Starting phenix.real_space_refine on Thu Jul 2 22:16:34 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7pmh_13533/07_2026/7pmh_13533.cif Found real_map, /net/cci-nas-00/data/ceres_data/7pmh_13533/07_2026/7pmh_13533.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/7pmh_13533/07_2026/7pmh_13533.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7pmh_13533/07_2026/7pmh_13533.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7pmh_13533/07_2026/7pmh_13533.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7pmh_13533/07_2026/7pmh_13533.map" model { file = "/net/cci-nas-00/data/ceres_data/7pmh_13533/07_2026/7pmh_13533.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7pmh_13533/07_2026/7pmh_13533.cif" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } 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= 0.001 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: 6 Type Number sf(0) Gaussians P 5 5.49 5 Mg 3 5.21 5 S 63 5.16 5 C 6461 2.51 5 N 1724 2.21 5 O 1898 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 52 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 10154 Number of models: 1 Model: "" Number of chains: 7 Chain: "B" Number of atoms: 1059 Number of conformers: 1 Conformer: "" Number of residues, atoms: 139, 1059 Classifications: {'peptide': 139} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 3, 'TRANS': 135} Chain breaks: 2 Unresolved non-hydrogen bonds: 45 Unresolved non-hydrogen angles: 53 Unresolved non-hydrogen dihedrals: 37 Planarities with less than four sites: {'GLU:plan': 3, 'ASP:plan': 2, 'ARG:plan': 2, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 31 Chain: "A" Number of atoms: 6070 Number of conformers: 1 Conformer: "" Number of residues, atoms: 742, 6070 Classifications: {'peptide': 742} Link IDs: {'PTRANS': 26, 'TRANS': 715} Chain breaks: 5 Chain: "C" Number of atoms: 2909 Number of conformers: 1 Conformer: "" Number of residues, atoms: 372, 2909 Classifications: {'peptide': 372} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 352} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'HIC:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "H" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 29 Classifications: {'peptide': 3} Link IDs: {'TRANS': 2} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'EEP:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "H" Number of atoms: 26 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 26 Classifications: {'peptide': 4} Link IDs: {'TRANS': 3} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'HYP:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "A" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' MG': 2, 'ANP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 1.63, per 1000 atoms: 0.16 Number of scatterers: 10154 At special positions: 0 Unit cell: (102.3, 128.7, 157.3, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 63 16.00 P 5 15.00 Mg 3 11.99 O 1898 8.00 N 1724 7.00 C 6461 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 - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied TRANS " TRP H 1 " - " ALA H 7 " " DTH H 4 " - " ALA H 3 " Time building additional restraints: 0.70 Conformation dependent library (CDL) restraints added in 307.2 milliseconds 2460 Ramachandran restraints generated. 1230 Oldfield, 0 Emsley, 1230 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Skipped Input residue name is d-peptide pdb=" CB DTH H 4 " Number of C-beta restraints generated: 2374 Finding SS restraints... Secondary structure from input PDB file: 62 helices and 15 sheets defined 55.0% alpha, 13.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.28 Creating SS restraints... Processing helix chain 'B' and resid 5 through 19 Processing helix chain 'B' and resid 29 through 39 removed outlier: 4.287A pdb=" N GLY B 33 " --> pdb=" O TYR B 29 " (cutoff:3.500A) removed outlier: 4.777A pdb=" N ASP B 34 " --> pdb=" O SER B 30 " (cutoff:3.500A) Processing helix chain 'B' and resid 44 through 52 Processing helix chain 'B' and resid 56 through 63 Processing helix chain 'B' and resid 67 through 79 Proline residue: B 72 - end of helix Processing helix chain 'B' and resid 87 through 95 Processing helix chain 'B' and resid 106 through 116 Processing helix chain 'B' and resid 121 through 130 Processing helix chain 'B' and resid 141 through 150 Processing helix chain 'A' and resid 81 through 95 Processing helix chain 'A' and resid 116 through 119 removed outlier: 4.497A pdb=" N TYR A 119 " --> pdb=" O LEU A 116 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 116 through 119' Processing helix chain 'A' and resid 120 through 128 Processing helix chain 'A' and resid 131 through 135 Processing helix chain 'A' and resid 138 through 154 removed outlier: 3.783A pdb=" N GLN A 149 " --> pdb=" O GLU A 145 " (cutoff:3.500A) Processing helix chain 'A' and resid 168 through 184 removed outlier: 3.733A pdb=" N PHE A 180 " --> pdb=" O ALA A 176 " (cutoff:3.500A) Processing helix chain 'A' and resid 191 through 198 Processing helix chain 'A' and resid 199 through 207 Processing helix chain 'A' and resid 245 through 250 Processing helix chain 'A' and resid 259 through 268 removed outlier: 4.163A pdb=" N TYR A 263 " --> pdb=" O TYR A 259 " (cutoff:3.500A) Processing helix chain 'A' and resid 269 through 271 No H-bonds generated for 'chain 'A' and resid 269 through 271' Processing helix chain 'A' and resid 273 through 278 Processing helix chain 'A' and resid 285 through 290 removed outlier: 3.864A pdb=" N GLN A 290 " --> pdb=" O HIS A 286 " (cutoff:3.500A) Processing helix chain 'A' and resid 300 through 315 removed outlier: 3.712A pdb=" N GLU A 304 " --> pdb=" O ASP A 300 " (cutoff:3.500A) removed outlier: 4.203A pdb=" N VAL A 306 " --> pdb=" O ALA A 302 " (cutoff:3.500A) Processing helix chain 'A' and resid 318 through 336 removed outlier: 3.624A pdb=" N MET A 323 " --> pdb=" O ASP A 319 " (cutoff:3.500A) Processing helix chain 'A' and resid 354 through 365 Processing helix chain 'A' and resid 367 through 375 Processing helix chain 'A' and resid 392 through 424 Processing helix chain 'A' and resid 448 through 481 Processing helix chain 'A' and resid 483 through 487 removed outlier: 3.766A pdb=" N LEU A 486 " --> pdb=" O PRO A 483 " (cutoff:3.500A) Processing helix chain 'A' and resid 492 through 500 Processing helix chain 'A' and resid 504 through 515 removed outlier: 3.821A pdb=" N LYS A 514 " --> pdb=" O ASP A 510 " (cutoff:3.500A) Processing helix chain 'A' and resid 519 through 532 removed outlier: 3.525A pdb=" N GLN A 525 " --> pdb=" O ASP A 521 " (cutoff:3.500A) Processing helix chain 'A' and resid 563 through 569 removed outlier: 3.607A pdb=" N LYS A 567 " --> pdb=" O GLY A 563 " (cutoff:3.500A) Processing helix chain 'A' and resid 573 through 582 removed outlier: 3.607A pdb=" N ILE A 577 " --> pdb=" O TYR A 573 " (cutoff:3.500A) Processing helix chain 'A' and resid 587 through 594 removed outlier: 4.034A pdb=" N PHE A 593 " --> pdb=" O LEU A 589 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N GLN A 594 " --> pdb=" O PRO A 590 " (cutoff:3.500A) Processing helix chain 'A' and resid 630 through 634 Processing helix chain 'A' and resid 635 through 654 removed outlier: 3.905A pdb=" N ALA A 653 " --> pdb=" O GLU A 649 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N THR A 654 " --> pdb=" O THR A 650 " (cutoff:3.500A) Processing helix chain 'A' and resid 674 through 685 removed outlier: 3.612A pdb=" N VAL A 679 " --> pdb=" O GLU A 675 " (cutoff:3.500A) Processing helix chain 'A' and resid 686 through 696 Processing helix chain 'A' and resid 704 through 712 Processing helix chain 'A' and resid 723 through 736 Processing helix chain 'A' and resid 754 through 792 Processing helix chain 'C' and resid 55 through 61 Processing helix chain 'C' and resid 79 through 93 removed outlier: 3.577A pdb=" N ILE C 85 " --> pdb=" O ASP C 81 " (cutoff:3.500A) Processing helix chain 'C' and resid 97 through 101 Processing helix chain 'C' and resid 112 through 126 removed outlier: 4.067A pdb=" N ARG C 116 " --> pdb=" O PRO C 112 " (cutoff:3.500A) Processing helix chain 'C' and resid 137 through 146 removed outlier: 3.667A pdb=" N SER C 141 " --> pdb=" O GLN C 137 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N LEU C 142 " --> pdb=" O ALA C 138 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N TYR C 143 " --> pdb=" O VAL C 139 " (cutoff:3.500A) Processing helix chain 'C' and resid 172 through 175 removed outlier: 3.747A pdb=" N ILE C 175 " --> pdb=" O PRO C 172 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 172 through 175' Processing helix chain 'C' and resid 182 through 196 removed outlier: 3.777A pdb=" N THR C 186 " --> pdb=" O GLY C 182 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N LYS C 191 " --> pdb=" O ASP C 187 " (cutoff:3.500A) Processing helix chain 'C' and resid 202 through 217 removed outlier: 3.529A pdb=" N GLU C 207 " --> pdb=" O THR C 203 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N ILE C 208 " --> pdb=" O ALA C 204 " (cutoff:3.500A) Processing helix chain 'C' and resid 222 through 233 Processing helix chain 'C' and resid 252 through 257 Processing helix chain 'C' and resid 258 through 262 Processing helix chain 'C' and resid 273 through 283 Processing helix chain 'C' and resid 289 through 294 Processing helix chain 'C' and resid 301 through 305 Processing helix chain 'C' and resid 308 through 321 Processing helix chain 'C' and resid 334 through 336 No H-bonds generated for 'chain 'C' and resid 334 through 336' Processing helix chain 'C' and resid 337 through 348 removed outlier: 3.682A pdb=" N SER C 348 " --> pdb=" O SER C 344 " (cutoff:3.500A) Processing helix chain 'C' and resid 349 through 355 removed outlier: 3.971A pdb=" N PHE C 352 " --> pdb=" O LEU C 349 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N GLN C 354 " --> pdb=" O THR C 351 " (cutoff:3.500A) Processing helix chain 'C' and resid 359 through 366 Processing helix chain 'C' and resid 368 through 374 removed outlier: 4.104A pdb=" N ARG C 372 " --> pdb=" O SER C 368 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 26 through 28 Processing sheet with id=AA2, first strand: chain 'B' and resid 103 through 105 Processing sheet with id=AA3, first strand: chain 'A' and resid 12 through 16 removed outlier: 7.066A pdb=" N GLN A 39 " --> pdb=" O LEU A 28 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N LEU A 48 " --> pdb=" O LEU A 40 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 100 through 103 removed outlier: 6.439A pdb=" N SER A 158 " --> pdb=" O HIS A 657 " (cutoff:3.500A) removed outlier: 7.913A pdb=" N VAL A 659 " --> pdb=" O SER A 158 " (cutoff:3.500A) removed outlier: 6.014A pdb=" N ILE A 160 " --> pdb=" O VAL A 659 " (cutoff:3.500A) removed outlier: 7.294A pdb=" N CYS A 661 " --> pdb=" O ILE A 160 " (cutoff:3.500A) removed outlier: 6.278A pdb=" N SER A 162 " --> pdb=" O CYS A 661 " (cutoff:3.500A) removed outlier: 6.662A pdb=" N GLN A 157 " --> pdb=" O GLY A 434 " (cutoff:3.500A) removed outlier: 8.035A pdb=" N LEU A 436 " --> pdb=" O GLN A 157 " (cutoff:3.500A) removed outlier: 6.695A pdb=" N ILE A 159 " --> pdb=" O LEU A 436 " (cutoff:3.500A) removed outlier: 7.676A pdb=" N ILE A 438 " --> pdb=" O ILE A 159 " (cutoff:3.500A) removed outlier: 5.960A pdb=" N VAL A 161 " --> pdb=" O ILE A 438 " (cutoff:3.500A) removed outlier: 4.147A pdb=" N GLY A 236 " --> pdb=" O GLY A 227 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 208 through 211 removed outlier: 5.392A pdb=" N ALA A 209 " --> pdb=" O ASN A 216 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 341 through 342 Processing sheet with id=AA7, first strand: chain 'A' and resid 377 through 382 Processing sheet with id=AA8, first strand: chain 'A' and resid 538 through 539 Processing sheet with id=AA9, first strand: chain 'A' and resid 700 through 703 removed outlier: 3.671A pdb=" N SER A 700 " --> pdb=" O PHE A 751 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 29 through 32 removed outlier: 3.691A pdb=" N THR C 106 " --> pdb=" O CYS C 10 " (cutoff:3.500A) removed outlier: 6.739A pdb=" N THR C 103 " --> pdb=" O TYR C 133 " (cutoff:3.500A) removed outlier: 8.072A pdb=" N ALA C 135 " --> pdb=" O THR C 103 " (cutoff:3.500A) removed outlier: 6.451A pdb=" N LEU C 105 " --> pdb=" O ALA C 135 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 53 through 54 Processing sheet with id=AB3, first strand: chain 'C' and resid 71 through 72 Processing sheet with id=AB4, first strand: chain 'C' and resid 169 through 170 Processing sheet with id=AB5, first strand: chain 'C' and resid 169 through 170 removed outlier: 6.092A pdb=" N ASN C 297 " --> pdb=" O ILE C 330 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 238 through 241 521 hydrogen bonds defined for protein. 1455 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.15 Time building geometry restraints manager: 0.91 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.31: 1694 1.31 - 1.44: 2739 1.44 - 1.56: 5823 1.56 - 1.69: 8 1.69 - 1.81: 103 Bond restraints: 10367 Sorted by residual: bond pdb=" O3A ANP A1901 " pdb=" PB ANP A1901 " ideal model delta sigma weight residual 1.700 1.551 0.149 2.00e-02 2.50e+03 5.53e+01 bond pdb=" CA EEP H 2 " pdb=" C EEP H 2 " ideal model delta sigma weight residual 1.572 1.439 0.133 2.00e-02 2.50e+03 4.39e+01 bond pdb=" N3B ANP A1901 " pdb=" PG ANP A1901 " ideal model delta sigma weight residual 1.795 1.690 0.105 2.00e-02 2.50e+03 2.75e+01 bond pdb=" O5' ANP A1901 " pdb=" PA ANP A1901 " ideal model delta sigma weight residual 1.655 1.571 0.084 2.00e-02 2.50e+03 1.76e+01 bond pdb=" C EEP H 2 " pdb=" O EEP H 2 " ideal model delta sigma weight residual 1.263 1.196 0.067 2.00e-02 2.50e+03 1.11e+01 ... (remaining 10362 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.25: 13806 3.25 - 6.50: 175 6.50 - 9.75: 18 9.75 - 13.00: 5 13.00 - 16.25: 1 Bond angle restraints: 14005 Sorted by residual: angle pdb=" C HYP H 6 " pdb=" N ALA H 7 " pdb=" CA ALA H 7 " ideal model delta sigma weight residual 121.70 110.78 10.92 1.80e+00 3.09e-01 3.68e+01 angle pdb=" N DTH H 4 " pdb=" CA DTH H 4 " pdb=" CB DTH H 4 " ideal model delta sigma weight residual 111.50 101.96 9.54 1.70e+00 3.46e-01 3.15e+01 angle pdb=" PB ANP A1901 " pdb=" N3B ANP A1901 " pdb=" PG ANP A1901 " ideal model delta sigma weight residual 126.95 110.70 16.25 3.00e+00 1.11e-01 2.94e+01 angle pdb=" C TRP H 1 " pdb=" CA TRP H 1 " pdb=" CB TRP H 1 " ideal model delta sigma weight residual 110.10 99.89 10.21 1.90e+00 2.77e-01 2.89e+01 angle pdb=" N GLY A 563 " pdb=" CA GLY A 563 " pdb=" C GLY A 563 " ideal model delta sigma weight residual 113.86 121.71 -7.85 1.50e+00 4.44e-01 2.74e+01 ... (remaining 14000 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 26.34: 5992 26.34 - 52.68: 192 52.68 - 79.02: 35 79.02 - 105.36: 15 105.36 - 131.70: 3 Dihedral angle restraints: 6237 sinusoidal: 2556 harmonic: 3681 Sorted by residual: dihedral pdb=" C5' ADP C 401 " pdb=" O5' ADP C 401 " pdb=" PA ADP C 401 " pdb=" O2A ADP C 401 " ideal model delta sinusoidal sigma weight residual 300.00 168.30 131.70 1 2.00e+01 2.50e-03 4.00e+01 dihedral pdb=" O1B ADP C 401 " pdb=" O3A ADP C 401 " pdb=" PB ADP C 401 " pdb=" PA ADP C 401 " ideal model delta sinusoidal sigma weight residual -60.00 67.81 -127.82 1 2.00e+01 2.50e-03 3.87e+01 dihedral pdb=" O2A ADP C 401 " pdb=" O3A ADP C 401 " pdb=" PA ADP C 401 " pdb=" PB ADP C 401 " ideal model delta sinusoidal sigma weight residual -60.00 64.63 -124.63 1 2.00e+01 2.50e-03 3.76e+01 ... (remaining 6234 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 1.036: 1528 1.036 - 2.072: 0 2.072 - 3.109: 0 3.109 - 4.145: 0 4.145 - 5.181: 2 Chirality restraints: 1530 Sorted by residual: chirality pdb=" CB DTH H 4 " pdb=" CA DTH H 4 " pdb=" OG1 DTH H 4 " pdb=" CG2 DTH H 4 " both_signs ideal model delta sigma weight residual False 2.55 -2.63 5.18 2.00e-01 2.50e+01 6.71e+02 chirality pdb=" CA DTH H 4 " pdb=" N DTH H 4 " pdb=" C DTH H 4 " pdb=" CB DTH H 4 " both_signs ideal model delta sigma weight residual False 2.53 -2.40 4.93 2.00e-01 2.50e+01 6.08e+02 chirality pdb=" C3' ANP A1901 " pdb=" C2' ANP A1901 " pdb=" C4' ANP A1901 " pdb=" O3' ANP A1901 " both_signs ideal model delta sigma weight residual False -2.36 -2.62 0.26 2.00e-01 2.50e+01 1.71e+00 ... (remaining 1527 not shown) Planarity restraints: 1787 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR C 306 " -0.006 2.00e-02 2.50e+03 3.77e-02 2.85e+01 pdb=" CG TYR C 306 " 0.002 2.00e-02 2.50e+03 pdb=" CD1 TYR C 306 " -0.049 2.00e-02 2.50e+03 pdb=" CD2 TYR C 306 " 0.001 2.00e-02 2.50e+03 pdb=" CE1 TYR C 306 " 0.053 2.00e-02 2.50e+03 pdb=" CE2 TYR C 306 " 0.003 2.00e-02 2.50e+03 pdb=" CZ TYR C 306 " 0.053 2.00e-02 2.50e+03 pdb=" OH TYR C 306 " -0.058 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG C 147 " -0.129 9.50e-02 1.11e+02 7.14e-02 2.41e+01 pdb=" NE ARG C 147 " 0.035 2.00e-02 2.50e+03 pdb=" CZ ARG C 147 " -0.080 2.00e-02 2.50e+03 pdb=" NH1 ARG C 147 " 0.028 2.00e-02 2.50e+03 pdb=" NH2 ARG C 147 " 0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 564 " -0.040 2.00e-02 2.50e+03 3.64e-02 2.32e+01 pdb=" CG PHE A 564 " 0.084 2.00e-02 2.50e+03 pdb=" CD1 PHE A 564 " -0.018 2.00e-02 2.50e+03 pdb=" CD2 PHE A 564 " -0.010 2.00e-02 2.50e+03 pdb=" CE1 PHE A 564 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 PHE A 564 " -0.008 2.00e-02 2.50e+03 pdb=" CZ PHE A 564 " -0.009 2.00e-02 2.50e+03 ... (remaining 1784 not shown) Histogram of nonbonded interaction distances: 1.73 - 2.37: 19 2.37 - 3.00: 5576 3.00 - 3.63: 14852 3.63 - 4.27: 22558 4.27 - 4.90: 38587 Nonbonded interactions: 81592 Sorted by model distance: nonbonded pdb=" CD1 TRP H 1 " pdb=" SG CYS H 5 " model vdw 1.732 3.620 nonbonded pdb=" O3G ANP A1901 " pdb="MG MG A1902 " model vdw 2.000 2.170 nonbonded pdb=" O1A ANP A1901 " pdb="MG MG A1903 " model vdw 2.020 2.170 nonbonded pdb=" O3B ADP C 401 " pdb="MG MG C 402 " model vdw 2.024 2.170 nonbonded pdb=" O1B ANP A1901 " pdb="MG MG A1903 " model vdw 2.038 2.170 ... (remaining 81587 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=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.010 Normalize map: mean=0, sd=1: 1.900 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: 0.180 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 7.760 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.010 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:1.080 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 11.040 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8282 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 : 0.009 0.149 10369 Z= 0.415 Angle : 1.008 16.253 14011 Z= 0.577 Chirality : 0.192 5.181 1530 Planarity : 0.008 0.089 1785 Dihedral : 14.972 131.704 3857 Min Nonbonded Distance : 1.732 Molprobity Statistics. All-atom Clashscore : 4.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.16 % Favored : 99.84 % Rotamer: Outliers : 0.09 % Allowed : 0.19 % Favored : 99.72 % Cbeta Deviations : 0.17 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.51 (0.20), residues: 1230 helix: -1.62 (0.17), residues: 599 sheet: 0.02 (0.36), residues: 166 loop : -0.16 (0.26), residues: 465 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.081 0.011 ARG C 147 TYR 0.058 0.007 TYR C 306 PHE 0.084 0.003 PHE A 564 TRP 0.045 0.005 TRP C 356 HIS 0.017 0.003 HIS C 275 Details of bonding type rmsd/Z covalent geometry : bond 0.00947 / 0.41 (10367) covalent geometry : angle 1.00485 / 0.58 (14005) hydrogen bonds : bond 0.15517 / 10.12 ( 519) hydrogen bonds : angle 7.41426 / 5.31 ( 1455) link_TRANS : bond 0.01705 / 0.86 ( 2) link_TRANS : angle 3.81068 / 2.59 ( 6) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2460 Ramachandran restraints generated. 1230 Oldfield, 0 Emsley, 1230 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2460 Ramachandran restraints generated. 1230 Oldfield, 0 Emsley, 1230 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 91 time to evaluate : 0.417 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 93 PHE cc_start: 0.8764 (m-80) cc_final: 0.8459 (m-80) outliers start: 1 outliers final: 1 residues processed: 92 average time/residue: 0.1351 time to fit residues: 16.8804 Evaluate side-chains 55 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 54 time to evaluate : 0.430 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 5 CYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 108 optimal weight: 0.8980 chunk 49 optimal weight: 0.9990 chunk 97 optimal weight: 3.9990 chunk 113 optimal weight: 2.9990 chunk 53 optimal weight: 0.9980 chunk 5 optimal weight: 20.0000 chunk 33 optimal weight: 0.9990 chunk 123 optimal weight: 1.9990 chunk 65 optimal weight: 0.0010 chunk 62 optimal weight: 0.8980 chunk 51 optimal weight: 0.8980 overall best weight: 0.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 75 GLN A 72 ASN ** A 81 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 200 ASN A 264 GLN A 290 GLN A 410 ASN A 775 GLN C 111 ASN C 137 GLN ** C 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 162 ASN C 371 HIS Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.049727 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2827 r_free = 0.2827 target = 0.035685 restraints weight = 57984.039| |-----------------------------------------------------------------------------| r_work (start): 0.2804 rms_B_bonded: 4.14 r_work: 0.2640 rms_B_bonded: 4.87 restraints_weight: 0.5000 r_work (final): 0.2640 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8755 moved from start: 0.1960 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 10369 Z= 0.138 Angle : 0.616 6.854 14011 Z= 0.328 Chirality : 0.043 0.165 1530 Planarity : 0.004 0.050 1785 Dihedral : 9.093 142.846 1386 Min Nonbonded Distance : 2.025 Molprobity Statistics. All-atom Clashscore : 5.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.24 % Favored : 99.76 % Rotamer: Outliers : 1.02 % Allowed : 3.61 % Favored : 95.37 % Cbeta Deviations : 0.08 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.76 (0.23), residues: 1230 helix: 0.75 (0.20), residues: 619 sheet: 0.47 (0.36), residues: 176 loop : 0.41 (0.30), residues: 435 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 784 TYR 0.021 0.002 TYR A 10 PHE 0.019 0.001 PHE A 564 TRP 0.024 0.002 TRP A 484 HIS 0.008 0.001 HIS C 275 Details of bonding type rmsd/Z covalent geometry : bond 0.00302 / 0.14 (10367) covalent geometry : angle 0.61598 / 0.33 (14005) hydrogen bonds : bond 0.04090 / 2.75 ( 519) hydrogen bonds : angle 5.23665 / 3.75 ( 1455) link_TRANS : bond 0.00272 / 0.13 ( 2) link_TRANS : angle 0.66521 / 0.44 ( 6) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2460 Ramachandran restraints generated. 1230 Oldfield, 0 Emsley, 1230 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2460 Ramachandran restraints generated. 1230 Oldfield, 0 Emsley, 1230 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 64 time to evaluate : 0.391 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 93 PHE cc_start: 0.9457 (m-80) cc_final: 0.8840 (m-80) REVERT: A 177 MET cc_start: 0.9519 (ttm) cc_final: 0.9141 (tmm) REVERT: A 478 MET cc_start: 0.8816 (mmp) cc_final: 0.8088 (mmp) REVERT: A 783 MET cc_start: 0.9335 (tpt) cc_final: 0.9043 (tpt) REVERT: C 190 MET cc_start: 0.8865 (mtp) cc_final: 0.8496 (mtt) REVERT: C 227 MET cc_start: 0.8773 (tpp) cc_final: 0.8478 (tpp) REVERT: C 313 MET cc_start: 0.9676 (tpp) cc_final: 0.9446 (mmt) outliers start: 11 outliers final: 3 residues processed: 67 average time/residue: 0.0979 time to fit residues: 9.7911 Evaluate side-chains 61 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 58 time to evaluate : 0.404 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 57 SER Chi-restraints excluded: chain A residue 722 SER Chi-restraints excluded: chain C residue 257 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 53 optimal weight: 0.9990 chunk 100 optimal weight: 3.9990 chunk 103 optimal weight: 4.9990 chunk 78 optimal weight: 0.0970 chunk 47 optimal weight: 0.7980 chunk 58 optimal weight: 0.8980 chunk 22 optimal weight: 0.9980 chunk 74 optimal weight: 0.9990 chunk 115 optimal weight: 0.9980 chunk 52 optimal weight: 0.9990 chunk 37 optimal weight: 1.9990 overall best weight: 0.7578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 72 ASN ** A 81 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 111 ASN ** C 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.049580 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2830 r_free = 0.2830 target = 0.035620 restraints weight = 57991.264| |-----------------------------------------------------------------------------| r_work (start): 0.2807 rms_B_bonded: 4.10 r_work: 0.2646 rms_B_bonded: 4.81 restraints_weight: 0.5000 r_work (final): 0.2646 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8749 moved from start: 0.2394 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 10369 Z= 0.123 Angle : 0.563 8.350 14011 Z= 0.293 Chirality : 0.041 0.175 1530 Planarity : 0.004 0.050 1785 Dihedral : 8.474 148.300 1385 Min Nonbonded Distance : 2.003 Molprobity Statistics. All-atom Clashscore : 4.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.57 % Favored : 99.43 % Rotamer: Outliers : 0.74 % Allowed : 4.90 % Favored : 94.36 % Cbeta Deviations : 0.08 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.34 (0.24), residues: 1230 helix: 1.38 (0.21), residues: 621 sheet: 0.77 (0.37), residues: 180 loop : 0.39 (0.31), residues: 429 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 21 TYR 0.015 0.001 TYR A 10 PHE 0.013 0.001 PHE C 255 TRP 0.027 0.002 TRP A 484 HIS 0.006 0.001 HIS C 275 Details of bonding type rmsd/Z covalent geometry : bond 0.00268 / 0.12 (10367) covalent geometry : angle 0.56348 / 0.29 (14005) hydrogen bonds : bond 0.03589 / 2.41 ( 519) hydrogen bonds : angle 4.80950 / 3.47 ( 1455) link_TRANS : bond 0.00127 / 0.06 ( 2) link_TRANS : angle 0.29240 / 0.20 ( 6) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2460 Ramachandran restraints generated. 1230 Oldfield, 0 Emsley, 1230 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2460 Ramachandran restraints generated. 1230 Oldfield, 0 Emsley, 1230 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 69 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 61 time to evaluate : 0.419 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 93 PHE cc_start: 0.9445 (m-80) cc_final: 0.8813 (m-10) REVERT: A 132 MET cc_start: 0.7342 (mmt) cc_final: 0.7040 (mmp) REVERT: A 135 MET cc_start: 0.8894 (ttp) cc_final: 0.8640 (ttt) REVERT: A 478 MET cc_start: 0.8995 (mmp) cc_final: 0.7813 (mmp) REVERT: A 783 MET cc_start: 0.9393 (tpt) cc_final: 0.9169 (tpp) REVERT: C 190 MET cc_start: 0.8911 (mtp) cc_final: 0.8569 (mtt) REVERT: C 205 GLU cc_start: 0.8976 (mt-10) cc_final: 0.8559 (mt-10) REVERT: C 227 MET cc_start: 0.8812 (tpp) cc_final: 0.8545 (tpp) REVERT: C 283 MET cc_start: 0.9161 (mmm) cc_final: 0.8907 (mmm) outliers start: 8 outliers final: 3 residues processed: 65 average time/residue: 0.1065 time to fit residues: 10.2186 Evaluate side-chains 57 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 54 time to evaluate : 0.402 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 57 SER Chi-restraints excluded: chain C residue 17 VAL Chi-restraints excluded: chain C residue 257 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 82 optimal weight: 3.9990 chunk 30 optimal weight: 0.0270 chunk 115 optimal weight: 0.0470 chunk 79 optimal weight: 5.9990 chunk 3 optimal weight: 0.2980 chunk 55 optimal weight: 0.9990 chunk 33 optimal weight: 0.8980 chunk 58 optimal weight: 0.8980 chunk 46 optimal weight: 7.9990 chunk 51 optimal weight: 0.7980 chunk 32 optimal weight: 0.4980 overall best weight: 0.3336 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 39 GLN A 72 ASN ** A 81 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 59 GLN C 111 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.050285 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2869 r_free = 0.2869 target = 0.036445 restraints weight = 57343.912| |-----------------------------------------------------------------------------| r_work (start): 0.2842 rms_B_bonded: 4.10 r_work: 0.2677 rms_B_bonded: 4.84 restraints_weight: 0.5000 r_work (final): 0.2677 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8739 moved from start: 0.2828 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 10369 Z= 0.095 Angle : 0.515 8.344 14011 Z= 0.267 Chirality : 0.040 0.174 1530 Planarity : 0.004 0.051 1785 Dihedral : 7.999 155.654 1385 Min Nonbonded Distance : 2.030 Molprobity Statistics. All-atom Clashscore : 4.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.98 % Favored : 99.02 % Rotamer: Outliers : 0.83 % Allowed : 5.64 % Favored : 93.52 % Cbeta Deviations : 0.08 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.69 (0.24), residues: 1230 helix: 1.77 (0.21), residues: 613 sheet: 0.91 (0.38), residues: 180 loop : 0.41 (0.30), residues: 437 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 784 TYR 0.010 0.001 TYR A 10 PHE 0.010 0.001 PHE C 255 TRP 0.049 0.002 TRP A 484 HIS 0.005 0.001 HIS A 81 Details of bonding type rmsd/Z covalent geometry : bond 0.00200 / 0.10 (10367) covalent geometry : angle 0.51497 / 0.27 (14005) hydrogen bonds : bond 0.03192 / 2.15 ( 519) hydrogen bonds : angle 4.56208 / 3.31 ( 1455) link_TRANS : bond 0.00036 / 0.02 ( 2) link_TRANS : angle 0.11067 / 0.09 ( 6) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2460 Ramachandran restraints generated. 1230 Oldfield, 0 Emsley, 1230 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2460 Ramachandran restraints generated. 1230 Oldfield, 0 Emsley, 1230 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 69 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 60 time to evaluate : 0.408 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 36 MET cc_start: 0.9218 (tpp) cc_final: 0.8992 (tpp) REVERT: B 93 PHE cc_start: 0.9431 (m-80) cc_final: 0.8812 (m-10) REVERT: A 132 MET cc_start: 0.6992 (mmt) cc_final: 0.6661 (mmp) REVERT: A 478 MET cc_start: 0.9164 (mmp) cc_final: 0.8856 (mmp) REVERT: C 190 MET cc_start: 0.8910 (mtp) cc_final: 0.8572 (mtt) REVERT: C 205 GLU cc_start: 0.8971 (mt-10) cc_final: 0.8614 (mt-10) REVERT: C 227 MET cc_start: 0.8833 (tpp) cc_final: 0.8342 (tmm) REVERT: C 283 MET cc_start: 0.9150 (mmm) cc_final: 0.8837 (mpp) outliers start: 9 outliers final: 5 residues processed: 67 average time/residue: 0.1073 time to fit residues: 10.6850 Evaluate side-chains 60 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 55 time to evaluate : 0.353 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 ASN Chi-restraints excluded: chain A residue 549 ILE Chi-restraints excluded: chain C residue 17 VAL Chi-restraints excluded: chain C residue 111 ASN Chi-restraints excluded: chain C residue 257 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 61 optimal weight: 0.8980 chunk 63 optimal weight: 2.9990 chunk 77 optimal weight: 4.9990 chunk 104 optimal weight: 0.6980 chunk 20 optimal weight: 0.5980 chunk 95 optimal weight: 1.9990 chunk 85 optimal weight: 3.9990 chunk 105 optimal weight: 0.9990 chunk 76 optimal weight: 0.6980 chunk 89 optimal weight: 3.9990 chunk 43 optimal weight: 1.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 81 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 111 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.049763 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2843 r_free = 0.2843 target = 0.035850 restraints weight = 58669.939| |-----------------------------------------------------------------------------| r_work (start): 0.2818 rms_B_bonded: 4.15 r_work: 0.2658 rms_B_bonded: 4.82 restraints_weight: 0.5000 r_work (final): 0.2658 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8746 moved from start: 0.2960 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 10369 Z= 0.114 Angle : 0.511 6.419 14011 Z= 0.261 Chirality : 0.040 0.176 1530 Planarity : 0.003 0.049 1785 Dihedral : 7.828 160.133 1385 Min Nonbonded Distance : 2.010 Molprobity Statistics. All-atom Clashscore : 4.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.38 % Favored : 98.62 % Rotamer: Outliers : 0.56 % Allowed : 6.85 % Favored : 92.60 % Cbeta Deviations : 0.08 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.79 (0.24), residues: 1230 helix: 1.85 (0.21), residues: 618 sheet: 1.12 (0.39), residues: 169 loop : 0.38 (0.30), residues: 443 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 701 TYR 0.009 0.001 TYR A 10 PHE 0.011 0.001 PHE C 255 TRP 0.030 0.001 TRP A 484 HIS 0.005 0.001 HIS A 81 Details of bonding type rmsd/Z covalent geometry : bond 0.00250 / 0.11 (10367) covalent geometry : angle 0.51067 / 0.26 (14005) hydrogen bonds : bond 0.03178 / 2.13 ( 519) hydrogen bonds : angle 4.50484 / 3.28 ( 1455) link_TRANS : bond 0.00117 / 0.06 ( 2) link_TRANS : angle 0.15590 / 0.09 ( 6) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2460 Ramachandran restraints generated. 1230 Oldfield, 0 Emsley, 1230 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2460 Ramachandran restraints generated. 1230 Oldfield, 0 Emsley, 1230 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 60 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 54 time to evaluate : 0.435 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 93 PHE cc_start: 0.9424 (m-80) cc_final: 0.8814 (m-10) REVERT: A 132 MET cc_start: 0.6870 (mmt) cc_final: 0.6504 (mmp) REVERT: A 135 MET cc_start: 0.8645 (ttp) cc_final: 0.8432 (ttp) REVERT: A 177 MET cc_start: 0.9447 (ptm) cc_final: 0.9082 (ppp) REVERT: A 305 MET cc_start: 0.9431 (tpp) cc_final: 0.9212 (tpp) REVERT: A 418 HIS cc_start: 0.9059 (OUTLIER) cc_final: 0.8728 (m-70) REVERT: A 478 MET cc_start: 0.9197 (mmp) cc_final: 0.8923 (mmp) REVERT: C 190 MET cc_start: 0.8954 (mtp) cc_final: 0.8613 (mtt) REVERT: C 205 GLU cc_start: 0.8976 (mt-10) cc_final: 0.8619 (mt-10) REVERT: C 227 MET cc_start: 0.8857 (tpp) cc_final: 0.8382 (tmm) REVERT: C 325 MET cc_start: 0.8705 (ptm) cc_final: 0.8209 (ptt) outliers start: 6 outliers final: 3 residues processed: 59 average time/residue: 0.1021 time to fit residues: 9.0753 Evaluate side-chains 56 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 52 time to evaluate : 0.409 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 418 HIS Chi-restraints excluded: chain A residue 549 ILE Chi-restraints excluded: chain C residue 17 VAL Chi-restraints excluded: chain C residue 257 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 43 optimal weight: 1.9990 chunk 62 optimal weight: 3.9990 chunk 73 optimal weight: 0.8980 chunk 49 optimal weight: 3.9990 chunk 30 optimal weight: 0.4980 chunk 66 optimal weight: 5.9990 chunk 96 optimal weight: 0.5980 chunk 33 optimal weight: 0.9980 chunk 85 optimal weight: 7.9990 chunk 35 optimal weight: 1.9990 chunk 19 optimal weight: 0.0970 overall best weight: 0.6178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 72 ASN ** A 81 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 111 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.049911 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2858 r_free = 0.2858 target = 0.036151 restraints weight = 57784.241| |-----------------------------------------------------------------------------| r_work (start): 0.2828 rms_B_bonded: 4.07 r_work: 0.2670 rms_B_bonded: 4.74 restraints_weight: 0.5000 r_work (final): 0.2670 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8745 moved from start: 0.3178 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 10369 Z= 0.102 Angle : 0.510 9.857 14011 Z= 0.258 Chirality : 0.040 0.175 1530 Planarity : 0.003 0.047 1785 Dihedral : 7.673 174.023 1385 Min Nonbonded Distance : 2.021 Molprobity Statistics. All-atom Clashscore : 4.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.46 % Favored : 98.54 % Rotamer: Outliers : 0.93 % Allowed : 6.85 % Favored : 92.23 % Cbeta Deviations : 0.08 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.84 (0.24), residues: 1230 helix: 1.92 (0.21), residues: 618 sheet: 1.24 (0.42), residues: 160 loop : 0.34 (0.30), residues: 452 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 701 TYR 0.008 0.001 TYR A 10 PHE 0.010 0.001 PHE C 255 TRP 0.021 0.001 TRP A 484 HIS 0.004 0.001 HIS A 81 Details of bonding type rmsd/Z covalent geometry : bond 0.00222 / 0.10 (10367) covalent geometry : angle 0.51058 / 0.26 (14005) hydrogen bonds : bond 0.03039 / 2.02 ( 519) hydrogen bonds : angle 4.40622 / 3.22 ( 1455) link_TRANS : bond 0.00092 / 0.05 ( 2) link_TRANS : angle 0.13116 / 0.09 ( 6) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2460 Ramachandran restraints generated. 1230 Oldfield, 0 Emsley, 1230 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2460 Ramachandran restraints generated. 1230 Oldfield, 0 Emsley, 1230 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 67 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 57 time to evaluate : 0.437 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 61 LYS cc_start: 0.8987 (mmmt) cc_final: 0.8659 (mmmt) REVERT: B 93 PHE cc_start: 0.9426 (m-80) cc_final: 0.8825 (m-10) REVERT: B 120 MET cc_start: 0.7969 (mmt) cc_final: 0.7472 (mmm) REVERT: A 132 MET cc_start: 0.6942 (mmt) cc_final: 0.6660 (mmp) REVERT: A 305 MET cc_start: 0.9455 (tpp) cc_final: 0.9129 (tpp) REVERT: A 418 HIS cc_start: 0.9053 (OUTLIER) cc_final: 0.8717 (m-70) REVERT: A 478 MET cc_start: 0.9194 (mmp) cc_final: 0.8865 (mmp) REVERT: C 190 MET cc_start: 0.8965 (mtp) cc_final: 0.8630 (mtt) REVERT: C 205 GLU cc_start: 0.9004 (mt-10) cc_final: 0.8670 (mt-10) REVERT: C 227 MET cc_start: 0.8865 (tpp) cc_final: 0.8396 (tmm) REVERT: C 283 MET cc_start: 0.9066 (mmm) cc_final: 0.8698 (mmm) REVERT: C 311 ASP cc_start: 0.9089 (t0) cc_final: 0.8851 (t0) REVERT: C 325 MET cc_start: 0.8997 (ptm) cc_final: 0.8357 (ptt) outliers start: 10 outliers final: 4 residues processed: 65 average time/residue: 0.0920 time to fit residues: 9.0341 Evaluate side-chains 58 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 53 time to evaluate : 0.296 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 418 HIS Chi-restraints excluded: chain A residue 549 ILE Chi-restraints excluded: chain C residue 17 VAL Chi-restraints excluded: chain C residue 111 ASN Chi-restraints excluded: chain C residue 257 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 57 optimal weight: 0.6980 chunk 114 optimal weight: 0.6980 chunk 92 optimal weight: 0.5980 chunk 122 optimal weight: 0.9990 chunk 20 optimal weight: 0.8980 chunk 78 optimal weight: 2.9990 chunk 34 optimal weight: 0.5980 chunk 106 optimal weight: 1.9990 chunk 67 optimal weight: 0.8980 chunk 11 optimal weight: 0.9990 chunk 10 optimal weight: 4.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 72 ASN ** A 81 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 111 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.049743 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2845 r_free = 0.2845 target = 0.035797 restraints weight = 58413.591| |-----------------------------------------------------------------------------| r_work (start): 0.2821 rms_B_bonded: 4.18 r_work: 0.2658 rms_B_bonded: 4.87 restraints_weight: 0.5000 r_work (final): 0.2658 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8763 moved from start: 0.3276 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 10369 Z= 0.109 Angle : 0.517 8.895 14011 Z= 0.261 Chirality : 0.040 0.173 1530 Planarity : 0.003 0.047 1785 Dihedral : 7.366 166.266 1385 Min Nonbonded Distance : 2.011 Molprobity Statistics. All-atom Clashscore : 5.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.63 % Favored : 98.37 % Rotamer: Outliers : 0.74 % Allowed : 7.77 % Favored : 91.49 % Cbeta Deviations : 0.08 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.84 (0.24), residues: 1230 helix: 1.96 (0.21), residues: 619 sheet: 1.27 (0.42), residues: 160 loop : 0.26 (0.29), residues: 451 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 701 TYR 0.008 0.001 TYR A 10 PHE 0.010 0.001 PHE C 255 TRP 0.019 0.001 TRP A 484 HIS 0.004 0.001 HIS A 81 Details of bonding type rmsd/Z covalent geometry : bond 0.00240 / 0.11 (10367) covalent geometry : angle 0.51743 / 0.26 (14005) hydrogen bonds : bond 0.03065 / 2.04 ( 519) hydrogen bonds : angle 4.39142 / 3.21 ( 1455) link_TRANS : bond 0.00109 / 0.05 ( 2) link_TRANS : angle 0.25944 / 0.16 ( 6) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2460 Ramachandran restraints generated. 1230 Oldfield, 0 Emsley, 1230 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2460 Ramachandran restraints generated. 1230 Oldfield, 0 Emsley, 1230 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 61 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 53 time to evaluate : 0.409 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 61 LYS cc_start: 0.9057 (mmmt) cc_final: 0.8751 (mmmt) REVERT: B 93 PHE cc_start: 0.9428 (m-80) cc_final: 0.8832 (m-10) REVERT: B 120 MET cc_start: 0.8022 (mmt) cc_final: 0.6983 (mmm) REVERT: A 177 MET cc_start: 0.9476 (ptm) cc_final: 0.8978 (ppp) REVERT: A 305 MET cc_start: 0.9452 (tpp) cc_final: 0.9110 (tpp) REVERT: A 478 MET cc_start: 0.9232 (mmp) cc_final: 0.8926 (mmp) REVERT: C 190 MET cc_start: 0.8986 (mtp) cc_final: 0.8654 (mtt) REVERT: C 205 GLU cc_start: 0.9022 (mt-10) cc_final: 0.8694 (mt-10) REVERT: C 227 MET cc_start: 0.8875 (tpp) cc_final: 0.8408 (tmm) REVERT: C 283 MET cc_start: 0.9096 (mmm) cc_final: 0.8720 (mmm) REVERT: C 311 ASP cc_start: 0.9129 (t0) cc_final: 0.8895 (t0) REVERT: C 325 MET cc_start: 0.9036 (ptm) cc_final: 0.8446 (ptt) outliers start: 8 outliers final: 5 residues processed: 59 average time/residue: 0.0901 time to fit residues: 7.8950 Evaluate side-chains 57 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 52 time to evaluate : 0.307 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 ASN Chi-restraints excluded: chain A residue 549 ILE Chi-restraints excluded: chain C residue 17 VAL Chi-restraints excluded: chain C residue 111 ASN Chi-restraints excluded: chain C residue 257 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 8 optimal weight: 4.9990 chunk 106 optimal weight: 1.9990 chunk 57 optimal weight: 1.9990 chunk 21 optimal weight: 0.7980 chunk 122 optimal weight: 0.9980 chunk 11 optimal weight: 3.9990 chunk 53 optimal weight: 1.9990 chunk 1 optimal weight: 10.0000 chunk 44 optimal weight: 4.9990 chunk 90 optimal weight: 0.8980 chunk 28 optimal weight: 3.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 81 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 290 GLN C 111 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.048972 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2815 r_free = 0.2815 target = 0.035004 restraints weight = 58297.765| |-----------------------------------------------------------------------------| r_work (start): 0.2797 rms_B_bonded: 4.10 r_work: 0.2634 rms_B_bonded: 4.79 restraints_weight: 0.5000 r_work (final): 0.2634 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8782 moved from start: 0.3241 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 10369 Z= 0.162 Angle : 0.552 8.259 14011 Z= 0.277 Chirality : 0.041 0.175 1530 Planarity : 0.003 0.046 1785 Dihedral : 6.893 141.676 1385 Min Nonbonded Distance : 1.980 Molprobity Statistics. All-atom Clashscore : 4.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Rotamer: Outliers : 0.46 % Allowed : 8.42 % Favored : 91.12 % Cbeta Deviations : 0.08 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.86 (0.25), residues: 1230 helix: 1.98 (0.21), residues: 619 sheet: 1.29 (0.42), residues: 160 loop : 0.25 (0.29), residues: 451 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 701 TYR 0.010 0.001 TYR A 259 PHE 0.013 0.001 PHE C 255 TRP 0.017 0.001 TRP A 484 HIS 0.004 0.001 HIS A 81 Details of bonding type rmsd/Z covalent geometry : bond 0.00362 / 0.16 (10367) covalent geometry : angle 0.55194 / 0.28 (14005) hydrogen bonds : bond 0.03240 / 2.17 ( 519) hydrogen bonds : angle 4.41751 / 3.23 ( 1455) link_TRANS : bond 0.00222 / 0.11 ( 2) link_TRANS : angle 0.37248 / 0.23 ( 6) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2460 Ramachandran restraints generated. 1230 Oldfield, 0 Emsley, 1230 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2460 Ramachandran restraints generated. 1230 Oldfield, 0 Emsley, 1230 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 59 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 54 time to evaluate : 0.417 Fit side-chains revert: symmetry clash REVERT: B 61 LYS cc_start: 0.9063 (mmmt) cc_final: 0.8756 (mmmt) REVERT: B 93 PHE cc_start: 0.9449 (m-80) cc_final: 0.8865 (m-10) REVERT: B 120 MET cc_start: 0.8068 (mmt) cc_final: 0.6744 (mmm) REVERT: A 177 MET cc_start: 0.9492 (ptm) cc_final: 0.9002 (ppp) REVERT: A 305 MET cc_start: 0.9463 (tpp) cc_final: 0.9085 (tpp) REVERT: A 478 MET cc_start: 0.9238 (mmp) cc_final: 0.8930 (mmp) REVERT: C 190 MET cc_start: 0.8996 (mtp) cc_final: 0.8661 (mtt) REVERT: C 205 GLU cc_start: 0.9006 (mt-10) cc_final: 0.8643 (mt-10) REVERT: C 227 MET cc_start: 0.8891 (tpp) cc_final: 0.8420 (tmm) REVERT: C 283 MET cc_start: 0.9051 (mmm) cc_final: 0.8795 (mmm) REVERT: C 311 ASP cc_start: 0.9143 (t0) cc_final: 0.8905 (t0) REVERT: C 325 MET cc_start: 0.9076 (ptm) cc_final: 0.8462 (ptt) outliers start: 5 outliers final: 5 residues processed: 58 average time/residue: 0.1047 time to fit residues: 9.0280 Evaluate side-chains 57 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 52 time to evaluate : 0.430 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 418 HIS Chi-restraints excluded: chain A residue 549 ILE Chi-restraints excluded: chain C residue 17 VAL Chi-restraints excluded: chain C residue 111 ASN Chi-restraints excluded: chain C residue 257 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 71 optimal weight: 2.9990 chunk 114 optimal weight: 0.9990 chunk 29 optimal weight: 4.9990 chunk 111 optimal weight: 2.9990 chunk 52 optimal weight: 1.9990 chunk 113 optimal weight: 0.9990 chunk 58 optimal weight: 0.9980 chunk 55 optimal weight: 0.2980 chunk 33 optimal weight: 0.9990 chunk 43 optimal weight: 0.6980 chunk 121 optimal weight: 0.6980 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 81 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.049368 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2830 r_free = 0.2830 target = 0.035368 restraints weight = 58148.941| |-----------------------------------------------------------------------------| r_work (start): 0.2809 rms_B_bonded: 4.15 r_work: 0.2645 rms_B_bonded: 4.85 restraints_weight: 0.5000 r_work (final): 0.2645 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8776 moved from start: 0.3357 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 10369 Z= 0.111 Angle : 0.523 7.966 14011 Z= 0.263 Chirality : 0.040 0.172 1530 Planarity : 0.003 0.046 1785 Dihedral : 6.417 120.628 1385 Min Nonbonded Distance : 2.013 Molprobity Statistics. All-atom Clashscore : 4.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Rotamer: Outliers : 0.46 % Allowed : 8.05 % Favored : 91.49 % Cbeta Deviations : 0.08 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.90 (0.24), residues: 1230 helix: 2.07 (0.22), residues: 613 sheet: 1.29 (0.42), residues: 160 loop : 0.21 (0.29), residues: 457 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 701 TYR 0.008 0.001 TYR A 10 PHE 0.010 0.001 PHE C 255 TRP 0.018 0.001 TRP A 484 HIS 0.004 0.001 HIS A 81 Details of bonding type rmsd/Z covalent geometry : bond 0.00249 / 0.11 (10367) covalent geometry : angle 0.52339 / 0.26 (14005) hydrogen bonds : bond 0.03078 / 2.06 ( 519) hydrogen bonds : angle 4.38027 / 3.21 ( 1455) link_TRANS : bond 0.00099 / 0.05 ( 2) link_TRANS : angle 0.24140 / 0.14 ( 6) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2460 Ramachandran restraints generated. 1230 Oldfield, 0 Emsley, 1230 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2460 Ramachandran restraints generated. 1230 Oldfield, 0 Emsley, 1230 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 57 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 52 time to evaluate : 0.408 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 61 LYS cc_start: 0.9065 (mmmt) cc_final: 0.8745 (mmmt) REVERT: B 93 PHE cc_start: 0.9455 (m-80) cc_final: 0.8882 (m-10) REVERT: B 120 MET cc_start: 0.8075 (mmt) cc_final: 0.6800 (mmm) REVERT: A 177 MET cc_start: 0.9477 (ptm) cc_final: 0.9083 (ppp) REVERT: A 305 MET cc_start: 0.9512 (tpp) cc_final: 0.9104 (tpp) REVERT: A 418 HIS cc_start: 0.9029 (OUTLIER) cc_final: 0.8691 (m-70) REVERT: A 478 MET cc_start: 0.9255 (mmp) cc_final: 0.8948 (mmp) REVERT: C 190 MET cc_start: 0.8994 (mtp) cc_final: 0.8661 (mtt) REVERT: C 205 GLU cc_start: 0.9006 (mt-10) cc_final: 0.8630 (mt-10) REVERT: C 227 MET cc_start: 0.8887 (tpp) cc_final: 0.8427 (tmm) REVERT: C 283 MET cc_start: 0.9024 (mmm) cc_final: 0.8589 (mpp) REVERT: C 311 ASP cc_start: 0.9145 (t0) cc_final: 0.8907 (t0) REVERT: C 325 MET cc_start: 0.9121 (ptm) cc_final: 0.8516 (ptt) outliers start: 5 outliers final: 3 residues processed: 56 average time/residue: 0.0942 time to fit residues: 8.0103 Evaluate side-chains 56 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 52 time to evaluate : 0.305 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 418 HIS Chi-restraints excluded: chain A residue 549 ILE Chi-restraints excluded: chain C residue 17 VAL Chi-restraints excluded: chain C residue 257 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 94 optimal weight: 3.9990 chunk 91 optimal weight: 8.9990 chunk 67 optimal weight: 1.9990 chunk 19 optimal weight: 4.9990 chunk 55 optimal weight: 5.9990 chunk 53 optimal weight: 3.9990 chunk 59 optimal weight: 0.9990 chunk 86 optimal weight: 2.9990 chunk 113 optimal weight: 0.9980 chunk 50 optimal weight: 1.9990 chunk 40 optimal weight: 3.9990 overall best weight: 1.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 81 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 373 HIS C 111 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.048039 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2779 r_free = 0.2779 target = 0.034081 restraints weight = 58133.320| |-----------------------------------------------------------------------------| r_work (start): 0.2761 rms_B_bonded: 4.08 r_work: 0.2597 rms_B_bonded: 4.79 restraints_weight: 0.5000 r_work (final): 0.2597 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8820 moved from start: 0.3279 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 10369 Z= 0.206 Angle : 0.574 8.021 14011 Z= 0.290 Chirality : 0.042 0.173 1530 Planarity : 0.004 0.045 1785 Dihedral : 6.433 115.629 1385 Min Nonbonded Distance : 1.962 Molprobity Statistics. All-atom Clashscore : 5.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 0.46 % Allowed : 8.23 % Favored : 91.30 % Cbeta Deviations : 0.08 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.78 (0.25), residues: 1230 helix: 1.90 (0.21), residues: 623 sheet: 1.32 (0.40), residues: 169 loop : 0.15 (0.30), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 64 TYR 0.012 0.001 TYR A 10 PHE 0.013 0.001 PHE C 255 TRP 0.020 0.002 TRP A 484 HIS 0.004 0.001 HIS A 418 Details of bonding type rmsd/Z covalent geometry : bond 0.00461 / 0.21 (10367) covalent geometry : angle 0.57402 / 0.29 (14005) hydrogen bonds : bond 0.03550 / 2.38 ( 519) hydrogen bonds : angle 4.53369 / 3.32 ( 1455) link_TRANS : bond 0.00298 / 0.14 ( 2) link_TRANS : angle 0.55322 / 0.34 ( 6) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2460 Ramachandran restraints generated. 1230 Oldfield, 0 Emsley, 1230 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2460 Ramachandran restraints generated. 1230 Oldfield, 0 Emsley, 1230 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 57 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 52 time to evaluate : 0.329 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 93 PHE cc_start: 0.9465 (m-80) cc_final: 0.8896 (m-10) REVERT: B 120 MET cc_start: 0.8106 (mmt) cc_final: 0.7081 (mmm) REVERT: A 177 MET cc_start: 0.9489 (ptm) cc_final: 0.9068 (ppp) REVERT: A 305 MET cc_start: 0.9554 (tpp) cc_final: 0.9145 (tpp) REVERT: A 478 MET cc_start: 0.9250 (mmp) cc_final: 0.8947 (mmp) REVERT: C 190 MET cc_start: 0.9017 (mtp) cc_final: 0.8680 (mtt) REVERT: C 205 GLU cc_start: 0.8996 (mt-10) cc_final: 0.8640 (mt-10) REVERT: C 225 ASN cc_start: 0.9260 (m-40) cc_final: 0.9039 (m-40) REVERT: C 227 MET cc_start: 0.8899 (tpp) cc_final: 0.8430 (tmm) REVERT: C 283 MET cc_start: 0.9053 (mmm) cc_final: 0.8815 (mmm) REVERT: C 311 ASP cc_start: 0.9172 (t0) cc_final: 0.8928 (t0) REVERT: C 325 MET cc_start: 0.9063 (ptm) cc_final: 0.8372 (ptt) outliers start: 5 outliers final: 3 residues processed: 57 average time/residue: 0.0901 time to fit residues: 7.7088 Evaluate side-chains 54 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 51 time to evaluate : 0.260 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 549 ILE Chi-restraints excluded: chain C residue 17 VAL Chi-restraints excluded: chain C residue 257 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 50 optimal weight: 0.7980 chunk 97 optimal weight: 0.8980 chunk 1 optimal weight: 8.9990 chunk 115 optimal weight: 2.9990 chunk 83 optimal weight: 4.9990 chunk 43 optimal weight: 0.7980 chunk 4 optimal weight: 0.0970 chunk 9 optimal weight: 9.9990 chunk 14 optimal weight: 0.8980 chunk 29 optimal weight: 0.9990 chunk 66 optimal weight: 0.7980 overall best weight: 0.6778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 81 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 111 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3337 r_free = 0.3337 target = 0.049139 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2821 r_free = 0.2821 target = 0.035109 restraints weight = 57785.835| |-----------------------------------------------------------------------------| r_work (start): 0.2802 rms_B_bonded: 4.14 r_work: 0.2637 rms_B_bonded: 4.84 restraints_weight: 0.5000 r_work (final): 0.2637 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8787 moved from start: 0.3467 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 10369 Z= 0.109 Angle : 0.532 8.121 14011 Z= 0.267 Chirality : 0.040 0.167 1530 Planarity : 0.003 0.046 1785 Dihedral : 6.125 108.258 1385 Min Nonbonded Distance : 2.022 Molprobity Statistics. All-atom Clashscore : 4.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.71 % Favored : 98.29 % Rotamer: Outliers : 0.46 % Allowed : 8.14 % Favored : 91.40 % Cbeta Deviations : 0.08 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.93 (0.25), residues: 1230 helix: 2.13 (0.22), residues: 612 sheet: 1.30 (0.42), residues: 160 loop : 0.17 (0.29), residues: 458 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 701 TYR 0.008 0.001 TYR A 10 PHE 0.010 0.001 PHE C 255 TRP 0.019 0.001 TRP A 484 HIS 0.005 0.001 HIS A 81 Details of bonding type rmsd/Z covalent geometry : bond 0.00244 / 0.11 (10367) covalent geometry : angle 0.53224 / 0.27 (14005) hydrogen bonds : bond 0.03101 / 2.07 ( 519) hydrogen bonds : angle 4.39982 / 3.22 ( 1455) link_TRANS : bond 0.00079 / 0.04 ( 2) link_TRANS : angle 0.21387 / 0.13 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2294.37 seconds wall clock time: 40 minutes 16.87 seconds (2416.87 seconds total)