Starting phenix.real_space_refine on Mon Jan 13 23:58:45 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8wyi_37929/01_2025/8wyi_37929.cif Found real_map, /net/cci-nas-00/data/ceres_data/8wyi_37929/01_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_37929/01_2025/8wyi_37929.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8wyi_37929/01_2025/8wyi_37929.map" model { file = "/net/cci-nas-00/data/ceres_data/8wyi_37929/01_2025/8wyi_37929.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8wyi_37929/01_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): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/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: 3.15, per 1000 atoms: 0.68 Number of scatterers: 4659 At special positions: 0 Unit cell: (70.0245, 89.4159, 107.73, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 37 16.00 O 861 8.00 N 743 7.00 C 3018 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=8, symmetry=0 Simple disulfide: pdb=" SG CYS a 32 " - pdb=" SG CYS b 32 " distance=2.03 Simple disulfide: pdb=" SG CYS d 37 " - pdb=" SG CYS d 73 " distance=2.04 Simple disulfide: pdb=" SG CYS d 93 " - pdb=" SG CYS d 96 " distance=2.03 Simple disulfide: pdb=" SG CYS e 49 " - pdb=" SG CYS e 98 " distance=2.03 Simple disulfide: pdb=" SG CYS e 119 " - pdb=" SG CYS e 122 " distance=2.03 Simple disulfide: pdb=" SG CYS f 49 " - pdb=" SG CYS f 98 " distance=2.03 Simple disulfide: pdb=" SG CYS g 46 " - pdb=" SG CYS g 87 " distance=2.03 Simple disulfide: pdb=" SG CYS g 104 " - pdb=" SG CYS g 107 " distance=2.02 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 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: 0.94 Conformation dependent library (CDL) restraints added in 506.0 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: 0.39 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: 1.02 Time building geometry restraints manager: 1.13 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: 0.350 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: 0.160 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 13.840 Find NCS groups from input model: 0.120 Set up NCS constraints: 0.010 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:2.580 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.140 ------------------------------------------------------------------------------- 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 : 0.490 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: 0.1617 time to fit residues: 31.6984 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 : 0.524 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain d residue 31 ASP Chi-restraints excluded: chain f residue 97 VAL Chi-restraints excluded: chain f residue 138 ILE Chi-restraints excluded: chain m residue 258 THR Chi-restraints excluded: chain m residue 290 TRP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 46 optimal weight: 3.9990 chunk 41 optimal weight: 8.9990 chunk 23 optimal weight: 0.9980 chunk 14 optimal weight: 0.9980 chunk 28 optimal weight: 3.9990 chunk 22 optimal weight: 0.4980 chunk 43 optimal weight: 7.9990 chunk 16 optimal weight: 0.9980 chunk 26 optimal weight: 1.9990 chunk 32 optimal weight: 3.9990 chunk 49 optimal weight: 0.7980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: d 38 ASN e 62 ASN f 33 GLN ** g 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 278 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4088 r_free = 0.4088 target = 0.170296 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3721 r_free = 0.3721 target = 0.137524 restraints weight = 6460.433| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3766 r_free = 0.3766 target = 0.141126 restraints weight = 4119.963| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3796 r_free = 0.3796 target = 0.143551 restraints weight = 3063.135| |-----------------------------------------------------------------------------| r_work (final): 0.3780 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7435 moved from start: 0.1609 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 4746 Z= 0.238 Angle : 0.813 9.832 6428 Z= 0.398 Chirality : 0.043 0.173 753 Planarity : 0.005 0.054 791 Dihedral : 6.173 53.445 642 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 11.65 Ramachandran Plot: Outliers : 1.23 % Allowed : 13.31 % Favored : 85.46 % Rotamer: Outliers : 8.41 % Allowed : 33.46 % Favored : 58.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.89 (0.36), residues: 571 helix: 3.44 (0.31), residues: 222 sheet: -3.26 (0.58), residues: 64 loop : -3.55 (0.28), residues: 285 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP d 43 HIS 0.003 0.001 HIS e 81 PHE 0.010 0.001 PHE g 56 TYR 0.019 0.001 TYR n 283 ARG 0.005 0.001 ARG e 115 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1142 Ramachandran restraints generated. 571 Oldfield, 0 Emsley, 571 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1142 Ramachandran restraints generated. 571 Oldfield, 0 Emsley, 571 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 523 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 151 time to evaluate : 0.522 Fit side-chains revert: symmetry clash REVERT: d 91 ARG cc_start: 0.8940 (OUTLIER) cc_final: 0.8695 (tmm160) REVERT: g 55 TRP cc_start: 0.6156 (m100) cc_final: 0.5499 (m100) outliers start: 44 outliers final: 27 residues processed: 177 average time/residue: 0.1551 time to fit residues: 34.8727 Evaluate side-chains 168 residues out of total 523 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 140 time to evaluate : 0.487 ------------------------------------------------------------------------------- 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 153 LYS Chi-restraints excluded: chain f residue 40 ILE Chi-restraints excluded: chain f residue 47 LEU Chi-restraints excluded: chain f residue 48 THR Chi-restraints excluded: chain f residue 97 VAL Chi-restraints excluded: chain f residue 138 ILE Chi-restraints excluded: chain g residue 35 ASP Chi-restraints excluded: chain g residue 53 ILE Chi-restraints excluded: chain g residue 97 LEU Chi-restraints excluded: chain g residue 133 VAL Chi-restraints excluded: chain m residue 268 VAL Chi-restraints excluded: chain m residue 286 THR Chi-restraints excluded: chain n residue 276 LEU Chi-restraints excluded: chain n residue 293 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 53 optimal weight: 0.5980 chunk 5 optimal weight: 0.2980 chunk 14 optimal weight: 0.9990 chunk 3 optimal weight: 0.4980 chunk 41 optimal weight: 5.9990 chunk 23 optimal weight: 4.9990 chunk 49 optimal weight: 0.9980 chunk 32 optimal weight: 1.9990 chunk 37 optimal weight: 0.6980 chunk 6 optimal weight: 2.9990 chunk 7 optimal weight: 4.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- 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 = 0.4175 r_free = 0.4175 target = 0.178003 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3855 r_free = 0.3855 target = 0.147898 restraints weight = 6492.985| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3873 r_free = 0.3873 target = 0.149960 restraints weight = 4141.407| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3889 r_free = 0.3889 target = 0.151523 restraints weight = 3381.694| |-----------------------------------------------------------------------------| r_work (final): 0.3870 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7439 moved from start: 0.2240 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= 0.210 Angle : 0.765 9.461 6428 Z= 0.377 Chirality : 0.042 0.220 753 Planarity : 0.004 0.044 791 Dihedral : 5.199 34.043 637 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 10.58 Ramachandran Plot: Outliers : 1.05 % Allowed : 11.21 % Favored : 87.74 % Rotamer: Outliers : 8.99 % Allowed : 33.65 % Favored : 57.36 % 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: -0.72 (0.35), residues: 571 helix: 3.53 (0.31), residues: 222 sheet: -3.14 (0.58), residues: 62 loop : -3.42 (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 0.007 0.001 PHE g 56 TYR 0.016 0.001 TYR b 33 ARG 0.003 0.000 ARG e 115 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1142 Ramachandran restraints generated. 571 Oldfield, 0 Emsley, 571 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1142 Ramachandran restraints generated. 571 Oldfield, 0 Emsley, 571 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 523 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 153 time to evaluate : 0.476 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: e 36 TYR cc_start: 0.8648 (m-10) cc_final: 0.8306 (m-10) REVERT: f 36 TYR cc_start: 0.5948 (OUTLIER) cc_final: 0.5407 (t80) REVERT: m 285 MET cc_start: 0.8787 (tpp) cc_final: 0.8394 (tpp) outliers start: 47 outliers final: 27 residues processed: 182 average time/residue: 0.1557 time to fit residues: 35.9737 Evaluate side-chains 172 residues out of total 523 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 144 time to evaluate : 0.527 ------------------------------------------------------------------------------- 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 97 LEU Chi-restraints excluded: chain g residue 98 GLN Chi-restraints excluded: chain m residue 268 VAL Chi-restraints excluded: chain m residue 271 LEU Chi-restraints excluded: chain m residue 290 TRP Chi-restraints excluded: chain m residue 291 SER Chi-restraints excluded: chain n residue 276 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 36 optimal weight: 0.6980 chunk 18 optimal weight: 1.9990 chunk 48 optimal weight: 2.9990 chunk 49 optimal weight: 1.9990 chunk 3 optimal weight: 2.9990 chunk 20 optimal weight: 2.9990 chunk 5 optimal weight: 0.0370 chunk 39 optimal weight: 0.5980 chunk 46 optimal weight: 0.6980 chunk 41 optimal weight: 4.9990 chunk 38 optimal weight: 3.9990 overall best weight: 0.8060 ------------------------------------------------------------------------------- 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 = 0.4143 r_free = 0.4143 target = 0.175135 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3780 r_free = 0.3780 target = 0.142064 restraints weight = 6571.177| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3825 r_free = 0.3825 target = 0.146067 restraints weight = 4091.921| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3857 r_free = 0.3857 target = 0.148792 restraints weight = 2991.496| |-----------------------------------------------------------------------------| r_work (final): 0.3836 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7460 moved from start: 0.2857 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= 0.219 Angle : 0.794 12.929 6428 Z= 0.381 Chirality : 0.043 0.231 753 Planarity : 0.004 0.040 791 Dihedral : 5.084 34.857 637 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 12.29 Ramachandran Plot: Outliers : 1.05 % Allowed : 12.43 % Favored : 86.51 % Rotamer: Outliers : 10.13 % Allowed : 35.37 % 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: -0.66 (0.36), residues: 571 helix: 3.50 (0.31), residues: 222 sheet: -3.07 (0.53), residues: 82 loop : -3.28 (0.29), residues: 267 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP d 43 HIS 0.002 0.001 HIS e 81 PHE 0.009 0.001 PHE n 296 TYR 0.017 0.001 TYR f 52 ARG 0.003 0.000 ARG e 115 *********************** 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 198 residues out of total 523 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 145 time to evaluate : 0.553 Fit side-chains REVERT: b 34 LEU cc_start: 0.7731 (OUTLIER) cc_final: 0.7461 (tm) REVERT: e 85 LYS cc_start: 0.8191 (pttp) cc_final: 0.7826 (mtpp) REVERT: f 36 TYR cc_start: 0.6315 (OUTLIER) cc_final: 0.5302 (t80) REVERT: m 285 MET cc_start: 0.8772 (tpp) cc_final: 0.8409 (tpp) outliers start: 53 outliers final: 35 residues processed: 179 average time/residue: 0.1563 time to fit residues: 35.5905 Evaluate side-chains 180 residues out of total 523 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 143 time to evaluate : 0.508 ------------------------------------------------------------------------------- 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 b residue 45 ILE Chi-restraints excluded: chain d residue 31 ASP Chi-restraints excluded: chain d residue 53 SER Chi-restraints excluded: chain d residue 85 THR Chi-restraints excluded: chain d residue 113 ILE Chi-restraints excluded: chain d residue 115 THR Chi-restraints excluded: chain e residue 45 VAL Chi-restraints excluded: chain e residue 48 THR Chi-restraints excluded: chain e residue 57 ILE Chi-restraints excluded: chain e residue 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 92 GLN Chi-restraints excluded: chain f residue 97 VAL Chi-restraints excluded: chain f residue 112 LEU Chi-restraints excluded: chain f residue 125 MET Chi-restraints excluded: chain f residue 138 ILE Chi-restraints excluded: chain g residue 30 LEU Chi-restraints excluded: chain g residue 35 ASP Chi-restraints excluded: chain g residue 44 LEU Chi-restraints excluded: chain g residue 53 ILE Chi-restraints excluded: chain g residue 92 ASN Chi-restraints excluded: chain g residue 97 LEU Chi-restraints excluded: chain g residue 103 MET Chi-restraints excluded: chain g residue 124 VAL Chi-restraints excluded: chain m residue 268 VAL Chi-restraints excluded: chain m residue 291 SER 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: 0.9980 chunk 6 optimal weight: 0.9990 chunk 45 optimal weight: 0.9980 chunk 16 optimal weight: 1.9990 chunk 54 optimal weight: 0.9980 chunk 48 optimal weight: 0.8980 chunk 2 optimal weight: 1.9990 chunk 13 optimal weight: 1.9990 chunk 33 optimal weight: 9.9990 chunk 20 optimal weight: 1.9990 chunk 42 optimal weight: 4.9990 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: f 33 GLN ** g 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 98 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 = 0.4123 r_free = 0.4123 target = 0.173509 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3761 r_free = 0.3761 target = 0.140498 restraints weight = 6747.743| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3807 r_free = 0.3807 target = 0.144458 restraints weight = 4198.850| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3838 r_free = 0.3838 target = 0.147171 restraints weight = 3069.264| |-----------------------------------------------------------------------------| r_work (final): 0.3818 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7516 moved from start: 0.3249 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 4746 Z= 0.233 Angle : 0.790 11.061 6428 Z= 0.382 Chirality : 0.044 0.234 753 Planarity : 0.004 0.037 791 Dihedral : 5.164 35.080 637 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 13.89 Ramachandran Plot: Outliers : 0.88 % Allowed : 11.38 % Favored : 87.74 % Rotamer: Outliers : 11.66 % Allowed : 31.93 % Favored : 56.41 % 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: -0.56 (0.35), residues: 571 helix: 3.57 (0.31), residues: 222 sheet: -3.00 (0.59), residues: 62 loop : -3.26 (0.28), residues: 287 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP d 43 HIS 0.002 0.001 HIS g 29 PHE 0.011 0.001 PHE f 110 TYR 0.021 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 212 residues out of total 523 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 151 time to evaluate : 0.586 Fit side-chains revert: symmetry clash REVERT: b 34 LEU cc_start: 0.7697 (OUTLIER) cc_final: 0.7439 (tm) REVERT: e 61 HIS cc_start: 0.7616 (OUTLIER) cc_final: 0.6384 (p90) REVERT: e 128 MET cc_start: 0.6495 (tmm) cc_final: 0.6207 (tmm) REVERT: f 36 TYR cc_start: 0.6600 (OUTLIER) cc_final: 0.5400 (t80) REVERT: m 285 MET cc_start: 0.8777 (tpp) cc_final: 0.8561 (tpp) outliers start: 61 outliers final: 42 residues processed: 190 average time/residue: 0.1432 time to fit residues: 35.4100 Evaluate side-chains 194 residues out of total 523 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 149 time to evaluate : 0.493 ------------------------------------------------------------------------------- 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 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 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 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 95 LYS 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 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: 7.9990 chunk 3 optimal weight: 1.9990 chunk 21 optimal weight: 0.6980 chunk 31 optimal weight: 0.4980 chunk 9 optimal weight: 6.9990 chunk 43 optimal weight: 0.6980 chunk 42 optimal weight: 5.9990 chunk 53 optimal weight: 0.9980 chunk 10 optimal weight: 0.8980 chunk 22 optimal weight: 0.9990 chunk 24 optimal weight: 0.8980 overall best weight: 0.7380 ------------------------------------------------------------------------------- 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 ** g 29 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 278 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4135 r_free = 0.4135 target = 0.174942 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3819 r_free = 0.3819 target = 0.144597 restraints weight = 6658.666| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3845 r_free = 0.3845 target = 0.147956 restraints weight = 4295.140| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3860 r_free = 0.3860 target = 0.149325 restraints weight = 3160.522| |-----------------------------------------------------------------------------| r_work (final): 0.3838 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7480 moved from start: 0.3650 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 4746 Z= 0.221 Angle : 0.803 10.683 6428 Z= 0.389 Chirality : 0.043 0.230 753 Planarity : 0.004 0.036 791 Dihedral : 5.115 36.184 637 Min Nonbonded Distance : 2.354 Molprobity Statistics. All-atom Clashscore : 12.72 Ramachandran Plot: Outliers : 0.88 % Allowed : 11.73 % Favored : 87.39 % Rotamer: Outliers : 10.13 % Allowed : 34.99 % Favored : 54.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.18 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.52 (0.36), residues: 571 helix: 3.60 (0.31), residues: 222 sheet: -2.83 (0.54), residues: 82 loop : -3.22 (0.29), residues: 267 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP d 43 HIS 0.003 0.001 HIS g 29 PHE 0.011 0.001 PHE g 56 TYR 0.036 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 198 residues out of total 523 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 145 time to evaluate : 0.534 Fit side-chains revert: symmetry clash REVERT: b 34 LEU cc_start: 0.7667 (OUTLIER) cc_final: 0.7421 (tm) REVERT: d 56 THR cc_start: 0.8512 (m) cc_final: 0.8301 (p) REVERT: e 61 HIS cc_start: 0.7604 (OUTLIER) cc_final: 0.6410 (p90) REVERT: e 85 LYS cc_start: 0.8076 (pttm) cc_final: 0.7831 (mtpp) REVERT: e 128 MET cc_start: 0.6476 (tmm) cc_final: 0.6160 (tmm) REVERT: g 110 LEU cc_start: 0.8485 (OUTLIER) cc_final: 0.8204 (mt) outliers start: 53 outliers final: 41 residues processed: 178 average time/residue: 0.1448 time to fit residues: 33.2925 Evaluate side-chains 187 residues out of total 523 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 143 time to evaluate : 0.496 ------------------------------------------------------------------------------- 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 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 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 48 THR 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 138 ILE 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 45 THR 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 95 LYS Chi-restraints excluded: chain g residue 97 LEU Chi-restraints excluded: chain g residue 99 VAL 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 291 SER 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 48 optimal weight: 0.5980 chunk 4 optimal weight: 2.9990 chunk 37 optimal weight: 0.9980 chunk 1 optimal weight: 0.9990 chunk 23 optimal weight: 3.9990 chunk 17 optimal weight: 0.9980 chunk 53 optimal weight: 0.9990 chunk 52 optimal weight: 1.9990 chunk 36 optimal weight: 0.0270 chunk 39 optimal weight: 0.0000 chunk 51 optimal weight: 0.6980 overall best weight: 0.4642 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: f 33 GLN ** g 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 278 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4157 r_free = 0.4157 target = 0.177141 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3818 r_free = 0.3818 target = 0.145165 restraints weight = 6639.350| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3862 r_free = 0.3862 target = 0.149095 restraints weight = 4122.672| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3891 r_free = 0.3891 target = 0.151745 restraints weight = 3013.232| |-----------------------------------------------------------------------------| r_work (final): 0.3874 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7429 moved from start: 0.3825 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 4746 Z= 0.205 Angle : 0.785 9.498 6428 Z= 0.380 Chirality : 0.042 0.222 753 Planarity : 0.004 0.038 791 Dihedral : 5.053 36.637 637 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 10.68 Ramachandran Plot: Outliers : 0.88 % Allowed : 11.21 % Favored : 87.92 % Rotamer: Outliers : 9.56 % Allowed : 34.61 % 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: -0.38 (0.36), residues: 571 helix: 3.66 (0.30), residues: 222 sheet: -2.68 (0.55), residues: 82 loop : -3.13 (0.30), residues: 267 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP d 43 HIS 0.004 0.001 HIS g 29 PHE 0.006 0.001 PHE g 56 TYR 0.035 0.001 TYR f 99 ARG 0.002 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 201 residues out of total 523 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 151 time to evaluate : 0.517 Fit side-chains revert: symmetry clash REVERT: b 34 LEU cc_start: 0.7585 (OUTLIER) cc_final: 0.7336 (tm) REVERT: b 54 LYS cc_start: 0.7873 (tptp) cc_final: 0.7424 (tptp) REVERT: e 61 HIS cc_start: 0.7259 (OUTLIER) cc_final: 0.6255 (p90) REVERT: e 128 MET cc_start: 0.6436 (tmm) cc_final: 0.6081 (tmm) REVERT: f 36 TYR cc_start: 0.6252 (OUTLIER) cc_final: 0.4893 (t80) REVERT: f 137 ASP cc_start: 0.8539 (t70) cc_final: 0.7845 (t0) outliers start: 50 outliers final: 39 residues processed: 181 average time/residue: 0.1478 time to fit residues: 34.7159 Evaluate side-chains 189 residues out of total 523 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 147 time to evaluate : 0.529 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 34 LEU Chi-restraints excluded: chain a residue 51 LEU Chi-restraints excluded: chain b residue 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 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 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 29 HIS 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 124 VAL Chi-restraints excluded: chain g residue 135 PHE 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 300 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 7 optimal weight: 0.0010 chunk 24 optimal weight: 1.9990 chunk 54 optimal weight: 1.9990 chunk 20 optimal weight: 0.6980 chunk 53 optimal weight: 0.5980 chunk 48 optimal weight: 0.7980 chunk 52 optimal weight: 0.7980 chunk 9 optimal weight: 2.9990 chunk 43 optimal weight: 6.9990 chunk 26 optimal weight: 0.7980 chunk 5 optimal weight: 0.0570 overall best weight: 0.4304 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: f 33 GLN ** g 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 278 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4175 r_free = 0.4175 target = 0.178691 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3838 r_free = 0.3838 target = 0.146710 restraints weight = 6590.324| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3879 r_free = 0.3879 target = 0.150520 restraints weight = 4183.960| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3907 r_free = 0.3907 target = 0.153136 restraints weight = 3073.066| |-----------------------------------------------------------------------------| r_work (final): 0.3894 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7408 moved from start: 0.4209 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= 0.203 Angle : 0.778 9.861 6428 Z= 0.376 Chirality : 0.042 0.217 753 Planarity : 0.004 0.038 791 Dihedral : 4.936 37.908 637 Min Nonbonded Distance : 2.417 Molprobity Statistics. All-atom Clashscore : 9.83 Ramachandran Plot: Outliers : 0.88 % Allowed : 10.86 % Favored : 88.27 % Rotamer: Outliers : 8.03 % Allowed : 36.71 % 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: -0.28 (0.36), residues: 571 helix: 3.70 (0.30), residues: 222 sheet: -2.52 (0.56), residues: 82 loop : -3.06 (0.30), residues: 267 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.002 TRP d 43 HIS 0.004 0.001 HIS g 29 PHE 0.010 0.001 PHE g 56 TYR 0.033 0.001 TYR f 99 ARG 0.002 0.000 ARG e 115 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1142 Ramachandran restraints generated. 571 Oldfield, 0 Emsley, 571 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1142 Ramachandran restraints generated. 571 Oldfield, 0 Emsley, 571 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 523 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 146 time to evaluate : 0.460 Fit side-chains revert: symmetry clash REVERT: b 34 LEU cc_start: 0.7578 (OUTLIER) cc_final: 0.7353 (tm) REVERT: b 54 LYS cc_start: 0.7910 (tptp) cc_final: 0.7485 (tptp) REVERT: e 61 HIS cc_start: 0.7096 (OUTLIER) cc_final: 0.6399 (p90) REVERT: e 128 MET cc_start: 0.6439 (tmm) cc_final: 0.6056 (tmm) REVERT: f 37 LYS cc_start: 0.6870 (tppt) cc_final: 0.6043 (ttmm) REVERT: f 128 MET cc_start: 0.7235 (tmm) cc_final: 0.5901 (tpt) REVERT: f 137 ASP cc_start: 0.8527 (t70) cc_final: 0.7879 (t0) REVERT: g 110 LEU cc_start: 0.8527 (OUTLIER) cc_final: 0.8229 (mt) outliers start: 42 outliers final: 32 residues processed: 173 average time/residue: 0.1520 time to fit residues: 33.5357 Evaluate side-chains 175 residues out of total 523 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 140 time to evaluate : 0.500 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 34 LEU Chi-restraints excluded: chain a residue 51 LEU Chi-restraints excluded: chain b residue 31 LEU Chi-restraints excluded: chain b residue 34 LEU Chi-restraints excluded: chain b residue 45 ILE 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 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 152 SER 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 30 LEU Chi-restraints excluded: chain g residue 44 LEU 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 104 CYS 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 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: 1.9990 chunk 46 optimal weight: 0.0060 chunk 2 optimal weight: 0.6980 chunk 35 optimal weight: 0.5980 chunk 16 optimal weight: 0.9980 chunk 23 optimal weight: 2.9990 chunk 39 optimal weight: 1.9990 chunk 42 optimal weight: 0.9990 chunk 9 optimal weight: 0.0970 chunk 12 optimal weight: 0.0030 chunk 41 optimal weight: 4.9990 overall best weight: 0.2804 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: e 81 HIS f 33 GLN ** g 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 278 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4202 r_free = 0.4202 target = 0.180943 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3868 r_free = 0.3868 target = 0.148926 restraints weight = 6655.857| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3913 r_free = 0.3913 target = 0.152886 restraints weight = 4187.551| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3938 r_free = 0.3938 target = 0.155277 restraints weight = 3058.385| |-----------------------------------------------------------------------------| r_work (final): 0.3920 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7377 moved from start: 0.4364 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 4746 Z= 0.202 Angle : 0.785 9.856 6428 Z= 0.377 Chirality : 0.042 0.211 753 Planarity : 0.004 0.040 791 Dihedral : 4.851 36.269 637 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 10.15 Ramachandran Plot: Outliers : 0.88 % Allowed : 11.03 % Favored : 88.09 % Rotamer: Outliers : 6.69 % Allowed : 38.43 % 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: -0.24 (0.36), residues: 571 helix: 3.72 (0.31), residues: 222 sheet: -2.43 (0.56), residues: 82 loop : -3.06 (0.30), residues: 267 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.002 TRP d 43 HIS 0.003 0.001 HIS g 29 PHE 0.007 0.001 PHE g 56 TYR 0.043 0.001 TYR g 34 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 175 residues out of total 523 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 140 time to evaluate : 0.504 Fit side-chains revert: symmetry clash REVERT: b 34 LEU cc_start: 0.7553 (OUTLIER) cc_final: 0.7317 (tm) REVERT: b 54 LYS cc_start: 0.7806 (tptp) cc_final: 0.7406 (tptp) REVERT: e 128 MET cc_start: 0.6399 (tmm) cc_final: 0.6025 (tmm) REVERT: f 37 LYS cc_start: 0.6755 (tppt) cc_final: 0.6025 (ttmm) REVERT: f 56 GLU cc_start: 0.7644 (mm-30) cc_final: 0.7433 (tt0) REVERT: f 128 MET cc_start: 0.7062 (tmm) cc_final: 0.5634 (tpt) REVERT: f 137 ASP cc_start: 0.8519 (t70) cc_final: 0.7891 (t0) REVERT: m 290 TRP cc_start: 0.5719 (OUTLIER) cc_final: 0.5382 (m100) outliers start: 35 outliers final: 28 residues processed: 160 average time/residue: 0.1578 time to fit residues: 32.1774 Evaluate side-chains 167 residues out of total 523 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 137 time to evaluate : 0.495 ------------------------------------------------------------------------------- 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 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 29 HIS Chi-restraints excluded: chain g residue 30 LEU Chi-restraints excluded: chain g residue 44 LEU 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 104 CYS 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 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: 1.9990 chunk 28 optimal weight: 0.8980 chunk 34 optimal weight: 0.6980 chunk 43 optimal weight: 0.0030 chunk 19 optimal weight: 4.9990 chunk 10 optimal weight: 0.9980 chunk 35 optimal weight: 0.4980 chunk 54 optimal weight: 1.9990 chunk 0 optimal weight: 1.9990 chunk 44 optimal weight: 0.9980 overall best weight: 0.6190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: f 33 GLN ** g 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 278 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4167 r_free = 0.4167 target = 0.177901 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3825 r_free = 0.3825 target = 0.145138 restraints weight = 6632.795| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3869 r_free = 0.3869 target = 0.149015 restraints weight = 4199.984| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3899 r_free = 0.3899 target = 0.151671 restraints weight = 3094.678| |-----------------------------------------------------------------------------| r_work (final): 0.3884 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7435 moved from start: 0.4644 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 4746 Z= 0.216 Angle : 0.812 12.173 6428 Z= 0.387 Chirality : 0.043 0.208 753 Planarity : 0.004 0.040 791 Dihedral : 4.843 36.964 637 Min Nonbonded Distance : 2.353 Molprobity Statistics. All-atom Clashscore : 10.47 Ramachandran Plot: Outliers : 0.88 % Allowed : 10.51 % Favored : 88.62 % Rotamer: Outliers : 7.27 % Allowed : 38.05 % 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: 3.71 (0.31), residues: 222 sheet: -2.47 (0.56), residues: 82 loop : -3.08 (0.30), residues: 267 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.043 0.002 TRP d 43 HIS 0.003 0.001 HIS g 29 PHE 0.008 0.001 PHE g 56 TYR 0.030 0.001 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: 38 poor density : 144 time to evaluate : 0.523 Fit side-chains revert: symmetry clash REVERT: b 34 LEU cc_start: 0.7686 (OUTLIER) cc_final: 0.7446 (tm) REVERT: b 54 LYS cc_start: 0.7965 (tptp) cc_final: 0.7546 (tptp) REVERT: d 83 GLU cc_start: 0.7821 (pm20) cc_final: 0.7542 (mp0) REVERT: e 61 HIS cc_start: 0.7252 (OUTLIER) cc_final: 0.6587 (p90) REVERT: e 85 LYS cc_start: 0.8016 (pttm) cc_final: 0.7782 (mtpp) REVERT: e 128 MET cc_start: 0.6370 (tmm) cc_final: 0.6022 (tmm) REVERT: f 37 LYS cc_start: 0.6891 (tppt) cc_final: 0.6090 (ttmm) REVERT: f 128 MET cc_start: 0.6999 (tmm) cc_final: 0.5707 (tpt) REVERT: g 55 TRP cc_start: 0.4920 (m100) cc_final: 0.4264 (m100) REVERT: m 290 TRP cc_start: 0.5774 (OUTLIER) cc_final: 0.5353 (m100) outliers start: 38 outliers final: 31 residues processed: 170 average time/residue: 0.1525 time to fit residues: 33.1311 Evaluate side-chains 177 residues out of total 523 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 143 time to evaluate : 0.545 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 34 LEU Chi-restraints excluded: chain a residue 51 LEU Chi-restraints excluded: chain b residue 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 107 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 66 ILE Chi-restraints excluded: chain e residue 119 CYS Chi-restraints excluded: chain e residue 152 SER 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 29 HIS Chi-restraints excluded: chain g residue 30 LEU Chi-restraints excluded: chain g residue 44 LEU 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 99 VAL Chi-restraints excluded: chain g residue 104 CYS Chi-restraints excluded: chain m residue 268 VAL Chi-restraints excluded: chain m residue 271 LEU Chi-restraints excluded: chain m residue 290 TRP Chi-restraints excluded: chain n residue 276 LEU Chi-restraints excluded: chain n residue 300 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 24 optimal weight: 0.9980 chunk 15 optimal weight: 7.9990 chunk 11 optimal weight: 3.9990 chunk 5 optimal weight: 0.0170 chunk 32 optimal weight: 1.9990 chunk 47 optimal weight: 4.9990 chunk 25 optimal weight: 6.9990 chunk 43 optimal weight: 0.7980 chunk 9 optimal weight: 0.9990 chunk 51 optimal weight: 0.9990 chunk 12 optimal weight: 0.9980 overall best weight: 0.7620 ------------------------------------------------------------------------------- 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 ** g 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 278 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4157 r_free = 0.4157 target = 0.176551 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3806 r_free = 0.3806 target = 0.143625 restraints weight = 6683.640| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3850 r_free = 0.3850 target = 0.147469 restraints weight = 4239.532| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3880 r_free = 0.3880 target = 0.150105 restraints weight = 3130.845| |-----------------------------------------------------------------------------| r_work (final): 0.3861 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7465 moved from start: 0.4740 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= 0.231 Angle : 0.812 10.536 6428 Z= 0.389 Chirality : 0.043 0.209 753 Planarity : 0.004 0.039 791 Dihedral : 4.883 35.215 637 Min Nonbonded Distance : 2.358 Molprobity Statistics. All-atom Clashscore : 11.01 Ramachandran Plot: Outliers : 0.88 % Allowed : 11.38 % Favored : 87.74 % Rotamer: Outliers : 7.27 % Allowed : 39.01 % Favored : 53.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.30 (0.36), residues: 571 helix: 3.65 (0.31), residues: 223 sheet: -2.38 (0.57), residues: 82 loop : -3.13 (0.30), residues: 266 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.045 0.002 TRP d 43 HIS 0.003 0.001 HIS g 29 PHE 0.006 0.001 PHE f 110 TYR 0.034 0.002 TYR f 99 ARG 0.002 0.000 ARG e 117 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1827.58 seconds wall clock time: 33 minutes 33.28 seconds (2013.28 seconds total)