Starting phenix.real_space_refine on Wed Apr 30 23:14:12 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8blw_16114/04_2025/8blw_16114.cif Found real_map, /net/cci-nas-00/data/ceres_data/8blw_16114/04_2025/8blw_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_16114/04_2025/8blw_16114.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8blw_16114/04_2025/8blw_16114.map" model { file = "/net/cci-nas-00/data/ceres_data/8blw_16114/04_2025/8blw_16114.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8blw_16114/04_2025/8blw_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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/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: 6.47, per 1000 atoms: 0.65 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: 2.55 Conformation dependent library (CDL) restraints added in 1.9 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: 1.34 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: 3.00 Time building geometry restraints manager: 2.88 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: 3.860 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: 0.070 Set scattering table: 0.090 Process input model: 26.570 Find NCS groups from input model: 0.200 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.480 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.680 ------------------------------------------------------------------------------- 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 10104 Z= 0.257 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 Details of bonding type rmsd hydrogen bonds : bond 0.13204 ( 306) hydrogen bonds : angle 7.87148 ( 819) covalent geometry : bond 0.00549 (10103) covalent geometry : angle 1.04846 (13719) Misc. bond : bond 0.00105 ( 1) *********************** 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 : 1.155 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: 0.1960 time to fit residues: 33.5062 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 : 1.192 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4024 r_free = 0.4024 target = 0.145173 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3587 r_free = 0.3587 target = 0.108497 restraints weight = 13077.907| |-----------------------------------------------------------------------------| r_work (start): 0.3585 rms_B_bonded: 2.46 r_work: 0.3475 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.3317 rms_B_bonded: 4.68 restraints_weight: 0.2500 r_work (final): 0.3317 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7739 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 10104 Z= 0.209 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 Details of bonding type rmsd hydrogen bonds : bond 0.03771 ( 306) hydrogen bonds : angle 6.74533 ( 819) covalent geometry : bond 0.00459 (10103) covalent geometry : angle 0.63079 (13719) Misc. bond : bond 0.00313 ( 1) *********************** 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 : 0.928 Fit side-chains revert: symmetry clash REVERT: A 113 ASP cc_start: 0.7968 (t70) cc_final: 0.7616 (t0) REVERT: A 304 GLU cc_start: 0.8090 (tm-30) cc_final: 0.7678 (tm-30) REVERT: A 363 LEU cc_start: 0.8788 (tp) cc_final: 0.8448 (tt) REVERT: A 495 TYR cc_start: 0.7861 (t80) cc_final: 0.7583 (t80) REVERT: B 326 GLN cc_start: 0.7876 (mp10) cc_final: 0.7627 (mp10) REVERT: B 369 ASN cc_start: 0.8397 (t0) cc_final: 0.8101 (t0) REVERT: B 508 TRP cc_start: 0.7686 (m100) cc_final: 0.6756 (m100) REVERT: B 597 TRP cc_start: 0.8815 (p-90) cc_final: 0.7935 (p-90) REVERT: B 616 TRP cc_start: 0.8640 (m-10) cc_final: 0.8198 (m-10) outliers start: 12 outliers final: 7 residues processed: 96 average time/residue: 0.1793 time to fit residues: 26.2626 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 : 1.056 ------------------------------------------------------------------------------- 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 31 optimal weight: 3.9990 chunk 38 optimal weight: 4.9990 chunk 58 optimal weight: 2.9990 chunk 91 optimal weight: 0.7980 chunk 35 optimal weight: 0.9980 chunk 101 optimal weight: 4.9990 chunk 48 optimal weight: 2.9990 chunk 1 optimal weight: 1.9990 chunk 94 optimal weight: 0.6980 chunk 60 optimal weight: 1.9990 chunk 95 optimal weight: 0.5980 overall best weight: 1.0182 ------------------------------------------------------------------------------- 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 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3952 r_free = 0.3952 target = 0.135997 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3545 r_free = 0.3545 target = 0.099340 restraints weight = 14425.542| |-----------------------------------------------------------------------------| r_work (start): 0.3529 rms_B_bonded: 2.76 r_work: 0.3431 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work: 0.3288 rms_B_bonded: 4.95 restraints_weight: 0.2500 r_work (final): 0.3288 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7602 moved from start: 0.2056 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 10104 Z= 0.193 Angle : 0.594 8.664 13719 Z= 0.316 Chirality : 0.047 0.221 1489 Planarity : 0.004 0.063 1796 Dihedral : 5.220 24.943 1390 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 10.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.67 % Favored : 92.33 % Rotamer: Outliers : 2.25 % Allowed : 10.13 % Favored : 87.62 % 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: -1.90 (0.24), residues: 1238 helix: -1.20 (0.69), residues: 56 sheet: -0.88 (0.22), residues: 548 loop : -1.56 (0.24), residues: 634 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 399 HIS 0.007 0.001 HIS B 429 PHE 0.019 0.001 PHE A 520 TYR 0.020 0.002 TYR A 269 ARG 0.003 0.000 ARG A 129 Details of bonding type rmsd hydrogen bonds : bond 0.03497 ( 306) hydrogen bonds : angle 6.58654 ( 819) covalent geometry : bond 0.00423 (10103) covalent geometry : angle 0.59390 (13719) Misc. bond : bond 0.00189 ( 1) *********************** 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: 24 poor density : 71 time to evaluate : 1.131 Fit side-chains REVERT: A 113 ASP cc_start: 0.8081 (t70) cc_final: 0.7773 (t0) REVERT: A 297 ILE cc_start: 0.8877 (OUTLIER) cc_final: 0.8664 (mp) REVERT: A 460 ASP cc_start: 0.8572 (m-30) cc_final: 0.8231 (m-30) REVERT: A 495 TYR cc_start: 0.7904 (t80) cc_final: 0.7614 (t80) REVERT: B 326 GLN cc_start: 0.8056 (mp10) cc_final: 0.7776 (mp10) REVERT: B 340 TYR cc_start: 0.8615 (m-10) cc_final: 0.8373 (m-10) REVERT: B 476 GLN cc_start: 0.7820 (mm-40) cc_final: 0.6175 (pm20) REVERT: B 508 TRP cc_start: 0.7604 (m100) cc_final: 0.6601 (m100) REVERT: B 597 TRP cc_start: 0.8718 (p-90) cc_final: 0.7812 (p-90) REVERT: B 616 TRP cc_start: 0.8625 (m-10) cc_final: 0.8232 (m-10) outliers start: 24 outliers final: 16 residues processed: 86 average time/residue: 0.1798 time to fit residues: 25.0959 Evaluate side-chains 84 residues out of total 1077 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 67 time to evaluate : 0.966 ------------------------------------------------------------------------------- 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 297 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 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 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 18 optimal weight: 0.2980 chunk 22 optimal weight: 2.9990 chunk 16 optimal weight: 4.9990 chunk 1 optimal weight: 1.9990 chunk 105 optimal weight: 8.9990 chunk 94 optimal weight: 1.9990 chunk 33 optimal weight: 0.8980 chunk 38 optimal weight: 0.6980 chunk 80 optimal weight: 0.9990 chunk 86 optimal weight: 0.0040 chunk 19 optimal weight: 0.8980 overall best weight: 0.5592 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3982 r_free = 0.3982 target = 0.138200 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3583 r_free = 0.3583 target = 0.101490 restraints weight = 14245.671| |-----------------------------------------------------------------------------| r_work (start): 0.3580 rms_B_bonded: 2.82 r_work: 0.3454 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.3454 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7484 moved from start: 0.2230 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 10104 Z= 0.129 Angle : 0.546 8.457 13719 Z= 0.290 Chirality : 0.046 0.219 1489 Planarity : 0.003 0.039 1796 Dihedral : 4.845 21.150 1390 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 9.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.43 % Favored : 92.57 % Rotamer: Outliers : 2.06 % Allowed : 11.16 % Favored : 86.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.73 (0.24), residues: 1238 helix: -0.98 (0.71), residues: 56 sheet: -0.84 (0.23), residues: 546 loop : -1.39 (0.24), residues: 636 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 590 HIS 0.004 0.001 HIS B 429 PHE 0.016 0.001 PHE A 296 TYR 0.021 0.001 TYR A 269 ARG 0.003 0.000 ARG B 141 Details of bonding type rmsd hydrogen bonds : bond 0.03048 ( 306) hydrogen bonds : angle 6.27054 ( 819) covalent geometry : bond 0.00276 (10103) covalent geometry : angle 0.54556 (13719) Misc. bond : bond 0.00136 ( 1) *********************** 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: 22 poor density : 82 time to evaluate : 1.034 Fit side-chains revert: symmetry clash REVERT: A 113 ASP cc_start: 0.7952 (t70) cc_final: 0.7577 (t0) REVERT: A 297 ILE cc_start: 0.8739 (OUTLIER) cc_final: 0.8525 (mp) REVERT: A 304 GLU cc_start: 0.8021 (tm-30) cc_final: 0.7465 (tm-30) REVERT: A 460 ASP cc_start: 0.8488 (m-30) cc_final: 0.8129 (m-30) REVERT: A 495 TYR cc_start: 0.7757 (t80) cc_final: 0.7449 (t80) REVERT: B 44 VAL cc_start: 0.7898 (OUTLIER) cc_final: 0.7693 (m) REVERT: B 326 GLN cc_start: 0.7940 (mp10) cc_final: 0.7694 (mp10) REVERT: B 340 TYR cc_start: 0.8381 (m-10) cc_final: 0.8156 (m-10) REVERT: B 429 HIS cc_start: 0.7960 (m90) cc_final: 0.7462 (m170) REVERT: B 508 TRP cc_start: 0.7597 (m100) cc_final: 0.6571 (m100) REVERT: B 541 TRP cc_start: 0.7971 (p-90) cc_final: 0.7557 (p-90) outliers start: 22 outliers final: 17 residues processed: 98 average time/residue: 0.1753 time to fit residues: 26.5666 Evaluate side-chains 92 residues out of total 1077 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 73 time to evaluate : 1.018 ------------------------------------------------------------------------------- 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 219 TYR Chi-restraints excluded: chain A residue 233 VAL Chi-restraints excluded: chain A residue 297 ILE 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 439 HIS 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 650 LEU Chi-restraints excluded: chain B residue 44 VAL Chi-restraints excluded: chain B residue 56 SER Chi-restraints excluded: chain B residue 213 ILE 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 33 optimal weight: 3.9990 chunk 66 optimal weight: 2.9990 chunk 98 optimal weight: 6.9990 chunk 111 optimal weight: 5.9990 chunk 88 optimal weight: 3.9990 chunk 108 optimal weight: 7.9990 chunk 84 optimal weight: 3.9990 chunk 64 optimal weight: 0.8980 chunk 71 optimal weight: 0.0370 chunk 91 optimal weight: 0.4980 chunk 75 optimal weight: 3.9990 overall best weight: 1.6862 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3699 r_free = 0.3699 target = 0.123096 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3246 r_free = 0.3246 target = 0.084920 restraints weight = 14820.111| |-----------------------------------------------------------------------------| r_work (start): 0.3197 rms_B_bonded: 3.07 r_work: 0.3083 rms_B_bonded: 3.32 restraints_weight: 0.5000 r_work (final): 0.3083 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7139 moved from start: 0.2984 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.048 10104 Z= 0.300 Angle : 0.658 11.518 13719 Z= 0.348 Chirality : 0.049 0.194 1489 Planarity : 0.004 0.037 1796 Dihedral : 5.341 28.614 1390 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 11.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.45 % Favored : 90.55 % Rotamer: Outliers : 3.38 % Allowed : 11.54 % Favored : 85.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.03 (0.24), residues: 1238 helix: -0.79 (0.73), residues: 55 sheet: -1.16 (0.22), residues: 543 loop : -1.50 (0.25), residues: 640 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 187 HIS 0.007 0.001 HIS B 429 PHE 0.021 0.002 PHE B 421 TYR 0.023 0.002 TYR A 267 ARG 0.003 0.001 ARG A 454 Details of bonding type rmsd hydrogen bonds : bond 0.03657 ( 306) hydrogen bonds : angle 6.79165 ( 819) covalent geometry : bond 0.00672 (10103) covalent geometry : angle 0.65818 (13719) Misc. bond : bond 0.00152 ( 1) *********************** 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 111 residues out of total 1077 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 75 time to evaluate : 1.171 Fit side-chains REVERT: A 297 ILE cc_start: 0.8531 (OUTLIER) cc_final: 0.8303 (mp) REVERT: A 386 SER cc_start: 0.8565 (t) cc_final: 0.8286 (m) REVERT: A 495 TYR cc_start: 0.7549 (t80) cc_final: 0.7324 (t80) REVERT: B 44 VAL cc_start: 0.7786 (OUTLIER) cc_final: 0.7526 (m) REVERT: B 45 PHE cc_start: 0.7198 (m-10) cc_final: 0.6985 (m-10) REVERT: B 326 GLN cc_start: 0.7882 (mp10) cc_final: 0.7468 (mp10) REVERT: B 338 GLU cc_start: 0.8519 (OUTLIER) cc_final: 0.8200 (tp30) REVERT: B 340 TYR cc_start: 0.8301 (m-10) cc_final: 0.7757 (m-10) REVERT: B 347 ASP cc_start: 0.7901 (m-30) cc_final: 0.7345 (m-30) REVERT: B 419 ASP cc_start: 0.8991 (m-30) cc_final: 0.8780 (p0) REVERT: B 476 GLN cc_start: 0.7920 (mm-40) cc_final: 0.6192 (pm20) REVERT: B 508 TRP cc_start: 0.7247 (m100) cc_final: 0.6209 (m100) REVERT: B 541 TRP cc_start: 0.7851 (p-90) cc_final: 0.7445 (p-90) REVERT: B 597 TRP cc_start: 0.8512 (p-90) cc_final: 0.7625 (p-90) REVERT: B 616 TRP cc_start: 0.8740 (m-10) cc_final: 0.8361 (m-10) outliers start: 36 outliers final: 21 residues processed: 101 average time/residue: 0.1748 time to fit residues: 27.9896 Evaluate side-chains 90 residues out of total 1077 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 66 time to evaluate : 1.178 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 110 VAL 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 297 ILE 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 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 241 VAL Chi-restraints excluded: chain B residue 274 LEU Chi-restraints excluded: chain B residue 338 GLU Chi-restraints excluded: chain B residue 493 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 86 optimal weight: 0.9980 chunk 92 optimal weight: 0.4980 chunk 16 optimal weight: 0.6980 chunk 67 optimal weight: 1.9990 chunk 32 optimal weight: 3.9990 chunk 50 optimal weight: 0.6980 chunk 72 optimal weight: 0.0670 chunk 39 optimal weight: 0.5980 chunk 87 optimal weight: 0.6980 chunk 65 optimal weight: 0.8980 chunk 9 optimal weight: 0.5980 overall best weight: 0.4918 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 124 GLN ** 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: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3755 r_free = 0.3755 target = 0.127513 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.089551 restraints weight = 14565.117| |-----------------------------------------------------------------------------| r_work (start): 0.3281 rms_B_bonded: 3.08 r_work: 0.3163 rms_B_bonded: 3.44 restraints_weight: 0.5000 r_work (final): 0.3163 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7115 moved from start: 0.2874 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 10104 Z= 0.133 Angle : 0.561 9.042 13719 Z= 0.297 Chirality : 0.046 0.221 1489 Planarity : 0.003 0.036 1796 Dihedral : 4.910 22.474 1390 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 10.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.75 % Favored : 92.25 % Rotamer: Outliers : 2.72 % Allowed : 13.13 % Favored : 84.15 % 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: -1.85 (0.24), residues: 1238 helix: -0.87 (0.73), residues: 55 sheet: -1.05 (0.22), residues: 547 loop : -1.34 (0.25), residues: 636 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 590 HIS 0.002 0.000 HIS B 254 PHE 0.019 0.001 PHE A 311 TYR 0.019 0.001 TYR A 269 ARG 0.003 0.000 ARG B 141 Details of bonding type rmsd hydrogen bonds : bond 0.03054 ( 306) hydrogen bonds : angle 6.36418 ( 819) covalent geometry : bond 0.00285 (10103) covalent geometry : angle 0.56051 (13719) Misc. bond : bond 0.00103 ( 1) *********************** 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 100 residues out of total 1077 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 71 time to evaluate : 1.300 Fit side-chains REVERT: A 297 ILE cc_start: 0.8508 (OUTLIER) cc_final: 0.8279 (mp) REVERT: A 495 TYR cc_start: 0.7572 (t80) cc_final: 0.7048 (t80) REVERT: B 44 VAL cc_start: 0.7643 (OUTLIER) cc_final: 0.7336 (m) REVERT: B 45 PHE cc_start: 0.7156 (m-10) cc_final: 0.6931 (m-10) REVERT: B 338 GLU cc_start: 0.8352 (OUTLIER) cc_final: 0.7972 (tp30) REVERT: B 340 TYR cc_start: 0.8255 (m-10) cc_final: 0.7785 (m-10) REVERT: B 508 TRP cc_start: 0.7192 (m100) cc_final: 0.6195 (m100) REVERT: B 597 TRP cc_start: 0.8450 (p-90) cc_final: 0.7491 (p-90) REVERT: B 616 TRP cc_start: 0.8641 (m-10) cc_final: 0.8210 (m-10) outliers start: 29 outliers final: 16 residues processed: 95 average time/residue: 0.2049 time to fit residues: 31.4006 Evaluate side-chains 86 residues out of total 1077 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 67 time to evaluate : 2.106 ------------------------------------------------------------------------------- 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 233 VAL Chi-restraints excluded: chain A residue 297 ILE Chi-restraints excluded: chain A residue 401 THR Chi-restraints excluded: chain A residue 410 VAL Chi-restraints excluded: chain A residue 439 HIS Chi-restraints excluded: chain A residue 481 ILE Chi-restraints excluded: chain A residue 489 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 155 TYR Chi-restraints excluded: chain B residue 338 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 105 optimal weight: 9.9990 chunk 43 optimal weight: 0.9990 chunk 27 optimal weight: 0.9990 chunk 4 optimal weight: 0.9990 chunk 106 optimal weight: 0.9990 chunk 32 optimal weight: 0.0570 chunk 0 optimal weight: 7.9990 chunk 46 optimal weight: 1.9990 chunk 90 optimal weight: 0.6980 chunk 49 optimal weight: 0.8980 chunk 93 optimal weight: 1.9990 overall best weight: 0.7302 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3749 r_free = 0.3749 target = 0.126868 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.089003 restraints weight = 14741.308| |-----------------------------------------------------------------------------| r_work (start): 0.3279 rms_B_bonded: 3.10 r_work: 0.3157 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work (final): 0.3157 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7130 moved from start: 0.2965 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 10104 Z= 0.155 Angle : 0.578 9.310 13719 Z= 0.303 Chirality : 0.047 0.241 1489 Planarity : 0.003 0.038 1796 Dihedral : 4.849 23.773 1390 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 11.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.32 % Favored : 91.68 % Rotamer: Outliers : 2.63 % Allowed : 12.85 % Favored : 84.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.85 (0.24), residues: 1238 helix: -1.01 (0.72), residues: 55 sheet: -1.06 (0.22), residues: 548 loop : -1.30 (0.25), residues: 635 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 0.018 0.001 PHE A 311 TYR 0.021 0.001 TYR A 269 ARG 0.003 0.000 ARG B 141 Details of bonding type rmsd hydrogen bonds : bond 0.03077 ( 306) hydrogen bonds : angle 6.25859 ( 819) covalent geometry : bond 0.00340 (10103) covalent geometry : angle 0.57769 (13719) Misc. bond : bond 0.00105 ( 1) *********************** 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 99 residues out of total 1077 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 71 time to evaluate : 1.293 Fit side-chains REVERT: A 297 ILE cc_start: 0.8532 (OUTLIER) cc_final: 0.8303 (mp) REVERT: A 495 TYR cc_start: 0.7617 (t80) cc_final: 0.7312 (t80) REVERT: A 636 TYR cc_start: 0.6948 (t80) cc_final: 0.6690 (t80) REVERT: B 44 VAL cc_start: 0.7650 (OUTLIER) cc_final: 0.7341 (m) REVERT: B 45 PHE cc_start: 0.7143 (m-10) cc_final: 0.6909 (m-10) REVERT: B 326 GLN cc_start: 0.7809 (mp10) cc_final: 0.7394 (mp10) REVERT: B 338 GLU cc_start: 0.8412 (OUTLIER) cc_final: 0.8036 (tp30) REVERT: B 340 TYR cc_start: 0.8244 (m-10) cc_final: 0.7756 (m-10) REVERT: B 374 SER cc_start: 0.8517 (t) cc_final: 0.8281 (p) REVERT: B 476 GLN cc_start: 0.7988 (mm-40) cc_final: 0.6269 (pm20) REVERT: B 508 TRP cc_start: 0.7179 (m100) cc_final: 0.6172 (m100) REVERT: B 597 TRP cc_start: 0.8462 (p-90) cc_final: 0.7490 (p-90) REVERT: B 616 TRP cc_start: 0.8590 (m-10) cc_final: 0.8151 (m-10) outliers start: 28 outliers final: 21 residues processed: 92 average time/residue: 0.1701 time to fit residues: 25.2612 Evaluate side-chains 93 residues out of total 1077 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 69 time to evaluate : 1.159 ------------------------------------------------------------------------------- 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 297 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 481 ILE Chi-restraints excluded: chain A residue 489 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 155 TYR Chi-restraints excluded: chain B residue 241 VAL Chi-restraints excluded: chain B residue 274 LEU Chi-restraints excluded: chain B residue 338 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 80 optimal weight: 0.7980 chunk 82 optimal weight: 0.7980 chunk 120 optimal weight: 9.9990 chunk 44 optimal weight: 1.9990 chunk 102 optimal weight: 0.7980 chunk 14 optimal weight: 0.8980 chunk 1 optimal weight: 1.9990 chunk 46 optimal weight: 0.8980 chunk 119 optimal weight: 10.0000 chunk 30 optimal weight: 0.7980 chunk 99 optimal weight: 0.9990 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** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3746 r_free = 0.3746 target = 0.126548 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.088719 restraints weight = 14754.161| |-----------------------------------------------------------------------------| r_work (start): 0.3274 rms_B_bonded: 3.09 r_work: 0.3121 rms_B_bonded: 3.55 restraints_weight: 0.5000 r_work (final): 0.3121 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7155 moved from start: 0.3072 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 10104 Z= 0.164 Angle : 0.578 9.779 13719 Z= 0.303 Chirality : 0.047 0.233 1489 Planarity : 0.003 0.038 1796 Dihedral : 4.853 24.788 1390 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 11.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.16 % Favored : 91.84 % Rotamer: Outliers : 2.81 % Allowed : 13.13 % Favored : 84.05 % 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: -1.89 (0.24), residues: 1238 helix: -1.04 (0.71), residues: 55 sheet: -1.12 (0.22), residues: 548 loop : -1.30 (0.25), residues: 635 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 590 HIS 0.002 0.001 HIS A 80 PHE 0.022 0.001 PHE A 311 TYR 0.021 0.001 TYR A 269 ARG 0.003 0.000 ARG B 141 Details of bonding type rmsd hydrogen bonds : bond 0.03092 ( 306) hydrogen bonds : angle 6.23814 ( 819) covalent geometry : bond 0.00361 (10103) covalent geometry : angle 0.57751 (13719) Misc. bond : bond 0.00107 ( 1) *********************** 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 102 residues out of total 1077 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 72 time to evaluate : 1.128 Fit side-chains revert: symmetry clash REVERT: A 297 ILE cc_start: 0.8513 (OUTLIER) cc_final: 0.8286 (mp) REVERT: A 495 TYR cc_start: 0.7619 (t80) cc_final: 0.7304 (t80) REVERT: A 505 ASN cc_start: 0.8736 (OUTLIER) cc_final: 0.8532 (m-40) REVERT: A 636 TYR cc_start: 0.7035 (t80) cc_final: 0.6798 (t80) REVERT: B 44 VAL cc_start: 0.7680 (OUTLIER) cc_final: 0.7369 (m) REVERT: B 45 PHE cc_start: 0.7180 (m-10) cc_final: 0.6954 (m-10) REVERT: B 326 GLN cc_start: 0.7819 (mp10) cc_final: 0.7427 (mp10) REVERT: B 338 GLU cc_start: 0.8479 (OUTLIER) cc_final: 0.8117 (tp30) REVERT: B 340 TYR cc_start: 0.8278 (m-10) cc_final: 0.7739 (m-10) REVERT: B 374 SER cc_start: 0.8561 (t) cc_final: 0.8322 (p) REVERT: B 508 TRP cc_start: 0.7214 (m100) cc_final: 0.6205 (m100) REVERT: B 597 TRP cc_start: 0.8495 (p-90) cc_final: 0.7507 (p-90) REVERT: B 616 TRP cc_start: 0.8621 (m-10) cc_final: 0.8156 (m-10) outliers start: 30 outliers final: 21 residues processed: 95 average time/residue: 0.1626 time to fit residues: 24.9215 Evaluate side-chains 95 residues out of total 1077 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 70 time to evaluate : 1.011 ------------------------------------------------------------------------------- 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 297 ILE Chi-restraints excluded: chain A residue 365 THR 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 481 ILE Chi-restraints excluded: chain A residue 505 ASN 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 338 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 110 optimal weight: 0.0870 chunk 80 optimal weight: 0.9980 chunk 33 optimal weight: 0.9980 chunk 59 optimal weight: 1.9990 chunk 84 optimal weight: 2.9990 chunk 108 optimal weight: 6.9990 chunk 73 optimal weight: 1.9990 chunk 49 optimal weight: 1.9990 chunk 22 optimal weight: 0.9990 chunk 31 optimal weight: 0.9990 chunk 61 optimal weight: 0.9990 overall best weight: 0.8162 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3741 r_free = 0.3741 target = 0.126385 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.088593 restraints weight = 14653.110| |-----------------------------------------------------------------------------| r_work (start): 0.3269 rms_B_bonded: 3.08 r_work: 0.3151 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work (final): 0.3151 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7144 moved from start: 0.3141 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 10104 Z= 0.164 Angle : 0.583 9.613 13719 Z= 0.305 Chirality : 0.047 0.229 1489 Planarity : 0.003 0.038 1796 Dihedral : 4.832 25.023 1390 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 11.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.56 % Favored : 91.44 % Rotamer: Outliers : 2.91 % Allowed : 13.04 % Favored : 84.05 % 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: -1.92 (0.24), residues: 1238 helix: -1.01 (0.71), residues: 55 sheet: -1.17 (0.22), residues: 549 loop : -1.30 (0.25), residues: 634 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 0.021 0.001 PHE A 311 TYR 0.020 0.001 TYR A 269 ARG 0.003 0.000 ARG B 141 Details of bonding type rmsd hydrogen bonds : bond 0.03084 ( 306) hydrogen bonds : angle 6.21150 ( 819) covalent geometry : bond 0.00360 (10103) covalent geometry : angle 0.58254 (13719) Misc. bond : bond 0.00104 ( 1) *********************** 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 107 residues out of total 1077 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 76 time to evaluate : 1.143 Fit side-chains revert: symmetry clash REVERT: A 297 ILE cc_start: 0.8520 (OUTLIER) cc_final: 0.8291 (mp) REVERT: A 372 MET cc_start: 0.7653 (ttt) cc_final: 0.7383 (ttt) REVERT: A 495 TYR cc_start: 0.7609 (t80) cc_final: 0.7037 (t80) REVERT: A 636 TYR cc_start: 0.7076 (t80) cc_final: 0.6843 (t80) REVERT: B 44 VAL cc_start: 0.7658 (OUTLIER) cc_final: 0.7340 (m) REVERT: B 45 PHE cc_start: 0.7215 (m-10) cc_final: 0.7005 (m-10) REVERT: B 326 GLN cc_start: 0.7814 (mp10) cc_final: 0.7387 (mp10) REVERT: B 338 GLU cc_start: 0.8446 (OUTLIER) cc_final: 0.8066 (tp30) REVERT: B 340 TYR cc_start: 0.8271 (m-10) cc_final: 0.7702 (m-10) REVERT: B 374 SER cc_start: 0.8598 (t) cc_final: 0.8396 (p) REVERT: B 508 TRP cc_start: 0.7137 (m100) cc_final: 0.6115 (m100) REVERT: B 597 TRP cc_start: 0.8447 (p-90) cc_final: 0.7448 (p-90) REVERT: B 616 TRP cc_start: 0.8626 (m-10) cc_final: 0.8145 (m-10) outliers start: 31 outliers final: 23 residues processed: 98 average time/residue: 0.1623 time to fit residues: 25.5790 Evaluate side-chains 94 residues out of total 1077 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 68 time to evaluate : 1.126 ------------------------------------------------------------------------------- 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 297 ILE Chi-restraints excluded: chain A residue 365 THR Chi-restraints excluded: chain A residue 397 ASN 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 481 ILE Chi-restraints excluded: chain A residue 489 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 306 THR Chi-restraints excluded: chain B residue 338 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 37 optimal weight: 2.9990 chunk 94 optimal weight: 1.9990 chunk 2 optimal weight: 1.9990 chunk 67 optimal weight: 2.9990 chunk 32 optimal weight: 0.0570 chunk 71 optimal weight: 0.0030 chunk 46 optimal weight: 3.9990 chunk 74 optimal weight: 0.7980 chunk 22 optimal weight: 0.9980 chunk 83 optimal weight: 3.9990 chunk 35 optimal weight: 4.9990 overall best weight: 0.7710 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3740 r_free = 0.3740 target = 0.126421 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.088688 restraints weight = 14565.600| |-----------------------------------------------------------------------------| r_work (start): 0.3271 rms_B_bonded: 3.07 r_work: 0.3121 rms_B_bonded: 3.53 restraints_weight: 0.5000 r_work (final): 0.3121 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7154 moved from start: 0.3189 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 10104 Z= 0.159 Angle : 0.586 9.890 13719 Z= 0.307 Chirality : 0.047 0.227 1489 Planarity : 0.003 0.038 1796 Dihedral : 4.812 24.875 1390 Min Nonbonded Distance : 2.314 Molprobity Statistics. All-atom Clashscore : 11.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.32 % Favored : 91.68 % Rotamer: Outliers : 2.63 % Allowed : 13.60 % Favored : 83.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.91 (0.24), residues: 1238 helix: -0.99 (0.72), residues: 55 sheet: -1.17 (0.22), residues: 547 loop : -1.29 (0.25), residues: 636 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 590 HIS 0.003 0.001 HIS B 603 PHE 0.020 0.001 PHE A 311 TYR 0.020 0.001 TYR A 269 ARG 0.003 0.000 ARG B 141 Details of bonding type rmsd hydrogen bonds : bond 0.03053 ( 306) hydrogen bonds : angle 6.19939 ( 819) covalent geometry : bond 0.00350 (10103) covalent geometry : angle 0.58596 (13719) Misc. bond : bond 0.00102 ( 1) ********************** 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 98 residues out of total 1077 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 70 time to evaluate : 1.476 Fit side-chains revert: symmetry clash REVERT: A 297 ILE cc_start: 0.8507 (OUTLIER) cc_final: 0.8282 (mp) REVERT: A 495 TYR cc_start: 0.7587 (t80) cc_final: 0.7018 (t80) REVERT: A 636 TYR cc_start: 0.7121 (t80) cc_final: 0.6885 (t80) REVERT: B 44 VAL cc_start: 0.7621 (OUTLIER) cc_final: 0.7294 (m) REVERT: B 45 PHE cc_start: 0.7242 (m-10) cc_final: 0.7038 (m-10) REVERT: B 326 GLN cc_start: 0.7825 (mp10) cc_final: 0.7429 (mp10) REVERT: B 338 GLU cc_start: 0.8476 (OUTLIER) cc_final: 0.8141 (tp30) REVERT: B 340 TYR cc_start: 0.8289 (m-10) cc_final: 0.7737 (m-10) REVERT: B 374 SER cc_start: 0.8645 (t) cc_final: 0.8414 (p) REVERT: B 508 TRP cc_start: 0.7125 (m100) cc_final: 0.6089 (m100) REVERT: B 597 TRP cc_start: 0.8455 (p-90) cc_final: 0.7471 (p-90) REVERT: B 616 TRP cc_start: 0.8634 (m-10) cc_final: 0.8175 (m-10) outliers start: 28 outliers final: 22 residues processed: 89 average time/residue: 0.2090 time to fit residues: 30.1738 Evaluate side-chains 94 residues out of total 1077 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 69 time to evaluate : 1.251 ------------------------------------------------------------------------------- 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 297 ILE Chi-restraints excluded: chain A residue 365 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 481 ILE Chi-restraints excluded: chain A residue 489 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 306 THR Chi-restraints excluded: chain B residue 338 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 5 optimal weight: 0.1980 chunk 101 optimal weight: 2.9990 chunk 79 optimal weight: 3.9990 chunk 15 optimal weight: 0.0970 chunk 43 optimal weight: 2.9990 chunk 13 optimal weight: 0.9980 chunk 83 optimal weight: 0.6980 chunk 52 optimal weight: 0.3980 chunk 88 optimal weight: 0.4980 chunk 54 optimal weight: 1.9990 chunk 6 optimal weight: 0.7980 overall best weight: 0.3778 ------------------------------------------------------------------------------- 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 = 0.3776 r_free = 0.3776 target = 0.129235 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.091394 restraints weight = 14521.326| |-----------------------------------------------------------------------------| r_work (start): 0.3304 rms_B_bonded: 3.18 r_work: 0.3186 rms_B_bonded: 3.50 restraints_weight: 0.5000 r_work (final): 0.3186 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7083 moved from start: 0.3114 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 10104 Z= 0.114 Angle : 0.563 9.765 13719 Z= 0.295 Chirality : 0.046 0.223 1489 Planarity : 0.003 0.038 1796 Dihedral : 4.617 23.138 1390 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 10.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.08 % Favored : 91.92 % Rotamer: Outliers : 2.35 % Allowed : 14.26 % Favored : 83.40 % 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 (0.25), residues: 1238 helix: -0.49 (0.78), residues: 50 sheet: -1.13 (0.22), residues: 552 loop : -1.24 (0.26), residues: 636 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 590 HIS 0.002 0.001 HIS B 603 PHE 0.022 0.001 PHE A 311 TYR 0.021 0.001 TYR A 269 ARG 0.004 0.000 ARG B 141 Details of bonding type rmsd hydrogen bonds : bond 0.02807 ( 306) hydrogen bonds : angle 5.96001 ( 819) covalent geometry : bond 0.00240 (10103) covalent geometry : angle 0.56318 (13719) Misc. bond : bond 0.00085 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5339.16 seconds wall clock time: 95 minutes 15.78 seconds (5715.78 seconds total)