimal weight: 0.8980 chunk 31 optimal weight: 3.9990 chunk 56 optimal weight: 0.4980 chunk 22 optimal weight: 0.6980 chunk 64 optimal weight: 4.9990 chunk 67 optimal weight: 2.9990 chunk 47 optimal weight: 1.9990 chunk 75 optimal weight: 0.9980 chunk 46 optimal weight: 0.9980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 460 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7148 moved from start: 0.4057 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 7283 Z= 0.204 Angle : 0.669 11.346 9923 Z= 0.330 Chirality : 0.043 0.272 1043 Planarity : 0.004 0.039 1191 Dihedral : 10.347 93.853 984 Min Nonbonded Distance : 2.192 Molprobity Statistics. All-atom Clashscore : 8.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.45 % Favored : 94.55 % Rotamer: Outliers : 2.87 % Allowed : 25.44 % Favored : 71.68 % 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 (0.30), residues: 808 helix: 1.01 (0.21), residues: 588 sheet: None (None), residues: 0 loop : -2.31 (0.41), residues: 220 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 186 HIS 0.004 0.001 HIS A 215 PHE 0.015 0.001 PHE A 486 TYR 0.022 0.002 TYR A 142 ARG 0.007 0.001 ARG A 319 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1616 Ramachandran restraints generated. 808 Oldfield, 0 Emsley, 808 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1616 Ramachandran restraints generated. 808 Oldfield, 0 Emsley, 808 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 736 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 116 time to evaluate : 0.821 Fit side-chains REVERT: A 125 ARG cc_start: 0.7304 (ttm-80) cc_final: 0.6897 (mtp85) REVERT: A 228 MET cc_start: 0.8190 (ttt) cc_final: 0.5790 (tpp) REVERT: A 406 ASP cc_start: 0.7505 (p0) cc_final: 0.7175 (p0) REVERT: A 449 MET cc_start: 0.7984 (ttm) cc_final: 0.7570 (ttm) REVERT: B 228 MET cc_start: 0.7434 (ptp) cc_final: 0.5238 (mmt) REVERT: B 229 ILE cc_start: 0.8197 (tt) cc_final: 0.7884 (pp) REVERT: B 331 PHE cc_start: 0.7876 (t80) cc_final: 0.7587 (t80) REVERT: B 357 PHE cc_start: 0.6715 (OUTLIER) cc_final: 0.5841 (t80) REVERT: B 446 SER cc_start: 0.8025 (m) cc_final: 0.7682 (p) REVERT: B 472 TYR cc_start: 0.5649 (OUTLIER) cc_final: 0.4832 (t80) REVERT: B 495 LYS cc_start: 0.7041 (mmpt) cc_final: 0.6663 (tptt) outliers start: 21 outliers final: 15 residues processed: 132 average time/residue: 0.7173 time to fit residues: 102.9967 Evaluate side-chains 133 residues out of total 736 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 116 time to evaluate : 0.744 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 133 LEU Chi-restraints excluded: chain A residue 269 SER Chi-restraints excluded: chain A residue 278 VAL Chi-restraints excluded: chain A residue 472 TYR Chi-restraints excluded: chain A residue 502 LEU Chi-restraints excluded: chain A residue 523 TYR Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 183 THR Chi-restraints excluded: chain B residue 198 VAL Chi-restraints excluded: chain B residue 243 VAL Chi-restraints excluded: chain B residue 269 SER Chi-restraints excluded: chain B residue 318 VAL Chi-restraints excluded: chain B residue 338 TYR Chi-restraints excluded: chain B residue 357 PHE Chi-restraints excluded: chain B residue 472 TYR Chi-restraints excluded: chain B residue 478 LEU Chi-restraints excluded: chain B residue 523 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 36 optimal weight: 0.0770 chunk 52 optimal weight: 0.9980 chunk 79 optimal weight: 0.7980 chunk 73 optimal weight: 4.9990 chunk 63 optimal weight: 0.8980 chunk 6 optimal weight: 0.9980 chunk 49 optimal weight: 1.9990 chunk 38 optimal weight: 0.9990 chunk 50 optimal weight: 1.9990 chunk 67 optimal weight: 1.9990 chunk 19 optimal weight: 0.1980 overall best weight: 0.5938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 460 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7138 moved from start: 0.4135 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 7283 Z= 0.175 Angle : 0.649 10.409 9923 Z= 0.320 Chirality : 0.042 0.282 1043 Planarity : 0.004 0.039 1191 Dihedral : 10.281 94.114 984 Min Nonbonded Distance : 2.206 Molprobity Statistics. All-atom Clashscore : 9.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.57 % Favored : 94.43 % Rotamer: Outliers : 2.46 % Allowed : 25.72 % Favored : 71.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.30 (0.30), residues: 808 helix: 1.11 (0.21), residues: 587 sheet: None (None), residues: 0 loop : -2.31 (0.41), residues: 221 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 186 HIS 0.004 0.001 HIS A 215 PHE 0.015 0.001 PHE A 225 TYR 0.023 0.001 TYR A 142 ARG 0.007 0.000 ARG A 319 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1616 Ramachandran restraints generated. 808 Oldfield, 0 Emsley, 808 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1616 Ramachandran restraints generated. 808 Oldfield, 0 Emsley, 808 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 736 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 116 time to evaluate : 0.778 Fit side-chains REVERT: A 125 ARG cc_start: 0.7281 (ttm-80) cc_final: 0.6884 (mtp85) REVERT: A 228 MET cc_start: 0.8187 (ttt) cc_final: 0.5780 (tpp) REVERT: A 372 PRO cc_start: 0.7740 (Cg_exo) cc_final: 0.7485 (Cg_endo) REVERT: A 406 ASP cc_start: 0.7582 (p0) cc_final: 0.7240 (p0) REVERT: A 449 MET cc_start: 0.7980 (ttm) cc_final: 0.7555 (ttm) REVERT: B 229 ILE cc_start: 0.8141 (tt) cc_final: 0.7836 (pp) REVERT: B 331 PHE cc_start: 0.7855 (t80) cc_final: 0.7567 (t80) REVERT: B 446 SER cc_start: 0.7893 (m) cc_final: 0.7642 (p) REVERT: B 472 TYR cc_start: 0.5754 (OUTLIER) cc_final: 0.5036 (t80) REVERT: B 495 LYS cc_start: 0.7031 (mmpt) cc_final: 0.6675 (tptt) outliers start: 18 outliers final: 13 residues processed: 129 average time/residue: 0.7766 time to fit residues: 108.7490 Evaluate side-chains 128 residues out of total 736 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 114 time to evaluate : 0.701 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 133 LEU Chi-restraints excluded: chain A residue 269 SER Chi-restraints excluded: chain A residue 472 TYR Chi-restraints excluded: chain A residue 502 LEU Chi-restraints excluded: chain A residue 523 TYR Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 198 VAL Chi-restraints excluded: chain B residue 243 VAL Chi-restraints excluded: chain B residue 318 VAL Chi-restraints excluded: chain B residue 338 TYR Chi-restraints excluded: chain B residue 364 LEU Chi-restraints excluded: chain B residue 472 TYR Chi-restraints excluded: chain B residue 478 LEU Chi-restraints excluded: chain B residue 523 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 58 optimal weight: 0.9990 chunk 9 optimal weight: 6.9990 chunk 17 optimal weight: 2.9990 chunk 63 optimal weight: 0.9990 chunk 26 optimal weight: 2.9990 chunk 65 optimal weight: 0.6980 chunk 8 optimal weight: 0.9980 chunk 11 optimal weight: 0.7980 chunk 55 optimal weight: 0.9980 chunk 3 optimal weight: 0.9980 chunk 45 optimal weight: 0.0980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 460 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4051 r_free = 0.4051 target = 0.164523 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3826 r_free = 0.3826 target = 0.145412 restraints weight = 12184.807| |-----------------------------------------------------------------------------| r_work (start): 0.3819 rms_B_bonded: 2.38 r_work: 0.3711 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work (final): 0.3711 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7346 moved from start: 0.4150 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 7283 Z= 0.190 Angle : 0.655 10.292 9923 Z= 0.327 Chirality : 0.043 0.261 1043 Planarity : 0.004 0.039 1191 Dihedral : 10.282 94.395 984 Min Nonbonded Distance : 2.213 Molprobity Statistics. All-atom Clashscore : 9.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.82 % Favored : 94.18 % Rotamer: Outliers : 3.15 % Allowed : 24.90 % Favored : 71.96 % 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: 0.30 (0.30), residues: 808 helix: 1.11 (0.21), residues: 587 sheet: None (None), residues: 0 loop : -2.33 (0.40), residues: 221 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 186 HIS 0.004 0.001 HIS A 215 PHE 0.013 0.001 PHE A 486 TYR 0.021 0.002 TYR A 161 ARG 0.007 0.000 ARG A 319 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2526.41 seconds wall clock time: 45 minutes 43.83 seconds (2743.83 seconds total)