Starting phenix.real_space_refine on Tue Sep 24 10:00:02 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ck6_30382/09_2024/7ck6_30382.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ck6_30382/09_2024/7ck6_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ck6_30382/09_2024/7ck6_30382.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ck6_30382/09_2024/7ck6_30382.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ck6_30382/09_2024/7ck6_30382.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ck6_30382/09_2024/7ck6_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-5461/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: 5.04, per 1000 atoms: 0.68 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: 1.83 Conformation dependent library (CDL) restraints added in 1.0 seconds 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: 0.79 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: 2.08 Time building geometry restraints manager: 2.09 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: 0.960 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: 0.280 Check model and map are aligned: 0.060 Set scattering table: 0.070 Process input model: 20.090 Find NCS groups from input model: 0.250 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.730 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.490 ------------------------------------------------------------------------------- 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= 0.501 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 *********************** 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 fitting. 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: 0.2819 time to fit residues: 108.7768 Evaluate side-chains 178 residues out of total 800 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 165 time to evaluate : 0.889 ------------------------------------------------------------------------------- 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 238 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7599 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 0.051 7621 Z= 0.321 Angle : 0.912 11.253 10299 Z= 0.458 Chirality : 0.049 0.313 1143 Planarity : 0.006 0.055 1310 Dihedral : 7.803 55.103 1070 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 16.33 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: 2.61 (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 *********************** 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 fitting. rotamer outliers: 45 poor density : 186 time to evaluate : 1.107 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: C 97 LEU cc_start: 0.8877 (tp) cc_final: 0.8580 (tp) REVERT: I 17 LYS cc_start: 0.9622 (mttt) cc_final: 0.9232 (mtmt) REVERT: I 31 PHE cc_start: 0.8873 (t80) cc_final: 0.8648 (t80) REVERT: I 38 LEU cc_start: 0.9003 (mm) cc_final: 0.8798 (mm) REVERT: J 17 LYS cc_start: 0.9544 (mttt) cc_final: 0.9136 (mtmt) REVERT: J 31 PHE cc_start: 0.8944 (t80) cc_final: 0.8698 (t80) outliers start: 45 outliers final: 20 residues processed: 207 average time/residue: 0.2212 time to fit residues: 62.1742 Evaluate side-chains 176 residues out of total 800 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 156 time to evaluate : 0.831 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 96 ILE 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 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 44 optimal weight: 7.9990 chunk 24 optimal weight: 1.9990 chunk 66 optimal weight: 0.0570 chunk 54 optimal weight: 3.9990 chunk 22 optimal weight: 5.9990 chunk 80 optimal weight: 1.9990 chunk 86 optimal weight: 1.9990 chunk 71 optimal weight: 5.9990 chunk 79 optimal weight: 10.0000 chunk 27 optimal weight: 0.9990 chunk 64 optimal weight: 2.9990 overall best weight: 1.4106 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7575 moved from start: 0.5574 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 7621 Z= 0.221 Angle : 0.850 11.029 10299 Z= 0.412 Chirality : 0.049 0.309 1143 Planarity : 0.005 0.048 1310 Dihedral : 7.228 58.827 1055 Min Nonbonded Distance : 2.417 Molprobity Statistics. All-atom Clashscore : 12.86 Ramachandran Plot: Outliers : 0.22 % Allowed : 6.99 % Favored : 92.79 % Rotamer: Outliers : 4.25 % Allowed : 23.38 % Favored : 72.38 % 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: 1.25 (0.28), residues: 916 helix: 2.67 (0.28), residues: 310 sheet: 1.21 (0.25), residues: 370 loop : -2.55 (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 0.028 0.002 PHE C 101 TYR 0.032 0.002 TYR J 34 ARG 0.005 0.001 ARG A 173 *********************** 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 211 residues out of total 800 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 177 time to evaluate : 0.862 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 280 ASP cc_start: 0.7626 (p0) cc_final: 0.7323 (p0) REVERT: B 280 ASP cc_start: 0.7604 (p0) cc_final: 0.7261 (p0) REVERT: B 294 MET cc_start: 0.8123 (tpt) cc_final: 0.7687 (tpt) REVERT: E 64 ASP cc_start: 0.7233 (OUTLIER) cc_final: 0.6874 (t70) REVERT: F 64 ASP cc_start: 0.7135 (OUTLIER) cc_final: 0.6799 (t70) REVERT: I 16 MET cc_start: 0.9070 (ppp) cc_final: 0.8849 (ppp) REVERT: I 38 LEU cc_start: 0.8903 (mm) cc_final: 0.8537 (mm) outliers start: 34 outliers final: 19 residues processed: 197 average time/residue: 0.1899 time to fit residues: 49.8664 Evaluate side-chains 172 residues out of total 800 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 151 time to evaluate : 0.866 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 THR Chi-restraints excluded: chain A residue 109 LEU 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 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 64 ASP Chi-restraints excluded: chain F residue 45 LEU Chi-restraints excluded: chain F residue 46 ILE Chi-restraints excluded: chain F residue 64 ASP 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 79 optimal weight: 8.9990 chunk 60 optimal weight: 4.9990 chunk 41 optimal weight: 10.0000 chunk 8 optimal weight: 6.9990 chunk 38 optimal weight: 10.0000 chunk 53 optimal weight: 0.9980 chunk 80 optimal weight: 0.0670 chunk 85 optimal weight: 0.7980 chunk 76 optimal weight: 0.4980 chunk 22 optimal weight: 4.9990 chunk 70 optimal weight: 5.9990 overall best weight: 1.4720 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 167 GLN ** A 238 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7587 moved from start: 0.6078 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 7621 Z= 0.216 Angle : 0.879 14.286 10299 Z= 0.414 Chirality : 0.048 0.254 1143 Planarity : 0.005 0.048 1310 Dihedral : 7.127 55.984 1053 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 14.06 Ramachandran Plot: Outliers : 0.22 % Allowed : 5.68 % Favored : 94.10 % Rotamer: Outliers : 4.25 % Allowed : 26.00 % Favored : 69.75 % 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: 1.36 (0.29), residues: 916 helix: 2.72 (0.29), residues: 310 sheet: 1.21 (0.26), residues: 370 loop : -2.27 (0.42), residues: 236 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP G 54 HIS 0.005 0.001 HIS B 238 PHE 0.023 0.002 PHE J 31 TYR 0.018 0.001 TYR J 34 ARG 0.008 0.001 ARG B 293 *********************** 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 192 residues out of total 800 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 158 time to evaluate : 0.795 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: A 235 LEU cc_start: 0.8515 (tt) cc_final: 0.8310 (tp) REVERT: A 280 ASP cc_start: 0.7669 (p0) cc_final: 0.7344 (p0) REVERT: B 150 LEU cc_start: 0.8448 (mp) cc_final: 0.8245 (tt) REVERT: B 154 MET cc_start: 0.6726 (tpt) cc_final: 0.6523 (tpt) REVERT: B 280 ASP cc_start: 0.7662 (p0) cc_final: 0.7278 (p0) REVERT: E 32 TYR cc_start: 0.8376 (t80) cc_final: 0.8156 (t80) REVERT: E 64 ASP cc_start: 0.7293 (OUTLIER) cc_final: 0.6975 (t70) REVERT: F 32 TYR cc_start: 0.8263 (t80) cc_final: 0.7921 (t80) REVERT: F 64 ASP cc_start: 0.7194 (OUTLIER) cc_final: 0.6860 (t70) REVERT: I 38 LEU cc_start: 0.8912 (mm) cc_final: 0.8511 (mm) REVERT: J 29 ARG cc_start: 0.9000 (mtm180) cc_final: 0.8748 (mpp80) outliers start: 34 outliers final: 21 residues processed: 177 average time/residue: 0.1852 time to fit residues: 44.7024 Evaluate side-chains 167 residues out of total 800 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 144 time to evaluate : 0.788 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 THR Chi-restraints excluded: chain A residue 147 PHE Chi-restraints excluded: chain A residue 165 ILE 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 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 96 VAL Chi-restraints excluded: chain D residue 71 LEU Chi-restraints excluded: chain D residue 72 PHE Chi-restraints excluded: chain E residue 64 ASP Chi-restraints excluded: chain F residue 46 ILE Chi-restraints excluded: chain F residue 64 ASP Chi-restraints excluded: chain G residue 36 PHE Chi-restraints excluded: chain H residue 32 ILE Chi-restraints excluded: chain H residue 34 LEU Chi-restraints excluded: chain H residue 52 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 48 optimal weight: 7.9990 chunk 1 optimal weight: 8.9990 chunk 63 optimal weight: 0.9980 chunk 35 optimal weight: 10.0000 chunk 72 optimal weight: 7.9990 chunk 58 optimal weight: 2.9990 chunk 0 optimal weight: 8.9990 chunk 43 optimal weight: 10.0000 chunk 76 optimal weight: 3.9990 chunk 21 optimal weight: 6.9990 chunk 28 optimal weight: 9.9990 overall best weight: 4.5988 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7712 moved from start: 0.6551 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.036 7621 Z= 0.362 Angle : 0.904 11.699 10299 Z= 0.440 Chirality : 0.050 0.200 1143 Planarity : 0.006 0.060 1310 Dihedral : 7.791 56.843 1052 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 17.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.10 % Favored : 92.90 % Rotamer: Outliers : 5.12 % Allowed : 26.12 % Favored : 68.75 % 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: 1.12 (0.29), residues: 916 helix: 2.37 (0.29), residues: 310 sheet: 1.14 (0.26), residues: 370 loop : -2.29 (0.43), residues: 236 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP B 322 HIS 0.005 0.002 HIS B 238 PHE 0.020 0.002 PHE E 41 TYR 0.017 0.002 TYR B 275 ARG 0.005 0.001 ARG A 293 *********************** 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 188 residues out of total 800 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 147 time to evaluate : 0.872 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 280 ASP cc_start: 0.7879 (p0) cc_final: 0.7552 (p0) REVERT: B 280 ASP cc_start: 0.7870 (p0) cc_final: 0.7498 (p0) REVERT: C 95 LEU cc_start: 0.8711 (OUTLIER) cc_final: 0.8471 (mp) REVERT: C 113 GLN cc_start: 0.9102 (mm-40) cc_final: 0.8711 (mm-40) REVERT: E 64 ASP cc_start: 0.7301 (OUTLIER) cc_final: 0.6994 (t70) REVERT: F 45 LEU cc_start: 0.8489 (OUTLIER) cc_final: 0.8279 (pp) REVERT: F 64 ASP cc_start: 0.7215 (OUTLIER) cc_final: 0.6891 (t70) REVERT: I 16 MET cc_start: 0.9108 (ppp) cc_final: 0.8896 (ppp) REVERT: I 38 LEU cc_start: 0.8957 (mm) cc_final: 0.8630 (mm) REVERT: J 29 ARG cc_start: 0.9014 (mtm180) cc_final: 0.8574 (mpp80) outliers start: 41 outliers final: 23 residues processed: 168 average time/residue: 0.1714 time to fit residues: 39.2968 Evaluate side-chains 165 residues out of total 800 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 138 time to evaluate : 0.777 ------------------------------------------------------------------------------- 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 118 THR Chi-restraints excluded: chain A residue 147 PHE Chi-restraints excluded: chain A residue 165 ILE 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 96 ILE Chi-restraints excluded: chain B residue 118 THR Chi-restraints excluded: chain B residue 147 PHE 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 96 VAL 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 D residue 114 LEU Chi-restraints excluded: chain E residue 47 LEU Chi-restraints excluded: chain E residue 64 ASP Chi-restraints excluded: chain F residue 45 LEU Chi-restraints excluded: chain F residue 64 ASP Chi-restraints excluded: chain G residue 32 ILE Chi-restraints excluded: chain G residue 36 PHE Chi-restraints excluded: chain H residue 32 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 76 optimal weight: 0.9990 chunk 16 optimal weight: 1.9990 chunk 49 optimal weight: 5.9990 chunk 20 optimal weight: 4.9990 chunk 85 optimal weight: 0.0870 chunk 70 optimal weight: 0.7980 chunk 39 optimal weight: 6.9990 chunk 7 optimal weight: 7.9990 chunk 28 optimal weight: 9.9990 chunk 44 optimal weight: 7.9990 chunk 82 optimal weight: 0.1980 overall best weight: 0.8162 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 238 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 112 HIS ** B 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 112 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7623 moved from start: 0.6710 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 7621 Z= 0.200 Angle : 0.907 16.075 10299 Z= 0.414 Chirality : 0.049 0.307 1143 Planarity : 0.005 0.052 1310 Dihedral : 7.285 59.715 1050 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 12.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.90 % Favored : 94.10 % Rotamer: Outliers : 2.38 % Allowed : 28.88 % Favored : 68.75 % 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: 1.28 (0.29), residues: 916 helix: 2.50 (0.29), residues: 310 sheet: 1.20 (0.26), residues: 370 loop : -2.15 (0.43), residues: 236 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP G 54 HIS 0.003 0.001 HIS B 238 PHE 0.023 0.002 PHE E 41 TYR 0.021 0.001 TYR J 34 ARG 0.004 0.000 ARG A 293 *********************** 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 177 residues out of total 800 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 158 time to evaluate : 0.811 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: A 280 ASP cc_start: 0.7732 (p0) cc_final: 0.7372 (p0) REVERT: B 280 ASP cc_start: 0.7776 (p0) cc_final: 0.7402 (p0) REVERT: C 113 GLN cc_start: 0.9101 (mm-40) cc_final: 0.8754 (mm-40) REVERT: E 64 ASP cc_start: 0.7378 (OUTLIER) cc_final: 0.7168 (t70) REVERT: F 64 ASP cc_start: 0.7198 (OUTLIER) cc_final: 0.6869 (t70) REVERT: I 16 MET cc_start: 0.8979 (ppp) cc_final: 0.8778 (ppp) REVERT: J 29 ARG cc_start: 0.9010 (mtm180) cc_final: 0.8466 (mtm180) outliers start: 19 outliers final: 11 residues processed: 168 average time/residue: 0.1739 time to fit residues: 39.8390 Evaluate side-chains 161 residues out of total 800 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 148 time to evaluate : 0.880 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 THR Chi-restraints excluded: chain A residue 147 PHE Chi-restraints excluded: chain A residue 165 ILE Chi-restraints excluded: chain A residue 250 LEU Chi-restraints excluded: chain B residue 82 THR Chi-restraints excluded: chain B residue 147 PHE Chi-restraints excluded: chain C residue 71 LEU 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 64 ASP Chi-restraints excluded: chain F residue 45 LEU Chi-restraints excluded: chain F residue 64 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 9 optimal weight: 8.9990 chunk 48 optimal weight: 7.9990 chunk 62 optimal weight: 3.9990 chunk 71 optimal weight: 4.9990 chunk 47 optimal weight: 9.9990 chunk 84 optimal weight: 3.9990 chunk 53 optimal weight: 6.9990 chunk 51 optimal weight: 4.9990 chunk 39 optimal weight: 7.9990 chunk 52 optimal weight: 1.9990 chunk 33 optimal weight: 5.9990 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 130 HIS A 161 ASN ** 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: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7708 moved from start: 0.6921 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.061 7621 Z= 0.329 Angle : 0.920 15.198 10299 Z= 0.433 Chirality : 0.049 0.348 1143 Planarity : 0.005 0.050 1310 Dihedral : 7.526 58.227 1050 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 15.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.77 % Favored : 93.23 % Rotamer: Outliers : 3.62 % Allowed : 28.38 % 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: 1.08 (0.29), residues: 916 helix: 2.32 (0.29), residues: 310 sheet: 1.00 (0.26), residues: 374 loop : -2.10 (0.44), residues: 232 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP E 57 HIS 0.004 0.001 HIS B 238 PHE 0.025 0.002 PHE E 41 TYR 0.014 0.002 TYR B 129 ARG 0.005 0.001 ARG A 88 *********************** 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 175 residues out of total 800 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 146 time to evaluate : 0.808 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 280 ASP cc_start: 0.7892 (p0) cc_final: 0.7537 (p0) REVERT: B 280 ASP cc_start: 0.7880 (p0) cc_final: 0.7491 (p0) REVERT: C 113 GLN cc_start: 0.9316 (mm-40) cc_final: 0.9031 (mm-40) REVERT: I 16 MET cc_start: 0.9112 (ppp) cc_final: 0.8909 (ppp) REVERT: I 29 ARG cc_start: 0.9011 (mtm180) cc_final: 0.8480 (mtm180) REVERT: J 29 ARG cc_start: 0.9006 (mtm180) cc_final: 0.8545 (mpp80) REVERT: J 45 LEU cc_start: 0.8749 (pp) cc_final: 0.8434 (mp) outliers start: 29 outliers final: 18 residues processed: 161 average time/residue: 0.1773 time to fit residues: 39.0253 Evaluate side-chains 163 residues out of total 800 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 145 time to evaluate : 0.819 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 THR Chi-restraints excluded: chain A residue 147 PHE Chi-restraints excluded: chain A residue 165 ILE 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 133 VAL Chi-restraints excluded: chain B residue 147 PHE Chi-restraints excluded: chain B residue 249 SER Chi-restraints excluded: chain C residue 71 LEU Chi-restraints excluded: chain C residue 104 GLU Chi-restraints excluded: chain C residue 114 LEU 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 47 LEU Chi-restraints excluded: chain G residue 15 LEU Chi-restraints excluded: chain H residue 32 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 50 optimal weight: 2.9990 chunk 25 optimal weight: 4.9990 chunk 16 optimal weight: 7.9990 chunk 53 optimal weight: 6.9990 chunk 57 optimal weight: 0.9980 chunk 41 optimal weight: 9.9990 chunk 7 optimal weight: 5.9990 chunk 66 optimal weight: 5.9990 chunk 77 optimal weight: 7.9990 chunk 81 optimal weight: 10.0000 chunk 74 optimal weight: 0.9980 overall best weight: 3.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 130 HIS ** A 238 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 130 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 267 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7705 moved from start: 0.7128 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 7621 Z= 0.282 Angle : 0.945 14.238 10299 Z= 0.438 Chirality : 0.050 0.389 1143 Planarity : 0.005 0.050 1310 Dihedral : 7.522 59.565 1050 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 14.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.77 % Favored : 93.23 % Rotamer: Outliers : 3.75 % Allowed : 28.50 % Favored : 67.75 % 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: 1.07 (0.29), residues: 916 helix: 2.22 (0.29), residues: 316 sheet: 0.97 (0.26), residues: 374 loop : -2.05 (0.45), residues: 226 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP E 57 HIS 0.007 0.001 HIS B 130 PHE 0.040 0.002 PHE C 101 TYR 0.015 0.001 TYR J 34 ARG 0.006 0.001 ARG B 88 *********************** 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 180 residues out of total 800 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 150 time to evaluate : 0.883 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: B 280 ASP cc_start: 0.7833 (p0) cc_final: 0.7478 (p0) REVERT: C 113 GLN cc_start: 0.9220 (mm-40) cc_final: 0.8889 (mm-40) REVERT: I 16 MET cc_start: 0.9117 (ppp) cc_final: 0.8871 (ppp) REVERT: I 29 ARG cc_start: 0.8995 (mtm180) cc_final: 0.8680 (mtm180) outliers start: 30 outliers final: 19 residues processed: 166 average time/residue: 0.1724 time to fit residues: 39.2142 Evaluate side-chains 164 residues out of total 800 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 145 time to evaluate : 0.878 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 THR Chi-restraints excluded: chain A residue 138 THR Chi-restraints excluded: chain A residue 147 PHE Chi-restraints excluded: chain A residue 165 ILE 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 133 VAL 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 F residue 40 ASP Chi-restraints excluded: chain F residue 51 LEU Chi-restraints excluded: chain G residue 32 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 79 optimal weight: 5.9990 chunk 81 optimal weight: 7.9990 chunk 47 optimal weight: 9.9990 chunk 34 optimal weight: 0.0570 chunk 62 optimal weight: 2.9990 chunk 24 optimal weight: 0.3980 chunk 71 optimal weight: 10.0000 chunk 74 optimal weight: 5.9990 chunk 78 optimal weight: 5.9990 chunk 51 optimal weight: 8.9990 chunk 83 optimal weight: 3.9990 overall best weight: 2.6904 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 130 HIS ** A 238 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7703 moved from start: 0.7273 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 7621 Z= 0.263 Angle : 0.954 14.216 10299 Z= 0.442 Chirality : 0.050 0.407 1143 Planarity : 0.005 0.053 1310 Dihedral : 7.591 58.668 1050 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 14.79 Ramachandran Plot: Outliers : 0.11 % Allowed : 6.99 % Favored : 92.90 % Rotamer: Outliers : 2.62 % Allowed : 29.25 % Favored : 68.12 % 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: 1.09 (0.29), residues: 916 helix: 2.21 (0.29), residues: 316 sheet: 1.02 (0.26), residues: 372 loop : -2.05 (0.45), residues: 228 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 0.045 0.002 PHE C 101 TYR 0.016 0.001 TYR I 34 ARG 0.004 0.001 ARG B 88 *********************** 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 168 residues out of total 800 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 147 time to evaluate : 0.889 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: B 280 ASP cc_start: 0.7823 (p0) cc_final: 0.7461 (p0) REVERT: C 113 GLN cc_start: 0.9200 (mm-40) cc_final: 0.8800 (mm-40) REVERT: I 29 ARG cc_start: 0.8967 (mtm180) cc_final: 0.8628 (mtm180) REVERT: I 38 LEU cc_start: 0.8965 (OUTLIER) cc_final: 0.8634 (mm) REVERT: J 29 ARG cc_start: 0.8795 (mtp180) cc_final: 0.8583 (mpp80) outliers start: 21 outliers final: 17 residues processed: 158 average time/residue: 0.1846 time to fit residues: 39.3725 Evaluate side-chains 164 residues out of total 800 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 146 time to evaluate : 0.842 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 THR Chi-restraints excluded: chain A residue 138 THR Chi-restraints excluded: chain A residue 147 PHE Chi-restraints excluded: chain A residue 150 LEU 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 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 47 LEU Chi-restraints excluded: chain F residue 51 LEU Chi-restraints excluded: chain H residue 32 ILE Chi-restraints excluded: chain I residue 38 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 51 optimal weight: 9.9990 chunk 39 optimal weight: 8.9990 chunk 58 optimal weight: 0.6980 chunk 87 optimal weight: 5.9990 chunk 80 optimal weight: 0.0370 chunk 69 optimal weight: 2.9990 chunk 7 optimal weight: 7.9990 chunk 53 optimal weight: 0.9980 chunk 42 optimal weight: 4.9990 chunk 55 optimal weight: 5.9990 chunk 74 optimal weight: 5.9990 overall best weight: 1.9462 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 163 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 238 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 163 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7684 moved from start: 0.7376 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 7621 Z= 0.240 Angle : 1.000 15.790 10299 Z= 0.456 Chirality : 0.051 0.401 1143 Planarity : 0.005 0.052 1310 Dihedral : 7.466 59.201 1050 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 15.26 Ramachandran Plot: Outliers : 0.11 % Allowed : 6.77 % Favored : 93.12 % Rotamer: Outliers : 2.38 % Allowed : 30.12 % Favored : 67.50 % 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: 1.22 (0.29), residues: 916 helix: 2.32 (0.29), residues: 316 sheet: 1.14 (0.27), residues: 370 loop : -2.04 (0.44), residues: 230 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP E 57 HIS 0.003 0.001 HIS A 238 PHE 0.026 0.002 PHE E 41 TYR 0.068 0.002 TYR J 34 ARG 0.004 0.000 ARG B 88 ********************** 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 170 residues out of total 800 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 151 time to evaluate : 0.865 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: B 280 ASP cc_start: 0.7789 (p0) cc_final: 0.7422 (p0) REVERT: C 113 GLN cc_start: 0.9208 (mm-40) cc_final: 0.8817 (mm-40) REVERT: I 38 LEU cc_start: 0.8939 (OUTLIER) cc_final: 0.8617 (mm) REVERT: J 29 ARG cc_start: 0.8824 (mtp180) cc_final: 0.8534 (mpp80) outliers start: 19 outliers final: 15 residues processed: 160 average time/residue: 0.1718 time to fit residues: 37.6868 Evaluate side-chains 163 residues out of total 800 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 147 time to evaluate : 0.762 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 THR Chi-restraints excluded: chain A residue 138 THR 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 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 47 LEU Chi-restraints excluded: chain H residue 32 ILE Chi-restraints excluded: chain I residue 38 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 21 optimal weight: 7.9990 chunk 64 optimal weight: 0.6980 chunk 10 optimal weight: 9.9990 chunk 19 optimal weight: 3.9990 chunk 69 optimal weight: 0.9980 chunk 29 optimal weight: 2.9990 chunk 71 optimal weight: 0.9980 chunk 8 optimal weight: 5.9990 chunk 12 optimal weight: 5.9990 chunk 61 optimal weight: 10.0000 chunk 3 optimal weight: 1.9990 overall best weight: 1.5384 ------------------------------------------------------------------------------- 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 163 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3806 r_free = 0.3806 target = 0.069277 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.051953 restraints weight = 31818.706| |-----------------------------------------------------------------------------| r_work (start): 0.3381 rms_B_bonded: 4.99 r_work (final): 0.3381 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8070 moved from start: 0.7476 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= 0.228 Angle : 0.981 15.242 10299 Z= 0.451 Chirality : 0.051 0.391 1143 Planarity : 0.005 0.052 1310 Dihedral : 7.350 59.376 1050 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 14.33 Ramachandran Plot: Outliers : 0.11 % Allowed : 6.44 % Favored : 93.45 % Rotamer: Outliers : 2.50 % Allowed : 30.38 % Favored : 67.12 % 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: 1.25 (0.29), residues: 916 helix: 2.38 (0.29), residues: 316 sheet: 1.04 (0.27), residues: 374 loop : -1.89 (0.44), residues: 226 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP G 54 HIS 0.004 0.001 HIS A 238 PHE 0.027 0.002 PHE E 41 TYR 0.018 0.001 TYR I 34 ARG 0.004 0.001 ARG B 88 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1918.30 seconds wall clock time: 34 minutes 54.69 seconds (2094.69 seconds total)