Starting phenix.real_space_refine on Mon Jun 24 19:47:39 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wyi_37929/06_2024/8wyi_37929.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wyi_37929/06_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_37929/06_2024/8wyi_37929.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wyi_37929/06_2024/8wyi_37929.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wyi_37929/06_2024/8wyi_37929.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wyi_37929/06_2024/8wyi_37929.pdb" } 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: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/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: 3.28, per 1000 atoms: 0.70 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: 1.87 Conformation dependent library (CDL) restraints added in 805.2 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: 0.43 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: 1.07 Time building geometry restraints manager: 2.01 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 2.520 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 2.520 ... (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 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: 0.390 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: 1.850 Check model and map are aligned: 0.030 Set scattering table: 0.050 Process input model: 17.300 Find NCS groups from input model: 0.220 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:2.870 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.730 ------------------------------------------------------------------------------- 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 : 0.496 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: 0.1625 time to fit residues: 31.8538 Evaluate side-chains 152 residues out of total 523 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 147 time to evaluate : 0.536 ------------------------------------------------------------------------------- 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: 2.9990 chunk 41 optimal weight: 5.9990 chunk 23 optimal weight: 0.9990 chunk 14 optimal weight: 1.9990 chunk 28 optimal weight: 1.9990 chunk 22 optimal weight: 0.4980 chunk 43 optimal weight: 4.9990 chunk 16 optimal weight: 0.6980 chunk 26 optimal weight: 0.5980 chunk 32 optimal weight: 0.8980 chunk 49 optimal weight: 2.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** d 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** f 33 GLN g 92 ASN ** 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: 0.6567 moved from start: 0.1520 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 4746 Z= 0.219 Angle : 0.784 10.067 6428 Z= 0.381 Chirality : 0.043 0.172 753 Planarity : 0.005 0.052 791 Dihedral : 6.109 54.827 642 Min Nonbonded Distance : 2.234 Molprobity Statistics. All-atom Clashscore : 14.53 Ramachandran Plot: Outliers : 1.23 % Allowed : 13.49 % Favored : 85.29 % Rotamer: Outliers : 8.60 % Allowed : 33.27 % 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: -0.84 (0.36), residues: 571 helix: 3.48 (0.32), residues: 222 sheet: -3.32 (0.59), residues: 64 loop : -3.49 (0.28), residues: 285 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP d 43 HIS 0.002 0.001 HIS e 81 PHE 0.010 0.001 PHE m 281 TYR 0.021 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 197 residues out of total 523 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 152 time to evaluate : 0.547 Fit side-chains revert: symmetry clash REVERT: e 70 GLU cc_start: 0.7512 (tp30) cc_final: 0.6844 (mp0) REVERT: e 85 LYS cc_start: 0.8845 (mtpp) cc_final: 0.8274 (pttp) REVERT: e 128 MET cc_start: 0.6253 (tmm) cc_final: 0.6013 (tmm) REVERT: g 55 TRP cc_start: 0.5585 (m100) cc_final: 0.5115 (m100) REVERT: g 72 TRP cc_start: 0.8169 (t-100) cc_final: 0.7929 (t-100) REVERT: m 285 MET cc_start: 0.7680 (tpp) cc_final: 0.7477 (tpp) outliers start: 45 outliers final: 25 residues processed: 178 average time/residue: 0.1467 time to fit residues: 33.3374 Evaluate side-chains 167 residues out of total 523 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 142 time to evaluate : 0.493 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 44 VAL Chi-restraints excluded: chain a residue 51 LEU 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 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 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 112 LEU Chi-restraints excluded: chain f residue 138 ILE 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: 3.9990 chunk 15 optimal weight: 0.9980 chunk 41 optimal weight: 0.9980 chunk 34 optimal weight: 0.8980 chunk 13 optimal weight: 0.8980 chunk 50 optimal weight: 0.8980 chunk 54 optimal weight: 0.8980 chunk 44 optimal weight: 0.9980 chunk 49 optimal weight: 0.6980 chunk 17 optimal weight: 3.9990 chunk 40 optimal weight: 5.9990 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 ** both conformations clash, **PLEASE CHECK MANUALLY** 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: 0.6600 moved from start: 0.2217 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= 0.217 Angle : 0.747 9.855 6428 Z= 0.366 Chirality : 0.042 0.208 753 Planarity : 0.004 0.044 791 Dihedral : 5.072 33.404 637 Min Nonbonded Distance : 2.223 Molprobity Statistics. All-atom Clashscore : 14.42 Ramachandran Plot: Outliers : 1.23 % Allowed : 11.38 % Favored : 87.39 % Rotamer: Outliers : 10.90 % Allowed : 33.08 % 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: -0.81 (0.36), residues: 571 helix: 3.55 (0.31), residues: 222 sheet: -3.35 (0.57), residues: 64 loop : -3.51 (0.28), residues: 285 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP d 43 HIS 0.002 0.001 HIS e 81 PHE 0.006 0.001 PHE g 56 TYR 0.012 0.001 TYR f 96 ARG 0.004 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 214 residues out of total 523 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 157 time to evaluate : 0.597 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: e 61 HIS cc_start: 0.6537 (OUTLIER) cc_final: 0.5277 (p90) REVERT: e 64 LYS cc_start: 0.8013 (pptt) cc_final: 0.7805 (pptt) REVERT: e 70 GLU cc_start: 0.7634 (tp30) cc_final: 0.6959 (mp0) REVERT: e 85 LYS cc_start: 0.8834 (mtpp) cc_final: 0.8224 (pttp) REVERT: e 123 MET cc_start: 0.6941 (OUTLIER) cc_final: 0.6559 (pmm) REVERT: e 128 MET cc_start: 0.6116 (OUTLIER) cc_final: 0.5862 (tmm) REVERT: f 37 LYS cc_start: 0.6743 (tppt) cc_final: 0.6532 (tppt) REVERT: g 55 TRP cc_start: 0.5650 (m100) cc_final: 0.5207 (m100) REVERT: g 72 TRP cc_start: 0.8196 (t-100) cc_final: 0.7955 (t-100) REVERT: g 109 GLU cc_start: 0.7817 (tt0) cc_final: 0.7476 (tt0) outliers start: 57 outliers final: 36 residues processed: 191 average time/residue: 0.1475 time to fit residues: 36.1595 Evaluate side-chains 190 residues out of total 523 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 151 time to evaluate : 0.478 ------------------------------------------------------------------------------- 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 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 85 THR Chi-restraints excluded: chain d residue 88 VAL 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 57 ILE Chi-restraints excluded: chain e residue 61 HIS 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 128 MET 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 84 LEU Chi-restraints excluded: chain f residue 97 VAL Chi-restraints excluded: chain f residue 107 ASP 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 45 THR 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 271 LEU Chi-restraints excluded: chain m residue 286 THR Chi-restraints excluded: chain m residue 290 TRP Chi-restraints excluded: chain m residue 292 SER Chi-restraints excluded: chain n residue 276 LEU Chi-restraints excluded: chain n residue 293 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 49 optimal weight: 2.9990 chunk 37 optimal weight: 0.6980 chunk 25 optimal weight: 0.9980 chunk 5 optimal weight: 0.0070 chunk 23 optimal weight: 3.9990 chunk 33 optimal weight: 0.0040 chunk 50 optimal weight: 0.5980 chunk 53 optimal weight: 0.6980 chunk 26 optimal weight: 0.8980 chunk 47 optimal weight: 0.9990 chunk 14 optimal weight: 0.7980 overall best weight: 0.4010 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** d 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** f 33 GLN g 98 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: 0.6554 moved from start: 0.2716 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= 0.193 Angle : 0.762 12.868 6428 Z= 0.360 Chirality : 0.042 0.239 753 Planarity : 0.004 0.038 791 Dihedral : 5.000 35.663 637 Min Nonbonded Distance : 2.194 Molprobity Statistics. All-atom Clashscore : 13.68 Ramachandran Plot: Outliers : 0.88 % Allowed : 12.26 % Favored : 86.87 % Rotamer: Outliers : 8.41 % Allowed : 36.71 % Favored : 54.88 % 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: -0.70 (0.36), residues: 571 helix: 3.54 (0.31), residues: 222 sheet: -3.39 (0.56), residues: 62 loop : -3.32 (0.28), residues: 287 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP d 43 HIS 0.002 0.001 HIS e 81 PHE 0.008 0.001 PHE g 56 TYR 0.014 0.001 TYR f 36 ARG 0.003 0.000 ARG d 57 *********************** 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: 44 poor density : 147 time to evaluate : 0.627 Fit side-chains revert: symmetry clash REVERT: b 54 LYS cc_start: 0.6923 (tptp) cc_final: 0.6529 (tptp) REVERT: e 61 HIS cc_start: 0.6424 (OUTLIER) cc_final: 0.5435 (p90) REVERT: e 70 GLU cc_start: 0.7619 (tp30) cc_final: 0.6919 (mp0) REVERT: e 85 LYS cc_start: 0.8803 (mtpp) cc_final: 0.8176 (pttp) REVERT: e 117 ARG cc_start: 0.7086 (tpp80) cc_final: 0.6860 (tpp80) REVERT: e 123 MET cc_start: 0.6953 (OUTLIER) cc_final: 0.6627 (pmm) REVERT: e 128 MET cc_start: 0.6048 (OUTLIER) cc_final: 0.5771 (tmm) REVERT: f 60 GLN cc_start: 0.6614 (OUTLIER) cc_final: 0.6357 (mm-40) REVERT: g 55 TRP cc_start: 0.5399 (m100) cc_final: 0.5171 (m100) REVERT: g 95 LYS cc_start: 0.8155 (mtpp) cc_final: 0.7951 (pttt) REVERT: n 287 LEU cc_start: 0.8210 (OUTLIER) cc_final: 0.8006 (tm) outliers start: 44 outliers final: 25 residues processed: 174 average time/residue: 0.1513 time to fit residues: 33.6981 Evaluate side-chains 174 residues out of total 523 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 144 time to evaluate : 0.553 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 32 CYS Chi-restraints excluded: chain a residue 51 LEU Chi-restraints excluded: chain b residue 31 LEU Chi-restraints excluded: chain d residue 58 LEU Chi-restraints excluded: chain d residue 59 ASP 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 123 MET Chi-restraints excluded: chain e residue 124 GLU Chi-restraints excluded: chain e residue 128 MET Chi-restraints excluded: chain e residue 146 LEU Chi-restraints excluded: chain e residue 153 LYS Chi-restraints excluded: chain f residue 48 THR Chi-restraints excluded: chain f residue 60 GLN Chi-restraints excluded: chain f residue 81 HIS Chi-restraints excluded: chain f residue 84 LEU Chi-restraints excluded: chain f residue 112 LEU Chi-restraints excluded: chain f residue 122 CYS Chi-restraints excluded: chain f residue 138 ILE Chi-restraints excluded: chain g residue 30 LEU Chi-restraints excluded: chain g residue 53 ILE Chi-restraints excluded: chain g residue 92 ASN Chi-restraints excluded: chain g residue 97 LEU Chi-restraints excluded: chain n residue 276 LEU Chi-restraints excluded: chain n residue 287 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 44 optimal weight: 0.9990 chunk 30 optimal weight: 8.9990 chunk 0 optimal weight: 3.9990 chunk 39 optimal weight: 0.0370 chunk 21 optimal weight: 0.9990 chunk 45 optimal weight: 0.8980 chunk 36 optimal weight: 0.3980 chunk 27 optimal weight: 5.9990 chunk 47 optimal weight: 7.9990 chunk 13 optimal weight: 1.9990 chunk 17 optimal weight: 4.9990 overall best weight: 0.6662 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** d 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 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: 0.6586 moved from start: 0.2999 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= 0.202 Angle : 0.758 10.950 6428 Z= 0.365 Chirality : 0.042 0.234 753 Planarity : 0.004 0.036 791 Dihedral : 4.894 34.638 636 Min Nonbonded Distance : 2.194 Molprobity Statistics. All-atom Clashscore : 13.78 Ramachandran Plot: Outliers : 0.88 % Allowed : 12.43 % Favored : 86.69 % Rotamer: Outliers : 9.18 % Allowed : 35.56 % Favored : 55.26 % 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: -0.65 (0.36), residues: 571 helix: 3.56 (0.31), residues: 222 sheet: -3.04 (0.52), residues: 80 loop : -3.32 (0.28), residues: 269 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP d 43 HIS 0.001 0.000 HIS g 29 PHE 0.007 0.001 PHE f 110 TYR 0.019 0.001 TYR f 96 ARG 0.003 0.000 ARG d 57 *********************** 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 195 residues out of total 523 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 147 time to evaluate : 0.572 Fit side-chains revert: symmetry clash REVERT: b 54 LYS cc_start: 0.7029 (tptp) cc_final: 0.6680 (tptp) REVERT: e 61 HIS cc_start: 0.6518 (OUTLIER) cc_final: 0.5733 (p90) REVERT: e 70 GLU cc_start: 0.7752 (tp30) cc_final: 0.6987 (mp0) REVERT: e 85 LYS cc_start: 0.8841 (mtpp) cc_final: 0.8129 (pttp) REVERT: e 123 MET cc_start: 0.6994 (OUTLIER) cc_final: 0.6687 (pmm) REVERT: e 128 MET cc_start: 0.6137 (OUTLIER) cc_final: 0.5763 (tmm) REVERT: f 37 LYS cc_start: 0.6667 (tppt) cc_final: 0.6419 (tttt) REVERT: f 49 CYS cc_start: 0.5911 (OUTLIER) cc_final: 0.4957 (p) REVERT: g 55 TRP cc_start: 0.5432 (m100) cc_final: 0.5161 (m100) REVERT: g 72 TRP cc_start: 0.8227 (t-100) cc_final: 0.7886 (t-100) outliers start: 48 outliers final: 33 residues processed: 177 average time/residue: 0.1349 time to fit residues: 30.9474 Evaluate side-chains 179 residues out of total 523 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 142 time to evaluate : 0.493 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 32 CYS 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 53 SER 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 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 128 MET Chi-restraints excluded: chain e residue 153 LYS Chi-restraints excluded: chain f residue 48 THR Chi-restraints excluded: chain f residue 49 CYS Chi-restraints excluded: chain f residue 81 HIS Chi-restraints excluded: chain f residue 84 LEU Chi-restraints excluded: chain f residue 112 LEU Chi-restraints excluded: chain f residue 122 CYS Chi-restraints excluded: chain f residue 138 ILE Chi-restraints excluded: chain g residue 30 LEU Chi-restraints excluded: chain g residue 44 LEU Chi-restraints excluded: chain g residue 45 THR 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 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 47 optimal weight: 3.9990 chunk 10 optimal weight: 1.9990 chunk 31 optimal weight: 2.9990 chunk 13 optimal weight: 0.8980 chunk 53 optimal weight: 0.8980 chunk 44 optimal weight: 0.0980 chunk 24 optimal weight: 0.9980 chunk 4 optimal weight: 1.9990 chunk 17 optimal weight: 10.0000 chunk 27 optimal weight: 3.9990 chunk 51 optimal weight: 0.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** d 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** f 33 GLN ** g 98 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: 0.6603 moved from start: 0.3442 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 4746 Z= 0.207 Angle : 0.753 10.527 6428 Z= 0.362 Chirality : 0.042 0.221 753 Planarity : 0.004 0.040 791 Dihedral : 4.892 35.234 636 Min Nonbonded Distance : 2.168 Molprobity Statistics. All-atom Clashscore : 12.82 Ramachandran Plot: Outliers : 0.88 % Allowed : 12.43 % Favored : 86.69 % Rotamer: Outliers : 10.90 % Allowed : 34.61 % 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: -0.57 (0.36), residues: 571 helix: 3.62 (0.31), residues: 222 sheet: -2.96 (0.53), residues: 80 loop : -3.29 (0.28), residues: 269 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP d 43 HIS 0.002 0.001 HIS g 29 PHE 0.014 0.001 PHE g 56 TYR 0.035 0.002 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 202 residues out of total 523 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 145 time to evaluate : 0.485 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: b 54 LYS cc_start: 0.7039 (tptp) cc_final: 0.6693 (tptp) REVERT: d 27 GLU cc_start: 0.7709 (pm20) cc_final: 0.7405 (pm20) REVERT: e 61 HIS cc_start: 0.6601 (OUTLIER) cc_final: 0.5606 (p90) REVERT: e 70 GLU cc_start: 0.7789 (tp30) cc_final: 0.7000 (mp0) REVERT: e 85 LYS cc_start: 0.8877 (mtpp) cc_final: 0.8185 (pttp) REVERT: e 123 MET cc_start: 0.7052 (OUTLIER) cc_final: 0.6822 (pmm) REVERT: e 128 MET cc_start: 0.6190 (OUTLIER) cc_final: 0.5803 (tmm) REVERT: f 37 LYS cc_start: 0.6841 (tppt) cc_final: 0.6556 (tttt) REVERT: f 60 GLN cc_start: 0.7039 (OUTLIER) cc_final: 0.6837 (mm-40) REVERT: g 55 TRP cc_start: 0.5332 (m100) cc_final: 0.5083 (m100) REVERT: g 72 TRP cc_start: 0.8248 (t-100) cc_final: 0.8003 (t-100) outliers start: 57 outliers final: 40 residues processed: 182 average time/residue: 0.1323 time to fit residues: 31.4598 Evaluate side-chains 184 residues out of total 523 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 140 time to evaluate : 0.532 ------------------------------------------------------------------------------- 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 44 VAL 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 53 SER 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 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 123 MET Chi-restraints excluded: chain e residue 124 GLU Chi-restraints excluded: chain e residue 128 MET Chi-restraints excluded: chain e residue 146 LEU Chi-restraints excluded: chain e residue 153 LYS Chi-restraints excluded: chain f residue 48 THR Chi-restraints excluded: chain f residue 60 GLN Chi-restraints excluded: chain f residue 81 HIS Chi-restraints excluded: chain f residue 84 LEU 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 35 ASP Chi-restraints excluded: chain g residue 44 LEU Chi-restraints excluded: chain g residue 45 THR 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 133 VAL Chi-restraints excluded: chain m residue 268 VAL Chi-restraints excluded: chain n residue 276 LEU Chi-restraints excluded: chain n residue 293 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 5 optimal weight: 5.9990 chunk 30 optimal weight: 7.9990 chunk 38 optimal weight: 1.9990 chunk 44 optimal weight: 0.9990 chunk 29 optimal weight: 0.9990 chunk 53 optimal weight: 0.5980 chunk 33 optimal weight: 0.6980 chunk 32 optimal weight: 0.9980 chunk 24 optimal weight: 0.5980 chunk 21 optimal weight: 0.7980 chunk 31 optimal weight: 0.6980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** d 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 62 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: 0.6599 moved from start: 0.3610 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 4746 Z= 0.203 Angle : 0.755 9.446 6428 Z= 0.364 Chirality : 0.043 0.233 753 Planarity : 0.004 0.039 791 Dihedral : 4.865 36.426 636 Min Nonbonded Distance : 2.168 Molprobity Statistics. All-atom Clashscore : 12.29 Ramachandran Plot: Outliers : 0.88 % Allowed : 11.91 % Favored : 87.22 % Rotamer: Outliers : 10.33 % Allowed : 36.33 % 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: -0.46 (0.36), residues: 571 helix: 3.68 (0.31), residues: 222 sheet: -2.83 (0.53), residues: 80 loop : -3.21 (0.29), residues: 269 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP d 43 HIS 0.003 0.001 HIS g 29 PHE 0.009 0.001 PHE g 56 TYR 0.030 0.001 TYR f 99 ARG 0.003 0.000 ARG d 91 *********************** 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: 54 poor density : 144 time to evaluate : 0.546 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: b 54 LYS cc_start: 0.7115 (tptp) cc_final: 0.6778 (tptp) REVERT: d 27 GLU cc_start: 0.7722 (pm20) cc_final: 0.7442 (pm20) REVERT: e 61 HIS cc_start: 0.6419 (OUTLIER) cc_final: 0.5771 (p90) REVERT: e 70 GLU cc_start: 0.7913 (tp30) cc_final: 0.7131 (mp0) REVERT: e 85 LYS cc_start: 0.8856 (mtpp) cc_final: 0.8174 (pttp) REVERT: e 123 MET cc_start: 0.7086 (OUTLIER) cc_final: 0.6865 (pmm) REVERT: e 128 MET cc_start: 0.6220 (OUTLIER) cc_final: 0.5854 (tmm) REVERT: f 37 LYS cc_start: 0.6951 (tppt) cc_final: 0.6647 (tttt) REVERT: f 49 CYS cc_start: 0.5949 (OUTLIER) cc_final: 0.5436 (p) REVERT: f 137 ASP cc_start: 0.7847 (t70) cc_final: 0.7455 (t0) REVERT: g 55 TRP cc_start: 0.5317 (m100) cc_final: 0.5003 (m100) REVERT: g 110 LEU cc_start: 0.7629 (OUTLIER) cc_final: 0.7380 (mt) outliers start: 54 outliers final: 39 residues processed: 179 average time/residue: 0.1327 time to fit residues: 30.9682 Evaluate side-chains 184 residues out of total 523 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 140 time to evaluate : 0.497 ------------------------------------------------------------------------------- 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 b residue 28 ASP 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 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 128 MET Chi-restraints excluded: chain e residue 146 LEU Chi-restraints excluded: chain f residue 48 THR Chi-restraints excluded: chain f residue 49 CYS Chi-restraints excluded: chain f residue 81 HIS Chi-restraints excluded: chain f residue 84 LEU Chi-restraints excluded: chain f residue 107 ASP 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 30 LEU Chi-restraints excluded: chain g residue 35 ASP Chi-restraints excluded: chain g residue 44 LEU Chi-restraints excluded: chain g residue 45 THR 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 133 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 Chi-restraints excluded: chain n residue 293 VAL Chi-restraints excluded: chain n residue 300 THR 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: 2.9990 chunk 33 optimal weight: 4.9990 chunk 36 optimal weight: 0.4980 chunk 26 optimal weight: 0.9980 chunk 4 optimal weight: 0.9980 chunk 41 optimal weight: 5.9990 chunk 48 optimal weight: 1.9990 chunk 50 optimal weight: 0.6980 chunk 46 optimal weight: 2.9990 chunk 49 optimal weight: 1.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** d 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 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: 0.6619 moved from start: 0.3969 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= 0.214 Angle : 0.751 9.701 6428 Z= 0.363 Chirality : 0.043 0.226 753 Planarity : 0.004 0.038 791 Dihedral : 4.839 38.409 636 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 12.29 Ramachandran Plot: Outliers : 0.88 % Allowed : 12.08 % Favored : 87.04 % Rotamer: Outliers : 9.18 % Allowed : 37.09 % Favored : 53.73 % 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: -0.46 (0.36), residues: 571 helix: 3.67 (0.31), residues: 222 sheet: -2.77 (0.54), residues: 80 loop : -3.22 (0.29), residues: 269 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP d 43 HIS 0.003 0.001 HIS g 29 PHE 0.012 0.001 PHE g 56 TYR 0.032 0.001 TYR f 99 ARG 0.003 0.000 ARG d 91 *********************** 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 196 residues out of total 523 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 148 time to evaluate : 0.529 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: b 54 LYS cc_start: 0.7163 (tptp) cc_final: 0.6832 (tptp) REVERT: d 27 GLU cc_start: 0.7734 (pm20) cc_final: 0.7447 (pm20) REVERT: e 70 GLU cc_start: 0.7932 (tp30) cc_final: 0.7174 (mp0) REVERT: e 85 LYS cc_start: 0.8842 (mtpp) cc_final: 0.8117 (pttp) REVERT: e 117 ARG cc_start: 0.6966 (tpp80) cc_final: 0.6661 (tpp80) REVERT: e 123 MET cc_start: 0.7148 (OUTLIER) cc_final: 0.6905 (pmm) REVERT: e 128 MET cc_start: 0.6231 (OUTLIER) cc_final: 0.5865 (tmm) REVERT: e 150 TYR cc_start: 0.7864 (t80) cc_final: 0.7621 (t80) REVERT: f 37 LYS cc_start: 0.6975 (tppt) cc_final: 0.6654 (tttt) REVERT: g 55 TRP cc_start: 0.5361 (m100) cc_final: 0.5056 (m100) REVERT: g 110 LEU cc_start: 0.7671 (OUTLIER) cc_final: 0.7358 (mt) outliers start: 48 outliers final: 37 residues processed: 177 average time/residue: 0.1406 time to fit residues: 32.6952 Evaluate side-chains 187 residues out of total 523 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 147 time to evaluate : 0.474 ------------------------------------------------------------------------------- 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 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 46 LEU 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 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 48 THR Chi-restraints excluded: chain e residue 57 ILE 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 128 MET 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 107 ASP Chi-restraints excluded: chain f residue 138 ILE Chi-restraints excluded: chain f residue 145 LEU 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 45 THR 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 133 VAL Chi-restraints excluded: chain m residue 268 VAL Chi-restraints excluded: chain n residue 276 LEU Chi-restraints excluded: chain n residue 293 VAL Chi-restraints excluded: chain n residue 300 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 50 optimal weight: 1.9990 chunk 29 optimal weight: 0.5980 chunk 21 optimal weight: 1.9990 chunk 38 optimal weight: 3.9990 chunk 15 optimal weight: 0.9980 chunk 44 optimal weight: 0.7980 chunk 46 optimal weight: 0.8980 chunk 49 optimal weight: 0.9990 chunk 32 optimal weight: 0.6980 chunk 52 optimal weight: 1.9990 chunk 31 optimal weight: 0.0060 overall best weight: 0.5996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** d 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** f 33 GLN f 92 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: 0.6603 moved from start: 0.4087 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 4746 Z= 0.205 Angle : 0.770 11.419 6428 Z= 0.369 Chirality : 0.043 0.216 753 Planarity : 0.004 0.038 791 Dihedral : 4.808 37.061 636 Min Nonbonded Distance : 2.149 Molprobity Statistics. All-atom Clashscore : 12.39 Ramachandran Plot: Outliers : 0.88 % Allowed : 11.91 % Favored : 87.22 % Rotamer: Outliers : 7.65 % Allowed : 39.96 % Favored : 52.39 % 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: -0.38 (0.36), residues: 571 helix: 3.69 (0.31), residues: 222 sheet: -2.66 (0.54), residues: 80 loop : -3.16 (0.30), residues: 269 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.002 TRP d 43 HIS 0.003 0.001 HIS g 29 PHE 0.009 0.001 PHE g 56 TYR 0.030 0.001 TYR f 99 ARG 0.003 0.000 ARG d 91 *********************** 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 190 residues out of total 523 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 150 time to evaluate : 0.549 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: b 54 LYS cc_start: 0.7129 (tptp) cc_final: 0.6783 (tptp) REVERT: d 27 GLU cc_start: 0.7698 (pm20) cc_final: 0.7365 (pm20) REVERT: e 70 GLU cc_start: 0.7919 (tp30) cc_final: 0.7172 (mp0) REVERT: e 117 ARG cc_start: 0.6956 (tpp80) cc_final: 0.6659 (tpp80) REVERT: e 123 MET cc_start: 0.7141 (OUTLIER) cc_final: 0.6909 (pmm) REVERT: e 128 MET cc_start: 0.6250 (OUTLIER) cc_final: 0.5889 (tmm) REVERT: f 37 LYS cc_start: 0.6988 (tppt) cc_final: 0.6624 (tttt) REVERT: f 137 ASP cc_start: 0.7655 (t70) cc_final: 0.7078 (t0) REVERT: g 55 TRP cc_start: 0.5226 (m100) cc_final: 0.4953 (m100) REVERT: g 109 GLU cc_start: 0.7842 (tt0) cc_final: 0.7630 (tp30) REVERT: g 110 LEU cc_start: 0.7673 (OUTLIER) cc_final: 0.7453 (mt) outliers start: 40 outliers final: 35 residues processed: 174 average time/residue: 0.1433 time to fit residues: 32.2049 Evaluate side-chains 185 residues out of total 523 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 147 time to evaluate : 0.514 ------------------------------------------------------------------------------- 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 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 58 LEU Chi-restraints excluded: chain d residue 64 ILE Chi-restraints excluded: chain d residue 73 CYS Chi-restraints excluded: chain d residue 107 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 57 ILE 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 128 MET Chi-restraints excluded: chain f residue 33 GLN Chi-restraints excluded: chain f residue 48 THR Chi-restraints excluded: chain f residue 107 ASP 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 30 LEU Chi-restraints excluded: chain g residue 35 ASP Chi-restraints excluded: chain g residue 44 LEU Chi-restraints excluded: chain g residue 45 THR 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 m residue 268 VAL Chi-restraints excluded: chain n residue 276 LEU Chi-restraints excluded: chain n residue 293 VAL 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: 3.9990 chunk 36 optimal weight: 0.9990 chunk 54 optimal weight: 0.5980 chunk 50 optimal weight: 0.1980 chunk 43 optimal weight: 0.9990 chunk 4 optimal weight: 0.8980 chunk 33 optimal weight: 0.0980 chunk 26 optimal weight: 0.8980 chunk 34 optimal weight: 0.8980 chunk 46 optimal weight: 0.5980 chunk 13 optimal weight: 0.6980 overall best weight: 0.4380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** d 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 81 HIS f 33 GLN f 92 GLN ** 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: 0.6583 moved from start: 0.4323 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 4746 Z= 0.198 Angle : 0.758 10.009 6428 Z= 0.364 Chirality : 0.042 0.207 753 Planarity : 0.004 0.040 791 Dihedral : 4.736 36.604 636 Min Nonbonded Distance : 2.098 Molprobity Statistics. All-atom Clashscore : 12.07 Ramachandran Plot: Outliers : 0.88 % Allowed : 11.21 % Favored : 87.92 % Rotamer: Outliers : 7.07 % Allowed : 40.15 % Favored : 52.77 % 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: -0.32 (0.36), residues: 571 helix: 3.74 (0.31), residues: 222 sheet: -2.43 (0.57), residues: 74 loop : -3.20 (0.29), residues: 275 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.002 TRP d 43 HIS 0.003 0.001 HIS g 29 PHE 0.012 0.001 PHE g 56 TYR 0.032 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 187 residues out of total 523 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 150 time to evaluate : 0.483 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: b 54 LYS cc_start: 0.7155 (tptp) cc_final: 0.6816 (tptp) REVERT: e 59 TRP cc_start: 0.6970 (m100) cc_final: 0.6409 (m100) REVERT: e 70 GLU cc_start: 0.7896 (tp30) cc_final: 0.7149 (mp0) REVERT: e 74 ASN cc_start: 0.8150 (m-40) cc_final: 0.7278 (p0) REVERT: e 123 MET cc_start: 0.7189 (OUTLIER) cc_final: 0.6899 (pmm) REVERT: e 128 MET cc_start: 0.6229 (OUTLIER) cc_final: 0.5868 (tmm) REVERT: f 37 LYS cc_start: 0.6925 (tppt) cc_final: 0.6526 (tttt) REVERT: f 56 GLU cc_start: 0.8214 (mm-30) cc_final: 0.7794 (tt0) REVERT: f 137 ASP cc_start: 0.7660 (t70) cc_final: 0.7083 (t0) REVERT: g 55 TRP cc_start: 0.5199 (m100) cc_final: 0.4915 (m100) outliers start: 37 outliers final: 29 residues processed: 170 average time/residue: 0.1485 time to fit residues: 32.2982 Evaluate side-chains 178 residues out of total 523 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 147 time to evaluate : 0.549 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 31 LEU 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 b residue 28 ASP Chi-restraints excluded: chain b residue 31 LEU Chi-restraints excluded: chain d residue 58 LEU Chi-restraints excluded: chain d residue 64 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 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 128 MET Chi-restraints excluded: chain f residue 48 THR Chi-restraints excluded: chain f residue 107 ASP 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 44 LEU Chi-restraints excluded: chain g residue 45 THR 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 m residue 268 VAL Chi-restraints excluded: chain m residue 286 THR 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: 7.9990 chunk 12 optimal weight: 4.9990 chunk 43 optimal weight: 5.9990 chunk 18 optimal weight: 5.9990 chunk 44 optimal weight: 0.8980 chunk 5 optimal weight: 4.9990 chunk 8 optimal weight: 0.6980 chunk 38 optimal weight: 7.9990 chunk 2 optimal weight: 0.4980 chunk 31 optimal weight: 0.7980 overall best weight: 1.5782 ------------------------------------------------------------------------------- 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 275 GLN ** n 278 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4058 r_free = 0.4058 target = 0.167624 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3683 r_free = 0.3683 target = 0.134164 restraints weight = 6476.641| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3727 r_free = 0.3727 target = 0.137801 restraints weight = 4154.661| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3757 r_free = 0.3757 target = 0.140304 restraints weight = 3115.791| |-----------------------------------------------------------------------------| r_work (final): 0.3758 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7619 moved from start: 0.4497 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 4746 Z= 0.303 Angle : 0.842 10.429 6428 Z= 0.408 Chirality : 0.044 0.213 753 Planarity : 0.004 0.037 791 Dihedral : 4.970 34.847 636 Min Nonbonded Distance : 2.172 Molprobity Statistics. All-atom Clashscore : 15.71 Ramachandran Plot: Outliers : 0.88 % Allowed : 12.26 % Favored : 86.87 % Rotamer: Outliers : 8.41 % Allowed : 38.81 % Favored : 52.77 % 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: -0.48 (0.36), residues: 571 helix: 3.58 (0.31), residues: 222 sheet: -2.50 (0.54), residues: 80 loop : -3.28 (0.30), residues: 269 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.003 TRP d 43 HIS 0.002 0.001 HIS d 89 PHE 0.013 0.002 PHE n 296 TYR 0.032 0.002 TYR f 99 ARG 0.004 0.001 ARG d 91 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1435.94 seconds wall clock time: 26 minutes 18.69 seconds (1578.69 seconds total)