Starting phenix.real_space_refine on Wed Mar 12 18:20:15 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7z24_14457/03_2025/7z24_14457.cif Found real_map, /net/cci-nas-00/data/ceres_data/7z24_14457/03_2025/7z24_14457.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.32 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7z24_14457/03_2025/7z24_14457.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7z24_14457/03_2025/7z24_14457.map" model { file = "/net/cci-nas-00/data/ceres_data/7z24_14457/03_2025/7z24_14457.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7z24_14457/03_2025/7z24_14457.cif" } resolution = 3.32 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= 0.024 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 35 5.49 5 S 13 5.16 5 C 5266 2.51 5 N 1378 2.21 5 O 1611 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 9 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib" Total number of atoms: 8303 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 4260 Number of conformers: 1 Conformer: "" Number of residues, atoms: 527, 4260 Classifications: {'peptide': 527} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PCIS': 2, 'PTRANS': 34, 'TRANS': 490} Chain breaks: 2 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 30 Unresolved non-hydrogen angles: 37 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 11 Chain: "B" Number of atoms: 3303 Number of conformers: 1 Conformer: "" Number of residues, atoms: 402, 3303 Classifications: {'peptide': 402} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 30, 'TRANS': 371} Chain breaks: 2 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 22 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 19 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 2} Unresolved non-hydrogen planarities: 10 Chain: "E" Number of atoms: 720 Number of conformers: 1 Conformer: "" Number of residues, atoms: 36, 720 Classifications: {'DNA': 34, 'RNA': 2} Modifications used: {'5*END': 1, 'rna3p': 2} Link IDs: {'rna3p': 35} Unresolved chain link angles: 1 Unresolved chain link dihedrals: 2 Unresolved non-hydrogen bonds: 22 Unresolved non-hydrogen angles: 35 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {' DA%5*END:plan2': 1, ' DA%5*END:plan': 1} Unresolved non-hydrogen planarities: 13 Chain: "A" Number of atoms: 20 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 20 Unusual residues: {'NVP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 6.02, per 1000 atoms: 0.73 Number of scatterers: 8303 At special positions: 0 Unit cell: (97, 109.61, 101.85, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 13 16.00 P 35 15.00 O 1611 8.00 N 1378 7.00 C 5266 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 Time building additional restraints: 3.31 Conformation dependent library (CDL) restraints added in 1.6 seconds 1834 Ramachandran restraints generated. 917 Oldfield, 0 Emsley, 917 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1750 Finding SS restraints... Secondary structure from input PDB file: 32 helices and 11 sheets defined 39.8% alpha, 15.7% beta 13 base pairs and 26 stacking pairs defined. Time for finding SS restraints: 3.19 Creating SS restraints... Processing helix chain 'A' and resid 27 through 45 removed outlier: 3.931A pdb=" N VAL A 35 " --> pdb=" O ILE A 31 " (cutoff:3.500A) removed outlier: 4.655A pdb=" N GLU A 36 " --> pdb=" O LYS A 32 " (cutoff:3.500A) removed outlier: 4.864A pdb=" N ILE A 37 " --> pdb=" O ALA A 33 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N GLU A 44 " --> pdb=" O GLU A 40 " (cutoff:3.500A) Processing helix chain 'A' and resid 77 through 84 Processing helix chain 'A' and resid 96 through 100 Processing helix chain 'A' and resid 113 through 117 Processing helix chain 'A' and resid 121 through 127 removed outlier: 4.340A pdb=" N LYS A 126 " --> pdb=" O ASP A 123 " (cutoff:3.500A) Processing helix chain 'A' and resid 155 through 175 Proline residue: A 170 - end of helix Processing helix chain 'A' and resid 194 through 212 removed outlier: 3.580A pdb=" N THR A 200 " --> pdb=" O GLY A 196 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N TRP A 212 " --> pdb=" O HIS A 208 " (cutoff:3.500A) Processing helix chain 'A' and resid 218 through 222 Processing helix chain 'A' and resid 253 through 268 Processing helix chain 'A' and resid 276 through 282 removed outlier: 3.917A pdb=" N LEU A 282 " --> pdb=" O GLN A 278 " (cutoff:3.500A) Processing helix chain 'A' and resid 296 through 312 removed outlier: 4.529A pdb=" N GLU A 312 " --> pdb=" O GLU A 308 " (cutoff:3.500A) Processing helix chain 'A' and resid 363 through 384 Processing helix chain 'A' and resid 394 through 405 Processing helix chain 'A' and resid 473 through 488 removed outlier: 4.006A pdb=" N ILE A 482 " --> pdb=" O GLU A 478 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N TYR A 483 " --> pdb=" O LEU A 479 " (cutoff:3.500A) Processing helix chain 'A' and resid 499 through 508 removed outlier: 3.891A pdb=" N ALA A 508 " --> pdb=" O GLY A 504 " (cutoff:3.500A) Processing helix chain 'A' and resid 515 through 528 removed outlier: 3.602A pdb=" N LYS A 527 " --> pdb=" O GLU A 523 " (cutoff:3.500A) Processing helix chain 'A' and resid 542 through 546 removed outlier: 3.576A pdb=" N GLU A 546 " --> pdb=" O GLY A 543 " (cutoff:3.500A) Processing helix chain 'B' and resid 27 through 44 removed outlier: 3.528A pdb=" N LEU B 34 " --> pdb=" O LYS B 30 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N LYS B 43 " --> pdb=" O THR B 39 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N GLU B 44 " --> pdb=" O GLU B 40 " (cutoff:3.500A) Processing helix chain 'B' and resid 77 through 85 Processing helix chain 'B' and resid 85 through 90 Processing helix chain 'B' and resid 98 through 102 removed outlier: 3.650A pdb=" N LYS B 101 " --> pdb=" O ALA B 98 " (cutoff:3.500A) Processing helix chain 'B' and resid 112 through 117 removed outlier: 3.823A pdb=" N SER B 117 " --> pdb=" O ALA B 114 " (cutoff:3.500A) Processing helix chain 'B' and resid 124 through 129 removed outlier: 3.853A pdb=" N ALA B 129 " --> pdb=" O LYS B 126 " (cutoff:3.500A) Processing helix chain 'B' and resid 134 through 138 Processing helix chain 'B' and resid 155 through 160 Processing helix chain 'B' and resid 160 through 173 Proline residue: B 170 - end of helix Processing helix chain 'B' and resid 194 through 212 removed outlier: 3.524A pdb=" N THR B 200 " --> pdb=" O GLY B 196 " (cutoff:3.500A) Processing helix chain 'B' and resid 254 through 271 removed outlier: 4.251A pdb=" N GLN B 269 " --> pdb=" O ASN B 265 " (cutoff:3.500A) removed outlier: 4.243A pdb=" N ILE B 270 " --> pdb=" O TRP B 266 " (cutoff:3.500A) Processing helix chain 'B' and resid 296 through 312 removed outlier: 3.765A pdb=" N GLU B 308 " --> pdb=" O ALA B 304 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N LYS B 311 " --> pdb=" O ARG B 307 " (cutoff:3.500A) Processing helix chain 'B' and resid 364 through 384 Processing helix chain 'B' and resid 394 through 402 Processing helix chain 'B' and resid 403 through 405 No H-bonds generated for 'chain 'B' and resid 403 through 405' Processing sheet with id=AA1, first strand: chain 'A' and resid 47 through 50 removed outlier: 4.605A pdb=" N ARG A 143 " --> pdb=" O ILE A 50 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 105 through 110 Processing sheet with id=AA3, first strand: chain 'A' and resid 227 through 229 removed outlier: 3.720A pdb=" N LYS A 238 " --> pdb=" O HIS A 235 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 348 through 354 removed outlier: 6.628A pdb=" N ILE A 341 " --> pdb=" O LEU A 349 " (cutoff:3.500A) removed outlier: 4.616A pdb=" N THR A 351 " --> pdb=" O TYR A 339 " (cutoff:3.500A) removed outlier: 6.728A pdb=" N TYR A 339 " --> pdb=" O THR A 351 " (cutoff:3.500A) removed outlier: 4.406A pdb=" N LYS A 353 " --> pdb=" O TRP A 337 " (cutoff:3.500A) removed outlier: 6.664A pdb=" N TRP A 337 " --> pdb=" O LYS A 353 " (cutoff:3.500A) removed outlier: 6.181A pdb=" N GLN A 336 " --> pdb=" O GLN A 332 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N LYS A 390 " --> pdb=" O ALA A 327 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N ILE A 329 " --> pdb=" O LYS A 390 " (cutoff:3.500A) removed outlier: 6.626A pdb=" N PHE A 389 " --> pdb=" O GLU A 415 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 361 through 362 removed outlier: 3.528A pdb=" N THR A 362 " --> pdb=" O LYS A 512 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N LYS A 512 " --> pdb=" O THR A 362 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'A' and resid 464 through 470 removed outlier: 3.531A pdb=" N LYS A 465 " --> pdb=" O TYR A 457 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N LEU A 452 " --> pdb=" O ASN A 447 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N TYR A 441 " --> pdb=" O VAL A 458 " (cutoff:3.500A) removed outlier: 6.689A pdb=" N GLU A 438 " --> pdb=" O ASN A 494 " (cutoff:3.500A) removed outlier: 7.774A pdb=" N VAL A 496 " --> pdb=" O GLU A 438 " (cutoff:3.500A) removed outlier: 6.713A pdb=" N PHE A 440 " --> pdb=" O VAL A 496 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 60 through 63 Processing sheet with id=AA8, first strand: chain 'B' and resid 179 through 183 Processing sheet with id=AA9, first strand: chain 'B' and resid 130 through 132 Processing sheet with id=AB1, first strand: chain 'B' and resid 252 through 253 removed outlier: 4.239A pdb=" N TRP B 252 " --> pdb=" O ILE B 293 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 347 through 355 removed outlier: 8.868A pdb=" N ASN B 348 " --> pdb=" O GLN B 343 " (cutoff:3.500A) removed outlier: 7.290A pdb=" N GLN B 343 " --> pdb=" O ASN B 348 " (cutoff:3.500A) removed outlier: 6.061A pdb=" N GLN B 336 " --> pdb=" O GLN B 332 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N ILE B 329 " --> pdb=" O LYS B 390 " (cutoff:3.500A) removed outlier: 6.174A pdb=" N PHE B 389 " --> pdb=" O GLU B 415 " (cutoff:3.500A) 310 hydrogen bonds defined for protein. 840 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 36 hydrogen bonds 72 hydrogen bond angles 0 basepair planarities 13 basepair parallelities 26 stacking parallelities Total time for adding SS restraints: 3.09 Time building geometry restraints manager: 2.96 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 1472 1.33 - 1.45: 2307 1.45 - 1.57: 4721 1.57 - 1.69: 71 1.69 - 1.81: 23 Bond restraints: 8594 Sorted by residual: bond pdb=" N GLU B 169 " pdb=" CA GLU B 169 " ideal model delta sigma weight residual 1.459 1.500 -0.040 1.04e-02 9.25e+03 1.51e+01 bond pdb=" N VAL B 241 " pdb=" CA VAL B 241 " ideal model delta sigma weight residual 1.457 1.501 -0.045 1.19e-02 7.06e+03 1.40e+01 bond pdb=" N ILE B 293 " pdb=" CA ILE B 293 " ideal model delta sigma weight residual 1.456 1.488 -0.032 8.70e-03 1.32e+04 1.35e+01 bond pdb=" N ILE B 244 " pdb=" CA ILE B 244 " ideal model delta sigma weight residual 1.457 1.501 -0.044 1.22e-02 6.72e+03 1.29e+01 bond pdb=" N GLY B 285 " pdb=" CA GLY B 285 " ideal model delta sigma weight residual 1.444 1.478 -0.035 1.02e-02 9.61e+03 1.15e+01 ... (remaining 8589 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.75: 11443 2.75 - 5.51: 357 5.51 - 8.26: 29 8.26 - 11.02: 3 11.02 - 13.77: 2 Bond angle restraints: 11834 Sorted by residual: angle pdb=" C5' DG E 12 " pdb=" C4' DG E 12 " pdb=" O4' DG E 12 " ideal model delta sigma weight residual 109.40 123.17 -13.77 1.50e+00 4.44e-01 8.43e+01 angle pdb=" C5' DT E 13 " pdb=" C4' DT E 13 " pdb=" O4' DT E 13 " ideal model delta sigma weight residual 109.40 122.69 -13.29 1.50e+00 4.44e-01 7.85e+01 angle pdb=" C5' DG E 19 " pdb=" C4' DG E 19 " pdb=" O4' DG E 19 " ideal model delta sigma weight residual 109.40 120.19 -10.79 1.50e+00 4.44e-01 5.17e+01 angle pdb=" C HIS B 235 " pdb=" CA HIS B 235 " pdb=" CB HIS B 235 " ideal model delta sigma weight residual 110.08 117.91 -7.83 1.15e+00 7.56e-01 4.63e+01 angle pdb=" C3' OMC E 2 " pdb=" C2' OMC E 2 " pdb=" C1' OMC E 2 " ideal model delta sigma weight residual 101.30 106.98 -5.68 1.00e+00 1.00e+00 3.22e+01 ... (remaining 11829 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 19.40: 4354 19.40 - 38.80: 495 38.80 - 58.20: 137 58.20 - 77.59: 31 77.59 - 96.99: 8 Dihedral angle restraints: 5025 sinusoidal: 2313 harmonic: 2712 Sorted by residual: dihedral pdb=" C PHE B 346 " pdb=" N PHE B 346 " pdb=" CA PHE B 346 " pdb=" CB PHE B 346 " ideal model delta harmonic sigma weight residual -122.60 -133.18 10.58 0 2.50e+00 1.60e-01 1.79e+01 dihedral pdb=" C GLU B 291 " pdb=" N GLU B 291 " pdb=" CA GLU B 291 " pdb=" CB GLU B 291 " ideal model delta harmonic sigma weight residual -122.60 -132.67 10.07 0 2.50e+00 1.60e-01 1.62e+01 dihedral pdb=" CD ARG A 277 " pdb=" NE ARG A 277 " pdb=" CZ ARG A 277 " pdb=" NH1 ARG A 277 " ideal model delta sinusoidal sigma weight residual 0.00 32.46 -32.46 1 1.00e+01 1.00e-02 1.50e+01 ... (remaining 5022 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.109: 1140 0.109 - 0.217: 125 0.217 - 0.326: 23 0.326 - 0.434: 2 0.434 - 0.543: 2 Chirality restraints: 1292 Sorted by residual: chirality pdb=" C4' DG E 12 " pdb=" C5' DG E 12 " pdb=" O4' DG E 12 " pdb=" C3' DG E 12 " both_signs ideal model delta sigma weight residual False -2.53 -1.98 -0.54 2.00e-01 2.50e+01 7.36e+00 chirality pdb=" C4' DT E 13 " pdb=" C5' DT E 13 " pdb=" O4' DT E 13 " pdb=" C3' DT E 13 " both_signs ideal model delta sigma weight residual False -2.53 -2.07 -0.45 2.00e-01 2.50e+01 5.09e+00 chirality pdb=" C4' DC E 20 " pdb=" C5' DC E 20 " pdb=" O4' DC E 20 " pdb=" C3' DC E 20 " both_signs ideal model delta sigma weight residual False -2.53 -2.17 -0.36 2.00e-01 2.50e+01 3.16e+00 ... (remaining 1289 not shown) Planarity restraints: 1367 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG A 277 " 0.582 9.50e-02 1.11e+02 2.61e-01 4.16e+01 pdb=" NE ARG A 277 " -0.035 2.00e-02 2.50e+03 pdb=" CZ ARG A 277 " -0.007 2.00e-02 2.50e+03 pdb=" NH1 ARG A 277 " -0.004 2.00e-02 2.50e+03 pdb=" NH2 ARG A 277 " 0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C THR B 419 " 0.079 5.00e-02 4.00e+02 1.17e-01 2.20e+01 pdb=" N PRO B 420 " -0.203 5.00e-02 4.00e+02 pdb=" CA PRO B 420 " 0.062 5.00e-02 4.00e+02 pdb=" CD PRO B 420 " 0.061 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU A 246 " -0.057 5.00e-02 4.00e+02 8.69e-02 1.21e+01 pdb=" N PRO A 247 " 0.150 5.00e-02 4.00e+02 pdb=" CA PRO A 247 " -0.046 5.00e-02 4.00e+02 pdb=" CD PRO A 247 " -0.047 5.00e-02 4.00e+02 ... (remaining 1364 not shown) Histogram of nonbonded interaction distances: 2.39 - 2.89: 3009 2.89 - 3.39: 7440 3.39 - 3.89: 13877 3.89 - 4.40: 15907 4.40 - 4.90: 26057 Nonbonded interactions: 66290 Sorted by model distance: nonbonded pdb=" O VAL A 276 " pdb=" OG SER A 280 " model vdw 2.387 3.040 nonbonded pdb=" OG1 THR A 286 " pdb=" OE2 GLU A 291 " model vdw 2.390 3.040 nonbonded pdb=" O TYR B 56 " pdb=" NH2 ARG B 143 " model vdw 2.417 3.120 nonbonded pdb=" N THR B 290 " pdb=" OG1 THR B 290 " model vdw 2.459 2.496 nonbonded pdb=" OE1 GLN A 330 " pdb=" NE2 GLN A 340 " model vdw 2.466 3.120 ... (remaining 66285 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: 19.570 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: 0.020 Extract box with map and model: 11.020 Check model and map are aligned: 0.060 Set scattering table: 0.080 Process input model: 27.060 Find NCS groups from input model: 0.080 Set up NCS constraints: 0.040 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:2.850 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 60.790 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6867 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 : 0.007 0.087 8594 Z= 0.469 Angle : 1.050 13.772 11834 Z= 0.706 Chirality : 0.076 0.543 1292 Planarity : 0.010 0.261 1367 Dihedral : 18.098 96.992 3275 Min Nonbonded Distance : 2.387 Molprobity Statistics. All-atom Clashscore : 7.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 2.07 % Allowed : 3.04 % Favored : 94.89 % Cbeta Deviations : 0.23 % Peptide Plane: Cis-proline : 3.03 % 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: -0.18 (0.28), residues: 917 helix: 1.09 (0.30), residues: 311 sheet: -0.29 (0.40), residues: 177 loop : -0.90 (0.29), residues: 429 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.043 0.002 TRP B 414 HIS 0.006 0.001 HIS A 315 PHE 0.021 0.002 PHE A 124 TYR 0.020 0.002 TYR A 532 ARG 0.004 0.001 ARG B 211 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1834 Ramachandran restraints generated. 917 Oldfield, 0 Emsley, 917 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1834 Ramachandran restraints generated. 917 Oldfield, 0 Emsley, 917 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 121 time to evaluate : 0.912 Fit side-chains revert: symmetry clash REVERT: A 498 ASN cc_start: 0.6968 (t0) cc_final: 0.6588 (t0) REVERT: B 280 SER cc_start: 0.7756 (p) cc_final: 0.7080 (t) outliers start: 17 outliers final: 9 residues processed: 134 average time/residue: 0.2633 time to fit residues: 49.6691 Evaluate side-chains 105 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 96 time to evaluate : 0.761 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 THR Chi-restraints excluded: chain A residue 186 ASP Chi-restraints excluded: chain B residue 101 LYS Chi-restraints excluded: chain B residue 214 LEU Chi-restraints excluded: chain B residue 241 VAL Chi-restraints excluded: chain B residue 282 LEU Chi-restraints excluded: chain B residue 290 THR Chi-restraints excluded: chain B residue 314 VAL Chi-restraints excluded: chain B residue 317 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 80 optimal weight: 10.0000 chunk 72 optimal weight: 7.9990 chunk 39 optimal weight: 5.9990 chunk 24 optimal weight: 10.0000 chunk 48 optimal weight: 10.0000 chunk 38 optimal weight: 2.9990 chunk 74 optimal weight: 20.0000 chunk 28 optimal weight: 5.9990 chunk 45 optimal weight: 0.9980 chunk 55 optimal weight: 3.9990 chunk 86 optimal weight: 1.9990 overall best weight: 3.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 182 GLN A 255 ASN A 332 GLN ** A 494 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 242 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4346 r_free = 0.4346 target = 0.214479 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3971 r_free = 0.3971 target = 0.175041 restraints weight = 8615.425| |-----------------------------------------------------------------------------| r_work (start): 0.3940 rms_B_bonded: 1.97 r_work: 0.3678 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work (final): 0.3678 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7063 moved from start: 0.1052 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 8594 Z= 0.229 Angle : 0.608 7.592 11834 Z= 0.321 Chirality : 0.042 0.144 1292 Planarity : 0.006 0.077 1367 Dihedral : 16.966 81.922 1360 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 7.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.18 % Favored : 97.82 % Rotamer: Outliers : 2.07 % Allowed : 9.85 % Favored : 88.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: -0.13 (0.28), residues: 917 helix: 1.00 (0.29), residues: 331 sheet: -0.17 (0.40), residues: 172 loop : -0.89 (0.30), residues: 414 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP B 402 HIS 0.004 0.001 HIS B 235 PHE 0.019 0.002 PHE B 87 TYR 0.012 0.002 TYR A 501 ARG 0.004 0.001 ARG A 78 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1834 Ramachandran restraints generated. 917 Oldfield, 0 Emsley, 917 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1834 Ramachandran restraints generated. 917 Oldfield, 0 Emsley, 917 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 103 time to evaluate : 0.839 Fit side-chains REVERT: A 31 ILE cc_start: 0.4799 (mt) cc_final: 0.4545 (mp) REVERT: A 78 ARG cc_start: 0.6150 (mmp80) cc_final: 0.5334 (mmt-90) REVERT: A 147 ASN cc_start: 0.7267 (m110) cc_final: 0.6710 (t0) REVERT: A 375 ILE cc_start: 0.8398 (OUTLIER) cc_final: 0.8137 (mt) REVERT: A 530 LYS cc_start: 0.7021 (mtpt) cc_final: 0.6757 (mtmt) REVERT: B 280 SER cc_start: 0.7785 (p) cc_final: 0.7336 (t) outliers start: 17 outliers final: 12 residues processed: 116 average time/residue: 0.2000 time to fit residues: 32.7112 Evaluate side-chains 108 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 95 time to evaluate : 0.846 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 THR Chi-restraints excluded: chain A residue 375 ILE Chi-restraints excluded: chain A residue 442 VAL Chi-restraints excluded: chain B residue 101 LYS Chi-restraints excluded: chain B residue 105 SER Chi-restraints excluded: chain B residue 142 ILE Chi-restraints excluded: chain B residue 234 LEU Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain B residue 241 VAL Chi-restraints excluded: chain B residue 282 LEU Chi-restraints excluded: chain B residue 290 THR Chi-restraints excluded: chain B residue 314 VAL Chi-restraints excluded: chain B residue 317 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 23 optimal weight: 10.0000 chunk 77 optimal weight: 0.6980 chunk 5 optimal weight: 0.1980 chunk 31 optimal weight: 3.9990 chunk 64 optimal weight: 9.9990 chunk 79 optimal weight: 8.9990 chunk 59 optimal weight: 4.9990 chunk 22 optimal weight: 8.9990 chunk 66 optimal weight: 7.9990 chunk 62 optimal weight: 20.0000 chunk 87 optimal weight: 0.8980 overall best weight: 2.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 182 GLN A 332 GLN ** A 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 494 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 498 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 545 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 373 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4359 r_free = 0.4359 target = 0.216394 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3990 r_free = 0.3990 target = 0.177148 restraints weight = 8731.841| |-----------------------------------------------------------------------------| r_work (start): 0.3954 rms_B_bonded: 1.92 r_work: 0.3703 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work (final): 0.3703 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7033 moved from start: 0.1458 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 8594 Z= 0.181 Angle : 0.541 7.738 11834 Z= 0.283 Chirality : 0.041 0.138 1292 Planarity : 0.005 0.062 1367 Dihedral : 16.495 81.713 1356 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 5.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.18 % Favored : 97.82 % Rotamer: Outliers : 2.43 % Allowed : 12.17 % Favored : 85.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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 (0.28), residues: 917 helix: 1.22 (0.30), residues: 331 sheet: -0.05 (0.40), residues: 166 loop : -0.69 (0.30), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 402 HIS 0.003 0.001 HIS B 235 PHE 0.022 0.001 PHE B 87 TYR 0.014 0.001 TYR A 501 ARG 0.005 0.001 ARG A 83 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1834 Ramachandran restraints generated. 917 Oldfield, 0 Emsley, 917 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1834 Ramachandran restraints generated. 917 Oldfield, 0 Emsley, 917 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 109 time to evaluate : 0.923 Fit side-chains REVERT: A 29 GLU cc_start: 0.5281 (OUTLIER) cc_final: 0.4753 (tp30) REVERT: A 147 ASN cc_start: 0.7289 (m110) cc_final: 0.6741 (t0) REVERT: A 375 ILE cc_start: 0.8378 (OUTLIER) cc_final: 0.8141 (mt) REVERT: A 530 LYS cc_start: 0.6940 (mtpt) cc_final: 0.6698 (mtmt) REVERT: B 233 GLU cc_start: 0.6454 (mp0) cc_final: 0.6244 (pm20) REVERT: B 280 SER cc_start: 0.7767 (p) cc_final: 0.7231 (t) outliers start: 20 outliers final: 12 residues processed: 123 average time/residue: 0.2143 time to fit residues: 37.6318 Evaluate side-chains 115 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 101 time to evaluate : 0.942 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 GLU Chi-restraints excluded: chain A residue 338 THR Chi-restraints excluded: chain A residue 375 ILE Chi-restraints excluded: chain A residue 442 VAL Chi-restraints excluded: chain B residue 105 SER Chi-restraints excluded: chain B residue 142 ILE Chi-restraints excluded: chain B residue 234 LEU Chi-restraints excluded: chain B residue 241 VAL Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain B residue 282 LEU Chi-restraints excluded: chain B residue 290 THR Chi-restraints excluded: chain B residue 314 VAL Chi-restraints excluded: chain B residue 317 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 45 optimal weight: 5.9990 chunk 73 optimal weight: 0.0980 chunk 52 optimal weight: 8.9990 chunk 90 optimal weight: 10.0000 chunk 70 optimal weight: 5.9990 chunk 55 optimal weight: 4.9990 chunk 93 optimal weight: 20.0000 chunk 50 optimal weight: 0.2980 chunk 43 optimal weight: 7.9990 chunk 38 optimal weight: 5.9990 chunk 78 optimal weight: 40.0000 overall best weight: 3.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 175 ASN ** A 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 494 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 498 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 545 ASN ** 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 = 0.4345 r_free = 0.4345 target = 0.214646 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3972 r_free = 0.3972 target = 0.175256 restraints weight = 8714.246| |-----------------------------------------------------------------------------| r_work (start): 0.3969 rms_B_bonded: 1.92 r_work: 0.3706 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work (final): 0.3706 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7077 moved from start: 0.1521 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 8594 Z= 0.223 Angle : 0.566 9.529 11834 Z= 0.294 Chirality : 0.042 0.164 1292 Planarity : 0.005 0.056 1367 Dihedral : 16.581 82.132 1351 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 5.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 2.31 % Allowed : 13.75 % Favored : 83.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: 0.04 (0.28), residues: 917 helix: 1.13 (0.29), residues: 331 sheet: -0.00 (0.42), residues: 155 loop : -0.79 (0.30), residues: 431 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 402 HIS 0.004 0.001 HIS A 315 PHE 0.020 0.002 PHE B 87 TYR 0.015 0.002 TYR A 501 ARG 0.005 0.000 ARG A 83 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1834 Ramachandran restraints generated. 917 Oldfield, 0 Emsley, 917 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1834 Ramachandran restraints generated. 917 Oldfield, 0 Emsley, 917 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 102 time to evaluate : 0.873 Fit side-chains REVERT: A 34 LEU cc_start: 0.4536 (OUTLIER) cc_final: 0.4327 (tt) REVERT: A 147 ASN cc_start: 0.7347 (m110) cc_final: 0.6769 (t0) REVERT: A 375 ILE cc_start: 0.8395 (OUTLIER) cc_final: 0.8163 (mt) REVERT: A 530 LYS cc_start: 0.7016 (mtpt) cc_final: 0.6746 (mtmt) REVERT: B 233 GLU cc_start: 0.6571 (mp0) cc_final: 0.6350 (pm20) outliers start: 19 outliers final: 14 residues processed: 115 average time/residue: 0.1889 time to fit residues: 30.9936 Evaluate side-chains 117 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 101 time to evaluate : 1.068 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 LEU Chi-restraints excluded: chain A residue 186 ASP Chi-restraints excluded: chain A residue 309 ILE Chi-restraints excluded: chain A residue 338 THR Chi-restraints excluded: chain A residue 375 ILE Chi-restraints excluded: chain A residue 442 VAL Chi-restraints excluded: chain B residue 105 SER Chi-restraints excluded: chain B residue 142 ILE Chi-restraints excluded: chain B residue 234 LEU Chi-restraints excluded: chain B residue 241 VAL Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain B residue 282 LEU Chi-restraints excluded: chain B residue 290 THR Chi-restraints excluded: chain B residue 314 VAL Chi-restraints excluded: chain B residue 317 VAL Chi-restraints excluded: chain B residue 377 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 50 optimal weight: 0.9990 chunk 32 optimal weight: 9.9990 chunk 84 optimal weight: 0.6980 chunk 78 optimal weight: 20.0000 chunk 79 optimal weight: 10.0000 chunk 37 optimal weight: 5.9990 chunk 11 optimal weight: 20.0000 chunk 81 optimal weight: 8.9990 chunk 24 optimal weight: 3.9990 chunk 22 optimal weight: 0.0000 chunk 0 optimal weight: 20.0000 overall best weight: 2.3390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 336 GLN A 428 GLN ** A 494 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 498 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 545 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4360 r_free = 0.4360 target = 0.216436 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3991 r_free = 0.3991 target = 0.177034 restraints weight = 8563.228| |-----------------------------------------------------------------------------| r_work (start): 0.3988 rms_B_bonded: 1.82 r_work: 0.3726 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work (final): 0.3726 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7053 moved from start: 0.1716 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 8594 Z= 0.181 Angle : 0.531 8.543 11834 Z= 0.276 Chirality : 0.041 0.138 1292 Planarity : 0.005 0.051 1367 Dihedral : 16.565 81.654 1351 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 5.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % Rotamer: Outliers : 2.43 % Allowed : 15.09 % Favored : 82.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: 0.22 (0.28), residues: 917 helix: 1.29 (0.30), residues: 332 sheet: -0.02 (0.40), residues: 163 loop : -0.67 (0.30), residues: 422 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 402 HIS 0.003 0.001 HIS A 315 PHE 0.021 0.001 PHE B 87 TYR 0.013 0.001 TYR A 501 ARG 0.006 0.000 ARG A 83 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1834 Ramachandran restraints generated. 917 Oldfield, 0 Emsley, 917 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1834 Ramachandran restraints generated. 917 Oldfield, 0 Emsley, 917 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 105 time to evaluate : 0.904 Fit side-chains REVERT: A 29 GLU cc_start: 0.5362 (OUTLIER) cc_final: 0.4719 (tp30) REVERT: A 34 LEU cc_start: 0.4503 (OUTLIER) cc_final: 0.4250 (tt) REVERT: A 147 ASN cc_start: 0.7334 (m110) cc_final: 0.6758 (t0) REVERT: A 375 ILE cc_start: 0.8319 (OUTLIER) cc_final: 0.8082 (mt) REVERT: A 530 LYS cc_start: 0.7047 (mtpt) cc_final: 0.6831 (mtmt) REVERT: B 233 GLU cc_start: 0.6561 (mp0) cc_final: 0.6351 (pm20) REVERT: B 280 SER cc_start: 0.7926 (p) cc_final: 0.7375 (t) outliers start: 20 outliers final: 14 residues processed: 120 average time/residue: 0.1993 time to fit residues: 33.5324 Evaluate side-chains 117 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 100 time to evaluate : 0.822 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 GLU Chi-restraints excluded: chain A residue 34 LEU Chi-restraints excluded: chain A residue 179 VAL Chi-restraints excluded: chain A residue 338 THR Chi-restraints excluded: chain A residue 365 VAL Chi-restraints excluded: chain A residue 375 ILE Chi-restraints excluded: chain A residue 380 ILE Chi-restraints excluded: chain A residue 442 VAL Chi-restraints excluded: chain B residue 105 SER Chi-restraints excluded: chain B residue 142 ILE Chi-restraints excluded: chain B residue 234 LEU Chi-restraints excluded: chain B residue 241 VAL Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain B residue 282 LEU Chi-restraints excluded: chain B residue 290 THR Chi-restraints excluded: chain B residue 314 VAL Chi-restraints excluded: chain B residue 317 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 11 optimal weight: 20.0000 chunk 8 optimal weight: 2.9990 chunk 59 optimal weight: 10.0000 chunk 94 optimal weight: 10.0000 chunk 40 optimal weight: 10.0000 chunk 50 optimal weight: 0.7980 chunk 42 optimal weight: 20.0000 chunk 57 optimal weight: 6.9990 chunk 38 optimal weight: 4.9990 chunk 5 optimal weight: 3.9990 chunk 76 optimal weight: 10.0000 overall best weight: 3.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 494 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 498 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 545 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 373 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4338 r_free = 0.4338 target = 0.214008 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3959 r_free = 0.3959 target = 0.174127 restraints weight = 8665.178| |-----------------------------------------------------------------------------| r_work (start): 0.3956 rms_B_bonded: 1.83 r_work: 0.3701 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work (final): 0.3701 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7086 moved from start: 0.1697 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 8594 Z= 0.240 Angle : 0.576 10.625 11834 Z= 0.298 Chirality : 0.042 0.192 1292 Planarity : 0.005 0.049 1367 Dihedral : 16.749 81.814 1351 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 5.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 2.80 % Allowed : 15.33 % Favored : 81.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: 0.03 (0.28), residues: 917 helix: 1.16 (0.29), residues: 331 sheet: -0.09 (0.40), residues: 159 loop : -0.81 (0.30), residues: 427 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 402 HIS 0.006 0.001 HIS A 315 PHE 0.025 0.002 PHE B 87 TYR 0.018 0.002 TYR A 501 ARG 0.006 0.001 ARG A 83 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1834 Ramachandran restraints generated. 917 Oldfield, 0 Emsley, 917 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1834 Ramachandran restraints generated. 917 Oldfield, 0 Emsley, 917 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 101 time to evaluate : 0.858 Fit side-chains REVERT: A 34 LEU cc_start: 0.4378 (OUTLIER) cc_final: 0.4117 (tt) REVERT: A 147 ASN cc_start: 0.7251 (m110) cc_final: 0.6764 (t0) REVERT: A 375 ILE cc_start: 0.8410 (OUTLIER) cc_final: 0.8183 (mt) REVERT: B 206 ARG cc_start: 0.7225 (ttp80) cc_final: 0.6516 (ttp-170) REVERT: B 233 GLU cc_start: 0.6541 (mp0) cc_final: 0.6310 (pm20) REVERT: B 280 SER cc_start: 0.8001 (p) cc_final: 0.7452 (t) outliers start: 23 outliers final: 18 residues processed: 117 average time/residue: 0.2002 time to fit residues: 32.9618 Evaluate side-chains 117 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 97 time to evaluate : 0.878 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 LEU Chi-restraints excluded: chain A residue 179 VAL Chi-restraints excluded: chain A residue 186 ASP Chi-restraints excluded: chain A residue 309 ILE Chi-restraints excluded: chain A residue 338 THR Chi-restraints excluded: chain A residue 365 VAL Chi-restraints excluded: chain A residue 375 ILE Chi-restraints excluded: chain A residue 442 VAL Chi-restraints excluded: chain B residue 105 SER Chi-restraints excluded: chain B residue 142 ILE Chi-restraints excluded: chain B residue 234 LEU Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain B residue 241 VAL Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain B residue 279 LEU Chi-restraints excluded: chain B residue 282 LEU Chi-restraints excluded: chain B residue 290 THR Chi-restraints excluded: chain B residue 314 VAL Chi-restraints excluded: chain B residue 317 VAL Chi-restraints excluded: chain B residue 377 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 32 optimal weight: 9.9990 chunk 73 optimal weight: 0.9990 chunk 41 optimal weight: 10.0000 chunk 48 optimal weight: 9.9990 chunk 87 optimal weight: 0.9980 chunk 75 optimal weight: 10.0000 chunk 16 optimal weight: 7.9990 chunk 90 optimal weight: 7.9990 chunk 14 optimal weight: 5.9990 chunk 51 optimal weight: 8.9990 chunk 9 optimal weight: 2.9990 overall best weight: 3.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4339 r_free = 0.4339 target = 0.214139 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3964 r_free = 0.3964 target = 0.174667 restraints weight = 8625.818| |-----------------------------------------------------------------------------| r_work (start): 0.3944 rms_B_bonded: 1.75 r_work: 0.3701 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.3555 rms_B_bonded: 4.94 restraints_weight: 0.2500 r_work (final): 0.3555 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7196 moved from start: 0.1746 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 8594 Z= 0.231 Angle : 0.572 11.010 11834 Z= 0.296 Chirality : 0.042 0.176 1292 Planarity : 0.005 0.047 1367 Dihedral : 16.765 81.599 1351 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 6.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 2.92 % Allowed : 15.21 % Favored : 81.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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 (0.28), residues: 917 helix: 1.17 (0.29), residues: 333 sheet: -0.23 (0.39), residues: 170 loop : -0.71 (0.30), residues: 414 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 402 HIS 0.006 0.001 HIS A 315 PHE 0.025 0.002 PHE B 87 TYR 0.017 0.002 TYR A 501 ARG 0.006 0.000 ARG A 83 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1834 Ramachandran restraints generated. 917 Oldfield, 0 Emsley, 917 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1834 Ramachandran restraints generated. 917 Oldfield, 0 Emsley, 917 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 96 time to evaluate : 0.977 Fit side-chains REVERT: A 34 LEU cc_start: 0.4393 (OUTLIER) cc_final: 0.4091 (tt) REVERT: A 375 ILE cc_start: 0.8420 (OUTLIER) cc_final: 0.8186 (mt) REVERT: B 206 ARG cc_start: 0.7198 (ttp80) cc_final: 0.6499 (ttp-170) REVERT: B 233 GLU cc_start: 0.6669 (mp0) cc_final: 0.6416 (pm20) REVERT: B 280 SER cc_start: 0.8018 (p) cc_final: 0.7437 (t) outliers start: 24 outliers final: 18 residues processed: 114 average time/residue: 0.2476 time to fit residues: 40.1697 Evaluate side-chains 115 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 95 time to evaluate : 0.984 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 LEU Chi-restraints excluded: chain A residue 179 VAL Chi-restraints excluded: chain A residue 186 ASP Chi-restraints excluded: chain A residue 309 ILE Chi-restraints excluded: chain A residue 338 THR Chi-restraints excluded: chain A residue 365 VAL Chi-restraints excluded: chain A residue 375 ILE Chi-restraints excluded: chain A residue 442 VAL Chi-restraints excluded: chain B residue 105 SER Chi-restraints excluded: chain B residue 142 ILE Chi-restraints excluded: chain B residue 234 LEU Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain B residue 241 VAL Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain B residue 279 LEU Chi-restraints excluded: chain B residue 282 LEU Chi-restraints excluded: chain B residue 290 THR Chi-restraints excluded: chain B residue 314 VAL Chi-restraints excluded: chain B residue 317 VAL Chi-restraints excluded: chain B residue 377 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/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-5624/modules/cctbx_project/iotbx/cli_parser.py", line 980, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/phenix/phenix/programs/real_space_refine.py", line 210, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/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-5624/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 767, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/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-5624/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-5624/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-5624/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-5624/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-5624/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-5624/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/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-5624/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-5624/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1525, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1427, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1308, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 70.5721 > 50: distance: 38 - 40: 34.530 distance: 40 - 41: 40.720 distance: 40 - 46: 47.878 distance: 41 - 44: 57.204 distance: 42 - 43: 40.991 distance: 42 - 47: 38.979 distance: 45 - 46: 42.028 distance: 47 - 48: 56.187 distance: 48 - 49: 22.946 distance: 48 - 51: 40.241 distance: 49 - 50: 18.389 distance: 49 - 56: 20.589 distance: 52 - 53: 70.048 distance: 53 - 55: 39.716 distance: 56 - 57: 41.106 distance: 57 - 60: 39.991 distance: 58 - 59: 40.647 distance: 60 - 61: 38.568 distance: 61 - 63: 56.852 distance: 64 - 70: 55.833 distance: 65 - 66: 8.079 distance: 65 - 68: 56.521 distance: 66 - 67: 52.990 distance: 66 - 71: 7.240 distance: 68 - 69: 27.874 distance: 69 - 70: 28.534 distance: 71 - 72: 40.110 distance: 72 - 73: 39.310 distance: 73 - 74: 40.425 distance: 75 - 76: 10.321 distance: 76 - 77: 27.212 distance: 76 - 78: 11.456 distance: 79 - 81: 39.426 distance: 80 - 81: 50.869 distance: 81 - 82: 40.770 distance: 83 - 84: 39.804 distance: 84 - 85: 39.376 distance: 85 - 86: 39.995 distance: 85 - 88: 39.776 distance: 88 - 89: 40.344 distance: 89 - 90: 39.829 distance: 89 - 92: 56.583 distance: 90 - 95: 39.464 distance: 92 - 93: 40.047 distance: 97 - 98: 66.132 distance: 97 - 102: 60.889 distance: 102 - 103: 43.278 distance: 104 - 109: 56.267 distance: 106 - 108: 56.875 distance: 109 - 110: 57.577 distance: 110 - 111: 38.555 distance: 110 - 113: 40.584 distance: 111 - 120: 34.771 distance: 113 - 114: 40.090 distance: 114 - 115: 55.389 distance: 115 - 117: 41.051 distance: 116 - 118: 39.921 distance: 118 - 119: 56.738