Starting phenix.real_space_refine on Tue Mar 3 13:09:31 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7x26_32959/03_2026/7x26_32959_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/7x26_32959/03_2026/7x26_32959.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.685 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7x26_32959/03_2026/7x26_32959_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7x26_32959/03_2026/7x26_32959_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7x26_32959/03_2026/7x26_32959.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7x26_32959/03_2026/7x26_32959.map" } resolution = 3.685 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= 0.000 sd= 0.001 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 21 5.16 5 C 3040 2.51 5 N 803 2.21 5 O 964 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 12 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: 4828 Number of models: 1 Model: "" Number of chains: 3 Chain: "H" Number of atoms: 1633 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 221, 1627 Classifications: {'peptide': 221} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 208} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'TYR:plan': 1} Unresolved non-hydrogen planarities: 7 Conformer: "B" Number of residues, atoms: 221, 1627 Classifications: {'peptide': 221} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 208} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'TYR:plan': 1} Unresolved non-hydrogen planarities: 7 bond proxies already assigned to first conformer: 1655 Chain: "I" Number of atoms: 1594 Number of conformers: 1 Conformer: "" Number of residues, atoms: 208, 1594 Classifications: {'peptide': 208} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'CIS': 2, 'PTRANS': 14, 'TRANS': 191} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "K" Number of atoms: 1601 Number of conformers: 1 Conformer: "" Number of residues, atoms: 212, 1601 Classifications: {'peptide': 212} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PCIS': 2, 'PTRANS': 10, 'TRANS': 199} Unresolved non-hydrogen bonds: 26 Unresolved non-hydrogen angles: 34 Unresolved non-hydrogen dihedrals: 23 Planarities with less than four sites: {'PHE:plan': 1, 'TYR:plan': 1, 'GLU:plan': 1, 'GLN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 24 Time building chain proxies: 1.48, per 1000 atoms: 0.31 Number of scatterers: 4828 At special positions: 0 Unit cell: (79.0225, 83.3525, 130.982, 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 21 16.00 O 964 8.00 N 803 7.00 C 3040 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=8, symmetry=0 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.04 Simple disulfide: pdb=" SG CYS H 147 " - pdb=" SG CYS H 203 " distance=2.01 Simple disulfide: pdb=" SG CYS I 383 " - pdb=" SG CYS I 407 " distance=2.02 Simple disulfide: pdb=" SG CYS I 425 " - pdb=" SG CYS I 478 " distance=2.03 Simple disulfide: pdb=" SG CYS I 437 " - pdb=" SG CYS I 585 " distance=2.06 Simple disulfide: pdb=" SG CYS I 503 " - pdb=" SG CYS I 526 " distance=2.02 Simple disulfide: pdb=" SG CYS K 23 " - pdb=" SG CYS K 89 " distance=2.04 Simple disulfide: pdb=" SG CYS K 135 " - pdb=" SG CYS K 195 " 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: 0.39 Conformation dependent library (CDL) restraints added in 329.1 milliseconds 1274 Ramachandran restraints generated. 637 Oldfield, 0 Emsley, 637 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1188 Finding SS restraints... Secondary structure from input PDB file: 9 helices and 13 sheets defined 7.3% alpha, 23.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.18 Creating SS restraints... Processing helix chain 'H' and resid 87 through 91 removed outlier: 3.691A pdb=" N ASP H 90 " --> pdb=" O THR H 87 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N THR H 91 " --> pdb=" O SER H 88 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 87 through 91' Processing helix chain 'H' and resid 161 through 165 Processing helix chain 'I' and resid 385 through 390 removed outlier: 3.998A pdb=" N SER I 390 " --> pdb=" O PRO I 387 " (cutoff:3.500A) Processing helix chain 'I' and resid 395 through 399 Processing helix chain 'I' and resid 411 through 416 Processing helix chain 'I' and resid 431 through 435 removed outlier: 3.705A pdb=" N SER I 435 " --> pdb=" O ALA I 432 " (cutoff:3.500A) Processing helix chain 'I' and resid 449 through 453 removed outlier: 3.637A pdb=" N MET I 452 " --> pdb=" O PRO I 449 " (cutoff:3.500A) Processing helix chain 'I' and resid 524 through 528 removed outlier: 4.085A pdb=" N SER I 528 " --> pdb=" O PRO I 525 " (cutoff:3.500A) Processing helix chain 'K' and resid 80 through 84 removed outlier: 3.651A pdb=" N SER K 84 " --> pdb=" O PRO K 81 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'H' and resid 11 through 12 removed outlier: 3.644A pdb=" N TYR H 94 " --> pdb=" O THR H 114 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N GLY H 49 " --> pdb=" O TRP H 36 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'H' and resid 21 through 23 Processing sheet with id=AA3, first strand: chain 'H' and resid 143 through 145 Processing sheet with id=AA4, first strand: chain 'H' and resid 148 through 152 removed outlier: 4.636A pdb=" N LEU H 148 " --> pdb=" O SER H 187 " (cutoff:3.500A) removed outlier: 6.444A pdb=" N SER H 187 " --> pdb=" O LEU H 148 " (cutoff:3.500A) removed outlier: 4.843A pdb=" N LYS H 150 " --> pdb=" O LEU H 185 " (cutoff:3.500A) removed outlier: 6.865A pdb=" N LEU H 185 " --> pdb=" O LYS H 150 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N TYR H 152 " --> pdb=" O TYR H 183 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'H' and resid 157 through 160 Processing sheet with id=AA6, first strand: chain 'I' and resid 400 through 404 removed outlier: 3.754A pdb=" N LYS I 400 " --> pdb=" O TYR I 445 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N TYR I 445 " --> pdb=" O LYS I 400 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'I' and resid 408 through 409 Processing sheet with id=AA8, first strand: chain 'I' and resid 513 through 515 removed outlier: 3.699A pdb=" N TYR I 497 " --> pdb=" O VAL I 561 " (cutoff:3.500A) removed outlier: 6.577A pdb=" N SER I 557 " --> pdb=" O ASN I 501 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'K' and resid 11 through 13 removed outlier: 5.677A pdb=" N LEU K 11 " --> pdb=" O GLU K 106 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'K' and resid 19 through 21 removed outlier: 3.795A pdb=" N ASP K 71 " --> pdb=" O SER K 68 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'K' and resid 49 through 50 Processing sheet with id=AB3, first strand: chain 'K' and resid 115 through 118 removed outlier: 3.613A pdb=" N SER K 163 " --> pdb=" O SER K 177 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'K' and resid 154 through 155 113 hydrogen bonds defined for protein. 233 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: 0.64 Time building geometry restraints manager: 0.53 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 1055 1.33 - 1.45: 1105 1.45 - 1.57: 2753 1.57 - 1.69: 0 1.69 - 1.81: 26 Bond restraints: 4939 Sorted by residual: bond pdb=" C SER H 186 " pdb=" O SER H 186 " ideal model delta sigma weight residual 1.236 1.362 -0.126 1.21e-02 6.83e+03 1.08e+02 bond pdb=" C SER H 160 " pdb=" O SER H 160 " ideal model delta sigma weight residual 1.234 1.358 -0.124 1.22e-02 6.72e+03 1.03e+02 bond pdb=" N VAL H 191 " pdb=" CA VAL H 191 " ideal model delta sigma weight residual 1.457 1.493 -0.036 9.00e-03 1.23e+04 1.58e+01 bond pdb=" N VAL K 192 " pdb=" CA VAL K 192 " ideal model delta sigma weight residual 1.457 1.498 -0.041 1.15e-02 7.56e+03 1.30e+01 bond pdb=" N ILE K 59 " pdb=" CA ILE K 59 " ideal model delta sigma weight residual 1.460 1.492 -0.032 9.30e-03 1.16e+04 1.20e+01 ... (remaining 4934 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.47: 6135 2.47 - 4.94: 563 4.94 - 7.41: 15 7.41 - 9.88: 9 9.88 - 12.34: 10 Bond angle restraints: 6732 Sorted by residual: angle pdb=" O SER H 186 " pdb=" C SER H 186 " pdb=" CA ASER H 186 " ideal model delta sigma weight residual 120.38 132.17 -11.79 1.09e+00 8.42e-01 1.17e+02 angle pdb=" O SER H 186 " pdb=" C SER H 186 " pdb=" CA BSER H 186 " ideal model delta sigma weight residual 120.38 132.13 -11.75 1.09e+00 8.42e-01 1.16e+02 angle pdb=" O SER H 160 " pdb=" C SER H 160 " pdb=" CA ASER H 160 " ideal model delta sigma weight residual 120.92 133.26 -12.34 1.15e+00 7.56e-01 1.15e+02 angle pdb=" O SER H 160 " pdb=" C SER H 160 " pdb=" CA BSER H 160 " ideal model delta sigma weight residual 120.92 133.26 -12.34 1.15e+00 7.56e-01 1.15e+02 angle pdb=" CA ASER H 160 " pdb=" C SER H 160 " pdb=" N TRP H 161 " ideal model delta sigma weight residual 115.86 104.32 11.54 1.24e+00 6.50e-01 8.66e+01 ... (remaining 6727 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.15: 2626 16.15 - 32.30: 263 32.30 - 48.44: 69 48.44 - 64.59: 13 64.59 - 80.74: 9 Dihedral angle restraints: 2980 sinusoidal: 1121 harmonic: 1859 Sorted by residual: dihedral pdb=" CA GLU H 155 " pdb=" C GLU H 155 " pdb=" N PRO H 156 " pdb=" CA PRO H 156 " ideal model delta harmonic sigma weight residual 0.00 40.97 -40.97 0 5.00e+00 4.00e-02 6.71e+01 dihedral pdb=" CA ASN I 521 " pdb=" C ASN I 521 " pdb=" N GLN I 522 " pdb=" CA GLN I 522 " ideal model delta harmonic sigma weight residual 180.00 149.27 30.73 0 5.00e+00 4.00e-02 3.78e+01 dihedral pdb=" CA ASP K 61 " pdb=" C ASP K 61 " pdb=" N ARG K 62 " pdb=" CA ARG K 62 " ideal model delta harmonic sigma weight residual 180.00 149.99 30.01 0 5.00e+00 4.00e-02 3.60e+01 ... (remaining 2977 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.085: 539 0.085 - 0.169: 186 0.169 - 0.254: 44 0.254 - 0.339: 2 0.339 - 0.423: 3 Chirality restraints: 774 Sorted by residual: chirality pdb=" CA GLN H 199 " pdb=" N GLN H 199 " pdb=" C GLN H 199 " pdb=" CB GLN H 199 " both_signs ideal model delta sigma weight residual False 2.51 2.09 0.42 2.00e-01 2.50e+01 4.48e+00 chirality pdb=" CA BSER H 186 " pdb=" N SER H 186 " pdb=" C SER H 186 " pdb=" CB BSER H 186 " both_signs ideal model delta sigma weight residual False 2.51 2.16 0.35 2.00e-01 2.50e+01 3.04e+00 chirality pdb=" CA ASER H 186 " pdb=" N SER H 186 " pdb=" C SER H 186 " pdb=" CB ASER H 186 " both_signs ideal model delta sigma weight residual False 2.51 2.16 0.35 2.00e-01 2.50e+01 3.01e+00 ... (remaining 771 not shown) Planarity restraints: 861 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLN K 91 " 0.012 2.00e-02 2.50e+03 2.53e-02 6.39e+00 pdb=" C GLN K 91 " -0.044 2.00e-02 2.50e+03 pdb=" O GLN K 91 " 0.017 2.00e-02 2.50e+03 pdb=" N TYR K 92 " 0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C SER H 160 " -0.039 2.00e-02 2.50e+03 2.27e-02 5.17e+00 pdb=" O SER H 160 " 0.016 2.00e-02 2.50e+03 pdb=" CA ASER H 160 " 0.012 2.00e-02 2.50e+03 pdb=" N TRP H 161 " 0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C SER H 160 " -0.039 2.00e-02 2.50e+03 2.27e-02 5.17e+00 pdb=" O SER H 160 " 0.016 2.00e-02 2.50e+03 pdb=" CA BSER H 160 " 0.012 2.00e-02 2.50e+03 pdb=" N TRP H 161 " 0.012 2.00e-02 2.50e+03 ... (remaining 858 not shown) Histogram of nonbonded interaction distances: 2.19 - 2.73: 334 2.73 - 3.27: 4653 3.27 - 3.81: 7236 3.81 - 4.36: 9557 4.36 - 4.90: 15675 Nonbonded interactions: 37455 Sorted by model distance: nonbonded pdb=" O ASN I 521 " pdb=" N TYR I 523 " model vdw 2.186 3.120 nonbonded pdb=" O ALA H 121 " pdb=" OG SER H 122 " model vdw 2.260 3.040 nonbonded pdb=" OD1 ASN I 436 " pdb=" OH TYR I 438 " model vdw 2.268 3.040 nonbonded pdb=" O PRO I 463 " pdb=" ND2 ASN I 468 " model vdw 2.269 3.120 nonbonded pdb=" O LEU I 456 " pdb=" OG SER I 457 " model vdw 2.355 3.040 ... (remaining 37450 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=0.40 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: 2.460 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: 0.100 Check model and map are aligned: 0.010 Set scattering table: 0.020 Process input model: 6.470 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:1.080 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 10.160 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7211 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 : 0.011 0.126 4947 Z= 0.824 Angle : 1.462 12.344 6748 Z= 1.021 Chirality : 0.087 0.423 774 Planarity : 0.005 0.048 861 Dihedral : 14.527 80.739 1768 Min Nonbonded Distance : 2.186 Molprobity Statistics. All-atom Clashscore : 10.90 Ramachandran Plot: Outliers : 2.52 % Allowed : 16.38 % Favored : 81.10 % Rotamer: Outliers : 9.27 % Allowed : 6.18 % Favored : 84.55 % Cbeta Deviations : 0.17 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.33 % Twisted Proline : 2.63 % Twisted General : 0.33 % 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: -3.21 (0.32), residues: 637 helix: -3.94 (0.94), residues: 12 sheet: -1.45 (0.34), residues: 249 loop : -2.65 (0.29), residues: 376 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG H 50 TYR 0.031 0.002 TYR I 438 PHE 0.013 0.002 PHE I 467 TRP 0.013 0.002 TRP K 36 HIS 0.004 0.001 HIS K 199 Details of bonding type rmsd covalent geometry : bond 0.01137 ( 4939) covalent geometry : angle 1.46038 ( 6732) SS BOND : bond 0.01373 ( 8) SS BOND : angle 2.06288 ( 16) hydrogen bonds : bond 0.20904 ( 113) hydrogen bonds : angle 9.01767 ( 233) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1274 Ramachandran restraints generated. 637 Oldfield, 0 Emsley, 637 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1274 Ramachandran restraints generated. 637 Oldfield, 0 Emsley, 637 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 145 time to evaluate : 0.113 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 157 VAL cc_start: 0.8806 (OUTLIER) cc_final: 0.8562 (p) REVERT: H 189 VAL cc_start: 0.5888 (OUTLIER) cc_final: 0.5677 (p) REVERT: I 438 TYR cc_start: 0.8187 (m-80) cc_final: 0.7808 (m-80) REVERT: I 502 LYS cc_start: 0.7873 (mtpp) cc_final: 0.7376 (mttp) REVERT: K 13 LEU cc_start: 0.7239 (OUTLIER) cc_final: 0.6639 (mt) REVERT: K 75 THR cc_start: 0.7424 (OUTLIER) cc_final: 0.6916 (p) REVERT: K 97 TRP cc_start: 0.7650 (m-10) cc_final: 0.7202 (m-10) REVERT: K 136 LEU cc_start: 0.8169 (tp) cc_final: 0.7948 (tt) outliers start: 51 outliers final: 14 residues processed: 174 average time/residue: 0.0833 time to fit residues: 17.9211 Evaluate side-chains 111 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 93 time to evaluate : 0.158 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 18 VAL Chi-restraints excluded: chain H residue 80 TYR Chi-restraints excluded: chain H residue 131 LEU Chi-restraints excluded: chain H residue 157 VAL Chi-restraints excluded: chain H residue 170 VAL Chi-restraints excluded: chain H residue 189 VAL Chi-restraints excluded: chain H residue 195 SER Chi-restraints excluded: chain H residue 196 LEU Chi-restraints excluded: chain H residue 200 THR Chi-restraints excluded: chain K residue 13 LEU Chi-restraints excluded: chain K residue 54 SER Chi-restraints excluded: chain K residue 75 THR Chi-restraints excluded: chain K residue 111 VAL Chi-restraints excluded: chain K residue 116 VAL Chi-restraints excluded: chain K residue 133 VAL Chi-restraints excluded: chain K residue 147 VAL Chi-restraints excluded: chain K residue 148 GLN Chi-restraints excluded: chain K residue 164 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 54 optimal weight: 0.0030 chunk 24 optimal weight: 0.3980 chunk 48 optimal weight: 0.8980 chunk 56 optimal weight: 0.7980 chunk 26 optimal weight: 0.7980 chunk 2 optimal weight: 0.9980 chunk 16 optimal weight: 0.7980 chunk 61 optimal weight: 0.7980 chunk 32 optimal weight: 0.5980 chunk 31 optimal weight: 1.9990 chunk 25 optimal weight: 0.8980 overall best weight: 0.5190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 486 HIS I 519 ASN I 582 ASN K 6 GLN K 90 GLN K 148 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4101 r_free = 0.4101 target = 0.171092 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3895 r_free = 0.3895 target = 0.153600 restraints weight = 16228.114| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3917 r_free = 0.3917 target = 0.157638 restraints weight = 8307.028| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3919 r_free = 0.3919 target = 0.157857 restraints weight = 4974.562| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3929 r_free = 0.3929 target = 0.158646 restraints weight = 3540.682| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3942 r_free = 0.3942 target = 0.159803 restraints weight = 2786.201| |-----------------------------------------------------------------------------| r_work (final): 0.3957 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3957 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3957 r_free = 0.3957 target_work(ls_wunit_k1) = 0.157 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3957 r_free = 0.3957 target_work(ls_wunit_k1) = 0.157 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3957 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7450 moved from start: 0.2663 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 4947 Z= 0.169 Angle : 0.769 11.769 6748 Z= 0.396 Chirality : 0.048 0.249 774 Planarity : 0.005 0.039 861 Dihedral : 8.597 59.887 714 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 12.16 Ramachandran Plot: Outliers : 0.47 % Allowed : 9.76 % Favored : 89.76 % Rotamer: Outliers : 5.82 % Allowed : 13.27 % Favored : 80.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.89 % Cis-general : 0.33 % 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: -2.87 (0.32), residues: 637 helix: -3.95 (1.03), residues: 12 sheet: -1.44 (0.32), residues: 264 loop : -2.22 (0.31), residues: 361 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG K 24 TYR 0.020 0.002 TYR I 445 PHE 0.018 0.002 PHE I 423 TRP 0.013 0.002 TRP K 97 HIS 0.003 0.001 HIS H 207 Details of bonding type rmsd covalent geometry : bond 0.00395 ( 4939) covalent geometry : angle 0.76757 ( 6732) SS BOND : bond 0.00280 ( 8) SS BOND : angle 1.16388 ( 16) hydrogen bonds : bond 0.03250 ( 113) hydrogen bonds : angle 6.32430 ( 233) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1274 Ramachandran restraints generated. 637 Oldfield, 0 Emsley, 637 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1274 Ramachandran restraints generated. 637 Oldfield, 0 Emsley, 637 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 91 time to evaluate : 0.127 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 13 LEU cc_start: 0.6994 (OUTLIER) cc_final: 0.6240 (mt) REVERT: K 75 THR cc_start: 0.7334 (OUTLIER) cc_final: 0.7019 (p) REVERT: K 76 ILE cc_start: 0.6971 (mt) cc_final: 0.6634 (mt) REVERT: K 143 ARG cc_start: 0.6171 (mtp85) cc_final: 0.5805 (ttm-80) outliers start: 32 outliers final: 18 residues processed: 115 average time/residue: 0.0896 time to fit residues: 12.8073 Evaluate side-chains 99 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 79 time to evaluate : 0.193 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 18 VAL Chi-restraints excluded: chain H residue 29 PHE Chi-restraints excluded: chain H residue 80 TYR Chi-restraints excluded: chain H residue 131 LEU Chi-restraints excluded: chain H residue 138 THR Chi-restraints excluded: chain H residue 157 VAL Chi-restraints excluded: chain H residue 170 VAL Chi-restraints excluded: chain H residue 218 VAL Chi-restraints excluded: chain I residue 417 LEU Chi-restraints excluded: chain I residue 426 SER Chi-restraints excluded: chain I residue 521 ASN Chi-restraints excluded: chain K residue 13 LEU Chi-restraints excluded: chain K residue 21 LEU Chi-restraints excluded: chain K residue 75 THR Chi-restraints excluded: chain K residue 111 VAL Chi-restraints excluded: chain K residue 116 VAL Chi-restraints excluded: chain K residue 133 VAL Chi-restraints excluded: chain K residue 164 VAL Chi-restraints excluded: chain K residue 197 VAL Chi-restraints excluded: chain K residue 206 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 33 optimal weight: 1.9990 chunk 55 optimal weight: 3.9990 chunk 19 optimal weight: 0.0270 chunk 28 optimal weight: 0.6980 chunk 50 optimal weight: 0.7980 chunk 34 optimal weight: 1.9990 chunk 21 optimal weight: 0.0670 chunk 25 optimal weight: 0.7980 chunk 42 optimal weight: 0.6980 chunk 59 optimal weight: 0.6980 chunk 57 optimal weight: 0.9990 overall best weight: 0.4376 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 62 GLN I 486 HIS K 90 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4015 r_free = 0.4015 target = 0.163818 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3817 r_free = 0.3817 target = 0.146330 restraints weight = 13327.880| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3818 r_free = 0.3818 target = 0.147401 restraints weight = 7837.951| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3835 r_free = 0.3835 target = 0.149044 restraints weight = 5427.512| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3840 r_free = 0.3840 target = 0.149568 restraints weight = 3531.882| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3846 r_free = 0.3846 target = 0.150095 restraints weight = 3406.584| |-----------------------------------------------------------------------------| r_work (final): 0.3837 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3837 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3837 r_free = 0.3837 target_work(ls_wunit_k1) = 0.149 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3837 r_free = 0.3837 target_work(ls_wunit_k1) = 0.149 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3837 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7454 moved from start: 0.3260 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 4947 Z= 0.141 Angle : 0.688 11.224 6748 Z= 0.351 Chirality : 0.046 0.234 774 Planarity : 0.004 0.031 861 Dihedral : 6.915 50.755 704 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 9.96 Ramachandran Plot: Outliers : 0.47 % Allowed : 9.92 % Favored : 89.61 % Rotamer: Outliers : 5.45 % Allowed : 17.09 % Favored : 77.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.89 % Cis-general : 0.33 % 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: -2.55 (0.33), residues: 637 helix: -4.04 (0.65), residues: 30 sheet: -0.79 (0.33), residues: 255 loop : -2.23 (0.32), residues: 352 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG K 24 TYR 0.017 0.002 TYR H 183 PHE 0.014 0.001 PHE I 423 TRP 0.012 0.001 TRP H 161 HIS 0.002 0.001 HIS H 207 Details of bonding type rmsd covalent geometry : bond 0.00327 ( 4939) covalent geometry : angle 0.68747 ( 6732) SS BOND : bond 0.00246 ( 8) SS BOND : angle 0.73626 ( 16) hydrogen bonds : bond 0.03173 ( 113) hydrogen bonds : angle 5.90756 ( 233) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1274 Ramachandran restraints generated. 637 Oldfield, 0 Emsley, 637 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1274 Ramachandran restraints generated. 637 Oldfield, 0 Emsley, 637 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 90 time to evaluate : 0.160 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 157 VAL cc_start: 0.8853 (OUTLIER) cc_final: 0.8633 (p) REVERT: H 214 VAL cc_start: 0.8079 (OUTLIER) cc_final: 0.7716 (m) REVERT: K 13 LEU cc_start: 0.7024 (OUTLIER) cc_final: 0.6271 (mt) REVERT: K 75 THR cc_start: 0.7356 (OUTLIER) cc_final: 0.7041 (p) REVERT: K 76 ILE cc_start: 0.6888 (mt) cc_final: 0.6490 (mt) REVERT: K 143 ARG cc_start: 0.6491 (mtp85) cc_final: 0.6088 (ttm-80) outliers start: 30 outliers final: 18 residues processed: 111 average time/residue: 0.0756 time to fit residues: 10.6450 Evaluate side-chains 102 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 80 time to evaluate : 0.177 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 18 VAL Chi-restraints excluded: chain H residue 29 PHE Chi-restraints excluded: chain H residue 80 TYR Chi-restraints excluded: chain H residue 131 LEU Chi-restraints excluded: chain H residue 157 VAL Chi-restraints excluded: chain H residue 170 VAL Chi-restraints excluded: chain H residue 214 VAL Chi-restraints excluded: chain H residue 218 VAL Chi-restraints excluded: chain I residue 417 LEU Chi-restraints excluded: chain I residue 521 ASN Chi-restraints excluded: chain I residue 581 THR Chi-restraints excluded: chain K residue 13 LEU Chi-restraints excluded: chain K residue 21 LEU Chi-restraints excluded: chain K residue 75 THR Chi-restraints excluded: chain K residue 90 GLN Chi-restraints excluded: chain K residue 111 VAL Chi-restraints excluded: chain K residue 116 VAL Chi-restraints excluded: chain K residue 133 VAL Chi-restraints excluded: chain K residue 147 VAL Chi-restraints excluded: chain K residue 164 VAL Chi-restraints excluded: chain K residue 172 SER Chi-restraints excluded: chain K residue 206 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 9 optimal weight: 1.9990 chunk 23 optimal weight: 0.9990 chunk 30 optimal weight: 0.8980 chunk 6 optimal weight: 0.9990 chunk 38 optimal weight: 0.8980 chunk 15 optimal weight: 0.9990 chunk 24 optimal weight: 0.6980 chunk 42 optimal weight: 1.9990 chunk 14 optimal weight: 0.0470 chunk 16 optimal weight: 0.8980 chunk 3 optimal weight: 0.7980 overall best weight: 0.6678 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 206 ASN I 486 HIS K 90 GLN ** K 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3971 r_free = 0.3971 target = 0.160413 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3752 r_free = 0.3752 target = 0.141169 restraints weight = 29392.218| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3779 r_free = 0.3779 target = 0.145449 restraints weight = 18733.521| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3817 r_free = 0.3817 target = 0.149240 restraints weight = 5623.468| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3825 r_free = 0.3825 target = 0.149943 restraints weight = 3060.338| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3830 r_free = 0.3830 target = 0.150360 restraints weight = 2667.224| |-----------------------------------------------------------------------------| r_work (final): 0.3824 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3823 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3823 r_free = 0.3823 target_work(ls_wunit_k1) = 0.147 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3823 r_free = 0.3823 target_work(ls_wunit_k1) = 0.147 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3823 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7482 moved from start: 0.3584 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 4947 Z= 0.178 Angle : 0.720 11.679 6748 Z= 0.368 Chirality : 0.047 0.237 774 Planarity : 0.005 0.041 861 Dihedral : 6.952 52.168 704 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 11.53 Ramachandran Plot: Outliers : 0.47 % Allowed : 8.82 % Favored : 90.71 % Rotamer: Outliers : 5.45 % Allowed : 19.09 % Favored : 75.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.89 % Cis-general : 0.33 % 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 (0.32), residues: 637 helix: -4.55 (0.58), residues: 24 sheet: -0.92 (0.33), residues: 262 loop : -2.07 (0.32), residues: 351 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG K 24 TYR 0.018 0.002 TYR H 183 PHE 0.016 0.002 PHE I 423 TRP 0.010 0.001 TRP K 97 HIS 0.002 0.001 HIS H 207 Details of bonding type rmsd covalent geometry : bond 0.00420 ( 4939) covalent geometry : angle 0.71937 ( 6732) SS BOND : bond 0.00285 ( 8) SS BOND : angle 0.95044 ( 16) hydrogen bonds : bond 0.03182 ( 113) hydrogen bonds : angle 5.84602 ( 233) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1274 Ramachandran restraints generated. 637 Oldfield, 0 Emsley, 637 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1274 Ramachandran restraints generated. 637 Oldfield, 0 Emsley, 637 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 79 time to evaluate : 0.188 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 13 LEU cc_start: 0.7136 (OUTLIER) cc_final: 0.6832 (mt) REVERT: K 75 THR cc_start: 0.7292 (OUTLIER) cc_final: 0.6952 (p) REVERT: K 76 ILE cc_start: 0.7040 (mt) cc_final: 0.6675 (mt) REVERT: K 143 ARG cc_start: 0.6370 (mtp85) cc_final: 0.6036 (ttm-80) outliers start: 30 outliers final: 20 residues processed: 103 average time/residue: 0.0809 time to fit residues: 10.4872 Evaluate side-chains 98 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 76 time to evaluate : 0.112 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 18 VAL Chi-restraints excluded: chain H residue 29 PHE Chi-restraints excluded: chain H residue 80 TYR Chi-restraints excluded: chain H residue 131 LEU Chi-restraints excluded: chain H residue 138 THR Chi-restraints excluded: chain H residue 170 VAL Chi-restraints excluded: chain H residue 218 VAL Chi-restraints excluded: chain I residue 417 LEU Chi-restraints excluded: chain I residue 426 SER Chi-restraints excluded: chain I residue 480 ILE Chi-restraints excluded: chain I residue 521 ASN Chi-restraints excluded: chain I residue 545 LEU Chi-restraints excluded: chain K residue 13 LEU Chi-restraints excluded: chain K residue 75 THR Chi-restraints excluded: chain K residue 111 VAL Chi-restraints excluded: chain K residue 116 VAL Chi-restraints excluded: chain K residue 133 VAL Chi-restraints excluded: chain K residue 147 VAL Chi-restraints excluded: chain K residue 164 VAL Chi-restraints excluded: chain K residue 172 SER Chi-restraints excluded: chain K residue 197 VAL Chi-restraints excluded: chain K residue 206 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 19 optimal weight: 0.8980 chunk 38 optimal weight: 0.5980 chunk 32 optimal weight: 0.9990 chunk 43 optimal weight: 1.9990 chunk 2 optimal weight: 0.6980 chunk 49 optimal weight: 1.9990 chunk 25 optimal weight: 0.7980 chunk 57 optimal weight: 0.6980 chunk 27 optimal weight: 0.1980 chunk 7 optimal weight: 0.6980 chunk 59 optimal weight: 3.9990 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 486 HIS K 148 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3974 r_free = 0.3974 target = 0.160503 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3746 r_free = 0.3746 target = 0.140809 restraints weight = 25722.693| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3782 r_free = 0.3782 target = 0.145673 restraints weight = 14740.954| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3812 r_free = 0.3812 target = 0.148613 restraints weight = 5086.720| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3821 r_free = 0.3821 target = 0.149390 restraints weight = 2979.838| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3826 r_free = 0.3826 target = 0.149757 restraints weight = 2102.548| |-----------------------------------------------------------------------------| r_work (final): 0.3820 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3818 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3818 r_free = 0.3818 target_work(ls_wunit_k1) = 0.147 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3818 r_free = 0.3818 target_work(ls_wunit_k1) = 0.147 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3818 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7494 moved from start: 0.3895 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 4947 Z= 0.159 Angle : 0.695 11.356 6748 Z= 0.352 Chirality : 0.046 0.238 774 Planarity : 0.005 0.034 861 Dihedral : 6.741 50.556 703 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 10.17 Ramachandran Plot: Outliers : 0.47 % Allowed : 10.08 % Favored : 89.45 % Rotamer: Outliers : 5.82 % Allowed : 19.45 % Favored : 74.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.89 % Cis-general : 0.33 % 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 (0.32), residues: 637 helix: -4.37 (0.76), residues: 18 sheet: -0.75 (0.33), residues: 257 loop : -2.04 (0.31), residues: 362 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG H 98 TYR 0.015 0.002 TYR H 183 PHE 0.014 0.001 PHE I 423 TRP 0.009 0.001 TRP K 97 HIS 0.001 0.001 HIS K 199 Details of bonding type rmsd covalent geometry : bond 0.00375 ( 4939) covalent geometry : angle 0.69456 ( 6732) SS BOND : bond 0.00303 ( 8) SS BOND : angle 0.95189 ( 16) hydrogen bonds : bond 0.03068 ( 113) hydrogen bonds : angle 5.73657 ( 233) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1274 Ramachandran restraints generated. 637 Oldfield, 0 Emsley, 637 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1274 Ramachandran restraints generated. 637 Oldfield, 0 Emsley, 637 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 80 time to evaluate : 0.135 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 75 THR cc_start: 0.7186 (OUTLIER) cc_final: 0.6834 (p) REVERT: K 76 ILE cc_start: 0.6872 (mt) cc_final: 0.6617 (mt) REVERT: K 124 GLU cc_start: 0.7215 (tm-30) cc_final: 0.6830 (tm-30) REVERT: K 143 ARG cc_start: 0.6540 (mtp85) cc_final: 0.6247 (ttm-80) outliers start: 32 outliers final: 22 residues processed: 104 average time/residue: 0.0822 time to fit residues: 10.7793 Evaluate side-chains 99 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 76 time to evaluate : 0.180 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 18 VAL Chi-restraints excluded: chain H residue 29 PHE Chi-restraints excluded: chain H residue 80 TYR Chi-restraints excluded: chain H residue 131 LEU Chi-restraints excluded: chain H residue 138 THR Chi-restraints excluded: chain H residue 170 VAL Chi-restraints excluded: chain H residue 214 VAL Chi-restraints excluded: chain H residue 218 VAL Chi-restraints excluded: chain I residue 417 LEU Chi-restraints excluded: chain I residue 426 SER Chi-restraints excluded: chain I residue 451 SER Chi-restraints excluded: chain I residue 521 ASN Chi-restraints excluded: chain I residue 545 LEU Chi-restraints excluded: chain I residue 581 THR Chi-restraints excluded: chain K residue 21 LEU Chi-restraints excluded: chain K residue 75 THR Chi-restraints excluded: chain K residue 111 VAL Chi-restraints excluded: chain K residue 116 VAL Chi-restraints excluded: chain K residue 133 VAL Chi-restraints excluded: chain K residue 147 VAL Chi-restraints excluded: chain K residue 164 VAL Chi-restraints excluded: chain K residue 172 SER Chi-restraints excluded: chain K residue 206 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 36 optimal weight: 0.9990 chunk 39 optimal weight: 0.9990 chunk 11 optimal weight: 1.9990 chunk 32 optimal weight: 0.2980 chunk 10 optimal weight: 2.9990 chunk 15 optimal weight: 0.8980 chunk 1 optimal weight: 0.4980 chunk 14 optimal weight: 0.9980 chunk 53 optimal weight: 0.5980 chunk 49 optimal weight: 2.9990 chunk 51 optimal weight: 0.3980 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 486 HIS K 90 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3981 r_free = 0.3981 target = 0.160861 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3758 r_free = 0.3758 target = 0.141402 restraints weight = 22872.227| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3792 r_free = 0.3792 target = 0.146473 restraints weight = 13894.378| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3815 r_free = 0.3815 target = 0.148607 restraints weight = 4822.275| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3826 r_free = 0.3826 target = 0.149577 restraints weight = 3118.903| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3835 r_free = 0.3835 target = 0.150415 restraints weight = 2194.343| |-----------------------------------------------------------------------------| r_work (final): 0.3828 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3835 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3835 r_free = 0.3835 target_work(ls_wunit_k1) = 0.148 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3835 r_free = 0.3835 target_work(ls_wunit_k1) = 0.148 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3835 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7486 moved from start: 0.4077 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 4947 Z= 0.152 Angle : 0.693 11.243 6748 Z= 0.347 Chirality : 0.046 0.232 774 Planarity : 0.005 0.034 861 Dihedral : 6.499 49.875 701 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 10.69 Ramachandran Plot: Outliers : 0.47 % Allowed : 9.45 % Favored : 90.08 % Rotamer: Outliers : 4.73 % Allowed : 20.00 % Favored : 75.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.89 % Cis-general : 0.33 % 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 (0.32), residues: 637 helix: -3.85 (0.76), residues: 24 sheet: -0.69 (0.32), residues: 265 loop : -2.19 (0.31), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG H 98 TYR 0.015 0.002 TYR H 183 PHE 0.012 0.001 PHE I 423 TRP 0.013 0.001 TRP K 97 HIS 0.002 0.001 HIS I 486 Details of bonding type rmsd covalent geometry : bond 0.00357 ( 4939) covalent geometry : angle 0.69247 ( 6732) SS BOND : bond 0.00288 ( 8) SS BOND : angle 0.94666 ( 16) hydrogen bonds : bond 0.02926 ( 113) hydrogen bonds : angle 5.70746 ( 233) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1274 Ramachandran restraints generated. 637 Oldfield, 0 Emsley, 637 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1274 Ramachandran restraints generated. 637 Oldfield, 0 Emsley, 637 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 80 time to evaluate : 0.192 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 29 PHE cc_start: 0.7851 (OUTLIER) cc_final: 0.7614 (t80) REVERT: K 75 THR cc_start: 0.7168 (OUTLIER) cc_final: 0.6816 (p) REVERT: K 76 ILE cc_start: 0.6862 (mt) cc_final: 0.6580 (mt) REVERT: K 124 GLU cc_start: 0.7120 (tm-30) cc_final: 0.6669 (tm-30) REVERT: K 143 ARG cc_start: 0.6473 (mtp85) cc_final: 0.6105 (ttm170) outliers start: 26 outliers final: 21 residues processed: 98 average time/residue: 0.0870 time to fit residues: 10.7373 Evaluate side-chains 98 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 75 time to evaluate : 0.173 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 18 VAL Chi-restraints excluded: chain H residue 29 PHE Chi-restraints excluded: chain H residue 80 TYR Chi-restraints excluded: chain H residue 131 LEU Chi-restraints excluded: chain H residue 138 THR Chi-restraints excluded: chain H residue 170 VAL Chi-restraints excluded: chain H residue 214 VAL Chi-restraints excluded: chain H residue 218 VAL Chi-restraints excluded: chain I residue 388 LEU Chi-restraints excluded: chain I residue 417 LEU Chi-restraints excluded: chain I residue 426 SER Chi-restraints excluded: chain I residue 451 SER Chi-restraints excluded: chain I residue 480 ILE Chi-restraints excluded: chain I residue 512 THR Chi-restraints excluded: chain I residue 521 ASN Chi-restraints excluded: chain I residue 545 LEU Chi-restraints excluded: chain K residue 75 THR Chi-restraints excluded: chain K residue 111 VAL Chi-restraints excluded: chain K residue 116 VAL Chi-restraints excluded: chain K residue 133 VAL Chi-restraints excluded: chain K residue 164 VAL Chi-restraints excluded: chain K residue 172 SER Chi-restraints excluded: chain K residue 206 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 1 optimal weight: 0.7980 chunk 62 optimal weight: 0.4980 chunk 31 optimal weight: 1.9990 chunk 18 optimal weight: 0.7980 chunk 58 optimal weight: 3.9990 chunk 43 optimal weight: 1.9990 chunk 47 optimal weight: 0.9980 chunk 36 optimal weight: 0.0040 chunk 56 optimal weight: 2.9990 chunk 44 optimal weight: 0.9990 chunk 10 optimal weight: 1.9990 overall best weight: 0.6192 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 486 HIS ** K 148 GLN ** 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 = 0.3962 r_free = 0.3962 target = 0.159169 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3746 r_free = 0.3746 target = 0.140746 restraints weight = 18274.539| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3772 r_free = 0.3772 target = 0.144942 restraints weight = 10480.930| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3780 r_free = 0.3780 target = 0.145647 restraints weight = 5028.756| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3791 r_free = 0.3791 target = 0.146568 restraints weight = 3604.329| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3811 r_free = 0.3811 target = 0.148371 restraints weight = 2645.149| |-----------------------------------------------------------------------------| r_work (final): 0.3813 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3809 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3809 r_free = 0.3809 target_work(ls_wunit_k1) = 0.146 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3809 r_free = 0.3809 target_work(ls_wunit_k1) = 0.146 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3809 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7519 moved from start: 0.4247 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 4947 Z= 0.167 Angle : 0.704 11.497 6748 Z= 0.354 Chirality : 0.046 0.236 774 Planarity : 0.004 0.034 861 Dihedral : 6.555 50.095 701 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 10.38 Ramachandran Plot: Outliers : 0.47 % Allowed : 11.02 % Favored : 88.50 % Rotamer: Outliers : 5.45 % Allowed : 19.64 % Favored : 74.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.89 % Cis-general : 0.33 % 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: -2.32 (0.32), residues: 637 helix: -4.44 (0.71), residues: 18 sheet: -0.68 (0.32), residues: 265 loop : -2.12 (0.31), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG H 98 TYR 0.021 0.002 TYR H 183 PHE 0.016 0.002 PHE I 423 TRP 0.012 0.001 TRP K 97 HIS 0.002 0.001 HIS I 486 Details of bonding type rmsd covalent geometry : bond 0.00394 ( 4939) covalent geometry : angle 0.70328 ( 6732) SS BOND : bond 0.00321 ( 8) SS BOND : angle 0.98805 ( 16) hydrogen bonds : bond 0.03070 ( 113) hydrogen bonds : angle 5.70632 ( 233) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1274 Ramachandran restraints generated. 637 Oldfield, 0 Emsley, 637 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1274 Ramachandran restraints generated. 637 Oldfield, 0 Emsley, 637 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 79 time to evaluate : 0.173 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 29 PHE cc_start: 0.7766 (OUTLIER) cc_final: 0.7487 (t80) REVERT: H 32 TYR cc_start: 0.8167 (m-80) cc_final: 0.7905 (m-80) REVERT: I 536 GLU cc_start: 0.8167 (mm-30) cc_final: 0.7474 (mt-10) REVERT: K 75 THR cc_start: 0.7193 (OUTLIER) cc_final: 0.6839 (p) REVERT: K 76 ILE cc_start: 0.6810 (mt) cc_final: 0.6523 (mt) REVERT: K 124 GLU cc_start: 0.7199 (tm-30) cc_final: 0.6642 (tm-30) REVERT: K 143 ARG cc_start: 0.6671 (mtp85) cc_final: 0.6276 (ttm170) outliers start: 30 outliers final: 24 residues processed: 100 average time/residue: 0.0801 time to fit residues: 10.1803 Evaluate side-chains 99 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 73 time to evaluate : 0.153 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 18 VAL Chi-restraints excluded: chain H residue 29 PHE Chi-restraints excluded: chain H residue 80 TYR Chi-restraints excluded: chain H residue 131 LEU Chi-restraints excluded: chain H residue 138 THR Chi-restraints excluded: chain H residue 170 VAL Chi-restraints excluded: chain H residue 214 VAL Chi-restraints excluded: chain H residue 218 VAL Chi-restraints excluded: chain I residue 388 LEU Chi-restraints excluded: chain I residue 417 LEU Chi-restraints excluded: chain I residue 426 SER Chi-restraints excluded: chain I residue 451 SER Chi-restraints excluded: chain I residue 480 ILE Chi-restraints excluded: chain I residue 486 HIS Chi-restraints excluded: chain I residue 512 THR Chi-restraints excluded: chain I residue 521 ASN Chi-restraints excluded: chain I residue 530 VAL Chi-restraints excluded: chain I residue 545 LEU Chi-restraints excluded: chain I residue 581 THR Chi-restraints excluded: chain K residue 75 THR Chi-restraints excluded: chain K residue 111 VAL Chi-restraints excluded: chain K residue 116 VAL Chi-restraints excluded: chain K residue 133 VAL Chi-restraints excluded: chain K residue 164 VAL Chi-restraints excluded: chain K residue 172 SER Chi-restraints excluded: chain K residue 206 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 29 optimal weight: 1.9990 chunk 35 optimal weight: 0.8980 chunk 1 optimal weight: 0.6980 chunk 42 optimal weight: 1.9990 chunk 39 optimal weight: 2.9990 chunk 48 optimal weight: 1.9990 chunk 43 optimal weight: 0.9980 chunk 14 optimal weight: 0.8980 chunk 60 optimal weight: 3.9990 chunk 58 optimal weight: 0.9980 chunk 23 optimal weight: 0.4980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 211 ASN I 486 HIS ** K 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3952 r_free = 0.3952 target = 0.158350 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3731 r_free = 0.3731 target = 0.139054 restraints weight = 23014.369| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3764 r_free = 0.3764 target = 0.144118 restraints weight = 14392.212| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3788 r_free = 0.3788 target = 0.146356 restraints weight = 4650.854| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3796 r_free = 0.3796 target = 0.147058 restraints weight = 2998.989| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3803 r_free = 0.3803 target = 0.147692 restraints weight = 2200.695| |-----------------------------------------------------------------------------| r_work (final): 0.3797 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3795 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3795 r_free = 0.3795 target_work(ls_wunit_k1) = 0.145 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3795 r_free = 0.3795 target_work(ls_wunit_k1) = 0.145 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3795 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7543 moved from start: 0.4343 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 4947 Z= 0.202 Angle : 0.749 11.597 6748 Z= 0.377 Chirality : 0.048 0.236 774 Planarity : 0.005 0.040 861 Dihedral : 6.730 52.929 701 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 11.11 Ramachandran Plot: Outliers : 0.47 % Allowed : 11.34 % Favored : 88.19 % Rotamer: Outliers : 5.27 % Allowed : 20.36 % Favored : 74.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.89 % Cis-general : 0.33 % 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: -2.48 (0.32), residues: 637 helix: -4.49 (0.69), residues: 18 sheet: -0.82 (0.33), residues: 242 loop : -2.13 (0.30), residues: 377 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG H 98 TYR 0.021 0.002 TYR H 183 PHE 0.017 0.002 PHE I 423 TRP 0.016 0.001 TRP K 97 HIS 0.002 0.001 HIS I 486 Details of bonding type rmsd covalent geometry : bond 0.00482 ( 4939) covalent geometry : angle 0.74781 ( 6732) SS BOND : bond 0.00357 ( 8) SS BOND : angle 1.16476 ( 16) hydrogen bonds : bond 0.03206 ( 113) hydrogen bonds : angle 5.80226 ( 233) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1274 Ramachandran restraints generated. 637 Oldfield, 0 Emsley, 637 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1274 Ramachandran restraints generated. 637 Oldfield, 0 Emsley, 637 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 74 time to evaluate : 0.290 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 29 PHE cc_start: 0.7834 (OUTLIER) cc_final: 0.7471 (t80) REVERT: I 480 ILE cc_start: 0.8404 (OUTLIER) cc_final: 0.8128 (mt) REVERT: I 536 GLU cc_start: 0.8162 (mm-30) cc_final: 0.7480 (mt-10) REVERT: K 75 THR cc_start: 0.7178 (OUTLIER) cc_final: 0.6833 (p) REVERT: K 76 ILE cc_start: 0.6859 (OUTLIER) cc_final: 0.6509 (mt) REVERT: K 124 GLU cc_start: 0.7221 (tm-30) cc_final: 0.6765 (tm-30) REVERT: K 143 ARG cc_start: 0.6638 (mtp85) cc_final: 0.6252 (ttm170) outliers start: 29 outliers final: 23 residues processed: 93 average time/residue: 0.0834 time to fit residues: 9.8169 Evaluate side-chains 100 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 73 time to evaluate : 0.137 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 18 VAL Chi-restraints excluded: chain H residue 29 PHE Chi-restraints excluded: chain H residue 80 TYR Chi-restraints excluded: chain H residue 131 LEU Chi-restraints excluded: chain H residue 138 THR Chi-restraints excluded: chain H residue 170 VAL Chi-restraints excluded: chain H residue 214 VAL Chi-restraints excluded: chain H residue 218 VAL Chi-restraints excluded: chain I residue 388 LEU Chi-restraints excluded: chain I residue 417 LEU Chi-restraints excluded: chain I residue 426 SER Chi-restraints excluded: chain I residue 451 SER Chi-restraints excluded: chain I residue 480 ILE Chi-restraints excluded: chain I residue 486 HIS Chi-restraints excluded: chain I residue 512 THR Chi-restraints excluded: chain I residue 521 ASN Chi-restraints excluded: chain I residue 530 VAL Chi-restraints excluded: chain I residue 545 LEU Chi-restraints excluded: chain I residue 581 THR Chi-restraints excluded: chain K residue 75 THR Chi-restraints excluded: chain K residue 76 ILE Chi-restraints excluded: chain K residue 111 VAL Chi-restraints excluded: chain K residue 116 VAL Chi-restraints excluded: chain K residue 133 VAL Chi-restraints excluded: chain K residue 164 VAL Chi-restraints excluded: chain K residue 172 SER Chi-restraints excluded: chain K residue 206 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 10 optimal weight: 1.9990 chunk 18 optimal weight: 1.9990 chunk 0 optimal weight: 2.9990 chunk 48 optimal weight: 1.9990 chunk 9 optimal weight: 0.6980 chunk 4 optimal weight: 1.9990 chunk 17 optimal weight: 0.7980 chunk 45 optimal weight: 0.7980 chunk 24 optimal weight: 0.8980 chunk 41 optimal weight: 0.6980 chunk 57 optimal weight: 0.8980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 211 ASN I 486 HIS ** K 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3948 r_free = 0.3948 target = 0.158135 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3741 r_free = 0.3741 target = 0.140240 restraints weight = 18242.339| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3768 r_free = 0.3768 target = 0.144320 restraints weight = 10328.965| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3769 r_free = 0.3769 target = 0.144628 restraints weight = 5463.238| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3781 r_free = 0.3781 target = 0.145609 restraints weight = 3705.903| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3801 r_free = 0.3801 target = 0.147466 restraints weight = 2792.443| |-----------------------------------------------------------------------------| r_work (final): 0.3795 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3794 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3794 r_free = 0.3794 target_work(ls_wunit_k1) = 0.145 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3794 r_free = 0.3794 target_work(ls_wunit_k1) = 0.145 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3794 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7539 moved from start: 0.4416 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 4947 Z= 0.200 Angle : 0.754 11.645 6748 Z= 0.380 Chirality : 0.048 0.244 774 Planarity : 0.005 0.036 861 Dihedral : 6.804 54.276 701 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 10.90 Ramachandran Plot: Outliers : 0.47 % Allowed : 11.81 % Favored : 87.72 % Rotamer: Outliers : 5.27 % Allowed : 20.36 % Favored : 74.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.89 % Cis-general : 0.33 % 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: -2.57 (0.31), residues: 637 helix: -4.51 (0.69), residues: 18 sheet: -0.93 (0.33), residues: 242 loop : -2.16 (0.30), residues: 377 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG H 98 TYR 0.021 0.002 TYR H 183 PHE 0.017 0.002 PHE I 423 TRP 0.015 0.002 TRP K 97 HIS 0.002 0.001 HIS H 207 Details of bonding type rmsd covalent geometry : bond 0.00476 ( 4939) covalent geometry : angle 0.75298 ( 6732) SS BOND : bond 0.00367 ( 8) SS BOND : angle 1.12505 ( 16) hydrogen bonds : bond 0.03209 ( 113) hydrogen bonds : angle 5.84874 ( 233) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1274 Ramachandran restraints generated. 637 Oldfield, 0 Emsley, 637 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1274 Ramachandran restraints generated. 637 Oldfield, 0 Emsley, 637 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 77 time to evaluate : 0.179 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 29 PHE cc_start: 0.7885 (OUTLIER) cc_final: 0.7473 (t80) REVERT: H 32 TYR cc_start: 0.8256 (m-80) cc_final: 0.7924 (m-80) REVERT: I 480 ILE cc_start: 0.8383 (OUTLIER) cc_final: 0.8104 (mt) REVERT: I 536 GLU cc_start: 0.8183 (mm-30) cc_final: 0.7571 (mt-10) REVERT: K 75 THR cc_start: 0.7183 (OUTLIER) cc_final: 0.6838 (p) REVERT: K 76 ILE cc_start: 0.6857 (OUTLIER) cc_final: 0.6505 (mt) REVERT: K 124 GLU cc_start: 0.7182 (tm-30) cc_final: 0.6674 (tm-30) REVERT: K 143 ARG cc_start: 0.6723 (mtp85) cc_final: 0.6333 (ttm170) outliers start: 29 outliers final: 23 residues processed: 96 average time/residue: 0.0812 time to fit residues: 9.9541 Evaluate side-chains 102 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 75 time to evaluate : 0.176 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 18 VAL Chi-restraints excluded: chain H residue 29 PHE Chi-restraints excluded: chain H residue 80 TYR Chi-restraints excluded: chain H residue 131 LEU Chi-restraints excluded: chain H residue 138 THR Chi-restraints excluded: chain H residue 170 VAL Chi-restraints excluded: chain H residue 214 VAL Chi-restraints excluded: chain H residue 218 VAL Chi-restraints excluded: chain I residue 388 LEU Chi-restraints excluded: chain I residue 417 LEU Chi-restraints excluded: chain I residue 426 SER Chi-restraints excluded: chain I residue 451 SER Chi-restraints excluded: chain I residue 480 ILE Chi-restraints excluded: chain I residue 486 HIS Chi-restraints excluded: chain I residue 512 THR Chi-restraints excluded: chain I residue 521 ASN Chi-restraints excluded: chain I residue 530 VAL Chi-restraints excluded: chain I residue 545 LEU Chi-restraints excluded: chain I residue 581 THR Chi-restraints excluded: chain K residue 75 THR Chi-restraints excluded: chain K residue 76 ILE Chi-restraints excluded: chain K residue 111 VAL Chi-restraints excluded: chain K residue 116 VAL Chi-restraints excluded: chain K residue 133 VAL Chi-restraints excluded: chain K residue 164 VAL Chi-restraints excluded: chain K residue 172 SER Chi-restraints excluded: chain K residue 206 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 18 optimal weight: 0.6980 chunk 10 optimal weight: 1.9990 chunk 58 optimal weight: 5.9990 chunk 19 optimal weight: 0.7980 chunk 50 optimal weight: 0.6980 chunk 48 optimal weight: 0.5980 chunk 21 optimal weight: 0.7980 chunk 55 optimal weight: 1.9990 chunk 53 optimal weight: 0.5980 chunk 7 optimal weight: 0.6980 chunk 33 optimal weight: 0.4980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 211 ASN I 486 HIS ** K 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3958 r_free = 0.3958 target = 0.159087 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3740 r_free = 0.3740 target = 0.139916 restraints weight = 23662.871| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3774 r_free = 0.3774 target = 0.144625 restraints weight = 15001.997| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3806 r_free = 0.3806 target = 0.147716 restraints weight = 5024.080| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3810 r_free = 0.3810 target = 0.148086 restraints weight = 2889.331| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3818 r_free = 0.3818 target = 0.148761 restraints weight = 2219.027| |-----------------------------------------------------------------------------| r_work (final): 0.3811 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3812 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3812 r_free = 0.3812 target_work(ls_wunit_k1) = 0.146 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3812 r_free = 0.3812 target_work(ls_wunit_k1) = 0.146 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3812 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7512 moved from start: 0.4476 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 4947 Z= 0.173 Angle : 0.737 11.406 6748 Z= 0.370 Chirality : 0.047 0.244 774 Planarity : 0.005 0.038 861 Dihedral : 6.757 55.863 701 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 10.69 Ramachandran Plot: Outliers : 0.31 % Allowed : 11.02 % Favored : 88.66 % Rotamer: Outliers : 5.27 % Allowed : 20.91 % Favored : 73.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.89 % Cis-general : 0.33 % 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: -2.53 (0.32), residues: 637 helix: -4.51 (0.70), residues: 18 sheet: -0.93 (0.33), residues: 243 loop : -2.11 (0.30), residues: 376 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG H 98 TYR 0.018 0.002 TYR H 183 PHE 0.015 0.002 PHE I 423 TRP 0.016 0.001 TRP K 97 HIS 0.003 0.001 HIS I 486 Details of bonding type rmsd covalent geometry : bond 0.00410 ( 4939) covalent geometry : angle 0.73628 ( 6732) SS BOND : bond 0.00326 ( 8) SS BOND : angle 1.07579 ( 16) hydrogen bonds : bond 0.03071 ( 113) hydrogen bonds : angle 5.77290 ( 233) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1274 Ramachandran restraints generated. 637 Oldfield, 0 Emsley, 637 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1274 Ramachandran restraints generated. 637 Oldfield, 0 Emsley, 637 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 76 time to evaluate : 0.175 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 29 PHE cc_start: 0.7888 (OUTLIER) cc_final: 0.7524 (t80) REVERT: H 32 TYR cc_start: 0.8235 (m-80) cc_final: 0.7938 (m-80) REVERT: I 536 GLU cc_start: 0.8218 (mm-30) cc_final: 0.7547 (mt-10) REVERT: K 75 THR cc_start: 0.7143 (OUTLIER) cc_final: 0.6808 (p) REVERT: K 76 ILE cc_start: 0.6807 (OUTLIER) cc_final: 0.6464 (mt) REVERT: K 124 GLU cc_start: 0.7313 (tm-30) cc_final: 0.6820 (tm-30) REVERT: K 143 ARG cc_start: 0.6665 (mtp85) cc_final: 0.6225 (ttm170) outliers start: 29 outliers final: 22 residues processed: 94 average time/residue: 0.0810 time to fit residues: 9.6614 Evaluate side-chains 99 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 74 time to evaluate : 0.180 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 18 VAL Chi-restraints excluded: chain H residue 29 PHE Chi-restraints excluded: chain H residue 80 TYR Chi-restraints excluded: chain H residue 131 LEU Chi-restraints excluded: chain H residue 138 THR Chi-restraints excluded: chain H residue 170 VAL Chi-restraints excluded: chain H residue 214 VAL Chi-restraints excluded: chain H residue 218 VAL Chi-restraints excluded: chain I residue 388 LEU Chi-restraints excluded: chain I residue 417 LEU Chi-restraints excluded: chain I residue 426 SER Chi-restraints excluded: chain I residue 451 SER Chi-restraints excluded: chain I residue 480 ILE Chi-restraints excluded: chain I residue 512 THR Chi-restraints excluded: chain I residue 521 ASN Chi-restraints excluded: chain I residue 530 VAL Chi-restraints excluded: chain I residue 545 LEU Chi-restraints excluded: chain I residue 581 THR Chi-restraints excluded: chain K residue 75 THR Chi-restraints excluded: chain K residue 76 ILE Chi-restraints excluded: chain K residue 111 VAL Chi-restraints excluded: chain K residue 116 VAL Chi-restraints excluded: chain K residue 133 VAL Chi-restraints excluded: chain K residue 172 SER Chi-restraints excluded: chain K residue 206 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 49 optimal weight: 2.9990 chunk 42 optimal weight: 0.9990 chunk 52 optimal weight: 1.9990 chunk 9 optimal weight: 0.7980 chunk 50 optimal weight: 0.3980 chunk 8 optimal weight: 0.5980 chunk 31 optimal weight: 0.9990 chunk 22 optimal weight: 0.9990 chunk 43 optimal weight: 0.1980 chunk 14 optimal weight: 0.9990 chunk 3 optimal weight: 0.4980 overall best weight: 0.4980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 211 ASN I 486 HIS ** K 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3975 r_free = 0.3975 target = 0.160565 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3761 r_free = 0.3761 target = 0.141536 restraints weight = 19502.822| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3800 r_free = 0.3800 target = 0.147008 restraints weight = 12787.032| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3810 r_free = 0.3810 target = 0.147878 restraints weight = 4611.556| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3817 r_free = 0.3817 target = 0.148532 restraints weight = 3323.865| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3824 r_free = 0.3824 target = 0.149138 restraints weight = 2796.952| |-----------------------------------------------------------------------------| r_work (final): 0.3821 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3820 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3820 r_free = 0.3820 target_work(ls_wunit_k1) = 0.147 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3820 r_free = 0.3820 target_work(ls_wunit_k1) = 0.147 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3820 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7496 moved from start: 0.4574 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 4947 Z= 0.151 Angle : 0.715 11.038 6748 Z= 0.357 Chirality : 0.046 0.231 774 Planarity : 0.004 0.039 861 Dihedral : 6.557 58.642 700 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 9.64 Ramachandran Plot: Outliers : 0.31 % Allowed : 10.71 % Favored : 88.98 % Rotamer: Outliers : 4.36 % Allowed : 21.82 % Favored : 73.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.89 % Cis-general : 0.33 % 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: -2.56 (0.31), residues: 637 helix: -3.94 (0.74), residues: 24 sheet: -0.95 (0.32), residues: 243 loop : -2.12 (0.30), residues: 370 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG K 143 TYR 0.015 0.002 TYR H 183 PHE 0.013 0.001 PHE I 423 TRP 0.014 0.001 TRP K 97 HIS 0.002 0.001 HIS H 207 Details of bonding type rmsd covalent geometry : bond 0.00357 ( 4939) covalent geometry : angle 0.71376 ( 6732) SS BOND : bond 0.00291 ( 8) SS BOND : angle 1.02579 ( 16) hydrogen bonds : bond 0.02927 ( 113) hydrogen bonds : angle 5.64196 ( 233) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1079.04 seconds wall clock time: 19 minutes 22.18 seconds (1162.18 seconds total)