Starting phenix.real_space_refine on Fri Dec 8 22:39:50 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8exq_28659/12_2023/8exq_28659.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8exq_28659/12_2023/8exq_28659.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8exq_28659/12_2023/8exq_28659.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8exq_28659/12_2023/8exq_28659.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8exq_28659/12_2023/8exq_28659.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8exq_28659/12_2023/8exq_28659.pdb" } resolution = 4.9 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= 0.003 sd= 0.045 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians Zn 2 6.06 5 S 38 5.16 5 C 6112 2.51 5 N 1534 2.21 5 O 1618 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B PHE 12": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 22": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 29": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 30": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 36": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 55": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 121": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 130": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 137": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 151": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 155": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 178": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 187": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 217": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 274": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 275": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 313": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 317": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 328": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 347": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 373": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 385": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 419": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 441": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 442": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 453": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 463": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 478": "OD1" <-> "OD2" Residue "B PHE 501": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 524": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 544": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 552": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 553": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 12": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 29": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 30": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 40": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 50": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 192": "OD1" <-> "OD2" Residue "A PHE 217": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 274": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 275": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 284": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 313": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 317": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 328": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 347": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 373": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 374": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 385": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 394": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 398": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 419": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 442": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 463": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 471": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 478": "OD1" <-> "OD2" Residue "A PHE 501": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 521": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 544": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 553": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/chem_data/mon_lib" Total number of atoms: 9304 Number of models: 1 Model: "" Number of chains: 4 Chain: "B" Number of atoms: 4651 Number of conformers: 1 Conformer: "" Number of residues, atoms: 554, 4651 Classifications: {'peptide': 554} Link IDs: {'PTRANS': 11, 'TRANS': 542} Chain breaks: 1 Chain: "A" Number of atoms: 4651 Number of conformers: 1 Conformer: "" Number of residues, atoms: 554, 4651 Classifications: {'peptide': 554} Link IDs: {'PTRANS': 11, 'TRANS': 542} Chain breaks: 1 Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Time building chain proxies: 5.84, per 1000 atoms: 0.63 Number of scatterers: 9304 At special positions: 0 Unit cell: (73.9927, 108.282, 135.353, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Zn 2 29.99 S 38 16.00 O 1618 8.00 N 1534 7.00 C 6112 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: 3.68 Conformation dependent library (CDL) restraints added in 1.7 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 701 " pdb="ZN ZN A 701 " - pdb=" NE2 HIS A 201 " pdb="ZN ZN A 701 " - pdb=" NE2 HIS A 205 " pdb=" ZN B 701 " pdb="ZN ZN B 701 " - pdb=" NE2 HIS B 201 " pdb="ZN ZN B 701 " - pdb=" NE2 HIS B 205 " 2200 Ramachandran restraints generated. 1100 Oldfield, 0 Emsley, 1100 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2140 Finding SS restraints... Secondary structure from input PDB file: 54 helices and 6 sheets defined 57.5% alpha, 16.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.16 Creating SS restraints... Processing helix chain 'B' and resid 2 through 31 Processing helix chain 'B' and resid 35 through 38 Processing helix chain 'B' and resid 39 through 46 Processing helix chain 'B' and resid 99 through 133 removed outlier: 3.571A pdb=" N ASP B 103 " --> pdb=" O TRP B 99 " (cutoff:3.500A) Processing helix chain 'B' and resid 139 through 151 Processing helix chain 'B' and resid 184 through 189 Processing helix chain 'B' and resid 190 through 193 Processing helix chain 'B' and resid 194 through 208 Processing helix chain 'B' and resid 209 through 224 Processing helix chain 'B' and resid 229 through 251 removed outlier: 3.969A pdb=" N ARG B 235 " --> pdb=" O HIS B 231 " (cutoff:3.500A) Processing helix chain 'B' and resid 252 through 253 No H-bonds generated for 'chain 'B' and resid 252 through 253' Processing helix chain 'B' and resid 254 through 256 No H-bonds generated for 'chain 'B' and resid 254 through 256' Processing helix chain 'B' and resid 257 through 268 removed outlier: 3.647A pdb=" N SER B 268 " --> pdb=" O SER B 264 " (cutoff:3.500A) Processing helix chain 'B' and resid 289 through 300 Processing helix chain 'B' and resid 308 through 327 Processing helix chain 'B' and resid 332 through 337 Processing helix chain 'B' and resid 352 through 357 Processing helix chain 'B' and resid 377 through 382 Processing helix chain 'B' and resid 387 through 389 No H-bonds generated for 'chain 'B' and resid 387 through 389' Processing helix chain 'B' and resid 390 through 402 removed outlier: 4.270A pdb=" N TYR B 394 " --> pdb=" O THR B 390 " (cutoff:3.500A) Processing helix chain 'B' and resid 421 through 425 Processing helix chain 'B' and resid 429 through 436 Processing helix chain 'B' and resid 438 through 448 Processing helix chain 'B' and resid 450 through 462 Processing helix chain 'B' and resid 483 through 497 Processing helix chain 'B' and resid 502 through 513 Processing helix chain 'B' and resid 564 through 579 Processing helix chain 'A' and resid 2 through 31 Processing helix chain 'A' and resid 35 through 38 Processing helix chain 'A' and resid 39 through 46 removed outlier: 3.563A pdb=" N LEU A 43 " --> pdb=" O TRP A 39 " (cutoff:3.500A) Processing helix chain 'A' and resid 47 through 51 Processing helix chain 'A' and resid 99 through 132 Processing helix chain 'A' and resid 139 through 152 removed outlier: 4.659A pdb=" N ASN A 152 " --> pdb=" O THR A 148 " (cutoff:3.500A) Processing helix chain 'A' and resid 185 through 187 No H-bonds generated for 'chain 'A' and resid 185 through 187' Processing helix chain 'A' and resid 194 through 208 Processing helix chain 'A' and resid 209 through 224 Processing helix chain 'A' and resid 228 through 233 Processing helix chain 'A' and resid 233 through 252 removed outlier: 3.620A pdb=" N ASN A 252 " --> pdb=" O PHE A 248 " (cutoff:3.500A) Processing helix chain 'A' and resid 253 through 256 removed outlier: 5.426A pdb=" N ASN A 256 " --> pdb=" O ILE A 253 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 253 through 256' Processing helix chain 'A' and resid 257 through 272 Processing helix chain 'A' and resid 289 through 300 Processing helix chain 'A' and resid 308 through 327 Processing helix chain 'A' and resid 333 through 337 Processing helix chain 'A' and resid 352 through 357 Processing helix chain 'A' and resid 377 through 382 Processing helix chain 'A' and resid 387 through 389 No H-bonds generated for 'chain 'A' and resid 387 through 389' Processing helix chain 'A' and resid 390 through 402 removed outlier: 4.455A pdb=" N TYR A 394 " --> pdb=" O THR A 390 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N MET A 397 " --> pdb=" O ILE A 393 " (cutoff:3.500A) Processing helix chain 'A' and resid 421 through 425 Processing helix chain 'A' and resid 429 through 436 Processing helix chain 'A' and resid 438 through 449 Processing helix chain 'A' and resid 450 through 461 Processing helix chain 'A' and resid 483 through 497 Processing helix chain 'A' and resid 502 through 513 Processing helix chain 'A' and resid 564 through 579 Processing sheet with id=AA1, first strand: chain 'B' and resid 90 through 94 removed outlier: 6.686A pdb=" N PHE B 90 " --> pdb=" O THR A 529 " (cutoff:3.500A) removed outlier: 7.505A pdb=" N ILE A 531 " --> pdb=" O PHE B 90 " (cutoff:3.500A) removed outlier: 6.018A pdb=" N THR B 92 " --> pdb=" O ILE A 531 " (cutoff:3.500A) removed outlier: 6.536A pdb=" N VAL A 532 " --> pdb=" O TYR A 536 " (cutoff:3.500A) removed outlier: 5.510A pdb=" N TYR A 536 " --> pdb=" O VAL A 532 " (cutoff:3.500A) removed outlier: 6.822A pdb=" N ASP A 346 " --> pdb=" O TYR A 373 " (cutoff:3.500A) removed outlier: 7.964A pdb=" N ILE A 375 " --> pdb=" O ASP A 346 " (cutoff:3.500A) removed outlier: 6.819A pdb=" N GLN A 348 " --> pdb=" O ILE A 375 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 90 through 94 removed outlier: 6.686A pdb=" N PHE B 90 " --> pdb=" O THR A 529 " (cutoff:3.500A) removed outlier: 7.505A pdb=" N ILE A 531 " --> pdb=" O PHE B 90 " (cutoff:3.500A) removed outlier: 6.018A pdb=" N THR B 92 " --> pdb=" O ILE A 531 " (cutoff:3.500A) removed outlier: 5.929A pdb=" N GLY A 525 " --> pdb=" O LEU A 514 " (cutoff:3.500A) removed outlier: 5.673A pdb=" N LEU A 514 " --> pdb=" O GLY A 525 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 160 through 164 removed outlier: 6.457A pdb=" N VAL B 160 " --> pdb=" O ILE B 180 " (cutoff:3.500A) removed outlier: 7.570A pdb=" N ILE B 182 " --> pdb=" O VAL B 160 " (cutoff:3.500A) removed outlier: 6.752A pdb=" N ARG B 162 " --> pdb=" O ILE B 182 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 346 through 350 removed outlier: 6.693A pdb=" N ASP B 346 " --> pdb=" O TYR B 373 " (cutoff:3.500A) removed outlier: 7.987A pdb=" N ILE B 375 " --> pdb=" O ASP B 346 " (cutoff:3.500A) removed outlier: 6.863A pdb=" N GLN B 348 " --> pdb=" O ILE B 375 " (cutoff:3.500A) removed outlier: 5.573A pdb=" N TYR B 536 " --> pdb=" O VAL B 532 " (cutoff:3.500A) removed outlier: 6.531A pdb=" N VAL B 532 " --> pdb=" O TYR B 536 " (cutoff:3.500A) removed outlier: 6.068A pdb=" N GLY B 525 " --> pdb=" O LEU B 514 " (cutoff:3.500A) removed outlier: 5.467A pdb=" N LEU B 514 " --> pdb=" O GLY B 525 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 346 through 350 removed outlier: 6.693A pdb=" N ASP B 346 " --> pdb=" O TYR B 373 " (cutoff:3.500A) removed outlier: 7.987A pdb=" N ILE B 375 " --> pdb=" O ASP B 346 " (cutoff:3.500A) removed outlier: 6.863A pdb=" N GLN B 348 " --> pdb=" O ILE B 375 " (cutoff:3.500A) removed outlier: 5.573A pdb=" N TYR B 536 " --> pdb=" O VAL B 532 " (cutoff:3.500A) removed outlier: 6.531A pdb=" N VAL B 532 " --> pdb=" O TYR B 536 " (cutoff:3.500A) removed outlier: 8.784A pdb=" N THR A 92 " --> pdb=" O THR B 527 " (cutoff:3.500A) removed outlier: 7.290A pdb=" N THR B 529 " --> pdb=" O THR A 92 " (cutoff:3.500A) removed outlier: 7.718A pdb=" N ILE A 94 " --> pdb=" O THR B 529 " (cutoff:3.500A) removed outlier: 6.772A pdb=" N ILE B 531 " --> pdb=" O ILE A 94 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 136 through 137 538 hydrogen bonds defined for protein. 1542 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: 3.68 Time building geometry restraints manager: 3.90 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 2085 1.32 - 1.46: 3022 1.46 - 1.59: 4346 1.59 - 1.73: 11 1.73 - 1.86: 68 Bond restraints: 9532 Sorted by residual: bond pdb=" CB HIS B 201 " pdb=" CG HIS B 201 " ideal model delta sigma weight residual 1.497 1.397 0.100 1.40e-02 5.10e+03 5.14e+01 bond pdb=" CB HIS B 153 " pdb=" CG HIS B 153 " ideal model delta sigma weight residual 1.497 1.418 0.079 1.40e-02 5.10e+03 3.22e+01 bond pdb=" CB TYR B 552 " pdb=" CG TYR B 552 " ideal model delta sigma weight residual 1.512 1.397 0.115 2.20e-02 2.07e+03 2.75e+01 bond pdb=" CB PHE A 90 " pdb=" CG PHE A 90 " ideal model delta sigma weight residual 1.502 1.385 0.117 2.30e-02 1.89e+03 2.58e+01 bond pdb=" CG MET B 494 " pdb=" SD MET B 494 " ideal model delta sigma weight residual 1.803 1.678 0.125 2.50e-02 1.60e+03 2.52e+01 ... (remaining 9527 not shown) Histogram of bond angle deviations from ideal: 93.13 - 101.33: 10 101.33 - 109.53: 1736 109.53 - 117.73: 5347 117.73 - 125.93: 5601 125.93 - 134.13: 142 Bond angle restraints: 12836 Sorted by residual: angle pdb=" CA PHE A 313 " pdb=" CB PHE A 313 " pdb=" CG PHE A 313 " ideal model delta sigma weight residual 113.80 105.83 7.97 1.00e+00 1.00e+00 6.36e+01 angle pdb=" CA ASP A 550 " pdb=" CB ASP A 550 " pdb=" CG ASP A 550 " ideal model delta sigma weight residual 112.60 120.57 -7.97 1.00e+00 1.00e+00 6.36e+01 angle pdb=" C SER B 386 " pdb=" N PRO B 387 " pdb=" CA PRO B 387 " ideal model delta sigma weight residual 119.56 127.47 -7.91 1.01e+00 9.80e-01 6.13e+01 angle pdb=" C TYR B 419 " pdb=" N PRO B 420 " pdb=" CA PRO B 420 " ideal model delta sigma weight residual 119.56 127.53 -7.97 1.02e+00 9.61e-01 6.11e+01 angle pdb=" C TYR A 419 " pdb=" N PRO A 420 " pdb=" CA PRO A 420 " ideal model delta sigma weight residual 119.56 127.44 -7.88 1.02e+00 9.61e-01 5.96e+01 ... (remaining 12831 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.91: 5476 17.91 - 35.81: 176 35.81 - 53.72: 26 53.72 - 71.62: 9 71.62 - 89.53: 7 Dihedral angle restraints: 5694 sinusoidal: 2374 harmonic: 3320 Sorted by residual: dihedral pdb=" C ILE B 48 " pdb=" N ILE B 48 " pdb=" CA ILE B 48 " pdb=" CB ILE B 48 " ideal model delta harmonic sigma weight residual -122.00 -131.80 9.80 0 2.50e+00 1.60e-01 1.54e+01 dihedral pdb=" C PHE B 501 " pdb=" N PHE B 501 " pdb=" CA PHE B 501 " pdb=" CB PHE B 501 " ideal model delta harmonic sigma weight residual -122.60 -113.60 -9.00 0 2.50e+00 1.60e-01 1.30e+01 dihedral pdb=" C TYR B 385 " pdb=" N TYR B 385 " pdb=" CA TYR B 385 " pdb=" CB TYR B 385 " ideal model delta harmonic sigma weight residual -122.60 -113.89 -8.71 0 2.50e+00 1.60e-01 1.21e+01 ... (remaining 5691 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.095: 923 0.095 - 0.189: 364 0.189 - 0.284: 87 0.284 - 0.379: 13 0.379 - 0.473: 1 Chirality restraints: 1388 Sorted by residual: chirality pdb=" CB ILE B 531 " pdb=" CA ILE B 531 " pdb=" CG1 ILE B 531 " pdb=" CG2 ILE B 531 " both_signs ideal model delta sigma weight residual False 2.64 2.17 0.47 2.00e-01 2.50e+01 5.60e+00 chirality pdb=" CA PHE A 313 " pdb=" N PHE A 313 " pdb=" C PHE A 313 " pdb=" CB PHE A 313 " both_signs ideal model delta sigma weight residual False 2.51 2.13 0.38 2.00e-01 2.50e+01 3.54e+00 chirality pdb=" CA ASN B 436 " pdb=" N ASN B 436 " pdb=" C ASN B 436 " pdb=" CB ASN B 436 " both_signs ideal model delta sigma weight residual False 2.51 2.15 0.36 2.00e-01 2.50e+01 3.25e+00 ... (remaining 1385 not shown) Planarity restraints: 1574 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR A 36 " -0.077 2.00e-02 2.50e+03 4.24e-02 3.60e+01 pdb=" CG TYR A 36 " 0.029 2.00e-02 2.50e+03 pdb=" CD1 TYR A 36 " 0.028 2.00e-02 2.50e+03 pdb=" CD2 TYR A 36 " 0.033 2.00e-02 2.50e+03 pdb=" CE1 TYR A 36 " 0.024 2.00e-02 2.50e+03 pdb=" CE2 TYR A 36 " 0.023 2.00e-02 2.50e+03 pdb=" CZ TYR A 36 " 0.009 2.00e-02 2.50e+03 pdb=" OH TYR A 36 " -0.067 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 540 " -0.075 2.00e-02 2.50e+03 3.64e-02 3.32e+01 pdb=" CG TRP A 540 " 0.018 2.00e-02 2.50e+03 pdb=" CD1 TRP A 540 " 0.035 2.00e-02 2.50e+03 pdb=" CD2 TRP A 540 " 0.030 2.00e-02 2.50e+03 pdb=" NE1 TRP A 540 " 0.009 2.00e-02 2.50e+03 pdb=" CE2 TRP A 540 " -0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP A 540 " 0.038 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 540 " -0.048 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 540 " 0.023 2.00e-02 2.50e+03 pdb=" CH2 TRP A 540 " -0.029 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR B 373 " 0.064 2.00e-02 2.50e+03 3.95e-02 3.12e+01 pdb=" CG TYR B 373 " -0.006 2.00e-02 2.50e+03 pdb=" CD1 TYR B 373 " -0.031 2.00e-02 2.50e+03 pdb=" CD2 TYR B 373 " -0.026 2.00e-02 2.50e+03 pdb=" CE1 TYR B 373 " -0.024 2.00e-02 2.50e+03 pdb=" CE2 TYR B 373 " -0.040 2.00e-02 2.50e+03 pdb=" CZ TYR B 373 " -0.005 2.00e-02 2.50e+03 pdb=" OH TYR B 373 " 0.068 2.00e-02 2.50e+03 ... (remaining 1571 not shown) Histogram of nonbonded interaction distances: 2.00 - 2.58: 67 2.58 - 3.16: 8618 3.16 - 3.74: 15153 3.74 - 4.32: 22622 4.32 - 4.90: 34188 Nonbonded interactions: 80648 Sorted by model distance: nonbonded pdb=" OE1 GLU A 242 " pdb="ZN ZN A 701 " model vdw 2.002 2.230 nonbonded pdb=" OE2 GLU A 242 " pdb="ZN ZN A 701 " model vdw 2.033 2.230 nonbonded pdb=" OE2 GLU B 242 " pdb="ZN ZN B 701 " model vdw 2.044 2.230 nonbonded pdb=" OE1 GLU B 242 " pdb="ZN ZN B 701 " model vdw 2.061 2.230 nonbonded pdb=" CD GLU A 242 " pdb="ZN ZN A 701 " model vdw 2.345 2.460 ... (remaining 80643 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 'B' } Set up NCS constraints Number of NCS constrained groups: 1 pdb_interpretation.ncs_group { reference = chain 'A' selection = chain 'B' } Set refine NCS operators NCS operators will be refined. 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 group one per residue 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: 0.080 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 1.010 Check model and map are aligned: 0.140 Set scattering table: 0.090 Process input model: 31.420 Find NCS groups from input model: 0.500 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.010 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.190 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.470 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4707 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 : 0.020 0.130 9532 Z= 1.264 Angle : 1.739 10.276 12836 Z= 1.191 Chirality : 0.104 0.473 1388 Planarity : 0.009 0.044 1574 Dihedral : 10.285 89.529 3554 Min Nonbonded Distance : 2.002 Molprobity Statistics. All-atom Clashscore : 1.81 Ramachandran Plot: Outliers : 0.18 % Allowed : 2.55 % Favored : 97.27 % Rotamer: Outliers : 0.00 % Allowed : 0.77 % Favored : 99.23 % 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: 0.34 (0.24), residues: 1100 helix: 0.79 (0.20), residues: 534 sheet: -0.15 (0.46), residues: 117 loop : -0.21 (0.30), residues: 449 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.075 0.013 TRP A 540 HIS 0.009 0.002 HIS A 153 PHE 0.037 0.007 PHE A 274 TYR 0.077 0.012 TYR A 36 ARG 0.007 0.001 ARG A 162 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2200 Ramachandran restraints generated. 1100 Oldfield, 0 Emsley, 1100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2200 Ramachandran restraints generated. 1100 Oldfield, 0 Emsley, 1100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 518 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 195 time to evaluate : 0.516 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 195 average time/residue: 0.1846 time to fit residues: 44.0922 Evaluate side-chains 111 residues out of total 518 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 111 time to evaluate : 0.498 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.7468 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 92 optimal weight: 0.2980 chunk 83 optimal weight: 5.9990 chunk 46 optimal weight: 0.9980 chunk 28 optimal weight: 2.9990 chunk 56 optimal weight: 0.0000 chunk 44 optimal weight: 4.9990 chunk 86 optimal weight: 0.0050 chunk 33 optimal weight: 0.0050 chunk 52 optimal weight: 5.9990 chunk 64 optimal weight: 7.9990 chunk 99 optimal weight: 0.0030 overall best weight: 0.0622 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 218 ASN A 241 ASN A 282 HIS ** A 302 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 538 ASN ** A 567 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4441 moved from start: 1.0616 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 9532 Z= 0.250 Angle : 0.768 8.362 12836 Z= 0.426 Chirality : 0.046 0.148 1388 Planarity : 0.005 0.042 1574 Dihedral : 5.568 29.011 1208 Min Nonbonded Distance : 2.088 Molprobity Statistics. All-atom Clashscore : 17.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 0.39 % Allowed : 3.47 % Favored : 96.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.55 (0.25), residues: 1100 helix: 1.34 (0.21), residues: 570 sheet: 0.02 (0.46), residues: 122 loop : -0.88 (0.29), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP B 414 HIS 0.008 0.001 HIS A 213 PHE 0.037 0.003 PHE B 14 TYR 0.027 0.002 TYR B 524 ARG 0.003 0.001 ARG A 28 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1100 Ramachandran restraints generated. 550 Oldfield, 0 Emsley, 550 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1100 Ramachandran restraints generated. 550 Oldfield, 0 Emsley, 550 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 518 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 156 time to evaluate : 0.551 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 outliers start: 2 outliers final: 0 residues processed: 156 average time/residue: 0.1901 time to fit residues: 36.9252 Evaluate side-chains 115 residues out of total 518 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 115 time to evaluate : 0.559 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.7510 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 55 optimal weight: 10.0000 chunk 31 optimal weight: 0.0170 chunk 83 optimal weight: 2.9990 chunk 68 optimal weight: 1.9990 chunk 27 optimal weight: 4.9990 chunk 100 optimal weight: 3.9990 chunk 108 optimal weight: 4.9990 chunk 89 optimal weight: 5.9990 chunk 99 optimal weight: 30.0000 chunk 34 optimal weight: 5.9990 chunk 80 optimal weight: 9.9990 overall best weight: 2.8026 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 31 ASN A 213 HIS A 487 GLN A 567 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4729 moved from start: 1.1347 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 9532 Z= 0.236 Angle : 0.709 11.046 12836 Z= 0.394 Chirality : 0.044 0.187 1388 Planarity : 0.005 0.042 1574 Dihedral : 5.486 29.821 1208 Min Nonbonded Distance : 2.001 Molprobity Statistics. All-atom Clashscore : 20.37 Ramachandran Plot: Outliers : 0.18 % Allowed : 3.64 % Favored : 96.18 % Rotamer: Outliers : 0.00 % Allowed : 3.67 % Favored : 96.33 % 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: -0.34 (0.24), residues: 1100 helix: 0.38 (0.20), residues: 572 sheet: 0.34 (0.44), residues: 136 loop : -1.24 (0.31), residues: 392 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP B 414 HIS 0.006 0.001 HIS B 213 PHE 0.046 0.003 PHE B 14 TYR 0.025 0.002 TYR A 524 ARG 0.005 0.001 ARG A 293 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1100 Ramachandran restraints generated. 550 Oldfield, 0 Emsley, 550 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1100 Ramachandran restraints generated. 550 Oldfield, 0 Emsley, 550 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 518 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 142 time to evaluate : 0.499 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 outliers start: 0 outliers final: 0 residues processed: 142 average time/residue: 0.1722 time to fit residues: 30.6299 Evaluate side-chains 112 residues out of total 518 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 112 time to evaluate : 0.492 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.7441 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 98 optimal weight: 0.0770 chunk 75 optimal weight: 1.9990 chunk 51 optimal weight: 0.6980 chunk 11 optimal weight: 0.8980 chunk 47 optimal weight: 3.9990 chunk 67 optimal weight: 2.9990 chunk 100 optimal weight: 4.9990 chunk 106 optimal weight: 0.6980 chunk 52 optimal weight: 7.9990 chunk 95 optimal weight: 10.0000 chunk 28 optimal weight: 3.9990 overall best weight: 0.8740 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 285 ASN ** A 518 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 567 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4638 moved from start: 1.1661 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 9532 Z= 0.202 Angle : 0.683 7.898 12836 Z= 0.375 Chirality : 0.042 0.158 1388 Planarity : 0.004 0.040 1574 Dihedral : 5.115 21.258 1208 Min Nonbonded Distance : 2.136 Molprobity Statistics. All-atom Clashscore : 18.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.55 % Favored : 95.45 % Rotamer: Outliers : 0.39 % Allowed : 3.09 % Favored : 96.53 % 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: -0.31 (0.24), residues: 1100 helix: 0.45 (0.21), residues: 568 sheet: 0.25 (0.44), residues: 132 loop : -1.22 (0.30), residues: 400 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 414 HIS 0.016 0.001 HIS B 239 PHE 0.043 0.002 PHE B 14 TYR 0.025 0.002 TYR A 544 ARG 0.007 0.001 ARG A 247 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1100 Ramachandran restraints generated. 550 Oldfield, 0 Emsley, 550 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1100 Ramachandran restraints generated. 550 Oldfield, 0 Emsley, 550 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 518 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 136 time to evaluate : 0.558 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 outliers start: 2 outliers final: 0 residues processed: 138 average time/residue: 0.1535 time to fit residues: 27.8383 Evaluate side-chains 110 residues out of total 518 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 110 time to evaluate : 0.700 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.8996 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 88 optimal weight: 0.0050 chunk 60 optimal weight: 0.6980 chunk 1 optimal weight: 7.9990 chunk 79 optimal weight: 20.0000 chunk 43 optimal weight: 3.9990 chunk 90 optimal weight: 3.9990 chunk 73 optimal weight: 5.9990 chunk 0 optimal weight: 10.0000 chunk 54 optimal weight: 1.9990 chunk 95 optimal weight: 7.9990 chunk 26 optimal weight: 7.9990 overall best weight: 2.1400 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 518 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 567 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4759 moved from start: 1.1884 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 9532 Z= 0.207 Angle : 0.667 10.848 12836 Z= 0.364 Chirality : 0.041 0.134 1388 Planarity : 0.004 0.040 1574 Dihedral : 5.036 20.285 1208 Min Nonbonded Distance : 2.181 Molprobity Statistics. All-atom Clashscore : 19.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.27 % Favored : 94.73 % Rotamer: Outliers : 0.19 % Allowed : 2.51 % Favored : 97.30 % 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 (0.24), residues: 1100 helix: 0.51 (0.20), residues: 570 sheet: 0.39 (0.43), residues: 132 loop : -1.38 (0.30), residues: 398 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP B 414 HIS 0.014 0.001 HIS B 239 PHE 0.033 0.002 PHE B 14 TYR 0.018 0.002 TYR A 32 ARG 0.006 0.001 ARG B 247 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1100 Ramachandran restraints generated. 550 Oldfield, 0 Emsley, 550 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1100 Ramachandran restraints generated. 550 Oldfield, 0 Emsley, 550 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 518 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 140 time to evaluate : 0.555 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 outliers start: 1 outliers final: 1 residues processed: 140 average time/residue: 0.1489 time to fit residues: 27.1083 Evaluate side-chains 111 residues out of total 518 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 110 time to evaluate : 0.561 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0722 time to fit residues: 0.9173 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 35 optimal weight: 3.9990 chunk 95 optimal weight: 8.9990 chunk 21 optimal weight: 8.9990 chunk 62 optimal weight: 8.9990 chunk 26 optimal weight: 9.9990 chunk 106 optimal weight: 0.8980 chunk 88 optimal weight: 0.2980 chunk 49 optimal weight: 3.9990 chunk 8 optimal weight: 2.9990 chunk 55 optimal weight: 9.9990 chunk 102 optimal weight: 2.9990 overall best weight: 2.2386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 282 HIS ** A 518 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 567 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4796 moved from start: 1.2334 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 9532 Z= 0.208 Angle : 0.665 14.149 12836 Z= 0.363 Chirality : 0.042 0.150 1388 Planarity : 0.004 0.038 1574 Dihedral : 5.052 18.994 1208 Min Nonbonded Distance : 2.096 Molprobity Statistics. All-atom Clashscore : 22.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.82 % Favored : 94.18 % Rotamer: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % 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: -0.57 (0.24), residues: 1100 helix: 0.35 (0.20), residues: 580 sheet: 0.26 (0.42), residues: 132 loop : -1.65 (0.29), residues: 388 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP B 414 HIS 0.012 0.002 HIS B 239 PHE 0.036 0.002 PHE A 14 TYR 0.020 0.002 TYR A 544 ARG 0.004 0.001 ARG B 247 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1100 Ramachandran restraints generated. 550 Oldfield, 0 Emsley, 550 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1100 Ramachandran restraints generated. 550 Oldfield, 0 Emsley, 550 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 518 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 137 time to evaluate : 0.541 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 137 average time/residue: 0.1422 time to fit residues: 25.5974 Evaluate side-chains 108 residues out of total 518 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 108 time to evaluate : 0.564 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.7222 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 11 optimal weight: 1.9990 chunk 60 optimal weight: 0.0000 chunk 77 optimal weight: 7.9990 chunk 89 optimal weight: 0.0470 chunk 59 optimal weight: 0.0770 chunk 106 optimal weight: 0.9990 chunk 66 optimal weight: 1.9990 chunk 64 optimal weight: 0.7980 chunk 48 optimal weight: 0.0970 chunk 65 optimal weight: 2.9990 chunk 42 optimal weight: 4.9990 overall best weight: 0.2038 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 518 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 567 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4664 moved from start: 1.2689 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 9532 Z= 0.191 Angle : 0.702 11.719 12836 Z= 0.372 Chirality : 0.044 0.245 1388 Planarity : 0.004 0.039 1574 Dihedral : 4.888 19.304 1208 Min Nonbonded Distance : 2.215 Molprobity Statistics. All-atom Clashscore : 19.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.55 % Favored : 95.45 % Rotamer: Outliers : 0.00 % Allowed : 1.35 % Favored : 98.65 % 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: -0.47 (0.24), residues: 1100 helix: 0.40 (0.20), residues: 578 sheet: 0.35 (0.43), residues: 132 loop : -1.57 (0.30), residues: 390 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.003 TRP A 414 HIS 0.004 0.001 HIS A 213 PHE 0.030 0.002 PHE A 14 TYR 0.018 0.002 TYR B 127 ARG 0.003 0.000 ARG A 209 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1100 Ramachandran restraints generated. 550 Oldfield, 0 Emsley, 550 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1100 Ramachandran restraints generated. 550 Oldfield, 0 Emsley, 550 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 518 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 144 time to evaluate : 0.494 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 outliers start: 0 outliers final: 0 residues processed: 144 average time/residue: 0.1568 time to fit residues: 28.6650 Evaluate side-chains 116 residues out of total 518 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 116 time to evaluate : 0.494 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.7189 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 63 optimal weight: 0.9990 chunk 31 optimal weight: 0.0040 chunk 20 optimal weight: 0.9990 chunk 67 optimal weight: 0.0570 chunk 72 optimal weight: 3.9990 chunk 52 optimal weight: 6.9990 chunk 9 optimal weight: 1.9990 chunk 83 optimal weight: 0.9990 chunk 96 optimal weight: 5.9990 chunk 101 optimal weight: 0.0770 chunk 92 optimal weight: 2.9990 overall best weight: 0.4272 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 518 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 567 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4658 moved from start: 1.2957 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 9532 Z= 0.185 Angle : 0.649 6.268 12836 Z= 0.364 Chirality : 0.043 0.185 1388 Planarity : 0.004 0.043 1574 Dihedral : 4.744 18.286 1208 Min Nonbonded Distance : 2.191 Molprobity Statistics. All-atom Clashscore : 18.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.82 % Favored : 94.18 % Rotamer: Outliers : 0.00 % Allowed : 0.58 % Favored : 99.42 % 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: -0.59 (0.24), residues: 1100 helix: 0.43 (0.20), residues: 578 sheet: 0.18 (0.46), residues: 124 loop : -1.76 (0.29), residues: 398 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.003 TRP B 414 HIS 0.003 0.001 HIS A 418 PHE 0.041 0.002 PHE A 14 TYR 0.031 0.001 TYR A 127 ARG 0.002 0.000 ARG A 294 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1100 Ramachandran restraints generated. 550 Oldfield, 0 Emsley, 550 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1100 Ramachandran restraints generated. 550 Oldfield, 0 Emsley, 550 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 518 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 140 time to evaluate : 0.527 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 140 average time/residue: 0.1737 time to fit residues: 31.4005 Evaluate side-chains 108 residues out of total 518 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 108 time to evaluate : 0.545 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.7134 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 98 optimal weight: 0.5980 chunk 101 optimal weight: 0.0070 chunk 59 optimal weight: 0.0770 chunk 43 optimal weight: 0.5980 chunk 77 optimal weight: 0.7980 chunk 30 optimal weight: 2.9990 chunk 89 optimal weight: 6.9990 chunk 93 optimal weight: 0.0040 chunk 64 optimal weight: 0.9990 chunk 104 optimal weight: 4.9990 chunk 63 optimal weight: 0.8980 overall best weight: 0.2568 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 518 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 567 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4635 moved from start: 1.3211 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 9532 Z= 0.183 Angle : 0.683 9.484 12836 Z= 0.371 Chirality : 0.043 0.192 1388 Planarity : 0.004 0.041 1574 Dihedral : 4.730 19.619 1208 Min Nonbonded Distance : 2.228 Molprobity Statistics. All-atom Clashscore : 18.09 Ramachandran Plot: Outliers : 0.36 % Allowed : 5.64 % Favored : 94.00 % Rotamer: Outliers : 0.00 % Allowed : 1.16 % Favored : 98.84 % 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 (0.24), residues: 1100 helix: 0.44 (0.20), residues: 582 sheet: 0.16 (0.46), residues: 124 loop : -1.74 (0.29), residues: 394 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP A 414 HIS 0.005 0.001 HIS A 418 PHE 0.031 0.002 PHE B 14 TYR 0.016 0.001 TYR B 441 ARG 0.008 0.001 ARG B 23 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1100 Ramachandran restraints generated. 550 Oldfield, 0 Emsley, 550 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1100 Ramachandran restraints generated. 550 Oldfield, 0 Emsley, 550 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 518 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 140 time to evaluate : 0.552 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 outliers start: 0 outliers final: 0 residues processed: 140 average time/residue: 0.1721 time to fit residues: 31.1950 Evaluate side-chains 113 residues out of total 518 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 113 time to evaluate : 0.568 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.7843 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 49 optimal weight: 0.9990 chunk 72 optimal weight: 3.9990 chunk 109 optimal weight: 0.0050 chunk 100 optimal weight: 0.9980 chunk 87 optimal weight: 0.0040 chunk 9 optimal weight: 0.9990 chunk 67 optimal weight: 0.0670 chunk 53 optimal weight: 0.2980 chunk 69 optimal weight: 0.7980 chunk 92 optimal weight: 5.9990 chunk 26 optimal weight: 5.9990 overall best weight: 0.2344 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 153 HIS ** A 518 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 567 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4615 moved from start: 1.3358 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 9532 Z= 0.179 Angle : 0.670 7.689 12836 Z= 0.365 Chirality : 0.042 0.173 1388 Planarity : 0.004 0.037 1574 Dihedral : 4.678 18.742 1208 Min Nonbonded Distance : 2.062 Molprobity Statistics. All-atom Clashscore : 17.56 Ramachandran Plot: Outliers : 0.18 % Allowed : 5.82 % Favored : 94.00 % Rotamer: Outliers : 0.00 % Allowed : 0.77 % Favored : 99.23 % 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: -0.61 (0.24), residues: 1100 helix: 0.33 (0.20), residues: 586 sheet: 0.28 (0.47), residues: 124 loop : -1.69 (0.30), residues: 390 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP B 414 HIS 0.005 0.001 HIS A 418 PHE 0.042 0.002 PHE A 14 TYR 0.014 0.001 TYR A 544 ARG 0.006 0.001 ARG A 247 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1100 Ramachandran restraints generated. 550 Oldfield, 0 Emsley, 550 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1100 Ramachandran restraints generated. 550 Oldfield, 0 Emsley, 550 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 518 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 133 time to evaluate : 0.538 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 outliers start: 0 outliers final: 0 residues processed: 133 average time/residue: 0.1471 time to fit residues: 25.4403 Evaluate side-chains 113 residues out of total 518 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 113 time to evaluate : 0.542 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.7731 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 80 optimal weight: 10.0000 chunk 12 optimal weight: 0.9990 chunk 24 optimal weight: 2.9990 chunk 87 optimal weight: 0.0670 chunk 36 optimal weight: 0.9980 chunk 89 optimal weight: 0.0470 chunk 11 optimal weight: 0.9980 chunk 16 optimal weight: 0.9990 chunk 76 optimal weight: 5.9990 chunk 4 optimal weight: 0.0870 chunk 63 optimal weight: 0.9980 overall best weight: 0.4394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 153 HIS ** A 518 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 567 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4562 r_free = 0.4562 target = 0.186213 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.4134 r_free = 0.4134 target = 0.147283 restraints weight = 14546.151| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.4185 r_free = 0.4185 target = 0.151385 restraints weight = 10049.061| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.4220 r_free = 0.4220 target = 0.154332 restraints weight = 7333.989| |-----------------------------------------------------------------------------| r_work (final): 0.4171 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6415 moved from start: 1.3568 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 9532 Z= 0.185 Angle : 0.672 8.010 12836 Z= 0.372 Chirality : 0.043 0.254 1388 Planarity : 0.004 0.042 1574 Dihedral : 4.619 22.606 1208 Min Nonbonded Distance : 2.069 Molprobity Statistics. All-atom Clashscore : 17.77 Ramachandran Plot: Outliers : 0.18 % Allowed : 5.27 % Favored : 94.55 % Rotamer: Outliers : 0.00 % Allowed : 0.58 % Favored : 99.42 % 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: -0.50 (0.25), residues: 1100 helix: 0.45 (0.21), residues: 586 sheet: 0.35 (0.48), residues: 124 loop : -1.72 (0.30), residues: 390 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.003 TRP B 414 HIS 0.002 0.001 HIS A 418 PHE 0.039 0.002 PHE A 14 TYR 0.016 0.001 TYR B 441 ARG 0.004 0.000 ARG A 247 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1772.52 seconds wall clock time: 33 minutes 27.20 seconds (2007.20 seconds total)