Starting phenix.real_space_refine on Tue Aug 6 01:29:02 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8r22_18833/08_2024/8r22_18833.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8r22_18833/08_2024/8r22_18833.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8r22_18833/08_2024/8r22_18833.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8r22_18833/08_2024/8r22_18833.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8r22_18833/08_2024/8r22_18833.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8r22_18833/08_2024/8r22_18833.cif" } resolution = 3.9 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= 0.000 sd= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians Zn 1 6.06 5 S 106 5.16 5 C 9620 2.51 5 N 2556 2.21 5 O 2786 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ASP 2": "OD1" <-> "OD2" Residue "A GLU 30": "OE1" <-> "OE2" Residue "A GLU 41": "OE1" <-> "OE2" Residue "A GLU 87": "OE1" <-> "OE2" Residue "A ARG 111": "NH1" <-> "NH2" Residue "A ASP 200": "OD1" <-> "OD2" Residue "A PHE 272": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 281": "OE1" <-> "OE2" Residue "A PHE 317": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 444": "OE1" <-> "OE2" Residue "A GLU 455": "OE1" <-> "OE2" Residue "A GLU 545": "OE1" <-> "OE2" Residue "A PHE 593": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 595": "OE1" <-> "OE2" Residue "A PHE 607": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 622": "OD1" <-> "OD2" Residue "A ARG 644": "NH1" <-> "NH2" Residue "A ASP 645": "OD1" <-> "OD2" Residue "A ASP 647": "OD1" <-> "OD2" Residue "A GLU 690": "OE1" <-> "OE2" Residue "A PHE 725": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 782": "OE1" <-> "OE2" Residue "A ASP 805": "OD1" <-> "OD2" Residue "B GLU 87": "OE1" <-> "OE2" Residue "B ASP 97": "OD1" <-> "OD2" Residue "B TYR 104": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 139": "OE1" <-> "OE2" Residue "B GLU 174": "OE1" <-> "OE2" Residue "B TYR 182": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 290": "NH1" <-> "NH2" Residue "B ASP 386": "OD1" <-> "OD2" Residue "B PHE 402": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 424": "OE1" <-> "OE2" Residue "B ASP 426": "OD1" <-> "OD2" Residue "B GLU 431": "OE1" <-> "OE2" Residue "B ASP 449": "OD1" <-> "OD2" Residue "B ARG 511": "NH1" <-> "NH2" Residue "C ARG 17": "NH1" <-> "NH2" Residue "C ARG 43": "NH1" <-> "NH2" Residue "C ARG 44": "NH1" <-> "NH2" Residue "C ASP 47": "OD1" <-> "OD2" Residue "C ASP 72": "OD1" <-> "OD2" Residue "C GLU 82": "OE1" <-> "OE2" Residue "C TYR 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 106": "OD1" <-> "OD2" Residue "C PHE 121": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 145": "OD1" <-> "OD2" Residue "C GLU 149": "OE1" <-> "OE2" Residue "C GLU 171": "OE1" <-> "OE2" Residue "C ARG 217": "NH1" <-> "NH2" Residue "C ARG 219": "NH1" <-> "NH2" Residue "C PHE 240": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 244": "NH1" <-> "NH2" Residue "C GLU 253": "OE1" <-> "OE2" Residue "C TYR 278": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 312": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 314": "OD1" <-> "OD2" Residue "C GLU 373": "OE1" <-> "OE2" Residue "C TYR 386": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 389": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 428": "OE1" <-> "OE2" Residue "C TYR 436": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 2": "OD1" <-> "OD2" Residue "D PHE 18": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 22": "OD1" <-> "OD2" Residue "D PHE 39": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 43": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 59": "NH1" <-> "NH2" Residue "D ASP 83": "OD1" <-> "OD2" Residue "D ASP 88": "OD1" <-> "OD2" Residue "D ASP 116": "OD1" <-> "OD2" Residue "D ASP 173": "OD1" <-> "OD2" Residue "D GLU 179": "OE1" <-> "OE2" Residue "D PHE 193": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 204": "OD1" <-> "OD2" Residue "D GLU 213": "OE1" <-> "OE2" Residue "D ASP 254": "OD1" <-> "OD2" Residue "D GLU 277": "OE1" <-> "OE2" Residue "D PHE 296": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 297": "OD1" <-> "OD2" Residue "D TYR 303": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 332": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 363": "OD1" <-> "OD2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/chem_data/mon_lib" Total number of atoms: 15069 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 5404 Number of conformers: 1 Conformer: "" Number of residues, atoms: 710, 5404 Classifications: {'peptide': 710} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 41, 'TRANS': 667} Chain breaks: 8 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "B" Number of atoms: 3454 Number of conformers: 1 Conformer: "" Number of residues, atoms: 451, 3454 Classifications: {'peptide': 451} Incomplete info: {'truncation_to_alanine': 25} Link IDs: {'PCIS': 4, 'PTRANS': 31, 'TRANS': 415} Chain breaks: 3 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 91 Unresolved non-hydrogen angles: 115 Unresolved non-hydrogen dihedrals: 80 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'GLN:plan1': 1, 'ARG:plan': 1, 'ASN:plan1': 1, 'TRP:plan': 1, 'ASP:plan': 2, 'PHE:plan': 1, 'GLU:plan': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 42 Chain: "C" Number of atoms: 3447 Number of conformers: 1 Conformer: "" Number of residues, atoms: 436, 3447 Classifications: {'peptide': 436} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 19, 'TRANS': 416} Chain breaks: 1 Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 19 Unresolved non-hydrogen dihedrals: 13 Planarities with less than four sites: {'HIS:plan': 1, 'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 13 Chain: "D" Number of atoms: 2763 Number of conformers: 1 Conformer: "" Number of residues, atoms: 353, 2763 Classifications: {'peptide': 353} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 22, 'TRANS': 329} Chain breaks: 4 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" N PRO A 492 " occ=0.25 ... (5 atoms not shown) pdb=" CD PRO A 492 " occ=0.25 Time building chain proxies: 8.23, per 1000 atoms: 0.55 Number of scatterers: 15069 At special positions: 0 Unit cell: (133.32, 124.08, 133.32, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Zn 1 29.99 S 106 16.00 O 2786 8.00 N 2556 7.00 C 9620 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: 5.73 Conformation dependent library (CDL) restraints added in 2.7 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN C 800 " pdb="ZN ZN C 800 " - pdb=" ND1 HIS C 70 " pdb="ZN ZN C 800 " - pdb=" NE2 HIS C 68 " pdb="ZN ZN C 800 " - pdb=" NE2 HIS C 157 " 3820 Ramachandran restraints generated. 1910 Oldfield, 0 Emsley, 1910 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3664 Finding SS restraints... Secondary structure from input PDB file: 63 helices and 0 sheets defined 36.2% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.05 Creating SS restraints... Processing helix chain 'A' and resid 9 through 17 removed outlier: 3.994A pdb=" N VAL A 17 " --> pdb=" O CYS A 13 " (cutoff:3.500A) Processing helix chain 'A' and resid 27 through 39 Processing helix chain 'A' and resid 46 through 51 Processing helix chain 'A' and resid 55 through 61 Processing helix chain 'A' and resid 73 through 83 Processing helix chain 'A' and resid 87 through 92 Processing helix chain 'A' and resid 99 through 103 Processing helix chain 'A' and resid 117 through 130 Processing helix chain 'A' and resid 134 through 139 Processing helix chain 'A' and resid 146 through 152 Processing helix chain 'A' and resid 158 through 175 Processing helix chain 'A' and resid 193 through 205 Processing helix chain 'A' and resid 211 through 224 Processing helix chain 'A' and resid 231 through 247 removed outlier: 3.522A pdb=" N ALA A 235 " --> pdb=" O PRO A 231 " (cutoff:3.500A) Proline residue: A 242 - end of helix Processing helix chain 'A' and resid 258 through 267 Processing helix chain 'A' and resid 279 through 289 Processing helix chain 'A' and resid 295 through 303 Processing helix chain 'A' and resid 310 through 329 Proline residue: A 323 - end of helix Processing helix chain 'A' and resid 349 through 356 Processing helix chain 'A' and resid 358 through 375 Processing helix chain 'A' and resid 388 through 402 Processing helix chain 'A' and resid 410 through 418 Processing helix chain 'A' and resid 424 through 435 Processing helix chain 'A' and resid 443 through 457 Processing helix chain 'A' and resid 464 through 478 Processing helix chain 'A' and resid 494 through 508 Proline residue: A 503 - end of helix Processing helix chain 'A' and resid 514 through 530 Processing helix chain 'A' and resid 535 through 543 Processing helix chain 'A' and resid 546 through 552 Processing helix chain 'A' and resid 559 through 575 Processing helix chain 'A' and resid 590 through 601 removed outlier: 4.029A pdb=" N GLU A 595 " --> pdb=" O SER A 591 " (cutoff:3.500A) Processing helix chain 'A' and resid 607 through 621 Processing helix chain 'A' and resid 631 through 642 Processing helix chain 'A' and resid 650 through 665 Processing helix chain 'A' and resid 688 through 697 Processing helix chain 'A' and resid 700 through 708 Processing helix chain 'A' and resid 713 through 733 Processing helix chain 'A' and resid 769 through 778 Processing helix chain 'A' and resid 781 through 788 Processing helix chain 'A' and resid 799 through 808 Processing helix chain 'B' and resid 110 through 115 Processing helix chain 'B' and resid 127 through 145 Processing helix chain 'B' and resid 159 through 163 Processing helix chain 'B' and resid 184 through 192 Processing helix chain 'B' and resid 274 through 289 Processing helix chain 'B' and resid 304 through 318 Processing helix chain 'B' and resid 333 through 341 Processing helix chain 'B' and resid 383 through 386 No H-bonds generated for 'chain 'B' and resid 383 through 386' Processing helix chain 'B' and resid 404 through 412 Processing helix chain 'B' and resid 429 through 433 Processing helix chain 'B' and resid 454 through 464 Processing helix chain 'C' and resid 57 through 60 No H-bonds generated for 'chain 'C' and resid 57 through 60' Processing helix chain 'C' and resid 77 through 78 No H-bonds generated for 'chain 'C' and resid 77 through 78' Processing helix chain 'C' and resid 94 through 113 Proline residue: C 101 - end of helix Processing helix chain 'C' and resid 123 through 130 Processing helix chain 'C' and resid 214 through 231 removed outlier: 3.502A pdb=" N ARG C 231 " --> pdb=" O GLU C 227 " (cutoff:3.500A) Processing helix chain 'C' and resid 244 through 259 Processing helix chain 'C' and resid 275 through 280 Processing helix chain 'C' and resid 332 through 339 Processing helix chain 'C' and resid 359 through 363 Processing helix chain 'C' and resid 395 through 405 Processing helix chain 'C' and resid 420 through 431 removed outlier: 4.585A pdb=" N GLN C 425 " --> pdb=" O GLU C 421 " (cutoff:3.500A) Processing helix chain 'D' and resid 3 through 14 removed outlier: 3.896A pdb=" N ARG D 13 " --> pdb=" O VAL D 9 " (cutoff:3.500A) 438 hydrogen bonds defined for protein. 1314 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: 3.34 Time building geometry restraints manager: 6.18 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 4906 1.34 - 1.46: 2973 1.46 - 1.58: 7381 1.58 - 1.69: 0 1.69 - 1.81: 151 Bond restraints: 15411 Sorted by residual: bond pdb=" C HIS B 246 " pdb=" N PRO B 247 " ideal model delta sigma weight residual 1.326 1.357 -0.030 1.44e-02 4.82e+03 4.47e+00 bond pdb=" C ASP D 339 " pdb=" N PRO D 340 " ideal model delta sigma weight residual 1.334 1.366 -0.032 2.34e-02 1.83e+03 1.87e+00 bond pdb=" CG PRO B 390 " pdb=" CD PRO B 390 " ideal model delta sigma weight residual 1.512 1.482 0.030 2.70e-02 1.37e+03 1.20e+00 bond pdb=" C GLY C 156 " pdb=" O GLY C 156 " ideal model delta sigma weight residual 1.237 1.231 0.006 7.00e-03 2.04e+04 8.33e-01 bond pdb=" CG LEU A 509 " pdb=" CD2 LEU A 509 " ideal model delta sigma weight residual 1.521 1.491 0.030 3.30e-02 9.18e+02 8.32e-01 ... (remaining 15406 not shown) Histogram of bond angle deviations from ideal: 98.68 - 105.75: 436 105.75 - 112.83: 8410 112.83 - 119.90: 5082 119.90 - 126.98: 6803 126.98 - 134.05: 230 Bond angle restraints: 20961 Sorted by residual: angle pdb=" N THR C 324 " pdb=" CA THR C 324 " pdb=" C THR C 324 " ideal model delta sigma weight residual 109.30 116.38 -7.08 1.49e+00 4.50e-01 2.26e+01 angle pdb=" C ALA C 323 " pdb=" N THR C 324 " pdb=" CA THR C 324 " ideal model delta sigma weight residual 122.59 117.73 4.86 1.11e+00 8.12e-01 1.92e+01 angle pdb=" C ASP C 14 " pdb=" N VAL C 15 " pdb=" CA VAL C 15 " ideal model delta sigma weight residual 120.62 125.71 -5.09 1.64e+00 3.72e-01 9.61e+00 angle pdb=" C GLY B 396 " pdb=" N HIS B 397 " pdb=" CA HIS B 397 " ideal model delta sigma weight residual 120.69 111.57 9.12 2.95e+00 1.15e-01 9.56e+00 angle pdb=" C ALA B 109 " pdb=" N LEU B 110 " pdb=" CA LEU B 110 " ideal model delta sigma weight residual 119.78 123.27 -3.49 1.24e+00 6.50e-01 7.91e+00 ... (remaining 20956 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.93: 8271 17.93 - 35.87: 797 35.87 - 53.80: 140 53.80 - 71.73: 24 71.73 - 89.67: 13 Dihedral angle restraints: 9245 sinusoidal: 3606 harmonic: 5639 Sorted by residual: dihedral pdb=" CA GLU C 301 " pdb=" C GLU C 301 " pdb=" N PHE C 302 " pdb=" CA PHE C 302 " ideal model delta harmonic sigma weight residual -180.00 -155.62 -24.38 0 5.00e+00 4.00e-02 2.38e+01 dihedral pdb=" CA ALA A 255 " pdb=" C ALA A 255 " pdb=" N ALA A 256 " pdb=" CA ALA A 256 " ideal model delta harmonic sigma weight residual 180.00 156.61 23.39 0 5.00e+00 4.00e-02 2.19e+01 dihedral pdb=" CA SER B 223 " pdb=" C SER B 223 " pdb=" N ASN B 224 " pdb=" CA ASN B 224 " ideal model delta harmonic sigma weight residual 180.00 158.58 21.42 0 5.00e+00 4.00e-02 1.84e+01 ... (remaining 9242 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.032: 1393 0.032 - 0.063: 701 0.063 - 0.095: 204 0.095 - 0.127: 101 0.127 - 0.158: 17 Chirality restraints: 2416 Sorted by residual: chirality pdb=" CA VAL C 144 " pdb=" N VAL C 144 " pdb=" C VAL C 144 " pdb=" CB VAL C 144 " both_signs ideal model delta sigma weight residual False 2.44 2.60 -0.16 2.00e-01 2.50e+01 6.27e-01 chirality pdb=" CA VAL D 300 " pdb=" N VAL D 300 " pdb=" C VAL D 300 " pdb=" CB VAL D 300 " both_signs ideal model delta sigma weight residual False 2.44 2.60 -0.16 2.00e-01 2.50e+01 6.17e-01 chirality pdb=" CA ILE C 90 " pdb=" N ILE C 90 " pdb=" C ILE C 90 " pdb=" CB ILE C 90 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.69e-01 ... (remaining 2413 not shown) Planarity restraints: 2682 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PHE A 502 " -0.037 5.00e-02 4.00e+02 5.61e-02 5.04e+00 pdb=" N PRO A 503 " 0.097 5.00e-02 4.00e+02 pdb=" CA PRO A 503 " -0.028 5.00e-02 4.00e+02 pdb=" CD PRO A 503 " -0.032 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE C 283 " 0.036 5.00e-02 4.00e+02 5.47e-02 4.79e+00 pdb=" N PRO C 284 " -0.095 5.00e-02 4.00e+02 pdb=" CA PRO C 284 " 0.028 5.00e-02 4.00e+02 pdb=" CD PRO C 284 " 0.031 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLU A 105 " 0.035 5.00e-02 4.00e+02 5.33e-02 4.55e+00 pdb=" N PRO A 106 " -0.092 5.00e-02 4.00e+02 pdb=" CA PRO A 106 " 0.027 5.00e-02 4.00e+02 pdb=" CD PRO A 106 " 0.030 5.00e-02 4.00e+02 ... (remaining 2679 not shown) Histogram of nonbonded interaction distances: 2.10 - 2.66: 237 2.66 - 3.22: 14639 3.22 - 3.78: 22022 3.78 - 4.34: 29848 4.34 - 4.90: 49367 Nonbonded interactions: 116113 Sorted by model distance: nonbonded pdb=" OD2 ASP C 178 " pdb="ZN ZN C 800 " model vdw 2.098 2.230 nonbonded pdb=" OH TYR B 327 " pdb=" O ASP B 386 " model vdw 2.110 3.040 nonbonded pdb=" O LEU D 155 " pdb=" OG SER D 172 " model vdw 2.139 3.040 nonbonded pdb=" OE1 GLN D 301 " pdb=" OH TYR D 303 " model vdw 2.143 3.040 nonbonded pdb=" OG1 THR D 282 " pdb=" NE2 HIS D 347 " model vdw 2.177 3.120 ... (remaining 116108 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.25 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: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.780 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: 0.550 Check model and map are aligned: 0.110 Set scattering table: 0.120 Process input model: 41.650 Find NCS groups from input model: 0.180 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.990 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 46.470 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7735 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 : 0.004 0.037 15411 Z= 0.275 Angle : 0.673 12.234 20961 Z= 0.365 Chirality : 0.044 0.158 2416 Planarity : 0.005 0.056 2682 Dihedral : 14.653 89.667 5581 Min Nonbonded Distance : 2.098 Molprobity Statistics. All-atom Clashscore : 10.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.27 % Favored : 90.73 % Rotamer: Outliers : 0.00 % Allowed : 6.69 % Favored : 93.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.08 % 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: -4.23 (0.16), residues: 1910 helix: -1.69 (0.16), residues: 793 sheet: -3.14 (0.26), residues: 263 loop : -3.82 (0.18), residues: 854 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP D 7 HIS 0.005 0.001 HIS D 347 PHE 0.029 0.002 PHE B 509 TYR 0.023 0.002 TYR C 278 ARG 0.004 0.000 ARG D 84 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3820 Ramachandran restraints generated. 1910 Oldfield, 0 Emsley, 1910 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3820 Ramachandran restraints generated. 1910 Oldfield, 0 Emsley, 1910 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 227 residues out of total 1688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 227 time to evaluate : 1.826 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 373 GLU cc_start: 0.7851 (tt0) cc_final: 0.7478 (tm-30) REVERT: A 578 HIS cc_start: 0.7114 (m-70) cc_final: 0.6818 (m170) REVERT: A 657 LEU cc_start: 0.9093 (tp) cc_final: 0.8890 (tp) REVERT: A 781 LEU cc_start: 0.8420 (mm) cc_final: 0.8092 (mm) REVERT: B 93 LEU cc_start: 0.6701 (tp) cc_final: 0.6422 (tt) REVERT: B 184 MET cc_start: 0.7778 (mmm) cc_final: 0.7466 (mmm) REVERT: B 409 MET cc_start: 0.8914 (mtp) cc_final: 0.8690 (ttm) REVERT: C 30 MET cc_start: 0.8853 (ttm) cc_final: 0.8626 (ttm) REVERT: C 44 ARG cc_start: 0.7924 (ptp90) cc_final: 0.7624 (ptt-90) REVERT: C 50 TYR cc_start: 0.6388 (m-80) cc_final: 0.6109 (m-80) REVERT: C 62 ASP cc_start: 0.7928 (m-30) cc_final: 0.7719 (m-30) REVERT: C 130 MET cc_start: 0.8573 (mmp) cc_final: 0.8349 (mmp) REVERT: C 378 LEU cc_start: 0.6495 (tp) cc_final: 0.6150 (tt) REVERT: D 211 PRO cc_start: 0.2871 (Cg_endo) cc_final: 0.2541 (Cg_exo) REVERT: D 362 ASN cc_start: 0.8364 (p0) cc_final: 0.7966 (p0) REVERT: D 363 ASP cc_start: 0.6189 (t0) cc_final: 0.5683 (t0) outliers start: 0 outliers final: 0 residues processed: 227 average time/residue: 0.2807 time to fit residues: 93.2581 Evaluate side-chains 156 residues out of total 1688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 156 time to evaluate : 1.732 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 194 random chunks: chunk 163 optimal weight: 8.9990 chunk 147 optimal weight: 8.9990 chunk 81 optimal weight: 0.8980 chunk 50 optimal weight: 0.7980 chunk 99 optimal weight: 0.7980 chunk 78 optimal weight: 2.9990 chunk 152 optimal weight: 7.9990 chunk 58 optimal weight: 0.9990 chunk 92 optimal weight: 6.9990 chunk 113 optimal weight: 0.9990 chunk 176 optimal weight: 10.0000 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 201 HIS A 578 HIS A 653 GLN A 767 GLN B 15 ASN ** B 246 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 268 GLN ** B 284 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 482 GLN C 13 GLN C 119 ASN C 124 GLN C 137 HIS C 198 ASN C 429 GLN ** D 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 112 GLN D 367 HIS Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7713 moved from start: 0.1087 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 15411 Z= 0.194 Angle : 0.587 9.751 20961 Z= 0.295 Chirality : 0.043 0.147 2416 Planarity : 0.005 0.062 2682 Dihedral : 4.838 21.457 2063 Min Nonbonded Distance : 1.984 Molprobity Statistics. All-atom Clashscore : 7.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.33 % Favored : 92.67 % Rotamer: Outliers : 1.21 % Allowed : 12.06 % Favored : 86.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.81 (0.18), residues: 1910 helix: -0.30 (0.18), residues: 801 sheet: -2.47 (0.27), residues: 273 loop : -3.27 (0.19), residues: 836 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP D 283 HIS 0.006 0.001 HIS D 347 PHE 0.021 0.001 PHE C 312 TYR 0.023 0.001 TYR C 107 ARG 0.004 0.000 ARG A 562 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3820 Ramachandran restraints generated. 1910 Oldfield, 0 Emsley, 1910 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3820 Ramachandran restraints generated. 1910 Oldfield, 0 Emsley, 1910 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 208 residues out of total 1688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 188 time to evaluate : 1.745 Fit side-chains revert: symmetry clash REVERT: A 373 GLU cc_start: 0.7869 (tt0) cc_final: 0.7400 (tm-30) REVERT: B 32 MET cc_start: 0.7634 (mtm) cc_final: 0.7357 (mtm) REVERT: B 206 PHE cc_start: 0.6130 (m-80) cc_final: 0.5854 (m-80) REVERT: C 30 MET cc_start: 0.8828 (ttm) cc_final: 0.8575 (ttm) REVERT: C 50 TYR cc_start: 0.6349 (m-80) cc_final: 0.6132 (m-80) REVERT: C 62 ASP cc_start: 0.7919 (m-30) cc_final: 0.7659 (m-30) REVERT: C 378 LEU cc_start: 0.6602 (tp) cc_final: 0.6224 (tt) REVERT: C 382 MET cc_start: 0.8743 (ptm) cc_final: 0.8513 (ptp) REVERT: D 202 LEU cc_start: 0.6444 (OUTLIER) cc_final: 0.6172 (mt) REVERT: D 249 ARG cc_start: 0.6422 (ttt90) cc_final: 0.6001 (ptm-80) REVERT: D 362 ASN cc_start: 0.8380 (p0) cc_final: 0.7975 (p0) REVERT: D 363 ASP cc_start: 0.6122 (t0) cc_final: 0.5589 (t0) outliers start: 20 outliers final: 12 residues processed: 202 average time/residue: 0.2382 time to fit residues: 74.0108 Evaluate side-chains 165 residues out of total 1688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 152 time to evaluate : 1.640 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 143 HIS Chi-restraints excluded: chain A residue 688 LEU Chi-restraints excluded: chain B residue 332 VAL Chi-restraints excluded: chain C residue 216 CYS Chi-restraints excluded: chain D residue 29 VAL Chi-restraints excluded: chain D residue 86 ILE Chi-restraints excluded: chain D residue 118 ASP Chi-restraints excluded: chain D residue 176 ASP Chi-restraints excluded: chain D residue 202 LEU Chi-restraints excluded: chain D residue 344 VAL Chi-restraints excluded: chain D residue 367 HIS Chi-restraints excluded: chain D residue 368 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 194 random chunks: chunk 97 optimal weight: 5.9990 chunk 54 optimal weight: 2.9990 chunk 146 optimal weight: 2.9990 chunk 119 optimal weight: 3.9990 chunk 48 optimal weight: 1.9990 chunk 176 optimal weight: 5.9990 chunk 190 optimal weight: 0.0170 chunk 157 optimal weight: 0.7980 chunk 175 optimal weight: 0.7980 chunk 60 optimal weight: 0.8980 chunk 141 optimal weight: 0.9990 overall best weight: 0.7020 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 246 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 284 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 334 ASN C 119 ASN D 49 ASN D 367 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7693 moved from start: 0.1530 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 15411 Z= 0.171 Angle : 0.558 8.450 20961 Z= 0.279 Chirality : 0.041 0.146 2416 Planarity : 0.005 0.056 2682 Dihedral : 4.545 20.907 2063 Min Nonbonded Distance : 1.991 Molprobity Statistics. All-atom Clashscore : 6.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.81 % Favored : 93.19 % Rotamer: Outliers : 1.33 % Allowed : 14.17 % Favored : 84.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.07 (0.19), residues: 1910 helix: 0.38 (0.18), residues: 807 sheet: -2.01 (0.29), residues: 249 loop : -3.00 (0.20), residues: 854 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP D 283 HIS 0.004 0.001 HIS B 468 PHE 0.014 0.001 PHE B 509 TYR 0.018 0.001 TYR C 107 ARG 0.003 0.000 ARG A 610 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3820 Ramachandran restraints generated. 1910 Oldfield, 0 Emsley, 1910 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3820 Ramachandran restraints generated. 1910 Oldfield, 0 Emsley, 1910 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 1688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 178 time to evaluate : 1.595 Fit side-chains REVERT: A 264 LEU cc_start: 0.8734 (tp) cc_final: 0.8474 (mt) REVERT: A 373 GLU cc_start: 0.7778 (tt0) cc_final: 0.7329 (tm-30) REVERT: A 454 LEU cc_start: 0.9201 (tp) cc_final: 0.8796 (tt) REVERT: B 27 ASP cc_start: 0.7046 (m-30) cc_final: 0.6711 (m-30) REVERT: B 32 MET cc_start: 0.7614 (mtm) cc_final: 0.7305 (mtm) REVERT: B 287 LEU cc_start: 0.8912 (OUTLIER) cc_final: 0.8683 (tp) REVERT: B 486 MET cc_start: 0.7372 (mtm) cc_final: 0.6926 (tpt) REVERT: B 500 ARG cc_start: 0.7204 (ttt180) cc_final: 0.6956 (ttt180) REVERT: C 62 ASP cc_start: 0.7867 (m-30) cc_final: 0.7606 (m-30) REVERT: C 208 THR cc_start: 0.8614 (p) cc_final: 0.8242 (p) REVERT: C 259 MET cc_start: 0.7665 (mmm) cc_final: 0.7464 (mmm) REVERT: C 378 LEU cc_start: 0.6597 (tp) cc_final: 0.6200 (tt) REVERT: C 382 MET cc_start: 0.8650 (ptm) cc_final: 0.8437 (ptp) REVERT: D 202 LEU cc_start: 0.6323 (mt) cc_final: 0.6105 (mt) REVERT: D 214 ASN cc_start: 0.5502 (t0) cc_final: 0.5245 (t0) REVERT: D 241 ILE cc_start: 0.7621 (mp) cc_final: 0.7245 (mp) REVERT: D 249 ARG cc_start: 0.6374 (ttt90) cc_final: 0.5757 (ptm-80) REVERT: D 362 ASN cc_start: 0.8346 (p0) cc_final: 0.7933 (p0) REVERT: D 363 ASP cc_start: 0.6207 (t0) cc_final: 0.5669 (t0) outliers start: 22 outliers final: 14 residues processed: 193 average time/residue: 0.2523 time to fit residues: 74.1789 Evaluate side-chains 170 residues out of total 1688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 155 time to evaluate : 1.902 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 143 HIS Chi-restraints excluded: chain A residue 294 HIS Chi-restraints excluded: chain A residue 398 LEU Chi-restraints excluded: chain A residue 688 LEU Chi-restraints excluded: chain B residue 237 VAL Chi-restraints excluded: chain B residue 287 LEU Chi-restraints excluded: chain B residue 332 VAL Chi-restraints excluded: chain B residue 504 VAL Chi-restraints excluded: chain C residue 216 CYS Chi-restraints excluded: chain D residue 29 VAL Chi-restraints excluded: chain D residue 118 ASP Chi-restraints excluded: chain D residue 151 HIS Chi-restraints excluded: chain D residue 344 VAL Chi-restraints excluded: chain D residue 368 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 194 random chunks: chunk 174 optimal weight: 7.9990 chunk 132 optimal weight: 4.9990 chunk 91 optimal weight: 6.9990 chunk 19 optimal weight: 2.9990 chunk 84 optimal weight: 0.0770 chunk 118 optimal weight: 0.9980 chunk 177 optimal weight: 7.9990 chunk 187 optimal weight: 10.0000 chunk 92 optimal weight: 5.9990 chunk 167 optimal weight: 0.5980 chunk 50 optimal weight: 0.7980 overall best weight: 1.0940 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 284 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 49 ASN D 367 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7710 moved from start: 0.1729 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 15411 Z= 0.204 Angle : 0.552 7.937 20961 Z= 0.275 Chirality : 0.042 0.148 2416 Planarity : 0.005 0.046 2682 Dihedral : 4.414 20.223 2063 Min Nonbonded Distance : 2.054 Molprobity Statistics. All-atom Clashscore : 6.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.17 % Favored : 92.83 % Rotamer: Outliers : 2.53 % Allowed : 14.66 % Favored : 82.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.67 (0.19), residues: 1910 helix: 0.69 (0.18), residues: 812 sheet: -1.69 (0.31), residues: 240 loop : -2.81 (0.20), residues: 858 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP D 283 HIS 0.007 0.001 HIS C 157 PHE 0.010 0.001 PHE B 281 TYR 0.024 0.001 TYR C 107 ARG 0.004 0.000 ARG C 217 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3820 Ramachandran restraints generated. 1910 Oldfield, 0 Emsley, 1910 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3820 Ramachandran restraints generated. 1910 Oldfield, 0 Emsley, 1910 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 225 residues out of total 1688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 183 time to evaluate : 1.706 Fit side-chains REVERT: A 191 TRP cc_start: 0.7071 (m-10) cc_final: 0.6752 (m-10) REVERT: A 264 LEU cc_start: 0.8748 (tp) cc_final: 0.8519 (mp) REVERT: A 373 GLU cc_start: 0.7831 (tt0) cc_final: 0.7305 (tm-30) REVERT: A 454 LEU cc_start: 0.9241 (tp) cc_final: 0.8882 (tt) REVERT: B 27 ASP cc_start: 0.7143 (m-30) cc_final: 0.6835 (m-30) REVERT: B 93 LEU cc_start: 0.5755 (tt) cc_final: 0.5471 (tt) REVERT: B 287 LEU cc_start: 0.8902 (OUTLIER) cc_final: 0.8667 (tp) REVERT: B 486 MET cc_start: 0.7375 (mtm) cc_final: 0.6904 (tpt) REVERT: B 500 ARG cc_start: 0.7192 (ttt180) cc_final: 0.6988 (ttt180) REVERT: C 5 ARG cc_start: 0.7410 (mtt90) cc_final: 0.7177 (mtm110) REVERT: C 62 ASP cc_start: 0.7920 (m-30) cc_final: 0.7640 (m-30) REVERT: C 208 THR cc_start: 0.8664 (p) cc_final: 0.8313 (p) REVERT: C 273 GLU cc_start: 0.5578 (OUTLIER) cc_final: 0.5312 (mp0) REVERT: C 278 TYR cc_start: 0.5561 (p90) cc_final: 0.4893 (p90) REVERT: C 378 LEU cc_start: 0.6501 (tp) cc_final: 0.6126 (tt) REVERT: D 202 LEU cc_start: 0.6288 (OUTLIER) cc_final: 0.6044 (mt) REVERT: D 207 GLN cc_start: 0.6877 (tm-30) cc_final: 0.6478 (tm-30) REVERT: D 241 ILE cc_start: 0.7498 (mp) cc_final: 0.7151 (mp) REVERT: D 249 ARG cc_start: 0.6396 (ttt90) cc_final: 0.5752 (ptm-80) REVERT: D 362 ASN cc_start: 0.8361 (p0) cc_final: 0.7932 (p0) REVERT: D 363 ASP cc_start: 0.6217 (t0) cc_final: 0.5703 (t0) outliers start: 42 outliers final: 24 residues processed: 217 average time/residue: 0.2697 time to fit residues: 88.5224 Evaluate side-chains 193 residues out of total 1688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 166 time to evaluate : 1.829 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 130 LEU Chi-restraints excluded: chain A residue 143 HIS Chi-restraints excluded: chain A residue 398 LEU Chi-restraints excluded: chain A residue 688 LEU Chi-restraints excluded: chain A residue 692 LEU Chi-restraints excluded: chain B residue 237 VAL Chi-restraints excluded: chain B residue 287 LEU Chi-restraints excluded: chain B residue 332 VAL Chi-restraints excluded: chain B residue 504 VAL Chi-restraints excluded: chain C residue 150 ILE Chi-restraints excluded: chain C residue 182 THR Chi-restraints excluded: chain C residue 205 THR Chi-restraints excluded: chain C residue 216 CYS Chi-restraints excluded: chain C residue 269 THR Chi-restraints excluded: chain C residue 273 GLU Chi-restraints excluded: chain C residue 314 ASP Chi-restraints excluded: chain C residue 434 ASN Chi-restraints excluded: chain D residue 29 VAL Chi-restraints excluded: chain D residue 49 ASN Chi-restraints excluded: chain D residue 118 ASP Chi-restraints excluded: chain D residue 151 HIS Chi-restraints excluded: chain D residue 161 VAL Chi-restraints excluded: chain D residue 174 VAL Chi-restraints excluded: chain D residue 202 LEU Chi-restraints excluded: chain D residue 344 VAL Chi-restraints excluded: chain D residue 368 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 194 random chunks: chunk 156 optimal weight: 0.6980 chunk 106 optimal weight: 0.6980 chunk 2 optimal weight: 5.9990 chunk 139 optimal weight: 6.9990 chunk 77 optimal weight: 3.9990 chunk 160 optimal weight: 5.9990 chunk 129 optimal weight: 4.9990 chunk 0 optimal weight: 9.9990 chunk 95 optimal weight: 0.6980 chunk 168 optimal weight: 3.9990 chunk 47 optimal weight: 0.6980 overall best weight: 1.3582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 219 ASN ** B 284 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 49 ASN D 367 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7720 moved from start: 0.1830 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 15411 Z= 0.233 Angle : 0.568 8.431 20961 Z= 0.280 Chirality : 0.042 0.152 2416 Planarity : 0.005 0.045 2682 Dihedral : 4.427 20.340 2063 Min Nonbonded Distance : 2.019 Molprobity Statistics. All-atom Clashscore : 6.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.28 % Favored : 92.72 % Rotamer: Outliers : 2.23 % Allowed : 16.16 % Favored : 81.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.53 (0.19), residues: 1910 helix: 0.78 (0.18), residues: 813 sheet: -1.56 (0.32), residues: 246 loop : -2.74 (0.20), residues: 851 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP D 283 HIS 0.008 0.001 HIS C 157 PHE 0.014 0.001 PHE C 312 TYR 0.031 0.001 TYR C 107 ARG 0.004 0.000 ARG C 211 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3820 Ramachandran restraints generated. 1910 Oldfield, 0 Emsley, 1910 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3820 Ramachandran restraints generated. 1910 Oldfield, 0 Emsley, 1910 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 208 residues out of total 1688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 171 time to evaluate : 1.742 Fit side-chains REVERT: A 264 LEU cc_start: 0.8799 (tp) cc_final: 0.8563 (mp) REVERT: A 373 GLU cc_start: 0.7850 (tt0) cc_final: 0.7377 (tm-30) REVERT: B 27 ASP cc_start: 0.7219 (m-30) cc_final: 0.6905 (m-30) REVERT: B 287 LEU cc_start: 0.8916 (OUTLIER) cc_final: 0.8710 (tp) REVERT: B 486 MET cc_start: 0.7416 (mtm) cc_final: 0.7014 (tpt) REVERT: B 500 ARG cc_start: 0.7189 (ttt180) cc_final: 0.6923 (ttt180) REVERT: C 62 ASP cc_start: 0.7964 (m-30) cc_final: 0.7670 (m-30) REVERT: C 208 THR cc_start: 0.8651 (p) cc_final: 0.8283 (p) REVERT: C 273 GLU cc_start: 0.5502 (OUTLIER) cc_final: 0.5244 (mp0) REVERT: C 278 TYR cc_start: 0.5573 (p90) cc_final: 0.4817 (p90) REVERT: C 378 LEU cc_start: 0.6491 (tp) cc_final: 0.6077 (tt) REVERT: D 241 ILE cc_start: 0.7509 (mp) cc_final: 0.7162 (mp) REVERT: D 249 ARG cc_start: 0.6430 (ttt90) cc_final: 0.5765 (ptm-80) REVERT: D 362 ASN cc_start: 0.8368 (p0) cc_final: 0.7947 (p0) REVERT: D 363 ASP cc_start: 0.6244 (t0) cc_final: 0.5692 (t0) outliers start: 37 outliers final: 28 residues processed: 196 average time/residue: 0.2631 time to fit residues: 78.1636 Evaluate side-chains 185 residues out of total 1688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 155 time to evaluate : 1.625 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 130 LEU Chi-restraints excluded: chain A residue 143 HIS Chi-restraints excluded: chain A residue 294 HIS Chi-restraints excluded: chain A residue 398 LEU Chi-restraints excluded: chain A residue 688 LEU Chi-restraints excluded: chain A residue 692 LEU Chi-restraints excluded: chain A residue 781 LEU Chi-restraints excluded: chain B residue 237 VAL Chi-restraints excluded: chain B residue 287 LEU Chi-restraints excluded: chain B residue 332 VAL Chi-restraints excluded: chain B residue 504 VAL Chi-restraints excluded: chain C residue 1 MET Chi-restraints excluded: chain C residue 150 ILE Chi-restraints excluded: chain C residue 157 HIS Chi-restraints excluded: chain C residue 182 THR Chi-restraints excluded: chain C residue 216 CYS Chi-restraints excluded: chain C residue 269 THR Chi-restraints excluded: chain C residue 273 GLU Chi-restraints excluded: chain C residue 302 PHE Chi-restraints excluded: chain C residue 434 ASN Chi-restraints excluded: chain D residue 29 VAL Chi-restraints excluded: chain D residue 118 ASP Chi-restraints excluded: chain D residue 141 VAL Chi-restraints excluded: chain D residue 151 HIS Chi-restraints excluded: chain D residue 161 VAL Chi-restraints excluded: chain D residue 174 VAL Chi-restraints excluded: chain D residue 176 ASP Chi-restraints excluded: chain D residue 344 VAL Chi-restraints excluded: chain D residue 368 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 194 random chunks: chunk 63 optimal weight: 0.9990 chunk 168 optimal weight: 7.9990 chunk 37 optimal weight: 0.4980 chunk 110 optimal weight: 0.9980 chunk 46 optimal weight: 1.9990 chunk 187 optimal weight: 7.9990 chunk 155 optimal weight: 2.9990 chunk 86 optimal weight: 0.8980 chunk 15 optimal weight: 3.9990 chunk 62 optimal weight: 1.9990 chunk 98 optimal weight: 0.7980 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 246 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 284 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 335 GLN D 367 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7696 moved from start: 0.2038 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 15411 Z= 0.173 Angle : 0.539 7.614 20961 Z= 0.267 Chirality : 0.041 0.145 2416 Planarity : 0.004 0.045 2682 Dihedral : 4.253 20.003 2063 Min Nonbonded Distance : 2.043 Molprobity Statistics. All-atom Clashscore : 6.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.18 % Favored : 93.82 % Rotamer: Outliers : 2.41 % Allowed : 16.41 % Favored : 81.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.24 (0.20), residues: 1910 helix: 1.02 (0.19), residues: 813 sheet: -1.40 (0.32), residues: 256 loop : -2.60 (0.20), residues: 841 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP D 283 HIS 0.008 0.001 HIS C 157 PHE 0.014 0.001 PHE C 312 TYR 0.020 0.001 TYR C 107 ARG 0.004 0.000 ARG A 177 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3820 Ramachandran restraints generated. 1910 Oldfield, 0 Emsley, 1910 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3820 Ramachandran restraints generated. 1910 Oldfield, 0 Emsley, 1910 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 213 residues out of total 1688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 173 time to evaluate : 1.566 Fit side-chains REVERT: A 373 GLU cc_start: 0.7829 (tt0) cc_final: 0.7357 (tm-30) REVERT: A 454 LEU cc_start: 0.9166 (tp) cc_final: 0.8798 (tt) REVERT: B 27 ASP cc_start: 0.7269 (m-30) cc_final: 0.6964 (m-30) REVERT: B 486 MET cc_start: 0.7543 (mtm) cc_final: 0.7037 (tpt) REVERT: B 500 ARG cc_start: 0.7162 (ttt180) cc_final: 0.6924 (ttt180) REVERT: C 62 ASP cc_start: 0.7842 (m-30) cc_final: 0.7546 (m-30) REVERT: C 208 THR cc_start: 0.8635 (p) cc_final: 0.8279 (p) REVERT: C 273 GLU cc_start: 0.5538 (OUTLIER) cc_final: 0.5254 (mp0) REVERT: C 278 TYR cc_start: 0.5561 (p90) cc_final: 0.4802 (p90) REVERT: C 310 ARG cc_start: 0.6604 (ttp80) cc_final: 0.6358 (ttp80) REVERT: D 207 GLN cc_start: 0.6177 (tm-30) cc_final: 0.5964 (tm-30) REVERT: D 241 ILE cc_start: 0.7480 (mp) cc_final: 0.7147 (mp) REVERT: D 249 ARG cc_start: 0.6500 (ttt90) cc_final: 0.5934 (ptm-80) REVERT: D 362 ASN cc_start: 0.8345 (p0) cc_final: 0.7916 (p0) REVERT: D 363 ASP cc_start: 0.6160 (t0) cc_final: 0.5610 (t0) outliers start: 40 outliers final: 31 residues processed: 203 average time/residue: 0.2477 time to fit residues: 76.5578 Evaluate side-chains 193 residues out of total 1688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 161 time to evaluate : 1.636 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 THR Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 130 LEU Chi-restraints excluded: chain A residue 143 HIS Chi-restraints excluded: chain A residue 294 HIS Chi-restraints excluded: chain A residue 398 LEU Chi-restraints excluded: chain A residue 688 LEU Chi-restraints excluded: chain A residue 692 LEU Chi-restraints excluded: chain A residue 781 LEU Chi-restraints excluded: chain B residue 332 VAL Chi-restraints excluded: chain B residue 504 VAL Chi-restraints excluded: chain C residue 1 MET Chi-restraints excluded: chain C residue 149 GLU Chi-restraints excluded: chain C residue 150 ILE Chi-restraints excluded: chain C residue 157 HIS Chi-restraints excluded: chain C residue 182 THR Chi-restraints excluded: chain C residue 205 THR Chi-restraints excluded: chain C residue 216 CYS Chi-restraints excluded: chain C residue 269 THR Chi-restraints excluded: chain C residue 273 GLU Chi-restraints excluded: chain C residue 302 PHE Chi-restraints excluded: chain C residue 314 ASP Chi-restraints excluded: chain C residue 434 ASN Chi-restraints excluded: chain D residue 29 VAL Chi-restraints excluded: chain D residue 118 ASP Chi-restraints excluded: chain D residue 141 VAL Chi-restraints excluded: chain D residue 151 HIS Chi-restraints excluded: chain D residue 174 VAL Chi-restraints excluded: chain D residue 176 ASP Chi-restraints excluded: chain D residue 291 LEU Chi-restraints excluded: chain D residue 344 VAL Chi-restraints excluded: chain D residue 368 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 194 random chunks: chunk 180 optimal weight: 0.3980 chunk 21 optimal weight: 0.7980 chunk 106 optimal weight: 1.9990 chunk 137 optimal weight: 0.6980 chunk 158 optimal weight: 3.9990 chunk 104 optimal weight: 0.6980 chunk 186 optimal weight: 2.9990 chunk 117 optimal weight: 0.0570 chunk 113 optimal weight: 6.9990 chunk 86 optimal weight: 3.9990 chunk 115 optimal weight: 6.9990 overall best weight: 0.5298 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 219 ASN ** B 246 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 367 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7672 moved from start: 0.2244 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 15411 Z= 0.149 Angle : 0.533 7.770 20961 Z= 0.264 Chirality : 0.041 0.148 2416 Planarity : 0.005 0.086 2682 Dihedral : 4.100 19.619 2063 Min Nonbonded Distance : 2.082 Molprobity Statistics. All-atom Clashscore : 6.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.92 % Favored : 94.08 % Rotamer: Outliers : 2.35 % Allowed : 16.83 % Favored : 80.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.08 % 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: -0.98 (0.20), residues: 1910 helix: 1.23 (0.19), residues: 811 sheet: -1.19 (0.33), residues: 255 loop : -2.46 (0.21), residues: 844 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP D 283 HIS 0.007 0.001 HIS C 157 PHE 0.010 0.001 PHE A 705 TYR 0.019 0.001 TYR C 107 ARG 0.007 0.000 ARG A 785 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3820 Ramachandran restraints generated. 1910 Oldfield, 0 Emsley, 1910 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3820 Ramachandran restraints generated. 1910 Oldfield, 0 Emsley, 1910 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 1688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 170 time to evaluate : 1.691 Fit side-chains REVERT: A 373 GLU cc_start: 0.7790 (tt0) cc_final: 0.7336 (tm-30) REVERT: A 454 LEU cc_start: 0.9124 (tp) cc_final: 0.8778 (tt) REVERT: B 27 ASP cc_start: 0.7175 (m-30) cc_final: 0.6873 (m-30) REVERT: B 93 LEU cc_start: 0.6066 (OUTLIER) cc_final: 0.5718 (tt) REVERT: B 486 MET cc_start: 0.7527 (mtm) cc_final: 0.7016 (tpt) REVERT: B 500 ARG cc_start: 0.7177 (ttt180) cc_final: 0.6946 (ttt-90) REVERT: C 62 ASP cc_start: 0.7732 (m-30) cc_final: 0.7468 (m-30) REVERT: C 208 THR cc_start: 0.8547 (p) cc_final: 0.8175 (p) REVERT: C 273 GLU cc_start: 0.5256 (OUTLIER) cc_final: 0.4995 (mp0) REVERT: C 278 TYR cc_start: 0.5537 (p90) cc_final: 0.4768 (p90) REVERT: D 241 ILE cc_start: 0.7508 (mp) cc_final: 0.7151 (mp) REVERT: D 249 ARG cc_start: 0.6444 (ttt90) cc_final: 0.6028 (ptm-80) REVERT: D 362 ASN cc_start: 0.8321 (p0) cc_final: 0.7888 (p0) REVERT: D 363 ASP cc_start: 0.6144 (t0) cc_final: 0.5594 (t0) outliers start: 39 outliers final: 29 residues processed: 199 average time/residue: 0.2501 time to fit residues: 75.9540 Evaluate side-chains 194 residues out of total 1688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 163 time to evaluate : 1.559 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 THR Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 130 LEU Chi-restraints excluded: chain A residue 143 HIS Chi-restraints excluded: chain A residue 294 HIS Chi-restraints excluded: chain A residue 398 LEU Chi-restraints excluded: chain A residue 688 LEU Chi-restraints excluded: chain A residue 701 PHE Chi-restraints excluded: chain B residue 12 LEU Chi-restraints excluded: chain B residue 93 LEU Chi-restraints excluded: chain B residue 332 VAL Chi-restraints excluded: chain B residue 504 VAL Chi-restraints excluded: chain C residue 150 ILE Chi-restraints excluded: chain C residue 157 HIS Chi-restraints excluded: chain C residue 182 THR Chi-restraints excluded: chain C residue 205 THR Chi-restraints excluded: chain C residue 216 CYS Chi-restraints excluded: chain C residue 269 THR Chi-restraints excluded: chain C residue 273 GLU Chi-restraints excluded: chain C residue 302 PHE Chi-restraints excluded: chain C residue 314 ASP Chi-restraints excluded: chain C residue 355 VAL Chi-restraints excluded: chain C residue 434 ASN Chi-restraints excluded: chain D residue 29 VAL Chi-restraints excluded: chain D residue 118 ASP Chi-restraints excluded: chain D residue 141 VAL Chi-restraints excluded: chain D residue 151 HIS Chi-restraints excluded: chain D residue 174 VAL Chi-restraints excluded: chain D residue 176 ASP Chi-restraints excluded: chain D residue 344 VAL Chi-restraints excluded: chain D residue 368 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 194 random chunks: chunk 74 optimal weight: 1.9990 chunk 111 optimal weight: 0.9980 chunk 56 optimal weight: 0.0030 chunk 36 optimal weight: 0.5980 chunk 118 optimal weight: 2.9990 chunk 127 optimal weight: 0.8980 chunk 92 optimal weight: 4.9990 chunk 17 optimal weight: 6.9990 chunk 146 optimal weight: 0.9990 chunk 170 optimal weight: 10.0000 chunk 179 optimal weight: 7.9990 overall best weight: 0.6992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 246 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 367 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7672 moved from start: 0.2332 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 15411 Z= 0.162 Angle : 0.546 8.033 20961 Z= 0.270 Chirality : 0.041 0.144 2416 Planarity : 0.004 0.049 2682 Dihedral : 4.033 19.695 2063 Min Nonbonded Distance : 2.083 Molprobity Statistics. All-atom Clashscore : 6.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.92 % Favored : 94.08 % Rotamer: Outliers : 2.23 % Allowed : 17.31 % Favored : 80.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.08 % 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: -0.87 (0.20), residues: 1910 helix: 1.33 (0.19), residues: 811 sheet: -1.29 (0.33), residues: 256 loop : -2.35 (0.21), residues: 843 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.001 TRP D 283 HIS 0.007 0.001 HIS C 157 PHE 0.010 0.001 PHE A 705 TYR 0.027 0.001 TYR C 107 ARG 0.015 0.000 ARG A 785 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3820 Ramachandran restraints generated. 1910 Oldfield, 0 Emsley, 1910 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3820 Ramachandran restraints generated. 1910 Oldfield, 0 Emsley, 1910 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 1688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 169 time to evaluate : 1.735 Fit side-chains REVERT: A 373 GLU cc_start: 0.7830 (tt0) cc_final: 0.7276 (tm-30) REVERT: A 454 LEU cc_start: 0.9156 (tp) cc_final: 0.8758 (tt) REVERT: B 27 ASP cc_start: 0.7238 (m-30) cc_final: 0.6941 (m-30) REVERT: B 93 LEU cc_start: 0.6080 (OUTLIER) cc_final: 0.5749 (tt) REVERT: B 486 MET cc_start: 0.7591 (mtm) cc_final: 0.6782 (tpt) REVERT: B 500 ARG cc_start: 0.7190 (ttt180) cc_final: 0.6965 (ttt-90) REVERT: C 35 MET cc_start: 0.8335 (ttt) cc_final: 0.8045 (ttt) REVERT: C 62 ASP cc_start: 0.7749 (m-30) cc_final: 0.7497 (m-30) REVERT: C 208 THR cc_start: 0.8541 (p) cc_final: 0.8164 (p) REVERT: C 273 GLU cc_start: 0.5225 (OUTLIER) cc_final: 0.4951 (mp0) REVERT: C 278 TYR cc_start: 0.5532 (p90) cc_final: 0.4823 (p90) REVERT: D 241 ILE cc_start: 0.7458 (mp) cc_final: 0.7092 (mp) REVERT: D 249 ARG cc_start: 0.6508 (ttt90) cc_final: 0.6126 (ptm-80) REVERT: D 362 ASN cc_start: 0.8316 (p0) cc_final: 0.7900 (p0) REVERT: D 363 ASP cc_start: 0.6175 (t0) cc_final: 0.5622 (t0) outliers start: 37 outliers final: 33 residues processed: 198 average time/residue: 0.2515 time to fit residues: 75.7701 Evaluate side-chains 194 residues out of total 1688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 159 time to evaluate : 1.673 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 THR Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 130 LEU Chi-restraints excluded: chain A residue 143 HIS Chi-restraints excluded: chain A residue 294 HIS Chi-restraints excluded: chain A residue 398 LEU Chi-restraints excluded: chain A residue 688 LEU Chi-restraints excluded: chain A residue 692 LEU Chi-restraints excluded: chain A residue 701 PHE Chi-restraints excluded: chain B residue 12 LEU Chi-restraints excluded: chain B residue 88 THR Chi-restraints excluded: chain B residue 93 LEU Chi-restraints excluded: chain B residue 237 VAL Chi-restraints excluded: chain B residue 332 VAL Chi-restraints excluded: chain B residue 504 VAL Chi-restraints excluded: chain C residue 149 GLU Chi-restraints excluded: chain C residue 150 ILE Chi-restraints excluded: chain C residue 157 HIS Chi-restraints excluded: chain C residue 182 THR Chi-restraints excluded: chain C residue 205 THR Chi-restraints excluded: chain C residue 216 CYS Chi-restraints excluded: chain C residue 269 THR Chi-restraints excluded: chain C residue 273 GLU Chi-restraints excluded: chain C residue 302 PHE Chi-restraints excluded: chain C residue 314 ASP Chi-restraints excluded: chain C residue 355 VAL Chi-restraints excluded: chain C residue 434 ASN Chi-restraints excluded: chain D residue 29 VAL Chi-restraints excluded: chain D residue 141 VAL Chi-restraints excluded: chain D residue 151 HIS Chi-restraints excluded: chain D residue 161 VAL Chi-restraints excluded: chain D residue 174 VAL Chi-restraints excluded: chain D residue 291 LEU Chi-restraints excluded: chain D residue 344 VAL Chi-restraints excluded: chain D residue 368 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 194 random chunks: chunk 163 optimal weight: 10.0000 chunk 174 optimal weight: 0.0770 chunk 179 optimal weight: 0.8980 chunk 104 optimal weight: 1.9990 chunk 75 optimal weight: 6.9990 chunk 136 optimal weight: 0.9990 chunk 53 optimal weight: 2.9990 chunk 157 optimal weight: 0.9990 chunk 164 optimal weight: 1.9990 chunk 173 optimal weight: 4.9990 chunk 114 optimal weight: 0.9990 overall best weight: 0.7944 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 246 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 284 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 367 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7676 moved from start: 0.2419 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 15411 Z= 0.170 Angle : 0.544 8.206 20961 Z= 0.269 Chirality : 0.041 0.145 2416 Planarity : 0.004 0.044 2682 Dihedral : 4.018 19.506 2063 Min Nonbonded Distance : 2.086 Molprobity Statistics. All-atom Clashscore : 6.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.07 % Favored : 93.93 % Rotamer: Outliers : 2.35 % Allowed : 17.31 % Favored : 80.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.08 % 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: -0.76 (0.20), residues: 1910 helix: 1.40 (0.19), residues: 808 sheet: -1.34 (0.32), residues: 269 loop : -2.21 (0.21), residues: 833 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.001 TRP D 283 HIS 0.007 0.001 HIS C 157 PHE 0.011 0.001 PHE A 701 TYR 0.024 0.001 TYR C 107 ARG 0.014 0.000 ARG A 785 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3820 Ramachandran restraints generated. 1910 Oldfield, 0 Emsley, 1910 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3820 Ramachandran restraints generated. 1910 Oldfield, 0 Emsley, 1910 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 1688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 166 time to evaluate : 1.636 Fit side-chains revert: symmetry clash REVERT: A 373 GLU cc_start: 0.7830 (tt0) cc_final: 0.7279 (tm-30) REVERT: A 454 LEU cc_start: 0.9168 (tp) cc_final: 0.8779 (tt) REVERT: B 27 ASP cc_start: 0.7264 (m-30) cc_final: 0.6948 (m-30) REVERT: B 93 LEU cc_start: 0.6109 (OUTLIER) cc_final: 0.5785 (tt) REVERT: B 486 MET cc_start: 0.7516 (mtm) cc_final: 0.7090 (tpt) REVERT: B 500 ARG cc_start: 0.7193 (ttt180) cc_final: 0.6947 (ttt180) REVERT: C 35 MET cc_start: 0.8381 (ttt) cc_final: 0.8150 (ttt) REVERT: C 62 ASP cc_start: 0.7769 (m-30) cc_final: 0.7483 (m-30) REVERT: C 208 THR cc_start: 0.8532 (p) cc_final: 0.8159 (p) REVERT: C 259 MET cc_start: 0.7744 (mmm) cc_final: 0.7493 (mmm) REVERT: C 273 GLU cc_start: 0.5314 (OUTLIER) cc_final: 0.5042 (mp0) REVERT: C 278 TYR cc_start: 0.5520 (p90) cc_final: 0.4863 (p90) REVERT: C 387 MET cc_start: 0.7220 (mtt) cc_final: 0.6915 (mtt) REVERT: D 241 ILE cc_start: 0.7442 (OUTLIER) cc_final: 0.7085 (mp) REVERT: D 249 ARG cc_start: 0.6515 (ttt90) cc_final: 0.5987 (ptm-80) REVERT: D 362 ASN cc_start: 0.8315 (p0) cc_final: 0.7895 (p0) REVERT: D 363 ASP cc_start: 0.6196 (t0) cc_final: 0.5634 (t0) outliers start: 39 outliers final: 35 residues processed: 196 average time/residue: 0.2639 time to fit residues: 78.9471 Evaluate side-chains 200 residues out of total 1688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 162 time to evaluate : 1.982 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 THR Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 130 LEU Chi-restraints excluded: chain A residue 143 HIS Chi-restraints excluded: chain A residue 294 HIS Chi-restraints excluded: chain A residue 398 LEU Chi-restraints excluded: chain A residue 688 LEU Chi-restraints excluded: chain A residue 689 THR Chi-restraints excluded: chain A residue 692 LEU Chi-restraints excluded: chain A residue 701 PHE Chi-restraints excluded: chain B residue 12 LEU Chi-restraints excluded: chain B residue 93 LEU Chi-restraints excluded: chain B residue 237 VAL Chi-restraints excluded: chain B residue 332 VAL Chi-restraints excluded: chain B residue 504 VAL Chi-restraints excluded: chain C residue 125 MET Chi-restraints excluded: chain C residue 149 GLU Chi-restraints excluded: chain C residue 150 ILE Chi-restraints excluded: chain C residue 157 HIS Chi-restraints excluded: chain C residue 182 THR Chi-restraints excluded: chain C residue 205 THR Chi-restraints excluded: chain C residue 216 CYS Chi-restraints excluded: chain C residue 269 THR Chi-restraints excluded: chain C residue 273 GLU Chi-restraints excluded: chain C residue 302 PHE Chi-restraints excluded: chain C residue 314 ASP Chi-restraints excluded: chain C residue 355 VAL Chi-restraints excluded: chain C residue 434 ASN Chi-restraints excluded: chain D residue 29 VAL Chi-restraints excluded: chain D residue 141 VAL Chi-restraints excluded: chain D residue 151 HIS Chi-restraints excluded: chain D residue 161 VAL Chi-restraints excluded: chain D residue 174 VAL Chi-restraints excluded: chain D residue 180 LEU Chi-restraints excluded: chain D residue 241 ILE Chi-restraints excluded: chain D residue 291 LEU Chi-restraints excluded: chain D residue 344 VAL Chi-restraints excluded: chain D residue 368 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 194 random chunks: chunk 184 optimal weight: 6.9990 chunk 112 optimal weight: 4.9990 chunk 87 optimal weight: 4.9990 chunk 128 optimal weight: 0.7980 chunk 193 optimal weight: 6.9990 chunk 177 optimal weight: 1.9990 chunk 153 optimal weight: 3.9990 chunk 15 optimal weight: 3.9990 chunk 118 optimal weight: 0.8980 chunk 94 optimal weight: 0.8980 chunk 122 optimal weight: 0.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 246 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 284 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 367 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7692 moved from start: 0.2444 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 15411 Z= 0.206 Angle : 0.573 12.995 20961 Z= 0.282 Chirality : 0.042 0.167 2416 Planarity : 0.005 0.061 2682 Dihedral : 4.080 19.824 2063 Min Nonbonded Distance : 2.047 Molprobity Statistics. All-atom Clashscore : 6.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.65 % Favored : 93.35 % Rotamer: Outliers : 2.47 % Allowed : 17.61 % Favored : 79.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.08 % 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: -0.78 (0.20), residues: 1910 helix: 1.34 (0.19), residues: 810 sheet: -1.35 (0.32), residues: 272 loop : -2.19 (0.21), residues: 828 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.001 TRP D 283 HIS 0.007 0.001 HIS C 157 PHE 0.012 0.001 PHE A 705 TYR 0.022 0.001 TYR C 107 ARG 0.013 0.000 ARG A 785 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3820 Ramachandran restraints generated. 1910 Oldfield, 0 Emsley, 1910 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3820 Ramachandran restraints generated. 1910 Oldfield, 0 Emsley, 1910 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 1688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 165 time to evaluate : 1.645 Fit side-chains REVERT: A 373 GLU cc_start: 0.7871 (tt0) cc_final: 0.7328 (tm-30) REVERT: A 454 LEU cc_start: 0.9219 (tp) cc_final: 0.8864 (tt) REVERT: B 1 MET cc_start: 0.5631 (tmm) cc_final: 0.5414 (tmm) REVERT: B 27 ASP cc_start: 0.7311 (m-30) cc_final: 0.7013 (m-30) REVERT: B 93 LEU cc_start: 0.5769 (OUTLIER) cc_final: 0.5439 (tt) REVERT: B 500 ARG cc_start: 0.7163 (ttt180) cc_final: 0.6914 (ttt180) REVERT: C 62 ASP cc_start: 0.7896 (m-30) cc_final: 0.7610 (m-30) REVERT: C 208 THR cc_start: 0.8532 (p) cc_final: 0.8158 (p) REVERT: C 259 MET cc_start: 0.7430 (mmm) cc_final: 0.7179 (mmm) REVERT: C 273 GLU cc_start: 0.5333 (OUTLIER) cc_final: 0.5052 (mp0) REVERT: C 278 TYR cc_start: 0.5484 (p90) cc_final: 0.4699 (p90) REVERT: D 241 ILE cc_start: 0.7425 (OUTLIER) cc_final: 0.7081 (mp) REVERT: D 249 ARG cc_start: 0.6547 (ttt90) cc_final: 0.5989 (ptm-80) REVERT: D 362 ASN cc_start: 0.8325 (p0) cc_final: 0.7912 (p0) REVERT: D 363 ASP cc_start: 0.6308 (t0) cc_final: 0.5699 (t0) outliers start: 41 outliers final: 34 residues processed: 195 average time/residue: 0.2529 time to fit residues: 75.7422 Evaluate side-chains 196 residues out of total 1688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 159 time to evaluate : 1.714 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 THR Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 130 LEU Chi-restraints excluded: chain A residue 143 HIS Chi-restraints excluded: chain A residue 294 HIS Chi-restraints excluded: chain A residue 398 LEU Chi-restraints excluded: chain A residue 688 LEU Chi-restraints excluded: chain A residue 689 THR Chi-restraints excluded: chain A residue 692 LEU Chi-restraints excluded: chain A residue 701 PHE Chi-restraints excluded: chain B residue 88 THR Chi-restraints excluded: chain B residue 93 LEU Chi-restraints excluded: chain B residue 237 VAL Chi-restraints excluded: chain B residue 332 VAL Chi-restraints excluded: chain B residue 504 VAL Chi-restraints excluded: chain C residue 149 GLU Chi-restraints excluded: chain C residue 150 ILE Chi-restraints excluded: chain C residue 157 HIS Chi-restraints excluded: chain C residue 182 THR Chi-restraints excluded: chain C residue 205 THR Chi-restraints excluded: chain C residue 216 CYS Chi-restraints excluded: chain C residue 269 THR Chi-restraints excluded: chain C residue 273 GLU Chi-restraints excluded: chain C residue 302 PHE Chi-restraints excluded: chain C residue 314 ASP Chi-restraints excluded: chain C residue 355 VAL Chi-restraints excluded: chain C residue 431 LEU Chi-restraints excluded: chain C residue 434 ASN Chi-restraints excluded: chain D residue 29 VAL Chi-restraints excluded: chain D residue 141 VAL Chi-restraints excluded: chain D residue 151 HIS Chi-restraints excluded: chain D residue 161 VAL Chi-restraints excluded: chain D residue 174 VAL Chi-restraints excluded: chain D residue 180 LEU Chi-restraints excluded: chain D residue 241 ILE Chi-restraints excluded: chain D residue 344 VAL Chi-restraints excluded: chain D residue 368 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 194 random chunks: chunk 163 optimal weight: 5.9990 chunk 47 optimal weight: 0.1980 chunk 141 optimal weight: 0.9990 chunk 22 optimal weight: 1.9990 chunk 42 optimal weight: 0.5980 chunk 154 optimal weight: 3.9990 chunk 64 optimal weight: 3.9990 chunk 158 optimal weight: 0.7980 chunk 19 optimal weight: 0.0050 chunk 28 optimal weight: 0.9980 chunk 135 optimal weight: 0.5980 overall best weight: 0.4394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 246 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 276 ASN D 367 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3757 r_free = 0.3757 target = 0.139164 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.111667 restraints weight = 25115.062| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.111545 restraints weight = 36295.903| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.112529 restraints weight = 37257.814| |-----------------------------------------------------------------------------| r_work (final): 0.3391 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3392 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3392 r_free = 0.3392 target_work(ls_wunit_k1) = 0.112 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3389 r_free = 0.3389 target_work(ls_wunit_k1) = 0.112 | | occupancies: max = 1.00 min = 1.00 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3389 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7604 moved from start: 0.2659 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 15411 Z= 0.145 Angle : 0.559 11.789 20961 Z= 0.271 Chirality : 0.041 0.174 2416 Planarity : 0.004 0.062 2682 Dihedral : 3.913 19.175 2063 Min Nonbonded Distance : 2.144 Molprobity Statistics. All-atom Clashscore : 6.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.13 % Favored : 94.87 % Rotamer: Outliers : 2.17 % Allowed : 18.15 % Favored : 79.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.08 % 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: -0.64 (0.20), residues: 1910 helix: 1.47 (0.19), residues: 808 sheet: -1.32 (0.32), residues: 284 loop : -2.11 (0.21), residues: 818 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.001 TRP D 283 HIS 0.006 0.001 HIS C 157 PHE 0.013 0.001 PHE A 705 TYR 0.023 0.001 TYR C 107 ARG 0.019 0.000 ARG A 785 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2774.32 seconds wall clock time: 51 minutes 53.73 seconds (3113.73 seconds total)