Starting phenix.real_space_refine on Fri Jul 25 15:01:30 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7ck6_30382/07_2025/7ck6_30382.cif Found real_map, /net/cci-nas-00/data/ceres_data/7ck6_30382/07_2025/7ck6_30382.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7ck6_30382/07_2025/7ck6_30382.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7ck6_30382/07_2025/7ck6_30382.map" model { file = "/net/cci-nas-00/data/ceres_data/7ck6_30382/07_2025/7ck6_30382.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7ck6_30382/07_2025/7ck6_30382.cif" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 1 5.49 5 S 32 5.16 5 C 4808 2.51 5 N 1281 2.21 5 O 1338 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 26 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib" Total number of atoms: 7460 Number of models: 1 Model: "" Number of chains: 11 Chain: "A" Number of atoms: 2179 Number of conformers: 1 Conformer: "" Number of residues, atoms: 284, 2179 Classifications: {'peptide': 284} Link IDs: {'PTRANS': 13, 'TRANS': 270} Chain: "B" Number of atoms: 2179 Number of conformers: 1 Conformer: "" Number of residues, atoms: 284, 2179 Classifications: {'peptide': 284} Link IDs: {'PTRANS': 13, 'TRANS': 270} Chain: "C" Number of atoms: 444 Number of conformers: 1 Conformer: "" Number of residues, atoms: 53, 444 Classifications: {'peptide': 53} Link IDs: {'PTRANS': 1, 'TRANS': 51} Chain: "D" Number of atoms: 444 Number of conformers: 1 Conformer: "" Number of residues, atoms: 53, 444 Classifications: {'peptide': 53} Link IDs: {'PTRANS': 1, 'TRANS': 51} Chain: "E" Number of atoms: 361 Number of conformers: 1 Conformer: "" Number of residues, atoms: 44, 361 Classifications: {'peptide': 44} Link IDs: {'TRANS': 43} Chain: "F" Number of atoms: 361 Number of conformers: 1 Conformer: "" Number of residues, atoms: 44, 361 Classifications: {'peptide': 44} Link IDs: {'TRANS': 43} Chain: "G" Number of atoms: 399 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 399 Classifications: {'peptide': 49} Link IDs: {'PTRANS': 4, 'TRANS': 44} Chain: "H" Number of atoms: 399 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 399 Classifications: {'peptide': 49} Link IDs: {'PTRANS': 4, 'TRANS': 44} Chain: "I" Number of atoms: 320 Number of conformers: 1 Conformer: "" Number of residues, atoms: 38, 320 Classifications: {'peptide': 38} Link IDs: {'PTRANS': 2, 'TRANS': 35} Chain: "J" Number of atoms: 320 Number of conformers: 1 Conformer: "" Number of residues, atoms: 38, 320 Classifications: {'peptide': 38} Link IDs: {'PTRANS': 2, 'TRANS': 35} Chain: "A" Number of atoms: 54 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 54 Unusual residues: {'PC1': 1} Classifications: {'undetermined': 1} Time building chain proxies: 4.89, per 1000 atoms: 0.66 Number of scatterers: 7460 At special positions: 0 Unit cell: (111.24, 145.8, 96.12, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 32 16.00 P 1 15.00 O 1338 8.00 N 1281 7.00 C 4808 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.71 Conformation dependent library (CDL) restraints added in 964.1 milliseconds 1832 Ramachandran restraints generated. 916 Oldfield, 0 Emsley, 916 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1716 Finding SS restraints... Secondary structure from input PDB file: 17 helices and 2 sheets defined 37.0% alpha, 33.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.72 Creating SS restraints... Processing helix chain 'A' and resid 83 through 86 Processing helix chain 'A' and resid 87 through 92 Processing helix chain 'B' and resid 83 through 86 Processing helix chain 'B' and resid 87 through 92 Processing helix chain 'C' and resid 67 through 118 Proline residue: C 98 - end of helix removed outlier: 3.784A pdb=" N GLU C 102 " --> pdb=" O PRO C 98 " (cutoff:3.500A) Processing helix chain 'D' and resid 67 through 96 Processing helix chain 'D' and resid 96 through 118 Processing helix chain 'E' and resid 24 through 35 Processing helix chain 'E' and resid 42 through 66 removed outlier: 3.509A pdb=" N GLY E 50 " --> pdb=" O ILE E 46 " (cutoff:3.500A) Processing helix chain 'F' and resid 24 through 35 Processing helix chain 'F' and resid 43 through 66 Processing helix chain 'G' and resid 7 through 37 removed outlier: 3.892A pdb=" N TRP G 25 " --> pdb=" O PHE G 21 " (cutoff:3.500A) removed outlier: 5.252A pdb=" N ILE G 28 " --> pdb=" O ARG G 24 " (cutoff:3.500A) Proline residue: G 29 - end of helix Processing helix chain 'G' and resid 48 through 54 removed outlier: 3.567A pdb=" N LEU G 52 " --> pdb=" O THR G 48 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N LEU G 53 " --> pdb=" O VAL G 49 " (cutoff:3.500A) Processing helix chain 'H' and resid 7 through 37 removed outlier: 3.893A pdb=" N TRP H 25 " --> pdb=" O PHE H 21 " (cutoff:3.500A) removed outlier: 5.252A pdb=" N ILE H 28 " --> pdb=" O ARG H 24 " (cutoff:3.500A) Proline residue: H 29 - end of helix removed outlier: 3.505A pdb=" N LYS H 37 " --> pdb=" O TYR H 33 " (cutoff:3.500A) Processing helix chain 'H' and resid 48 through 54 removed outlier: 3.567A pdb=" N LEU H 52 " --> pdb=" O THR H 48 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N LEU H 53 " --> pdb=" O VAL H 49 " (cutoff:3.500A) Processing helix chain 'I' and resid 13 through 48 Proline residue: I 42 - end of helix removed outlier: 3.793A pdb=" N LYS I 47 " --> pdb=" O PHE I 43 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N LEU I 48 " --> pdb=" O ILE I 44 " (cutoff:3.500A) Processing helix chain 'J' and resid 13 through 48 Proline residue: J 42 - end of helix removed outlier: 3.793A pdb=" N LYS J 47 " --> pdb=" O PHE J 43 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N LEU J 48 " --> pdb=" O ILE J 44 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 351 through 353 removed outlier: 3.731A pdb=" N LYS A 351 " --> pdb=" O ASN A 346 " (cutoff:3.500A) removed outlier: 14.431A pdb=" N VAL A 186 " --> pdb=" O ASP A 209 " (cutoff:3.500A) removed outlier: 10.324A pdb=" N ASP A 209 " --> pdb=" O VAL A 186 " (cutoff:3.500A) removed outlier: 7.387A pdb=" N TRP A 188 " --> pdb=" O ASN A 207 " (cutoff:3.500A) removed outlier: 7.157A pdb=" N SER A 214 " --> pdb=" O PRO A 208 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N PHE A 301 " --> pdb=" O VAL A 318 " (cutoff:3.500A) removed outlier: 4.560A pdb=" N ILE A 323 " --> pdb=" O ASP A 319 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N LEU A 337 " --> pdb=" O LEU A 332 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 351 through 353 removed outlier: 3.669A pdb=" N LYS B 351 " --> pdb=" O ASN B 346 " (cutoff:3.500A) removed outlier: 14.430A pdb=" N VAL B 186 " --> pdb=" O ASP B 209 " (cutoff:3.500A) removed outlier: 10.325A pdb=" N ASP B 209 " --> pdb=" O VAL B 186 " (cutoff:3.500A) removed outlier: 7.388A pdb=" N TRP B 188 " --> pdb=" O ASN B 207 " (cutoff:3.500A) removed outlier: 7.157A pdb=" N SER B 214 " --> pdb=" O PRO B 208 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N PHE B 301 " --> pdb=" O VAL B 318 " (cutoff:3.500A) removed outlier: 4.561A pdb=" N ILE B 323 " --> pdb=" O ASP B 319 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N LEU B 337 " --> pdb=" O LEU B 332 " (cutoff:3.500A) 518 hydrogen bonds defined for protein. 1494 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: 2.23 Time building geometry restraints manager: 2.06 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.33: 2343 1.33 - 1.45: 1063 1.45 - 1.57: 4157 1.57 - 1.69: 2 1.69 - 1.80: 56 Bond restraints: 7621 Sorted by residual: bond pdb=" C31 PC1 A 401 " pdb=" O31 PC1 A 401 " ideal model delta sigma weight residual 1.330 1.455 -0.125 2.00e-02 2.50e+03 3.88e+01 bond pdb=" C21 PC1 A 401 " pdb=" O21 PC1 A 401 " ideal model delta sigma weight residual 1.331 1.454 -0.123 2.00e-02 2.50e+03 3.76e+01 bond pdb=" CA HIS A 347 " pdb=" C HIS A 347 " ideal model delta sigma weight residual 1.523 1.473 0.050 1.34e-02 5.57e+03 1.42e+01 bond pdb=" CA PRO A 333 " pdb=" C PRO A 333 " ideal model delta sigma weight residual 1.517 1.551 -0.034 9.30e-03 1.16e+04 1.33e+01 bond pdb=" CA PRO B 333 " pdb=" C PRO B 333 " ideal model delta sigma weight residual 1.517 1.551 -0.034 9.30e-03 1.16e+04 1.32e+01 ... (remaining 7616 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.67: 9909 2.67 - 5.35: 329 5.35 - 8.02: 45 8.02 - 10.69: 12 10.69 - 13.36: 4 Bond angle restraints: 10299 Sorted by residual: angle pdb=" N PRO A 333 " pdb=" CA PRO A 333 " pdb=" C PRO A 333 " ideal model delta sigma weight residual 110.70 124.06 -13.36 1.22e+00 6.72e-01 1.20e+02 angle pdb=" N PRO B 333 " pdb=" CA PRO B 333 " pdb=" C PRO B 333 " ideal model delta sigma weight residual 110.70 124.05 -13.35 1.22e+00 6.72e-01 1.20e+02 angle pdb=" C GLU H 46 " pdb=" N PRO H 47 " pdb=" CA PRO H 47 " ideal model delta sigma weight residual 119.84 132.57 -12.73 1.25e+00 6.40e-01 1.04e+02 angle pdb=" C GLU G 46 " pdb=" N PRO G 47 " pdb=" CA PRO G 47 " ideal model delta sigma weight residual 119.84 132.41 -12.57 1.25e+00 6.40e-01 1.01e+02 angle pdb=" N THR B 292 " pdb=" CA THR B 292 " pdb=" C THR B 292 " ideal model delta sigma weight residual 111.14 119.93 -8.79 1.08e+00 8.57e-01 6.62e+01 ... (remaining 10294 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.13: 3951 15.13 - 30.26: 468 30.26 - 45.39: 82 45.39 - 60.51: 24 60.51 - 75.64: 7 Dihedral angle restraints: 4532 sinusoidal: 1864 harmonic: 2668 Sorted by residual: dihedral pdb=" N GLN B 182 " pdb=" C GLN B 182 " pdb=" CA GLN B 182 " pdb=" CB GLN B 182 " ideal model delta harmonic sigma weight residual 122.80 134.15 -11.35 0 2.50e+00 1.60e-01 2.06e+01 dihedral pdb=" N GLN A 182 " pdb=" C GLN A 182 " pdb=" CA GLN A 182 " pdb=" CB GLN A 182 " ideal model delta harmonic sigma weight residual 122.80 134.05 -11.25 0 2.50e+00 1.60e-01 2.02e+01 dihedral pdb=" C GLN B 182 " pdb=" N GLN B 182 " pdb=" CA GLN B 182 " pdb=" CB GLN B 182 " ideal model delta harmonic sigma weight residual -122.60 -133.46 10.86 0 2.50e+00 1.60e-01 1.89e+01 ... (remaining 4529 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.096: 1029 0.096 - 0.192: 96 0.192 - 0.288: 13 0.288 - 0.384: 3 0.384 - 0.480: 2 Chirality restraints: 1143 Sorted by residual: chirality pdb=" CA GLN B 182 " pdb=" N GLN B 182 " pdb=" C GLN B 182 " pdb=" CB GLN B 182 " both_signs ideal model delta sigma weight residual False 2.51 2.03 0.48 2.00e-01 2.50e+01 5.76e+00 chirality pdb=" CA GLN A 182 " pdb=" N GLN A 182 " pdb=" C GLN A 182 " pdb=" CB GLN A 182 " both_signs ideal model delta sigma weight residual False 2.51 2.04 0.48 2.00e-01 2.50e+01 5.65e+00 chirality pdb=" CA PRO A 333 " pdb=" N PRO A 333 " pdb=" C PRO A 333 " pdb=" CB PRO A 333 " both_signs ideal model delta sigma weight residual False 2.72 2.38 0.34 2.00e-01 2.50e+01 2.81e+00 ... (remaining 1140 not shown) Planarity restraints: 1310 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLU H 46 " -0.044 5.00e-02 4.00e+02 6.54e-02 6.84e+00 pdb=" N PRO H 47 " 0.113 5.00e-02 4.00e+02 pdb=" CA PRO H 47 " -0.039 5.00e-02 4.00e+02 pdb=" CD PRO H 47 " -0.031 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLU G 46 " 0.044 5.00e-02 4.00e+02 6.54e-02 6.84e+00 pdb=" N PRO G 47 " -0.113 5.00e-02 4.00e+02 pdb=" CA PRO G 47 " 0.038 5.00e-02 4.00e+02 pdb=" CD PRO G 47 " 0.031 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA THR C 66 " -0.012 2.00e-02 2.50e+03 2.53e-02 6.38e+00 pdb=" C THR C 66 " 0.044 2.00e-02 2.50e+03 pdb=" O THR C 66 " -0.017 2.00e-02 2.50e+03 pdb=" N PHE C 67 " -0.015 2.00e-02 2.50e+03 ... (remaining 1307 not shown) Histogram of nonbonded interaction distances: 1.65 - 2.30: 29 2.30 - 2.95: 3720 2.95 - 3.60: 10402 3.60 - 4.25: 14230 4.25 - 4.90: 25368 Nonbonded interactions: 53749 Sorted by model distance: nonbonded pdb=" O ASN F 39 " pdb=" CE2 PHE F 41 " model vdw 1.652 3.340 nonbonded pdb=" O LEU H 30 " pdb=" CD2 LEU H 34 " model vdw 1.677 3.460 nonbonded pdb=" O ASP F 37 " pdb=" OD1 ASP F 40 " model vdw 1.722 3.040 nonbonded pdb=" OG1 THR B 297 " pdb=" ND2 ASN F 48 " model vdw 1.824 3.120 nonbonded pdb=" O LEU G 30 " pdb=" CD2 LEU G 34 " model vdw 1.843 3.460 ... (remaining 53744 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 Found NCS groups: ncs_group { reference = (chain 'A' and resid 77 through 360) selection = chain 'B' } ncs_group { reference = chain 'C' selection = chain 'D' } ncs_group { reference = chain 'E' selection = chain 'F' } ncs_group { reference = chain 'G' selection = chain 'H' } ncs_group { reference = chain 'I' selection = chain 'J' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.710 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.290 Check model and map are aligned: 0.050 Set scattering table: 0.070 Process input model: 20.270 Find NCS groups from input model: 0.240 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.110 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.780 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7424 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 : 0.008 0.125 7621 Z= 0.400 Angle : 1.142 13.363 10299 Z= 0.740 Chirality : 0.065 0.480 1143 Planarity : 0.005 0.065 1310 Dihedral : 13.465 75.643 2816 Min Nonbonded Distance : 1.652 Molprobity Statistics. All-atom Clashscore : 36.32 Ramachandran Plot: Outliers : 0.76 % Allowed : 6.11 % Favored : 93.12 % Rotamer: Outliers : 4.12 % Allowed : 12.38 % Favored : 83.50 % Cbeta Deviations : 0.23 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.38 (0.28), residues: 916 helix: 2.24 (0.30), residues: 300 sheet: 0.39 (0.27), residues: 378 loop : -2.66 (0.34), residues: 238 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 86 HIS 0.003 0.001 HIS A 220 PHE 0.031 0.002 PHE A 344 TYR 0.018 0.002 TYR A 129 ARG 0.004 0.000 ARG I 21 Details of bonding type rmsd hydrogen bonds : bond 0.16553 ( 518) hydrogen bonds : angle 6.11566 ( 1494) covalent geometry : bond 0.00771 ( 7621) covalent geometry : angle 1.14224 (10299) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1832 Ramachandran restraints generated. 916 Oldfield, 0 Emsley, 916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1832 Ramachandran restraints generated. 916 Oldfield, 0 Emsley, 916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 338 residues out of total 800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 305 time to evaluate : 0.879 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 296 ASP cc_start: 0.7206 (m-30) cc_final: 0.6706 (m-30) REVERT: C 97 LEU cc_start: 0.8892 (tp) cc_final: 0.8643 (tp) REVERT: C 114 LEU cc_start: 0.9313 (OUTLIER) cc_final: 0.9088 (mt) REVERT: I 38 LEU cc_start: 0.9032 (mm) cc_final: 0.8766 (mm) outliers start: 33 outliers final: 12 residues processed: 319 average time/residue: 0.2925 time to fit residues: 112.7711 Evaluate side-chains 178 residues out of total 800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 165 time to evaluate : 0.840 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 144 THR Chi-restraints excluded: chain A residue 147 PHE Chi-restraints excluded: chain A residue 182 GLN Chi-restraints excluded: chain A residue 296 ASP Chi-restraints excluded: chain B residue 144 THR Chi-restraints excluded: chain B residue 147 PHE Chi-restraints excluded: chain B residue 182 GLN Chi-restraints excluded: chain C residue 99 VAL Chi-restraints excluded: chain C residue 114 LEU Chi-restraints excluded: chain D residue 99 VAL Chi-restraints excluded: chain F residue 40 ASP Chi-restraints excluded: chain F residue 46 ILE Chi-restraints excluded: chain G residue 34 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 74 optimal weight: 7.9990 chunk 66 optimal weight: 6.9990 chunk 37 optimal weight: 0.4980 chunk 22 optimal weight: 7.9990 chunk 44 optimal weight: 7.9990 chunk 35 optimal weight: 5.9990 chunk 68 optimal weight: 3.9990 chunk 26 optimal weight: 4.9990 chunk 41 optimal weight: 9.9990 chunk 51 optimal weight: 3.9990 chunk 79 optimal weight: 2.9990 overall best weight: 3.2988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 97 GLN A 114 GLN ** A 163 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 182 GLN A 220 HIS A 223 GLN ** A 238 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 353 GLN B 97 GLN B 114 GLN ** B 163 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 182 GLN B 220 HIS B 223 GLN B 353 GLN C 110 GLN E 23 ASN E 61 ASN F 61 ASN G 10 GLN H 10 GLN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3873 r_free = 0.3873 target = 0.071313 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.053674 restraints weight = 30974.768| |-----------------------------------------------------------------------------| r_work (start): 0.3429 rms_B_bonded: 4.92 r_work (final): 0.3429 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8053 moved from start: 0.4894 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 7621 Z= 0.221 Angle : 0.909 11.196 10299 Z= 0.456 Chirality : 0.049 0.306 1143 Planarity : 0.006 0.055 1310 Dihedral : 7.805 55.149 1070 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 16.39 Ramachandran Plot: Outliers : 0.22 % Allowed : 5.68 % Favored : 94.10 % Rotamer: Outliers : 5.62 % Allowed : 21.50 % Favored : 72.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.05 (0.28), residues: 916 helix: 2.62 (0.28), residues: 308 sheet: 1.01 (0.26), residues: 376 loop : -2.70 (0.38), residues: 232 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP G 54 HIS 0.006 0.001 HIS A 112 PHE 0.020 0.002 PHE F 41 TYR 0.019 0.002 TYR A 129 ARG 0.009 0.001 ARG J 18 Details of bonding type rmsd hydrogen bonds : bond 0.05162 ( 518) hydrogen bonds : angle 5.24087 ( 1494) covalent geometry : bond 0.00490 ( 7621) covalent geometry : angle 0.90924 (10299) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1832 Ramachandran restraints generated. 916 Oldfield, 0 Emsley, 916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1832 Ramachandran restraints generated. 916 Oldfield, 0 Emsley, 916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 231 residues out of total 800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 186 time to evaluate : 0.863 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 128 ASN cc_start: 0.7912 (OUTLIER) cc_final: 0.7374 (t0) REVERT: A 150 LEU cc_start: 0.9286 (mp) cc_final: 0.8662 (tt) REVERT: A 154 MET cc_start: 0.8527 (ttt) cc_final: 0.8121 (tpt) REVERT: A 270 MET cc_start: 0.8368 (mpp) cc_final: 0.8116 (mpp) REVERT: B 128 ASN cc_start: 0.7429 (OUTLIER) cc_final: 0.7019 (t0) REVERT: B 154 MET cc_start: 0.8448 (ttt) cc_final: 0.8056 (tpt) REVERT: B 270 MET cc_start: 0.8378 (mpp) cc_final: 0.8113 (mpp) REVERT: C 97 LEU cc_start: 0.9406 (tp) cc_final: 0.9021 (tp) REVERT: C 101 PHE cc_start: 0.9316 (m-80) cc_final: 0.8989 (m-80) REVERT: C 108 MET cc_start: 0.9515 (mmp) cc_final: 0.9115 (mmp) REVERT: E 62 LEU cc_start: 0.9457 (mm) cc_final: 0.9246 (mm) REVERT: I 17 LYS cc_start: 0.9687 (mttt) cc_final: 0.9366 (mtmt) REVERT: I 38 LEU cc_start: 0.9268 (mm) cc_final: 0.9056 (mm) REVERT: J 17 LYS cc_start: 0.9599 (mttt) cc_final: 0.9258 (mtmt) outliers start: 45 outliers final: 20 residues processed: 207 average time/residue: 0.1884 time to fit residues: 52.1952 Evaluate side-chains 181 residues out of total 800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 159 time to evaluate : 0.805 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 96 ILE Chi-restraints excluded: chain A residue 128 ASN Chi-restraints excluded: chain A residue 147 PHE Chi-restraints excluded: chain A residue 250 LEU Chi-restraints excluded: chain B residue 96 ILE Chi-restraints excluded: chain B residue 128 ASN Chi-restraints excluded: chain B residue 147 PHE Chi-restraints excluded: chain B residue 250 LEU Chi-restraints excluded: chain C residue 71 LEU Chi-restraints excluded: chain C residue 72 PHE Chi-restraints excluded: chain C residue 95 LEU Chi-restraints excluded: chain C residue 99 VAL Chi-restraints excluded: chain D residue 71 LEU Chi-restraints excluded: chain D residue 72 PHE Chi-restraints excluded: chain D residue 93 MET Chi-restraints excluded: chain D residue 96 VAL Chi-restraints excluded: chain F residue 40 ASP Chi-restraints excluded: chain F residue 45 LEU Chi-restraints excluded: chain F residue 46 ILE Chi-restraints excluded: chain F residue 56 VAL Chi-restraints excluded: chain G residue 53 LEU Chi-restraints excluded: chain I residue 48 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 52 optimal weight: 4.9990 chunk 6 optimal weight: 0.7980 chunk 21 optimal weight: 10.0000 chunk 25 optimal weight: 1.9990 chunk 62 optimal weight: 2.9990 chunk 38 optimal weight: 9.9990 chunk 36 optimal weight: 9.9990 chunk 69 optimal weight: 3.9990 chunk 5 optimal weight: 2.9990 chunk 34 optimal weight: 0.9990 chunk 86 optimal weight: 4.9990 overall best weight: 1.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 238 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3846 r_free = 0.3846 target = 0.071364 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.053247 restraints weight = 31627.588| |-----------------------------------------------------------------------------| r_work (start): 0.3399 rms_B_bonded: 5.11 r_work (final): 0.3399 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8038 moved from start: 0.5586 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 7621 Z= 0.164 Angle : 0.832 11.493 10299 Z= 0.408 Chirality : 0.048 0.287 1143 Planarity : 0.005 0.049 1310 Dihedral : 7.255 59.951 1055 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 13.19 Ramachandran Plot: Outliers : 0.22 % Allowed : 7.10 % Favored : 92.69 % Rotamer: Outliers : 4.62 % Allowed : 23.62 % Favored : 71.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.33 (0.28), residues: 916 helix: 2.78 (0.28), residues: 310 sheet: 1.23 (0.25), residues: 370 loop : -2.52 (0.39), residues: 236 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP G 54 HIS 0.005 0.001 HIS B 238 PHE 0.018 0.002 PHE I 31 TYR 0.033 0.002 TYR J 34 ARG 0.005 0.001 ARG A 173 Details of bonding type rmsd hydrogen bonds : bond 0.04594 ( 518) hydrogen bonds : angle 4.99614 ( 1494) covalent geometry : bond 0.00360 ( 7621) covalent geometry : angle 0.83192 (10299) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1832 Ramachandran restraints generated. 916 Oldfield, 0 Emsley, 916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1832 Ramachandran restraints generated. 916 Oldfield, 0 Emsley, 916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 213 residues out of total 800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 176 time to evaluate : 0.802 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 128 ASN cc_start: 0.8013 (OUTLIER) cc_final: 0.7359 (t0) REVERT: A 150 LEU cc_start: 0.9286 (mp) cc_final: 0.8720 (tt) REVERT: A 154 MET cc_start: 0.8600 (ttt) cc_final: 0.8218 (tpt) REVERT: A 280 ASP cc_start: 0.8941 (p0) cc_final: 0.8651 (p0) REVERT: B 128 ASN cc_start: 0.7560 (OUTLIER) cc_final: 0.7082 (t0) REVERT: B 150 LEU cc_start: 0.9276 (mp) cc_final: 0.8695 (tt) REVERT: B 154 MET cc_start: 0.8502 (ttt) cc_final: 0.8140 (tpt) REVERT: B 280 ASP cc_start: 0.8937 (p0) cc_final: 0.8650 (p0) REVERT: C 97 LEU cc_start: 0.9359 (tp) cc_final: 0.8863 (tp) REVERT: C 101 PHE cc_start: 0.9317 (m-80) cc_final: 0.8898 (m-80) REVERT: C 108 MET cc_start: 0.9529 (mmp) cc_final: 0.9209 (mmp) REVERT: E 62 LEU cc_start: 0.9452 (OUTLIER) cc_final: 0.9247 (mm) REVERT: I 38 LEU cc_start: 0.9104 (mm) cc_final: 0.8805 (mm) outliers start: 37 outliers final: 18 residues processed: 196 average time/residue: 0.1841 time to fit residues: 48.3023 Evaluate side-chains 176 residues out of total 800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 155 time to evaluate : 0.804 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 THR Chi-restraints excluded: chain A residue 128 ASN Chi-restraints excluded: chain A residue 147 PHE Chi-restraints excluded: chain A residue 218 VAL Chi-restraints excluded: chain A residue 250 LEU Chi-restraints excluded: chain B residue 82 THR Chi-restraints excluded: chain B residue 128 ASN Chi-restraints excluded: chain B residue 147 PHE Chi-restraints excluded: chain B residue 218 VAL Chi-restraints excluded: chain B residue 250 LEU Chi-restraints excluded: chain C residue 71 LEU Chi-restraints excluded: chain C residue 72 PHE Chi-restraints excluded: chain C residue 95 LEU Chi-restraints excluded: chain C residue 99 VAL Chi-restraints excluded: chain D residue 71 LEU Chi-restraints excluded: chain D residue 72 PHE Chi-restraints excluded: chain D residue 114 LEU Chi-restraints excluded: chain E residue 62 LEU Chi-restraints excluded: chain F residue 45 LEU Chi-restraints excluded: chain F residue 46 ILE Chi-restraints excluded: chain I residue 48 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 71 optimal weight: 0.0050 chunk 82 optimal weight: 0.7980 chunk 48 optimal weight: 5.9990 chunk 86 optimal weight: 3.9990 chunk 83 optimal weight: 3.9990 chunk 85 optimal weight: 1.9990 chunk 50 optimal weight: 4.9990 chunk 4 optimal weight: 3.9990 chunk 13 optimal weight: 0.0020 chunk 55 optimal weight: 0.7980 chunk 15 optimal weight: 0.0270 overall best weight: 0.3260 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 167 GLN B 167 GLN ** B 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 116 GLN D 116 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3854 r_free = 0.3854 target = 0.072233 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.054450 restraints weight = 31926.351| |-----------------------------------------------------------------------------| r_work (start): 0.3434 rms_B_bonded: 5.15 r_work (final): 0.3434 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8003 moved from start: 0.6055 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 7621 Z= 0.155 Angle : 0.901 15.003 10299 Z= 0.420 Chirality : 0.049 0.282 1143 Planarity : 0.005 0.048 1310 Dihedral : 6.979 55.864 1053 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 12.73 Ramachandran Plot: Outliers : 0.22 % Allowed : 5.46 % Favored : 94.32 % Rotamer: Outliers : 3.62 % Allowed : 26.75 % Favored : 69.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.50 (0.29), residues: 916 helix: 2.83 (0.29), residues: 310 sheet: 1.20 (0.26), residues: 372 loop : -2.07 (0.43), residues: 234 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP G 54 HIS 0.005 0.001 HIS B 238 PHE 0.023 0.002 PHE I 31 TYR 0.052 0.001 TYR J 34 ARG 0.011 0.001 ARG B 293 Details of bonding type rmsd hydrogen bonds : bond 0.04121 ( 518) hydrogen bonds : angle 4.83069 ( 1494) covalent geometry : bond 0.00320 ( 7621) covalent geometry : angle 0.90066 (10299) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1832 Ramachandran restraints generated. 916 Oldfield, 0 Emsley, 916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1832 Ramachandran restraints generated. 916 Oldfield, 0 Emsley, 916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 172 time to evaluate : 1.082 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 116 ASN cc_start: 0.9041 (p0) cc_final: 0.8803 (m-40) REVERT: A 128 ASN cc_start: 0.7889 (OUTLIER) cc_final: 0.7288 (t0) REVERT: A 150 LEU cc_start: 0.9304 (mp) cc_final: 0.8694 (tt) REVERT: A 154 MET cc_start: 0.8527 (ttt) cc_final: 0.8162 (tpt) REVERT: A 235 LEU cc_start: 0.9243 (tt) cc_final: 0.9031 (tp) REVERT: A 280 ASP cc_start: 0.8961 (p0) cc_final: 0.8628 (p0) REVERT: A 322 TRP cc_start: 0.8803 (m100) cc_final: 0.8500 (m-90) REVERT: B 116 ASN cc_start: 0.9027 (p0) cc_final: 0.8823 (m-40) REVERT: B 128 ASN cc_start: 0.7354 (OUTLIER) cc_final: 0.6877 (t0) REVERT: B 150 LEU cc_start: 0.9289 (mp) cc_final: 0.8717 (tt) REVERT: B 154 MET cc_start: 0.8482 (ttt) cc_final: 0.8095 (tpt) REVERT: B 280 ASP cc_start: 0.8897 (p0) cc_final: 0.8562 (p0) REVERT: B 296 ASP cc_start: 0.9053 (t0) cc_final: 0.8728 (t0) REVERT: C 97 LEU cc_start: 0.9304 (tp) cc_final: 0.8761 (tp) REVERT: C 101 PHE cc_start: 0.9295 (m-80) cc_final: 0.8897 (m-80) REVERT: C 108 MET cc_start: 0.9572 (mmp) cc_final: 0.9277 (mmp) REVERT: D 108 MET cc_start: 0.9614 (mmp) cc_final: 0.9413 (mmp) REVERT: E 62 LEU cc_start: 0.9486 (OUTLIER) cc_final: 0.9248 (mm) REVERT: F 32 TYR cc_start: 0.8540 (t80) cc_final: 0.8197 (t80) REVERT: I 34 TYR cc_start: 0.9161 (t80) cc_final: 0.8930 (t80) REVERT: I 38 LEU cc_start: 0.9228 (mm) cc_final: 0.8827 (mm) REVERT: J 29 ARG cc_start: 0.9345 (mtm180) cc_final: 0.8944 (mpp80) outliers start: 29 outliers final: 15 residues processed: 186 average time/residue: 0.1776 time to fit residues: 45.2887 Evaluate side-chains 175 residues out of total 800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 157 time to evaluate : 0.807 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 109 LEU Chi-restraints excluded: chain A residue 128 ASN Chi-restraints excluded: chain A residue 147 PHE Chi-restraints excluded: chain A residue 218 VAL Chi-restraints excluded: chain A residue 250 LEU Chi-restraints excluded: chain B residue 82 THR Chi-restraints excluded: chain B residue 128 ASN Chi-restraints excluded: chain B residue 147 PHE Chi-restraints excluded: chain B residue 218 VAL Chi-restraints excluded: chain B residue 250 LEU Chi-restraints excluded: chain C residue 71 LEU Chi-restraints excluded: chain D residue 71 LEU Chi-restraints excluded: chain D residue 72 PHE Chi-restraints excluded: chain E residue 62 LEU Chi-restraints excluded: chain F residue 24 VAL Chi-restraints excluded: chain F residue 45 LEU Chi-restraints excluded: chain H residue 34 LEU Chi-restraints excluded: chain I residue 48 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 39 optimal weight: 5.9990 chunk 62 optimal weight: 5.9990 chunk 47 optimal weight: 9.9990 chunk 15 optimal weight: 9.9990 chunk 65 optimal weight: 2.9990 chunk 25 optimal weight: 6.9990 chunk 30 optimal weight: 5.9990 chunk 4 optimal weight: 3.9990 chunk 67 optimal weight: 6.9990 chunk 70 optimal weight: 2.9990 chunk 29 optimal weight: 0.7980 overall best weight: 3.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 238 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 311 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 112 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3804 r_free = 0.3804 target = 0.069648 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.052025 restraints weight = 32335.402| |-----------------------------------------------------------------------------| r_work (start): 0.3364 rms_B_bonded: 4.97 r_work (final): 0.3364 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8084 moved from start: 0.6394 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 7621 Z= 0.202 Angle : 0.864 11.980 10299 Z= 0.412 Chirality : 0.048 0.249 1143 Planarity : 0.005 0.060 1310 Dihedral : 7.414 59.109 1050 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 15.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.33 % Favored : 93.67 % Rotamer: Outliers : 4.62 % Allowed : 26.12 % Favored : 69.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.47 (0.29), residues: 916 helix: 2.81 (0.29), residues: 310 sheet: 1.21 (0.25), residues: 368 loop : -2.08 (0.42), residues: 238 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP E 57 HIS 0.005 0.001 HIS B 238 PHE 0.022 0.002 PHE E 41 TYR 0.019 0.002 TYR A 129 ARG 0.007 0.001 ARG B 293 Details of bonding type rmsd hydrogen bonds : bond 0.04435 ( 518) hydrogen bonds : angle 4.90066 ( 1494) covalent geometry : bond 0.00450 ( 7621) covalent geometry : angle 0.86416 (10299) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1832 Ramachandran restraints generated. 916 Oldfield, 0 Emsley, 916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1832 Ramachandran restraints generated. 916 Oldfield, 0 Emsley, 916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 159 time to evaluate : 0.913 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 116 ASN cc_start: 0.9102 (p0) cc_final: 0.8901 (m-40) REVERT: A 128 ASN cc_start: 0.7899 (OUTLIER) cc_final: 0.7310 (t0) REVERT: A 154 MET cc_start: 0.8526 (ttt) cc_final: 0.8121 (tpt) REVERT: A 280 ASP cc_start: 0.8989 (p0) cc_final: 0.8672 (p0) REVERT: B 280 ASP cc_start: 0.8981 (p0) cc_final: 0.8648 (p0) REVERT: C 97 LEU cc_start: 0.9342 (tp) cc_final: 0.8771 (tp) REVERT: C 101 PHE cc_start: 0.9314 (m-80) cc_final: 0.8892 (m-80) REVERT: C 108 MET cc_start: 0.9574 (mmp) cc_final: 0.9206 (mmp) REVERT: E 62 LEU cc_start: 0.9470 (OUTLIER) cc_final: 0.9218 (mm) REVERT: F 47 LEU cc_start: 0.9747 (tt) cc_final: 0.9502 (pp) REVERT: I 38 LEU cc_start: 0.9252 (mm) cc_final: 0.8890 (mm) REVERT: J 29 ARG cc_start: 0.9315 (mtm180) cc_final: 0.8900 (mtm180) REVERT: J 45 LEU cc_start: 0.8998 (pp) cc_final: 0.8679 (mp) outliers start: 37 outliers final: 24 residues processed: 179 average time/residue: 0.1735 time to fit residues: 42.7686 Evaluate side-chains 176 residues out of total 800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 150 time to evaluate : 0.876 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 THR Chi-restraints excluded: chain A residue 96 ILE Chi-restraints excluded: chain A residue 128 ASN Chi-restraints excluded: chain A residue 147 PHE Chi-restraints excluded: chain A residue 191 ASP Chi-restraints excluded: chain A residue 218 VAL Chi-restraints excluded: chain A residue 228 CYS Chi-restraints excluded: chain A residue 250 LEU Chi-restraints excluded: chain B residue 82 THR Chi-restraints excluded: chain B residue 96 ILE Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 147 PHE Chi-restraints excluded: chain B residue 218 VAL Chi-restraints excluded: chain B residue 250 LEU Chi-restraints excluded: chain C residue 71 LEU Chi-restraints excluded: chain C residue 72 PHE Chi-restraints excluded: chain C residue 104 GLU Chi-restraints excluded: chain D residue 71 LEU Chi-restraints excluded: chain D residue 72 PHE Chi-restraints excluded: chain D residue 114 LEU Chi-restraints excluded: chain E residue 62 LEU Chi-restraints excluded: chain F residue 51 LEU Chi-restraints excluded: chain G residue 32 ILE Chi-restraints excluded: chain G residue 36 PHE Chi-restraints excluded: chain H residue 32 ILE Chi-restraints excluded: chain I residue 48 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 77 optimal weight: 20.0000 chunk 29 optimal weight: 4.9990 chunk 67 optimal weight: 10.0000 chunk 9 optimal weight: 4.9990 chunk 1 optimal weight: 3.9990 chunk 73 optimal weight: 0.9980 chunk 28 optimal weight: 9.9990 chunk 65 optimal weight: 9.9990 chunk 13 optimal weight: 0.0670 chunk 23 optimal weight: 4.9990 chunk 61 optimal weight: 20.0000 overall best weight: 3.0124 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 238 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 112 HIS ** B 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 113 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 = 0.3799 r_free = 0.3799 target = 0.068958 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.051684 restraints weight = 32357.806| |-----------------------------------------------------------------------------| r_work (start): 0.3365 rms_B_bonded: 4.97 r_work (final): 0.3365 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8074 moved from start: 0.6675 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 7621 Z= 0.186 Angle : 0.893 13.304 10299 Z= 0.416 Chirality : 0.048 0.261 1143 Planarity : 0.005 0.051 1310 Dihedral : 7.356 57.750 1050 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 14.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.00 % Favored : 94.00 % Rotamer: Outliers : 3.38 % Allowed : 27.62 % Favored : 69.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.27 (0.29), residues: 916 helix: 2.61 (0.29), residues: 310 sheet: 0.99 (0.25), residues: 378 loop : -2.06 (0.44), residues: 228 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP E 57 HIS 0.005 0.001 HIS B 117 PHE 0.024 0.002 PHE E 41 TYR 0.016 0.002 TYR J 34 ARG 0.004 0.001 ARG A 293 Details of bonding type rmsd hydrogen bonds : bond 0.04313 ( 518) hydrogen bonds : angle 4.83507 ( 1494) covalent geometry : bond 0.00409 ( 7621) covalent geometry : angle 0.89269 (10299) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1832 Ramachandran restraints generated. 916 Oldfield, 0 Emsley, 916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1832 Ramachandran restraints generated. 916 Oldfield, 0 Emsley, 916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 155 time to evaluate : 0.807 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 128 ASN cc_start: 0.7890 (OUTLIER) cc_final: 0.7209 (t0) REVERT: A 154 MET cc_start: 0.8563 (ttt) cc_final: 0.8011 (tpt) REVERT: A 280 ASP cc_start: 0.9005 (p0) cc_final: 0.8683 (p0) REVERT: B 198 ASP cc_start: 0.9240 (p0) cc_final: 0.8901 (t0) REVERT: B 280 ASP cc_start: 0.8993 (p0) cc_final: 0.8650 (p0) REVERT: C 97 LEU cc_start: 0.9357 (tp) cc_final: 0.8777 (tp) REVERT: C 101 PHE cc_start: 0.9322 (m-80) cc_final: 0.8904 (m-80) REVERT: C 108 MET cc_start: 0.9495 (mmp) cc_final: 0.9210 (mmp) REVERT: C 113 GLN cc_start: 0.9410 (mm-40) cc_final: 0.9089 (mm-40) REVERT: E 62 LEU cc_start: 0.9446 (OUTLIER) cc_final: 0.9212 (mm) REVERT: F 47 LEU cc_start: 0.9760 (tt) cc_final: 0.9541 (pp) REVERT: J 29 ARG cc_start: 0.9330 (mtm180) cc_final: 0.8839 (mpp80) outliers start: 27 outliers final: 17 residues processed: 166 average time/residue: 0.1785 time to fit residues: 41.1939 Evaluate side-chains 168 residues out of total 800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 149 time to evaluate : 0.827 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 THR Chi-restraints excluded: chain A residue 128 ASN Chi-restraints excluded: chain A residue 147 PHE Chi-restraints excluded: chain A residue 191 ASP Chi-restraints excluded: chain A residue 228 CYS Chi-restraints excluded: chain A residue 250 LEU Chi-restraints excluded: chain A residue 291 SER Chi-restraints excluded: chain B residue 82 THR Chi-restraints excluded: chain B residue 147 PHE Chi-restraints excluded: chain B residue 250 LEU Chi-restraints excluded: chain C residue 71 LEU Chi-restraints excluded: chain C residue 104 GLU Chi-restraints excluded: chain D residue 71 LEU Chi-restraints excluded: chain D residue 72 PHE Chi-restraints excluded: chain D residue 96 VAL Chi-restraints excluded: chain E residue 47 LEU Chi-restraints excluded: chain E residue 62 LEU Chi-restraints excluded: chain G residue 32 ILE Chi-restraints excluded: chain G residue 36 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 7 optimal weight: 9.9990 chunk 18 optimal weight: 9.9990 chunk 8 optimal weight: 1.9990 chunk 39 optimal weight: 7.9990 chunk 68 optimal weight: 0.7980 chunk 35 optimal weight: 1.9990 chunk 23 optimal weight: 0.0270 chunk 62 optimal weight: 0.9990 chunk 55 optimal weight: 0.9980 chunk 44 optimal weight: 7.9990 chunk 3 optimal weight: 2.9990 overall best weight: 0.9642 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 112 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3825 r_free = 0.3825 target = 0.070547 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.053120 restraints weight = 32185.916| |-----------------------------------------------------------------------------| r_work (start): 0.3400 rms_B_bonded: 5.02 r_work (final): 0.3400 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8048 moved from start: 0.6834 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 7621 Z= 0.141 Angle : 0.893 15.049 10299 Z= 0.409 Chirality : 0.047 0.171 1143 Planarity : 0.005 0.050 1310 Dihedral : 7.152 59.491 1050 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 12.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.00 % Favored : 94.00 % Rotamer: Outliers : 2.62 % Allowed : 29.38 % Favored : 68.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.43 (0.29), residues: 916 helix: 2.60 (0.29), residues: 316 sheet: 1.20 (0.26), residues: 370 loop : -2.02 (0.44), residues: 230 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP E 57 HIS 0.004 0.001 HIS A 117 PHE 0.027 0.002 PHE I 31 TYR 0.021 0.001 TYR J 34 ARG 0.004 0.000 ARG B 88 Details of bonding type rmsd hydrogen bonds : bond 0.04074 ( 518) hydrogen bonds : angle 4.63751 ( 1494) covalent geometry : bond 0.00300 ( 7621) covalent geometry : angle 0.89349 (10299) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1832 Ramachandran restraints generated. 916 Oldfield, 0 Emsley, 916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1832 Ramachandran restraints generated. 916 Oldfield, 0 Emsley, 916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 161 time to evaluate : 0.956 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 128 ASN cc_start: 0.7791 (OUTLIER) cc_final: 0.7122 (t0) REVERT: A 154 MET cc_start: 0.8503 (ttt) cc_final: 0.8066 (tpt) REVERT: A 280 ASP cc_start: 0.8956 (p0) cc_final: 0.8596 (p0) REVERT: B 154 MET cc_start: 0.8301 (ttt) cc_final: 0.7726 (tpt) REVERT: B 198 ASP cc_start: 0.9207 (p0) cc_final: 0.8884 (t0) REVERT: B 280 ASP cc_start: 0.8978 (p0) cc_final: 0.8602 (p0) REVERT: C 97 LEU cc_start: 0.9301 (tp) cc_final: 0.8657 (tp) REVERT: C 101 PHE cc_start: 0.9278 (m-80) cc_final: 0.8870 (m-80) REVERT: E 62 LEU cc_start: 0.9446 (mm) cc_final: 0.9194 (mm) REVERT: I 20 MET cc_start: 0.9511 (ptp) cc_final: 0.9296 (ptp) REVERT: I 23 ASP cc_start: 0.9253 (m-30) cc_final: 0.9046 (p0) REVERT: J 31 PHE cc_start: 0.9400 (t80) cc_final: 0.9123 (t80) outliers start: 21 outliers final: 13 residues processed: 170 average time/residue: 0.1798 time to fit residues: 41.8241 Evaluate side-chains 164 residues out of total 800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 150 time to evaluate : 0.836 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 THR Chi-restraints excluded: chain A residue 128 ASN Chi-restraints excluded: chain A residue 147 PHE Chi-restraints excluded: chain A residue 250 LEU Chi-restraints excluded: chain B residue 82 THR Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 147 PHE Chi-restraints excluded: chain C residue 71 LEU Chi-restraints excluded: chain C residue 104 GLU Chi-restraints excluded: chain C residue 112 GLN Chi-restraints excluded: chain D residue 71 LEU Chi-restraints excluded: chain D residue 72 PHE Chi-restraints excluded: chain E residue 47 LEU Chi-restraints excluded: chain F residue 45 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 30 optimal weight: 0.9980 chunk 48 optimal weight: 6.9990 chunk 51 optimal weight: 3.9990 chunk 25 optimal weight: 0.9980 chunk 63 optimal weight: 1.9990 chunk 83 optimal weight: 1.9990 chunk 54 optimal weight: 2.9990 chunk 35 optimal weight: 5.9990 chunk 49 optimal weight: 10.0000 chunk 78 optimal weight: 5.9990 chunk 43 optimal weight: 10.0000 overall best weight: 1.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 116 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3809 r_free = 0.3809 target = 0.069814 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.052555 restraints weight = 32571.706| |-----------------------------------------------------------------------------| r_work (start): 0.3390 rms_B_bonded: 5.01 r_work (final): 0.3390 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8062 moved from start: 0.6965 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 7621 Z= 0.154 Angle : 0.937 15.377 10299 Z= 0.426 Chirality : 0.049 0.422 1143 Planarity : 0.005 0.050 1310 Dihedral : 7.138 58.417 1050 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 14.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.11 % Favored : 93.89 % Rotamer: Outliers : 2.38 % Allowed : 30.62 % Favored : 67.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.36 (0.29), residues: 916 helix: 2.48 (0.29), residues: 316 sheet: 1.19 (0.26), residues: 372 loop : -2.01 (0.45), residues: 228 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP E 57 HIS 0.004 0.001 HIS A 238 PHE 0.025 0.002 PHE C 92 TYR 0.017 0.001 TYR I 34 ARG 0.005 0.001 ARG B 88 Details of bonding type rmsd hydrogen bonds : bond 0.04105 ( 518) hydrogen bonds : angle 4.66246 ( 1494) covalent geometry : bond 0.00340 ( 7621) covalent geometry : angle 0.93665 (10299) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1832 Ramachandran restraints generated. 916 Oldfield, 0 Emsley, 916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1832 Ramachandran restraints generated. 916 Oldfield, 0 Emsley, 916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 153 time to evaluate : 1.384 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 88 ARG cc_start: 0.8467 (ttm110) cc_final: 0.8180 (ttm110) REVERT: A 128 ASN cc_start: 0.7743 (OUTLIER) cc_final: 0.7075 (t0) REVERT: A 154 MET cc_start: 0.8500 (ttt) cc_final: 0.8072 (tpt) REVERT: A 280 ASP cc_start: 0.9013 (p0) cc_final: 0.8669 (p0) REVERT: B 88 ARG cc_start: 0.8455 (ttm110) cc_final: 0.8164 (ttm110) REVERT: B 154 MET cc_start: 0.8330 (ttt) cc_final: 0.7763 (tpt) REVERT: B 198 ASP cc_start: 0.9279 (p0) cc_final: 0.8996 (t0) REVERT: B 280 ASP cc_start: 0.9024 (p0) cc_final: 0.8673 (p0) REVERT: C 97 LEU cc_start: 0.9322 (tp) cc_final: 0.9038 (tp) REVERT: E 62 LEU cc_start: 0.9452 (OUTLIER) cc_final: 0.9204 (mm) outliers start: 19 outliers final: 13 residues processed: 162 average time/residue: 0.2748 time to fit residues: 63.2638 Evaluate side-chains 163 residues out of total 800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 148 time to evaluate : 1.059 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 THR Chi-restraints excluded: chain A residue 128 ASN Chi-restraints excluded: chain A residue 147 PHE Chi-restraints excluded: chain A residue 250 LEU Chi-restraints excluded: chain B residue 82 THR Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 147 PHE Chi-restraints excluded: chain C residue 71 LEU Chi-restraints excluded: chain C residue 104 GLU Chi-restraints excluded: chain D residue 71 LEU Chi-restraints excluded: chain D residue 72 PHE Chi-restraints excluded: chain D residue 96 VAL Chi-restraints excluded: chain E residue 47 LEU Chi-restraints excluded: chain E residue 62 LEU Chi-restraints excluded: chain F residue 45 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 22 optimal weight: 5.9990 chunk 74 optimal weight: 5.9990 chunk 1 optimal weight: 2.9990 chunk 45 optimal weight: 6.9990 chunk 79 optimal weight: 9.9990 chunk 8 optimal weight: 6.9990 chunk 55 optimal weight: 3.9990 chunk 87 optimal weight: 2.9990 chunk 17 optimal weight: 10.0000 chunk 38 optimal weight: 8.9990 chunk 59 optimal weight: 3.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 238 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3774 r_free = 0.3774 target = 0.068224 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.050789 restraints weight = 33280.359| |-----------------------------------------------------------------------------| r_work (start): 0.3334 rms_B_bonded: 5.00 r_work (final): 0.3334 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8116 moved from start: 0.7173 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 7621 Z= 0.229 Angle : 0.965 14.494 10299 Z= 0.452 Chirality : 0.049 0.379 1143 Planarity : 0.005 0.070 1310 Dihedral : 7.525 58.902 1050 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 17.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.88 % Favored : 93.12 % Rotamer: Outliers : 2.62 % Allowed : 30.50 % Favored : 66.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.13 (0.29), residues: 916 helix: 2.08 (0.28), residues: 316 sheet: 1.14 (0.26), residues: 374 loop : -1.96 (0.46), residues: 226 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP A 259 HIS 0.004 0.001 HIS A 130 PHE 0.026 0.002 PHE C 92 TYR 0.018 0.002 TYR B 129 ARG 0.014 0.001 ARG C 117 Details of bonding type rmsd hydrogen bonds : bond 0.04523 ( 518) hydrogen bonds : angle 4.87006 ( 1494) covalent geometry : bond 0.00507 ( 7621) covalent geometry : angle 0.96539 (10299) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1832 Ramachandran restraints generated. 916 Oldfield, 0 Emsley, 916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1832 Ramachandran restraints generated. 916 Oldfield, 0 Emsley, 916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 145 time to evaluate : 0.793 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 128 ASN cc_start: 0.7919 (OUTLIER) cc_final: 0.7469 (t0) REVERT: A 280 ASP cc_start: 0.9013 (p0) cc_final: 0.8676 (p0) REVERT: B 198 ASP cc_start: 0.9318 (p0) cc_final: 0.8970 (t0) REVERT: B 280 ASP cc_start: 0.9009 (p0) cc_final: 0.8665 (p0) REVERT: C 97 LEU cc_start: 0.9342 (tp) cc_final: 0.8685 (tp) REVERT: C 101 PHE cc_start: 0.9355 (m-80) cc_final: 0.8957 (m-80) REVERT: E 62 LEU cc_start: 0.9426 (OUTLIER) cc_final: 0.9185 (mm) REVERT: I 20 MET cc_start: 0.9448 (ptp) cc_final: 0.9208 (ptp) REVERT: I 29 ARG cc_start: 0.9250 (mtm180) cc_final: 0.8932 (mtm180) REVERT: J 29 ARG cc_start: 0.9196 (mtp180) cc_final: 0.8685 (mpp80) outliers start: 21 outliers final: 15 residues processed: 154 average time/residue: 0.2992 time to fit residues: 64.1761 Evaluate side-chains 161 residues out of total 800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 144 time to evaluate : 1.139 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 THR Chi-restraints excluded: chain A residue 128 ASN Chi-restraints excluded: chain A residue 147 PHE Chi-restraints excluded: chain A residue 249 SER Chi-restraints excluded: chain A residue 250 LEU Chi-restraints excluded: chain A residue 291 SER Chi-restraints excluded: chain B residue 82 THR Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 147 PHE Chi-restraints excluded: chain B residue 218 VAL Chi-restraints excluded: chain C residue 71 LEU Chi-restraints excluded: chain C residue 104 GLU Chi-restraints excluded: chain D residue 71 LEU Chi-restraints excluded: chain D residue 72 PHE Chi-restraints excluded: chain D residue 96 VAL Chi-restraints excluded: chain E residue 62 LEU Chi-restraints excluded: chain G residue 32 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 5 optimal weight: 6.9990 chunk 9 optimal weight: 2.9990 chunk 44 optimal weight: 10.0000 chunk 60 optimal weight: 0.3980 chunk 55 optimal weight: 2.9990 chunk 37 optimal weight: 10.0000 chunk 72 optimal weight: 2.9990 chunk 50 optimal weight: 5.9990 chunk 74 optimal weight: 7.9990 chunk 67 optimal weight: 10.0000 chunk 69 optimal weight: 9.9990 overall best weight: 3.0788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 238 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3780 r_free = 0.3780 target = 0.068329 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.051088 restraints weight = 32717.055| |-----------------------------------------------------------------------------| r_work (start): 0.3343 rms_B_bonded: 4.98 r_work (final): 0.3343 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8103 moved from start: 0.7301 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 7621 Z= 0.193 Angle : 0.983 15.512 10299 Z= 0.455 Chirality : 0.050 0.376 1143 Planarity : 0.006 0.090 1310 Dihedral : 7.465 58.738 1050 Min Nonbonded Distance : 2.408 Molprobity Statistics. All-atom Clashscore : 16.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.88 % Favored : 93.12 % Rotamer: Outliers : 2.38 % Allowed : 31.00 % Favored : 66.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.17 (0.29), residues: 916 helix: 2.08 (0.29), residues: 316 sheet: 1.20 (0.26), residues: 374 loop : -1.96 (0.45), residues: 226 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 259 HIS 0.003 0.001 HIS A 112 PHE 0.028 0.002 PHE C 92 TYR 0.017 0.002 TYR I 34 ARG 0.017 0.001 ARG C 117 Details of bonding type rmsd hydrogen bonds : bond 0.04380 ( 518) hydrogen bonds : angle 4.81334 ( 1494) covalent geometry : bond 0.00433 ( 7621) covalent geometry : angle 0.98325 (10299) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1832 Ramachandran restraints generated. 916 Oldfield, 0 Emsley, 916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1832 Ramachandran restraints generated. 916 Oldfield, 0 Emsley, 916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 146 time to evaluate : 0.906 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 128 ASN cc_start: 0.7973 (OUTLIER) cc_final: 0.7525 (t0) REVERT: A 280 ASP cc_start: 0.9010 (p0) cc_final: 0.8674 (p0) REVERT: B 198 ASP cc_start: 0.9295 (p0) cc_final: 0.8925 (t0) REVERT: B 280 ASP cc_start: 0.9034 (p0) cc_final: 0.8709 (p0) REVERT: C 97 LEU cc_start: 0.9345 (tp) cc_final: 0.9040 (tp) REVERT: E 62 LEU cc_start: 0.9428 (OUTLIER) cc_final: 0.9176 (mm) REVERT: I 29 ARG cc_start: 0.9265 (mtm180) cc_final: 0.8941 (mtm180) REVERT: J 29 ARG cc_start: 0.9193 (mtp180) cc_final: 0.8676 (mpp80) outliers start: 19 outliers final: 15 residues processed: 154 average time/residue: 0.1836 time to fit residues: 38.7791 Evaluate side-chains 164 residues out of total 800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 147 time to evaluate : 0.856 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 THR Chi-restraints excluded: chain A residue 128 ASN Chi-restraints excluded: chain A residue 147 PHE Chi-restraints excluded: chain A residue 250 LEU Chi-restraints excluded: chain B residue 82 THR Chi-restraints excluded: chain B residue 118 THR Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 147 PHE Chi-restraints excluded: chain B residue 218 VAL Chi-restraints excluded: chain C residue 71 LEU Chi-restraints excluded: chain C residue 104 GLU Chi-restraints excluded: chain D residue 71 LEU Chi-restraints excluded: chain D residue 72 PHE Chi-restraints excluded: chain D residue 96 VAL Chi-restraints excluded: chain E residue 62 LEU Chi-restraints excluded: chain F residue 51 LEU Chi-restraints excluded: chain G residue 32 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 59 optimal weight: 0.9990 chunk 30 optimal weight: 2.9990 chunk 56 optimal weight: 9.9990 chunk 80 optimal weight: 0.7980 chunk 39 optimal weight: 5.9990 chunk 76 optimal weight: 0.3980 chunk 47 optimal weight: 10.0000 chunk 38 optimal weight: 5.9990 chunk 32 optimal weight: 0.9990 chunk 29 optimal weight: 5.9990 chunk 87 optimal weight: 4.9990 overall best weight: 1.2386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 238 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 140 GLN ** B 267 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 = 0.3800 r_free = 0.3800 target = 0.069510 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.052068 restraints weight = 32293.858| |-----------------------------------------------------------------------------| r_work (start): 0.3378 rms_B_bonded: 5.02 r_work (final): 0.3378 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8082 moved from start: 0.7380 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 7621 Z= 0.151 Angle : 0.987 15.513 10299 Z= 0.449 Chirality : 0.050 0.391 1143 Planarity : 0.005 0.076 1310 Dihedral : 7.211 59.704 1050 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 14.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.33 % Favored : 93.67 % Rotamer: Outliers : 2.12 % Allowed : 30.88 % Favored : 67.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.31 (0.29), residues: 916 helix: 2.29 (0.29), residues: 316 sheet: 1.22 (0.26), residues: 374 loop : -1.93 (0.45), residues: 226 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP E 57 HIS 0.004 0.001 HIS A 238 PHE 0.030 0.001 PHE C 92 TYR 0.015 0.001 TYR J 34 ARG 0.015 0.001 ARG C 117 Details of bonding type rmsd hydrogen bonds : bond 0.04079 ( 518) hydrogen bonds : angle 4.68772 ( 1494) covalent geometry : bond 0.00330 ( 7621) covalent geometry : angle 0.98675 (10299) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4118.00 seconds wall clock time: 73 minutes 0.36 seconds (4380.36 seconds total)