Starting phenix.real_space_refine on Mon Jul 28 20:57:16 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6qma_4593/07_2025/6qma_4593.cif Found real_map, /net/cci-nas-00/data/ceres_data/6qma_4593/07_2025/6qma_4593.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6qma_4593/07_2025/6qma_4593.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6qma_4593/07_2025/6qma_4593.map" model { file = "/net/cci-nas-00/data/ceres_data/6qma_4593/07_2025/6qma_4593.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6qma_4593/07_2025/6qma_4593.cif" } resolution = 3.7 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= 0.011 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians Ca 4 9.91 5 S 40 5.16 5 C 6970 2.51 5 N 1786 2.21 5 O 1916 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 66 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib" Total number of atoms: 10716 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 5356 Number of conformers: 1 Conformer: "" Number of residues, atoms: 662, 5356 Classifications: {'peptide': 662} Link IDs: {'PTRANS': 28, 'TRANS': 633} Chain breaks: 5 Chain: "A" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' CA': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Restraints were copied for chains: B Time building chain proxies: 10.10, per 1000 atoms: 0.94 Number of scatterers: 10716 At special positions: 0 Unit cell: (120.428, 110.308, 106.26, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Ca 4 19.99 S 40 16.00 O 1916 8.00 N 1786 7.00 C 6970 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.53 Conformation dependent library (CDL) restraints added in 1.2 seconds 2600 Ramachandran restraints generated. 1300 Oldfield, 0 Emsley, 1300 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2512 Finding SS restraints... Secondary structure from input PDB file: 48 helices and 4 sheets defined 74.0% alpha, 2.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.97 Creating SS restraints... Processing helix chain 'A' and resid 32 through 50 Processing helix chain 'A' and resid 72 through 90 removed outlier: 3.720A pdb=" N HIS A 90 " --> pdb=" O GLY A 86 " (cutoff:3.500A) Processing helix chain 'A' and resid 102 through 108 Processing helix chain 'A' and resid 111 through 125 Processing helix chain 'A' and resid 152 through 166 Processing helix chain 'A' and resid 170 through 182 removed outlier: 3.827A pdb=" N ILE A 174 " --> pdb=" O GLU A 170 " (cutoff:3.500A) Processing helix chain 'A' and resid 182 through 211 removed outlier: 4.864A pdb=" N ILE A 201 " --> pdb=" O ARG A 197 " (cutoff:3.500A) Proline residue: A 202 - end of helix Processing helix chain 'A' and resid 217 through 246 removed outlier: 3.659A pdb=" N ALA A 221 " --> pdb=" O SER A 217 " (cutoff:3.500A) Processing helix chain 'A' and resid 280 through 318 removed outlier: 4.135A pdb=" N ARG A 284 " --> pdb=" O PRO A 280 " (cutoff:3.500A) removed outlier: 4.323A pdb=" N ILE A 292 " --> pdb=" O GLN A 288 " (cutoff:3.500A) Proline residue: A 293 - end of helix Processing helix chain 'A' and resid 325 through 358 Proline residue: A 332 - end of helix Proline residue: A 341 - end of helix Processing helix chain 'A' and resid 362 through 391 removed outlier: 6.152A pdb=" N ALA A 385 " --> pdb=" O THR A 381 " (cutoff:3.500A) removed outlier: 5.187A pdb=" N LEU A 386 " --> pdb=" O SER A 382 " (cutoff:3.500A) Processing helix chain 'A' and resid 400 through 415 removed outlier: 3.673A pdb=" N LEU A 404 " --> pdb=" O LEU A 400 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N THR A 413 " --> pdb=" O ALA A 409 " (cutoff:3.500A) Processing helix chain 'A' and resid 431 through 453 removed outlier: 3.624A pdb=" N ASN A 435 " --> pdb=" O ALA A 431 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N VAL A 453 " --> pdb=" O PHE A 449 " (cutoff:3.500A) Processing helix chain 'A' and resid 453 through 468 Processing helix chain 'A' and resid 477 through 481 removed outlier: 3.507A pdb=" N GLU A 480 " --> pdb=" O GLU A 477 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N GLU A 481 " --> pdb=" O ASP A 478 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 477 through 481' Processing helix chain 'A' and resid 482 through 495 removed outlier: 3.543A pdb=" N ARG A 488 " --> pdb=" O GLU A 484 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N THR A 494 " --> pdb=" O ARG A 490 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N LEU A 495 " --> pdb=" O GLU A 491 " (cutoff:3.500A) Processing helix chain 'A' and resid 500 through 518 removed outlier: 3.876A pdb=" N SER A 518 " --> pdb=" O VAL A 514 " (cutoff:3.500A) Processing helix chain 'A' and resid 523 through 543 removed outlier: 4.225A pdb=" N ALA A 540 " --> pdb=" O LEU A 536 " (cutoff:3.500A) Processing helix chain 'A' and resid 559 through 585 removed outlier: 4.152A pdb=" N THR A 563 " --> pdb=" O GLY A 559 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N ILE A 574 " --> pdb=" O TRP A 570 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N ASN A 585 " --> pdb=" O TYR A 581 " (cutoff:3.500A) Processing helix chain 'A' and resid 598 through 627 Processing helix chain 'A' and resid 629 through 650 removed outlier: 3.937A pdb=" N GLN A 633 " --> pdb=" O SER A 629 " (cutoff:3.500A) Processing helix chain 'A' and resid 666 through 684 removed outlier: 3.509A pdb=" N ILE A 684 " --> pdb=" O ARG A 680 " (cutoff:3.500A) Processing helix chain 'A' and resid 689 through 696 Processing helix chain 'A' and resid 700 through 718 Processing helix chain 'B' and resid 32 through 50 Processing helix chain 'B' and resid 72 through 90 removed outlier: 3.720A pdb=" N HIS B 90 " --> pdb=" O GLY B 86 " (cutoff:3.500A) Processing helix chain 'B' and resid 102 through 108 Processing helix chain 'B' and resid 111 through 125 Processing helix chain 'B' and resid 152 through 166 Processing helix chain 'B' and resid 170 through 182 removed outlier: 3.827A pdb=" N ILE B 174 " --> pdb=" O GLU B 170 " (cutoff:3.500A) Processing helix chain 'B' and resid 182 through 211 removed outlier: 4.864A pdb=" N ILE B 201 " --> pdb=" O ARG B 197 " (cutoff:3.500A) Proline residue: B 202 - end of helix Processing helix chain 'B' and resid 217 through 246 removed outlier: 3.659A pdb=" N ALA B 221 " --> pdb=" O SER B 217 " (cutoff:3.500A) Processing helix chain 'B' and resid 280 through 318 removed outlier: 4.134A pdb=" N ARG B 284 " --> pdb=" O PRO B 280 " (cutoff:3.500A) removed outlier: 4.324A pdb=" N ILE B 292 " --> pdb=" O GLN B 288 " (cutoff:3.500A) Proline residue: B 293 - end of helix Processing helix chain 'B' and resid 325 through 358 Proline residue: B 332 - end of helix Proline residue: B 341 - end of helix Processing helix chain 'B' and resid 362 through 391 removed outlier: 6.152A pdb=" N ALA B 385 " --> pdb=" O THR B 381 " (cutoff:3.500A) removed outlier: 5.187A pdb=" N LEU B 386 " --> pdb=" O SER B 382 " (cutoff:3.500A) Processing helix chain 'B' and resid 400 through 415 removed outlier: 3.673A pdb=" N LEU B 404 " --> pdb=" O LEU B 400 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N THR B 413 " --> pdb=" O ALA B 409 " (cutoff:3.500A) Processing helix chain 'B' and resid 431 through 453 removed outlier: 3.623A pdb=" N ASN B 435 " --> pdb=" O ALA B 431 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N VAL B 453 " --> pdb=" O PHE B 449 " (cutoff:3.500A) Processing helix chain 'B' and resid 453 through 468 Processing helix chain 'B' and resid 477 through 481 removed outlier: 3.508A pdb=" N GLU B 480 " --> pdb=" O GLU B 477 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N GLU B 481 " --> pdb=" O ASP B 478 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 477 through 481' Processing helix chain 'B' and resid 482 through 495 removed outlier: 3.543A pdb=" N ARG B 488 " --> pdb=" O GLU B 484 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N THR B 494 " --> pdb=" O ARG B 490 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N LEU B 495 " --> pdb=" O GLU B 491 " (cutoff:3.500A) Processing helix chain 'B' and resid 500 through 518 removed outlier: 3.877A pdb=" N SER B 518 " --> pdb=" O VAL B 514 " (cutoff:3.500A) Processing helix chain 'B' and resid 523 through 543 removed outlier: 4.226A pdb=" N ALA B 540 " --> pdb=" O LEU B 536 " (cutoff:3.500A) Processing helix chain 'B' and resid 559 through 585 removed outlier: 4.152A pdb=" N THR B 563 " --> pdb=" O GLY B 559 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N ILE B 574 " --> pdb=" O TRP B 570 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N ASN B 585 " --> pdb=" O TYR B 581 " (cutoff:3.500A) Processing helix chain 'B' and resid 598 through 627 Processing helix chain 'B' and resid 629 through 650 removed outlier: 3.937A pdb=" N GLN B 633 " --> pdb=" O SER B 629 " (cutoff:3.500A) Processing helix chain 'B' and resid 666 through 684 removed outlier: 3.510A pdb=" N ILE B 684 " --> pdb=" O ARG B 680 " (cutoff:3.500A) Processing helix chain 'B' and resid 689 through 696 Processing helix chain 'B' and resid 700 through 718 Processing sheet with id=AA1, first strand: chain 'A' and resid 52 through 59 removed outlier: 4.102A pdb=" N SER A 63 " --> pdb=" O GLY A 59 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 265 through 266 removed outlier: 3.708A pdb=" N HIS A 265 " --> pdb=" O VAL A 278 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 52 through 59 removed outlier: 4.102A pdb=" N SER B 63 " --> pdb=" O GLY B 59 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 265 through 266 removed outlier: 3.707A pdb=" N HIS B 265 " --> pdb=" O VAL B 278 " (cutoff:3.500A) 746 hydrogen bonds defined for protein. 2232 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: 3.08 Time building geometry restraints manager: 3.00 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: 3337 1.34 - 1.46: 1926 1.46 - 1.57: 5663 1.57 - 1.69: 0 1.69 - 1.81: 66 Bond restraints: 10992 Sorted by residual: bond pdb=" C ILE B 292 " pdb=" N PRO B 293 " ideal model delta sigma weight residual 1.335 1.393 -0.059 1.28e-02 6.10e+03 2.10e+01 bond pdb=" C ILE A 292 " pdb=" N PRO A 293 " ideal model delta sigma weight residual 1.335 1.393 -0.058 1.28e-02 6.10e+03 2.08e+01 bond pdb=" C THR A 340 " pdb=" N PRO A 341 " ideal model delta sigma weight residual 1.335 1.391 -0.055 1.36e-02 5.41e+03 1.67e+01 bond pdb=" C THR B 340 " pdb=" N PRO B 341 " ideal model delta sigma weight residual 1.335 1.391 -0.055 1.36e-02 5.41e+03 1.65e+01 bond pdb=" C ILE A 394 " pdb=" N PRO A 395 " ideal model delta sigma weight residual 1.334 1.386 -0.052 2.34e-02 1.83e+03 4.94e+00 ... (remaining 10987 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.23: 14457 2.23 - 4.46: 403 4.46 - 6.69: 30 6.69 - 8.92: 16 8.92 - 11.15: 4 Bond angle restraints: 14910 Sorted by residual: angle pdb=" C VAL A 454 " pdb=" N VAL A 455 " pdb=" CA VAL A 455 " ideal model delta sigma weight residual 120.33 124.43 -4.10 8.00e-01 1.56e+00 2.63e+01 angle pdb=" C VAL B 454 " pdb=" N VAL B 455 " pdb=" CA VAL B 455 " ideal model delta sigma weight residual 120.33 124.40 -4.07 8.00e-01 1.56e+00 2.59e+01 angle pdb=" N VAL A 248 " pdb=" CA VAL A 248 " pdb=" CB VAL A 248 " ideal model delta sigma weight residual 112.28 106.95 5.33 1.33e+00 5.65e-01 1.61e+01 angle pdb=" N VAL B 248 " pdb=" CA VAL B 248 " pdb=" CB VAL B 248 " ideal model delta sigma weight residual 112.28 106.95 5.33 1.33e+00 5.65e-01 1.60e+01 angle pdb=" N ILE A 543 " pdb=" CA ILE A 543 " pdb=" C ILE A 543 " ideal model delta sigma weight residual 112.50 107.23 5.27 1.39e+00 5.18e-01 1.44e+01 ... (remaining 14905 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.22: 5694 17.22 - 34.44: 598 34.44 - 51.67: 128 51.67 - 68.89: 20 68.89 - 86.11: 20 Dihedral angle restraints: 6460 sinusoidal: 2592 harmonic: 3868 Sorted by residual: dihedral pdb=" CA GLN A 648 " pdb=" C GLN A 648 " pdb=" N GLU A 649 " pdb=" CA GLU A 649 " ideal model delta harmonic sigma weight residual 180.00 162.35 17.65 0 5.00e+00 4.00e-02 1.25e+01 dihedral pdb=" CA GLN B 648 " pdb=" C GLN B 648 " pdb=" N GLU B 649 " pdb=" CA GLU B 649 " ideal model delta harmonic sigma weight residual 180.00 162.35 17.65 0 5.00e+00 4.00e-02 1.25e+01 dihedral pdb=" CA THR B 135 " pdb=" C THR B 135 " pdb=" N PRO B 136 " pdb=" CA PRO B 136 " ideal model delta harmonic sigma weight residual 180.00 -163.86 -16.14 0 5.00e+00 4.00e-02 1.04e+01 ... (remaining 6457 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.051: 1253 0.051 - 0.101: 258 0.101 - 0.151: 109 0.151 - 0.202: 8 0.202 - 0.252: 4 Chirality restraints: 1632 Sorted by residual: chirality pdb=" CB VAL A 248 " pdb=" CA VAL A 248 " pdb=" CG1 VAL A 248 " pdb=" CG2 VAL A 248 " both_signs ideal model delta sigma weight residual False -2.63 -2.38 -0.25 2.00e-01 2.50e+01 1.59e+00 chirality pdb=" CB VAL B 248 " pdb=" CA VAL B 248 " pdb=" CG1 VAL B 248 " pdb=" CG2 VAL B 248 " both_signs ideal model delta sigma weight residual False -2.63 -2.38 -0.25 2.00e-01 2.50e+01 1.59e+00 chirality pdb=" CB VAL B 500 " pdb=" CA VAL B 500 " pdb=" CG1 VAL B 500 " pdb=" CG2 VAL B 500 " both_signs ideal model delta sigma weight residual False -2.63 -2.42 -0.21 2.00e-01 2.50e+01 1.12e+00 ... (remaining 1629 not shown) Planarity restraints: 1894 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASN B 532 " -0.014 2.00e-02 2.50e+03 2.80e-02 7.82e+00 pdb=" C ASN B 532 " 0.048 2.00e-02 2.50e+03 pdb=" O ASN B 532 " -0.018 2.00e-02 2.50e+03 pdb=" N TRP B 533 " -0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASN A 532 " 0.014 2.00e-02 2.50e+03 2.77e-02 7.67e+00 pdb=" C ASN A 532 " -0.048 2.00e-02 2.50e+03 pdb=" O ASN A 532 " 0.018 2.00e-02 2.50e+03 pdb=" N TRP A 533 " 0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C HIS A 401 " -0.045 5.00e-02 4.00e+02 6.69e-02 7.16e+00 pdb=" N PRO A 402 " 0.116 5.00e-02 4.00e+02 pdb=" CA PRO A 402 " -0.033 5.00e-02 4.00e+02 pdb=" CD PRO A 402 " -0.038 5.00e-02 4.00e+02 ... (remaining 1891 not shown) Histogram of nonbonded interaction distances: 1.97 - 2.56: 80 2.56 - 3.14: 8263 3.14 - 3.73: 17645 3.73 - 4.31: 22665 4.31 - 4.90: 37794 Nonbonded interactions: 86447 Sorted by model distance: nonbonded pdb=" OE2 GLU A 313 " pdb=" OD1 ASN A 317 " model vdw 1.974 3.040 nonbonded pdb=" OE2 GLU B 313 " pdb=" OD1 ASN B 317 " model vdw 1.974 3.040 nonbonded pdb=" OE1 GLN B 445 " pdb=" ND2 ASN B 531 " model vdw 2.294 3.120 nonbonded pdb=" OE1 GLN A 445 " pdb=" ND2 ASN A 531 " model vdw 2.294 3.120 nonbonded pdb=" O TYR B 120 " pdb=" OG1 THR B 124 " model vdw 2.307 3.040 ... (remaining 86442 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: 0.05 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } 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 group one per residue 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: 0.560 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: 0.390 Check model and map are aligned: 0.070 Set scattering table: 0.100 Process input model: 29.090 Find NCS groups from input model: 0.190 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.610 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.040 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8168 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 : 0.006 0.065 10992 Z= 0.268 Angle : 0.880 11.150 14910 Z= 0.508 Chirality : 0.050 0.252 1632 Planarity : 0.007 0.067 1894 Dihedral : 15.235 86.108 3948 Min Nonbonded Distance : 1.974 Molprobity Statistics. All-atom Clashscore : 4.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 0.18 % Allowed : 7.56 % Favored : 92.27 % 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: -3.00 (0.18), residues: 1300 helix: -1.54 (0.13), residues: 934 sheet: -2.21 (0.62), residues: 68 loop : -2.77 (0.29), residues: 298 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP B 235 HIS 0.006 0.001 HIS B 143 PHE 0.032 0.002 PHE A 396 TYR 0.021 0.002 TYR B 279 ARG 0.004 0.001 ARG A 549 Details of bonding type rmsd hydrogen bonds : bond 0.11760 ( 746) hydrogen bonds : angle 6.07795 ( 2232) covalent geometry : bond 0.00559 (10992) covalent geometry : angle 0.88009 (14910) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2600 Ramachandran restraints generated. 1300 Oldfield, 0 Emsley, 1300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2600 Ramachandran restraints generated. 1300 Oldfield, 0 Emsley, 1300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 1138 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 167 time to evaluate : 1.324 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 45 ARG cc_start: 0.8162 (mmm-85) cc_final: 0.7960 (tpp80) outliers start: 2 outliers final: 0 residues processed: 167 average time/residue: 0.2632 time to fit residues: 59.9119 Evaluate side-chains 119 residues out of total 1138 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 119 time to evaluate : 1.220 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 111 optimal weight: 0.9990 chunk 100 optimal weight: 8.9990 chunk 55 optimal weight: 6.9990 chunk 34 optimal weight: 0.7980 chunk 67 optimal weight: 10.0000 chunk 53 optimal weight: 0.6980 chunk 103 optimal weight: 2.9990 chunk 40 optimal weight: 6.9990 chunk 62 optimal weight: 20.0000 chunk 77 optimal weight: 7.9990 chunk 119 optimal weight: 0.8980 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 58 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 151 HIS A 156 ASN A 317 ASN A 378 ASN A 435 ASN ** B 58 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 151 HIS B 156 ASN B 317 ASN B 378 ASN B 435 ASN B 641 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3616 r_free = 0.3616 target = 0.109108 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3158 r_free = 0.3158 target = 0.082384 restraints weight = 24234.574| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3205 r_free = 0.3205 target = 0.084903 restraints weight = 12756.554| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3234 r_free = 0.3234 target = 0.086455 restraints weight = 8848.959| |-----------------------------------------------------------------------------| r_work (final): 0.3237 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8183 moved from start: 0.1604 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 10992 Z= 0.150 Angle : 0.571 7.892 14910 Z= 0.303 Chirality : 0.038 0.135 1632 Planarity : 0.005 0.049 1894 Dihedral : 4.395 15.809 1422 Min Nonbonded Distance : 2.248 Molprobity Statistics. All-atom Clashscore : 6.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 2.46 % Allowed : 13.09 % Favored : 84.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.49 (0.22), residues: 1300 helix: 0.45 (0.15), residues: 936 sheet: -1.87 (0.67), residues: 68 loop : -2.22 (0.32), residues: 296 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 235 HIS 0.003 0.001 HIS A 58 PHE 0.014 0.001 PHE B 396 TYR 0.017 0.002 TYR B 26 ARG 0.004 0.000 ARG B 45 Details of bonding type rmsd hydrogen bonds : bond 0.04921 ( 746) hydrogen bonds : angle 4.49633 ( 2232) covalent geometry : bond 0.00317 (10992) covalent geometry : angle 0.57135 (14910) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2600 Ramachandran restraints generated. 1300 Oldfield, 0 Emsley, 1300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2600 Ramachandran restraints generated. 1300 Oldfield, 0 Emsley, 1300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 1138 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 137 time to evaluate : 1.246 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 378 ASN cc_start: 0.8958 (OUTLIER) cc_final: 0.8559 (t0) REVERT: A 384 MET cc_start: 0.8557 (tpp) cc_final: 0.8202 (mpp) REVERT: A 482 GLU cc_start: 0.8135 (OUTLIER) cc_final: 0.7727 (mt-10) REVERT: B 482 GLU cc_start: 0.8119 (OUTLIER) cc_final: 0.7880 (mt-10) outliers start: 28 outliers final: 16 residues processed: 158 average time/residue: 0.2488 time to fit residues: 56.2361 Evaluate side-chains 138 residues out of total 1138 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 119 time to evaluate : 1.282 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 211 LEU Chi-restraints excluded: chain A residue 223 LEU Chi-restraints excluded: chain A residue 244 VAL Chi-restraints excluded: chain A residue 252 SER Chi-restraints excluded: chain A residue 300 VAL Chi-restraints excluded: chain A residue 336 LEU Chi-restraints excluded: chain A residue 340 THR Chi-restraints excluded: chain A residue 378 ASN Chi-restraints excluded: chain A residue 482 GLU Chi-restraints excluded: chain B residue 66 VAL Chi-restraints excluded: chain B residue 211 LEU Chi-restraints excluded: chain B residue 223 LEU Chi-restraints excluded: chain B residue 244 VAL Chi-restraints excluded: chain B residue 252 SER Chi-restraints excluded: chain B residue 300 VAL Chi-restraints excluded: chain B residue 340 THR Chi-restraints excluded: chain B residue 482 GLU Chi-restraints excluded: chain B residue 716 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 96 optimal weight: 5.9990 chunk 46 optimal weight: 8.9990 chunk 117 optimal weight: 4.9990 chunk 81 optimal weight: 8.9990 chunk 63 optimal weight: 0.0010 chunk 84 optimal weight: 3.9990 chunk 74 optimal weight: 7.9990 chunk 110 optimal weight: 8.9990 chunk 60 optimal weight: 7.9990 chunk 123 optimal weight: 2.9990 chunk 34 optimal weight: 10.0000 overall best weight: 3.5994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 58 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 378 ASN ** B 58 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 378 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3555 r_free = 0.3555 target = 0.105254 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3079 r_free = 0.3079 target = 0.078102 restraints weight = 25063.163| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3125 r_free = 0.3125 target = 0.080506 restraints weight = 13511.376| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3153 r_free = 0.3153 target = 0.081948 restraints weight = 9528.634| |-----------------------------------------------------------------------------| r_work (final): 0.3154 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8275 moved from start: 0.2022 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.056 10992 Z= 0.275 Angle : 0.639 6.637 14910 Z= 0.342 Chirality : 0.042 0.166 1632 Planarity : 0.005 0.045 1894 Dihedral : 4.291 16.237 1422 Min Nonbonded Distance : 2.168 Molprobity Statistics. All-atom Clashscore : 8.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 3.69 % Allowed : 15.03 % Favored : 81.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.35 (0.23), residues: 1300 helix: 1.09 (0.16), residues: 940 sheet: -1.73 (0.66), residues: 68 loop : -1.99 (0.35), residues: 292 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A 235 HIS 0.004 0.001 HIS B 479 PHE 0.021 0.002 PHE B 189 TYR 0.019 0.002 TYR B 279 ARG 0.004 0.000 ARG B 548 Details of bonding type rmsd hydrogen bonds : bond 0.05282 ( 746) hydrogen bonds : angle 4.57321 ( 2232) covalent geometry : bond 0.00615 (10992) covalent geometry : angle 0.63898 (14910) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2600 Ramachandran restraints generated. 1300 Oldfield, 0 Emsley, 1300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2600 Ramachandran restraints generated. 1300 Oldfield, 0 Emsley, 1300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 1138 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 114 time to evaluate : 1.637 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 173 ASP cc_start: 0.8350 (OUTLIER) cc_final: 0.7982 (t0) REVERT: A 203 SER cc_start: 0.8875 (t) cc_final: 0.8409 (p) REVERT: B 173 ASP cc_start: 0.8366 (OUTLIER) cc_final: 0.8036 (t0) REVERT: B 203 SER cc_start: 0.8847 (t) cc_final: 0.8391 (p) REVERT: B 378 ASN cc_start: 0.9005 (OUTLIER) cc_final: 0.8390 (m-40) outliers start: 42 outliers final: 28 residues processed: 144 average time/residue: 0.2797 time to fit residues: 63.5168 Evaluate side-chains 142 residues out of total 1138 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 111 time to evaluate : 1.397 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 THR Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 173 ASP Chi-restraints excluded: chain A residue 200 VAL Chi-restraints excluded: chain A residue 211 LEU Chi-restraints excluded: chain A residue 223 LEU Chi-restraints excluded: chain A residue 244 VAL Chi-restraints excluded: chain A residue 252 SER Chi-restraints excluded: chain A residue 336 LEU Chi-restraints excluded: chain A residue 340 THR Chi-restraints excluded: chain A residue 451 THR Chi-restraints excluded: chain A residue 527 CYS Chi-restraints excluded: chain A residue 647 LEU Chi-restraints excluded: chain A residue 666 HIS Chi-restraints excluded: chain A residue 716 LEU Chi-restraints excluded: chain B residue 49 THR Chi-restraints excluded: chain B residue 66 VAL Chi-restraints excluded: chain B residue 173 ASP Chi-restraints excluded: chain B residue 200 VAL Chi-restraints excluded: chain B residue 211 LEU Chi-restraints excluded: chain B residue 223 LEU Chi-restraints excluded: chain B residue 244 VAL Chi-restraints excluded: chain B residue 252 SER Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain B residue 340 THR Chi-restraints excluded: chain B residue 378 ASN Chi-restraints excluded: chain B residue 451 THR Chi-restraints excluded: chain B residue 527 CYS Chi-restraints excluded: chain B residue 639 ARG Chi-restraints excluded: chain B residue 647 LEU Chi-restraints excluded: chain B residue 716 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 72 optimal weight: 5.9990 chunk 105 optimal weight: 8.9990 chunk 129 optimal weight: 1.9990 chunk 36 optimal weight: 1.9990 chunk 108 optimal weight: 3.9990 chunk 48 optimal weight: 0.0040 chunk 96 optimal weight: 3.9990 chunk 120 optimal weight: 0.7980 chunk 98 optimal weight: 2.9990 chunk 29 optimal weight: 9.9990 chunk 6 optimal weight: 10.0000 overall best weight: 1.5598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 58 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 378 ASN A 510 GLN ** B 58 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 378 ASN B 510 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3588 r_free = 0.3588 target = 0.107175 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3117 r_free = 0.3117 target = 0.080191 restraints weight = 24501.277| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3163 r_free = 0.3163 target = 0.082582 restraints weight = 13114.760| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3191 r_free = 0.3191 target = 0.084077 restraints weight = 9235.170| |-----------------------------------------------------------------------------| r_work (final): 0.3193 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8233 moved from start: 0.2124 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 10992 Z= 0.156 Angle : 0.554 6.800 14910 Z= 0.291 Chirality : 0.038 0.131 1632 Planarity : 0.004 0.043 1894 Dihedral : 4.160 14.660 1422 Min Nonbonded Distance : 2.229 Molprobity Statistics. All-atom Clashscore : 7.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.69 % Favored : 97.31 % Rotamer: Outliers : 2.99 % Allowed : 16.87 % Favored : 80.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.86 (0.23), residues: 1300 helix: 1.47 (0.16), residues: 940 sheet: -1.65 (0.68), residues: 68 loop : -1.83 (0.35), residues: 292 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A 235 HIS 0.003 0.001 HIS B 479 PHE 0.012 0.001 PHE A 640 TYR 0.017 0.002 TYR B 26 ARG 0.002 0.000 ARG B 115 Details of bonding type rmsd hydrogen bonds : bond 0.04786 ( 746) hydrogen bonds : angle 4.36647 ( 2232) covalent geometry : bond 0.00338 (10992) covalent geometry : angle 0.55395 (14910) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2600 Ramachandran restraints generated. 1300 Oldfield, 0 Emsley, 1300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2600 Ramachandran restraints generated. 1300 Oldfield, 0 Emsley, 1300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 1138 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 119 time to evaluate : 1.236 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 203 SER cc_start: 0.8867 (t) cc_final: 0.8436 (p) REVERT: A 378 ASN cc_start: 0.8957 (OUTLIER) cc_final: 0.8510 (t0) REVERT: B 203 SER cc_start: 0.8859 (t) cc_final: 0.8436 (p) outliers start: 34 outliers final: 24 residues processed: 142 average time/residue: 0.2557 time to fit residues: 58.0877 Evaluate side-chains 137 residues out of total 1138 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 112 time to evaluate : 1.994 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 THR Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 211 LEU Chi-restraints excluded: chain A residue 223 LEU Chi-restraints excluded: chain A residue 239 GLU Chi-restraints excluded: chain A residue 244 VAL Chi-restraints excluded: chain A residue 336 LEU Chi-restraints excluded: chain A residue 340 THR Chi-restraints excluded: chain A residue 378 ASN Chi-restraints excluded: chain A residue 527 CYS Chi-restraints excluded: chain A residue 639 ARG Chi-restraints excluded: chain A residue 647 LEU Chi-restraints excluded: chain A residue 716 LEU Chi-restraints excluded: chain B residue 54 THR Chi-restraints excluded: chain B residue 66 VAL Chi-restraints excluded: chain B residue 211 LEU Chi-restraints excluded: chain B residue 223 LEU Chi-restraints excluded: chain B residue 239 GLU Chi-restraints excluded: chain B residue 244 VAL Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain B residue 340 THR Chi-restraints excluded: chain B residue 378 ASN Chi-restraints excluded: chain B residue 527 CYS Chi-restraints excluded: chain B residue 647 LEU Chi-restraints excluded: chain B residue 716 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 100 optimal weight: 10.0000 chunk 129 optimal weight: 5.9990 chunk 103 optimal weight: 5.9990 chunk 125 optimal weight: 5.9990 chunk 128 optimal weight: 5.9990 chunk 15 optimal weight: 7.9990 chunk 75 optimal weight: 0.9980 chunk 104 optimal weight: 6.9990 chunk 131 optimal weight: 6.9990 chunk 21 optimal weight: 3.9990 chunk 58 optimal weight: 0.4980 overall best weight: 3.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 58 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 378 ASN ** B 58 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 156 ASN B 378 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.104645 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3070 r_free = 0.3070 target = 0.077679 restraints weight = 24844.198| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3116 r_free = 0.3116 target = 0.080016 restraints weight = 13492.907| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3144 r_free = 0.3144 target = 0.081454 restraints weight = 9564.011| |-----------------------------------------------------------------------------| r_work (final): 0.3147 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8291 moved from start: 0.2360 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.052 10992 Z= 0.264 Angle : 0.620 5.888 14910 Z= 0.329 Chirality : 0.041 0.133 1632 Planarity : 0.004 0.044 1894 Dihedral : 4.182 15.775 1422 Min Nonbonded Distance : 2.172 Molprobity Statistics. All-atom Clashscore : 8.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 4.31 % Allowed : 17.66 % Favored : 78.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.90 (0.23), residues: 1300 helix: 1.49 (0.16), residues: 942 sheet: -1.63 (0.70), residues: 66 loop : -1.80 (0.36), residues: 292 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A 235 HIS 0.004 0.001 HIS B 479 PHE 0.018 0.002 PHE A 189 TYR 0.019 0.002 TYR B 26 ARG 0.003 0.000 ARG B 548 Details of bonding type rmsd hydrogen bonds : bond 0.05061 ( 746) hydrogen bonds : angle 4.47781 ( 2232) covalent geometry : bond 0.00592 (10992) covalent geometry : angle 0.61986 (14910) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2600 Ramachandran restraints generated. 1300 Oldfield, 0 Emsley, 1300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2600 Ramachandran restraints generated. 1300 Oldfield, 0 Emsley, 1300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 1138 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 110 time to evaluate : 1.249 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 173 ASP cc_start: 0.8349 (OUTLIER) cc_final: 0.8013 (t0) REVERT: A 203 SER cc_start: 0.8905 (t) cc_final: 0.8415 (p) REVERT: A 384 MET cc_start: 0.8747 (tpp) cc_final: 0.8081 (mpp) REVERT: B 173 ASP cc_start: 0.8342 (OUTLIER) cc_final: 0.8008 (t0) REVERT: B 203 SER cc_start: 0.8874 (t) cc_final: 0.8436 (p) REVERT: B 384 MET cc_start: 0.8704 (tpp) cc_final: 0.7980 (mpp) outliers start: 49 outliers final: 37 residues processed: 143 average time/residue: 0.2244 time to fit residues: 51.2340 Evaluate side-chains 147 residues out of total 1138 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 108 time to evaluate : 1.362 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 LEU Chi-restraints excluded: chain A residue 49 THR Chi-restraints excluded: chain A residue 54 THR Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 173 ASP Chi-restraints excluded: chain A residue 200 VAL Chi-restraints excluded: chain A residue 211 LEU Chi-restraints excluded: chain A residue 223 LEU Chi-restraints excluded: chain A residue 244 VAL Chi-restraints excluded: chain A residue 252 SER Chi-restraints excluded: chain A residue 282 MET Chi-restraints excluded: chain A residue 336 LEU Chi-restraints excluded: chain A residue 340 THR Chi-restraints excluded: chain A residue 451 THR Chi-restraints excluded: chain A residue 527 CYS Chi-restraints excluded: chain A residue 639 ARG Chi-restraints excluded: chain A residue 647 LEU Chi-restraints excluded: chain A residue 666 HIS Chi-restraints excluded: chain A residue 716 LEU Chi-restraints excluded: chain B residue 43 LEU Chi-restraints excluded: chain B residue 49 THR Chi-restraints excluded: chain B residue 54 THR Chi-restraints excluded: chain B residue 66 VAL Chi-restraints excluded: chain B residue 156 ASN Chi-restraints excluded: chain B residue 173 ASP Chi-restraints excluded: chain B residue 200 VAL Chi-restraints excluded: chain B residue 211 LEU Chi-restraints excluded: chain B residue 223 LEU Chi-restraints excluded: chain B residue 244 VAL Chi-restraints excluded: chain B residue 252 SER Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain B residue 340 THR Chi-restraints excluded: chain B residue 378 ASN Chi-restraints excluded: chain B residue 451 THR Chi-restraints excluded: chain B residue 527 CYS Chi-restraints excluded: chain B residue 639 ARG Chi-restraints excluded: chain B residue 647 LEU Chi-restraints excluded: chain B residue 666 HIS Chi-restraints excluded: chain B residue 716 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 98 optimal weight: 0.5980 chunk 74 optimal weight: 9.9990 chunk 13 optimal weight: 2.9990 chunk 52 optimal weight: 4.9990 chunk 60 optimal weight: 9.9990 chunk 90 optimal weight: 5.9990 chunk 111 optimal weight: 0.9990 chunk 29 optimal weight: 9.9990 chunk 1 optimal weight: 0.8980 chunk 24 optimal weight: 6.9990 chunk 68 optimal weight: 6.9990 overall best weight: 2.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 58 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 156 ASN A 378 ASN B 58 HIS B 156 ASN B 378 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3572 r_free = 0.3572 target = 0.105982 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3096 r_free = 0.3096 target = 0.079013 restraints weight = 24921.812| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3143 r_free = 0.3143 target = 0.081388 restraints weight = 13429.173| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3171 r_free = 0.3171 target = 0.082880 restraints weight = 9462.983| |-----------------------------------------------------------------------------| r_work (final): 0.3175 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8262 moved from start: 0.2422 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 10992 Z= 0.184 Angle : 0.568 7.206 14910 Z= 0.300 Chirality : 0.039 0.131 1632 Planarity : 0.004 0.045 1894 Dihedral : 4.107 14.284 1422 Min Nonbonded Distance : 2.186 Molprobity Statistics. All-atom Clashscore : 7.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 4.48 % Allowed : 18.45 % Favored : 77.07 % 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: 1.12 (0.24), residues: 1300 helix: 1.65 (0.16), residues: 942 sheet: -1.37 (0.70), residues: 68 loop : -1.75 (0.36), residues: 290 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP A 235 HIS 0.005 0.001 HIS B 58 PHE 0.018 0.001 PHE B 335 TYR 0.018 0.002 TYR B 26 ARG 0.002 0.000 ARG A 548 Details of bonding type rmsd hydrogen bonds : bond 0.04819 ( 746) hydrogen bonds : angle 4.36849 ( 2232) covalent geometry : bond 0.00406 (10992) covalent geometry : angle 0.56823 (14910) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2600 Ramachandran restraints generated. 1300 Oldfield, 0 Emsley, 1300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2600 Ramachandran restraints generated. 1300 Oldfield, 0 Emsley, 1300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 1138 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 112 time to evaluate : 2.283 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 173 ASP cc_start: 0.8281 (OUTLIER) cc_final: 0.7923 (t0) REVERT: A 203 SER cc_start: 0.8891 (t) cc_final: 0.8476 (p) REVERT: A 378 ASN cc_start: 0.8954 (OUTLIER) cc_final: 0.8506 (t0) REVERT: A 384 MET cc_start: 0.8739 (tpp) cc_final: 0.8043 (mpp) REVERT: A 439 TYR cc_start: 0.7441 (m-80) cc_final: 0.6979 (m-80) REVERT: A 565 LEU cc_start: 0.9352 (OUTLIER) cc_final: 0.9083 (mp) REVERT: B 173 ASP cc_start: 0.8334 (OUTLIER) cc_final: 0.7984 (t0) REVERT: B 203 SER cc_start: 0.8890 (t) cc_final: 0.8514 (p) REVERT: B 384 MET cc_start: 0.8703 (tpp) cc_final: 0.8022 (mpp) REVERT: B 565 LEU cc_start: 0.9371 (OUTLIER) cc_final: 0.9104 (mp) outliers start: 51 outliers final: 40 residues processed: 148 average time/residue: 0.2975 time to fit residues: 67.2527 Evaluate side-chains 150 residues out of total 1138 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 105 time to evaluate : 2.204 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 LEU Chi-restraints excluded: chain A residue 49 THR Chi-restraints excluded: chain A residue 54 THR Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 156 ASN Chi-restraints excluded: chain A residue 173 ASP Chi-restraints excluded: chain A residue 200 VAL Chi-restraints excluded: chain A residue 211 LEU Chi-restraints excluded: chain A residue 223 LEU Chi-restraints excluded: chain A residue 240 VAL Chi-restraints excluded: chain A residue 244 VAL Chi-restraints excluded: chain A residue 252 SER Chi-restraints excluded: chain A residue 282 MET Chi-restraints excluded: chain A residue 336 LEU Chi-restraints excluded: chain A residue 340 THR Chi-restraints excluded: chain A residue 378 ASN Chi-restraints excluded: chain A residue 440 PHE Chi-restraints excluded: chain A residue 451 THR Chi-restraints excluded: chain A residue 527 CYS Chi-restraints excluded: chain A residue 565 LEU Chi-restraints excluded: chain A residue 639 ARG Chi-restraints excluded: chain A residue 647 LEU Chi-restraints excluded: chain A residue 666 HIS Chi-restraints excluded: chain A residue 716 LEU Chi-restraints excluded: chain B residue 43 LEU Chi-restraints excluded: chain B residue 49 THR Chi-restraints excluded: chain B residue 54 THR Chi-restraints excluded: chain B residue 66 VAL Chi-restraints excluded: chain B residue 173 ASP Chi-restraints excluded: chain B residue 200 VAL Chi-restraints excluded: chain B residue 211 LEU Chi-restraints excluded: chain B residue 223 LEU Chi-restraints excluded: chain B residue 240 VAL Chi-restraints excluded: chain B residue 244 VAL Chi-restraints excluded: chain B residue 252 SER Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain B residue 340 THR Chi-restraints excluded: chain B residue 378 ASN Chi-restraints excluded: chain B residue 440 PHE Chi-restraints excluded: chain B residue 451 THR Chi-restraints excluded: chain B residue 527 CYS Chi-restraints excluded: chain B residue 565 LEU Chi-restraints excluded: chain B residue 647 LEU Chi-restraints excluded: chain B residue 666 HIS Chi-restraints excluded: chain B residue 716 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 126 optimal weight: 0.9990 chunk 89 optimal weight: 0.9990 chunk 79 optimal weight: 0.8980 chunk 5 optimal weight: 5.9990 chunk 50 optimal weight: 0.9980 chunk 64 optimal weight: 8.9990 chunk 112 optimal weight: 0.9980 chunk 115 optimal weight: 6.9990 chunk 117 optimal weight: 3.9990 chunk 34 optimal weight: 3.9990 chunk 80 optimal weight: 0.6980 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 58 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 156 ASN A 378 ASN B 378 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3598 r_free = 0.3598 target = 0.107644 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3131 r_free = 0.3131 target = 0.080844 restraints weight = 24844.142| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3178 r_free = 0.3178 target = 0.083282 restraints weight = 13319.317| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3205 r_free = 0.3205 target = 0.084750 restraints weight = 9341.773| |-----------------------------------------------------------------------------| r_work (final): 0.3207 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8221 moved from start: 0.2483 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 10992 Z= 0.134 Angle : 0.546 8.137 14910 Z= 0.282 Chirality : 0.037 0.133 1632 Planarity : 0.004 0.045 1894 Dihedral : 3.999 14.463 1422 Min Nonbonded Distance : 2.213 Molprobity Statistics. All-atom Clashscore : 7.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 3.60 % Allowed : 19.60 % Favored : 76.80 % 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: 1.34 (0.24), residues: 1300 helix: 1.81 (0.16), residues: 940 sheet: -1.22 (0.73), residues: 68 loop : -1.67 (0.36), residues: 292 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP B 235 HIS 0.003 0.001 HIS A 265 PHE 0.013 0.001 PHE A 155 TYR 0.015 0.002 TYR B 26 ARG 0.003 0.000 ARG B 505 Details of bonding type rmsd hydrogen bonds : bond 0.04528 ( 746) hydrogen bonds : angle 4.22365 ( 2232) covalent geometry : bond 0.00280 (10992) covalent geometry : angle 0.54590 (14910) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2600 Ramachandran restraints generated. 1300 Oldfield, 0 Emsley, 1300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2600 Ramachandran restraints generated. 1300 Oldfield, 0 Emsley, 1300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 1138 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 120 time to evaluate : 1.284 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 173 ASP cc_start: 0.8302 (OUTLIER) cc_final: 0.7956 (t0) REVERT: A 203 SER cc_start: 0.8888 (t) cc_final: 0.8539 (p) REVERT: A 384 MET cc_start: 0.8706 (tpp) cc_final: 0.8026 (mpp) REVERT: A 565 LEU cc_start: 0.9316 (OUTLIER) cc_final: 0.9065 (mp) REVERT: A 575 THR cc_start: 0.9201 (m) cc_final: 0.8978 (p) REVERT: B 203 SER cc_start: 0.8879 (t) cc_final: 0.8543 (p) REVERT: B 384 MET cc_start: 0.8678 (tpp) cc_final: 0.8021 (mpp) REVERT: B 565 LEU cc_start: 0.9334 (OUTLIER) cc_final: 0.9099 (mp) REVERT: B 575 THR cc_start: 0.9205 (m) cc_final: 0.8981 (p) outliers start: 41 outliers final: 30 residues processed: 152 average time/residue: 0.1852 time to fit residues: 43.5617 Evaluate side-chains 145 residues out of total 1138 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 112 time to evaluate : 1.201 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 LEU Chi-restraints excluded: chain A residue 54 THR Chi-restraints excluded: chain A residue 135 THR Chi-restraints excluded: chain A residue 156 ASN Chi-restraints excluded: chain A residue 173 ASP Chi-restraints excluded: chain A residue 200 VAL Chi-restraints excluded: chain A residue 211 LEU Chi-restraints excluded: chain A residue 240 VAL Chi-restraints excluded: chain A residue 244 VAL Chi-restraints excluded: chain A residue 282 MET Chi-restraints excluded: chain A residue 336 LEU Chi-restraints excluded: chain A residue 340 THR Chi-restraints excluded: chain A residue 440 PHE Chi-restraints excluded: chain A residue 451 THR Chi-restraints excluded: chain A residue 565 LEU Chi-restraints excluded: chain A residue 639 ARG Chi-restraints excluded: chain A residue 647 LEU Chi-restraints excluded: chain A residue 716 LEU Chi-restraints excluded: chain B residue 43 LEU Chi-restraints excluded: chain B residue 54 THR Chi-restraints excluded: chain B residue 111 VAL Chi-restraints excluded: chain B residue 156 ASN Chi-restraints excluded: chain B residue 200 VAL Chi-restraints excluded: chain B residue 240 VAL Chi-restraints excluded: chain B residue 244 VAL Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain B residue 340 THR Chi-restraints excluded: chain B residue 378 ASN Chi-restraints excluded: chain B residue 440 PHE Chi-restraints excluded: chain B residue 451 THR Chi-restraints excluded: chain B residue 565 LEU Chi-restraints excluded: chain B residue 647 LEU Chi-restraints excluded: chain B residue 716 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 38 optimal weight: 6.9990 chunk 125 optimal weight: 6.9990 chunk 117 optimal weight: 5.9990 chunk 75 optimal weight: 5.9990 chunk 123 optimal weight: 3.9990 chunk 2 optimal weight: 3.9990 chunk 35 optimal weight: 8.9990 chunk 101 optimal weight: 10.0000 chunk 80 optimal weight: 0.7980 chunk 113 optimal weight: 0.3980 chunk 71 optimal weight: 0.9990 overall best weight: 2.0386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 58 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 156 ASN A 378 ASN B 378 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3584 r_free = 0.3584 target = 0.106645 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3113 r_free = 0.3113 target = 0.079881 restraints weight = 24840.554| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3159 r_free = 0.3159 target = 0.082252 restraints weight = 13469.724| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3185 r_free = 0.3185 target = 0.083678 restraints weight = 9523.816| |-----------------------------------------------------------------------------| r_work (final): 0.3185 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8248 moved from start: 0.2592 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 10992 Z= 0.176 Angle : 0.565 7.069 14910 Z= 0.293 Chirality : 0.039 0.136 1632 Planarity : 0.004 0.045 1894 Dihedral : 3.960 14.134 1422 Min Nonbonded Distance : 2.197 Molprobity Statistics. All-atom Clashscore : 7.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 4.39 % Allowed : 20.21 % Favored : 75.40 % 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: 1.42 (0.24), residues: 1300 helix: 1.86 (0.16), residues: 942 sheet: -1.20 (0.75), residues: 66 loop : -1.64 (0.36), residues: 292 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 235 HIS 0.003 0.001 HIS B 479 PHE 0.012 0.001 PHE A 640 TYR 0.016 0.002 TYR B 26 ARG 0.003 0.000 ARG B 505 Details of bonding type rmsd hydrogen bonds : bond 0.04589 ( 746) hydrogen bonds : angle 4.25105 ( 2232) covalent geometry : bond 0.00391 (10992) covalent geometry : angle 0.56471 (14910) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2600 Ramachandran restraints generated. 1300 Oldfield, 0 Emsley, 1300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2600 Ramachandran restraints generated. 1300 Oldfield, 0 Emsley, 1300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 1138 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 114 time to evaluate : 1.311 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 173 ASP cc_start: 0.8287 (OUTLIER) cc_final: 0.7934 (t0) REVERT: A 378 ASN cc_start: 0.8885 (OUTLIER) cc_final: 0.8503 (t0) REVERT: A 384 MET cc_start: 0.8732 (tpp) cc_final: 0.8054 (mpp) REVERT: A 565 LEU cc_start: 0.9342 (OUTLIER) cc_final: 0.9077 (mp) REVERT: B 173 ASP cc_start: 0.8324 (OUTLIER) cc_final: 0.7986 (t0) REVERT: B 384 MET cc_start: 0.8697 (tpp) cc_final: 0.8043 (mpp) REVERT: B 439 TYR cc_start: 0.7411 (m-80) cc_final: 0.6926 (m-80) REVERT: B 565 LEU cc_start: 0.9366 (OUTLIER) cc_final: 0.9118 (mp) outliers start: 50 outliers final: 39 residues processed: 150 average time/residue: 0.1944 time to fit residues: 44.3913 Evaluate side-chains 155 residues out of total 1138 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 111 time to evaluate : 1.242 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 LEU Chi-restraints excluded: chain A residue 49 THR Chi-restraints excluded: chain A residue 54 THR Chi-restraints excluded: chain A residue 111 VAL Chi-restraints excluded: chain A residue 135 THR Chi-restraints excluded: chain A residue 173 ASP Chi-restraints excluded: chain A residue 200 VAL Chi-restraints excluded: chain A residue 211 LEU Chi-restraints excluded: chain A residue 240 VAL Chi-restraints excluded: chain A residue 252 SER Chi-restraints excluded: chain A residue 282 MET Chi-restraints excluded: chain A residue 336 LEU Chi-restraints excluded: chain A residue 340 THR Chi-restraints excluded: chain A residue 378 ASN Chi-restraints excluded: chain A residue 440 PHE Chi-restraints excluded: chain A residue 451 THR Chi-restraints excluded: chain A residue 565 LEU Chi-restraints excluded: chain A residue 639 ARG Chi-restraints excluded: chain A residue 647 LEU Chi-restraints excluded: chain A residue 666 HIS Chi-restraints excluded: chain A residue 716 LEU Chi-restraints excluded: chain B residue 43 LEU Chi-restraints excluded: chain B residue 49 THR Chi-restraints excluded: chain B residue 54 THR Chi-restraints excluded: chain B residue 111 VAL Chi-restraints excluded: chain B residue 135 THR Chi-restraints excluded: chain B residue 156 ASN Chi-restraints excluded: chain B residue 173 ASP Chi-restraints excluded: chain B residue 200 VAL Chi-restraints excluded: chain B residue 211 LEU Chi-restraints excluded: chain B residue 240 VAL Chi-restraints excluded: chain B residue 244 VAL Chi-restraints excluded: chain B residue 252 SER Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain B residue 340 THR Chi-restraints excluded: chain B residue 378 ASN Chi-restraints excluded: chain B residue 440 PHE Chi-restraints excluded: chain B residue 451 THR Chi-restraints excluded: chain B residue 527 CYS Chi-restraints excluded: chain B residue 565 LEU Chi-restraints excluded: chain B residue 632 LEU Chi-restraints excluded: chain B residue 647 LEU Chi-restraints excluded: chain B residue 666 HIS Chi-restraints excluded: chain B residue 716 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 12 optimal weight: 5.9990 chunk 79 optimal weight: 0.7980 chunk 37 optimal weight: 3.9990 chunk 21 optimal weight: 3.9990 chunk 52 optimal weight: 0.9980 chunk 8 optimal weight: 0.6980 chunk 50 optimal weight: 0.9980 chunk 23 optimal weight: 0.9990 chunk 76 optimal weight: 2.9990 chunk 11 optimal weight: 9.9990 chunk 89 optimal weight: 3.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 58 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 378 ASN B 378 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3606 r_free = 0.3606 target = 0.107956 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3138 r_free = 0.3138 target = 0.081125 restraints weight = 24892.592| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3185 r_free = 0.3185 target = 0.083615 restraints weight = 13052.149| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3213 r_free = 0.3213 target = 0.085145 restraints weight = 9050.148| |-----------------------------------------------------------------------------| r_work (final): 0.3216 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8208 moved from start: 0.2632 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 10992 Z= 0.128 Angle : 0.546 7.721 14910 Z= 0.280 Chirality : 0.038 0.142 1632 Planarity : 0.004 0.045 1894 Dihedral : 3.931 13.908 1422 Min Nonbonded Distance : 2.213 Molprobity Statistics. All-atom Clashscore : 7.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 3.51 % Allowed : 21.27 % Favored : 75.22 % 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: 1.55 (0.24), residues: 1300 helix: 1.96 (0.16), residues: 940 sheet: -1.09 (0.74), residues: 68 loop : -1.58 (0.36), residues: 292 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP B 235 HIS 0.002 0.001 HIS B 265 PHE 0.015 0.001 PHE A 379 TYR 0.014 0.002 TYR B 26 ARG 0.003 0.000 ARG B 505 Details of bonding type rmsd hydrogen bonds : bond 0.04421 ( 746) hydrogen bonds : angle 4.16485 ( 2232) covalent geometry : bond 0.00273 (10992) covalent geometry : angle 0.54566 (14910) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2600 Ramachandran restraints generated. 1300 Oldfield, 0 Emsley, 1300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2600 Ramachandran restraints generated. 1300 Oldfield, 0 Emsley, 1300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 1138 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 124 time to evaluate : 1.205 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 384 MET cc_start: 0.8702 (tpp) cc_final: 0.7961 (mpp) REVERT: A 565 LEU cc_start: 0.9315 (OUTLIER) cc_final: 0.9068 (mp) REVERT: A 575 THR cc_start: 0.9194 (m) cc_final: 0.8974 (p) REVERT: B 384 MET cc_start: 0.8681 (tpp) cc_final: 0.7986 (mpp) REVERT: B 565 LEU cc_start: 0.9335 (OUTLIER) cc_final: 0.9104 (mp) REVERT: B 575 THR cc_start: 0.9195 (m) cc_final: 0.8975 (p) outliers start: 40 outliers final: 35 residues processed: 156 average time/residue: 0.1847 time to fit residues: 44.8857 Evaluate side-chains 150 residues out of total 1138 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 113 time to evaluate : 1.137 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 LEU Chi-restraints excluded: chain A residue 54 THR Chi-restraints excluded: chain A residue 111 VAL Chi-restraints excluded: chain A residue 135 THR Chi-restraints excluded: chain A residue 156 ASN Chi-restraints excluded: chain A residue 200 VAL Chi-restraints excluded: chain A residue 240 VAL Chi-restraints excluded: chain A residue 252 SER Chi-restraints excluded: chain A residue 282 MET Chi-restraints excluded: chain A residue 336 LEU Chi-restraints excluded: chain A residue 340 THR Chi-restraints excluded: chain A residue 378 ASN Chi-restraints excluded: chain A residue 440 PHE Chi-restraints excluded: chain A residue 451 THR Chi-restraints excluded: chain A residue 565 LEU Chi-restraints excluded: chain A residue 639 ARG Chi-restraints excluded: chain A residue 647 LEU Chi-restraints excluded: chain A residue 666 HIS Chi-restraints excluded: chain A residue 716 LEU Chi-restraints excluded: chain B residue 43 LEU Chi-restraints excluded: chain B residue 54 THR Chi-restraints excluded: chain B residue 111 VAL Chi-restraints excluded: chain B residue 156 ASN Chi-restraints excluded: chain B residue 200 VAL Chi-restraints excluded: chain B residue 211 LEU Chi-restraints excluded: chain B residue 240 VAL Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain B residue 340 THR Chi-restraints excluded: chain B residue 378 ASN Chi-restraints excluded: chain B residue 440 PHE Chi-restraints excluded: chain B residue 451 THR Chi-restraints excluded: chain B residue 527 CYS Chi-restraints excluded: chain B residue 565 LEU Chi-restraints excluded: chain B residue 632 LEU Chi-restraints excluded: chain B residue 647 LEU Chi-restraints excluded: chain B residue 666 HIS Chi-restraints excluded: chain B residue 716 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 78 optimal weight: 10.0000 chunk 100 optimal weight: 2.9990 chunk 63 optimal weight: 0.7980 chunk 24 optimal weight: 5.9990 chunk 75 optimal weight: 4.9990 chunk 58 optimal weight: 5.9990 chunk 69 optimal weight: 6.9990 chunk 115 optimal weight: 2.9990 chunk 97 optimal weight: 9.9990 chunk 74 optimal weight: 10.0000 chunk 47 optimal weight: 3.9990 overall best weight: 3.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 58 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 378 ASN B 378 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.105157 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3085 r_free = 0.3085 target = 0.078410 restraints weight = 25059.941| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3129 r_free = 0.3129 target = 0.080705 restraints weight = 13709.307| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3157 r_free = 0.3157 target = 0.082163 restraints weight = 9737.944| |-----------------------------------------------------------------------------| r_work (final): 0.3159 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8281 moved from start: 0.2716 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 10992 Z= 0.244 Angle : 0.623 6.899 14910 Z= 0.324 Chirality : 0.041 0.146 1632 Planarity : 0.004 0.046 1894 Dihedral : 3.969 14.058 1422 Min Nonbonded Distance : 2.168 Molprobity Statistics. All-atom Clashscore : 8.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.62 % Favored : 96.38 % Rotamer: Outliers : 3.69 % Allowed : 21.62 % Favored : 74.69 % 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: 1.46 (0.24), residues: 1300 helix: 1.91 (0.16), residues: 942 sheet: -1.13 (0.74), residues: 66 loop : -1.67 (0.36), residues: 292 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 235 HIS 0.004 0.001 HIS B 479 PHE 0.017 0.001 PHE A 189 TYR 0.018 0.002 TYR B 26 ARG 0.003 0.000 ARG A 548 Details of bonding type rmsd hydrogen bonds : bond 0.04773 ( 746) hydrogen bonds : angle 4.29751 ( 2232) covalent geometry : bond 0.00550 (10992) covalent geometry : angle 0.62349 (14910) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2600 Ramachandran restraints generated. 1300 Oldfield, 0 Emsley, 1300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2600 Ramachandran restraints generated. 1300 Oldfield, 0 Emsley, 1300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 1138 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 113 time to evaluate : 1.249 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 173 ASP cc_start: 0.8341 (OUTLIER) cc_final: 0.7979 (t0) REVERT: A 378 ASN cc_start: 0.8933 (OUTLIER) cc_final: 0.8576 (t0) REVERT: A 384 MET cc_start: 0.8755 (tpp) cc_final: 0.8096 (mpp) REVERT: A 565 LEU cc_start: 0.9363 (OUTLIER) cc_final: 0.9081 (mp) REVERT: B 173 ASP cc_start: 0.8349 (OUTLIER) cc_final: 0.8000 (t0) REVERT: B 384 MET cc_start: 0.8730 (tpp) cc_final: 0.8028 (mpp) REVERT: B 565 LEU cc_start: 0.9371 (OUTLIER) cc_final: 0.9086 (mp) outliers start: 42 outliers final: 36 residues processed: 147 average time/residue: 0.1734 time to fit residues: 40.2217 Evaluate side-chains 154 residues out of total 1138 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 113 time to evaluate : 1.203 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 LEU Chi-restraints excluded: chain A residue 54 THR Chi-restraints excluded: chain A residue 111 VAL Chi-restraints excluded: chain A residue 135 THR Chi-restraints excluded: chain A residue 156 ASN Chi-restraints excluded: chain A residue 173 ASP Chi-restraints excluded: chain A residue 200 VAL Chi-restraints excluded: chain A residue 240 VAL Chi-restraints excluded: chain A residue 252 SER Chi-restraints excluded: chain A residue 282 MET Chi-restraints excluded: chain A residue 336 LEU Chi-restraints excluded: chain A residue 340 THR Chi-restraints excluded: chain A residue 378 ASN Chi-restraints excluded: chain A residue 440 PHE Chi-restraints excluded: chain A residue 451 THR Chi-restraints excluded: chain A residue 527 CYS Chi-restraints excluded: chain A residue 565 LEU Chi-restraints excluded: chain A residue 639 ARG Chi-restraints excluded: chain A residue 647 LEU Chi-restraints excluded: chain A residue 666 HIS Chi-restraints excluded: chain A residue 716 LEU Chi-restraints excluded: chain B residue 43 LEU Chi-restraints excluded: chain B residue 54 THR Chi-restraints excluded: chain B residue 111 VAL Chi-restraints excluded: chain B residue 135 THR Chi-restraints excluded: chain B residue 156 ASN Chi-restraints excluded: chain B residue 173 ASP Chi-restraints excluded: chain B residue 200 VAL Chi-restraints excluded: chain B residue 211 LEU Chi-restraints excluded: chain B residue 240 VAL Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain B residue 340 THR Chi-restraints excluded: chain B residue 378 ASN Chi-restraints excluded: chain B residue 440 PHE Chi-restraints excluded: chain B residue 451 THR Chi-restraints excluded: chain B residue 527 CYS Chi-restraints excluded: chain B residue 565 LEU Chi-restraints excluded: chain B residue 632 LEU Chi-restraints excluded: chain B residue 647 LEU Chi-restraints excluded: chain B residue 666 HIS Chi-restraints excluded: chain B residue 716 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 106 optimal weight: 10.0000 chunk 34 optimal weight: 1.9990 chunk 78 optimal weight: 5.9990 chunk 38 optimal weight: 6.9990 chunk 58 optimal weight: 4.9990 chunk 48 optimal weight: 0.8980 chunk 28 optimal weight: 2.9990 chunk 8 optimal weight: 10.0000 chunk 5 optimal weight: 0.9980 chunk 37 optimal weight: 0.8980 chunk 0 optimal weight: 0.7980 overall best weight: 1.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 58 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 378 ASN B 378 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3596 r_free = 0.3596 target = 0.107303 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3127 r_free = 0.3127 target = 0.080541 restraints weight = 24672.572| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3173 r_free = 0.3173 target = 0.082998 restraints weight = 13053.523| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3202 r_free = 0.3202 target = 0.084514 restraints weight = 9105.681| |-----------------------------------------------------------------------------| r_work (final): 0.3206 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8215 moved from start: 0.2727 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 10992 Z= 0.138 Angle : 0.572 8.757 14910 Z= 0.292 Chirality : 0.038 0.156 1632 Planarity : 0.004 0.045 1894 Dihedral : 3.944 13.719 1422 Min Nonbonded Distance : 2.194 Molprobity Statistics. All-atom Clashscore : 7.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 3.60 % Allowed : 21.88 % Favored : 74.52 % 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: 1.59 (0.23), residues: 1300 helix: 1.99 (0.16), residues: 942 sheet: -1.02 (0.72), residues: 68 loop : -1.61 (0.36), residues: 290 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP B 235 HIS 0.003 0.001 HIS B 265 PHE 0.015 0.001 PHE A 379 TYR 0.015 0.002 TYR B 26 ARG 0.002 0.000 ARG B 505 Details of bonding type rmsd hydrogen bonds : bond 0.04530 ( 746) hydrogen bonds : angle 4.16487 ( 2232) covalent geometry : bond 0.00299 (10992) covalent geometry : angle 0.57154 (14910) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3612.25 seconds wall clock time: 67 minutes 30.14 seconds (4050.14 seconds total)