Starting phenix.real_space_refine on Mon Jun 24 18:52:25 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jty_36656/06_2024/8jty_36656.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jty_36656/06_2024/8jty_36656.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.26 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jty_36656/06_2024/8jty_36656.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jty_36656/06_2024/8jty_36656.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jty_36656/06_2024/8jty_36656.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jty_36656/06_2024/8jty_36656.pdb" } resolution = 3.26 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= -0.004 sd= 0.184 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: 4 Type Number sf(0) Gaussians S 34 5.16 5 C 2785 2.51 5 N 703 2.21 5 O 752 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B GLU 46": "OE1" <-> "OE2" Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/chem_data/mon_lib" Total number of atoms: 4274 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 3366 Number of conformers: 1 Conformer: "" Number of residues, atoms: 448, 3366 Classifications: {'peptide': 448} Incomplete info: {'truncation_to_alanine': 21} Link IDs: {'PTRANS': 22, 'TRANS': 425} Chain breaks: 1 Unresolved non-hydrogen bonds: 83 Unresolved non-hydrogen angles: 108 Unresolved non-hydrogen dihedrals: 69 Unresolved non-hydrogen chiralities: 10 Planarities with less than four sites: {'ASP:plan': 2, 'TRP:plan': 1, 'HIS:plan': 1, 'PHE:plan': 1, 'GLU:plan': 2, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 44 Chain: "B" Number of atoms: 908 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 908 Classifications: {'peptide': 118} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 3, 'TRANS': 114} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Time building chain proxies: 3.07, per 1000 atoms: 0.72 Number of scatterers: 4274 At special positions: 0 Unit cell: (57.62, 84.28, 126.42, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 34 16.00 O 752 8.00 N 703 7.00 C 2785 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS A 50 " - pdb=" SG CYS A 121 " distance=2.03 Simple disulfide: pdb=" SG CYS A 62 " - pdb=" SG CYS A 102 " distance=2.03 Simple disulfide: pdb=" SG CYS A 88 " - pdb=" SG CYS A 142 " distance=2.03 Simple disulfide: pdb=" SG CYS B 22 " - pdb=" SG CYS B 95 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.52 Conformation dependent library (CDL) restraints added in 781.5 milliseconds 1120 Ramachandran restraints generated. 560 Oldfield, 0 Emsley, 560 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1024 Finding SS restraints... Secondary structure from input PDB file: 23 helices and 5 sheets defined 59.2% alpha, 11.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.45 Creating SS restraints... Processing helix chain 'A' and resid 21 through 33 Processing helix chain 'A' and resid 37 through 41 Processing helix chain 'A' and resid 54 through 62 removed outlier: 3.568A pdb=" N LEU A 58 " --> pdb=" O GLY A 54 " (cutoff:3.500A) Processing helix chain 'A' and resid 67 through 74 removed outlier: 4.253A pdb=" N ASN A 71 " --> pdb=" O ALA A 67 " (cutoff:3.500A) Processing helix chain 'A' and resid 104 through 110 Processing helix chain 'A' and resid 133 through 139 Processing helix chain 'A' and resid 141 through 147 removed outlier: 4.768A pdb=" N TRP A 146 " --> pdb=" O ALA A 143 " (cutoff:3.500A) Processing helix chain 'A' and resid 148 through 170 removed outlier: 4.250A pdb=" N GLN A 152 " --> pdb=" O LEU A 148 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N LEU A 155 " --> pdb=" O PHE A 151 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N SER A 163 " --> pdb=" O PHE A 159 " (cutoff:3.500A) removed outlier: 4.187A pdb=" N LEU A 164 " --> pdb=" O LEU A 160 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N GLY A 165 " --> pdb=" O PHE A 161 " (cutoff:3.500A) removed outlier: 4.710A pdb=" N GLY A 167 " --> pdb=" O SER A 163 " (cutoff:3.500A) removed outlier: 4.841A pdb=" N TYR A 168 " --> pdb=" O LEU A 164 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N PHE A 169 " --> pdb=" O GLY A 165 " (cutoff:3.500A) Processing helix chain 'A' and resid 176 through 195 removed outlier: 4.106A pdb=" N LEU A 180 " --> pdb=" O LYS A 176 " (cutoff:3.500A) Processing helix chain 'A' and resid 198 through 228 removed outlier: 3.751A pdb=" N MET A 202 " --> pdb=" O ASN A 198 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N LEU A 211 " --> pdb=" O LEU A 207 " (cutoff:3.500A) removed outlier: 4.291A pdb=" N VAL A 212 " --> pdb=" O LEU A 208 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N LYS A 214 " --> pdb=" O GLY A 210 " (cutoff:3.500A) removed outlier: 4.244A pdb=" N ALA A 219 " --> pdb=" O GLY A 215 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N GLY A 220 " --> pdb=" O ASN A 216 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N TYR A 221 " --> pdb=" O TRP A 217 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N VAL A 228 " --> pdb=" O ILE A 224 " (cutoff:3.500A) Processing helix chain 'A' and resid 229 through 231 No H-bonds generated for 'chain 'A' and resid 229 through 231' Processing helix chain 'A' and resid 232 through 258 removed outlier: 3.580A pdb=" N LEU A 251 " --> pdb=" O GLY A 247 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N THR A 252 " --> pdb=" O LEU A 248 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N GLY A 253 " --> pdb=" O VAL A 249 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N TYR A 256 " --> pdb=" O THR A 252 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N ALA A 257 " --> pdb=" O GLY A 253 " (cutoff:3.500A) Processing helix chain 'A' and resid 260 through 277 Proline residue: A 271 - end of helix removed outlier: 3.523A pdb=" N LEU A 276 " --> pdb=" O THR A 272 " (cutoff:3.500A) removed outlier: 4.586A pdb=" N LEU A 277 " --> pdb=" O PHE A 273 " (cutoff:3.500A) Processing helix chain 'A' and resid 333 through 338 removed outlier: 3.988A pdb=" N LEU A 337 " --> pdb=" O PHE A 334 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N PHE A 338 " --> pdb=" O ALA A 335 " (cutoff:3.500A) Processing helix chain 'A' and resid 342 through 369 removed outlier: 4.648A pdb=" N ARG A 346 " --> pdb=" O ARG A 342 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N THR A 347 " --> pdb=" O LEU A 343 " (cutoff:3.500A) removed outlier: 4.455A pdb=" N PHE A 348 " --> pdb=" O ARG A 344 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N MET A 351 " --> pdb=" O THR A 347 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N ILE A 365 " --> pdb=" O TYR A 361 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N LEU A 366 " --> pdb=" O GLN A 362 " (cutoff:3.500A) Processing helix chain 'A' and resid 374 through 384 Processing helix chain 'A' and resid 386 through 396 removed outlier: 3.771A pdb=" N ALA A 390 " --> pdb=" O GLU A 386 " (cutoff:3.500A) Processing helix chain 'A' and resid 403 through 420 removed outlier: 3.564A pdb=" N ALA A 413 " --> pdb=" O SER A 409 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N GLY A 414 " --> pdb=" O ASN A 410 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N ALA A 416 " --> pdb=" O LEU A 412 " (cutoff:3.500A) removed outlier: 4.248A pdb=" N CYS A 417 " --> pdb=" O ALA A 413 " (cutoff:3.500A) Processing helix chain 'A' and resid 430 through 457 removed outlier: 3.605A pdb=" N ALA A 445 " --> pdb=" O GLY A 441 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ILE A 446 " --> pdb=" O ILE A 442 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N GLN A 447 " --> pdb=" O THR A 443 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N MET A 448 " --> pdb=" O ILE A 444 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N ILE A 449 " --> pdb=" O ALA A 445 " (cutoff:3.500A) Processing helix chain 'A' and resid 458 through 487 removed outlier: 4.456A pdb=" N MET A 467 " --> pdb=" O ASN A 463 " (cutoff:3.500A) Proline residue: A 481 - end of helix Processing helix chain 'A' and resid 494 through 507 removed outlier: 3.790A pdb=" N LEU A 498 " --> pdb=" O LEU A 494 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N PHE A 499 " --> pdb=" O PRO A 495 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N ALA A 500 " --> pdb=" O LEU A 496 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ALA A 507 " --> pdb=" O GLY A 503 " (cutoff:3.500A) Processing helix chain 'A' and resid 509 through 513 Processing helix chain 'B' and resid 27 through 32 removed outlier: 3.701A pdb=" N TYR B 31 " --> pdb=" O THR B 27 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N GLU B 32 " --> pdb=" O ILE B 28 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 27 through 32' Processing sheet with id=AA1, first strand: chain 'A' and resid 48 through 49 Processing sheet with id=AA2, first strand: chain 'A' and resid 89 through 91 removed outlier: 3.860A pdb=" N ARG A 90 " --> pdb=" O GLY A 119 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N GLY A 119 " --> pdb=" O ARG A 90 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'B' and resid 5 through 6 removed outlier: 3.850A pdb=" N GLN B 5 " --> pdb=" O ALA B 23 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 57 through 59 removed outlier: 3.821A pdb=" N ASN B 58 " --> pdb=" O THR B 50 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N THR B 50 " --> pdb=" O ASN B 58 " (cutoff:3.500A) removed outlier: 5.245A pdb=" N PHE B 47 " --> pdb=" O ARG B 38 " (cutoff:3.500A) removed outlier: 5.928A pdb=" N ARG B 38 " --> pdb=" O PHE B 47 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N ALA B 49 " --> pdb=" O TRP B 36 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N ILE B 51 " --> pdb=" O MET B 34 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N MET B 34 " --> pdb=" O ILE B 51 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ALA B 96 " --> pdb=" O GLY B 35 " (cutoff:3.500A) removed outlier: 7.101A pdb=" N CYS B 95 " --> pdb=" O TRP B 112 " (cutoff:3.500A) removed outlier: 4.304A pdb=" N TRP B 112 " --> pdb=" O CYS B 95 " (cutoff:3.500A) removed outlier: 6.613A pdb=" N VAL B 97 " --> pdb=" O ILE B 110 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 57 through 59 removed outlier: 3.821A pdb=" N ASN B 58 " --> pdb=" O THR B 50 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N THR B 50 " --> pdb=" O ASN B 58 " (cutoff:3.500A) removed outlier: 5.245A pdb=" N PHE B 47 " --> pdb=" O ARG B 38 " (cutoff:3.500A) removed outlier: 5.928A pdb=" N ARG B 38 " --> pdb=" O PHE B 47 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N ALA B 49 " --> pdb=" O TRP B 36 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N ILE B 51 " --> pdb=" O MET B 34 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N MET B 34 " --> pdb=" O ILE B 51 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ALA B 96 " --> pdb=" O GLY B 35 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N ALA B 91 " --> pdb=" O VAL B 118 " (cutoff:3.500A) 217 hydrogen bonds defined for protein. 615 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: 1.09 Time building geometry restraints manager: 1.69 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 1342 1.34 - 1.46: 1033 1.46 - 1.58: 1953 1.58 - 1.70: 0 1.70 - 1.81: 51 Bond restraints: 4379 Sorted by residual: bond pdb=" CD2 TRP A 125 " pdb=" CE2 TRP A 125 " ideal model delta sigma weight residual 1.409 1.464 -0.055 1.70e-02 3.46e+03 1.04e+01 bond pdb=" CA TRP A 64 " pdb=" C TRP A 64 " ideal model delta sigma weight residual 1.524 1.497 0.026 1.27e-02 6.20e+03 4.34e+00 bond pdb=" CG TRP A 125 " pdb=" CD2 TRP A 125 " ideal model delta sigma weight residual 1.433 1.469 -0.036 1.80e-02 3.09e+03 3.93e+00 bond pdb=" NE1 TRP A 125 " pdb=" CE2 TRP A 125 " ideal model delta sigma weight residual 1.370 1.350 0.020 1.10e-02 8.26e+03 3.22e+00 bond pdb=" CA TRP A 125 " pdb=" C TRP A 125 " ideal model delta sigma weight residual 1.523 1.500 0.023 1.34e-02 5.57e+03 2.97e+00 ... (remaining 4374 not shown) Histogram of bond angle deviations from ideal: 100.10 - 107.03: 132 107.03 - 113.95: 2423 113.95 - 120.87: 2096 120.87 - 127.80: 1277 127.80 - 134.72: 42 Bond angle restraints: 5970 Sorted by residual: angle pdb=" C SER A 65 " pdb=" N PRO A 66 " pdb=" CA PRO A 66 " ideal model delta sigma weight residual 119.32 114.35 4.97 1.14e+00 7.69e-01 1.90e+01 angle pdb=" N ASP A 398 " pdb=" CA ASP A 398 " pdb=" CB ASP A 398 " ideal model delta sigma weight residual 114.17 109.80 4.37 1.14e+00 7.69e-01 1.47e+01 angle pdb=" N ALA A 143 " pdb=" CA ALA A 143 " pdb=" C ALA A 143 " ideal model delta sigma weight residual 112.87 117.41 -4.54 1.20e+00 6.94e-01 1.43e+01 angle pdb=" N LEU A 70 " pdb=" CA LEU A 70 " pdb=" C LEU A 70 " ideal model delta sigma weight residual 110.97 106.92 4.05 1.09e+00 8.42e-01 1.38e+01 angle pdb=" N TRP A 125 " pdb=" CA TRP A 125 " pdb=" C TRP A 125 " ideal model delta sigma weight residual 110.80 117.12 -6.32 2.13e+00 2.20e-01 8.80e+00 ... (remaining 5965 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.80: 2203 17.80 - 35.59: 243 35.59 - 53.39: 81 53.39 - 71.18: 5 71.18 - 88.98: 7 Dihedral angle restraints: 2539 sinusoidal: 929 harmonic: 1610 Sorted by residual: dihedral pdb=" CB CYS A 62 " pdb=" SG CYS A 62 " pdb=" SG CYS A 102 " pdb=" CB CYS A 102 " ideal model delta sinusoidal sigma weight residual -86.00 -127.01 41.01 1 1.00e+01 1.00e-02 2.36e+01 dihedral pdb=" CB CYS A 88 " pdb=" SG CYS A 88 " pdb=" SG CYS A 142 " pdb=" CB CYS A 142 " ideal model delta sinusoidal sigma weight residual -86.00 -117.68 31.68 1 1.00e+01 1.00e-02 1.43e+01 dihedral pdb=" CA ASN A 453 " pdb=" CB ASN A 453 " pdb=" CG ASN A 453 " pdb=" OD1 ASN A 453 " ideal model delta sinusoidal sigma weight residual 120.00 -166.22 -73.78 2 2.00e+01 2.50e-03 1.11e+01 ... (remaining 2536 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.033: 455 0.033 - 0.066: 172 0.066 - 0.100: 36 0.100 - 0.133: 22 0.133 - 0.166: 3 Chirality restraints: 688 Sorted by residual: chirality pdb=" CA TRP A 125 " pdb=" N TRP A 125 " pdb=" C TRP A 125 " pdb=" CB TRP A 125 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.17 2.00e-01 2.50e+01 6.90e-01 chirality pdb=" CA ALA A 143 " pdb=" N ALA A 143 " pdb=" C ALA A 143 " pdb=" CB ALA A 143 " both_signs ideal model delta sigma weight residual False 2.48 2.34 0.15 2.00e-01 2.50e+01 5.54e-01 chirality pdb=" CB THR A 45 " pdb=" CA THR A 45 " pdb=" OG1 THR A 45 " pdb=" CG2 THR A 45 " both_signs ideal model delta sigma weight residual False 2.55 2.41 0.14 2.00e-01 2.50e+01 4.99e-01 ... (remaining 685 not shown) Planarity restraints: 751 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU A 270 " -0.038 5.00e-02 4.00e+02 5.72e-02 5.24e+00 pdb=" N PRO A 271 " 0.099 5.00e-02 4.00e+02 pdb=" CA PRO A 271 " -0.029 5.00e-02 4.00e+02 pdb=" CD PRO A 271 " -0.032 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ASP A 398 " 0.011 2.00e-02 2.50e+03 2.28e-02 5.19e+00 pdb=" C ASP A 398 " -0.039 2.00e-02 2.50e+03 pdb=" O ASP A 398 " 0.015 2.00e-02 2.50e+03 pdb=" N ARG A 399 " 0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL A 37 " 0.007 2.00e-02 2.50e+03 1.33e-02 1.78e+00 pdb=" C VAL A 37 " -0.023 2.00e-02 2.50e+03 pdb=" O VAL A 37 " 0.008 2.00e-02 2.50e+03 pdb=" N GLY A 38 " 0.008 2.00e-02 2.50e+03 ... (remaining 748 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.75: 563 2.75 - 3.29: 3887 3.29 - 3.83: 6527 3.83 - 4.36: 6841 4.36 - 4.90: 12819 Nonbonded interactions: 30637 Sorted by model distance: nonbonded pdb=" O GLY A 476 " pdb=" OG1 THR A 480 " model vdw 2.217 2.440 nonbonded pdb=" OG SER B 7 " pdb=" OG SER B 21 " model vdw 2.300 2.440 nonbonded pdb=" OH TYR B 37 " pdb=" O TRP B 106 " model vdw 2.338 2.440 nonbonded pdb=" OG SER A 52 " pdb=" NH2 ARG A 90 " model vdw 2.351 2.520 nonbonded pdb=" N GLU B 32 " pdb=" OE1 GLU B 32 " model vdw 2.361 2.520 ... (remaining 30632 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== 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: 1.070 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 3.690 Check model and map are aligned: 0.030 Set scattering table: 0.050 Process input model: 15.850 Find NCS groups from input model: 0.110 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.700 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.520 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7483 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 : 0.003 0.055 4379 Z= 0.191 Angle : 0.547 8.455 5970 Z= 0.301 Chirality : 0.040 0.166 688 Planarity : 0.004 0.057 751 Dihedral : 16.261 88.975 1503 Min Nonbonded Distance : 2.217 Molprobity Statistics. All-atom Clashscore : 4.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.00 % Favored : 95.00 % Rotamer: Outliers : 0.00 % Allowed : 23.41 % Favored : 76.59 % 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: -0.56 (0.36), residues: 560 helix: 0.66 (0.31), residues: 305 sheet: 0.52 (0.78), residues: 53 loop : -2.26 (0.38), residues: 202 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 261 HIS 0.001 0.001 HIS A 367 PHE 0.014 0.001 PHE A 275 TYR 0.007 0.001 TYR A 91 ARG 0.002 0.000 ARG B 45 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1120 Ramachandran restraints generated. 560 Oldfield, 0 Emsley, 560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1120 Ramachandran restraints generated. 560 Oldfield, 0 Emsley, 560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 50 residues out of total 464 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 50 time to evaluate : 0.428 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 50 average time/residue: 0.1818 time to fit residues: 11.5939 Evaluate side-chains 48 residues out of total 464 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 48 time to evaluate : 0.436 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 46 optimal weight: 2.9990 chunk 41 optimal weight: 0.8980 chunk 23 optimal weight: 0.0010 chunk 14 optimal weight: 1.9990 chunk 28 optimal weight: 0.7980 chunk 22 optimal weight: 1.9990 chunk 43 optimal weight: 1.9990 chunk 16 optimal weight: 0.6980 chunk 26 optimal weight: 0.0770 chunk 32 optimal weight: 1.9990 chunk 49 optimal weight: 5.9990 overall best weight: 0.4944 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7453 moved from start: 0.0711 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 4379 Z= 0.158 Angle : 0.498 7.659 5970 Z= 0.256 Chirality : 0.039 0.132 688 Planarity : 0.004 0.054 751 Dihedral : 3.676 13.518 610 Min Nonbonded Distance : 2.239 Molprobity Statistics. All-atom Clashscore : 2.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.82 % Favored : 95.18 % Rotamer: Outliers : 2.27 % Allowed : 21.59 % Favored : 76.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.30 (0.36), residues: 560 helix: 0.91 (0.31), residues: 315 sheet: 0.56 (0.77), residues: 53 loop : -2.35 (0.39), residues: 192 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 261 HIS 0.001 0.000 HIS A 49 PHE 0.016 0.001 PHE A 275 TYR 0.006 0.001 TYR A 91 ARG 0.002 0.000 ARG A 402 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1120 Ramachandran restraints generated. 560 Oldfield, 0 Emsley, 560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1120 Ramachandran restraints generated. 560 Oldfield, 0 Emsley, 560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 59 residues out of total 464 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 49 time to evaluate : 0.414 Fit side-chains REVERT: A 239 MET cc_start: 0.7118 (mmp) cc_final: 0.6656 (mmt) REVERT: A 398 ASP cc_start: 0.7496 (t0) cc_final: 0.7273 (t0) outliers start: 10 outliers final: 5 residues processed: 56 average time/residue: 0.1459 time to fit residues: 10.7269 Evaluate side-chains 53 residues out of total 464 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 48 time to evaluate : 0.416 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 45 THR Chi-restraints excluded: chain A residue 487 LEU Chi-restraints excluded: chain B residue 46 GLU Chi-restraints excluded: chain B residue 69 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 27 optimal weight: 0.2980 chunk 15 optimal weight: 7.9990 chunk 41 optimal weight: 0.9980 chunk 34 optimal weight: 0.6980 chunk 13 optimal weight: 2.9990 chunk 50 optimal weight: 7.9990 chunk 54 optimal weight: 3.9990 chunk 44 optimal weight: 3.9990 chunk 49 optimal weight: 0.7980 chunk 17 optimal weight: 0.9990 chunk 40 optimal weight: 3.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7497 moved from start: 0.0940 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 4379 Z= 0.183 Angle : 0.508 7.283 5970 Z= 0.260 Chirality : 0.039 0.134 688 Planarity : 0.004 0.054 751 Dihedral : 3.672 13.358 610 Min Nonbonded Distance : 2.250 Molprobity Statistics. All-atom Clashscore : 2.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.82 % Favored : 95.18 % Rotamer: Outliers : 3.18 % Allowed : 20.68 % Favored : 76.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.21 (0.36), residues: 560 helix: 0.99 (0.31), residues: 315 sheet: 0.60 (0.77), residues: 51 loop : -2.30 (0.39), residues: 194 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 261 HIS 0.001 0.000 HIS A 49 PHE 0.017 0.001 PHE A 275 TYR 0.006 0.001 TYR A 91 ARG 0.002 0.000 ARG B 45 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1120 Ramachandran restraints generated. 560 Oldfield, 0 Emsley, 560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1120 Ramachandran restraints generated. 560 Oldfield, 0 Emsley, 560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 63 residues out of total 464 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 49 time to evaluate : 0.423 Fit side-chains REVERT: A 398 ASP cc_start: 0.7581 (t0) cc_final: 0.7351 (t0) outliers start: 14 outliers final: 7 residues processed: 59 average time/residue: 0.1549 time to fit residues: 11.9376 Evaluate side-chains 56 residues out of total 464 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 49 time to evaluate : 0.431 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 45 THR Chi-restraints excluded: chain A residue 140 LEU Chi-restraints excluded: chain A residue 269 SER Chi-restraints excluded: chain A residue 273 PHE Chi-restraints excluded: chain A residue 487 LEU Chi-restraints excluded: chain B residue 46 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 49 optimal weight: 4.9990 chunk 37 optimal weight: 2.9990 chunk 25 optimal weight: 0.0570 chunk 5 optimal weight: 7.9990 chunk 23 optimal weight: 2.9990 chunk 33 optimal weight: 0.3980 chunk 50 optimal weight: 1.9990 chunk 53 optimal weight: 0.8980 chunk 26 optimal weight: 2.9990 chunk 47 optimal weight: 1.9990 chunk 14 optimal weight: 0.1980 overall best weight: 0.7100 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7490 moved from start: 0.1099 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 4379 Z= 0.175 Angle : 0.521 7.392 5970 Z= 0.259 Chirality : 0.039 0.133 688 Planarity : 0.004 0.054 751 Dihedral : 3.631 13.620 610 Min Nonbonded Distance : 2.247 Molprobity Statistics. All-atom Clashscore : 3.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.82 % Favored : 95.18 % Rotamer: Outliers : 3.18 % Allowed : 21.36 % Favored : 75.45 % 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: -0.15 (0.37), residues: 560 helix: 1.08 (0.31), residues: 315 sheet: 0.58 (0.77), residues: 51 loop : -2.35 (0.39), residues: 194 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 261 HIS 0.001 0.000 HIS A 49 PHE 0.017 0.001 PHE A 275 TYR 0.005 0.001 TYR A 91 ARG 0.001 0.000 ARG A 402 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1120 Ramachandran restraints generated. 560 Oldfield, 0 Emsley, 560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1120 Ramachandran restraints generated. 560 Oldfield, 0 Emsley, 560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 64 residues out of total 464 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 50 time to evaluate : 0.467 Fit side-chains REVERT: A 239 MET cc_start: 0.6941 (mmp) cc_final: 0.6507 (mmt) REVERT: A 398 ASP cc_start: 0.7584 (t0) cc_final: 0.7356 (t0) outliers start: 14 outliers final: 9 residues processed: 61 average time/residue: 0.1472 time to fit residues: 11.7896 Evaluate side-chains 59 residues out of total 464 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 50 time to evaluate : 0.433 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 45 THR Chi-restraints excluded: chain A residue 58 LEU Chi-restraints excluded: chain A residue 140 LEU Chi-restraints excluded: chain A residue 273 PHE Chi-restraints excluded: chain A residue 358 SER Chi-restraints excluded: chain A residue 487 LEU Chi-restraints excluded: chain B residue 46 GLU Chi-restraints excluded: chain B residue 50 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 44 optimal weight: 0.2980 chunk 30 optimal weight: 0.9980 chunk 0 optimal weight: 10.0000 chunk 39 optimal weight: 0.9980 chunk 21 optimal weight: 3.9990 chunk 45 optimal weight: 6.9990 chunk 36 optimal weight: 0.6980 chunk 27 optimal weight: 0.2980 chunk 47 optimal weight: 2.9990 chunk 13 optimal weight: 0.6980 chunk 17 optimal weight: 0.4980 overall best weight: 0.4980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7455 moved from start: 0.1184 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 4379 Z= 0.150 Angle : 0.494 7.465 5970 Z= 0.246 Chirality : 0.038 0.126 688 Planarity : 0.004 0.055 751 Dihedral : 3.512 13.709 610 Min Nonbonded Distance : 2.242 Molprobity Statistics. All-atom Clashscore : 3.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.82 % Favored : 95.18 % Rotamer: Outliers : 3.18 % Allowed : 21.36 % Favored : 75.45 % 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: -0.01 (0.37), residues: 560 helix: 1.22 (0.31), residues: 315 sheet: 0.65 (0.78), residues: 51 loop : -2.34 (0.39), residues: 194 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 261 HIS 0.001 0.000 HIS A 49 PHE 0.017 0.001 PHE A 275 TYR 0.004 0.001 TYR A 91 ARG 0.001 0.000 ARG B 45 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1120 Ramachandran restraints generated. 560 Oldfield, 0 Emsley, 560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1120 Ramachandran restraints generated. 560 Oldfield, 0 Emsley, 560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 64 residues out of total 464 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 50 time to evaluate : 0.448 Fit side-chains REVERT: A 398 ASP cc_start: 0.7529 (t0) cc_final: 0.7325 (t0) outliers start: 14 outliers final: 9 residues processed: 60 average time/residue: 0.1560 time to fit residues: 12.3984 Evaluate side-chains 59 residues out of total 464 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 50 time to evaluate : 0.435 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 THR Chi-restraints excluded: chain A residue 58 LEU Chi-restraints excluded: chain A residue 140 LEU Chi-restraints excluded: chain A residue 269 SER Chi-restraints excluded: chain A residue 273 PHE Chi-restraints excluded: chain A residue 358 SER Chi-restraints excluded: chain A residue 442 ILE Chi-restraints excluded: chain A residue 487 LEU Chi-restraints excluded: chain B residue 46 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 47 optimal weight: 1.9990 chunk 10 optimal weight: 0.9980 chunk 31 optimal weight: 1.9990 chunk 13 optimal weight: 0.7980 chunk 53 optimal weight: 0.8980 chunk 44 optimal weight: 3.9990 chunk 24 optimal weight: 0.9990 chunk 4 optimal weight: 0.9990 chunk 17 optimal weight: 4.9990 chunk 27 optimal weight: 0.5980 chunk 51 optimal weight: 5.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7512 moved from start: 0.1265 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 4379 Z= 0.192 Angle : 0.525 7.168 5970 Z= 0.263 Chirality : 0.039 0.134 688 Planarity : 0.004 0.053 751 Dihedral : 3.641 13.575 610 Min Nonbonded Distance : 2.245 Molprobity Statistics. All-atom Clashscore : 3.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.36 % Favored : 94.64 % Rotamer: Outliers : 3.41 % Allowed : 20.45 % Favored : 76.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.14 (0.37), residues: 560 helix: 1.12 (0.31), residues: 315 sheet: 0.34 (0.75), residues: 53 loop : -2.36 (0.39), residues: 192 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 261 HIS 0.001 0.000 HIS A 49 PHE 0.017 0.001 PHE A 275 TYR 0.005 0.001 TYR A 91 ARG 0.002 0.000 ARG B 45 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1120 Ramachandran restraints generated. 560 Oldfield, 0 Emsley, 560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1120 Ramachandran restraints generated. 560 Oldfield, 0 Emsley, 560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 69 residues out of total 464 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 54 time to evaluate : 0.460 Fit side-chains REVERT: A 398 ASP cc_start: 0.7588 (t0) cc_final: 0.7375 (t0) outliers start: 15 outliers final: 11 residues processed: 66 average time/residue: 0.1480 time to fit residues: 13.0258 Evaluate side-chains 63 residues out of total 464 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 52 time to evaluate : 0.452 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 THR Chi-restraints excluded: chain A residue 58 LEU Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 140 LEU Chi-restraints excluded: chain A residue 269 SER Chi-restraints excluded: chain A residue 273 PHE Chi-restraints excluded: chain A residue 358 SER Chi-restraints excluded: chain A residue 487 LEU Chi-restraints excluded: chain B residue 46 GLU Chi-restraints excluded: chain B residue 50 THR Chi-restraints excluded: chain B residue 69 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 5 optimal weight: 0.6980 chunk 30 optimal weight: 0.6980 chunk 38 optimal weight: 0.6980 chunk 44 optimal weight: 0.6980 chunk 29 optimal weight: 0.9980 chunk 53 optimal weight: 1.9990 chunk 33 optimal weight: 0.4980 chunk 32 optimal weight: 0.8980 chunk 24 optimal weight: 0.8980 chunk 21 optimal weight: 3.9990 chunk 31 optimal weight: 0.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7487 moved from start: 0.1281 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 4379 Z= 0.166 Angle : 0.499 7.316 5970 Z= 0.252 Chirality : 0.039 0.129 688 Planarity : 0.004 0.055 751 Dihedral : 3.584 13.835 610 Min Nonbonded Distance : 2.241 Molprobity Statistics. All-atom Clashscore : 3.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.82 % Favored : 95.18 % Rotamer: Outliers : 3.18 % Allowed : 20.91 % Favored : 75.91 % 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: -0.07 (0.37), residues: 560 helix: 1.19 (0.31), residues: 315 sheet: 0.41 (0.75), residues: 53 loop : -2.36 (0.39), residues: 192 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 261 HIS 0.001 0.000 HIS A 49 PHE 0.017 0.001 PHE A 275 TYR 0.005 0.001 TYR A 457 ARG 0.001 0.000 ARG B 45 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1120 Ramachandran restraints generated. 560 Oldfield, 0 Emsley, 560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1120 Ramachandran restraints generated. 560 Oldfield, 0 Emsley, 560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 63 residues out of total 464 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 49 time to evaluate : 0.462 Fit side-chains outliers start: 14 outliers final: 11 residues processed: 59 average time/residue: 0.1628 time to fit residues: 12.6729 Evaluate side-chains 60 residues out of total 464 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 49 time to evaluate : 0.451 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 THR Chi-restraints excluded: chain A residue 58 LEU Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 140 LEU Chi-restraints excluded: chain A residue 269 SER Chi-restraints excluded: chain A residue 273 PHE Chi-restraints excluded: chain A residue 358 SER Chi-restraints excluded: chain A residue 487 LEU Chi-restraints excluded: chain B residue 46 GLU Chi-restraints excluded: chain B residue 50 THR Chi-restraints excluded: chain B residue 69 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 15 optimal weight: 5.9990 chunk 10 optimal weight: 0.0040 chunk 33 optimal weight: 0.6980 chunk 36 optimal weight: 0.5980 chunk 26 optimal weight: 0.0010 chunk 4 optimal weight: 10.0000 chunk 41 optimal weight: 1.9990 chunk 48 optimal weight: 0.0370 chunk 50 optimal weight: 2.9990 chunk 46 optimal weight: 0.6980 chunk 49 optimal weight: 2.9990 overall best weight: 0.2676 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7414 moved from start: 0.1420 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 4379 Z= 0.133 Angle : 0.476 7.682 5970 Z= 0.240 Chirality : 0.037 0.122 688 Planarity : 0.004 0.056 751 Dihedral : 3.428 13.852 610 Min Nonbonded Distance : 2.242 Molprobity Statistics. All-atom Clashscore : 3.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.64 % Favored : 95.36 % Rotamer: Outliers : 2.27 % Allowed : 21.82 % Favored : 75.91 % 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: 0.17 (0.37), residues: 560 helix: 1.48 (0.32), residues: 307 sheet: 0.44 (0.75), residues: 53 loop : -2.26 (0.39), residues: 200 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 261 HIS 0.001 0.000 HIS A 367 PHE 0.018 0.001 PHE A 275 TYR 0.005 0.000 TYR A 457 ARG 0.002 0.000 ARG A 399 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1120 Ramachandran restraints generated. 560 Oldfield, 0 Emsley, 560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1120 Ramachandran restraints generated. 560 Oldfield, 0 Emsley, 560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 57 residues out of total 464 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 47 time to evaluate : 0.427 Fit side-chains REVERT: A 200 MET cc_start: 0.7349 (tpt) cc_final: 0.7072 (mmt) outliers start: 10 outliers final: 9 residues processed: 54 average time/residue: 0.1512 time to fit residues: 10.7061 Evaluate side-chains 55 residues out of total 464 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 46 time to evaluate : 0.494 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 THR Chi-restraints excluded: chain A residue 58 LEU Chi-restraints excluded: chain A residue 128 ASP Chi-restraints excluded: chain A residue 140 LEU Chi-restraints excluded: chain A residue 273 PHE Chi-restraints excluded: chain A residue 358 SER Chi-restraints excluded: chain A residue 364 LEU Chi-restraints excluded: chain A residue 442 ILE Chi-restraints excluded: chain B residue 46 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/cctbx_project/iotbx/cli_parser.py", line 946, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/phenix/phenix/programs/real_space_refine.py", line 200, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 700, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 764, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1477, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1379, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1260, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 50.9545 > 50: distance: 41 - 57: 4.637 distance: 46 - 64: 12.306 distance: 50 - 72: 11.159 distance: 54 - 77: 12.282 distance: 57 - 58: 6.129 distance: 58 - 59: 3.004 distance: 58 - 61: 3.959 distance: 59 - 60: 7.500 distance: 59 - 64: 8.263 distance: 60 - 86: 24.425 distance: 61 - 62: 5.668 distance: 61 - 63: 21.854 distance: 65 - 66: 8.731 distance: 65 - 68: 12.654 distance: 66 - 72: 3.433 distance: 67 - 94: 12.050 distance: 68 - 69: 5.732 distance: 69 - 70: 13.038 distance: 69 - 71: 17.161 distance: 72 - 73: 5.615 distance: 73 - 74: 10.599 distance: 73 - 76: 4.282 distance: 74 - 75: 13.921 distance: 74 - 77: 3.252 distance: 77 - 78: 4.619 distance: 78 - 79: 9.745 distance: 78 - 81: 6.901 distance: 79 - 80: 11.933 distance: 79 - 86: 13.744 distance: 81 - 82: 7.065 distance: 82 - 83: 7.172 distance: 83 - 85: 6.381 distance: 86 - 87: 14.682 distance: 87 - 88: 23.992 distance: 87 - 90: 13.645 distance: 88 - 89: 13.377 distance: 88 - 94: 13.400 distance: 90 - 91: 4.097 distance: 91 - 92: 13.123 distance: 91 - 93: 16.681 distance: 94 - 95: 13.512 distance: 95 - 96: 10.023 distance: 95 - 98: 5.325 distance: 96 - 97: 12.897 distance: 96 - 106: 18.762 distance: 98 - 99: 4.601 distance: 99 - 100: 10.666 distance: 99 - 101: 14.135 distance: 100 - 102: 6.906 distance: 101 - 103: 5.808 distance: 102 - 104: 14.984 distance: 103 - 104: 17.183 distance: 106 - 107: 14.801 distance: 106 - 112: 31.671 distance: 107 - 108: 10.218 distance: 107 - 110: 21.423 distance: 108 - 109: 13.542 distance: 108 - 113: 13.595 distance: 109 - 132: 26.979 distance: 110 - 111: 26.212 distance: 111 - 112: 11.927 distance: 113 - 114: 12.260 distance: 114 - 115: 3.583 distance: 114 - 117: 9.421 distance: 115 - 116: 6.629 distance: 115 - 120: 5.117 distance: 116 - 142: 7.778 distance: 117 - 118: 4.548 distance: 117 - 119: 10.741 distance: 120 - 121: 6.470 distance: 121 - 122: 6.294 distance: 121 - 124: 8.291 distance: 122 - 123: 5.933 distance: 122 - 125: 5.238 distance: 123 - 149: 10.887 distance: 125 - 126: 3.689 distance: 126 - 127: 6.807 distance: 126 - 129: 12.259 distance: 127 - 128: 9.352 distance: 127 - 132: 12.590 distance: 128 - 157: 23.162 distance: 129 - 130: 8.562 distance: 129 - 131: 12.048