Starting phenix.real_space_refine on Mon Jul 28 18:40:59 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7pmh_13533/07_2025/7pmh_13533.cif Found real_map, /net/cci-nas-00/data/ceres_data/7pmh_13533/07_2025/7pmh_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/7pmh_13533/07_2025/7pmh_13533.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7pmh_13533/07_2025/7pmh_13533.map" model { file = "/net/cci-nas-00/data/ceres_data/7pmh_13533/07_2025/7pmh_13533.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7pmh_13533/07_2025/7pmh_13533.cif" } resolution = 3.4 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= 0.001 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): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/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, 'ARG:plan': 2, 'ASN:plan1': 1, 'ASP:plan': 2} 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 Unresolved non-hydrogen dihedrals: 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} Modifications used: {'DTH_chir_02_both': 1, 'PEPT-D': 1} 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: 7.34, per 1000 atoms: 0.72 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: 2.85 Conformation dependent library (CDL) restraints added in 1.4 seconds 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: 1.36 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: 4.27 Time building geometry restraints manager: 3.34 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: 6003 26.34 - 52.68: 211 52.68 - 79.02: 42 79.02 - 105.36: 16 105.36 - 131.70: 3 Dihedral angle restraints: 6275 sinusoidal: 2594 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 6272 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.052: 1000 0.052 - 0.105: 415 0.105 - 0.157: 99 0.157 - 0.209: 13 0.209 - 0.261: 3 Chirality restraints: 1530 Sorted by residual: 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 chirality pdb=" CA GLU C 316 " pdb=" N GLU C 316 " pdb=" C GLU C 316 " pdb=" CB GLU C 316 " both_signs ideal model delta sigma weight residual False 2.51 2.29 0.22 2.00e-01 2.50e+01 1.21e+00 chirality pdb=" CA GLU C 226 " pdb=" N GLU C 226 " pdb=" C GLU C 226 " pdb=" CB GLU C 226 " both_signs ideal model delta sigma weight residual False 2.51 2.29 0.22 2.00e-01 2.50e+01 1.18e+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: 0.000 Normalize map: mean=0, sd=1: 2.200 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: 0.470 Check model and map are aligned: 0.090 Set scattering table: 0.110 Process input model: 29.470 Find NCS groups from input model: 0.150 Set up NCS constraints: 0.060 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: 0.010 Load rotamer database and sin/cos tables:3.380 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.950 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8192 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 : 0.058 0.261 1530 Planarity : 0.008 0.089 1785 Dihedral : 15.498 131.704 3895 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 (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: -1.51 (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 TRP 0.045 0.005 TRP C 356 HIS 0.017 0.003 HIS C 275 PHE 0.084 0.003 PHE A 564 TYR 0.058 0.007 TYR C 306 ARG 0.081 0.011 ARG C 147 Details of bonding type rmsd link_TRANS : bond 0.01705 ( 2) link_TRANS : angle 3.81068 ( 6) hydrogen bonds : bond 0.15517 ( 519) hydrogen bonds : angle 7.41426 ( 1455) covalent geometry : bond 0.00947 (10367) covalent geometry : angle 1.00485 (14005) *********************** 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 : 1.259 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: 0.3381 time to fit residues: 41.8941 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 : 1.268 ------------------------------------------------------------------------------- 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 104 optimal weight: 0.8980 chunk 93 optimal weight: 0.7980 chunk 52 optimal weight: 0.4980 chunk 32 optimal weight: 0.8980 chunk 63 optimal weight: 0.9980 chunk 50 optimal weight: 0.7980 chunk 97 optimal weight: 3.9990 chunk 37 optimal weight: 0.6980 chunk 59 optimal weight: 3.9990 chunk 72 optimal weight: 0.9980 chunk 112 optimal weight: 0.6980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 ** both conformations clash, **PLEASE CHECK MANUALLY** 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: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.048678 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2796 r_free = 0.2796 target = 0.035029 restraints weight = 57216.651| |-----------------------------------------------------------------------------| r_work (start): 0.2774 rms_B_bonded: 4.01 r_work: 0.2613 rms_B_bonded: 4.78 restraints_weight: 0.5000 r_work (final): 0.2613 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8655 moved from start: 0.2039 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= 0.136 Angle : 0.615 7.241 14011 Z= 0.326 Chirality : 0.043 0.210 1530 Planarity : 0.004 0.050 1785 Dihedral : 10.385 144.084 1424 Min Nonbonded Distance : 2.043 Molprobity Statistics. All-atom Clashscore : 5.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.24 % Favored : 99.76 % Rotamer: Outliers : 0.93 % Allowed : 3.52 % Favored : 95.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.84 (0.23), residues: 1230 helix: 0.82 (0.21), residues: 618 sheet: 0.58 (0.36), residues: 174 loop : 0.40 (0.30), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP A 484 HIS 0.007 0.001 HIS C 275 PHE 0.018 0.001 PHE A 564 TYR 0.021 0.001 TYR A 10 ARG 0.005 0.001 ARG C 95 Details of bonding type rmsd link_TRANS : bond 0.00160 ( 2) link_TRANS : angle 0.89307 ( 6) hydrogen bonds : bond 0.03947 ( 519) hydrogen bonds : angle 5.18574 ( 1455) covalent geometry : bond 0.00292 (10367) covalent geometry : angle 0.61440 (14005) *********************** 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 76 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 66 time to evaluate : 1.419 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 93 PHE cc_start: 0.9432 (m-80) cc_final: 0.8788 (m-10) REVERT: A 177 MET cc_start: 0.9511 (ttm) cc_final: 0.9157 (tmm) REVERT: A 478 MET cc_start: 0.8865 (mmp) cc_final: 0.8135 (mmp) REVERT: A 783 MET cc_start: 0.9348 (tpt) cc_final: 0.9140 (tpp) REVERT: C 190 MET cc_start: 0.8858 (mtp) cc_final: 0.8496 (mtt) REVERT: C 195 GLU cc_start: 0.8807 (OUTLIER) cc_final: 0.8446 (mt-10) REVERT: C 205 GLU cc_start: 0.8987 (mt-10) cc_final: 0.8575 (mt-10) REVERT: C 227 MET cc_start: 0.8764 (tpp) cc_final: 0.8451 (tpp) REVERT: C 313 MET cc_start: 0.9642 (tpp) cc_final: 0.9407 (mmt) outliers start: 10 outliers final: 2 residues processed: 68 average time/residue: 0.3138 time to fit residues: 31.1549 Evaluate side-chains 62 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 59 time to evaluate : 2.348 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 57 SER Chi-restraints excluded: chain C residue 195 GLU 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 45 optimal weight: 0.5980 chunk 71 optimal weight: 1.9990 chunk 63 optimal weight: 1.9990 chunk 84 optimal weight: 3.9990 chunk 22 optimal weight: 2.9990 chunk 64 optimal weight: 0.5980 chunk 48 optimal weight: 0.7980 chunk 74 optimal weight: 1.9990 chunk 90 optimal weight: 0.2980 chunk 42 optimal weight: 1.9990 chunk 69 optimal weight: 0.9990 overall best weight: 0.6582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 72 ASN ** A 81 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.048592 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2802 r_free = 0.2802 target = 0.035044 restraints weight = 57815.473| |-----------------------------------------------------------------------------| r_work (start): 0.2776 rms_B_bonded: 3.98 r_work: 0.2616 rms_B_bonded: 4.73 restraints_weight: 0.5000 r_work (final): 0.2616 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8653 moved from start: 0.2445 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= 0.116 Angle : 0.554 7.428 14011 Z= 0.288 Chirality : 0.041 0.168 1530 Planarity : 0.004 0.050 1785 Dihedral : 9.775 148.696 1423 Min Nonbonded Distance : 2.032 Molprobity Statistics. All-atom Clashscore : 4.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.57 % Favored : 99.43 % Rotamer: Outliers : 0.46 % Allowed : 5.09 % Favored : 94.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.38 (0.24), residues: 1230 helix: 1.41 (0.21), residues: 620 sheet: 0.78 (0.37), residues: 180 loop : 0.43 (0.31), residues: 430 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP A 484 HIS 0.006 0.001 HIS C 275 PHE 0.013 0.001 PHE C 255 TYR 0.014 0.001 TYR A 10 ARG 0.003 0.000 ARG B 21 Details of bonding type rmsd link_TRANS : bond 0.00215 ( 2) link_TRANS : angle 0.97173 ( 6) hydrogen bonds : bond 0.03541 ( 519) hydrogen bonds : angle 4.77915 ( 1455) covalent geometry : bond 0.00256 (10367) covalent geometry : angle 0.55329 (14005) *********************** 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 65 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 60 time to evaluate : 3.543 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 93 PHE cc_start: 0.9426 (m-80) cc_final: 0.8787 (m-10) REVERT: A 132 MET cc_start: 0.7173 (mmt) cc_final: 0.6870 (mmp) REVERT: A 135 MET cc_start: 0.8811 (ttp) cc_final: 0.8553 (ttt) REVERT: A 478 MET cc_start: 0.9045 (mmp) cc_final: 0.7842 (mmp) REVERT: A 783 MET cc_start: 0.9387 (tpt) cc_final: 0.9132 (tpp) REVERT: C 190 MET cc_start: 0.8905 (mtp) cc_final: 0.8564 (mtt) REVERT: C 205 GLU cc_start: 0.8991 (mt-10) cc_final: 0.8585 (mt-10) REVERT: C 227 MET cc_start: 0.8801 (tpp) cc_final: 0.8523 (tpp) REVERT: C 283 MET cc_start: 0.9212 (mmm) cc_final: 0.8929 (mmm) outliers start: 5 outliers final: 3 residues processed: 63 average time/residue: 0.3323 time to fit residues: 30.6246 Evaluate side-chains 56 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 53 time to evaluate : 1.457 ------------------------------------------------------------------------------- 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 100 optimal weight: 0.0770 chunk 20 optimal weight: 0.6980 chunk 52 optimal weight: 0.9980 chunk 59 optimal weight: 0.0050 chunk 75 optimal weight: 1.9990 chunk 19 optimal weight: 0.9990 chunk 82 optimal weight: 4.9990 chunk 121 optimal weight: 3.9990 chunk 87 optimal weight: 5.9990 chunk 70 optimal weight: 0.9990 chunk 63 optimal weight: 0.9990 overall best weight: 0.5554 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 39 GLN A 72 ASN ** A 81 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 59 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.048822 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2816 r_free = 0.2816 target = 0.035306 restraints weight = 57364.377| |-----------------------------------------------------------------------------| r_work (start): 0.2790 rms_B_bonded: 4.00 r_work: 0.2632 rms_B_bonded: 4.70 restraints_weight: 0.5000 r_work (final): 0.2632 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8648 moved from start: 0.2792 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= 0.103 Angle : 0.517 9.746 14011 Z= 0.267 Chirality : 0.040 0.165 1530 Planarity : 0.004 0.051 1785 Dihedral : 9.355 155.680 1423 Min Nonbonded Distance : 1.968 Molprobity Statistics. All-atom Clashscore : 4.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.06 % Favored : 98.94 % Rotamer: Outliers : 0.65 % Allowed : 5.83 % Favored : 93.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.72 (0.24), residues: 1230 helix: 1.78 (0.21), residues: 613 sheet: 1.00 (0.39), residues: 170 loop : 0.43 (0.30), residues: 447 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.054 0.002 TRP A 484 HIS 0.005 0.001 HIS A 81 PHE 0.011 0.001 PHE C 255 TYR 0.010 0.001 TYR A 10 ARG 0.003 0.000 ARG A 784 Details of bonding type rmsd link_TRANS : bond 0.00219 ( 2) link_TRANS : angle 0.95862 ( 6) hydrogen bonds : bond 0.03237 ( 519) hydrogen bonds : angle 4.57790 ( 1455) covalent geometry : bond 0.00223 (10367) covalent geometry : angle 0.51634 (14005) *********************** 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 66 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 59 time to evaluate : 1.444 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 93 PHE cc_start: 0.9411 (m-80) cc_final: 0.8790 (m-10) REVERT: A 132 MET cc_start: 0.7006 (mmt) cc_final: 0.6681 (mmp) REVERT: A 305 MET cc_start: 0.9466 (tpp) cc_final: 0.9138 (tpp) REVERT: A 478 MET cc_start: 0.9186 (mmp) cc_final: 0.8883 (mmp) REVERT: A 788 MET cc_start: 0.9222 (mpp) cc_final: 0.8984 (ptp) REVERT: C 190 MET cc_start: 0.8939 (mtp) cc_final: 0.8600 (mtt) REVERT: C 205 GLU cc_start: 0.8969 (mt-10) cc_final: 0.8590 (mt-10) REVERT: C 227 MET cc_start: 0.8831 (tpp) cc_final: 0.8327 (tmm) REVERT: C 283 MET cc_start: 0.9187 (mmm) cc_final: 0.8968 (mmm) outliers start: 7 outliers final: 3 residues processed: 64 average time/residue: 0.2840 time to fit residues: 26.7870 Evaluate side-chains 58 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 55 time to evaluate : 1.313 ------------------------------------------------------------------------------- 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 82 optimal weight: 2.9990 chunk 100 optimal weight: 3.9990 chunk 111 optimal weight: 2.9990 chunk 114 optimal weight: 0.9980 chunk 18 optimal weight: 1.9990 chunk 41 optimal weight: 0.6980 chunk 5 optimal weight: 8.9990 chunk 70 optimal weight: 0.9980 chunk 90 optimal weight: 3.9990 chunk 28 optimal weight: 5.9990 chunk 29 optimal weight: 0.9980 overall best weight: 1.1382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 72 ASN ** A 81 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.048000 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2782 r_free = 0.2782 target = 0.034426 restraints weight = 57488.625| |-----------------------------------------------------------------------------| r_work (start): 0.2758 rms_B_bonded: 3.98 r_work: 0.2600 rms_B_bonded: 4.68 restraints_weight: 0.5000 r_work (final): 0.2600 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8680 moved from start: 0.2938 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 10369 Z= 0.145 Angle : 0.519 6.547 14011 Z= 0.267 Chirality : 0.041 0.167 1530 Planarity : 0.004 0.049 1785 Dihedral : 9.254 164.595 1423 Min Nonbonded Distance : 1.982 Molprobity Statistics. All-atom Clashscore : 4.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.30 % Favored : 98.70 % Rotamer: Outliers : 0.74 % Allowed : 6.85 % Favored : 92.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.70 (0.24), residues: 1230 helix: 1.80 (0.21), residues: 625 sheet: 1.14 (0.41), residues: 159 loop : 0.26 (0.29), residues: 446 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.001 TRP A 484 HIS 0.004 0.001 HIS A 81 PHE 0.013 0.001 PHE C 255 TYR 0.011 0.001 TYR A 10 ARG 0.003 0.000 ARG A 789 Details of bonding type rmsd link_TRANS : bond 0.00180 ( 2) link_TRANS : angle 0.90703 ( 6) hydrogen bonds : bond 0.03349 ( 519) hydrogen bonds : angle 4.52719 ( 1455) covalent geometry : bond 0.00322 (10367) covalent geometry : angle 0.51912 (14005) *********************** 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 63 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 55 time to evaluate : 1.057 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 93 PHE cc_start: 0.9426 (m-80) cc_final: 0.8827 (m-10) REVERT: A 132 MET cc_start: 0.6895 (mmt) cc_final: 0.6526 (mmp) REVERT: A 177 MET cc_start: 0.9480 (ptm) cc_final: 0.9064 (ppp) REVERT: A 305 MET cc_start: 0.9478 (tpp) cc_final: 0.9122 (tpp) REVERT: A 478 MET cc_start: 0.9198 (mmp) cc_final: 0.8887 (mmp) REVERT: C 190 MET cc_start: 0.8987 (mtp) cc_final: 0.8648 (mtt) REVERT: C 205 GLU cc_start: 0.9006 (mt-10) cc_final: 0.8613 (mt-10) REVERT: C 227 MET cc_start: 0.8866 (tpp) cc_final: 0.8375 (tmm) outliers start: 8 outliers final: 4 residues processed: 61 average time/residue: 0.2251 time to fit residues: 20.4804 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 : 1.290 ------------------------------------------------------------------------------- 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 257 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 57 optimal weight: 0.6980 chunk 109 optimal weight: 0.7980 chunk 108 optimal weight: 0.9990 chunk 45 optimal weight: 0.4980 chunk 54 optimal weight: 4.9990 chunk 86 optimal weight: 0.7980 chunk 58 optimal weight: 0.7980 chunk 25 optimal weight: 2.9990 chunk 32 optimal weight: 3.9990 chunk 15 optimal weight: 5.9990 chunk 114 optimal weight: 0.6980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3302 r_free = 0.3302 target = 0.048310 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2798 r_free = 0.2798 target = 0.034752 restraints weight = 57822.489| |-----------------------------------------------------------------------------| r_work (start): 0.2776 rms_B_bonded: 4.02 r_work: 0.2616 rms_B_bonded: 4.71 restraints_weight: 0.5000 r_work (final): 0.2616 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8668 moved from start: 0.3135 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 10369 Z= 0.109 Angle : 0.515 9.466 14011 Z= 0.261 Chirality : 0.040 0.163 1530 Planarity : 0.003 0.047 1785 Dihedral : 9.218 179.587 1423 Min Nonbonded Distance : 1.995 Molprobity Statistics. All-atom Clashscore : 4.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.71 % Favored : 98.29 % Rotamer: Outliers : 0.65 % Allowed : 7.59 % Favored : 91.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.84 (0.24), residues: 1230 helix: 1.95 (0.21), residues: 618 sheet: 1.20 (0.40), residues: 169 loop : 0.30 (0.30), residues: 443 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP A 484 HIS 0.004 0.001 HIS A 81 PHE 0.011 0.001 PHE C 255 TYR 0.009 0.001 TYR A 10 ARG 0.005 0.000 ARG A 710 Details of bonding type rmsd link_TRANS : bond 0.00207 ( 2) link_TRANS : angle 0.94140 ( 6) hydrogen bonds : bond 0.03154 ( 519) hydrogen bonds : angle 4.44187 ( 1455) covalent geometry : bond 0.00238 (10367) covalent geometry : angle 0.51483 (14005) *********************** 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 65 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 58 time to evaluate : 1.234 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 93 PHE cc_start: 0.9420 (m-80) cc_final: 0.8826 (m-10) REVERT: B 120 MET cc_start: 0.8066 (mmt) cc_final: 0.6699 (mmm) REVERT: A 132 MET cc_start: 0.6871 (mmt) cc_final: 0.6566 (mmp) REVERT: A 177 MET cc_start: 0.9459 (ptm) cc_final: 0.9031 (ppp) REVERT: A 305 MET cc_start: 0.9516 (tpp) cc_final: 0.9088 (tpp) REVERT: A 418 HIS cc_start: 0.8989 (OUTLIER) cc_final: 0.8646 (m-70) REVERT: A 478 MET cc_start: 0.9213 (mmp) cc_final: 0.8873 (mmp) REVERT: C 190 MET cc_start: 0.8987 (mtp) cc_final: 0.8655 (mtt) REVERT: C 205 GLU cc_start: 0.9021 (mt-10) cc_final: 0.8734 (mt-10) REVERT: C 227 MET cc_start: 0.8877 (tpp) cc_final: 0.8401 (tmm) REVERT: C 283 MET cc_start: 0.9146 (mmm) cc_final: 0.8803 (mmm) REVERT: C 311 ASP cc_start: 0.9130 (t0) cc_final: 0.8896 (t0) outliers start: 7 outliers final: 3 residues processed: 63 average time/residue: 0.2441 time to fit residues: 22.9728 Evaluate side-chains 57 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 53 time to evaluate : 1.234 ------------------------------------------------------------------------------- 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 30 optimal weight: 0.0870 chunk 102 optimal weight: 5.9990 chunk 93 optimal weight: 4.9990 chunk 61 optimal weight: 2.9990 chunk 13 optimal weight: 0.9990 chunk 76 optimal weight: 0.8980 chunk 41 optimal weight: 0.9980 chunk 55 optimal weight: 3.9990 chunk 5 optimal weight: 6.9990 chunk 42 optimal weight: 0.8980 chunk 24 optimal weight: 0.8980 overall best weight: 0.7558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3303 r_free = 0.3303 target = 0.048332 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2795 r_free = 0.2795 target = 0.034678 restraints weight = 58765.173| |-----------------------------------------------------------------------------| r_work (start): 0.2772 rms_B_bonded: 4.03 r_work: 0.2613 rms_B_bonded: 4.74 restraints_weight: 0.5000 r_work (final): 0.2613 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8673 moved from start: 0.3256 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 10369 Z= 0.114 Angle : 0.528 9.167 14011 Z= 0.268 Chirality : 0.040 0.163 1530 Planarity : 0.003 0.046 1785 Dihedral : 8.595 149.516 1423 Min Nonbonded Distance : 1.993 Molprobity Statistics. All-atom Clashscore : 4.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.38 % Favored : 98.62 % Rotamer: Outliers : 0.37 % Allowed : 8.42 % Favored : 91.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.86 (0.24), residues: 1230 helix: 1.98 (0.21), residues: 618 sheet: 1.27 (0.42), residues: 160 loop : 0.27 (0.30), residues: 452 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 484 HIS 0.004 0.001 HIS A 81 PHE 0.010 0.001 PHE C 255 TYR 0.009 0.001 TYR A 10 ARG 0.002 0.000 ARG A 789 Details of bonding type rmsd link_TRANS : bond 0.00196 ( 2) link_TRANS : angle 0.91763 ( 6) hydrogen bonds : bond 0.03115 ( 519) hydrogen bonds : angle 4.40642 ( 1455) covalent geometry : bond 0.00254 (10367) covalent geometry : angle 0.52768 (14005) *********************** 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 59 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 55 time to evaluate : 1.255 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 93 PHE cc_start: 0.9423 (m-80) cc_final: 0.8840 (m-10) REVERT: B 120 MET cc_start: 0.8042 (mmt) cc_final: 0.6926 (mmm) REVERT: A 177 MET cc_start: 0.9419 (ptm) cc_final: 0.9077 (ppp) REVERT: A 305 MET cc_start: 0.9520 (tpp) cc_final: 0.9095 (tpp) REVERT: A 418 HIS cc_start: 0.8998 (OUTLIER) cc_final: 0.8650 (m-70) REVERT: A 478 MET cc_start: 0.9218 (mmp) cc_final: 0.8918 (mmp) REVERT: C 190 MET cc_start: 0.8997 (mtp) cc_final: 0.8665 (mtt) REVERT: C 205 GLU cc_start: 0.9003 (mt-10) cc_final: 0.8625 (mt-10) REVERT: C 227 MET cc_start: 0.8880 (tpp) cc_final: 0.8406 (tmm) REVERT: C 283 MET cc_start: 0.9125 (mmm) cc_final: 0.8847 (mmm) REVERT: C 311 ASP cc_start: 0.9142 (t0) cc_final: 0.8905 (t0) REVERT: C 325 MET cc_start: 0.8701 (ptp) cc_final: 0.8309 (ptt) outliers start: 4 outliers final: 3 residues processed: 58 average time/residue: 0.2376 time to fit residues: 20.7283 Evaluate side-chains 58 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 54 time to evaluate : 1.242 ------------------------------------------------------------------------------- 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 64 optimal weight: 4.9990 chunk 110 optimal weight: 5.9990 chunk 81 optimal weight: 0.1980 chunk 6 optimal weight: 2.9990 chunk 73 optimal weight: 2.9990 chunk 29 optimal weight: 2.9990 chunk 108 optimal weight: 0.4980 chunk 97 optimal weight: 0.9980 chunk 30 optimal weight: 2.9990 chunk 16 optimal weight: 0.0030 chunk 54 optimal weight: 3.9990 overall best weight: 0.9392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3296 r_free = 0.3296 target = 0.048112 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2786 r_free = 0.2786 target = 0.034455 restraints weight = 58486.031| |-----------------------------------------------------------------------------| r_work (start): 0.2763 rms_B_bonded: 4.03 r_work: 0.2605 rms_B_bonded: 4.73 restraints_weight: 0.5000 r_work (final): 0.2605 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8685 moved from start: 0.3338 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 10369 Z= 0.125 Angle : 0.525 8.538 14011 Z= 0.264 Chirality : 0.040 0.166 1530 Planarity : 0.003 0.045 1785 Dihedral : 8.039 114.265 1423 Min Nonbonded Distance : 1.988 Molprobity Statistics. All-atom Clashscore : 5.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Rotamer: Outliers : 0.46 % Allowed : 8.51 % Favored : 91.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.91 (0.25), residues: 1230 helix: 2.05 (0.21), residues: 618 sheet: 1.25 (0.42), residues: 160 loop : 0.26 (0.30), residues: 452 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 484 HIS 0.004 0.001 HIS A 81 PHE 0.011 0.001 PHE C 255 TYR 0.009 0.001 TYR A 10 ARG 0.002 0.000 ARG A 701 Details of bonding type rmsd link_TRANS : bond 0.00186 ( 2) link_TRANS : angle 0.88782 ( 6) hydrogen bonds : bond 0.03138 ( 519) hydrogen bonds : angle 4.38412 ( 1455) covalent geometry : bond 0.00281 (10367) covalent geometry : angle 0.52507 (14005) *********************** 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 : 1.289 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 57 SER cc_start: 0.8735 (OUTLIER) cc_final: 0.8324 (p) REVERT: B 93 PHE cc_start: 0.9430 (m-80) cc_final: 0.8847 (m-10) REVERT: B 120 MET cc_start: 0.8071 (mmt) cc_final: 0.7016 (mmm) REVERT: A 177 MET cc_start: 0.9410 (ptm) cc_final: 0.9074 (ppp) REVERT: A 305 MET cc_start: 0.9528 (tpp) cc_final: 0.9160 (tpp) REVERT: A 478 MET cc_start: 0.9239 (mmp) cc_final: 0.8942 (mmp) REVERT: C 190 MET cc_start: 0.9009 (mtp) cc_final: 0.8681 (mtt) REVERT: C 205 GLU cc_start: 0.9002 (mt-10) cc_final: 0.8623 (mt-10) REVERT: C 227 MET cc_start: 0.8885 (tpp) cc_final: 0.8415 (tmm) REVERT: C 283 MET cc_start: 0.9100 (mmm) cc_final: 0.8709 (mpp) REVERT: C 311 ASP cc_start: 0.9172 (t0) cc_final: 0.8937 (t0) outliers start: 5 outliers final: 4 residues processed: 57 average time/residue: 0.2338 time to fit residues: 20.4488 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 : 1.303 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 57 SER 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 116 optimal weight: 3.9990 chunk 19 optimal weight: 3.9990 chunk 105 optimal weight: 1.9990 chunk 79 optimal weight: 1.9990 chunk 18 optimal weight: 0.8980 chunk 30 optimal weight: 0.9990 chunk 65 optimal weight: 0.5980 chunk 82 optimal weight: 4.9990 chunk 74 optimal weight: 2.9990 chunk 26 optimal weight: 0.9980 chunk 45 optimal weight: 0.4980 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 72 ASN ** A 81 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.048264 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2797 r_free = 0.2797 target = 0.034696 restraints weight = 58296.150| |-----------------------------------------------------------------------------| r_work (start): 0.2772 rms_B_bonded: 4.01 r_work: 0.2612 rms_B_bonded: 4.72 restraints_weight: 0.5000 r_work (final): 0.2612 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8681 moved from start: 0.3402 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 10369 Z= 0.114 Angle : 0.523 8.121 14011 Z= 0.264 Chirality : 0.040 0.165 1530 Planarity : 0.003 0.045 1785 Dihedral : 7.972 112.946 1423 Min Nonbonded Distance : 1.998 Molprobity Statistics. All-atom Clashscore : 5.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Rotamer: Outliers : 0.65 % Allowed : 8.70 % Favored : 90.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.94 (0.25), residues: 1230 helix: 2.06 (0.21), residues: 619 sheet: 1.28 (0.42), residues: 160 loop : 0.27 (0.30), residues: 451 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 484 HIS 0.004 0.001 HIS A 81 PHE 0.010 0.001 PHE C 255 TYR 0.009 0.001 TYR A 10 ARG 0.005 0.000 ARG B 64 Details of bonding type rmsd link_TRANS : bond 0.00193 ( 2) link_TRANS : angle 0.88786 ( 6) hydrogen bonds : bond 0.03067 ( 519) hydrogen bonds : angle 4.36966 ( 1455) covalent geometry : bond 0.00254 (10367) covalent geometry : angle 0.52319 (14005) *********************** 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 61 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 54 time to evaluate : 1.201 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 93 PHE cc_start: 0.9432 (m-80) cc_final: 0.8850 (m-10) REVERT: B 120 MET cc_start: 0.8074 (mmt) cc_final: 0.7041 (mmm) REVERT: A 177 MET cc_start: 0.9411 (ptm) cc_final: 0.9044 (ppp) REVERT: A 305 MET cc_start: 0.9522 (tpp) cc_final: 0.9150 (tpp) REVERT: A 478 MET cc_start: 0.9216 (mmp) cc_final: 0.8912 (mmp) REVERT: A 759 LEU cc_start: 0.9635 (mt) cc_final: 0.9416 (tp) REVERT: C 190 MET cc_start: 0.9003 (mtp) cc_final: 0.8670 (mtt) REVERT: C 205 GLU cc_start: 0.9013 (mt-10) cc_final: 0.8653 (mt-10) REVERT: C 227 MET cc_start: 0.8887 (tpp) cc_final: 0.8420 (tmm) REVERT: C 311 ASP cc_start: 0.9168 (t0) cc_final: 0.8930 (t0) REVERT: C 325 MET cc_start: 0.8707 (ptp) cc_final: 0.8251 (ptt) outliers start: 7 outliers final: 6 residues processed: 59 average time/residue: 0.2150 time to fit residues: 19.4387 Evaluate side-chains 58 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 52 time to evaluate : 1.157 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 57 SER Chi-restraints excluded: chain A residue 72 ASN 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 22 optimal weight: 0.9990 chunk 36 optimal weight: 2.9990 chunk 52 optimal weight: 2.9990 chunk 84 optimal weight: 0.9980 chunk 54 optimal weight: 3.9990 chunk 45 optimal weight: 0.9990 chunk 89 optimal weight: 0.2980 chunk 17 optimal weight: 0.0570 chunk 81 optimal weight: 4.9990 chunk 68 optimal weight: 3.9990 chunk 62 optimal weight: 0.0670 overall best weight: 0.4838 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 72 ASN ** A 81 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.048603 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2813 r_free = 0.2813 target = 0.035067 restraints weight = 57920.828| |-----------------------------------------------------------------------------| r_work (start): 0.2789 rms_B_bonded: 4.01 r_work: 0.2631 rms_B_bonded: 4.71 restraints_weight: 0.5000 r_work (final): 0.2631 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8666 moved from start: 0.3524 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 10369 Z= 0.097 Angle : 0.531 8.889 14011 Z= 0.264 Chirality : 0.039 0.163 1530 Planarity : 0.003 0.046 1785 Dihedral : 7.895 108.094 1423 Min Nonbonded Distance : 2.006 Molprobity Statistics. All-atom Clashscore : 5.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Rotamer: Outliers : 0.65 % Allowed : 8.60 % Favored : 90.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.05 (0.25), residues: 1230 helix: 2.19 (0.22), residues: 607 sheet: 1.30 (0.42), residues: 160 loop : 0.34 (0.29), residues: 463 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 484 HIS 0.005 0.001 HIS A 81 PHE 0.009 0.001 PHE C 255 TYR 0.010 0.001 TYR A 127 ARG 0.003 0.000 ARG B 64 Details of bonding type rmsd link_TRANS : bond 0.00209 ( 2) link_TRANS : angle 0.90004 ( 6) hydrogen bonds : bond 0.02942 ( 519) hydrogen bonds : angle 4.31571 ( 1455) covalent geometry : bond 0.00215 (10367) covalent geometry : angle 0.53098 (14005) ********************** 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 63 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 56 time to evaluate : 1.193 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 61 LYS cc_start: 0.8971 (mmmt) cc_final: 0.8670 (ptpp) REVERT: B 93 PHE cc_start: 0.9424 (m-80) cc_final: 0.8815 (m-10) REVERT: B 120 MET cc_start: 0.8057 (mmt) cc_final: 0.7032 (mmm) REVERT: A 177 MET cc_start: 0.9411 (ptm) cc_final: 0.9050 (ppp) REVERT: A 305 MET cc_start: 0.9518 (tpp) cc_final: 0.9142 (tpp) REVERT: A 418 HIS cc_start: 0.9042 (OUTLIER) cc_final: 0.8670 (m-70) REVERT: A 478 MET cc_start: 0.9210 (mmp) cc_final: 0.8902 (mmp) REVERT: A 759 LEU cc_start: 0.9646 (mt) cc_final: 0.9430 (tp) REVERT: C 190 MET cc_start: 0.8987 (mtp) cc_final: 0.8655 (mtt) REVERT: C 205 GLU cc_start: 0.8981 (mt-10) cc_final: 0.8636 (mt-10) REVERT: C 227 MET cc_start: 0.8874 (tpp) cc_final: 0.8416 (tmm) REVERT: C 311 ASP cc_start: 0.9159 (t0) cc_final: 0.8921 (t0) REVERT: C 325 MET cc_start: 0.8717 (ptp) cc_final: 0.8261 (ptt) outliers start: 7 outliers final: 5 residues processed: 61 average time/residue: 0.2096 time to fit residues: 19.7573 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 : 1.182 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 57 SER Chi-restraints excluded: chain A residue 72 ASN 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 78 optimal weight: 1.9990 chunk 25 optimal weight: 0.0870 chunk 90 optimal weight: 0.4980 chunk 77 optimal weight: 4.9990 chunk 71 optimal weight: 1.9990 chunk 98 optimal weight: 0.7980 chunk 36 optimal weight: 0.6980 chunk 72 optimal weight: 0.7980 chunk 32 optimal weight: 0.9980 chunk 29 optimal weight: 0.9990 chunk 122 optimal weight: 0.7980 overall best weight: 0.5758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3310 r_free = 0.3310 target = 0.048574 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2814 r_free = 0.2814 target = 0.035095 restraints weight = 57628.401| |-----------------------------------------------------------------------------| r_work (start): 0.2789 rms_B_bonded: 3.98 r_work: 0.2630 rms_B_bonded: 4.71 restraints_weight: 0.5000 r_work (final): 0.2630 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8668 moved from start: 0.3590 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 10369 Z= 0.101 Angle : 0.530 8.870 14011 Z= 0.265 Chirality : 0.040 0.164 1530 Planarity : 0.003 0.045 1785 Dihedral : 7.841 105.606 1423 Min Nonbonded Distance : 2.006 Molprobity Statistics. All-atom Clashscore : 5.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Rotamer: Outliers : 0.46 % Allowed : 8.70 % Favored : 90.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.08 (0.25), residues: 1230 helix: 2.23 (0.22), residues: 606 sheet: 1.33 (0.42), residues: 160 loop : 0.34 (0.29), residues: 464 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 484 HIS 0.005 0.001 HIS A 81 PHE 0.019 0.001 PHE B 12 TYR 0.017 0.001 TYR C 279 ARG 0.002 0.000 ARG B 64 Details of bonding type rmsd link_TRANS : bond 0.00196 ( 2) link_TRANS : angle 0.87143 ( 6) hydrogen bonds : bond 0.02959 ( 519) hydrogen bonds : angle 4.28633 ( 1455) covalent geometry : bond 0.00225 (10367) covalent geometry : angle 0.52987 (14005) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5327.76 seconds wall clock time: 96 minutes 52.20 seconds (5812.20 seconds total)