Starting phenix.real_space_refine on Tue Mar 3 11:33:17 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7f62_31470/03_2026/7f62_31470.cif Found real_map, /net/cci-nas-00/data/ceres_data/7f62_31470/03_2026/7f62_31470.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7f62_31470/03_2026/7f62_31470.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7f62_31470/03_2026/7f62_31470.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7f62_31470/03_2026/7f62_31470.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7f62_31470/03_2026/7f62_31470.map" } resolution = 3.6 write_initial_geo_file = False refinement { macro_cycles = 10 } 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= 0.034 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 2104 2.51 5 N 552 2.21 5 O 647 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 3321 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 1579 Number of conformers: 1 Conformer: "" Number of residues, atoms: 199, 1579 Classifications: {'peptide': 199} Link IDs: {'PTRANS': 11, 'TRANS': 187} Chain breaks: 1 Chain: "H" Number of atoms: 914 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 914 Classifications: {'peptide': 119} Link IDs: {'PTRANS': 3, 'TRANS': 115} Chain: "L" Number of atoms: 828 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 828 Classifications: {'peptide': 109} Link IDs: {'PTRANS': 5, 'TRANS': 103} Time building chain proxies: 0.91, per 1000 atoms: 0.27 Number of scatterers: 3321 At special positions: 0 Unit cell: (77, 53.9, 102.3, 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 647 8.00 N 552 7.00 C 2104 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.04 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.03 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 89 " distance=2.03 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: 0.26 Conformation dependent library (CDL) restraints added in 132.5 milliseconds 838 Ramachandran restraints generated. 419 Oldfield, 0 Emsley, 419 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 784 Finding SS restraints... Secondary structure from input PDB file: 7 helices and 10 sheets defined 9.8% alpha, 21.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.12 Creating SS restraints... Processing helix chain 'A' and resid 337 through 343 removed outlier: 4.007A pdb=" N VAL A 341 " --> pdb=" O PRO A 337 " (cutoff:3.500A) Processing helix chain 'A' and resid 365 through 370 removed outlier: 3.936A pdb=" N TYR A 369 " --> pdb=" O TYR A 365 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 410 removed outlier: 5.197A pdb=" N ARG A 408 " --> pdb=" O ASP A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 422 removed outlier: 3.625A pdb=" N ASN A 422 " --> pdb=" O ILE A 418 " (cutoff:3.500A) Processing helix chain 'A' and resid 438 through 443 Processing helix chain 'H' and resid 61 through 65 removed outlier: 4.075A pdb=" N ALA H 64 " --> pdb=" O PRO H 61 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N THR H 65 " --> pdb=" O ASP H 62 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 61 through 65' Processing helix chain 'L' and resid 80 through 84 removed outlier: 3.998A pdb=" N ALA L 84 " --> pdb=" O ALA L 81 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 354 through 358 removed outlier: 3.561A pdb=" N VAL A 395 " --> pdb=" O ILE A 358 " (cutoff:3.500A) removed outlier: 4.414A pdb=" N VAL A 395 " --> pdb=" O SER A 514 " (cutoff:3.500A) removed outlier: 6.679A pdb=" N SER A 514 " --> pdb=" O VAL A 395 " (cutoff:3.500A) removed outlier: 4.390A pdb=" N ALA A 397 " --> pdb=" O VAL A 512 " (cutoff:3.500A) removed outlier: 6.499A pdb=" N VAL A 512 " --> pdb=" O ALA A 397 " (cutoff:3.500A) removed outlier: 4.425A pdb=" N SER A 399 " --> pdb=" O VAL A 510 " (cutoff:3.500A) removed outlier: 7.048A pdb=" N VAL A 510 " --> pdb=" O SER A 399 " (cutoff:3.500A) removed outlier: 4.548A pdb=" N VAL A 401 " --> pdb=" O TYR A 508 " (cutoff:3.500A) removed outlier: 6.400A pdb=" N TYR A 508 " --> pdb=" O VAL A 401 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 453 through 454 Processing sheet with id=AA3, first strand: chain 'A' and resid 473 through 474 Processing sheet with id=AA4, first strand: chain 'H' and resid 19 through 21 Processing sheet with id=AA5, first strand: chain 'H' and resid 57 through 59 removed outlier: 3.919A pdb=" N ASN H 59 " --> pdb=" O GLU H 50 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N GLU H 50 " --> pdb=" O ASN H 59 " (cutoff:3.500A) removed outlier: 6.653A pdb=" N TRP H 36 " --> pdb=" O VAL H 48 " (cutoff:3.500A) removed outlier: 4.951A pdb=" N GLU H 50 " --> pdb=" O MET H 34 " (cutoff:3.500A) removed outlier: 6.953A pdb=" N MET H 34 " --> pdb=" O GLU H 50 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'L' and resid 5 through 6 removed outlier: 4.072A pdb=" N SER L 71 " --> pdb=" O SER L 68 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N SER L 68 " --> pdb=" O SER L 71 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'L' and resid 12 through 14 removed outlier: 6.133A pdb=" N GLU L 106 " --> pdb=" O VAL L 13 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'L' and resid 35 through 36 removed outlier: 4.195A pdb=" N ILE L 49 " --> pdb=" O TRP L 36 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'L' and resid 86 through 87 removed outlier: 3.725A pdb=" N TYR L 87 " --> pdb=" O THR L 103 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'L' and resid 90 through 91 removed outlier: 3.741A pdb=" N GLN L 91 " --> pdb=" O THR L 98 " (cutoff:3.500A) removed outlier: 4.204A pdb=" N THR L 98 " --> pdb=" O GLN L 91 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 68 hydrogen bonds defined for protein. 153 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: 0.44 Time building geometry restraints manager: 0.36 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: 1046 1.34 - 1.46: 748 1.46 - 1.58: 1588 1.58 - 1.70: 0 1.70 - 1.82: 24 Bond restraints: 3406 Sorted by residual: bond pdb=" N TYR A 449 " pdb=" CA TYR A 449 " ideal model delta sigma weight residual 1.457 1.425 0.032 1.29e-02 6.01e+03 6.35e+00 bond pdb=" C ASN A 448 " pdb=" N TYR A 449 " ideal model delta sigma weight residual 1.332 1.301 0.031 1.40e-02 5.10e+03 5.04e+00 bond pdb=" C TYR A 449 " pdb=" O TYR A 449 " ideal model delta sigma weight residual 1.235 1.218 0.018 1.26e-02 6.30e+03 1.99e+00 bond pdb=" CE2 TYR A 449 " pdb=" CZ TYR A 449 " ideal model delta sigma weight residual 1.378 1.345 0.033 2.40e-02 1.74e+03 1.92e+00 bond pdb=" C SER L 95 " pdb=" O SER L 95 " ideal model delta sigma weight residual 1.241 1.231 0.011 9.80e-03 1.04e+04 1.19e+00 ... (remaining 3401 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.25: 4362 1.25 - 2.51: 205 2.51 - 3.76: 38 3.76 - 5.02: 17 5.02 - 6.27: 2 Bond angle restraints: 4624 Sorted by residual: angle pdb=" CA SER L 95 " pdb=" C SER L 95 " pdb=" N PRO L 96 " ideal model delta sigma weight residual 120.79 116.56 4.23 9.70e-01 1.06e+00 1.91e+01 angle pdb=" C SER L 95 " pdb=" N PRO L 96 " pdb=" CA PRO L 96 " ideal model delta sigma weight residual 119.99 124.05 -4.06 1.08e+00 8.57e-01 1.41e+01 angle pdb=" CA TYR A 449 " pdb=" CB TYR A 449 " pdb=" CG TYR A 449 " ideal model delta sigma weight residual 113.90 119.63 -5.73 1.80e+00 3.09e-01 1.01e+01 angle pdb=" N LEU A 452 " pdb=" CA LEU A 452 " pdb=" C LEU A 452 " ideal model delta sigma weight residual 109.41 113.80 -4.39 1.52e+00 4.33e-01 8.32e+00 angle pdb=" C PRO A 330 " pdb=" N ASN A 331 " pdb=" CA ASN A 331 " ideal model delta sigma weight residual 120.65 124.21 -3.56 1.32e+00 5.74e-01 7.27e+00 ... (remaining 4619 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.33: 1770 15.33 - 30.66: 174 30.66 - 45.99: 49 45.99 - 61.32: 12 61.32 - 76.65: 4 Dihedral angle restraints: 2009 sinusoidal: 771 harmonic: 1238 Sorted by residual: dihedral pdb=" CB CYS A 336 " pdb=" SG CYS A 336 " pdb=" SG CYS A 361 " pdb=" CB CYS A 361 " ideal model delta sinusoidal sigma weight residual 93.00 26.90 66.10 1 1.00e+01 1.00e-02 5.71e+01 dihedral pdb=" CA GLN H 3 " pdb=" C GLN H 3 " pdb=" N LEU H 4 " pdb=" CA LEU H 4 " ideal model delta harmonic sigma weight residual 180.00 151.87 28.13 0 5.00e+00 4.00e-02 3.16e+01 dihedral pdb=" CB CYS A 480 " pdb=" SG CYS A 480 " pdb=" SG CYS A 488 " pdb=" CB CYS A 488 " ideal model delta sinusoidal sigma weight residual -86.00 -132.09 46.09 1 1.00e+01 1.00e-02 2.94e+01 ... (remaining 2006 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.032: 308 0.032 - 0.063: 120 0.063 - 0.095: 41 0.095 - 0.127: 22 0.127 - 0.159: 4 Chirality restraints: 495 Sorted by residual: chirality pdb=" CB ILE L 49 " pdb=" CA ILE L 49 " pdb=" CG1 ILE L 49 " pdb=" CG2 ILE L 49 " both_signs ideal model delta sigma weight residual False 2.64 2.49 0.16 2.00e-01 2.50e+01 6.29e-01 chirality pdb=" CA VAL H 37 " pdb=" N VAL H 37 " pdb=" C VAL H 37 " pdb=" CB VAL H 37 " both_signs ideal model delta sigma weight residual False 2.44 2.59 -0.15 2.00e-01 2.50e+01 5.29e-01 chirality pdb=" CA VAL A 401 " pdb=" N VAL A 401 " pdb=" C VAL A 401 " pdb=" CB VAL A 401 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 4.31e-01 ... (remaining 492 not shown) Planarity restraints: 593 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASN A 448 " 0.010 2.00e-02 2.50e+03 2.00e-02 4.02e+00 pdb=" C ASN A 448 " -0.035 2.00e-02 2.50e+03 pdb=" O ASN A 448 " 0.013 2.00e-02 2.50e+03 pdb=" N TYR A 449 " 0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ALA A 520 " 0.031 5.00e-02 4.00e+02 4.67e-02 3.49e+00 pdb=" N PRO A 521 " -0.081 5.00e-02 4.00e+02 pdb=" CA PRO A 521 " 0.024 5.00e-02 4.00e+02 pdb=" CD PRO A 521 " 0.026 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS H 13 " -0.024 5.00e-02 4.00e+02 3.66e-02 2.14e+00 pdb=" N PRO H 14 " 0.063 5.00e-02 4.00e+02 pdb=" CA PRO H 14 " -0.019 5.00e-02 4.00e+02 pdb=" CD PRO H 14 " -0.020 5.00e-02 4.00e+02 ... (remaining 590 not shown) Histogram of nonbonded interaction distances: 1.92 - 2.52: 44 2.52 - 3.11: 2497 3.11 - 3.71: 5200 3.71 - 4.30: 7066 4.30 - 4.90: 11389 Nonbonded interactions: 26196 Sorted by model distance: nonbonded pdb=" O VAL L 29 " pdb=" ND1 HIS L 93 " model vdw 1.925 3.120 nonbonded pdb=" CE2 TYR L 33 " pdb=" CD2 HIS L 93 " model vdw 1.951 3.560 nonbonded pdb=" CD2 TYR L 33 " pdb=" CD2 HIS L 93 " model vdw 1.983 3.560 nonbonded pdb=" OH TYR H 60 " pdb=" O THR H 65 " model vdw 2.177 3.040 nonbonded pdb=" OG1 THR H 33 " pdb=" O PHE H 99 " model vdw 2.207 3.040 ... (remaining 26191 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 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: 2.890 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.060 Check model and map are aligned: 0.000 Set scattering table: 0.010 Process input model: 4.800 Find NCS groups from input model: 0.020 Set up NCS constraints: 0.000 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:1.530 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 9.310 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6210 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 3412 Z= 0.150 Angle : 0.651 6.271 4636 Z= 0.370 Chirality : 0.043 0.159 495 Planarity : 0.004 0.047 593 Dihedral : 13.209 76.650 1207 Min Nonbonded Distance : 1.925 Molprobity Statistics. All-atom Clashscore : 19.73 Ramachandran Plot: Outliers : 0.24 % Allowed : 8.11 % Favored : 91.65 % Rotamer: Outliers : 1.38 % Allowed : 1.65 % Favored : 96.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.76 (0.39), residues: 419 helix: -4.04 (0.68), residues: 30 sheet: -0.91 (0.48), residues: 123 loop : -2.11 (0.36), residues: 266 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 457 TYR 0.013 0.001 TYR H 95 PHE 0.011 0.001 PHE H 27 TRP 0.014 0.002 TRP L 48 HIS 0.002 0.001 HIS L 35 Details of bonding type rmsd covalent geometry : bond 0.00266 ( 3406) covalent geometry : angle 0.64918 ( 4624) SS BOND : bond 0.00421 ( 6) SS BOND : angle 1.18306 ( 12) hydrogen bonds : bond 0.21588 ( 68) hydrogen bonds : angle 9.80983 ( 153) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 838 Ramachandran restraints generated. 419 Oldfield, 0 Emsley, 419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 838 Ramachandran restraints generated. 419 Oldfield, 0 Emsley, 419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 363 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 93 time to evaluate : 0.122 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 365 TYR cc_start: 0.9212 (m-80) cc_final: 0.8985 (m-80) REVERT: A 451 TYR cc_start: 0.4870 (OUTLIER) cc_final: 0.4556 (m-10) REVERT: A 489 TYR cc_start: 0.7475 (m-80) cc_final: 0.7107 (m-10) REVERT: H 4 LEU cc_start: 0.6373 (mt) cc_final: 0.5859 (mp) REVERT: H 101 ASN cc_start: 0.7598 (p0) cc_final: 0.7169 (p0) REVERT: H 103 GLU cc_start: 0.7792 (tp30) cc_final: 0.7303 (tm-30) REVERT: L 75 THR cc_start: 0.7609 (t) cc_final: 0.7089 (m) outliers start: 5 outliers final: 2 residues processed: 98 average time/residue: 0.1063 time to fit residues: 11.7943 Evaluate side-chains 54 residues out of total 363 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 51 time to evaluate : 0.126 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 449 TYR Chi-restraints excluded: chain A residue 451 TYR Chi-restraints excluded: chain L residue 94 ARG Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 24 optimal weight: 0.6980 chunk 26 optimal weight: 2.9990 chunk 2 optimal weight: 2.9990 chunk 16 optimal weight: 2.9990 chunk 32 optimal weight: 6.9990 chunk 31 optimal weight: 5.9990 chunk 25 optimal weight: 0.0000 chunk 19 optimal weight: 0.9980 chunk 30 optimal weight: 5.9990 chunk 22 optimal weight: 3.9990 chunk 37 optimal weight: 5.9990 overall best weight: 1.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 493 GLN H 59 ASN H 74 ASN L 90 HIS L 93 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3986 r_free = 0.3986 target = 0.092590 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3678 r_free = 0.3678 target = 0.075317 restraints weight = 12674.852| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3725 r_free = 0.3725 target = 0.077954 restraints weight = 6510.933| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3754 r_free = 0.3754 target = 0.079620 restraints weight = 4367.852| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3776 r_free = 0.3776 target = 0.080792 restraints weight = 3415.687| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3790 r_free = 0.3790 target = 0.081561 restraints weight = 2894.828| |-----------------------------------------------------------------------------| r_work (final): 0.3788 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7456 moved from start: 0.3565 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 3412 Z= 0.165 Angle : 0.648 5.831 4636 Z= 0.340 Chirality : 0.046 0.153 495 Planarity : 0.005 0.046 593 Dihedral : 5.976 47.612 480 Min Nonbonded Distance : 2.571 Molprobity Statistics. All-atom Clashscore : 10.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.35 % Favored : 91.65 % Rotamer: Outliers : 3.03 % Allowed : 12.12 % Favored : 84.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.47 (0.39), residues: 419 helix: -3.33 (0.86), residues: 24 sheet: -0.92 (0.49), residues: 119 loop : -1.90 (0.35), residues: 276 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG H 38 TYR 0.017 0.002 TYR H 95 PHE 0.018 0.002 PHE L 63 TRP 0.024 0.002 TRP L 48 HIS 0.004 0.001 HIS L 35 Details of bonding type rmsd covalent geometry : bond 0.00380 ( 3406) covalent geometry : angle 0.64676 ( 4624) SS BOND : bond 0.00246 ( 6) SS BOND : angle 1.06125 ( 12) hydrogen bonds : bond 0.03778 ( 68) hydrogen bonds : angle 7.13902 ( 153) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 838 Ramachandran restraints generated. 419 Oldfield, 0 Emsley, 419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 838 Ramachandran restraints generated. 419 Oldfield, 0 Emsley, 419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 67 residues out of total 363 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 56 time to evaluate : 0.132 Fit side-chains revert: symmetry clash REVERT: A 480 CYS cc_start: 0.4355 (OUTLIER) cc_final: 0.3534 (m) REVERT: H 90 ASP cc_start: 0.8302 (t0) cc_final: 0.8068 (t0) REVERT: L 75 THR cc_start: 0.6491 (t) cc_final: 0.6002 (m) outliers start: 11 outliers final: 7 residues processed: 64 average time/residue: 0.0659 time to fit residues: 5.2269 Evaluate side-chains 53 residues out of total 363 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 45 time to evaluate : 0.130 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 442 ASP Chi-restraints excluded: chain A residue 480 CYS Chi-restraints excluded: chain H residue 18 LEU Chi-restraints excluded: chain H residue 20 LEU Chi-restraints excluded: chain H residue 28 THR Chi-restraints excluded: chain H residue 113 LEU Chi-restraints excluded: chain L residue 4 LEU Chi-restraints excluded: chain L residue 49 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 24 optimal weight: 2.9990 chunk 17 optimal weight: 4.9990 chunk 32 optimal weight: 2.9990 chunk 12 optimal weight: 0.8980 chunk 22 optimal weight: 2.9990 chunk 26 optimal weight: 2.9990 chunk 20 optimal weight: 20.0000 chunk 1 optimal weight: 4.9990 chunk 2 optimal weight: 0.9980 chunk 38 optimal weight: 1.9990 chunk 10 optimal weight: 6.9990 overall best weight: 1.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 74 ASN ** H 101 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 = 0.3893 r_free = 0.3893 target = 0.088149 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3579 r_free = 0.3579 target = 0.070928 restraints weight = 12671.604| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3624 r_free = 0.3624 target = 0.073448 restraints weight = 6589.636| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3654 r_free = 0.3654 target = 0.075130 restraints weight = 4420.846| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3675 r_free = 0.3675 target = 0.076228 restraints weight = 3418.539| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3686 r_free = 0.3686 target = 0.076940 restraints weight = 2893.038| |-----------------------------------------------------------------------------| r_work (final): 0.3680 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7561 moved from start: 0.4637 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 3412 Z= 0.193 Angle : 0.646 5.658 4636 Z= 0.341 Chirality : 0.047 0.148 495 Planarity : 0.005 0.044 593 Dihedral : 5.096 22.600 472 Min Nonbonded Distance : 2.592 Molprobity Statistics. All-atom Clashscore : 12.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.79 % Favored : 90.21 % Rotamer: Outliers : 5.23 % Allowed : 16.25 % Favored : 78.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.33 (0.39), residues: 419 helix: -3.17 (0.85), residues: 24 sheet: -0.73 (0.50), residues: 115 loop : -1.85 (0.35), residues: 280 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG H 38 TYR 0.011 0.001 TYR L 87 PHE 0.011 0.002 PHE A 456 TRP 0.019 0.002 TRP L 48 HIS 0.003 0.001 HIS L 35 Details of bonding type rmsd covalent geometry : bond 0.00440 ( 3406) covalent geometry : angle 0.64379 ( 4624) SS BOND : bond 0.00260 ( 6) SS BOND : angle 1.24229 ( 12) hydrogen bonds : bond 0.03985 ( 68) hydrogen bonds : angle 7.21715 ( 153) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 838 Ramachandran restraints generated. 419 Oldfield, 0 Emsley, 419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 838 Ramachandran restraints generated. 419 Oldfield, 0 Emsley, 419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 68 residues out of total 363 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 49 time to evaluate : 0.124 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 480 CYS cc_start: 0.4108 (OUTLIER) cc_final: 0.3757 (m) REVERT: H 80 TYR cc_start: 0.7131 (m-10) cc_final: 0.6867 (m-80) REVERT: H 90 ASP cc_start: 0.8540 (t0) cc_final: 0.8292 (t0) outliers start: 19 outliers final: 10 residues processed: 62 average time/residue: 0.0582 time to fit residues: 4.6086 Evaluate side-chains 52 residues out of total 363 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 41 time to evaluate : 0.121 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 480 CYS Chi-restraints excluded: chain H residue 20 LEU Chi-restraints excluded: chain H residue 28 THR Chi-restraints excluded: chain H residue 65 THR Chi-restraints excluded: chain H residue 70 ILE Chi-restraints excluded: chain H residue 79 LEU Chi-restraints excluded: chain H residue 113 LEU Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 33 TYR Chi-restraints excluded: chain L residue 49 ILE Chi-restraints excluded: chain L residue 59 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 8 optimal weight: 7.9990 chunk 2 optimal weight: 2.9990 chunk 12 optimal weight: 4.9990 chunk 39 optimal weight: 4.9990 chunk 19 optimal weight: 3.9990 chunk 13 optimal weight: 4.9990 chunk 28 optimal weight: 0.9980 chunk 18 optimal weight: 7.9990 chunk 0 optimal weight: 7.9990 chunk 27 optimal weight: 7.9990 chunk 35 optimal weight: 0.6980 overall best weight: 2.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 38 GLN ** 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 = 0.3829 r_free = 0.3829 target = 0.085261 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3513 r_free = 0.3513 target = 0.068191 restraints weight = 12753.139| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3555 r_free = 0.3555 target = 0.070474 restraints weight = 6666.336| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3583 r_free = 0.3583 target = 0.072042 restraints weight = 4557.964| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3603 r_free = 0.3603 target = 0.073085 restraints weight = 3566.923| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3613 r_free = 0.3613 target = 0.073702 restraints weight = 3044.949| |-----------------------------------------------------------------------------| r_work (final): 0.3604 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7666 moved from start: 0.5410 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.060 3412 Z= 0.252 Angle : 0.683 5.012 4636 Z= 0.367 Chirality : 0.048 0.153 495 Planarity : 0.005 0.044 593 Dihedral : 5.650 23.134 472 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 14.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.46 % Favored : 88.54 % Rotamer: Outliers : 5.79 % Allowed : 21.49 % Favored : 72.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.52 (0.38), residues: 419 helix: -2.98 (0.94), residues: 18 sheet: -0.85 (0.52), residues: 106 loop : -2.04 (0.33), residues: 295 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG H 38 TYR 0.012 0.002 TYR A 495 PHE 0.016 0.002 PHE H 29 TRP 0.015 0.002 TRP L 36 HIS 0.004 0.001 HIS L 35 Details of bonding type rmsd covalent geometry : bond 0.00564 ( 3406) covalent geometry : angle 0.68071 ( 4624) SS BOND : bond 0.00429 ( 6) SS BOND : angle 1.29245 ( 12) hydrogen bonds : bond 0.04521 ( 68) hydrogen bonds : angle 7.80926 ( 153) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 838 Ramachandran restraints generated. 419 Oldfield, 0 Emsley, 419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 838 Ramachandran restraints generated. 419 Oldfield, 0 Emsley, 419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 65 residues out of total 363 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 44 time to evaluate : 0.129 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 4 LEU cc_start: 0.6383 (OUTLIER) cc_final: 0.6024 (mt) REVERT: H 11 LEU cc_start: 0.7809 (OUTLIER) cc_final: 0.7475 (pp) REVERT: H 60 TYR cc_start: 0.7734 (OUTLIER) cc_final: 0.6959 (p90) REVERT: H 80 TYR cc_start: 0.7383 (m-10) cc_final: 0.7111 (m-80) REVERT: H 90 ASP cc_start: 0.8599 (t0) cc_final: 0.8370 (t0) outliers start: 21 outliers final: 11 residues processed: 57 average time/residue: 0.0657 time to fit residues: 4.6878 Evaluate side-chains 47 residues out of total 363 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 33 time to evaluate : 0.132 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 415 THR Chi-restraints excluded: chain H residue 4 LEU Chi-restraints excluded: chain H residue 11 LEU Chi-restraints excluded: chain H residue 20 LEU Chi-restraints excluded: chain H residue 28 THR Chi-restraints excluded: chain H residue 60 TYR Chi-restraints excluded: chain H residue 65 THR Chi-restraints excluded: chain H residue 70 ILE Chi-restraints excluded: chain H residue 79 LEU Chi-restraints excluded: chain H residue 112 THR Chi-restraints excluded: chain H residue 113 LEU Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 35 HIS Chi-restraints excluded: chain L residue 49 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 23 optimal weight: 3.9990 chunk 0 optimal weight: 8.9990 chunk 11 optimal weight: 2.9990 chunk 19 optimal weight: 5.9990 chunk 25 optimal weight: 2.9990 chunk 30 optimal weight: 3.9990 chunk 3 optimal weight: 7.9990 chunk 9 optimal weight: 0.0170 chunk 38 optimal weight: 0.9990 chunk 7 optimal weight: 1.9990 chunk 24 optimal weight: 2.9990 overall best weight: 1.8026 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3868 r_free = 0.3868 target = 0.086245 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3545 r_free = 0.3545 target = 0.069309 restraints weight = 12641.618| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.071708 restraints weight = 6612.889| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3618 r_free = 0.3618 target = 0.073263 restraints weight = 4493.333| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3635 r_free = 0.3635 target = 0.074227 restraints weight = 3517.332| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3645 r_free = 0.3645 target = 0.074867 restraints weight = 3013.493| |-----------------------------------------------------------------------------| r_work (final): 0.3639 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7636 moved from start: 0.5545 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 3412 Z= 0.175 Angle : 0.625 5.506 4636 Z= 0.331 Chirality : 0.046 0.149 495 Planarity : 0.006 0.048 593 Dihedral : 5.322 20.391 472 Min Nonbonded Distance : 2.577 Molprobity Statistics. All-atom Clashscore : 11.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.02 % Favored : 89.98 % Rotamer: Outliers : 5.23 % Allowed : 22.59 % Favored : 72.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.59 (0.37), residues: 419 helix: -2.81 (0.97), residues: 18 sheet: -0.82 (0.52), residues: 107 loop : -2.15 (0.32), residues: 294 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG L 62 TYR 0.009 0.001 TYR H 95 PHE 0.016 0.001 PHE H 68 TRP 0.013 0.002 TRP L 36 HIS 0.002 0.001 HIS L 93 Details of bonding type rmsd covalent geometry : bond 0.00397 ( 3406) covalent geometry : angle 0.62005 ( 4624) SS BOND : bond 0.00485 ( 6) SS BOND : angle 1.65114 ( 12) hydrogen bonds : bond 0.03755 ( 68) hydrogen bonds : angle 7.41683 ( 153) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 838 Ramachandran restraints generated. 419 Oldfield, 0 Emsley, 419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 838 Ramachandran restraints generated. 419 Oldfield, 0 Emsley, 419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 59 residues out of total 363 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 40 time to evaluate : 0.123 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 4 LEU cc_start: 0.6508 (OUTLIER) cc_final: 0.6191 (mt) REVERT: H 11 LEU cc_start: 0.7816 (OUTLIER) cc_final: 0.7495 (pp) REVERT: H 60 TYR cc_start: 0.7773 (OUTLIER) cc_final: 0.6611 (p90) REVERT: H 80 TYR cc_start: 0.7353 (m-10) cc_final: 0.7082 (m-80) REVERT: H 90 ASP cc_start: 0.8526 (t0) cc_final: 0.8280 (t0) outliers start: 19 outliers final: 10 residues processed: 53 average time/residue: 0.0466 time to fit residues: 3.1944 Evaluate side-chains 50 residues out of total 363 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 37 time to evaluate : 0.110 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 4 LEU Chi-restraints excluded: chain H residue 11 LEU Chi-restraints excluded: chain H residue 18 LEU Chi-restraints excluded: chain H residue 20 LEU Chi-restraints excluded: chain H residue 28 THR Chi-restraints excluded: chain H residue 60 TYR Chi-restraints excluded: chain H residue 65 THR Chi-restraints excluded: chain H residue 70 ILE Chi-restraints excluded: chain H residue 113 LEU Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 35 HIS Chi-restraints excluded: chain L residue 49 ILE Chi-restraints excluded: chain L residue 98 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 16 optimal weight: 2.9990 chunk 17 optimal weight: 0.8980 chunk 24 optimal weight: 3.9990 chunk 12 optimal weight: 1.9990 chunk 36 optimal weight: 8.9990 chunk 0 optimal weight: 8.9990 chunk 31 optimal weight: 0.0020 chunk 8 optimal weight: 2.9990 chunk 25 optimal weight: 1.9990 chunk 19 optimal weight: 0.1980 chunk 33 optimal weight: 1.9990 overall best weight: 1.0192 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4030 r_free = 0.4030 target = 0.094150 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3714 r_free = 0.3714 target = 0.076310 restraints weight = 12662.398| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3757 r_free = 0.3757 target = 0.078884 restraints weight = 6801.068| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3787 r_free = 0.3787 target = 0.080586 restraints weight = 4678.112| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3803 r_free = 0.3803 target = 0.081599 restraints weight = 3694.375| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3815 r_free = 0.3815 target = 0.082317 restraints weight = 3186.078| |-----------------------------------------------------------------------------| r_work (final): 0.3806 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7629 moved from start: 0.5614 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 3412 Z= 0.118 Angle : 0.572 5.038 4636 Z= 0.298 Chirality : 0.045 0.152 495 Planarity : 0.005 0.050 593 Dihedral : 4.883 19.612 472 Min Nonbonded Distance : 2.602 Molprobity Statistics. All-atom Clashscore : 9.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.79 % Favored : 90.21 % Rotamer: Outliers : 4.68 % Allowed : 22.87 % Favored : 72.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.52 (0.38), residues: 419 helix: -2.88 (0.97), residues: 18 sheet: -0.88 (0.50), residues: 113 loop : -2.06 (0.32), residues: 288 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG L 62 TYR 0.008 0.001 TYR L 92 PHE 0.017 0.001 PHE H 68 TRP 0.009 0.001 TRP L 48 HIS 0.002 0.001 HIS L 93 Details of bonding type rmsd covalent geometry : bond 0.00273 ( 3406) covalent geometry : angle 0.56977 ( 4624) SS BOND : bond 0.00375 ( 6) SS BOND : angle 1.21607 ( 12) hydrogen bonds : bond 0.03091 ( 68) hydrogen bonds : angle 7.01526 ( 153) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 838 Ramachandran restraints generated. 419 Oldfield, 0 Emsley, 419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 838 Ramachandran restraints generated. 419 Oldfield, 0 Emsley, 419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 61 residues out of total 363 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 44 time to evaluate : 0.141 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 4 LEU cc_start: 0.6618 (OUTLIER) cc_final: 0.6320 (mt) REVERT: H 11 LEU cc_start: 0.7895 (OUTLIER) cc_final: 0.7547 (pp) REVERT: H 60 TYR cc_start: 0.7518 (OUTLIER) cc_final: 0.6162 (p90) REVERT: H 80 TYR cc_start: 0.7287 (m-10) cc_final: 0.7038 (m-80) REVERT: H 90 ASP cc_start: 0.8372 (t0) cc_final: 0.8115 (t0) REVERT: L 94 ARG cc_start: 0.8172 (mtp-110) cc_final: 0.7947 (mmm-85) outliers start: 17 outliers final: 12 residues processed: 55 average time/residue: 0.0662 time to fit residues: 4.5412 Evaluate side-chains 55 residues out of total 363 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 40 time to evaluate : 0.136 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 4 LEU Chi-restraints excluded: chain H residue 11 LEU Chi-restraints excluded: chain H residue 18 LEU Chi-restraints excluded: chain H residue 20 LEU Chi-restraints excluded: chain H residue 28 THR Chi-restraints excluded: chain H residue 60 TYR Chi-restraints excluded: chain H residue 65 THR Chi-restraints excluded: chain H residue 70 ILE Chi-restraints excluded: chain H residue 113 LEU Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 33 TYR Chi-restraints excluded: chain L residue 35 HIS Chi-restraints excluded: chain L residue 49 ILE Chi-restraints excluded: chain L residue 98 THR Chi-restraints excluded: chain L residue 107 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 19 optimal weight: 2.9990 chunk 39 optimal weight: 0.9980 chunk 8 optimal weight: 4.9990 chunk 13 optimal weight: 5.9990 chunk 7 optimal weight: 1.9990 chunk 25 optimal weight: 0.7980 chunk 12 optimal weight: 6.9990 chunk 4 optimal weight: 2.9990 chunk 27 optimal weight: 0.5980 chunk 17 optimal weight: 5.9990 chunk 14 optimal weight: 3.9990 overall best weight: 1.4784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 74 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4021 r_free = 0.4021 target = 0.093853 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3711 r_free = 0.3711 target = 0.076278 restraints weight = 12896.559| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3753 r_free = 0.3753 target = 0.078688 restraints weight = 7047.984| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3782 r_free = 0.3782 target = 0.080337 restraints weight = 4904.856| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3800 r_free = 0.3800 target = 0.081366 restraints weight = 3893.116| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3810 r_free = 0.3810 target = 0.082029 restraints weight = 3351.868| |-----------------------------------------------------------------------------| r_work (final): 0.3793 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7668 moved from start: 0.5803 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 3412 Z= 0.147 Angle : 0.600 5.906 4636 Z= 0.313 Chirality : 0.045 0.153 495 Planarity : 0.005 0.046 593 Dihedral : 4.928 19.209 472 Min Nonbonded Distance : 2.561 Molprobity Statistics. All-atom Clashscore : 11.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.74 % Favored : 89.26 % Rotamer: Outliers : 4.96 % Allowed : 22.59 % Favored : 72.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.51 (0.38), residues: 419 helix: -3.59 (0.80), residues: 24 sheet: -0.70 (0.51), residues: 114 loop : -2.02 (0.33), residues: 281 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG L 62 TYR 0.008 0.001 TYR H 107 PHE 0.019 0.001 PHE H 68 TRP 0.010 0.001 TRP L 48 HIS 0.002 0.001 HIS L 93 Details of bonding type rmsd covalent geometry : bond 0.00335 ( 3406) covalent geometry : angle 0.59794 ( 4624) SS BOND : bond 0.00338 ( 6) SS BOND : angle 1.13310 ( 12) hydrogen bonds : bond 0.03486 ( 68) hydrogen bonds : angle 7.06433 ( 153) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 838 Ramachandran restraints generated. 419 Oldfield, 0 Emsley, 419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 838 Ramachandran restraints generated. 419 Oldfield, 0 Emsley, 419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 58 residues out of total 363 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 40 time to evaluate : 0.125 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 4 LEU cc_start: 0.6694 (OUTLIER) cc_final: 0.6313 (mt) REVERT: H 11 LEU cc_start: 0.7912 (OUTLIER) cc_final: 0.7550 (pp) REVERT: H 60 TYR cc_start: 0.7481 (OUTLIER) cc_final: 0.6052 (p90) REVERT: H 80 TYR cc_start: 0.7364 (m-10) cc_final: 0.7103 (m-80) REVERT: H 90 ASP cc_start: 0.8341 (t0) cc_final: 0.8085 (t0) outliers start: 18 outliers final: 11 residues processed: 52 average time/residue: 0.0591 time to fit residues: 3.9154 Evaluate side-chains 52 residues out of total 363 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 38 time to evaluate : 0.080 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 4 LEU Chi-restraints excluded: chain H residue 11 LEU Chi-restraints excluded: chain H residue 18 LEU Chi-restraints excluded: chain H residue 20 LEU Chi-restraints excluded: chain H residue 28 THR Chi-restraints excluded: chain H residue 60 TYR Chi-restraints excluded: chain H residue 65 THR Chi-restraints excluded: chain H residue 70 ILE Chi-restraints excluded: chain H residue 113 LEU Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 33 TYR Chi-restraints excluded: chain L residue 35 HIS Chi-restraints excluded: chain L residue 49 ILE Chi-restraints excluded: chain L residue 107 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 36 optimal weight: 0.9980 chunk 20 optimal weight: 20.0000 chunk 18 optimal weight: 0.9980 chunk 19 optimal weight: 0.2980 chunk 2 optimal weight: 3.9990 chunk 1 optimal weight: 2.9990 chunk 4 optimal weight: 10.0000 chunk 14 optimal weight: 4.9990 chunk 37 optimal weight: 0.9980 chunk 32 optimal weight: 0.9990 chunk 6 optimal weight: 1.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 98 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 = 0.4043 r_free = 0.4043 target = 0.095389 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3735 r_free = 0.3735 target = 0.077676 restraints weight = 13160.821| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3779 r_free = 0.3779 target = 0.080227 restraints weight = 7003.963| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3808 r_free = 0.3808 target = 0.081958 restraints weight = 4797.398| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3827 r_free = 0.3827 target = 0.083032 restraints weight = 3761.661| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3835 r_free = 0.3835 target = 0.083649 restraints weight = 3219.836| |-----------------------------------------------------------------------------| r_work (final): 0.3839 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7614 moved from start: 0.5857 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 3412 Z= 0.108 Angle : 0.577 5.256 4636 Z= 0.297 Chirality : 0.046 0.259 495 Planarity : 0.005 0.049 593 Dihedral : 4.712 20.649 472 Min Nonbonded Distance : 2.582 Molprobity Statistics. All-atom Clashscore : 9.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.59 % Favored : 91.41 % Rotamer: Outliers : 3.86 % Allowed : 22.87 % Favored : 73.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.43 (0.38), residues: 419 helix: -3.71 (0.78), residues: 24 sheet: -0.57 (0.51), residues: 114 loop : -1.99 (0.33), residues: 281 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG L 62 TYR 0.008 0.001 TYR L 92 PHE 0.021 0.001 PHE H 68 TRP 0.008 0.001 TRP L 48 HIS 0.002 0.001 HIS L 93 Details of bonding type rmsd covalent geometry : bond 0.00249 ( 3406) covalent geometry : angle 0.57535 ( 4624) SS BOND : bond 0.00302 ( 6) SS BOND : angle 1.03604 ( 12) hydrogen bonds : bond 0.02945 ( 68) hydrogen bonds : angle 6.87313 ( 153) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 838 Ramachandran restraints generated. 419 Oldfield, 0 Emsley, 419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 838 Ramachandran restraints generated. 419 Oldfield, 0 Emsley, 419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 59 residues out of total 363 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 45 time to evaluate : 0.126 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 4 LEU cc_start: 0.6564 (mt) cc_final: 0.6213 (mp) REVERT: H 11 LEU cc_start: 0.7791 (OUTLIER) cc_final: 0.7433 (pp) REVERT: H 60 TYR cc_start: 0.7420 (OUTLIER) cc_final: 0.6055 (p90) REVERT: H 80 TYR cc_start: 0.7374 (m-10) cc_final: 0.7106 (m-80) REVERT: H 90 ASP cc_start: 0.8282 (t0) cc_final: 0.8067 (t0) outliers start: 14 outliers final: 11 residues processed: 53 average time/residue: 0.0589 time to fit residues: 4.0111 Evaluate side-chains 51 residues out of total 363 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 38 time to evaluate : 0.125 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 415 THR Chi-restraints excluded: chain H residue 11 LEU Chi-restraints excluded: chain H residue 18 LEU Chi-restraints excluded: chain H residue 20 LEU Chi-restraints excluded: chain H residue 28 THR Chi-restraints excluded: chain H residue 60 TYR Chi-restraints excluded: chain H residue 65 THR Chi-restraints excluded: chain H residue 113 LEU Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 33 TYR Chi-restraints excluded: chain L residue 35 HIS Chi-restraints excluded: chain L residue 49 ILE Chi-restraints excluded: chain L residue 107 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 22 optimal weight: 5.9990 chunk 26 optimal weight: 0.0470 chunk 36 optimal weight: 10.0000 chunk 10 optimal weight: 7.9990 chunk 3 optimal weight: 9.9990 chunk 28 optimal weight: 0.9980 chunk 1 optimal weight: 1.9990 chunk 39 optimal weight: 1.9990 chunk 20 optimal weight: 20.0000 chunk 5 optimal weight: 1.9990 chunk 25 optimal weight: 0.5980 overall best weight: 1.1282 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4026 r_free = 0.4026 target = 0.094493 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3715 r_free = 0.3715 target = 0.076677 restraints weight = 12853.723| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3759 r_free = 0.3759 target = 0.079246 restraints weight = 6887.197| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3788 r_free = 0.3788 target = 0.080937 restraints weight = 4740.586| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3806 r_free = 0.3806 target = 0.081989 restraints weight = 3740.958| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3818 r_free = 0.3818 target = 0.082700 restraints weight = 3212.850| |-----------------------------------------------------------------------------| r_work (final): 0.3809 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7624 moved from start: 0.5977 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 3412 Z= 0.123 Angle : 0.600 6.097 4636 Z= 0.308 Chirality : 0.046 0.221 495 Planarity : 0.005 0.047 593 Dihedral : 4.725 19.946 472 Min Nonbonded Distance : 2.562 Molprobity Statistics. All-atom Clashscore : 10.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.50 % Favored : 89.50 % Rotamer: Outliers : 3.86 % Allowed : 23.69 % Favored : 72.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.39 (0.38), residues: 419 helix: -3.72 (0.92), residues: 18 sheet: -0.57 (0.51), residues: 114 loop : -2.00 (0.32), residues: 287 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG L 62 TYR 0.008 0.001 TYR H 107 PHE 0.018 0.001 PHE H 68 TRP 0.007 0.001 TRP L 48 HIS 0.002 0.001 HIS L 93 Details of bonding type rmsd covalent geometry : bond 0.00283 ( 3406) covalent geometry : angle 0.59831 ( 4624) SS BOND : bond 0.00312 ( 6) SS BOND : angle 1.02239 ( 12) hydrogen bonds : bond 0.03093 ( 68) hydrogen bonds : angle 6.83805 ( 153) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 838 Ramachandran restraints generated. 419 Oldfield, 0 Emsley, 419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 838 Ramachandran restraints generated. 419 Oldfield, 0 Emsley, 419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 53 residues out of total 363 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 39 time to evaluate : 0.132 Fit side-chains revert: symmetry clash REVERT: H 4 LEU cc_start: 0.6486 (OUTLIER) cc_final: 0.6137 (mp) REVERT: H 11 LEU cc_start: 0.7801 (OUTLIER) cc_final: 0.7448 (pp) REVERT: H 60 TYR cc_start: 0.7444 (OUTLIER) cc_final: 0.6049 (p90) REVERT: H 80 TYR cc_start: 0.7356 (m-10) cc_final: 0.7046 (m-80) REVERT: H 90 ASP cc_start: 0.8331 (t0) cc_final: 0.8094 (t0) REVERT: L 55 LEU cc_start: 0.8521 (mm) cc_final: 0.8228 (mm) outliers start: 14 outliers final: 11 residues processed: 47 average time/residue: 0.0505 time to fit residues: 3.1432 Evaluate side-chains 51 residues out of total 363 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 37 time to evaluate : 0.131 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 415 THR Chi-restraints excluded: chain H residue 4 LEU Chi-restraints excluded: chain H residue 11 LEU Chi-restraints excluded: chain H residue 18 LEU Chi-restraints excluded: chain H residue 20 LEU Chi-restraints excluded: chain H residue 28 THR Chi-restraints excluded: chain H residue 60 TYR Chi-restraints excluded: chain H residue 65 THR Chi-restraints excluded: chain H residue 113 LEU Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 33 TYR Chi-restraints excluded: chain L residue 35 HIS Chi-restraints excluded: chain L residue 49 ILE Chi-restraints excluded: chain L residue 107 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 11 optimal weight: 0.3980 chunk 38 optimal weight: 0.7980 chunk 39 optimal weight: 0.1980 chunk 36 optimal weight: 0.9990 chunk 4 optimal weight: 0.9990 chunk 17 optimal weight: 1.9990 chunk 8 optimal weight: 0.9990 chunk 33 optimal weight: 0.9990 chunk 26 optimal weight: 3.9990 chunk 30 optimal weight: 3.9990 chunk 16 optimal weight: 0.8980 overall best weight: 0.6582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 98 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 = 0.4052 r_free = 0.4052 target = 0.095894 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3748 r_free = 0.3748 target = 0.078411 restraints weight = 12834.032| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3790 r_free = 0.3790 target = 0.080892 restraints weight = 6897.688| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3819 r_free = 0.3819 target = 0.082600 restraints weight = 4772.477| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3838 r_free = 0.3838 target = 0.083695 restraints weight = 3763.383| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3850 r_free = 0.3850 target = 0.084396 restraints weight = 3223.091| |-----------------------------------------------------------------------------| r_work (final): 0.3854 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7584 moved from start: 0.6045 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 3412 Z= 0.100 Angle : 0.580 5.774 4636 Z= 0.297 Chirality : 0.045 0.190 495 Planarity : 0.005 0.047 593 Dihedral : 4.557 18.926 472 Min Nonbonded Distance : 2.564 Molprobity Statistics. All-atom Clashscore : 8.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.55 % Favored : 90.45 % Rotamer: Outliers : 2.75 % Allowed : 25.07 % Favored : 72.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.22 (0.38), residues: 419 helix: -3.83 (0.89), residues: 18 sheet: -0.40 (0.51), residues: 115 loop : -1.89 (0.33), residues: 286 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG L 62 TYR 0.008 0.001 TYR L 92 PHE 0.019 0.001 PHE H 68 TRP 0.007 0.001 TRP A 436 HIS 0.002 0.001 HIS L 93 Details of bonding type rmsd covalent geometry : bond 0.00232 ( 3406) covalent geometry : angle 0.57935 ( 4624) SS BOND : bond 0.00296 ( 6) SS BOND : angle 0.90504 ( 12) hydrogen bonds : bond 0.02770 ( 68) hydrogen bonds : angle 6.61756 ( 153) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 838 Ramachandran restraints generated. 419 Oldfield, 0 Emsley, 419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 838 Ramachandran restraints generated. 419 Oldfield, 0 Emsley, 419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 52 residues out of total 363 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 42 time to evaluate : 0.076 Fit side-chains revert: symmetry clash REVERT: A 332 ILE cc_start: 0.7433 (mm) cc_final: 0.7194 (mm) REVERT: H 11 LEU cc_start: 0.7731 (OUTLIER) cc_final: 0.7375 (pp) REVERT: H 60 TYR cc_start: 0.7306 (OUTLIER) cc_final: 0.5995 (p90) REVERT: H 80 TYR cc_start: 0.7297 (m-10) cc_final: 0.7021 (m-80) REVERT: H 90 ASP cc_start: 0.8241 (t0) cc_final: 0.7987 (t0) outliers start: 10 outliers final: 8 residues processed: 47 average time/residue: 0.0585 time to fit residues: 3.4134 Evaluate side-chains 48 residues out of total 363 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 38 time to evaluate : 0.125 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 415 THR Chi-restraints excluded: chain H residue 11 LEU Chi-restraints excluded: chain H residue 20 LEU Chi-restraints excluded: chain H residue 28 THR Chi-restraints excluded: chain H residue 60 TYR Chi-restraints excluded: chain H residue 113 LEU Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 33 TYR Chi-restraints excluded: chain L residue 35 HIS Chi-restraints excluded: chain L residue 49 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 34 optimal weight: 1.9990 chunk 11 optimal weight: 4.9990 chunk 38 optimal weight: 0.9980 chunk 26 optimal weight: 2.9990 chunk 20 optimal weight: 0.0000 chunk 6 optimal weight: 6.9990 chunk 13 optimal weight: 6.9990 chunk 17 optimal weight: 0.3980 chunk 7 optimal weight: 0.8980 chunk 16 optimal weight: 0.9990 chunk 32 optimal weight: 10.0000 overall best weight: 0.6586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4050 r_free = 0.4050 target = 0.095843 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3743 r_free = 0.3743 target = 0.078124 restraints weight = 12929.547| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3788 r_free = 0.3788 target = 0.080745 restraints weight = 6862.263| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3818 r_free = 0.3818 target = 0.082444 restraints weight = 4686.158| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3837 r_free = 0.3837 target = 0.083541 restraints weight = 3691.802| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.3849 r_free = 0.3849 target = 0.084266 restraints weight = 3159.682| |-----------------------------------------------------------------------------| r_work (final): 0.3857 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7574 moved from start: 0.6097 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 3412 Z= 0.099 Angle : 0.574 5.619 4636 Z= 0.293 Chirality : 0.045 0.193 495 Planarity : 0.005 0.048 593 Dihedral : 4.460 18.377 472 Min Nonbonded Distance : 2.569 Molprobity Statistics. All-atom Clashscore : 8.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.55 % Favored : 90.45 % Rotamer: Outliers : 2.75 % Allowed : 24.79 % Favored : 72.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.09 (0.38), residues: 419 helix: -3.68 (0.96), residues: 18 sheet: -0.29 (0.52), residues: 115 loop : -1.81 (0.33), residues: 286 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 346 TYR 0.008 0.001 TYR A 421 PHE 0.015 0.001 PHE H 68 TRP 0.007 0.001 TRP A 436 HIS 0.002 0.001 HIS L 93 Details of bonding type rmsd covalent geometry : bond 0.00231 ( 3406) covalent geometry : angle 0.57270 ( 4624) SS BOND : bond 0.00256 ( 6) SS BOND : angle 0.87491 ( 12) hydrogen bonds : bond 0.02759 ( 68) hydrogen bonds : angle 6.50386 ( 153) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 900.18 seconds wall clock time: 16 minutes 6.81 seconds (966.81 seconds total)