Starting phenix.real_space_refine on Fri Aug 2 19:19:25 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wyi_37929/08_2024/8wyi_37929.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wyi_37929/08_2024/8wyi_37929.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wyi_37929/08_2024/8wyi_37929.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wyi_37929/08_2024/8wyi_37929.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wyi_37929/08_2024/8wyi_37929.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wyi_37929/08_2024/8wyi_37929.cif" } resolution = 3.9 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= 0.004 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 37 5.16 5 C 3018 2.51 5 N 743 2.21 5 O 861 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "d GLU 28": "OE1" <-> "OE2" Residue "d GLU 45": "OE1" <-> "OE2" Residue "e GLU 56": "OE1" <-> "OE2" Residue "e GLU 91": "OE1" <-> "OE2" Residue "e GLU 120": "OE1" <-> "OE2" Residue "e GLU 124": "OE1" <-> "OE2" Residue "f GLU 56": "OE1" <-> "OE2" Residue "g GLU 122": "OE1" <-> "OE2" Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/chem_data/mon_lib" Total number of atoms: 4659 Number of models: 1 Model: "" Number of chains: 8 Chain: "a" Number of atoms: 245 Number of conformers: 1 Conformer: "" Number of residues, atoms: 30, 245 Classifications: {'peptide': 30} Link IDs: {'PTRANS': 1, 'TRANS': 28} Chain: "b" Number of atoms: 226 Number of conformers: 1 Conformer: "" Number of residues, atoms: 28, 226 Classifications: {'peptide': 28} Link IDs: {'PTRANS': 1, 'TRANS': 26} Chain: "d" Number of atoms: 821 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 821 Classifications: {'peptide': 106} Link IDs: {'PTRANS': 3, 'TRANS': 102} Chain: "e" Number of atoms: 959 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 959 Classifications: {'peptide': 121} Link IDs: {'PTRANS': 5, 'TRANS': 115} Chain: "f" Number of atoms: 933 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 933 Classifications: {'peptide': 118} Link IDs: {'PTRANS': 5, 'TRANS': 112} Chain breaks: 1 Chain: "g" Number of atoms: 899 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 899 Classifications: {'peptide': 114} Link IDs: {'PTRANS': 2, 'TRANS': 111} Chain: "m" Number of atoms: 292 Number of conformers: 1 Conformer: "" Number of residues, atoms: 37, 292 Classifications: {'peptide': 37} Link IDs: {'TRANS': 36} Chain: "n" Number of atoms: 284 Number of conformers: 1 Conformer: "" Number of residues, atoms: 35, 284 Classifications: {'peptide': 35} Link IDs: {'TRANS': 34} Time building chain proxies: 3.16, per 1000 atoms: 0.68 Number of scatterers: 4659 At special positions: 0 Unit cell: (70.0245, 89.4159, 107.73, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 37 16.00 O 861 8.00 N 743 7.00 C 3018 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=8, symmetry=0 Simple disulfide: pdb=" SG CYS a 32 " - pdb=" SG CYS b 32 " distance=2.03 Simple disulfide: pdb=" SG CYS d 37 " - pdb=" SG CYS d 73 " distance=2.04 Simple disulfide: pdb=" SG CYS d 93 " - pdb=" SG CYS d 96 " distance=2.03 Simple disulfide: pdb=" SG CYS e 49 " - pdb=" SG CYS e 98 " distance=2.03 Simple disulfide: pdb=" SG CYS e 119 " - pdb=" SG CYS e 122 " distance=2.03 Simple disulfide: pdb=" SG CYS f 49 " - pdb=" SG CYS f 98 " distance=2.03 Simple disulfide: pdb=" SG CYS g 46 " - pdb=" SG CYS g 87 " distance=2.03 Simple disulfide: pdb=" SG CYS g 104 " - pdb=" SG CYS g 107 " distance=2.02 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 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: 1.97 Conformation dependent library (CDL) restraints added in 866.7 milliseconds 1142 Ramachandran restraints generated. 571 Oldfield, 0 Emsley, 571 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1094 Finding SS restraints... Secondary structure from input PDB file: 9 helices and 7 sheets defined 39.9% alpha, 7.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.45 Creating SS restraints... Processing helix chain 'a' and resid 27 through 55 Processing helix chain 'b' and resid 28 through 54 removed outlier: 3.691A pdb=" N CYS b 32 " --> pdb=" O ASP b 28 " (cutoff:3.500A) Processing helix chain 'd' and resid 100 through 127 Processing helix chain 'e' and resid 70 through 74 removed outlier: 3.779A pdb=" N ASN e 74 " --> pdb=" O ASP e 71 " (cutoff:3.500A) Processing helix chain 'e' and resid 126 through 152 removed outlier: 3.820A pdb=" N VAL e 130 " --> pdb=" O ASP e 126 " (cutoff:3.500A) Processing helix chain 'f' and resid 126 through 154 Processing helix chain 'g' and resid 113 through 137 Processing helix chain 'm' and resid 260 through 290 removed outlier: 3.989A pdb=" N TRP m 290 " --> pdb=" O THR m 286 " (cutoff:3.500A) Processing helix chain 'n' and resid 272 through 305 Processing sheet with id=AA1, first strand: chain 'd' and resid 45 through 46 removed outlier: 3.573A pdb=" N GLU d 45 " --> pdb=" O ILE d 70 " (cutoff:3.500A) removed outlier: 5.888A pdb=" N THR d 85 " --> pdb=" O TYR e 111 " (cutoff:3.500A) removed outlier: 6.803A pdb=" N TYR e 113 " --> pdb=" O THR d 85 " (cutoff:3.500A) removed outlier: 5.435A pdb=" N GLN d 87 " --> pdb=" O TYR e 113 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'd' and resid 96 through 97 Processing sheet with id=AA3, first strand: chain 'e' and resid 37 through 41 removed outlier: 3.667A pdb=" N LEU e 47 " --> pdb=" O LEU e 82 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N LEU e 82 " --> pdb=" O LEU e 47 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'f' and resid 37 through 41 Processing sheet with id=AA5, first strand: chain 'f' and resid 58 through 60 removed outlier: 3.729A pdb=" N GLN f 60 " --> pdb=" O VAL f 97 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N VAL f 97 " --> pdb=" O GLN f 60 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'f' and resid 114 through 116 removed outlier: 7.024A pdb=" N ARG f 115 " --> pdb=" O ARG g 102 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'g' and resid 32 through 34 removed outlier: 4.548A pdb=" N LEU g 43 " --> pdb=" O TYR g 34 " (cutoff:3.500A) 222 hydrogen bonds defined for protein. 639 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: 1.05 Time building geometry restraints manager: 1.99 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 1447 1.34 - 1.47: 1129 1.47 - 1.59: 2119 1.59 - 1.71: 0 1.71 - 1.83: 51 Bond restraints: 4746 Sorted by residual: bond pdb=" CB ARG m 288 " pdb=" CG ARG m 288 " ideal model delta sigma weight residual 1.520 1.562 -0.042 3.00e-02 1.11e+03 1.99e+00 bond pdb=" CB GLU e 79 " pdb=" CG GLU e 79 " ideal model delta sigma weight residual 1.520 1.561 -0.041 3.00e-02 1.11e+03 1.90e+00 bond pdb=" C ASP a 28 " pdb=" N PRO a 29 " ideal model delta sigma weight residual 1.335 1.352 -0.017 1.30e-02 5.92e+03 1.72e+00 bond pdb=" CB LYS g 69 " pdb=" CG LYS g 69 " ideal model delta sigma weight residual 1.520 1.559 -0.039 3.00e-02 1.11e+03 1.69e+00 bond pdb=" N ASP d 59 " pdb=" CA ASP d 59 " ideal model delta sigma weight residual 1.457 1.474 -0.017 1.29e-02 6.01e+03 1.64e+00 ... (remaining 4741 not shown) Histogram of bond angle deviations from ideal: 99.50 - 106.43: 89 106.43 - 113.37: 2594 113.37 - 120.31: 1677 120.31 - 127.24: 2028 127.24 - 134.18: 40 Bond angle restraints: 6428 Sorted by residual: angle pdb=" N GLN f 51 " pdb=" CA GLN f 51 " pdb=" C GLN f 51 " ideal model delta sigma weight residual 114.75 108.19 6.56 1.26e+00 6.30e-01 2.71e+01 angle pdb=" C LEU d 58 " pdb=" N ASP d 59 " pdb=" CA ASP d 59 " ideal model delta sigma weight residual 121.54 129.79 -8.25 1.91e+00 2.74e-01 1.87e+01 angle pdb=" N GLU e 70 " pdb=" CA GLU e 70 " pdb=" C GLU e 70 " ideal model delta sigma weight residual 113.23 108.00 5.23 1.22e+00 6.72e-01 1.84e+01 angle pdb=" CA CYS d 96 " pdb=" CB CYS d 96 " pdb=" SG CYS d 96 " ideal model delta sigma weight residual 114.40 123.30 -8.90 2.30e+00 1.89e-01 1.50e+01 angle pdb=" CA LYS g 69 " pdb=" CB LYS g 69 " pdb=" CG LYS g 69 " ideal model delta sigma weight residual 114.10 121.75 -7.65 2.00e+00 2.50e-01 1.46e+01 ... (remaining 6423 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.78: 2353 17.78 - 35.55: 372 35.55 - 53.33: 97 53.33 - 71.10: 11 71.10 - 88.88: 8 Dihedral angle restraints: 2841 sinusoidal: 1132 harmonic: 1709 Sorted by residual: dihedral pdb=" CB CYS g 104 " pdb=" SG CYS g 104 " pdb=" SG CYS g 107 " pdb=" CB CYS g 107 " ideal model delta sinusoidal sigma weight residual 93.00 -179.98 -87.02 1 1.00e+01 1.00e-02 9.10e+01 dihedral pdb=" CB CYS e 119 " pdb=" SG CYS e 119 " pdb=" SG CYS e 122 " pdb=" CB CYS e 122 " ideal model delta sinusoidal sigma weight residual -86.00 -151.04 65.04 1 1.00e+01 1.00e-02 5.55e+01 dihedral pdb=" CB CYS a 32 " pdb=" SG CYS a 32 " pdb=" SG CYS b 32 " pdb=" CB CYS b 32 " ideal model delta sinusoidal sigma weight residual 93.00 142.20 -49.20 1 1.00e+01 1.00e-02 3.33e+01 ... (remaining 2838 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.045: 550 0.045 - 0.090: 160 0.090 - 0.135: 37 0.135 - 0.180: 4 0.180 - 0.225: 2 Chirality restraints: 753 Sorted by residual: chirality pdb=" CA ASP d 59 " pdb=" N ASP d 59 " pdb=" C ASP d 59 " pdb=" CB ASP d 59 " both_signs ideal model delta sigma weight residual False 2.51 2.29 0.22 2.00e-01 2.50e+01 1.26e+00 chirality pdb=" CB ILE n 299 " pdb=" CA ILE n 299 " pdb=" CG1 ILE n 299 " pdb=" CG2 ILE n 299 " both_signs ideal model delta sigma weight residual False 2.64 2.46 0.19 2.00e-01 2.50e+01 8.98e-01 chirality pdb=" CA ASN d 36 " pdb=" N ASN d 36 " pdb=" C ASN d 36 " pdb=" CB ASN d 36 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.15 2.00e-01 2.50e+01 5.43e-01 ... (remaining 750 not shown) Planarity restraints: 791 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C TYR e 52 " -0.045 5.00e-02 4.00e+02 6.86e-02 7.54e+00 pdb=" N PRO e 53 " 0.119 5.00e-02 4.00e+02 pdb=" CA PRO e 53 " -0.036 5.00e-02 4.00e+02 pdb=" CD PRO e 53 " -0.038 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TYR f 99 " 0.041 5.00e-02 4.00e+02 6.25e-02 6.25e+00 pdb=" N PRO f 100 " -0.108 5.00e-02 4.00e+02 pdb=" CA PRO f 100 " 0.033 5.00e-02 4.00e+02 pdb=" CD PRO f 100 " 0.034 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TRP d 43 " 0.016 2.00e-02 2.50e+03 1.35e-02 4.56e+00 pdb=" CG TRP d 43 " -0.037 2.00e-02 2.50e+03 pdb=" CD1 TRP d 43 " 0.014 2.00e-02 2.50e+03 pdb=" CD2 TRP d 43 " -0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP d 43 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP d 43 " -0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP d 43 " 0.005 2.00e-02 2.50e+03 pdb=" CZ2 TRP d 43 " 0.003 2.00e-02 2.50e+03 pdb=" CZ3 TRP d 43 " -0.000 2.00e-02 2.50e+03 pdb=" CH2 TRP d 43 " 0.000 2.00e-02 2.50e+03 ... (remaining 788 not shown) Histogram of nonbonded interaction distances: 2.07 - 2.63: 76 2.63 - 3.20: 4388 3.20 - 3.77: 7079 3.77 - 4.33: 8814 4.33 - 4.90: 14140 Nonbonded interactions: 34497 Sorted by model distance: nonbonded pdb=" O LEU m 289 " pdb=" CE3 TRP m 290 " model vdw 2.068 3.340 nonbonded pdb=" N GLN f 33 " pdb=" NE2 GLN f 33 " model vdw 2.160 3.200 nonbonded pdb=" OG SER m 291 " pdb=" N SER m 292 " model vdw 2.190 3.120 nonbonded pdb=" O LEU m 289 " pdb=" CD2 TRP m 290 " model vdw 2.214 3.260 nonbonded pdb=" ND2 ASN d 38 " pdb=" OG1 THR d 76 " model vdw 2.217 3.120 ... (remaining 34492 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 27 through 54) selection = chain 'b' } ncs_group { reference = (chain 'e' and (resid 33 through 69 or resid 74 through 153)) selection = (chain 'f' and resid 33 through 153) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.490 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.170 Check model and map are aligned: 0.030 Set scattering table: 0.050 Process input model: 16.810 Find NCS groups from input model: 0.120 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.530 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.220 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6547 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 : 0.004 0.042 4746 Z= 0.279 Angle : 1.061 9.939 6428 Z= 0.580 Chirality : 0.044 0.225 753 Planarity : 0.006 0.069 791 Dihedral : 18.199 88.877 1723 Min Nonbonded Distance : 2.068 Molprobity Statistics. All-atom Clashscore : 17.74 Ramachandran Plot: Outliers : 1.58 % Allowed : 11.21 % Favored : 87.22 % Rotamer: Outliers : 1.91 % Allowed : 42.07 % Favored : 56.02 % 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: -1.04 (0.35), residues: 571 helix: 3.06 (0.33), residues: 221 sheet: -2.21 (0.73), residues: 52 loop : -3.66 (0.27), residues: 298 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.003 TRP d 43 HIS 0.006 0.001 HIS d 89 PHE 0.018 0.002 PHE m 281 TYR 0.019 0.001 TYR g 34 ARG 0.006 0.001 ARG e 115 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1142 Ramachandran restraints generated. 571 Oldfield, 0 Emsley, 571 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1142 Ramachandran restraints generated. 571 Oldfield, 0 Emsley, 571 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 523 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 153 time to evaluate : 0.539 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: e 85 LYS cc_start: 0.8770 (mtpp) cc_final: 0.8254 (pttm) REVERT: e 117 ARG cc_start: 0.7608 (tpp80) cc_final: 0.7318 (tpp80) REVERT: f 126 ASP cc_start: 0.7698 (t70) cc_final: 0.7062 (p0) REVERT: g 55 TRP cc_start: 0.5446 (m100) cc_final: 0.4702 (m100) REVERT: g 72 TRP cc_start: 0.8170 (t-100) cc_final: 0.7878 (t-100) REVERT: g 84 MET cc_start: 0.5874 (mmm) cc_final: 0.5316 (mmm) outliers start: 10 outliers final: 5 residues processed: 156 average time/residue: 0.1581 time to fit residues: 31.1158 Evaluate side-chains 152 residues out of total 523 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 147 time to evaluate : 0.434 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain d residue 31 ASP Chi-restraints excluded: chain f residue 97 VAL Chi-restraints excluded: chain f residue 138 ILE Chi-restraints excluded: chain m residue 258 THR Chi-restraints excluded: chain m residue 290 TRP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 46 optimal weight: 3.9990 chunk 41 optimal weight: 8.9990 chunk 23 optimal weight: 0.9980 chunk 14 optimal weight: 0.9980 chunk 28 optimal weight: 3.9990 chunk 22 optimal weight: 0.4980 chunk 43 optimal weight: 7.9990 chunk 16 optimal weight: 0.9980 chunk 26 optimal weight: 1.9990 chunk 32 optimal weight: 3.9990 chunk 49 optimal weight: 0.7980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: d 38 ASN e 62 ASN f 33 GLN ** g 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 278 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6582 moved from start: 0.1609 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 4746 Z= 0.238 Angle : 0.813 9.832 6428 Z= 0.398 Chirality : 0.043 0.173 753 Planarity : 0.005 0.054 791 Dihedral : 6.173 53.445 642 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 11.65 Ramachandran Plot: Outliers : 1.23 % Allowed : 13.31 % Favored : 85.46 % Rotamer: Outliers : 8.41 % Allowed : 33.46 % Favored : 58.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.89 (0.36), residues: 571 helix: 3.44 (0.31), residues: 222 sheet: -3.26 (0.58), residues: 64 loop : -3.55 (0.28), residues: 285 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP d 43 HIS 0.003 0.001 HIS e 81 PHE 0.010 0.001 PHE g 56 TYR 0.019 0.001 TYR n 283 ARG 0.005 0.001 ARG e 115 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1142 Ramachandran restraints generated. 571 Oldfield, 0 Emsley, 571 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1142 Ramachandran restraints generated. 571 Oldfield, 0 Emsley, 571 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 523 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 151 time to evaluate : 0.548 Fit side-chains revert: symmetry clash REVERT: d 38 ASN cc_start: 0.8526 (OUTLIER) cc_final: 0.8199 (m-40) REVERT: d 91 ARG cc_start: 0.7834 (OUTLIER) cc_final: 0.7604 (tmm160) REVERT: e 70 GLU cc_start: 0.7550 (tp30) cc_final: 0.6884 (mp0) REVERT: e 85 LYS cc_start: 0.8847 (mtpp) cc_final: 0.8273 (pttp) REVERT: e 128 MET cc_start: 0.6308 (tmm) cc_final: 0.6051 (tmm) REVERT: g 55 TRP cc_start: 0.5611 (m100) cc_final: 0.5087 (m100) REVERT: g 72 TRP cc_start: 0.8212 (t-100) cc_final: 0.7896 (t-100) outliers start: 44 outliers final: 27 residues processed: 177 average time/residue: 0.1508 time to fit residues: 33.9868 Evaluate side-chains 169 residues out of total 523 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 140 time to evaluate : 0.520 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 44 VAL Chi-restraints excluded: chain a residue 51 LEU Chi-restraints excluded: chain b residue 31 LEU Chi-restraints excluded: chain d residue 38 ASN Chi-restraints excluded: chain d residue 85 THR Chi-restraints excluded: chain d residue 91 ARG Chi-restraints excluded: chain d residue 113 ILE Chi-restraints excluded: chain d residue 115 THR Chi-restraints excluded: chain d residue 124 CYS Chi-restraints excluded: chain e residue 45 VAL Chi-restraints excluded: chain e residue 48 THR Chi-restraints excluded: chain e residue 114 LEU Chi-restraints excluded: chain e residue 119 CYS Chi-restraints excluded: chain e residue 123 MET Chi-restraints excluded: chain e residue 124 GLU Chi-restraints excluded: chain e residue 153 LYS Chi-restraints excluded: chain f residue 40 ILE Chi-restraints excluded: chain f residue 47 LEU Chi-restraints excluded: chain f residue 48 THR Chi-restraints excluded: chain f residue 97 VAL Chi-restraints excluded: chain f residue 138 ILE Chi-restraints excluded: chain g residue 35 ASP Chi-restraints excluded: chain g residue 53 ILE Chi-restraints excluded: chain g residue 97 LEU Chi-restraints excluded: chain g residue 133 VAL Chi-restraints excluded: chain m residue 268 VAL Chi-restraints excluded: chain m residue 286 THR Chi-restraints excluded: chain n residue 276 LEU Chi-restraints excluded: chain n residue 293 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 27 optimal weight: 8.9990 chunk 15 optimal weight: 0.9980 chunk 41 optimal weight: 0.0970 chunk 34 optimal weight: 0.9980 chunk 13 optimal weight: 0.5980 chunk 50 optimal weight: 1.9990 chunk 54 optimal weight: 0.9990 chunk 44 optimal weight: 0.0670 chunk 49 optimal weight: 0.9980 chunk 17 optimal weight: 4.9990 chunk 40 optimal weight: 6.9990 overall best weight: 0.5516 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: d 38 ASN f 33 GLN ** n 278 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6572 moved from start: 0.2090 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 4746 Z= 0.204 Angle : 0.757 9.491 6428 Z= 0.373 Chirality : 0.042 0.222 753 Planarity : 0.004 0.044 791 Dihedral : 5.199 34.162 637 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 10.79 Ramachandran Plot: Outliers : 1.05 % Allowed : 11.21 % Favored : 87.74 % Rotamer: Outliers : 8.80 % Allowed : 34.03 % Favored : 57.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.74 (0.35), residues: 571 helix: 3.52 (0.31), residues: 222 sheet: -3.13 (0.58), residues: 62 loop : -3.45 (0.27), residues: 287 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP d 43 HIS 0.002 0.001 HIS g 29 PHE 0.008 0.001 PHE g 56 TYR 0.014 0.001 TYR b 33 ARG 0.003 0.000 ARG e 115 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1142 Ramachandran restraints generated. 571 Oldfield, 0 Emsley, 571 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1142 Ramachandran restraints generated. 571 Oldfield, 0 Emsley, 571 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 523 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 153 time to evaluate : 0.536 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: e 36 TYR cc_start: 0.7973 (m-10) cc_final: 0.7483 (m-10) REVERT: e 70 GLU cc_start: 0.7553 (tp30) cc_final: 0.6887 (mp0) REVERT: e 85 LYS cc_start: 0.8824 (mtpp) cc_final: 0.8260 (pttp) REVERT: e 117 ARG cc_start: 0.7469 (tpp80) cc_final: 0.6906 (tpp80) REVERT: e 123 MET cc_start: 0.7724 (OUTLIER) cc_final: 0.7498 (pmm) REVERT: e 128 MET cc_start: 0.6140 (tmm) cc_final: 0.5872 (tmm) REVERT: g 55 TRP cc_start: 0.5377 (m100) cc_final: 0.5164 (m100) REVERT: m 285 MET cc_start: 0.7720 (tpp) cc_final: 0.7452 (tpp) outliers start: 46 outliers final: 27 residues processed: 183 average time/residue: 0.1504 time to fit residues: 35.1027 Evaluate side-chains 174 residues out of total 523 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 146 time to evaluate : 0.529 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 32 CYS Chi-restraints excluded: chain a residue 34 LEU Chi-restraints excluded: chain a residue 51 LEU Chi-restraints excluded: chain d residue 31 ASP Chi-restraints excluded: chain d residue 38 ASN Chi-restraints excluded: chain d residue 64 ILE Chi-restraints excluded: chain d residue 85 THR Chi-restraints excluded: chain d residue 115 THR Chi-restraints excluded: chain e residue 45 VAL Chi-restraints excluded: chain e residue 48 THR Chi-restraints excluded: chain e residue 57 ILE Chi-restraints excluded: chain e residue 119 CYS Chi-restraints excluded: chain e residue 123 MET Chi-restraints excluded: chain e residue 124 GLU Chi-restraints excluded: chain e residue 153 LYS Chi-restraints excluded: chain f residue 48 THR Chi-restraints excluded: chain f residue 81 HIS Chi-restraints excluded: chain f residue 97 VAL Chi-restraints excluded: chain f residue 112 LEU Chi-restraints excluded: chain f residue 138 ILE Chi-restraints excluded: chain g residue 44 LEU Chi-restraints excluded: chain g residue 97 LEU Chi-restraints excluded: chain g residue 98 GLN Chi-restraints excluded: chain m residue 268 VAL Chi-restraints excluded: chain m residue 271 LEU Chi-restraints excluded: chain m residue 290 TRP Chi-restraints excluded: chain m residue 291 SER Chi-restraints excluded: chain n residue 276 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 49 optimal weight: 1.9990 chunk 37 optimal weight: 0.7980 chunk 25 optimal weight: 0.7980 chunk 5 optimal weight: 0.3980 chunk 23 optimal weight: 3.9990 chunk 33 optimal weight: 0.0970 chunk 50 optimal weight: 0.9980 chunk 53 optimal weight: 0.7980 chunk 26 optimal weight: 0.6980 chunk 47 optimal weight: 0.9990 chunk 14 optimal weight: 0.8980 overall best weight: 0.5578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: f 33 GLN ** n 278 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6570 moved from start: 0.2601 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 4746 Z= 0.202 Angle : 0.777 12.782 6428 Z= 0.373 Chirality : 0.042 0.233 753 Planarity : 0.004 0.040 791 Dihedral : 5.056 34.860 637 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 10.47 Ramachandran Plot: Outliers : 1.05 % Allowed : 12.08 % Favored : 86.87 % Rotamer: Outliers : 8.80 % Allowed : 34.42 % Favored : 56.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.70 (0.35), residues: 571 helix: 3.49 (0.31), residues: 222 sheet: -3.13 (0.58), residues: 62 loop : -3.35 (0.28), residues: 287 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP d 43 HIS 0.002 0.001 HIS g 29 PHE 0.006 0.001 PHE m 281 TYR 0.017 0.001 TYR f 52 ARG 0.003 0.001 ARG d 91 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1142 Ramachandran restraints generated. 571 Oldfield, 0 Emsley, 571 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1142 Ramachandran restraints generated. 571 Oldfield, 0 Emsley, 571 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 523 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 145 time to evaluate : 0.531 Fit side-chains REVERT: e 70 GLU cc_start: 0.7593 (tp30) cc_final: 0.6961 (mp0) REVERT: e 85 LYS cc_start: 0.8827 (mtpp) cc_final: 0.8212 (pttp) REVERT: e 117 ARG cc_start: 0.7101 (tpp80) cc_final: 0.6838 (tpp80) REVERT: e 123 MET cc_start: 0.7708 (mpp) cc_final: 0.7296 (pmm) REVERT: e 128 MET cc_start: 0.6135 (tmm) cc_final: 0.5820 (tmm) REVERT: f 36 TYR cc_start: 0.5355 (OUTLIER) cc_final: 0.4373 (t80) REVERT: g 72 TRP cc_start: 0.8181 (t-100) cc_final: 0.7780 (t-100) REVERT: g 95 LYS cc_start: 0.8112 (mtpp) cc_final: 0.7820 (pttt) REVERT: m 285 MET cc_start: 0.7798 (tpp) cc_final: 0.7562 (tpp) REVERT: n 287 LEU cc_start: 0.8218 (OUTLIER) cc_final: 0.8014 (tm) outliers start: 46 outliers final: 30 residues processed: 174 average time/residue: 0.1536 time to fit residues: 34.0789 Evaluate side-chains 175 residues out of total 523 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 143 time to evaluate : 0.475 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 35 LEU Chi-restraints excluded: chain a residue 44 VAL Chi-restraints excluded: chain a residue 51 LEU Chi-restraints excluded: chain b residue 31 LEU Chi-restraints excluded: chain d residue 31 ASP Chi-restraints excluded: chain d residue 58 LEU Chi-restraints excluded: chain d residue 73 CYS Chi-restraints excluded: chain d residue 85 THR Chi-restraints excluded: chain d residue 115 THR Chi-restraints excluded: chain e residue 45 VAL Chi-restraints excluded: chain e residue 48 THR Chi-restraints excluded: chain e residue 57 ILE Chi-restraints excluded: chain e residue 61 HIS Chi-restraints excluded: chain e residue 119 CYS Chi-restraints excluded: chain e residue 124 GLU Chi-restraints excluded: chain e residue 153 LYS Chi-restraints excluded: chain f residue 36 TYR Chi-restraints excluded: chain f residue 48 THR Chi-restraints excluded: chain f residue 81 HIS Chi-restraints excluded: chain f residue 97 VAL Chi-restraints excluded: chain f residue 112 LEU Chi-restraints excluded: chain f residue 125 MET Chi-restraints excluded: chain f residue 138 ILE Chi-restraints excluded: chain g residue 30 LEU Chi-restraints excluded: chain g residue 35 ASP Chi-restraints excluded: chain g residue 44 LEU Chi-restraints excluded: chain g residue 53 ILE Chi-restraints excluded: chain g residue 97 LEU Chi-restraints excluded: chain m residue 291 SER Chi-restraints excluded: chain n residue 276 LEU Chi-restraints excluded: chain n residue 287 LEU Chi-restraints excluded: chain n residue 293 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 44 optimal weight: 0.4980 chunk 30 optimal weight: 0.0970 chunk 0 optimal weight: 3.9990 chunk 39 optimal weight: 0.3980 chunk 21 optimal weight: 2.9990 chunk 45 optimal weight: 0.9980 chunk 36 optimal weight: 0.2980 chunk 27 optimal weight: 6.9990 chunk 47 optimal weight: 0.7980 chunk 13 optimal weight: 0.5980 chunk 17 optimal weight: 3.9990 overall best weight: 0.3778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: f 33 GLN ** g 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 278 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6550 moved from start: 0.2900 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 4746 Z= 0.190 Angle : 0.763 10.418 6428 Z= 0.366 Chirality : 0.043 0.223 753 Planarity : 0.004 0.036 791 Dihedral : 5.058 35.437 637 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 9.72 Ramachandran Plot: Outliers : 0.88 % Allowed : 10.86 % Favored : 88.27 % Rotamer: Outliers : 8.22 % Allowed : 35.76 % Favored : 56.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.55 (0.36), residues: 571 helix: 3.60 (0.31), residues: 222 sheet: -3.00 (0.52), residues: 82 loop : -3.21 (0.29), residues: 267 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.001 TRP d 43 HIS 0.002 0.001 HIS g 29 PHE 0.006 0.001 PHE f 110 TYR 0.018 0.001 TYR f 52 ARG 0.003 0.000 ARG d 91 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1142 Ramachandran restraints generated. 571 Oldfield, 0 Emsley, 571 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1142 Ramachandran restraints generated. 571 Oldfield, 0 Emsley, 571 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 523 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 150 time to evaluate : 0.563 Fit side-chains REVERT: b 54 LYS cc_start: 0.6765 (tptp) cc_final: 0.6441 (tptp) REVERT: e 70 GLU cc_start: 0.7551 (tp30) cc_final: 0.6846 (mp0) REVERT: e 85 LYS cc_start: 0.8764 (mtpp) cc_final: 0.8150 (pttp) REVERT: e 123 MET cc_start: 0.7765 (mpp) cc_final: 0.7344 (pmm) REVERT: f 36 TYR cc_start: 0.5121 (OUTLIER) cc_final: 0.4269 (t80) REVERT: g 72 TRP cc_start: 0.8130 (t-100) cc_final: 0.7869 (t-100) REVERT: g 95 LYS cc_start: 0.8156 (mtpp) cc_final: 0.7757 (pttt) REVERT: m 285 MET cc_start: 0.7845 (tpp) cc_final: 0.7625 (tpp) outliers start: 43 outliers final: 31 residues processed: 175 average time/residue: 0.1435 time to fit residues: 32.5052 Evaluate side-chains 176 residues out of total 523 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 144 time to evaluate : 0.512 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 34 LEU Chi-restraints excluded: chain a residue 51 LEU Chi-restraints excluded: chain b residue 31 LEU Chi-restraints excluded: chain b residue 46 LEU Chi-restraints excluded: chain d residue 31 ASP Chi-restraints excluded: chain d residue 58 LEU Chi-restraints excluded: chain d residue 64 ILE Chi-restraints excluded: chain d residue 73 CYS Chi-restraints excluded: chain d residue 78 ILE Chi-restraints excluded: chain d residue 85 THR Chi-restraints excluded: chain d residue 88 VAL Chi-restraints excluded: chain d residue 115 THR Chi-restraints excluded: chain e residue 45 VAL Chi-restraints excluded: chain e residue 48 THR Chi-restraints excluded: chain e residue 57 ILE Chi-restraints excluded: chain e residue 61 HIS Chi-restraints excluded: chain e residue 66 ILE Chi-restraints excluded: chain e residue 119 CYS Chi-restraints excluded: chain e residue 124 GLU Chi-restraints excluded: chain e residue 152 SER Chi-restraints excluded: chain e residue 153 LYS Chi-restraints excluded: chain f residue 36 TYR Chi-restraints excluded: chain f residue 48 THR Chi-restraints excluded: chain f residue 97 VAL Chi-restraints excluded: chain f residue 112 LEU Chi-restraints excluded: chain f residue 138 ILE Chi-restraints excluded: chain g residue 44 LEU Chi-restraints excluded: chain g residue 92 ASN Chi-restraints excluded: chain g residue 97 LEU Chi-restraints excluded: chain m residue 268 VAL Chi-restraints excluded: chain m residue 291 SER Chi-restraints excluded: chain n residue 276 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 47 optimal weight: 9.9990 chunk 10 optimal weight: 2.9990 chunk 31 optimal weight: 2.9990 chunk 13 optimal weight: 0.6980 chunk 53 optimal weight: 0.7980 chunk 44 optimal weight: 0.9980 chunk 24 optimal weight: 1.9990 chunk 4 optimal weight: 3.9990 chunk 17 optimal weight: 0.3980 chunk 27 optimal weight: 0.8980 chunk 51 optimal weight: 0.5980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: f 33 GLN ** g 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 278 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6575 moved from start: 0.3295 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 4746 Z= 0.207 Angle : 0.771 9.860 6428 Z= 0.371 Chirality : 0.042 0.225 753 Planarity : 0.004 0.033 791 Dihedral : 4.933 35.055 637 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 11.01 Ramachandran Plot: Outliers : 0.88 % Allowed : 11.21 % Favored : 87.92 % Rotamer: Outliers : 9.18 % Allowed : 35.37 % Favored : 55.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.48 (0.36), residues: 571 helix: 3.64 (0.31), residues: 222 sheet: -2.77 (0.54), residues: 80 loop : -3.24 (0.29), residues: 269 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP d 43 HIS 0.001 0.000 HIS g 29 PHE 0.007 0.001 PHE n 296 TYR 0.037 0.001 TYR f 99 ARG 0.003 0.001 ARG d 91 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1142 Ramachandran restraints generated. 571 Oldfield, 0 Emsley, 571 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1142 Ramachandran restraints generated. 571 Oldfield, 0 Emsley, 571 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 523 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 148 time to evaluate : 0.513 Fit side-chains REVERT: b 54 LYS cc_start: 0.6840 (tptp) cc_final: 0.6522 (tptp) REVERT: e 61 HIS cc_start: 0.6471 (OUTLIER) cc_final: 0.5345 (p90) REVERT: e 70 GLU cc_start: 0.7647 (tp30) cc_final: 0.6902 (mp0) REVERT: e 85 LYS cc_start: 0.8849 (mtpp) cc_final: 0.8234 (pttp) REVERT: e 117 ARG cc_start: 0.7133 (tpp80) cc_final: 0.6805 (tpp80) REVERT: e 123 MET cc_start: 0.7702 (mpp) cc_final: 0.7303 (pmm) REVERT: e 128 MET cc_start: 0.6192 (tmm) cc_final: 0.5761 (tmm) REVERT: f 36 TYR cc_start: 0.5221 (OUTLIER) cc_final: 0.4086 (t80) REVERT: f 60 GLN cc_start: 0.6775 (OUTLIER) cc_final: 0.6562 (mm-40) REVERT: f 137 ASP cc_start: 0.7858 (t70) cc_final: 0.7440 (t0) REVERT: g 61 MET cc_start: 0.7303 (tmm) cc_final: 0.7088 (tmm) REVERT: g 72 TRP cc_start: 0.8037 (t-100) cc_final: 0.7784 (t-100) REVERT: g 88 LYS cc_start: 0.7394 (mptt) cc_final: 0.7079 (mmtm) outliers start: 48 outliers final: 35 residues processed: 177 average time/residue: 0.1521 time to fit residues: 34.2839 Evaluate side-chains 184 residues out of total 523 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 146 time to evaluate : 0.516 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 34 LEU Chi-restraints excluded: chain a residue 44 VAL Chi-restraints excluded: chain a residue 51 LEU Chi-restraints excluded: chain b residue 31 LEU Chi-restraints excluded: chain b residue 45 ILE Chi-restraints excluded: chain d residue 31 ASP Chi-restraints excluded: chain d residue 64 ILE Chi-restraints excluded: chain d residue 73 CYS Chi-restraints excluded: chain d residue 78 ILE Chi-restraints excluded: chain d residue 85 THR Chi-restraints excluded: chain d residue 113 ILE Chi-restraints excluded: chain d residue 115 THR Chi-restraints excluded: chain e residue 45 VAL Chi-restraints excluded: chain e residue 48 THR Chi-restraints excluded: chain e residue 57 ILE Chi-restraints excluded: chain e residue 61 HIS Chi-restraints excluded: chain e residue 66 ILE Chi-restraints excluded: chain e residue 119 CYS Chi-restraints excluded: chain e residue 124 GLU Chi-restraints excluded: chain e residue 152 SER Chi-restraints excluded: chain e residue 153 LYS Chi-restraints excluded: chain f residue 36 TYR Chi-restraints excluded: chain f residue 60 GLN Chi-restraints excluded: chain f residue 81 HIS Chi-restraints excluded: chain f residue 97 VAL Chi-restraints excluded: chain f residue 112 LEU Chi-restraints excluded: chain f residue 138 ILE Chi-restraints excluded: chain g residue 30 LEU Chi-restraints excluded: chain g residue 54 THR Chi-restraints excluded: chain g residue 92 ASN Chi-restraints excluded: chain g residue 97 LEU Chi-restraints excluded: chain g residue 110 LEU Chi-restraints excluded: chain g residue 124 VAL Chi-restraints excluded: chain g residue 135 PHE Chi-restraints excluded: chain m residue 268 VAL Chi-restraints excluded: chain m residue 271 LEU Chi-restraints excluded: chain m residue 291 SER Chi-restraints excluded: chain n residue 276 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 5 optimal weight: 8.9990 chunk 30 optimal weight: 5.9990 chunk 38 optimal weight: 3.9990 chunk 44 optimal weight: 2.9990 chunk 29 optimal weight: 0.7980 chunk 53 optimal weight: 0.9990 chunk 33 optimal weight: 0.9990 chunk 32 optimal weight: 1.9990 chunk 24 optimal weight: 2.9990 chunk 21 optimal weight: 3.9990 chunk 31 optimal weight: 0.7980 overall best weight: 1.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: f 33 GLN ** g 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 278 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6630 moved from start: 0.3554 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 4746 Z= 0.247 Angle : 0.794 9.831 6428 Z= 0.386 Chirality : 0.043 0.229 753 Planarity : 0.004 0.036 791 Dihedral : 5.087 36.108 637 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 11.97 Ramachandran Plot: Outliers : 0.88 % Allowed : 10.86 % Favored : 88.27 % Rotamer: Outliers : 9.75 % Allowed : 35.37 % Favored : 54.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.18 % 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: -0.52 (0.36), residues: 571 helix: 3.64 (0.31), residues: 222 sheet: -2.74 (0.55), residues: 80 loop : -3.31 (0.29), residues: 269 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.002 TRP d 43 HIS 0.004 0.001 HIS g 29 PHE 0.009 0.001 PHE n 296 TYR 0.034 0.002 TYR f 99 ARG 0.003 0.000 ARG d 57 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1142 Ramachandran restraints generated. 571 Oldfield, 0 Emsley, 571 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1142 Ramachandran restraints generated. 571 Oldfield, 0 Emsley, 571 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 523 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 147 time to evaluate : 0.486 Fit side-chains REVERT: b 54 LYS cc_start: 0.6977 (tptp) cc_final: 0.6677 (tptp) REVERT: d 27 GLU cc_start: 0.7664 (pm20) cc_final: 0.7359 (pm20) REVERT: e 61 HIS cc_start: 0.6697 (OUTLIER) cc_final: 0.5878 (p90) REVERT: e 70 GLU cc_start: 0.7855 (tp30) cc_final: 0.7110 (mp0) REVERT: e 85 LYS cc_start: 0.8850 (mtpp) cc_final: 0.8200 (pttp) REVERT: e 123 MET cc_start: 0.7695 (mpp) cc_final: 0.7372 (pmm) REVERT: e 128 MET cc_start: 0.6294 (tmm) cc_final: 0.5863 (tmm) REVERT: f 36 TYR cc_start: 0.5030 (OUTLIER) cc_final: 0.4125 (t80) REVERT: f 60 GLN cc_start: 0.7013 (OUTLIER) cc_final: 0.6808 (mm-40) REVERT: f 137 ASP cc_start: 0.7832 (t70) cc_final: 0.7427 (t0) REVERT: g 72 TRP cc_start: 0.7989 (t-100) cc_final: 0.7699 (t-100) REVERT: g 95 LYS cc_start: 0.8449 (mtpp) cc_final: 0.8019 (ptmt) outliers start: 51 outliers final: 39 residues processed: 178 average time/residue: 0.1512 time to fit residues: 34.1776 Evaluate side-chains 185 residues out of total 523 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 143 time to evaluate : 0.513 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 44 VAL Chi-restraints excluded: chain a residue 51 LEU Chi-restraints excluded: chain b residue 28 ASP Chi-restraints excluded: chain b residue 31 LEU Chi-restraints excluded: chain b residue 45 ILE Chi-restraints excluded: chain b residue 46 LEU Chi-restraints excluded: chain d residue 31 ASP Chi-restraints excluded: chain d residue 33 VAL Chi-restraints excluded: chain d residue 53 SER Chi-restraints excluded: chain d residue 58 LEU Chi-restraints excluded: chain d residue 64 ILE Chi-restraints excluded: chain d residue 73 CYS Chi-restraints excluded: chain d residue 78 ILE Chi-restraints excluded: chain d residue 85 THR Chi-restraints excluded: chain d residue 107 ILE Chi-restraints excluded: chain d residue 113 ILE Chi-restraints excluded: chain d residue 115 THR Chi-restraints excluded: chain e residue 45 VAL Chi-restraints excluded: chain e residue 48 THR Chi-restraints excluded: chain e residue 57 ILE Chi-restraints excluded: chain e residue 61 HIS Chi-restraints excluded: chain e residue 66 ILE Chi-restraints excluded: chain e residue 119 CYS Chi-restraints excluded: chain e residue 124 GLU Chi-restraints excluded: chain e residue 152 SER Chi-restraints excluded: chain f residue 36 TYR Chi-restraints excluded: chain f residue 60 GLN Chi-restraints excluded: chain f residue 81 HIS Chi-restraints excluded: chain f residue 97 VAL Chi-restraints excluded: chain f residue 112 LEU Chi-restraints excluded: chain f residue 138 ILE Chi-restraints excluded: chain g residue 28 ASN Chi-restraints excluded: chain g residue 30 LEU Chi-restraints excluded: chain g residue 44 LEU Chi-restraints excluded: chain g residue 54 THR Chi-restraints excluded: chain g residue 92 ASN Chi-restraints excluded: chain g residue 97 LEU Chi-restraints excluded: chain g residue 124 VAL Chi-restraints excluded: chain m residue 268 VAL Chi-restraints excluded: chain m residue 291 SER Chi-restraints excluded: chain n residue 276 LEU Chi-restraints excluded: chain n residue 293 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 15 optimal weight: 0.9990 chunk 10 optimal weight: 0.0970 chunk 33 optimal weight: 0.8980 chunk 36 optimal weight: 0.8980 chunk 26 optimal weight: 0.7980 chunk 4 optimal weight: 0.5980 chunk 41 optimal weight: 0.0970 chunk 48 optimal weight: 0.9990 chunk 50 optimal weight: 1.9990 chunk 46 optimal weight: 0.7980 chunk 49 optimal weight: 0.6980 overall best weight: 0.4576 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: f 33 GLN f 121 ASN ** g 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 278 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6574 moved from start: 0.3901 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 4746 Z= 0.200 Angle : 0.772 9.868 6428 Z= 0.371 Chirality : 0.043 0.221 753 Planarity : 0.004 0.038 791 Dihedral : 4.991 40.204 637 Min Nonbonded Distance : 2.417 Molprobity Statistics. All-atom Clashscore : 9.72 Ramachandran Plot: Outliers : 0.88 % Allowed : 11.21 % Favored : 87.92 % Rotamer: Outliers : 7.84 % Allowed : 37.48 % Favored : 54.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.40 (0.36), residues: 571 helix: 3.72 (0.31), residues: 222 sheet: -2.65 (0.56), residues: 80 loop : -3.23 (0.29), residues: 269 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.002 TRP d 43 HIS 0.002 0.001 HIS g 29 PHE 0.008 0.001 PHE g 56 TYR 0.033 0.001 TYR f 99 ARG 0.002 0.000 ARG e 115 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1142 Ramachandran restraints generated. 571 Oldfield, 0 Emsley, 571 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1142 Ramachandran restraints generated. 571 Oldfield, 0 Emsley, 571 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 523 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 147 time to evaluate : 0.531 Fit side-chains REVERT: b 54 LYS cc_start: 0.6977 (tptp) cc_final: 0.6704 (tptp) REVERT: d 27 GLU cc_start: 0.7556 (pm20) cc_final: 0.7267 (pm20) REVERT: e 61 HIS cc_start: 0.6402 (OUTLIER) cc_final: 0.5609 (p90) REVERT: e 70 GLU cc_start: 0.7880 (tp30) cc_final: 0.7089 (mp0) REVERT: e 128 MET cc_start: 0.6264 (tmm) cc_final: 0.5822 (tmm) REVERT: e 150 TYR cc_start: 0.7898 (t80) cc_final: 0.7687 (t80) REVERT: e 153 LYS cc_start: 0.7910 (ptpt) cc_final: 0.7710 (ptpt) REVERT: f 36 TYR cc_start: 0.4738 (OUTLIER) cc_final: 0.3810 (t80) REVERT: f 37 LYS cc_start: 0.6607 (tppt) cc_final: 0.5634 (ttmm) REVERT: f 96 TYR cc_start: 0.7729 (m-80) cc_final: 0.7497 (m-80) REVERT: f 137 ASP cc_start: 0.7829 (t70) cc_final: 0.7424 (t0) REVERT: g 72 TRP cc_start: 0.7846 (t-100) cc_final: 0.7636 (t-100) REVERT: n 284 MET cc_start: 0.7806 (tpp) cc_final: 0.7573 (tpp) outliers start: 41 outliers final: 33 residues processed: 171 average time/residue: 0.1301 time to fit residues: 29.3811 Evaluate side-chains 177 residues out of total 523 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 142 time to evaluate : 0.531 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 51 LEU Chi-restraints excluded: chain b residue 28 ASP Chi-restraints excluded: chain b residue 31 LEU Chi-restraints excluded: chain b residue 46 LEU Chi-restraints excluded: chain d residue 31 ASP Chi-restraints excluded: chain d residue 58 LEU Chi-restraints excluded: chain d residue 64 ILE Chi-restraints excluded: chain d residue 73 CYS Chi-restraints excluded: chain d residue 85 THR Chi-restraints excluded: chain d residue 107 ILE Chi-restraints excluded: chain d residue 115 THR Chi-restraints excluded: chain e residue 45 VAL Chi-restraints excluded: chain e residue 48 THR Chi-restraints excluded: chain e residue 57 ILE Chi-restraints excluded: chain e residue 61 HIS Chi-restraints excluded: chain e residue 66 ILE Chi-restraints excluded: chain e residue 119 CYS Chi-restraints excluded: chain e residue 124 GLU Chi-restraints excluded: chain e residue 152 SER Chi-restraints excluded: chain f residue 36 TYR Chi-restraints excluded: chain f residue 48 THR Chi-restraints excluded: chain f residue 97 VAL Chi-restraints excluded: chain f residue 112 LEU Chi-restraints excluded: chain f residue 138 ILE Chi-restraints excluded: chain g residue 28 ASN Chi-restraints excluded: chain g residue 30 LEU Chi-restraints excluded: chain g residue 44 LEU Chi-restraints excluded: chain g residue 54 THR Chi-restraints excluded: chain g residue 92 ASN Chi-restraints excluded: chain g residue 97 LEU Chi-restraints excluded: chain g residue 103 MET Chi-restraints excluded: chain g residue 124 VAL Chi-restraints excluded: chain m residue 268 VAL Chi-restraints excluded: chain m residue 271 LEU Chi-restraints excluded: chain n residue 276 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 50 optimal weight: 0.5980 chunk 29 optimal weight: 0.4980 chunk 21 optimal weight: 1.9990 chunk 38 optimal weight: 5.9990 chunk 15 optimal weight: 1.9990 chunk 44 optimal weight: 0.0170 chunk 46 optimal weight: 0.9990 chunk 49 optimal weight: 0.9990 chunk 32 optimal weight: 1.9990 chunk 52 optimal weight: 0.8980 chunk 31 optimal weight: 0.7980 overall best weight: 0.5618 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: e 81 HIS f 33 GLN ** g 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 278 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6582 moved from start: 0.4074 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 4746 Z= 0.211 Angle : 0.788 9.676 6428 Z= 0.379 Chirality : 0.043 0.212 753 Planarity : 0.004 0.039 791 Dihedral : 4.921 37.548 637 Min Nonbonded Distance : 2.378 Molprobity Statistics. All-atom Clashscore : 10.68 Ramachandran Plot: Outliers : 0.88 % Allowed : 11.03 % Favored : 88.09 % Rotamer: Outliers : 8.60 % Allowed : 37.67 % Favored : 53.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.35 (0.36), residues: 571 helix: 3.70 (0.31), residues: 222 sheet: -2.54 (0.56), residues: 80 loop : -3.17 (0.30), residues: 269 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.002 TRP d 43 HIS 0.002 0.001 HIS g 29 PHE 0.006 0.001 PHE e 87 TYR 0.034 0.001 TYR f 99 ARG 0.002 0.000 ARG d 57 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1142 Ramachandran restraints generated. 571 Oldfield, 0 Emsley, 571 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1142 Ramachandran restraints generated. 571 Oldfield, 0 Emsley, 571 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 523 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 144 time to evaluate : 0.622 Fit side-chains revert: symmetry clash REVERT: b 54 LYS cc_start: 0.7016 (tptp) cc_final: 0.6727 (tptp) REVERT: d 27 GLU cc_start: 0.7545 (pm20) cc_final: 0.7254 (pm20) REVERT: d 83 GLU cc_start: 0.7923 (pm20) cc_final: 0.7617 (pm20) REVERT: e 61 HIS cc_start: 0.6351 (OUTLIER) cc_final: 0.5634 (p90) REVERT: e 70 GLU cc_start: 0.7870 (tp30) cc_final: 0.7148 (mp0) REVERT: e 74 ASN cc_start: 0.8173 (m-40) cc_final: 0.7349 (p0) REVERT: e 123 MET cc_start: 0.7256 (OUTLIER) cc_final: 0.6998 (pmm) REVERT: e 128 MET cc_start: 0.6272 (tmm) cc_final: 0.5829 (tmm) REVERT: e 150 TYR cc_start: 0.7863 (t80) cc_final: 0.7616 (t80) REVERT: e 153 LYS cc_start: 0.7710 (ptpt) cc_final: 0.7499 (ptpt) REVERT: f 37 LYS cc_start: 0.6681 (tppt) cc_final: 0.5777 (ttmm) REVERT: f 128 MET cc_start: 0.6878 (tmm) cc_final: 0.5568 (tpt) REVERT: f 137 ASP cc_start: 0.7813 (t70) cc_final: 0.7419 (t0) REVERT: g 95 LYS cc_start: 0.8484 (mtpp) cc_final: 0.8043 (ptpt) REVERT: g 109 GLU cc_start: 0.7912 (tt0) cc_final: 0.7577 (tt0) REVERT: m 290 TRP cc_start: 0.6644 (OUTLIER) cc_final: 0.5950 (m100) outliers start: 45 outliers final: 38 residues processed: 171 average time/residue: 0.1450 time to fit residues: 31.9421 Evaluate side-chains 183 residues out of total 523 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 142 time to evaluate : 0.525 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 31 LEU Chi-restraints excluded: chain a residue 51 LEU Chi-restraints excluded: chain b residue 28 ASP Chi-restraints excluded: chain b residue 31 LEU Chi-restraints excluded: chain b residue 46 LEU Chi-restraints excluded: chain d residue 31 ASP Chi-restraints excluded: chain d residue 58 LEU Chi-restraints excluded: chain d residue 64 ILE Chi-restraints excluded: chain d residue 73 CYS Chi-restraints excluded: chain d residue 85 THR Chi-restraints excluded: chain d residue 107 ILE Chi-restraints excluded: chain d residue 115 THR Chi-restraints excluded: chain e residue 45 VAL Chi-restraints excluded: chain e residue 48 THR Chi-restraints excluded: chain e residue 57 ILE Chi-restraints excluded: chain e residue 61 HIS Chi-restraints excluded: chain e residue 66 ILE Chi-restraints excluded: chain e residue 119 CYS Chi-restraints excluded: chain e residue 123 MET Chi-restraints excluded: chain e residue 124 GLU Chi-restraints excluded: chain e residue 152 SER Chi-restraints excluded: chain f residue 36 TYR Chi-restraints excluded: chain f residue 48 THR Chi-restraints excluded: chain f residue 81 HIS Chi-restraints excluded: chain f residue 97 VAL Chi-restraints excluded: chain f residue 112 LEU Chi-restraints excluded: chain f residue 138 ILE Chi-restraints excluded: chain f residue 145 LEU Chi-restraints excluded: chain g residue 28 ASN Chi-restraints excluded: chain g residue 30 LEU Chi-restraints excluded: chain g residue 44 LEU Chi-restraints excluded: chain g residue 54 THR Chi-restraints excluded: chain g residue 92 ASN Chi-restraints excluded: chain g residue 97 LEU Chi-restraints excluded: chain g residue 103 MET Chi-restraints excluded: chain g residue 124 VAL Chi-restraints excluded: chain m residue 268 VAL Chi-restraints excluded: chain m residue 271 LEU Chi-restraints excluded: chain m residue 290 TRP Chi-restraints excluded: chain n residue 276 LEU Chi-restraints excluded: chain n residue 300 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 24 optimal weight: 0.0970 chunk 36 optimal weight: 0.5980 chunk 54 optimal weight: 0.8980 chunk 50 optimal weight: 0.5980 chunk 43 optimal weight: 1.9990 chunk 4 optimal weight: 1.9990 chunk 33 optimal weight: 0.5980 chunk 26 optimal weight: 1.9990 chunk 34 optimal weight: 0.8980 chunk 46 optimal weight: 6.9990 chunk 13 optimal weight: 0.7980 overall best weight: 0.5378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: f 33 GLN ** g 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 278 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6574 moved from start: 0.4398 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 4746 Z= 0.211 Angle : 0.785 9.749 6428 Z= 0.376 Chirality : 0.042 0.209 753 Planarity : 0.004 0.040 791 Dihedral : 4.850 37.214 637 Min Nonbonded Distance : 2.363 Molprobity Statistics. All-atom Clashscore : 9.83 Ramachandran Plot: Outliers : 0.88 % Allowed : 10.33 % Favored : 88.79 % Rotamer: Outliers : 7.46 % Allowed : 38.05 % Favored : 54.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.31 (0.36), residues: 571 helix: 3.67 (0.31), residues: 222 sheet: -2.39 (0.56), residues: 81 loop : -3.14 (0.31), residues: 268 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.043 0.003 TRP d 43 HIS 0.002 0.001 HIS e 81 PHE 0.007 0.001 PHE g 56 TYR 0.034 0.001 TYR f 99 ARG 0.002 0.000 ARG d 91 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1142 Ramachandran restraints generated. 571 Oldfield, 0 Emsley, 571 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1142 Ramachandran restraints generated. 571 Oldfield, 0 Emsley, 571 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 523 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 146 time to evaluate : 0.551 Fit side-chains revert: symmetry clash REVERT: b 54 LYS cc_start: 0.7017 (tptp) cc_final: 0.6730 (tptp) REVERT: e 34 THR cc_start: 0.8201 (p) cc_final: 0.7987 (p) REVERT: e 61 HIS cc_start: 0.6276 (OUTLIER) cc_final: 0.5697 (p90) REVERT: e 70 GLU cc_start: 0.7887 (tp30) cc_final: 0.7145 (mp0) REVERT: e 74 ASN cc_start: 0.8165 (m-40) cc_final: 0.7306 (p0) REVERT: e 123 MET cc_start: 0.7282 (OUTLIER) cc_final: 0.7000 (pmm) REVERT: e 128 MET cc_start: 0.6260 (tmm) cc_final: 0.5822 (tmm) REVERT: e 153 LYS cc_start: 0.7763 (ptpt) cc_final: 0.7533 (ptpt) REVERT: f 37 LYS cc_start: 0.6689 (tppt) cc_final: 0.5766 (ttmm) REVERT: f 56 GLU cc_start: 0.8133 (mm-30) cc_final: 0.7738 (tt0) REVERT: f 128 MET cc_start: 0.6747 (tmm) cc_final: 0.5543 (tpt) REVERT: f 137 ASP cc_start: 0.7816 (t70) cc_final: 0.7423 (t0) REVERT: g 72 TRP cc_start: 0.7145 (t-100) cc_final: 0.6657 (t60) REVERT: g 109 GLU cc_start: 0.8048 (tt0) cc_final: 0.7782 (tt0) REVERT: m 290 TRP cc_start: 0.6468 (OUTLIER) cc_final: 0.5788 (m100) outliers start: 39 outliers final: 33 residues processed: 170 average time/residue: 0.1397 time to fit residues: 30.9938 Evaluate side-chains 182 residues out of total 523 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 146 time to evaluate : 0.541 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 31 LEU Chi-restraints excluded: chain a residue 51 LEU Chi-restraints excluded: chain b residue 28 ASP Chi-restraints excluded: chain b residue 31 LEU Chi-restraints excluded: chain b residue 45 ILE Chi-restraints excluded: chain b residue 46 LEU Chi-restraints excluded: chain d residue 64 ILE Chi-restraints excluded: chain d residue 73 CYS Chi-restraints excluded: chain d residue 85 THR Chi-restraints excluded: chain d residue 107 ILE Chi-restraints excluded: chain d residue 115 THR Chi-restraints excluded: chain e residue 48 THR Chi-restraints excluded: chain e residue 57 ILE Chi-restraints excluded: chain e residue 61 HIS Chi-restraints excluded: chain e residue 66 ILE Chi-restraints excluded: chain e residue 119 CYS Chi-restraints excluded: chain e residue 123 MET Chi-restraints excluded: chain e residue 124 GLU Chi-restraints excluded: chain e residue 152 SER Chi-restraints excluded: chain f residue 36 TYR Chi-restraints excluded: chain f residue 48 THR Chi-restraints excluded: chain f residue 97 VAL Chi-restraints excluded: chain f residue 112 LEU Chi-restraints excluded: chain f residue 138 ILE Chi-restraints excluded: chain g residue 28 ASN Chi-restraints excluded: chain g residue 30 LEU Chi-restraints excluded: chain g residue 44 LEU Chi-restraints excluded: chain g residue 54 THR Chi-restraints excluded: chain g residue 92 ASN Chi-restraints excluded: chain g residue 97 LEU Chi-restraints excluded: chain g residue 124 VAL Chi-restraints excluded: chain m residue 268 VAL Chi-restraints excluded: chain m residue 271 LEU Chi-restraints excluded: chain m residue 290 TRP Chi-restraints excluded: chain n residue 276 LEU Chi-restraints excluded: chain n residue 300 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 40 optimal weight: 6.9990 chunk 6 optimal weight: 6.9990 chunk 12 optimal weight: 0.3980 chunk 43 optimal weight: 0.0970 chunk 18 optimal weight: 0.9980 chunk 44 optimal weight: 0.9990 chunk 5 optimal weight: 0.6980 chunk 8 optimal weight: 0.0470 chunk 38 optimal weight: 3.9990 chunk 2 optimal weight: 0.8980 chunk 31 optimal weight: 0.5980 overall best weight: 0.3676 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: f 33 GLN ** g 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 278 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4196 r_free = 0.4196 target = 0.180652 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3857 r_free = 0.3857 target = 0.147937 restraints weight = 6475.544| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3898 r_free = 0.3898 target = 0.151615 restraints weight = 4167.365| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3926 r_free = 0.3926 target = 0.154095 restraints weight = 3134.343| |-----------------------------------------------------------------------------| r_work (final): 0.3910 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7417 moved from start: 0.4508 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 4746 Z= 0.204 Angle : 0.794 10.928 6428 Z= 0.383 Chirality : 0.043 0.208 753 Planarity : 0.004 0.040 791 Dihedral : 4.829 36.673 637 Min Nonbonded Distance : 2.361 Molprobity Statistics. All-atom Clashscore : 10.68 Ramachandran Plot: Outliers : 0.88 % Allowed : 11.21 % Favored : 87.92 % Rotamer: Outliers : 6.69 % Allowed : 39.96 % Favored : 53.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.27 (0.36), residues: 571 helix: 3.75 (0.31), residues: 222 sheet: -2.36 (0.57), residues: 80 loop : -3.17 (0.30), residues: 269 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.044 0.003 TRP d 43 HIS 0.002 0.001 HIS e 81 PHE 0.007 0.001 PHE m 281 TYR 0.033 0.001 TYR f 99 ARG 0.002 0.000 ARG e 115 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1460.18 seconds wall clock time: 26 minutes 31.50 seconds (1591.50 seconds total)