Starting phenix.real_space_refine on Thu Mar 6 02:58:47 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8wyi_37929/03_2025/8wyi_37929.cif Found real_map, /net/cci-nas-00/data/ceres_data/8wyi_37929/03_2025/8wyi_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/cci-nas-00/data/ceres_data/8wyi_37929/03_2025/8wyi_37929.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8wyi_37929/03_2025/8wyi_37929.map" model { file = "/net/cci-nas-00/data/ceres_data/8wyi_37929/03_2025/8wyi_37929.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8wyi_37929/03_2025/8wyi_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. Time to flip 8 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/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: 3.30, per 1000 atoms: 0.71 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 - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.19 Conformation dependent library (CDL) restraints added in 616.7 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: 0.42 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: 1.06 Time building geometry restraints manager: 1.44 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: 0.00 - 1.99: 6050 1.99 - 3.98: 302 3.98 - 5.96: 45 5.96 - 7.95: 22 7.95 - 9.94: 9 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: 0.560 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.180 Check model and map are aligned: 0.040 Set scattering table: 0.050 Process input model: 15.220 Find NCS groups from input model: 0.130 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:2.920 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.130 ------------------------------------------------------------------------------- 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 to be fit. rotamer outliers: 10 poor density : 153 time to evaluate : 0.469 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: 0.1639 time to fit residues: 32.0425 Evaluate side-chains 152 residues out of total 523 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 147 time to evaluate : 0.494 ------------------------------------------------------------------------------- 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: 0.6980 chunk 26 optimal weight: 1.9990 chunk 32 optimal weight: 3.9990 chunk 49 optimal weight: 0.7980 overall best weight: 0.7980 ------------------------------------------------------------------------------- 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 ** n 278 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4092 r_free = 0.4092 target = 0.170656 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3728 r_free = 0.3728 target = 0.138077 restraints weight = 6462.100| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3772 r_free = 0.3772 target = 0.141673 restraints weight = 4087.596| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3800 r_free = 0.3800 target = 0.143988 restraints weight = 3022.365| |-----------------------------------------------------------------------------| r_work (final): 0.3790 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7423 moved from start: 0.1662 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 4746 Z= 0.232 Angle : 0.807 9.845 6428 Z= 0.395 Chirality : 0.043 0.171 753 Planarity : 0.005 0.054 791 Dihedral : 6.170 53.693 642 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 11.43 Ramachandran Plot: Outliers : 1.23 % Allowed : 12.96 % Favored : 85.81 % Rotamer: Outliers : 8.60 % Allowed : 32.89 % Favored : 58.51 % 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: -0.88 (0.36), residues: 571 helix: 3.45 (0.31), residues: 222 sheet: -3.28 (0.58), residues: 64 loop : -3.54 (0.28), residues: 285 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP d 43 HIS 0.003 0.001 HIS e 81 PHE 0.010 0.001 PHE m 281 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 196 residues out of total 523 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 151 time to evaluate : 0.535 Fit side-chains revert: symmetry clash REVERT: d 91 ARG cc_start: 0.8936 (OUTLIER) cc_final: 0.8719 (tmm160) REVERT: g 55 TRP cc_start: 0.5929 (m100) cc_final: 0.5334 (m100) outliers start: 45 outliers final: 28 residues processed: 178 average time/residue: 0.1543 time to fit residues: 35.0258 Evaluate side-chains 170 residues out of total 523 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 141 time to evaluate : 0.506 ------------------------------------------------------------------------------- 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 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 136 VAL Chi-restraints excluded: chain e residue 153 LYS 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 m residue 290 TRP 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 53 optimal weight: 0.5980 chunk 5 optimal weight: 0.0060 chunk 14 optimal weight: 0.6980 chunk 3 optimal weight: 1.9990 chunk 41 optimal weight: 6.9990 chunk 23 optimal weight: 3.9990 chunk 49 optimal weight: 0.8980 chunk 32 optimal weight: 1.9990 chunk 37 optimal weight: 0.9990 chunk 6 optimal weight: 2.9990 chunk 7 optimal weight: 4.9990 overall best weight: 0.6398 ------------------------------------------------------------------------------- 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 f 92 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 = 0.4174 r_free = 0.4174 target = 0.177922 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3851 r_free = 0.3851 target = 0.147774 restraints weight = 6522.151| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3873 r_free = 0.3873 target = 0.150298 restraints weight = 4162.645| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3877 r_free = 0.3877 target = 0.150704 restraints weight = 3338.693| |-----------------------------------------------------------------------------| r_work (final): 0.3860 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7455 moved from start: 0.2265 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= 0.210 Angle : 0.767 9.502 6428 Z= 0.377 Chirality : 0.042 0.199 753 Planarity : 0.004 0.044 791 Dihedral : 5.736 53.149 639 Min Nonbonded Distance : 2.391 Molprobity Statistics. All-atom Clashscore : 11.43 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: -0.75 (0.35), residues: 571 helix: 3.51 (0.31), residues: 222 sheet: -3.18 (0.58), residues: 62 loop : -3.43 (0.28), residues: 287 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP d 43 HIS 0.002 0.001 HIS e 81 PHE 0.009 0.001 PHE m 281 TYR 0.014 0.001 TYR b 33 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 199 residues out of total 523 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 153 time to evaluate : 0.531 Fit side-chains revert: symmetry clash REVERT: e 36 TYR cc_start: 0.8634 (m-10) cc_final: 0.8293 (m-10) REVERT: e 133 ILE cc_start: 0.8988 (tp) cc_final: 0.8773 (tp) REVERT: f 36 TYR cc_start: 0.6084 (OUTLIER) cc_final: 0.5387 (t80) outliers start: 46 outliers final: 26 residues processed: 180 average time/residue: 0.1531 time to fit residues: 35.0378 Evaluate side-chains 172 residues out of total 523 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 145 time to evaluate : 0.489 ------------------------------------------------------------------------------- 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 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 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 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 271 LEU 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 36 optimal weight: 0.7980 chunk 18 optimal weight: 5.9990 chunk 48 optimal weight: 2.9990 chunk 49 optimal weight: 2.9990 chunk 3 optimal weight: 2.9990 chunk 20 optimal weight: 0.6980 chunk 5 optimal weight: 0.0170 chunk 39 optimal weight: 5.9990 chunk 46 optimal weight: 0.3980 chunk 41 optimal weight: 7.9990 chunk 38 optimal weight: 0.8980 overall best weight: 0.5618 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4173 r_free = 0.4173 target = 0.177909 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3815 r_free = 0.3815 target = 0.144992 restraints weight = 6570.877| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3860 r_free = 0.3860 target = 0.148992 restraints weight = 4061.114| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3890 r_free = 0.3890 target = 0.151728 restraints weight = 2972.125| |-----------------------------------------------------------------------------| r_work (final): 0.3857 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7411 moved from start: 0.2827 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= 0.198 Angle : 0.779 12.645 6428 Z= 0.373 Chirality : 0.043 0.233 753 Planarity : 0.004 0.039 791 Dihedral : 5.052 35.278 637 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 11.65 Ramachandran Plot: Outliers : 1.05 % Allowed : 11.91 % Favored : 87.04 % Rotamer: Outliers : 9.18 % Allowed : 35.18 % Favored : 55.64 % 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: 3.54 (0.31), residues: 222 sheet: -3.05 (0.54), residues: 80 loop : -3.30 (0.29), residues: 269 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP d 43 HIS 0.002 0.001 HIS g 29 PHE 0.006 0.001 PHE n 296 TYR 0.016 0.001 TYR f 52 ARG 0.003 0.000 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 193 residues out of total 523 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 145 time to evaluate : 0.550 Fit side-chains REVERT: b 34 LEU cc_start: 0.7686 (OUTLIER) cc_final: 0.7424 (tm) REVERT: e 85 LYS cc_start: 0.8153 (pttp) cc_final: 0.7806 (mtpp) REVERT: e 133 ILE cc_start: 0.8993 (tp) cc_final: 0.8768 (tp) REVERT: f 137 ASP cc_start: 0.8329 (t70) cc_final: 0.8100 (t70) REVERT: g 88 LYS cc_start: 0.8195 (mptt) cc_final: 0.7710 (mptt) outliers start: 48 outliers final: 30 residues processed: 175 average time/residue: 0.1513 time to fit residues: 33.8477 Evaluate side-chains 173 residues out of total 523 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 142 time to evaluate : 0.520 ------------------------------------------------------------------------------- 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 b residue 34 LEU Chi-restraints excluded: chain d residue 31 ASP Chi-restraints excluded: chain d residue 58 LEU 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 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 44 LEU Chi-restraints excluded: chain g residue 53 ILE 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 271 LEU Chi-restraints excluded: chain n residue 276 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 14 optimal weight: 0.9990 chunk 6 optimal weight: 4.9990 chunk 45 optimal weight: 0.8980 chunk 16 optimal weight: 3.9990 chunk 54 optimal weight: 0.9980 chunk 48 optimal weight: 0.6980 chunk 2 optimal weight: 0.9980 chunk 13 optimal weight: 0.5980 chunk 33 optimal weight: 0.4980 chunk 20 optimal weight: 0.9980 chunk 42 optimal weight: 1.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: f 33 GLN f 92 GLN ** n 278 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4150 r_free = 0.4150 target = 0.176011 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3825 r_free = 0.3825 target = 0.145357 restraints weight = 6679.006| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3846 r_free = 0.3846 target = 0.148084 restraints weight = 4382.581| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3852 r_free = 0.3852 target = 0.148634 restraints weight = 3432.733| |-----------------------------------------------------------------------------| r_work (final): 0.3838 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7481 moved from start: 0.3204 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= 0.209 Angle : 0.776 10.561 6428 Z= 0.376 Chirality : 0.043 0.231 753 Planarity : 0.004 0.037 791 Dihedral : 5.077 35.408 637 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 12.18 Ramachandran Plot: Outliers : 0.88 % Allowed : 11.03 % Favored : 88.09 % Rotamer: Outliers : 9.94 % Allowed : 34.23 % Favored : 55.83 % 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: 3.57 (0.31), residues: 222 sheet: -2.98 (0.54), residues: 80 loop : -3.19 (0.29), 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 0.007 0.001 PHE g 56 TYR 0.020 0.001 TYR f 52 ARG 0.004 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 197 residues out of total 523 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 145 time to evaluate : 0.491 Fit side-chains REVERT: b 34 LEU cc_start: 0.7722 (OUTLIER) cc_final: 0.7449 (tm) REVERT: b 54 LYS cc_start: 0.7889 (tptp) cc_final: 0.7392 (tptp) REVERT: e 61 HIS cc_start: 0.7367 (OUTLIER) cc_final: 0.6246 (p90) REVERT: e 85 LYS cc_start: 0.8023 (pttp) cc_final: 0.7765 (mtpp) REVERT: e 128 MET cc_start: 0.6484 (tmm) cc_final: 0.6171 (tmm) REVERT: e 133 ILE cc_start: 0.9075 (tp) cc_final: 0.8856 (tp) REVERT: f 36 TYR cc_start: 0.6465 (OUTLIER) cc_final: 0.5292 (t80) REVERT: f 90 LEU cc_start: 0.7819 (mt) cc_final: 0.7618 (mt) REVERT: f 137 ASP cc_start: 0.8487 (t70) cc_final: 0.7758 (t0) outliers start: 52 outliers final: 38 residues processed: 177 average time/residue: 0.1508 time to fit residues: 33.9067 Evaluate side-chains 185 residues out of total 523 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 144 time to evaluate : 0.562 ------------------------------------------------------------------------------- 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 34 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 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 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 84 LEU Chi-restraints excluded: chain f residue 97 VAL Chi-restraints excluded: chain f residue 112 LEU Chi-restraints excluded: chain f residue 122 CYS 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 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 28 optimal weight: 0.9990 chunk 3 optimal weight: 1.9990 chunk 21 optimal weight: 0.9990 chunk 31 optimal weight: 1.9990 chunk 9 optimal weight: 0.5980 chunk 43 optimal weight: 1.9990 chunk 42 optimal weight: 3.9990 chunk 53 optimal weight: 1.9990 chunk 10 optimal weight: 0.1980 chunk 22 optimal weight: 0.0980 chunk 24 optimal weight: 0.9990 overall best weight: 0.5784 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4166 r_free = 0.4166 target = 0.177404 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3815 r_free = 0.3815 target = 0.145147 restraints weight = 6601.562| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3860 r_free = 0.3860 target = 0.149050 restraints weight = 4103.425| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3885 r_free = 0.3885 target = 0.151454 restraints weight = 3004.848| |-----------------------------------------------------------------------------| r_work (final): 0.3868 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7432 moved from start: 0.3528 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= 0.209 Angle : 0.783 9.839 6428 Z= 0.380 Chirality : 0.042 0.231 753 Planarity : 0.004 0.036 791 Dihedral : 4.985 36.349 637 Min Nonbonded Distance : 2.348 Molprobity Statistics. All-atom Clashscore : 11.86 Ramachandran Plot: Outliers : 0.88 % Allowed : 11.03 % Favored : 88.09 % Rotamer: Outliers : 10.33 % Allowed : 34.42 % 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: -0.48 (0.36), residues: 571 helix: 3.62 (0.31), residues: 222 sheet: -2.88 (0.54), residues: 80 loop : -3.18 (0.29), residues: 269 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP d 43 HIS 0.005 0.001 HIS g 29 PHE 0.011 0.001 PHE g 56 TYR 0.038 0.001 TYR f 99 ARG 0.002 0.000 ARG d 57 *********************** 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 201 residues out of total 523 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 147 time to evaluate : 0.546 Fit side-chains REVERT: b 34 LEU cc_start: 0.7648 (OUTLIER) cc_final: 0.7398 (tm) REVERT: b 54 LYS cc_start: 0.7808 (tptp) cc_final: 0.7328 (tptp) REVERT: e 61 HIS cc_start: 0.7369 (OUTLIER) cc_final: 0.6154 (p90) REVERT: e 128 MET cc_start: 0.6415 (tmm) cc_final: 0.6090 (tmm) REVERT: e 133 ILE cc_start: 0.9062 (tp) cc_final: 0.8839 (tp) REVERT: f 36 TYR cc_start: 0.6306 (OUTLIER) cc_final: 0.4957 (t80) REVERT: f 137 ASP cc_start: 0.8479 (t70) cc_final: 0.7768 (t0) outliers start: 54 outliers final: 38 residues processed: 182 average time/residue: 0.1464 time to fit residues: 34.2772 Evaluate side-chains 183 residues out of total 523 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 142 time to evaluate : 0.543 ------------------------------------------------------------------------------- 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 34 LEU Chi-restraints excluded: chain d residue 31 ASP 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 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 84 LEU 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 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 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 m residue 291 SER 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 48 optimal weight: 0.8980 chunk 4 optimal weight: 1.9990 chunk 37 optimal weight: 0.7980 chunk 1 optimal weight: 1.9990 chunk 23 optimal weight: 4.9990 chunk 17 optimal weight: 0.9990 chunk 53 optimal weight: 0.8980 chunk 52 optimal weight: 0.6980 chunk 36 optimal weight: 0.4980 chunk 39 optimal weight: 5.9990 chunk 51 optimal weight: 0.6980 overall best weight: 0.7180 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4158 r_free = 0.4158 target = 0.176563 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3795 r_free = 0.3795 target = 0.143466 restraints weight = 6615.028| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3842 r_free = 0.3842 target = 0.147548 restraints weight = 4089.788| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3873 r_free = 0.3873 target = 0.150297 restraints weight = 2987.800| |-----------------------------------------------------------------------------| r_work (final): 0.3854 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7445 moved from start: 0.3717 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= 0.215 Angle : 0.782 9.550 6428 Z= 0.380 Chirality : 0.042 0.228 753 Planarity : 0.004 0.037 791 Dihedral : 5.056 35.869 637 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 10.90 Ramachandran Plot: Outliers : 0.88 % Allowed : 11.73 % Favored : 87.39 % Rotamer: Outliers : 10.52 % Allowed : 34.80 % 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: -0.35 (0.36), residues: 571 helix: 3.64 (0.31), residues: 222 sheet: -2.64 (0.56), residues: 80 loop : -3.07 (0.30), residues: 269 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 0.007 0.001 PHE g 56 TYR 0.034 0.001 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 197 residues out of total 523 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 142 time to evaluate : 0.494 Fit side-chains REVERT: b 34 LEU cc_start: 0.7664 (OUTLIER) cc_final: 0.7410 (tm) REVERT: b 54 LYS cc_start: 0.7895 (tptp) cc_final: 0.7458 (tptp) REVERT: e 61 HIS cc_start: 0.7468 (OUTLIER) cc_final: 0.6423 (p90) REVERT: e 85 LYS cc_start: 0.8057 (pttp) cc_final: 0.7823 (mtpp) REVERT: e 128 MET cc_start: 0.6445 (tmm) cc_final: 0.6106 (tmm) REVERT: f 36 TYR cc_start: 0.6255 (OUTLIER) cc_final: 0.4927 (t80) REVERT: f 137 ASP cc_start: 0.8480 (t70) cc_final: 0.7751 (t0) REVERT: g 110 LEU cc_start: 0.8441 (OUTLIER) cc_final: 0.8150 (mt) outliers start: 55 outliers final: 41 residues processed: 177 average time/residue: 0.1373 time to fit residues: 31.5629 Evaluate side-chains 184 residues out of total 523 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 139 time to evaluate : 0.555 ------------------------------------------------------------------------------- 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 34 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 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 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 84 LEU 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 29 HIS Chi-restraints excluded: chain g residue 30 LEU Chi-restraints excluded: chain g residue 35 ASP 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 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 m residue 291 SER 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 7 optimal weight: 4.9990 chunk 24 optimal weight: 0.6980 chunk 54 optimal weight: 1.9990 chunk 20 optimal weight: 0.4980 chunk 53 optimal weight: 0.5980 chunk 48 optimal weight: 0.9980 chunk 52 optimal weight: 0.9980 chunk 9 optimal weight: 2.9990 chunk 43 optimal weight: 1.9990 chunk 26 optimal weight: 0.7980 chunk 5 optimal weight: 0.0060 overall best weight: 0.5196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: f 33 GLN g 29 HIS ** n 278 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4176 r_free = 0.4176 target = 0.178567 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3824 r_free = 0.3824 target = 0.146135 restraints weight = 6604.561| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3869 r_free = 0.3869 target = 0.150054 restraints weight = 4197.132| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3899 r_free = 0.3899 target = 0.152714 restraints weight = 3092.107| |-----------------------------------------------------------------------------| r_work (final): 0.3880 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7430 moved from start: 0.4067 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 : 0.774 9.811 6428 Z= 0.375 Chirality : 0.043 0.221 753 Planarity : 0.004 0.038 791 Dihedral : 5.037 38.980 637 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 10.36 Ramachandran Plot: Outliers : 0.88 % Allowed : 10.51 % Favored : 88.62 % Rotamer: Outliers : 9.56 % Allowed : 35.76 % 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: -0.27 (0.36), residues: 571 helix: 3.72 (0.31), residues: 222 sheet: -2.48 (0.56), residues: 81 loop : -3.07 (0.30), residues: 268 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.002 TRP d 43 HIS 0.004 0.001 HIS g 29 PHE 0.010 0.001 PHE g 56 TYR 0.034 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 193 residues out of total 523 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 143 time to evaluate : 0.888 Fit side-chains REVERT: b 34 LEU cc_start: 0.7613 (OUTLIER) cc_final: 0.7384 (tm) REVERT: b 54 LYS cc_start: 0.7914 (tptp) cc_final: 0.7495 (tptp) REVERT: e 61 HIS cc_start: 0.7301 (OUTLIER) cc_final: 0.6411 (p90) REVERT: e 128 MET cc_start: 0.6356 (tmm) cc_final: 0.5998 (tmm) REVERT: f 37 LYS cc_start: 0.6762 (tppt) cc_final: 0.5947 (ttmm) REVERT: f 137 ASP cc_start: 0.8444 (t70) cc_final: 0.7789 (t0) REVERT: g 95 LYS cc_start: 0.7939 (OUTLIER) cc_final: 0.7687 (ptmt) REVERT: g 98 GLN cc_start: 0.6083 (OUTLIER) cc_final: 0.5602 (tm-30) REVERT: g 110 LEU cc_start: 0.8459 (OUTLIER) cc_final: 0.8136 (mt) outliers start: 50 outliers final: 35 residues processed: 175 average time/residue: 0.1443 time to fit residues: 32.5503 Evaluate side-chains 179 residues out of total 523 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 139 time to evaluate : 0.548 ------------------------------------------------------------------------------- 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 34 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 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 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 152 SER 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 30 LEU Chi-restraints excluded: chain g residue 35 ASP 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 95 LYS Chi-restraints excluded: chain g residue 97 LEU Chi-restraints excluded: chain g residue 98 GLN Chi-restraints excluded: chain g residue 110 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 291 SER 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 33 optimal weight: 0.9980 chunk 46 optimal weight: 0.9980 chunk 2 optimal weight: 0.0970 chunk 35 optimal weight: 1.9990 chunk 16 optimal weight: 0.8980 chunk 23 optimal weight: 2.9990 chunk 39 optimal weight: 0.0270 chunk 42 optimal weight: 0.9990 chunk 9 optimal weight: 6.9990 chunk 12 optimal weight: 0.5980 chunk 41 optimal weight: 0.0570 overall best weight: 0.3354 ------------------------------------------------------------------------------- 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 ** n 278 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4197 r_free = 0.4197 target = 0.180237 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3853 r_free = 0.3853 target = 0.147911 restraints weight = 6596.728| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3897 r_free = 0.3897 target = 0.151809 restraints weight = 4111.220| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3928 r_free = 0.3928 target = 0.154513 restraints weight = 3018.387| |-----------------------------------------------------------------------------| r_work (final): 0.3912 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7386 moved from start: 0.4240 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 4746 Z= 0.207 Angle : 0.779 9.836 6428 Z= 0.377 Chirality : 0.042 0.214 753 Planarity : 0.004 0.039 791 Dihedral : 4.907 37.588 637 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 9.40 Ramachandran Plot: Outliers : 0.88 % Allowed : 11.38 % Favored : 87.74 % Rotamer: Outliers : 7.84 % Allowed : 37.86 % Favored : 54.30 % 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: -0.23 (0.36), residues: 571 helix: 3.72 (0.31), residues: 222 sheet: -2.46 (0.56), residues: 81 loop : -3.02 (0.31), residues: 268 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.002 TRP d 43 HIS 0.002 0.000 HIS f 61 PHE 0.006 0.001 PHE g 56 TYR 0.031 0.001 TYR f 99 ARG 0.002 0.000 ARG e 115 *********************** 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 182 residues out of total 523 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 141 time to evaluate : 0.487 Fit side-chains REVERT: b 34 LEU cc_start: 0.7561 (OUTLIER) cc_final: 0.7323 (tm) REVERT: b 54 LYS cc_start: 0.7811 (tptp) cc_final: 0.7426 (tptp) REVERT: e 61 HIS cc_start: 0.7162 (OUTLIER) cc_final: 0.6686 (p90) REVERT: e 128 MET cc_start: 0.6324 (tmm) cc_final: 0.5983 (tmm) REVERT: f 37 LYS cc_start: 0.6691 (tppt) cc_final: 0.5966 (ttmm) REVERT: f 92 GLN cc_start: 0.6940 (tp-100) cc_final: 0.6166 (tt0) REVERT: f 128 MET cc_start: 0.6938 (tmm) cc_final: 0.5558 (tpt) REVERT: f 137 ASP cc_start: 0.8448 (t70) cc_final: 0.7907 (t0) REVERT: g 95 LYS cc_start: 0.7924 (OUTLIER) cc_final: 0.7666 (ptmt) REVERT: g 103 MET cc_start: 0.7190 (OUTLIER) cc_final: 0.6742 (mmm) REVERT: g 110 LEU cc_start: 0.8469 (OUTLIER) cc_final: 0.8101 (mt) REVERT: m 289 LEU cc_start: 0.8253 (mt) cc_final: 0.7410 (mt) REVERT: m 290 TRP cc_start: 0.5866 (m100) cc_final: 0.5569 (m100) outliers start: 41 outliers final: 28 residues processed: 168 average time/residue: 0.1475 time to fit residues: 31.8735 Evaluate side-chains 169 residues out of total 523 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 136 time to evaluate : 0.536 ------------------------------------------------------------------------------- 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 34 LEU Chi-restraints excluded: chain b residue 45 ILE 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 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 66 ILE Chi-restraints excluded: chain e residue 119 CYS Chi-restraints excluded: chain e residue 152 SER 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 44 LEU Chi-restraints excluded: chain g residue 54 THR Chi-restraints excluded: chain g residue 92 ASN Chi-restraints excluded: chain g residue 95 LYS Chi-restraints excluded: chain g residue 97 LEU Chi-restraints excluded: chain g residue 103 MET 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 286 THR Chi-restraints excluded: chain m residue 291 SER 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 4 optimal weight: 1.9990 chunk 1 optimal weight: 2.9990 chunk 28 optimal weight: 1.9990 chunk 34 optimal weight: 0.8980 chunk 43 optimal weight: 2.9990 chunk 19 optimal weight: 4.9990 chunk 10 optimal weight: 0.7980 chunk 35 optimal weight: 1.9990 chunk 54 optimal weight: 0.9990 chunk 0 optimal weight: 1.9990 chunk 44 optimal weight: 5.9990 overall best weight: 1.3386 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4104 r_free = 0.4104 target = 0.171493 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3722 r_free = 0.3722 target = 0.137341 restraints weight = 6573.291| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3768 r_free = 0.3768 target = 0.141178 restraints weight = 4188.142| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3798 r_free = 0.3798 target = 0.143716 restraints weight = 3113.518| |-----------------------------------------------------------------------------| r_work (final): 0.3781 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7567 moved from start: 0.4552 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 4746 Z= 0.285 Angle : 0.849 11.532 6428 Z= 0.409 Chirality : 0.045 0.222 753 Planarity : 0.004 0.039 791 Dihedral : 5.139 35.555 637 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 12.29 Ramachandran Plot: Outliers : 1.05 % Allowed : 12.08 % Favored : 86.87 % Rotamer: Outliers : 6.50 % Allowed : 39.58 % Favored : 53.92 % 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: 3.55 (0.30), residues: 223 sheet: -2.46 (0.56), residues: 81 loop : -3.15 (0.30), residues: 267 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.045 0.003 TRP d 43 HIS 0.003 0.001 HIS d 89 PHE 0.010 0.001 PHE n 296 TYR 0.028 0.002 TYR f 99 ARG 0.010 0.001 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 182 residues out of total 523 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 148 time to evaluate : 0.493 Fit side-chains REVERT: b 34 LEU cc_start: 0.7772 (OUTLIER) cc_final: 0.7522 (tm) REVERT: b 54 LYS cc_start: 0.8015 (tptp) cc_final: 0.7565 (tptp) REVERT: e 61 HIS cc_start: 0.7884 (OUTLIER) cc_final: 0.7076 (p90) REVERT: e 85 LYS cc_start: 0.8269 (pttp) cc_final: 0.7932 (mtpp) REVERT: e 128 MET cc_start: 0.6554 (tmm) cc_final: 0.6170 (tmm) REVERT: f 37 LYS cc_start: 0.7167 (tppt) cc_final: 0.6374 (ttmm) REVERT: f 137 ASP cc_start: 0.8473 (t70) cc_final: 0.7798 (t0) REVERT: g 95 LYS cc_start: 0.7975 (OUTLIER) cc_final: 0.7732 (ptmt) REVERT: m 260 LYS cc_start: 0.9047 (mppt) cc_final: 0.8841 (mppt) outliers start: 34 outliers final: 26 residues processed: 173 average time/residue: 0.1415 time to fit residues: 31.7512 Evaluate side-chains 173 residues out of total 523 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 144 time to evaluate : 0.580 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 51 LEU Chi-restraints excluded: chain b residue 31 LEU Chi-restraints excluded: chain b residue 34 LEU Chi-restraints excluded: chain b residue 45 ILE 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 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 66 ILE Chi-restraints excluded: chain e residue 119 CYS Chi-restraints excluded: chain e residue 152 SER Chi-restraints excluded: chain f residue 97 VAL 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 54 THR Chi-restraints excluded: chain g residue 92 ASN Chi-restraints excluded: chain g residue 95 LYS 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 286 THR Chi-restraints excluded: chain m residue 291 SER 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 15 optimal weight: 1.9990 chunk 11 optimal weight: 0.9980 chunk 5 optimal weight: 1.9990 chunk 32 optimal weight: 1.9990 chunk 47 optimal weight: 0.7980 chunk 25 optimal weight: 7.9990 chunk 43 optimal weight: 6.9990 chunk 9 optimal weight: 4.9990 chunk 51 optimal weight: 0.7980 chunk 12 optimal weight: 0.8980 overall best weight: 1.0982 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4114 r_free = 0.4114 target = 0.172635 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3748 r_free = 0.3748 target = 0.139167 restraints weight = 6648.584| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3793 r_free = 0.3793 target = 0.142947 restraints weight = 4240.859| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3822 r_free = 0.3822 target = 0.145454 restraints weight = 3162.198| |-----------------------------------------------------------------------------| r_work (final): 0.3803 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7545 moved from start: 0.4623 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 4746 Z= 0.262 Angle : 0.834 10.291 6428 Z= 0.406 Chirality : 0.044 0.215 753 Planarity : 0.004 0.039 791 Dihedral : 5.145 37.742 637 Min Nonbonded Distance : 2.360 Molprobity Statistics. All-atom Clashscore : 12.72 Ramachandran Plot: Outliers : 1.05 % Allowed : 11.73 % Favored : 87.22 % Rotamer: Outliers : 6.69 % Allowed : 41.49 % Favored : 51.82 % 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: -0.45 (0.36), residues: 571 helix: 3.50 (0.30), residues: 223 sheet: -2.48 (0.57), residues: 80 loop : -3.18 (0.30), residues: 268 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.046 0.003 TRP d 43 HIS 0.002 0.001 HIS e 81 PHE 0.009 0.001 PHE f 110 TYR 0.032 0.002 TYR f 99 ARG 0.009 0.001 ARG d 91 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1869.76 seconds wall clock time: 33 minutes 24.10 seconds (2004.10 seconds total)