Starting phenix.real_space_refine on Sun Dec 29 06:25:41 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8blw_16114/12_2024/8blw_16114.cif Found real_map, /net/cci-nas-00/data/ceres_data/8blw_16114/12_2024/8blw_16114.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.22 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8blw_16114/12_2024/8blw_16114.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8blw_16114/12_2024/8blw_16114.map" model { file = "/net/cci-nas-00/data/ceres_data/8blw_16114/12_2024/8blw_16114.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8blw_16114/12_2024/8blw_16114.cif" } resolution = 3.22 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= 0.001 sd= 0.019 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 18 5.16 5 C 6239 2.51 5 N 1683 2.21 5 O 1943 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 18 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/chem_data/mon_lib" Total number of atoms: 9883 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 4974 Number of conformers: 1 Conformer: "" Number of residues, atoms: 624, 4974 Classifications: {'peptide': 624} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 22, 'TRANS': 601} Chain breaks: 3 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 31 Unresolved non-hydrogen angles: 39 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1, 'ASN:plan1': 3, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 19 Chain: "B" Number of atoms: 4898 Number of conformers: 1 Conformer: "" Number of residues, atoms: 626, 4898 Classifications: {'peptide': 626} Link IDs: {'PTRANS': 23, 'TRANS': 602} Chain breaks: 1 Chain: "B" Number of atoms: 11 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 11 Unusual residues: {'GAL': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 6.54, per 1000 atoms: 0.66 Number of scatterers: 9883 At special positions: 0 Unit cell: (81.9, 71.89, 141.96, 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 18 16.00 O 1943 8.00 N 1683 7.00 C 6239 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=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 2.43 Conformation dependent library (CDL) restraints added in 1.2 seconds 2476 Ramachandran restraints generated. 1238 Oldfield, 0 Emsley, 1238 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2316 Finding SS restraints... Secondary structure from input PDB file: 11 helices and 20 sheets defined 5.7% alpha, 34.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.36 Creating SS restraints... Processing helix chain 'A' and resid 62 through 69 Processing helix chain 'A' and resid 74 through 79 removed outlier: 3.708A pdb=" N LYS A 79 " --> pdb=" O SER A 75 " (cutoff:3.500A) Processing helix chain 'A' and resid 126 through 130 removed outlier: 3.574A pdb=" N ARG A 129 " --> pdb=" O ASP A 126 " (cutoff:3.500A) Processing helix chain 'A' and resid 151 through 155 Processing helix chain 'A' and resid 457 through 462 Processing helix chain 'A' and resid 620 through 624 removed outlier: 3.594A pdb=" N ARG A 624 " --> pdb=" O SER A 621 " (cutoff:3.500A) Processing helix chain 'B' and resid 80 through 87 Processing helix chain 'B' and resid 195 through 199 Processing helix chain 'B' and resid 412 through 416 removed outlier: 3.578A pdb=" N ALA B 416 " --> pdb=" O THR B 413 " (cutoff:3.500A) Processing helix chain 'B' and resid 422 through 436 Processing helix chain 'B' and resid 613 through 615 No H-bonds generated for 'chain 'B' and resid 613 through 615' Processing sheet with id=AA1, first strand: chain 'A' and resid 58 through 61 removed outlier: 3.567A pdb=" N ARG A 137 " --> pdb=" O GLN A 164 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 85 through 87 Processing sheet with id=AA3, first strand: chain 'A' and resid 176 through 177 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 176 through 177 current: chain 'A' and resid 189 through 191 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 189 through 191 current: chain 'A' and resid 204 through 214 removed outlier: 4.443A pdb=" N GLU A 244 " --> pdb=" O SER A 272 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N SER A 272 " --> pdb=" O GLU A 244 " (cutoff:3.500A) removed outlier: 4.171A pdb=" N ALA A 254 " --> pdb=" O TRP A 262 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N TYR A 321 " --> pdb=" O LYS A 293 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 336 through 348 current: chain 'A' and resid 359 through 374 removed outlier: 6.886A pdb=" N SER A 360 " --> pdb=" O LYS A 394 " (cutoff:3.500A) removed outlier: 5.213A pdb=" N LYS A 394 " --> pdb=" O SER A 360 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N SER A 362 " --> pdb=" O ALA A 392 " (cutoff:3.500A) removed outlier: 4.399A pdb=" N LEU A 388 " --> pdb=" O ASP A 366 " (cutoff:3.500A) removed outlier: 4.741A pdb=" N ALA A 406 " --> pdb=" O GLY A 393 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N GLU A 442 " --> pdb=" O SER A 486 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 495 through 502 current: chain 'A' and resid 530 through 532 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 530 through 532 current: chain 'A' and resid 553 through 559 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 553 through 559 current: chain 'A' and resid 580 through 581 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 580 through 581 current: chain 'A' and resid 602 through 610 Processing sheet with id=AA4, first strand: chain 'A' and resid 222 through 224 Processing sheet with id=AA5, first strand: chain 'A' and resid 511 through 515 Processing sheet with id=AA6, first strand: chain 'A' and resid 661 through 663 removed outlier: 4.816A pdb=" N VAL A 663 " --> pdb=" O PHE A 666 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 76 through 78 removed outlier: 6.789A pdb=" N GLU B 51 " --> pdb=" O PHE B 373 " (cutoff:3.500A) removed outlier: 4.748A pdb=" N PHE B 373 " --> pdb=" O GLU B 51 " (cutoff:3.500A) removed outlier: 6.583A pdb=" N TYR B 53 " --> pdb=" O VAL B 371 " (cutoff:3.500A) removed outlier: 4.299A pdb=" N VAL B 371 " --> pdb=" O TYR B 53 " (cutoff:3.500A) removed outlier: 6.337A pdb=" N LEU B 55 " --> pdb=" O ASN B 369 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 94 through 100 removed outlier: 3.697A pdb=" N ILE B 128 " --> pdb=" O VAL B 114 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 140 through 145 removed outlier: 3.819A pdb=" N ALA B 142 " --> pdb=" O CYS B 153 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N THR B 158 " --> pdb=" O SER B 154 " (cutoff:3.500A) removed outlier: 6.454A pdb=" N VAL B 159 " --> pdb=" O ILE B 172 " (cutoff:3.500A) removed outlier: 4.364A pdb=" N ILE B 172 " --> pdb=" O VAL B 159 " (cutoff:3.500A) removed outlier: 6.593A pdb=" N ARG B 161 " --> pdb=" O GLU B 170 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 179 through 185 removed outlier: 4.388A pdb=" N ASP B 181 " --> pdb=" O SER B 192 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N THR B 207 " --> pdb=" O ASN B 193 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N LYS B 220 " --> pdb=" O VAL B 210 " (cutoff:3.500A) removed outlier: 7.016A pdb=" N ASP B 212 " --> pdb=" O GLU B 218 " (cutoff:3.500A) removed outlier: 6.875A pdb=" N GLU B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 228 through 233 removed outlier: 5.652A pdb=" N VAL B 242 " --> pdb=" O GLY B 229 " (cutoff:3.500A) removed outlier: 4.626A pdb=" N ILE B 231 " --> pdb=" O TYR B 240 " (cutoff:3.500A) removed outlier: 6.900A pdb=" N TYR B 240 " --> pdb=" O ILE B 231 " (cutoff:3.500A) removed outlier: 7.142A pdb=" N ALA B 238 " --> pdb=" O PRO B 233 " (cutoff:3.500A) removed outlier: 6.262A pdb=" N ASP B 259 " --> pdb=" O VAL B 265 " (cutoff:3.500A) removed outlier: 6.142A pdb=" N VAL B 265 " --> pdb=" O ASP B 259 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 275 through 279 removed outlier: 3.610A pdb=" N SER B 275 " --> pdb=" O TYR B 286 " (cutoff:3.500A) removed outlier: 6.653A pdb=" N VAL B 299 " --> pdb=" O ILE B 308 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 322 through 327 removed outlier: 6.856A pdb=" N THR B 337 " --> pdb=" O PHE B 323 " (cutoff:3.500A) removed outlier: 4.587A pdb=" N ILE B 325 " --> pdb=" O TYR B 335 " (cutoff:3.500A) removed outlier: 6.747A pdb=" N TYR B 335 " --> pdb=" O ILE B 325 " (cutoff:3.500A) removed outlier: 7.358A pdb=" N GLY B 346 " --> pdb=" O ASN B 362 " (cutoff:3.500A) removed outlier: 5.426A pdb=" N ASN B 362 " --> pdb=" O GLY B 346 " (cutoff:3.500A) removed outlier: 6.201A pdb=" N VAL B 348 " --> pdb=" O ARG B 360 " (cutoff:3.500A) removed outlier: 4.253A pdb=" N ARG B 360 " --> pdb=" O VAL B 348 " (cutoff:3.500A) removed outlier: 6.851A pdb=" N CYS B 350 " --> pdb=" O GLN B 358 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 399 through 403 removed outlier: 3.530A pdb=" N GLU B 401 " --> pdb=" O THR B 450 " (cutoff:3.500A) removed outlier: 5.917A pdb=" N VAL B 492 " --> pdb=" O LEU B 511 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 440 through 441 Processing sheet with id=AB7, first strand: chain 'B' and resid 457 through 458 Processing sheet with id=AB8, first strand: chain 'B' and resid 611 through 612 Processing sheet with id=AB9, first strand: chain 'B' and resid 548 through 551 removed outlier: 3.953A pdb=" N ARG B 540 " --> pdb=" O TYR B 530 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N ASN B 524 " --> pdb=" O GLY B 576 " (cutoff:3.500A) removed outlier: 6.245A pdb=" N GLY B 576 " --> pdb=" O ASN B 524 " (cutoff:3.500A) removed outlier: 4.454A pdb=" N GLU B 526 " --> pdb=" O PHE B 574 " (cutoff:3.500A) removed outlier: 6.618A pdb=" N PHE B 574 " --> pdb=" O GLU B 526 " (cutoff:3.500A) removed outlier: 4.435A pdb=" N THR B 528 " --> pdb=" O ILE B 572 " (cutoff:3.500A) removed outlier: 6.544A pdb=" N ILE B 572 " --> pdb=" O THR B 528 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 583 through 584 removed outlier: 3.868A pdb=" N VAL B 591 " --> pdb=" O ILE B 584 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 642 through 644 removed outlier: 6.030A pdb=" N GLY B 647 " --> pdb=" O VAL B 643 " (cutoff:3.500A) 306 hydrogen bonds defined for protein. 819 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.76 Time building geometry restraints manager: 2.78 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 3204 1.34 - 1.46: 2285 1.46 - 1.58: 4584 1.58 - 1.70: 1 1.70 - 1.82: 29 Bond restraints: 10103 Sorted by residual: bond pdb=" CG PRO A 175 " pdb=" CD PRO A 175 " ideal model delta sigma weight residual 1.503 1.363 0.140 3.40e-02 8.65e+02 1.69e+01 bond pdb=" C5 GAL B 701 " pdb=" O5 GAL B 701 " ideal model delta sigma weight residual 1.412 1.481 -0.069 2.00e-02 2.50e+03 1.20e+01 bond pdb=" CB PRO A 175 " pdb=" CG PRO A 175 " ideal model delta sigma weight residual 1.492 1.648 -0.156 5.00e-02 4.00e+02 9.75e+00 bond pdb=" N PRO A 175 " pdb=" CD PRO A 175 " ideal model delta sigma weight residual 1.473 1.511 -0.038 1.40e-02 5.10e+03 7.26e+00 bond pdb=" C1 GAL B 701 " pdb=" O5 GAL B 701 " ideal model delta sigma weight residual 1.407 1.451 -0.044 2.00e-02 2.50e+03 4.93e+00 ... (remaining 10098 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.50: 13498 3.50 - 6.99: 194 6.99 - 10.49: 22 10.49 - 13.98: 3 13.98 - 17.48: 2 Bond angle restraints: 13719 Sorted by residual: angle pdb=" CA PRO A 175 " pdb=" N PRO A 175 " pdb=" CD PRO A 175 " ideal model delta sigma weight residual 112.00 94.52 17.48 1.40e+00 5.10e-01 1.56e+02 angle pdb=" N PRO A 175 " pdb=" CD PRO A 175 " pdb=" CG PRO A 175 " ideal model delta sigma weight residual 103.20 92.83 10.37 1.50e+00 4.44e-01 4.78e+01 angle pdb=" C LYS B 147 " pdb=" N ASP B 148 " pdb=" CA ASP B 148 " ideal model delta sigma weight residual 121.54 132.39 -10.85 1.91e+00 2.74e-01 3.22e+01 angle pdb=" C GLN B 62 " pdb=" N ASN B 63 " pdb=" CA ASN B 63 " ideal model delta sigma weight residual 122.46 129.32 -6.86 1.41e+00 5.03e-01 2.36e+01 angle pdb=" N VAL B 44 " pdb=" CA VAL B 44 " pdb=" C VAL B 44 " ideal model delta sigma weight residual 106.21 111.38 -5.17 1.07e+00 8.73e-01 2.33e+01 ... (remaining 13714 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.45: 5612 22.45 - 44.90: 312 44.90 - 67.35: 30 67.35 - 89.80: 15 89.80 - 112.26: 3 Dihedral angle restraints: 5972 sinusoidal: 2339 harmonic: 3633 Sorted by residual: dihedral pdb=" CA GLN B 533 " pdb=" C GLN B 533 " pdb=" N PRO B 534 " pdb=" CA PRO B 534 " ideal model delta harmonic sigma weight residual 180.00 156.06 23.94 0 5.00e+00 4.00e-02 2.29e+01 dihedral pdb=" CA ARG A 454 " pdb=" C ARG A 454 " pdb=" N LEU A 455 " pdb=" CA LEU A 455 " ideal model delta harmonic sigma weight residual 180.00 157.35 22.65 0 5.00e+00 4.00e-02 2.05e+01 dihedral pdb=" CA PHE B 550 " pdb=" C PHE B 550 " pdb=" N VAL B 551 " pdb=" CA VAL B 551 " ideal model delta harmonic sigma weight residual 180.00 157.86 22.14 0 5.00e+00 4.00e-02 1.96e+01 ... (remaining 5969 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.085: 1266 0.085 - 0.171: 198 0.171 - 0.256: 24 0.256 - 0.341: 0 0.341 - 0.427: 1 Chirality restraints: 1489 Sorted by residual: chirality pdb=" CB ILE B 403 " pdb=" CA ILE B 403 " pdb=" CG1 ILE B 403 " pdb=" CG2 ILE B 403 " both_signs ideal model delta sigma weight residual False 2.64 2.22 0.43 2.00e-01 2.50e+01 4.55e+00 chirality pdb=" CB ILE A 551 " pdb=" CA ILE A 551 " pdb=" CG1 ILE A 551 " pdb=" CG2 ILE A 551 " both_signs ideal model delta sigma weight residual False 2.64 2.90 -0.25 2.00e-01 2.50e+01 1.62e+00 chirality pdb=" CB ILE A 535 " pdb=" CA ILE A 535 " pdb=" CG1 ILE A 535 " pdb=" CG2 ILE A 535 " both_signs ideal model delta sigma weight residual False 2.64 2.39 0.25 2.00e-01 2.50e+01 1.62e+00 ... (remaining 1486 not shown) Planarity restraints: 1796 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LYS A 174 " -0.127 5.00e-02 4.00e+02 1.75e-01 4.90e+01 pdb=" N PRO A 175 " 0.302 5.00e-02 4.00e+02 pdb=" CA PRO A 175 " -0.091 5.00e-02 4.00e+02 pdb=" CD PRO A 175 " -0.084 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA MET A 213 " -0.017 2.00e-02 2.50e+03 3.33e-02 1.11e+01 pdb=" C MET A 213 " 0.058 2.00e-02 2.50e+03 pdb=" O MET A 213 " -0.022 2.00e-02 2.50e+03 pdb=" N SER A 214 " -0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE A 551 " 0.014 2.00e-02 2.50e+03 2.83e-02 8.03e+00 pdb=" C ILE A 551 " -0.049 2.00e-02 2.50e+03 pdb=" O ILE A 551 " 0.019 2.00e-02 2.50e+03 pdb=" N ASN A 552 " 0.016 2.00e-02 2.50e+03 ... (remaining 1793 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.79: 2124 2.79 - 3.31: 8744 3.31 - 3.84: 16923 3.84 - 4.37: 19540 4.37 - 4.90: 34579 Nonbonded interactions: 81910 Sorted by model distance: nonbonded pdb=" O ALA A 82 " pdb=" OG1 THR A 558 " model vdw 2.257 3.040 nonbonded pdb=" OG SER B 324 " pdb=" O ASN B 369 " model vdw 2.291 3.040 nonbonded pdb=" OG1 THR A 598 " pdb=" O LEU A 601 " model vdw 2.296 3.040 nonbonded pdb=" OH TYR B 284 " pdb=" OE1 GLN B 353 " model vdw 2.298 3.040 nonbonded pdb=" OG1 THR B 478 " pdb=" O THR B 480 " model vdw 2.308 3.040 ... (remaining 81905 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.500 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.360 Check model and map are aligned: 0.060 Set scattering table: 0.080 Process input model: 26.210 Find NCS groups from input model: 0.180 Set up NCS constraints: 0.050 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:2.890 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.340 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7635 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 : 0.005 0.156 10103 Z= 0.354 Angle : 1.048 17.481 13719 Z= 0.577 Chirality : 0.063 0.427 1489 Planarity : 0.008 0.175 1796 Dihedral : 14.225 112.256 3656 Min Nonbonded Distance : 2.257 Molprobity Statistics. All-atom Clashscore : 6.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.29 % Favored : 90.71 % Rotamer: Outliers : 0.00 % Allowed : 0.19 % Favored : 99.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.93 (0.23), residues: 1238 helix: -2.85 (0.55), residues: 50 sheet: -0.41 (0.23), residues: 536 loop : -1.94 (0.23), residues: 652 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.002 TRP B 590 HIS 0.014 0.002 HIS A 80 PHE 0.035 0.003 PHE B 216 TYR 0.034 0.003 TYR A 395 ARG 0.014 0.001 ARG B 141 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2476 Ramachandran restraints generated. 1238 Oldfield, 0 Emsley, 1238 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2476 Ramachandran restraints generated. 1238 Oldfield, 0 Emsley, 1238 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 1077 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 106 time to evaluate : 1.128 Fit side-chains REVERT: A 113 ASP cc_start: 0.7168 (t70) cc_final: 0.6868 (t0) REVERT: B 369 ASN cc_start: 0.8108 (t0) cc_final: 0.7907 (t0) REVERT: B 429 HIS cc_start: 0.7729 (m-70) cc_final: 0.7399 (m170) REVERT: B 508 TRP cc_start: 0.7598 (m100) cc_final: 0.6735 (m100) REVERT: B 597 TRP cc_start: 0.8764 (p-90) cc_final: 0.7910 (p-90) REVERT: B 616 TRP cc_start: 0.8423 (m-10) cc_final: 0.8195 (m-10) outliers start: 0 outliers final: 0 residues processed: 106 average time/residue: 0.1749 time to fit residues: 29.2778 Evaluate side-chains 71 residues out of total 1077 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 71 time to evaluate : 1.150 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 104 optimal weight: 1.9990 chunk 93 optimal weight: 0.4980 chunk 52 optimal weight: 0.1980 chunk 32 optimal weight: 3.9990 chunk 63 optimal weight: 4.9990 chunk 50 optimal weight: 1.9990 chunk 97 optimal weight: 2.9990 chunk 37 optimal weight: 0.7980 chunk 59 optimal weight: 3.9990 chunk 72 optimal weight: 1.9990 chunk 112 optimal weight: 8.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 133 ASN ** A 322 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 420 ASN ** A 459 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 571 ASN ** A 580 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 87 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7780 moved from start: 0.1638 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 10103 Z= 0.303 Angle : 0.631 8.949 13719 Z= 0.337 Chirality : 0.048 0.210 1489 Planarity : 0.005 0.076 1796 Dihedral : 5.570 26.701 1390 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 9.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.19 % Favored : 92.81 % Rotamer: Outliers : 1.13 % Allowed : 8.26 % Favored : 90.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.93 (0.23), residues: 1238 helix: -1.27 (0.70), residues: 50 sheet: -0.81 (0.22), residues: 557 loop : -1.69 (0.24), residues: 631 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 399 HIS 0.002 0.001 HIS B 254 PHE 0.017 0.002 PHE A 311 TYR 0.022 0.002 TYR A 269 ARG 0.007 0.001 ARG A 454 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2476 Ramachandran restraints generated. 1238 Oldfield, 0 Emsley, 1238 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2476 Ramachandran restraints generated. 1238 Oldfield, 0 Emsley, 1238 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 1077 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 88 time to evaluate : 1.218 Fit side-chains revert: symmetry clash REVERT: A 113 ASP cc_start: 0.7605 (t70) cc_final: 0.7289 (t0) REVERT: A 304 GLU cc_start: 0.7666 (tm-30) cc_final: 0.7379 (tm-30) REVERT: A 363 LEU cc_start: 0.8744 (tp) cc_final: 0.8423 (tt) REVERT: B 326 GLN cc_start: 0.7937 (mp10) cc_final: 0.7638 (mp10) REVERT: B 369 ASN cc_start: 0.8430 (t0) cc_final: 0.8122 (t0) REVERT: B 508 TRP cc_start: 0.7537 (m100) cc_final: 0.6640 (m100) REVERT: B 597 TRP cc_start: 0.8791 (p-90) cc_final: 0.7890 (p-90) REVERT: B 616 TRP cc_start: 0.8624 (m-10) cc_final: 0.8170 (m-10) outliers start: 12 outliers final: 7 residues processed: 96 average time/residue: 0.1899 time to fit residues: 28.1027 Evaluate side-chains 73 residues out of total 1077 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 66 time to evaluate : 1.151 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 214 SER Chi-restraints excluded: chain A residue 365 THR Chi-restraints excluded: chain A residue 420 ASN Chi-restraints excluded: chain A residue 424 HIS Chi-restraints excluded: chain A residue 481 ILE Chi-restraints excluded: chain A residue 650 LEU Chi-restraints excluded: chain B residue 56 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 62 optimal weight: 1.9990 chunk 34 optimal weight: 0.9990 chunk 93 optimal weight: 0.7980 chunk 76 optimal weight: 0.8980 chunk 31 optimal weight: 4.9990 chunk 112 optimal weight: 7.9990 chunk 121 optimal weight: 2.9990 chunk 100 optimal weight: 0.0010 chunk 111 optimal weight: 4.9990 chunk 38 optimal weight: 0.8980 chunk 90 optimal weight: 2.9990 overall best weight: 0.7188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 322 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 459 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 478 GLN A 571 ASN ** A 580 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 665 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 429 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7774 moved from start: 0.1934 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 10103 Z= 0.215 Angle : 0.570 7.319 13719 Z= 0.304 Chirality : 0.047 0.218 1489 Planarity : 0.004 0.047 1796 Dihedral : 5.111 24.331 1390 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 9.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.67 % Favored : 92.33 % Rotamer: Outliers : 1.88 % Allowed : 10.04 % Favored : 88.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.82 (0.24), residues: 1238 helix: -1.19 (0.70), residues: 56 sheet: -0.80 (0.22), residues: 546 loop : -1.53 (0.24), residues: 636 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 399 HIS 0.008 0.001 HIS B 429 PHE 0.019 0.001 PHE A 520 TYR 0.020 0.001 TYR A 269 ARG 0.003 0.000 ARG A 129 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2476 Ramachandran restraints generated. 1238 Oldfield, 0 Emsley, 1238 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2476 Ramachandran restraints generated. 1238 Oldfield, 0 Emsley, 1238 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 1077 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 75 time to evaluate : 1.262 Fit side-chains revert: symmetry clash REVERT: A 113 ASP cc_start: 0.7601 (t70) cc_final: 0.7302 (t0) REVERT: A 363 LEU cc_start: 0.8780 (tp) cc_final: 0.8435 (tt) REVERT: A 460 ASP cc_start: 0.8436 (m-30) cc_final: 0.8219 (m-30) REVERT: B 326 GLN cc_start: 0.8050 (mp10) cc_final: 0.7778 (mp10) REVERT: B 476 GLN cc_start: 0.7743 (mm-40) cc_final: 0.6104 (pm20) REVERT: B 508 TRP cc_start: 0.7516 (m100) cc_final: 0.6530 (m100) REVERT: B 597 TRP cc_start: 0.8731 (p-90) cc_final: 0.7778 (p-90) REVERT: B 616 TRP cc_start: 0.8608 (m-10) cc_final: 0.8163 (m-10) outliers start: 20 outliers final: 14 residues processed: 89 average time/residue: 0.1695 time to fit residues: 24.4901 Evaluate side-chains 80 residues out of total 1077 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 66 time to evaluate : 1.169 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 196 LEU Chi-restraints excluded: chain A residue 214 SER Chi-restraints excluded: chain A residue 397 ASN Chi-restraints excluded: chain A residue 401 THR Chi-restraints excluded: chain A residue 424 HIS Chi-restraints excluded: chain A residue 481 ILE Chi-restraints excluded: chain A residue 535 ILE Chi-restraints excluded: chain A residue 538 THR Chi-restraints excluded: chain A residue 598 THR Chi-restraints excluded: chain A residue 650 LEU Chi-restraints excluded: chain B residue 56 SER Chi-restraints excluded: chain B residue 213 ILE Chi-restraints excluded: chain B residue 327 LEU Chi-restraints excluded: chain B residue 603 HIS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 111 optimal weight: 0.0670 chunk 84 optimal weight: 4.9990 chunk 58 optimal weight: 1.9990 chunk 12 optimal weight: 3.9990 chunk 53 optimal weight: 2.9990 chunk 75 optimal weight: 4.9990 chunk 113 optimal weight: 0.8980 chunk 119 optimal weight: 20.0000 chunk 59 optimal weight: 1.9990 chunk 107 optimal weight: 0.7980 chunk 32 optimal weight: 3.9990 overall best weight: 1.1522 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 209 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 322 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 459 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 571 ASN ** A 580 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 429 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7845 moved from start: 0.2520 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 10103 Z= 0.315 Angle : 0.602 10.470 13719 Z= 0.318 Chirality : 0.047 0.203 1489 Planarity : 0.004 0.039 1796 Dihedral : 5.120 22.237 1390 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 10.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.51 % Favored : 92.49 % Rotamer: Outliers : 2.35 % Allowed : 11.16 % Favored : 86.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.88 (0.24), residues: 1238 helix: -0.88 (0.71), residues: 55 sheet: -0.96 (0.22), residues: 543 loop : -1.48 (0.24), residues: 640 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 187 HIS 0.002 0.001 HIS B 557 PHE 0.017 0.002 PHE A 520 TYR 0.021 0.002 TYR A 269 ARG 0.003 0.001 ARG B 69 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2476 Ramachandran restraints generated. 1238 Oldfield, 0 Emsley, 1238 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2476 Ramachandran restraints generated. 1238 Oldfield, 0 Emsley, 1238 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 1077 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 79 time to evaluate : 1.149 Fit side-chains revert: symmetry clash REVERT: A 113 ASP cc_start: 0.7724 (t70) cc_final: 0.7384 (t0) REVERT: A 304 GLU cc_start: 0.7633 (tm-30) cc_final: 0.7281 (tm-30) REVERT: A 460 ASP cc_start: 0.8520 (m-30) cc_final: 0.8132 (m-30) REVERT: B 44 VAL cc_start: 0.8012 (OUTLIER) cc_final: 0.7810 (m) REVERT: B 326 GLN cc_start: 0.8188 (mp10) cc_final: 0.7867 (mp10) REVERT: B 340 TYR cc_start: 0.8682 (m-10) cc_final: 0.8414 (m-10) REVERT: B 347 ASP cc_start: 0.8453 (m-30) cc_final: 0.7985 (m-30) REVERT: B 429 HIS cc_start: 0.7922 (m90) cc_final: 0.7433 (m170) REVERT: B 508 TRP cc_start: 0.7515 (m100) cc_final: 0.7050 (m100) REVERT: B 541 TRP cc_start: 0.8070 (p-90) cc_final: 0.7646 (p-90) outliers start: 25 outliers final: 18 residues processed: 96 average time/residue: 0.1895 time to fit residues: 28.0566 Evaluate side-chains 90 residues out of total 1077 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 71 time to evaluate : 1.172 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 196 LEU Chi-restraints excluded: chain A residue 214 SER Chi-restraints excluded: chain A residue 219 TYR Chi-restraints excluded: chain A residue 233 VAL Chi-restraints excluded: chain A residue 355 ILE Chi-restraints excluded: chain A residue 365 THR Chi-restraints excluded: chain A residue 401 THR Chi-restraints excluded: chain A residue 424 HIS Chi-restraints excluded: chain A residue 439 HIS Chi-restraints excluded: chain A residue 481 ILE Chi-restraints excluded: chain A residue 535 ILE Chi-restraints excluded: chain A residue 538 THR Chi-restraints excluded: chain A residue 598 THR Chi-restraints excluded: chain A residue 622 ASP Chi-restraints excluded: chain A residue 650 LEU Chi-restraints excluded: chain B residue 44 VAL Chi-restraints excluded: chain B residue 56 SER Chi-restraints excluded: chain B residue 155 TYR Chi-restraints excluded: chain B residue 327 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 99 optimal weight: 0.9990 chunk 68 optimal weight: 1.9990 chunk 1 optimal weight: 0.9980 chunk 89 optimal weight: 0.9980 chunk 49 optimal weight: 0.8980 chunk 102 optimal weight: 6.9990 chunk 82 optimal weight: 2.9990 chunk 0 optimal weight: 3.9990 chunk 61 optimal weight: 0.6980 chunk 107 optimal weight: 4.9990 chunk 30 optimal weight: 0.8980 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 209 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 322 GLN A 571 ASN ** A 580 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7836 moved from start: 0.2671 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 10103 Z= 0.255 Angle : 0.571 8.979 13719 Z= 0.303 Chirality : 0.047 0.210 1489 Planarity : 0.003 0.038 1796 Dihedral : 4.973 22.061 1390 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 10.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.35 % Favored : 92.65 % Rotamer: Outliers : 3.00 % Allowed : 11.63 % Favored : 85.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.86 (0.24), residues: 1238 helix: -0.89 (0.73), residues: 55 sheet: -1.02 (0.22), residues: 543 loop : -1.38 (0.25), residues: 640 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 187 HIS 0.003 0.001 HIS B 429 PHE 0.018 0.001 PHE A 296 TYR 0.020 0.002 TYR A 269 ARG 0.002 0.000 ARG B 132 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2476 Ramachandran restraints generated. 1238 Oldfield, 0 Emsley, 1238 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2476 Ramachandran restraints generated. 1238 Oldfield, 0 Emsley, 1238 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 1077 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 73 time to evaluate : 0.990 Fit side-chains REVERT: A 113 ASP cc_start: 0.7689 (t70) cc_final: 0.7454 (t70) REVERT: B 44 VAL cc_start: 0.7931 (OUTLIER) cc_final: 0.7629 (m) REVERT: B 326 GLN cc_start: 0.8130 (mp10) cc_final: 0.7792 (mp10) REVERT: B 340 TYR cc_start: 0.8639 (m-10) cc_final: 0.8253 (m-10) REVERT: B 508 TRP cc_start: 0.7474 (m100) cc_final: 0.6516 (m100) REVERT: B 541 TRP cc_start: 0.8074 (p-90) cc_final: 0.7665 (p-90) REVERT: B 597 TRP cc_start: 0.8646 (p-90) cc_final: 0.7750 (p-90) REVERT: B 616 TRP cc_start: 0.8759 (m-10) cc_final: 0.8351 (m-10) outliers start: 32 outliers final: 22 residues processed: 95 average time/residue: 0.1749 time to fit residues: 26.0888 Evaluate side-chains 91 residues out of total 1077 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 68 time to evaluate : 1.200 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 110 VAL Chi-restraints excluded: chain A residue 165 THR Chi-restraints excluded: chain A residue 196 LEU Chi-restraints excluded: chain A residue 214 SER Chi-restraints excluded: chain A residue 219 TYR Chi-restraints excluded: chain A residue 233 VAL Chi-restraints excluded: chain A residue 350 SER Chi-restraints excluded: chain A residue 355 ILE Chi-restraints excluded: chain A residue 365 THR Chi-restraints excluded: chain A residue 401 THR Chi-restraints excluded: chain A residue 424 HIS Chi-restraints excluded: chain A residue 439 HIS Chi-restraints excluded: chain A residue 455 LEU Chi-restraints excluded: chain A residue 481 ILE Chi-restraints excluded: chain A residue 535 ILE Chi-restraints excluded: chain A residue 538 THR Chi-restraints excluded: chain A residue 598 THR Chi-restraints excluded: chain A residue 622 ASP Chi-restraints excluded: chain A residue 650 LEU Chi-restraints excluded: chain B residue 44 VAL Chi-restraints excluded: chain B residue 52 MET Chi-restraints excluded: chain B residue 155 TYR Chi-restraints excluded: chain B residue 274 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 40 optimal weight: 2.9990 chunk 107 optimal weight: 8.9990 chunk 23 optimal weight: 0.9980 chunk 70 optimal weight: 0.3980 chunk 29 optimal weight: 0.6980 chunk 119 optimal weight: 9.9990 chunk 99 optimal weight: 0.9980 chunk 55 optimal weight: 2.9990 chunk 9 optimal weight: 2.9990 chunk 39 optimal weight: 0.7980 chunk 62 optimal weight: 0.0050 overall best weight: 0.5794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 209 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 571 ASN ** A 580 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7809 moved from start: 0.2719 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 10103 Z= 0.191 Angle : 0.549 8.885 13719 Z= 0.291 Chirality : 0.046 0.237 1489 Planarity : 0.003 0.038 1796 Dihedral : 4.762 22.321 1390 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 10.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.75 % Favored : 92.25 % Rotamer: Outliers : 3.00 % Allowed : 12.20 % Favored : 84.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.74 (0.24), residues: 1238 helix: -0.40 (0.79), residues: 50 sheet: -0.97 (0.22), residues: 555 loop : -1.30 (0.25), residues: 633 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 590 HIS 0.001 0.000 HIS B 254 PHE 0.016 0.001 PHE A 296 TYR 0.021 0.001 TYR A 269 ARG 0.002 0.000 ARG B 141 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2476 Ramachandran restraints generated. 1238 Oldfield, 0 Emsley, 1238 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2476 Ramachandran restraints generated. 1238 Oldfield, 0 Emsley, 1238 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 1077 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 75 time to evaluate : 1.100 Fit side-chains REVERT: A 113 ASP cc_start: 0.7638 (t70) cc_final: 0.7391 (t70) REVERT: B 44 VAL cc_start: 0.7974 (OUTLIER) cc_final: 0.7755 (m) REVERT: B 326 GLN cc_start: 0.8087 (mp10) cc_final: 0.7747 (mp10) REVERT: B 340 TYR cc_start: 0.8547 (m-10) cc_final: 0.8196 (m-10) REVERT: B 476 GLN cc_start: 0.7877 (mm-40) cc_final: 0.6170 (pm20) REVERT: B 508 TRP cc_start: 0.7478 (m100) cc_final: 0.6425 (m100) REVERT: B 541 TRP cc_start: 0.8058 (p-90) cc_final: 0.7641 (p-90) REVERT: B 597 TRP cc_start: 0.8646 (p-90) cc_final: 0.7699 (p-90) REVERT: B 616 TRP cc_start: 0.8690 (m-10) cc_final: 0.8242 (m-10) outliers start: 32 outliers final: 20 residues processed: 100 average time/residue: 0.1855 time to fit residues: 28.6903 Evaluate side-chains 92 residues out of total 1077 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 71 time to evaluate : 1.232 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 110 VAL Chi-restraints excluded: chain A residue 165 THR Chi-restraints excluded: chain A residue 169 HIS Chi-restraints excluded: chain A residue 196 LEU Chi-restraints excluded: chain A residue 214 SER Chi-restraints excluded: chain A residue 219 TYR Chi-restraints excluded: chain A residue 233 VAL Chi-restraints excluded: chain A residue 355 ILE Chi-restraints excluded: chain A residue 401 THR Chi-restraints excluded: chain A residue 424 HIS Chi-restraints excluded: chain A residue 439 HIS Chi-restraints excluded: chain A residue 455 LEU Chi-restraints excluded: chain A residue 481 ILE Chi-restraints excluded: chain A residue 535 ILE Chi-restraints excluded: chain A residue 598 THR Chi-restraints excluded: chain A residue 622 ASP Chi-restraints excluded: chain A residue 650 LEU Chi-restraints excluded: chain B residue 44 VAL Chi-restraints excluded: chain B residue 52 MET Chi-restraints excluded: chain B residue 241 VAL Chi-restraints excluded: chain B residue 274 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 115 optimal weight: 0.0170 chunk 13 optimal weight: 3.9990 chunk 68 optimal weight: 0.8980 chunk 87 optimal weight: 0.8980 chunk 67 optimal weight: 0.7980 chunk 100 optimal weight: 0.3980 chunk 66 optimal weight: 0.6980 chunk 119 optimal weight: 10.0000 chunk 74 optimal weight: 0.5980 chunk 72 optimal weight: 0.8980 chunk 55 optimal weight: 2.9990 overall best weight: 0.5018 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 209 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 571 ASN ** A 580 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 665 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7798 moved from start: 0.2797 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 10103 Z= 0.180 Angle : 0.556 9.174 13719 Z= 0.292 Chirality : 0.046 0.222 1489 Planarity : 0.003 0.039 1796 Dihedral : 4.696 23.378 1390 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 10.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.51 % Favored : 92.49 % Rotamer: Outliers : 2.72 % Allowed : 12.66 % Favored : 84.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.72 (0.24), residues: 1238 helix: -0.62 (0.76), residues: 50 sheet: -1.00 (0.22), residues: 551 loop : -1.22 (0.25), residues: 637 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 590 HIS 0.005 0.001 HIS A 80 PHE 0.020 0.001 PHE B 421 TYR 0.022 0.001 TYR A 636 ARG 0.003 0.000 ARG B 141 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2476 Ramachandran restraints generated. 1238 Oldfield, 0 Emsley, 1238 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2476 Ramachandran restraints generated. 1238 Oldfield, 0 Emsley, 1238 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 1077 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 78 time to evaluate : 1.069 Fit side-chains REVERT: A 113 ASP cc_start: 0.7674 (t70) cc_final: 0.7391 (t70) REVERT: B 44 VAL cc_start: 0.7923 (OUTLIER) cc_final: 0.7704 (m) REVERT: B 326 GLN cc_start: 0.8061 (mp10) cc_final: 0.7724 (mp10) REVERT: B 340 TYR cc_start: 0.8541 (m-10) cc_final: 0.8247 (m-10) REVERT: B 508 TRP cc_start: 0.7462 (m100) cc_final: 0.6406 (m100) REVERT: B 597 TRP cc_start: 0.8644 (p-90) cc_final: 0.7686 (p-90) REVERT: B 616 TRP cc_start: 0.8694 (m-10) cc_final: 0.8211 (m-10) outliers start: 29 outliers final: 22 residues processed: 98 average time/residue: 0.1605 time to fit residues: 25.3018 Evaluate side-chains 94 residues out of total 1077 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 71 time to evaluate : 1.072 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 110 VAL Chi-restraints excluded: chain A residue 165 THR Chi-restraints excluded: chain A residue 169 HIS Chi-restraints excluded: chain A residue 196 LEU Chi-restraints excluded: chain A residue 214 SER Chi-restraints excluded: chain A residue 219 TYR Chi-restraints excluded: chain A residue 233 VAL Chi-restraints excluded: chain A residue 355 ILE Chi-restraints excluded: chain A residue 401 THR Chi-restraints excluded: chain A residue 410 VAL Chi-restraints excluded: chain A residue 424 HIS Chi-restraints excluded: chain A residue 439 HIS Chi-restraints excluded: chain A residue 455 LEU Chi-restraints excluded: chain A residue 481 ILE Chi-restraints excluded: chain A residue 535 ILE Chi-restraints excluded: chain A residue 538 THR Chi-restraints excluded: chain A residue 598 THR Chi-restraints excluded: chain A residue 622 ASP Chi-restraints excluded: chain A residue 650 LEU Chi-restraints excluded: chain B residue 44 VAL Chi-restraints excluded: chain B residue 52 MET Chi-restraints excluded: chain B residue 155 TYR Chi-restraints excluded: chain B residue 241 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 73 optimal weight: 1.9990 chunk 47 optimal weight: 0.7980 chunk 71 optimal weight: 1.9990 chunk 36 optimal weight: 0.8980 chunk 23 optimal weight: 0.6980 chunk 75 optimal weight: 0.6980 chunk 81 optimal weight: 0.9980 chunk 59 optimal weight: 3.9990 chunk 11 optimal weight: 1.9990 chunk 93 optimal weight: 1.9990 chunk 108 optimal weight: 5.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 209 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 571 ASN ** A 580 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 95 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7829 moved from start: 0.2943 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 10103 Z= 0.238 Angle : 0.580 9.542 13719 Z= 0.304 Chirality : 0.047 0.217 1489 Planarity : 0.003 0.038 1796 Dihedral : 4.771 25.605 1390 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 10.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.08 % Favored : 91.92 % Rotamer: Outliers : 2.91 % Allowed : 13.41 % Favored : 83.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.76 (0.24), residues: 1238 helix: -0.57 (0.77), residues: 49 sheet: -1.06 (0.23), residues: 548 loop : -1.21 (0.25), residues: 641 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 590 HIS 0.002 0.001 HIS A 80 PHE 0.023 0.001 PHE B 421 TYR 0.021 0.001 TYR A 269 ARG 0.004 0.000 ARG B 141 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2476 Ramachandran restraints generated. 1238 Oldfield, 0 Emsley, 1238 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2476 Ramachandran restraints generated. 1238 Oldfield, 0 Emsley, 1238 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 1077 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 74 time to evaluate : 1.192 Fit side-chains REVERT: A 113 ASP cc_start: 0.7752 (t70) cc_final: 0.7446 (t70) REVERT: B 44 VAL cc_start: 0.7934 (OUTLIER) cc_final: 0.7713 (m) REVERT: B 326 GLN cc_start: 0.8144 (mp10) cc_final: 0.7802 (mp10) REVERT: B 340 TYR cc_start: 0.8624 (m-10) cc_final: 0.8282 (m-10) REVERT: B 347 ASP cc_start: 0.8404 (m-30) cc_final: 0.7843 (m-30) REVERT: B 508 TRP cc_start: 0.7464 (m100) cc_final: 0.6466 (m100) REVERT: B 597 TRP cc_start: 0.8643 (p-90) cc_final: 0.7679 (p-90) REVERT: B 616 TRP cc_start: 0.8673 (m-10) cc_final: 0.8253 (m-10) outliers start: 31 outliers final: 24 residues processed: 96 average time/residue: 0.1548 time to fit residues: 24.6865 Evaluate side-chains 100 residues out of total 1077 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 75 time to evaluate : 1.118 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 110 VAL Chi-restraints excluded: chain A residue 165 THR Chi-restraints excluded: chain A residue 169 HIS Chi-restraints excluded: chain A residue 196 LEU Chi-restraints excluded: chain A residue 214 SER Chi-restraints excluded: chain A residue 219 TYR Chi-restraints excluded: chain A residue 233 VAL Chi-restraints excluded: chain A residue 350 SER Chi-restraints excluded: chain A residue 355 ILE Chi-restraints excluded: chain A residue 401 THR Chi-restraints excluded: chain A residue 410 VAL Chi-restraints excluded: chain A residue 424 HIS Chi-restraints excluded: chain A residue 439 HIS Chi-restraints excluded: chain A residue 455 LEU Chi-restraints excluded: chain A residue 481 ILE Chi-restraints excluded: chain A residue 535 ILE Chi-restraints excluded: chain A residue 538 THR Chi-restraints excluded: chain A residue 598 THR Chi-restraints excluded: chain A residue 622 ASP Chi-restraints excluded: chain A residue 650 LEU Chi-restraints excluded: chain B residue 44 VAL Chi-restraints excluded: chain B residue 52 MET Chi-restraints excluded: chain B residue 155 TYR Chi-restraints excluded: chain B residue 241 VAL Chi-restraints excluded: chain B residue 274 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 114 optimal weight: 2.9990 chunk 104 optimal weight: 20.0000 chunk 111 optimal weight: 0.9990 chunk 67 optimal weight: 2.9990 chunk 48 optimal weight: 0.1980 chunk 87 optimal weight: 1.9990 chunk 34 optimal weight: 0.0570 chunk 100 optimal weight: 0.0670 chunk 105 optimal weight: 5.9990 chunk 110 optimal weight: 0.7980 chunk 73 optimal weight: 1.9990 overall best weight: 0.4238 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 209 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 571 ASN ** A 580 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 665 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7787 moved from start: 0.2933 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 10103 Z= 0.165 Angle : 0.559 9.666 13719 Z= 0.293 Chirality : 0.046 0.225 1489 Planarity : 0.003 0.038 1796 Dihedral : 4.583 23.007 1390 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 9.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.19 % Favored : 92.81 % Rotamer: Outliers : 2.44 % Allowed : 13.88 % Favored : 83.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.66 (0.25), residues: 1238 helix: -0.60 (0.77), residues: 50 sheet: -0.98 (0.23), residues: 546 loop : -1.17 (0.26), residues: 642 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 590 HIS 0.002 0.001 HIS B 603 PHE 0.023 0.001 PHE B 421 TYR 0.021 0.001 TYR A 269 ARG 0.005 0.000 ARG B 141 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2476 Ramachandran restraints generated. 1238 Oldfield, 0 Emsley, 1238 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2476 Ramachandran restraints generated. 1238 Oldfield, 0 Emsley, 1238 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 1077 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 77 time to evaluate : 1.052 Fit side-chains REVERT: A 113 ASP cc_start: 0.7677 (t70) cc_final: 0.7369 (t70) REVERT: B 44 VAL cc_start: 0.7844 (OUTLIER) cc_final: 0.7619 (m) REVERT: B 326 GLN cc_start: 0.8022 (mp10) cc_final: 0.7669 (mp10) REVERT: B 340 TYR cc_start: 0.8556 (m-10) cc_final: 0.8188 (m-10) REVERT: B 508 TRP cc_start: 0.7442 (m100) cc_final: 0.6374 (m100) REVERT: B 597 TRP cc_start: 0.8651 (p-90) cc_final: 0.7699 (p-90) REVERT: B 616 TRP cc_start: 0.8705 (m-10) cc_final: 0.8274 (m-10) outliers start: 26 outliers final: 22 residues processed: 97 average time/residue: 0.1514 time to fit residues: 24.2660 Evaluate side-chains 95 residues out of total 1077 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 72 time to evaluate : 1.261 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 110 VAL Chi-restraints excluded: chain A residue 165 THR Chi-restraints excluded: chain A residue 169 HIS Chi-restraints excluded: chain A residue 196 LEU Chi-restraints excluded: chain A residue 214 SER Chi-restraints excluded: chain A residue 219 TYR Chi-restraints excluded: chain A residue 233 VAL Chi-restraints excluded: chain A residue 401 THR Chi-restraints excluded: chain A residue 410 VAL Chi-restraints excluded: chain A residue 424 HIS Chi-restraints excluded: chain A residue 439 HIS Chi-restraints excluded: chain A residue 455 LEU Chi-restraints excluded: chain A residue 481 ILE Chi-restraints excluded: chain A residue 535 ILE Chi-restraints excluded: chain A residue 538 THR Chi-restraints excluded: chain A residue 598 THR Chi-restraints excluded: chain A residue 622 ASP Chi-restraints excluded: chain A residue 650 LEU Chi-restraints excluded: chain B residue 44 VAL Chi-restraints excluded: chain B residue 52 MET Chi-restraints excluded: chain B residue 155 TYR Chi-restraints excluded: chain B residue 241 VAL Chi-restraints excluded: chain B residue 274 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 117 optimal weight: 3.9990 chunk 71 optimal weight: 0.9980 chunk 55 optimal weight: 2.9990 chunk 81 optimal weight: 0.8980 chunk 123 optimal weight: 6.9990 chunk 113 optimal weight: 3.9990 chunk 98 optimal weight: 6.9990 chunk 10 optimal weight: 0.1980 chunk 75 optimal weight: 0.8980 chunk 60 optimal weight: 0.9980 chunk 78 optimal weight: 0.6980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 209 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 571 ASN ** A 580 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 326 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7823 moved from start: 0.3018 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 10103 Z= 0.223 Angle : 0.578 9.615 13719 Z= 0.301 Chirality : 0.047 0.212 1489 Planarity : 0.003 0.039 1796 Dihedral : 4.653 25.901 1390 Min Nonbonded Distance : 2.316 Molprobity Statistics. All-atom Clashscore : 10.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.92 % Favored : 92.08 % Rotamer: Outliers : 2.44 % Allowed : 14.26 % Favored : 83.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.69 (0.25), residues: 1238 helix: -0.49 (0.78), residues: 49 sheet: -1.04 (0.23), residues: 546 loop : -1.15 (0.26), residues: 643 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 590 HIS 0.002 0.001 HIS B 603 PHE 0.026 0.001 PHE B 421 TYR 0.021 0.001 TYR A 269 ARG 0.004 0.000 ARG B 141 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2476 Ramachandran restraints generated. 1238 Oldfield, 0 Emsley, 1238 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2476 Ramachandran restraints generated. 1238 Oldfield, 0 Emsley, 1238 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 1077 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 74 time to evaluate : 1.107 Fit side-chains REVERT: A 113 ASP cc_start: 0.7733 (t70) cc_final: 0.7412 (t70) REVERT: B 44 VAL cc_start: 0.7906 (OUTLIER) cc_final: 0.7677 (m) REVERT: B 326 GLN cc_start: 0.8046 (OUTLIER) cc_final: 0.7700 (mp10) REVERT: B 340 TYR cc_start: 0.8622 (m-10) cc_final: 0.8193 (m-10) REVERT: B 508 TRP cc_start: 0.7440 (m100) cc_final: 0.6442 (m100) REVERT: B 597 TRP cc_start: 0.8645 (p-90) cc_final: 0.7696 (p-90) REVERT: B 616 TRP cc_start: 0.8668 (m-10) cc_final: 0.8230 (m-10) outliers start: 26 outliers final: 22 residues processed: 95 average time/residue: 0.1637 time to fit residues: 25.6321 Evaluate side-chains 98 residues out of total 1077 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 74 time to evaluate : 1.166 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 110 VAL Chi-restraints excluded: chain A residue 165 THR Chi-restraints excluded: chain A residue 169 HIS Chi-restraints excluded: chain A residue 196 LEU Chi-restraints excluded: chain A residue 214 SER Chi-restraints excluded: chain A residue 219 TYR Chi-restraints excluded: chain A residue 233 VAL Chi-restraints excluded: chain A residue 401 THR Chi-restraints excluded: chain A residue 410 VAL Chi-restraints excluded: chain A residue 424 HIS Chi-restraints excluded: chain A residue 439 HIS Chi-restraints excluded: chain A residue 455 LEU Chi-restraints excluded: chain A residue 481 ILE Chi-restraints excluded: chain A residue 535 ILE Chi-restraints excluded: chain A residue 538 THR Chi-restraints excluded: chain A residue 598 THR Chi-restraints excluded: chain A residue 622 ASP Chi-restraints excluded: chain A residue 650 LEU Chi-restraints excluded: chain B residue 44 VAL Chi-restraints excluded: chain B residue 52 MET Chi-restraints excluded: chain B residue 155 TYR Chi-restraints excluded: chain B residue 241 VAL Chi-restraints excluded: chain B residue 274 LEU Chi-restraints excluded: chain B residue 326 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 104 optimal weight: 0.0980 chunk 30 optimal weight: 3.9990 chunk 90 optimal weight: 0.2980 chunk 14 optimal weight: 0.7980 chunk 27 optimal weight: 0.9980 chunk 98 optimal weight: 5.9990 chunk 41 optimal weight: 0.8980 chunk 101 optimal weight: 5.9990 chunk 12 optimal weight: 0.8980 chunk 18 optimal weight: 0.0770 chunk 86 optimal weight: 0.8980 overall best weight: 0.4338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 209 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 580 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3780 r_free = 0.3780 target = 0.129481 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.091438 restraints weight = 14383.661| |-----------------------------------------------------------------------------| r_work (start): 0.3299 rms_B_bonded: 3.17 r_work: 0.3182 rms_B_bonded: 3.47 restraints_weight: 0.5000 r_work (final): 0.3182 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7079 moved from start: 0.3007 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 10103 Z= 0.168 Angle : 0.565 9.583 13719 Z= 0.294 Chirality : 0.046 0.213 1489 Planarity : 0.003 0.037 1796 Dihedral : 4.563 24.298 1390 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 10.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.92 % Favored : 92.08 % Rotamer: Outliers : 2.25 % Allowed : 14.54 % Favored : 83.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.66 (0.25), residues: 1238 helix: -0.50 (0.78), residues: 49 sheet: -1.02 (0.23), residues: 551 loop : -1.13 (0.26), residues: 638 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 590 HIS 0.002 0.000 HIS B 603 PHE 0.027 0.001 PHE B 421 TYR 0.021 0.001 TYR A 269 ARG 0.005 0.000 ARG B 141 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2196.70 seconds wall clock time: 41 minutes 27.97 seconds (2487.97 seconds total)