Starting phenix.real_space_refine on Mon Jan 20 03:45:31 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8xkx_38430/01_2025/8xkx_38430.cif Found real_map, /net/cci-nas-00/data/ceres_data/8xkx_38430/01_2025/8xkx_38430.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8xkx_38430/01_2025/8xkx_38430.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8xkx_38430/01_2025/8xkx_38430.map" model { file = "/net/cci-nas-00/data/ceres_data/8xkx_38430/01_2025/8xkx_38430.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8xkx_38430/01_2025/8xkx_38430.cif" } resolution = 3.7 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= 0.003 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians S 22 5.16 5 C 4810 2.51 5 N 1262 2.21 5 O 1424 1.98 5 H 7340 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 18 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/chem_data/mon_lib" Total number of atoms: 14858 Number of models: 1 Model: "" Number of chains: 5 Chain: "B" Number of atoms: 784 Number of conformers: 1 Conformer: "" Number of residues, atoms: 50, 784 Classifications: {'peptide': 50} Link IDs: {'PTRANS': 1, 'TRANS': 48} Chain: "C" Number of atoms: 637 Number of conformers: 1 Conformer: "" Number of residues, atoms: 37, 637 Classifications: {'peptide': 37} Link IDs: {'PTRANS': 1, 'TRANS': 35} Chain: "D" Number of atoms: 540 Number of conformers: 1 Conformer: "" Number of residues, atoms: 35, 540 Classifications: {'peptide': 35} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 31} Chain: "E" Number of atoms: 816 Number of conformers: 1 Conformer: "" Number of residues, atoms: 50, 816 Classifications: {'peptide': 50} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 45} Chain: "A" Number of atoms: 4652 Number of conformers: 1 Conformer: "" Number of residues, atoms: 307, 4652 Classifications: {'peptide': 307} Link IDs: {'PTRANS': 9, 'TRANS': 297} Chain breaks: 1 Restraints were copied for chains: G, J, F, H, I Time building chain proxies: 10.96, per 1000 atoms: 0.74 Number of scatterers: 14858 At special positions: 0 Unit cell: (136.74, 113.42, 97.52, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 22 16.00 O 1424 8.00 N 1262 7.00 C 4810 6.00 H 7340 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.87 Conformation dependent library (CDL) restraints added in 1.2 seconds 1868 Ramachandran restraints generated. 934 Oldfield, 0 Emsley, 934 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1792 Finding SS restraints... Secondary structure from input PDB file: 18 helices and 2 sheets defined 37.1% alpha, 30.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.18 Creating SS restraints... Processing helix chain 'B' and resid 86 through 135 Proline residue: B 112 - end of helix Processing helix chain 'C' and resid 14 through 49 Proline residue: C 39 - end of helix Processing helix chain 'D' and resid 30 through 51 removed outlier: 3.805A pdb=" N THR D 34 " --> pdb=" O SER D 30 " (cutoff:3.500A) removed outlier: 4.164A pdb=" N ILE D 35 " --> pdb=" O PRO D 31 " (cutoff:3.500A) Processing helix chain 'D' and resid 51 through 58 removed outlier: 4.044A pdb=" N ASP D 55 " --> pdb=" O SER D 51 " (cutoff:3.500A) Processing helix chain 'E' and resid 12 through 44 removed outlier: 3.778A pdb=" N TYR E 30 " --> pdb=" O ASN E 26 " (cutoff:3.500A) removed outlier: 6.270A pdb=" N ILE E 33 " --> pdb=" O HIS E 29 " (cutoff:3.500A) Proline residue: E 34 - end of helix Processing helix chain 'E' and resid 49 through 55 Processing helix chain 'A' and resid 49 through 54 removed outlier: 3.650A pdb=" N SER A 54 " --> pdb=" O HIS A 51 " (cutoff:3.500A) Processing helix chain 'A' and resid 67 through 72 Processing helix chain 'A' and resid 364 through 373 Processing helix chain 'G' and resid 87 through 135 Proline residue: G 112 - end of helix Processing helix chain 'H' and resid 14 through 49 Proline residue: H 39 - end of helix Processing helix chain 'I' and resid 30 through 51 removed outlier: 3.805A pdb=" N THR I 34 " --> pdb=" O SER I 30 " (cutoff:3.500A) removed outlier: 4.165A pdb=" N ILE I 35 " --> pdb=" O PRO I 31 " (cutoff:3.500A) Processing helix chain 'I' and resid 51 through 58 removed outlier: 4.044A pdb=" N ASP I 55 " --> pdb=" O SER I 51 " (cutoff:3.500A) Processing helix chain 'J' and resid 12 through 44 removed outlier: 3.778A pdb=" N TYR J 30 " --> pdb=" O ASN J 26 " (cutoff:3.500A) removed outlier: 6.270A pdb=" N ILE J 33 " --> pdb=" O HIS J 29 " (cutoff:3.500A) Proline residue: J 34 - end of helix Processing helix chain 'J' and resid 49 through 55 Processing helix chain 'F' and resid 49 through 54 removed outlier: 3.650A pdb=" N SER F 54 " --> pdb=" O HIS F 51 " (cutoff:3.500A) Processing helix chain 'F' and resid 67 through 72 Processing helix chain 'F' and resid 364 through 373 Processing sheet with id=AA1, first strand: chain 'A' and resid 351 through 355 removed outlier: 6.851A pdb=" N LEU A 209 " --> pdb=" O VAL A 205 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N GLY A 195 " --> pdb=" O ARG A 219 " (cutoff:3.500A) removed outlier: 7.417A pdb=" N THR A 194 " --> pdb=" O PRO A 185 " (cutoff:3.500A) removed outlier: 7.236A pdb=" N CYS A 165 " --> pdb=" O ASN A 184 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N SER A 136 " --> pdb=" O ASP A 132 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ALA A 115 " --> pdb=" O THR A 103 " (cutoff:3.500A) removed outlier: 6.753A pdb=" N PHE A 98 " --> pdb=" O PHE A 92 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N PHE A 92 " --> pdb=" O PHE A 98 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'F' and resid 351 through 355 removed outlier: 6.851A pdb=" N LEU F 209 " --> pdb=" O VAL F 205 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N GLY F 195 " --> pdb=" O ARG F 219 " (cutoff:3.500A) removed outlier: 7.417A pdb=" N THR F 194 " --> pdb=" O PRO F 185 " (cutoff:3.500A) removed outlier: 7.237A pdb=" N CYS F 165 " --> pdb=" O ASN F 184 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N SER F 136 " --> pdb=" O ASP F 132 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ALA F 115 " --> pdb=" O THR F 103 " (cutoff:3.500A) removed outlier: 6.752A pdb=" N PHE F 98 " --> pdb=" O PHE F 92 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N PHE F 92 " --> pdb=" O PHE F 98 " (cutoff:3.500A) 509 hydrogen bonds defined for protein. 1473 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: 6.95 Time building geometry restraints manager: 4.82 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 5.73: 14986 5.73 - 10.62: 30 10.62 - 15.51: 0 15.51 - 20.40: 2 20.40 - 25.29: 2 Warning: extremely large bond lengths. Bond restraints: 15020 Sorted by residual: bond pdb=" CG GLN F 99 " pdb=" HG1 GLN F 99 " ideal model delta sigma weight residual 0.970 25.289 -24.319 2.00e-02 2.50e+03 1.48e+06 bond pdb=" CG GLN A 99 " pdb=" HG1 GLN A 99 " ideal model delta sigma weight residual 0.970 25.289 -24.319 2.00e-02 2.50e+03 1.48e+06 bond pdb=" CB MET I 54 " pdb=" HB1 MET I 54 " ideal model delta sigma weight residual 0.970 16.180 -15.210 2.00e-02 2.50e+03 5.78e+05 bond pdb=" CB MET D 54 " pdb=" HB1 MET D 54 " ideal model delta sigma weight residual 0.970 16.180 -15.210 2.00e-02 2.50e+03 5.78e+05 bond pdb=" CB LEU I 53 " pdb=" HB1 LEU I 53 " ideal model delta sigma weight residual 0.970 9.599 -8.629 2.00e-02 2.50e+03 1.86e+05 ... (remaining 15015 not shown) Histogram of bond angle deviations from ideal: 0.00 - 20.32: 26854 20.32 - 40.65: 122 40.65 - 60.97: 24 60.97 - 81.29: 12 81.29 - 101.62: 10 Bond angle restraints: 27022 Sorted by residual: angle pdb=" HB1 ARG C 15 " pdb=" CB ARG C 15 " pdb=" HB2 ARG C 15 " ideal model delta sigma weight residual 110.00 8.38 101.62 3.00e+00 1.11e-01 1.15e+03 angle pdb=" HB1 ARG H 15 " pdb=" CB ARG H 15 " pdb=" HB2 ARG H 15 " ideal model delta sigma weight residual 110.00 8.39 101.61 3.00e+00 1.11e-01 1.15e+03 angle pdb=" HG1 GLU H 13 " pdb=" CG GLU H 13 " pdb=" HG2 GLU H 13 " ideal model delta sigma weight residual 110.00 15.74 94.26 3.00e+00 1.11e-01 9.87e+02 angle pdb=" HG1 GLU C 13 " pdb=" CG GLU C 13 " pdb=" HG2 GLU C 13 " ideal model delta sigma weight residual 110.00 15.75 94.25 3.00e+00 1.11e-01 9.87e+02 angle pdb=" HB1 ASP F 132 " pdb=" CB ASP F 132 " pdb=" HB2 ASP F 132 " ideal model delta sigma weight residual 110.00 17.00 93.00 3.00e+00 1.11e-01 9.61e+02 ... (remaining 27017 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.98: 6331 17.98 - 35.96: 609 35.96 - 53.95: 146 53.95 - 71.93: 28 71.93 - 89.91: 8 Dihedral angle restraints: 7122 sinusoidal: 3802 harmonic: 3320 Sorted by residual: dihedral pdb=" C ILE F 256 " pdb=" N ILE F 256 " pdb=" CA ILE F 256 " pdb=" CB ILE F 256 " ideal model delta harmonic sigma weight residual -122.00 -131.43 9.43 0 2.50e+00 1.60e-01 1.42e+01 dihedral pdb=" C ILE A 256 " pdb=" N ILE A 256 " pdb=" CA ILE A 256 " pdb=" CB ILE A 256 " ideal model delta harmonic sigma weight residual -122.00 -131.40 9.40 0 2.50e+00 1.60e-01 1.41e+01 dihedral pdb=" C LEU H 35 " pdb=" N LEU H 35 " pdb=" CA LEU H 35 " pdb=" CB LEU H 35 " ideal model delta harmonic sigma weight residual -122.60 -131.99 9.39 0 2.50e+00 1.60e-01 1.41e+01 ... (remaining 7119 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.074: 1058 0.074 - 0.148: 96 0.148 - 0.221: 2 0.221 - 0.295: 2 0.295 - 0.369: 16 Chirality restraints: 1174 Sorted by residual: chirality pdb=" CA GLN F 53 " pdb=" N GLN F 53 " pdb=" C GLN F 53 " pdb=" CB GLN F 53 " both_signs ideal model delta sigma weight residual False 2.51 2.14 0.37 2.00e-01 2.50e+01 3.41e+00 chirality pdb=" CA HIS F 49 " pdb=" N HIS F 49 " pdb=" C HIS F 49 " pdb=" CB HIS F 49 " both_signs ideal model delta sigma weight residual False 2.51 2.14 0.37 2.00e-01 2.50e+01 3.36e+00 chirality pdb=" CA SER F 158 " pdb=" N SER F 158 " pdb=" C SER F 158 " pdb=" CB SER F 158 " both_signs ideal model delta sigma weight residual False 2.51 2.14 0.37 2.00e-01 2.50e+01 3.36e+00 ... (remaining 1171 not shown) Planarity restraints: 2234 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CG GLN A 99 " -0.055 2.00e-02 2.50e+03 5.63e-02 4.75e+01 pdb=" CD GLN A 99 " 0.007 2.00e-02 2.50e+03 pdb=" OE1 GLN A 99 " 0.050 2.00e-02 2.50e+03 pdb=" NE2 GLN A 99 " 0.001 2.00e-02 2.50e+03 pdb="HE21 GLN A 99 " -0.083 2.00e-02 2.50e+03 pdb="HE22 GLN A 99 " 0.081 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLN F 99 " -0.054 2.00e-02 2.50e+03 5.63e-02 4.75e+01 pdb=" CD GLN F 99 " 0.006 2.00e-02 2.50e+03 pdb=" OE1 GLN F 99 " 0.050 2.00e-02 2.50e+03 pdb=" NE2 GLN F 99 " 0.001 2.00e-02 2.50e+03 pdb="HE21 GLN F 99 " -0.083 2.00e-02 2.50e+03 pdb="HE22 GLN F 99 " 0.081 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN F 154 " -0.048 2.00e-02 2.50e+03 5.49e-02 4.52e+01 pdb=" CG ASN F 154 " -0.009 2.00e-02 2.50e+03 pdb=" OD1 ASN F 154 " 0.055 2.00e-02 2.50e+03 pdb=" ND2 ASN F 154 " -0.000 2.00e-02 2.50e+03 pdb="HD21 ASN F 154 " 0.081 2.00e-02 2.50e+03 pdb="HD22 ASN F 154 " -0.079 2.00e-02 2.50e+03 ... (remaining 2231 not shown) Histogram of nonbonded interaction distances: 1.58 - 2.18: 711 2.18 - 2.79: 28575 2.79 - 3.39: 39555 3.39 - 4.00: 49834 4.00 - 4.60: 76046 Nonbonded interactions: 194721 Sorted by model distance: nonbonded pdb=" H ASP F 345 " pdb=" HA ASP F 345 " model vdw 1.576 1.816 nonbonded pdb=" H ASP A 345 " pdb=" HA ASP A 345 " model vdw 1.577 1.816 nonbonded pdb=" HA LEU D 37 " pdb=" HB3 LEU D 37 " model vdw 1.592 1.952 nonbonded pdb=" HA LEU I 37 " pdb=" HB3 LEU I 37 " model vdw 1.592 1.952 nonbonded pdb=" H ILE A 256 " pdb=" HA ILE A 256 " model vdw 1.594 1.816 ... (remaining 194716 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: 0.05 Found NCS groups: ncs_group { reference = chain 'B' selection = chain 'G' } ncs_group { reference = chain 'E' selection = chain 'J' } ncs_group { reference = chain 'A' selection = chain 'F' } ncs_group { reference = chain 'C' selection = chain 'H' } ncs_group { reference = chain 'D' selection = chain 'I' } 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: 0.610 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: 0.290 Extract box with map and model: 0.660 Check model and map are aligned: 0.120 Set scattering table: 0.160 Process input model: 38.350 Find NCS groups from input model: 0.210 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 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: 43.370 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7656 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 0.046 7680 Z= 0.250 Angle : 0.741 9.069 10412 Z= 0.471 Chirality : 0.058 0.369 1174 Planarity : 0.004 0.049 1332 Dihedral : 16.096 89.910 2750 Min Nonbonded Distance : 2.288 Molprobity Statistics. All-atom Clashscore : 4.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.93 % Favored : 98.07 % Rotamer: Outliers : 0.24 % Allowed : 25.98 % Favored : 73.78 % 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: 1.46 (0.29), residues: 934 helix: 3.12 (0.27), residues: 344 sheet: -0.01 (0.26), residues: 390 loop : -0.76 (0.46), residues: 200 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP J 32 HIS 0.007 0.001 HIS H 43 PHE 0.008 0.001 PHE F 359 TYR 0.021 0.001 TYR F 171 ARG 0.002 0.000 ARG F 52 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1868 Ramachandran restraints generated. 934 Oldfield, 0 Emsley, 934 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1868 Ramachandran restraints generated. 934 Oldfield, 0 Emsley, 934 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 188 time to evaluate : 1.346 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 2 outliers final: 2 residues processed: 190 average time/residue: 0.3756 time to fit residues: 99.1460 Evaluate side-chains 174 residues out of total 820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 172 time to evaluate : 1.349 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 261 ARG Chi-restraints excluded: chain F residue 261 ARG Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 77 optimal weight: 0.9990 chunk 69 optimal weight: 1.9990 chunk 38 optimal weight: 1.9990 chunk 23 optimal weight: 1.9990 chunk 47 optimal weight: 1.9990 chunk 37 optimal weight: 0.8980 chunk 72 optimal weight: 0.9980 chunk 27 optimal weight: 5.9990 chunk 43 optimal weight: 0.7980 chunk 53 optimal weight: 2.9990 chunk 83 optimal weight: 0.8980 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4218 r_free = 0.4218 target = 0.183643 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3800 r_free = 0.3800 target = 0.142938 restraints weight = 23001.999| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3805 r_free = 0.3805 target = 0.144308 restraints weight = 24556.228| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3828 r_free = 0.3828 target = 0.146768 restraints weight = 18282.502| |-----------------------------------------------------------------------------| r_work (final): 0.3812 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7611 moved from start: 0.1276 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 7680 Z= 0.238 Angle : 0.660 9.472 10412 Z= 0.354 Chirality : 0.058 0.441 1174 Planarity : 0.004 0.042 1332 Dihedral : 4.823 49.582 1014 Min Nonbonded Distance : 2.381 Molprobity Statistics. All-atom Clashscore : 4.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 3.66 % Allowed : 24.02 % Favored : 72.32 % 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: 1.39 (0.29), residues: 934 helix: 3.13 (0.27), residues: 344 sheet: -0.13 (0.26), residues: 390 loop : -0.73 (0.46), residues: 200 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP E 32 HIS 0.003 0.001 HIS H 43 PHE 0.013 0.001 PHE A 359 TYR 0.004 0.001 TYR F 232 ARG 0.002 0.000 ARG C 15 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1868 Ramachandran restraints generated. 934 Oldfield, 0 Emsley, 934 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1868 Ramachandran restraints generated. 934 Oldfield, 0 Emsley, 934 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 208 residues out of total 820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 178 time to evaluate : 1.203 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 15 ARG cc_start: 0.6906 (OUTLIER) cc_final: 0.6305 (mpt90) REVERT: A 164 MET cc_start: 0.7079 (OUTLIER) cc_final: 0.6829 (ttm) REVERT: H 15 ARG cc_start: 0.6909 (OUTLIER) cc_final: 0.6303 (mpt90) REVERT: F 164 MET cc_start: 0.7108 (OUTLIER) cc_final: 0.6845 (ttm) outliers start: 30 outliers final: 16 residues processed: 194 average time/residue: 0.4008 time to fit residues: 107.2737 Evaluate side-chains 185 residues out of total 820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 165 time to evaluate : 1.175 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 13 GLU Chi-restraints excluded: chain C residue 15 ARG Chi-restraints excluded: chain C residue 17 HIS Chi-restraints excluded: chain E residue 45 SER Chi-restraints excluded: chain A residue 76 LEU Chi-restraints excluded: chain A residue 132 ASP Chi-restraints excluded: chain A residue 164 MET Chi-restraints excluded: chain A residue 233 LEU Chi-restraints excluded: chain A residue 261 ARG Chi-restraints excluded: chain A residue 361 THR Chi-restraints excluded: chain H residue 13 GLU Chi-restraints excluded: chain H residue 15 ARG Chi-restraints excluded: chain H residue 17 HIS Chi-restraints excluded: chain J residue 45 SER Chi-restraints excluded: chain F residue 76 LEU Chi-restraints excluded: chain F residue 132 ASP Chi-restraints excluded: chain F residue 164 MET Chi-restraints excluded: chain F residue 233 LEU Chi-restraints excluded: chain F residue 261 ARG Chi-restraints excluded: chain F residue 361 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 7 optimal weight: 1.9990 chunk 31 optimal weight: 2.9990 chunk 86 optimal weight: 0.5980 chunk 43 optimal weight: 0.9980 chunk 76 optimal weight: 5.9990 chunk 25 optimal weight: 3.9990 chunk 91 optimal weight: 3.9990 chunk 89 optimal weight: 0.5980 chunk 90 optimal weight: 0.9980 chunk 47 optimal weight: 1.9990 chunk 16 optimal weight: 7.9990 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4260 r_free = 0.4260 target = 0.187635 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3849 r_free = 0.3849 target = 0.147799 restraints weight = 22819.596| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3851 r_free = 0.3851 target = 0.148577 restraints weight = 20601.035| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3884 r_free = 0.3884 target = 0.152227 restraints weight = 16553.082| |-----------------------------------------------------------------------------| r_work (final): 0.3805 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7553 moved from start: 0.1550 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 7680 Z= 0.210 Angle : 0.595 9.199 10412 Z= 0.318 Chirality : 0.058 0.434 1174 Planarity : 0.004 0.043 1332 Dihedral : 4.744 48.460 1014 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 4.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.93 % Favored : 98.07 % Rotamer: Outliers : 2.07 % Allowed : 25.98 % Favored : 71.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.28 (0.29), residues: 934 helix: 3.19 (0.27), residues: 344 sheet: -0.29 (0.26), residues: 388 loop : -0.85 (0.46), residues: 202 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP E 32 HIS 0.006 0.001 HIS C 43 PHE 0.013 0.001 PHE A 359 TYR 0.004 0.001 TYR A 114 ARG 0.002 0.000 ARG F 310 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1868 Ramachandran restraints generated. 934 Oldfield, 0 Emsley, 934 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1868 Ramachandran restraints generated. 934 Oldfield, 0 Emsley, 934 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 166 time to evaluate : 1.274 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 268 GLU cc_start: 0.8341 (OUTLIER) cc_final: 0.8108 (pt0) REVERT: F 268 GLU cc_start: 0.8357 (OUTLIER) cc_final: 0.8106 (pt0) REVERT: F 345 ASP cc_start: 0.7930 (t0) cc_final: 0.7568 (t0) outliers start: 17 outliers final: 15 residues processed: 177 average time/residue: 0.3864 time to fit residues: 94.8699 Evaluate side-chains 175 residues out of total 820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 158 time to evaluate : 1.278 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 95 SER Chi-restraints excluded: chain C residue 15 ARG Chi-restraints excluded: chain A residue 76 LEU Chi-restraints excluded: chain A residue 150 ILE Chi-restraints excluded: chain A residue 233 LEU Chi-restraints excluded: chain A residue 261 ARG Chi-restraints excluded: chain A residue 268 GLU Chi-restraints excluded: chain A residue 361 THR Chi-restraints excluded: chain G residue 95 SER Chi-restraints excluded: chain H residue 15 ARG Chi-restraints excluded: chain F residue 76 LEU Chi-restraints excluded: chain F residue 101 SER Chi-restraints excluded: chain F residue 150 ILE Chi-restraints excluded: chain F residue 233 LEU Chi-restraints excluded: chain F residue 261 ARG Chi-restraints excluded: chain F residue 268 GLU Chi-restraints excluded: chain F residue 361 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 26 optimal weight: 2.9990 chunk 58 optimal weight: 4.9990 chunk 10 optimal weight: 0.6980 chunk 50 optimal weight: 2.9990 chunk 22 optimal weight: 2.9990 chunk 73 optimal weight: 3.9990 chunk 55 optimal weight: 2.9990 chunk 53 optimal weight: 0.9990 chunk 84 optimal weight: 0.9990 chunk 77 optimal weight: 3.9990 chunk 90 optimal weight: 0.1980 overall best weight: 1.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4191 r_free = 0.4191 target = 0.180682 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3632 r_free = 0.3632 target = 0.128532 restraints weight = 23186.833| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 57)----------------| | r_work = 0.3684 r_free = 0.3684 target = 0.132981 restraints weight = 14206.496| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.3717 r_free = 0.3717 target = 0.135823 restraints weight = 10722.613| |-----------------------------------------------------------------------------| r_work (final): 0.3696 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7726 moved from start: 0.1805 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 7680 Z= 0.226 Angle : 0.582 9.134 10412 Z= 0.311 Chirality : 0.058 0.432 1174 Planarity : 0.003 0.041 1332 Dihedral : 4.686 47.856 1014 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 4.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 2.20 % Allowed : 25.73 % Favored : 72.07 % 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: 1.24 (0.29), residues: 934 helix: 3.24 (0.27), residues: 344 sheet: -0.38 (0.26), residues: 388 loop : -0.89 (0.46), residues: 202 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP J 32 HIS 0.004 0.001 HIS C 43 PHE 0.014 0.001 PHE A 359 TYR 0.005 0.001 TYR A 114 ARG 0.002 0.000 ARG F 310 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1868 Ramachandran restraints generated. 934 Oldfield, 0 Emsley, 934 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1868 Ramachandran restraints generated. 934 Oldfield, 0 Emsley, 934 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 169 time to evaluate : 1.235 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 268 GLU cc_start: 0.8414 (OUTLIER) cc_final: 0.8172 (pt0) REVERT: F 268 GLU cc_start: 0.8413 (OUTLIER) cc_final: 0.8164 (pt0) REVERT: F 345 ASP cc_start: 0.7907 (t0) cc_final: 0.7637 (t0) outliers start: 18 outliers final: 16 residues processed: 181 average time/residue: 0.3706 time to fit residues: 92.5747 Evaluate side-chains 182 residues out of total 820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 164 time to evaluate : 1.180 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 15 ARG Chi-restraints excluded: chain C residue 17 HIS Chi-restraints excluded: chain A residue 76 LEU Chi-restraints excluded: chain A residue 150 ILE Chi-restraints excluded: chain A residue 182 THR Chi-restraints excluded: chain A residue 233 LEU Chi-restraints excluded: chain A residue 261 ARG Chi-restraints excluded: chain A residue 268 GLU Chi-restraints excluded: chain A residue 361 THR Chi-restraints excluded: chain H residue 15 ARG Chi-restraints excluded: chain H residue 17 HIS Chi-restraints excluded: chain F residue 76 LEU Chi-restraints excluded: chain F residue 150 ILE Chi-restraints excluded: chain F residue 182 THR Chi-restraints excluded: chain F residue 233 LEU Chi-restraints excluded: chain F residue 261 ARG Chi-restraints excluded: chain F residue 268 GLU Chi-restraints excluded: chain F residue 361 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 81 optimal weight: 1.9990 chunk 0 optimal weight: 7.9990 chunk 40 optimal weight: 0.6980 chunk 20 optimal weight: 1.9990 chunk 75 optimal weight: 3.9990 chunk 66 optimal weight: 2.9990 chunk 82 optimal weight: 1.9990 chunk 64 optimal weight: 1.9990 chunk 50 optimal weight: 0.9980 chunk 9 optimal weight: 2.9990 chunk 73 optimal weight: 1.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4226 r_free = 0.4226 target = 0.184417 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 73)----------------| | r_work = 0.3685 r_free = 0.3685 target = 0.133540 restraints weight = 23275.367| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 53)----------------| | r_work = 0.3734 r_free = 0.3734 target = 0.137714 restraints weight = 14813.347| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3765 r_free = 0.3765 target = 0.140446 restraints weight = 11336.959| |-----------------------------------------------------------------------------| r_work (final): 0.3679 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7773 moved from start: 0.2005 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 7680 Z= 0.272 Angle : 0.595 9.119 10412 Z= 0.317 Chirality : 0.058 0.430 1174 Planarity : 0.003 0.041 1332 Dihedral : 4.740 48.957 1014 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 4.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 3.05 % Allowed : 25.85 % Favored : 71.10 % 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: 1.11 (0.29), residues: 934 helix: 3.24 (0.27), residues: 344 sheet: -0.53 (0.26), residues: 390 loop : -0.98 (0.47), residues: 200 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP F 260 HIS 0.005 0.001 HIS A 102 PHE 0.015 0.002 PHE B 87 TYR 0.006 0.001 TYR A 114 ARG 0.002 0.000 ARG A 310 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1868 Ramachandran restraints generated. 934 Oldfield, 0 Emsley, 934 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1868 Ramachandran restraints generated. 934 Oldfield, 0 Emsley, 934 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 169 time to evaluate : 1.157 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 345 ASP cc_start: 0.7903 (t0) cc_final: 0.7675 (t0) REVERT: F 94 MET cc_start: 0.8079 (tpp) cc_final: 0.7659 (tpp) REVERT: F 345 ASP cc_start: 0.7917 (t0) cc_final: 0.7684 (t0) outliers start: 25 outliers final: 22 residues processed: 185 average time/residue: 0.3610 time to fit residues: 92.4611 Evaluate side-chains 187 residues out of total 820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 165 time to evaluate : 1.163 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 95 SER Chi-restraints excluded: chain C residue 15 ARG Chi-restraints excluded: chain C residue 17 HIS Chi-restraints excluded: chain E residue 27 VAL Chi-restraints excluded: chain A residue 76 LEU Chi-restraints excluded: chain A residue 150 ILE Chi-restraints excluded: chain A residue 182 THR Chi-restraints excluded: chain A residue 233 LEU Chi-restraints excluded: chain A residue 261 ARG Chi-restraints excluded: chain A residue 268 GLU Chi-restraints excluded: chain A residue 361 THR Chi-restraints excluded: chain G residue 95 SER Chi-restraints excluded: chain H residue 15 ARG Chi-restraints excluded: chain H residue 17 HIS Chi-restraints excluded: chain J residue 27 VAL Chi-restraints excluded: chain F residue 76 LEU Chi-restraints excluded: chain F residue 150 ILE Chi-restraints excluded: chain F residue 182 THR Chi-restraints excluded: chain F residue 233 LEU Chi-restraints excluded: chain F residue 261 ARG Chi-restraints excluded: chain F residue 268 GLU Chi-restraints excluded: chain F residue 361 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 62 optimal weight: 6.9990 chunk 70 optimal weight: 1.9990 chunk 77 optimal weight: 0.6980 chunk 41 optimal weight: 0.0970 chunk 21 optimal weight: 0.8980 chunk 18 optimal weight: 0.5980 chunk 55 optimal weight: 2.9990 chunk 80 optimal weight: 2.9990 chunk 66 optimal weight: 0.3980 chunk 63 optimal weight: 0.9980 chunk 87 optimal weight: 0.6980 overall best weight: 0.4978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 43 HIS ** A 252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 43 HIS ** F 252 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 = 0.181567 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3633 r_free = 0.3633 target = 0.129001 restraints weight = 23176.829| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3686 r_free = 0.3686 target = 0.133446 restraints weight = 14285.652| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3711 r_free = 0.3711 target = 0.135830 restraints weight = 10789.114| |-----------------------------------------------------------------------------| r_work (final): 0.3690 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7727 moved from start: 0.2173 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 7680 Z= 0.154 Angle : 0.566 9.222 10412 Z= 0.300 Chirality : 0.057 0.428 1174 Planarity : 0.003 0.038 1332 Dihedral : 4.548 44.843 1014 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 4.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 2.07 % Allowed : 26.22 % Favored : 71.71 % 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: 1.23 (0.30), residues: 934 helix: 3.29 (0.27), residues: 344 sheet: -0.43 (0.27), residues: 390 loop : -0.88 (0.47), residues: 200 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 260 HIS 0.010 0.001 HIS C 43 PHE 0.015 0.001 PHE A 359 TYR 0.005 0.001 TYR A 217 ARG 0.001 0.000 ARG A 310 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1868 Ramachandran restraints generated. 934 Oldfield, 0 Emsley, 934 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1868 Ramachandran restraints generated. 934 Oldfield, 0 Emsley, 934 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 164 time to evaluate : 1.116 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 38 ASN cc_start: 0.8822 (m-40) cc_final: 0.8619 (m-40) REVERT: A 94 MET cc_start: 0.7886 (tpp) cc_final: 0.7546 (tpp) REVERT: F 268 GLU cc_start: 0.8363 (OUTLIER) cc_final: 0.8129 (pt0) outliers start: 17 outliers final: 16 residues processed: 176 average time/residue: 0.3800 time to fit residues: 92.2874 Evaluate side-chains 178 residues out of total 820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 161 time to evaluate : 1.100 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 15 ARG Chi-restraints excluded: chain C residue 17 HIS Chi-restraints excluded: chain A residue 76 LEU Chi-restraints excluded: chain A residue 182 THR Chi-restraints excluded: chain A residue 233 LEU Chi-restraints excluded: chain A residue 261 ARG Chi-restraints excluded: chain A residue 268 GLU Chi-restraints excluded: chain A residue 361 THR Chi-restraints excluded: chain G residue 124 ILE Chi-restraints excluded: chain H residue 15 ARG Chi-restraints excluded: chain H residue 17 HIS Chi-restraints excluded: chain F residue 76 LEU Chi-restraints excluded: chain F residue 182 THR Chi-restraints excluded: chain F residue 233 LEU Chi-restraints excluded: chain F residue 261 ARG Chi-restraints excluded: chain F residue 268 GLU Chi-restraints excluded: chain F residue 361 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 12 optimal weight: 6.9990 chunk 8 optimal weight: 1.9990 chunk 78 optimal weight: 4.9990 chunk 50 optimal weight: 1.9990 chunk 88 optimal weight: 1.9990 chunk 76 optimal weight: 6.9990 chunk 32 optimal weight: 1.9990 chunk 84 optimal weight: 2.9990 chunk 75 optimal weight: 0.9990 chunk 15 optimal weight: 0.9980 chunk 27 optimal weight: 4.9990 overall best weight: 1.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4167 r_free = 0.4167 target = 0.178544 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3621 r_free = 0.3621 target = 0.127850 restraints weight = 23350.545| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 54)----------------| | r_work = 0.3664 r_free = 0.3664 target = 0.131563 restraints weight = 14805.363| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3686 r_free = 0.3686 target = 0.133582 restraints weight = 11572.221| |-----------------------------------------------------------------------------| r_work (final): 0.3661 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7794 moved from start: 0.2281 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 7680 Z= 0.284 Angle : 0.590 9.337 10412 Z= 0.316 Chirality : 0.058 0.436 1174 Planarity : 0.003 0.037 1332 Dihedral : 4.632 46.469 1014 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 4.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.53 % Favored : 96.47 % Rotamer: Outliers : 3.66 % Allowed : 25.49 % Favored : 70.85 % 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: 1.16 (0.30), residues: 934 helix: 3.30 (0.27), residues: 344 sheet: -0.49 (0.27), residues: 388 loop : -1.02 (0.46), residues: 202 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP J 32 HIS 0.004 0.001 HIS A 102 PHE 0.012 0.002 PHE F 126 TYR 0.006 0.001 TYR A 114 ARG 0.002 0.000 ARG A 72 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1868 Ramachandran restraints generated. 934 Oldfield, 0 Emsley, 934 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1868 Ramachandran restraints generated. 934 Oldfield, 0 Emsley, 934 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 171 time to evaluate : 2.383 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 268 GLU cc_start: 0.8420 (OUTLIER) cc_final: 0.8196 (pt0) REVERT: A 345 ASP cc_start: 0.7853 (t0) cc_final: 0.7643 (t0) REVERT: F 94 MET cc_start: 0.8051 (tpp) cc_final: 0.7579 (tpp) REVERT: F 268 GLU cc_start: 0.8409 (OUTLIER) cc_final: 0.8179 (pt0) REVERT: F 345 ASP cc_start: 0.7896 (t0) cc_final: 0.7678 (t0) outliers start: 30 outliers final: 24 residues processed: 193 average time/residue: 0.3711 time to fit residues: 100.5498 Evaluate side-chains 193 residues out of total 820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 167 time to evaluate : 1.302 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 105 THR Chi-restraints excluded: chain B residue 124 ILE Chi-restraints excluded: chain C residue 15 ARG Chi-restraints excluded: chain C residue 17 HIS Chi-restraints excluded: chain A residue 76 LEU Chi-restraints excluded: chain A residue 101 SER Chi-restraints excluded: chain A residue 108 SER Chi-restraints excluded: chain A residue 136 SER Chi-restraints excluded: chain A residue 150 ILE Chi-restraints excluded: chain A residue 182 THR Chi-restraints excluded: chain A residue 233 LEU Chi-restraints excluded: chain A residue 261 ARG Chi-restraints excluded: chain A residue 268 GLU Chi-restraints excluded: chain A residue 339 LEU Chi-restraints excluded: chain A residue 361 THR Chi-restraints excluded: chain G residue 124 ILE Chi-restraints excluded: chain H residue 15 ARG Chi-restraints excluded: chain F residue 76 LEU Chi-restraints excluded: chain F residue 108 SER Chi-restraints excluded: chain F residue 150 ILE Chi-restraints excluded: chain F residue 182 THR Chi-restraints excluded: chain F residue 233 LEU Chi-restraints excluded: chain F residue 261 ARG Chi-restraints excluded: chain F residue 268 GLU Chi-restraints excluded: chain F residue 339 LEU Chi-restraints excluded: chain F residue 361 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 79 optimal weight: 9.9990 chunk 6 optimal weight: 1.9990 chunk 7 optimal weight: 0.9990 chunk 60 optimal weight: 6.9990 chunk 64 optimal weight: 0.7980 chunk 57 optimal weight: 10.0000 chunk 63 optimal weight: 0.9990 chunk 68 optimal weight: 2.9990 chunk 72 optimal weight: 2.9990 chunk 41 optimal weight: 0.4980 chunk 77 optimal weight: 0.8980 overall best weight: 0.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4188 r_free = 0.4188 target = 0.180741 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3622 r_free = 0.3622 target = 0.128191 restraints weight = 23179.879| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 57)----------------| | r_work = 0.3675 r_free = 0.3675 target = 0.132571 restraints weight = 14311.491| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 53)----------------| | r_work = 0.3709 r_free = 0.3709 target = 0.135450 restraints weight = 10847.479| |-----------------------------------------------------------------------------| r_work (final): 0.3685 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7741 moved from start: 0.2368 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 7680 Z= 0.186 Angle : 0.565 9.310 10412 Z= 0.301 Chirality : 0.057 0.432 1174 Planarity : 0.003 0.035 1332 Dihedral : 4.532 44.589 1014 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 4.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 2.68 % Allowed : 26.34 % Favored : 70.98 % 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: 1.21 (0.30), residues: 934 helix: 3.31 (0.27), residues: 344 sheet: -0.45 (0.27), residues: 388 loop : -0.97 (0.46), residues: 202 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP E 32 HIS 0.003 0.001 HIS J 29 PHE 0.010 0.001 PHE A 116 TYR 0.006 0.001 TYR E 30 ARG 0.001 0.000 ARG F 310 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1868 Ramachandran restraints generated. 934 Oldfield, 0 Emsley, 934 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1868 Ramachandran restraints generated. 934 Oldfield, 0 Emsley, 934 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 165 time to evaluate : 1.147 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 94 MET cc_start: 0.8017 (tpp) cc_final: 0.7608 (tpp) outliers start: 22 outliers final: 20 residues processed: 180 average time/residue: 0.3803 time to fit residues: 94.7773 Evaluate side-chains 183 residues out of total 820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 163 time to evaluate : 1.240 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 15 ARG Chi-restraints excluded: chain A residue 76 LEU Chi-restraints excluded: chain A residue 101 SER Chi-restraints excluded: chain A residue 150 ILE Chi-restraints excluded: chain A residue 182 THR Chi-restraints excluded: chain A residue 233 LEU Chi-restraints excluded: chain A residue 261 ARG Chi-restraints excluded: chain A residue 268 GLU Chi-restraints excluded: chain A residue 361 THR Chi-restraints excluded: chain G residue 105 THR Chi-restraints excluded: chain G residue 124 ILE Chi-restraints excluded: chain H residue 15 ARG Chi-restraints excluded: chain F residue 76 LEU Chi-restraints excluded: chain F residue 101 SER Chi-restraints excluded: chain F residue 150 ILE Chi-restraints excluded: chain F residue 182 THR Chi-restraints excluded: chain F residue 233 LEU Chi-restraints excluded: chain F residue 261 ARG Chi-restraints excluded: chain F residue 268 GLU Chi-restraints excluded: chain F residue 361 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 52 optimal weight: 1.9990 chunk 25 optimal weight: 3.9990 chunk 86 optimal weight: 1.9990 chunk 35 optimal weight: 0.9980 chunk 34 optimal weight: 1.9990 chunk 4 optimal weight: 3.9990 chunk 74 optimal weight: 6.9990 chunk 67 optimal weight: 1.9990 chunk 83 optimal weight: 0.6980 chunk 70 optimal weight: 2.9990 chunk 43 optimal weight: 0.9980 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 43 HIS ** F 252 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 = 0.4169 r_free = 0.4169 target = 0.178970 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3599 r_free = 0.3599 target = 0.126349 restraints weight = 23456.668| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.3651 r_free = 0.3651 target = 0.130723 restraints weight = 14424.566| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 58)----------------| | r_work = 0.3684 r_free = 0.3684 target = 0.133522 restraints weight = 10968.257| |-----------------------------------------------------------------------------| r_work (final): 0.3664 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7763 moved from start: 0.2476 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 7680 Z= 0.244 Angle : 0.579 9.268 10412 Z= 0.310 Chirality : 0.058 0.433 1174 Planarity : 0.003 0.036 1332 Dihedral : 4.568 44.881 1014 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 4.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Rotamer: Outliers : 3.17 % Allowed : 26.34 % Favored : 70.49 % 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: 1.20 (0.30), residues: 934 helix: 3.35 (0.27), residues: 344 sheet: -0.51 (0.27), residues: 388 loop : -0.94 (0.46), residues: 202 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP E 32 HIS 0.010 0.001 HIS H 43 PHE 0.011 0.001 PHE A 116 TYR 0.008 0.001 TYR J 38 ARG 0.001 0.000 ARG A 72 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1868 Ramachandran restraints generated. 934 Oldfield, 0 Emsley, 934 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1868 Ramachandran restraints generated. 934 Oldfield, 0 Emsley, 934 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 165 time to evaluate : 1.388 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 94 MET cc_start: 0.8013 (tpp) cc_final: 0.7627 (tpp) outliers start: 26 outliers final: 24 residues processed: 183 average time/residue: 0.3600 time to fit residues: 92.9484 Evaluate side-chains 188 residues out of total 820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 164 time to evaluate : 1.258 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 124 ILE Chi-restraints excluded: chain C residue 15 ARG Chi-restraints excluded: chain A residue 76 LEU Chi-restraints excluded: chain A residue 101 SER Chi-restraints excluded: chain A residue 108 SER Chi-restraints excluded: chain A residue 150 ILE Chi-restraints excluded: chain A residue 182 THR Chi-restraints excluded: chain A residue 233 LEU Chi-restraints excluded: chain A residue 268 GLU Chi-restraints excluded: chain A residue 351 THR Chi-restraints excluded: chain A residue 361 THR Chi-restraints excluded: chain G residue 105 THR Chi-restraints excluded: chain G residue 124 ILE Chi-restraints excluded: chain H residue 15 ARG Chi-restraints excluded: chain F residue 76 LEU Chi-restraints excluded: chain F residue 101 SER Chi-restraints excluded: chain F residue 108 SER Chi-restraints excluded: chain F residue 136 SER Chi-restraints excluded: chain F residue 150 ILE Chi-restraints excluded: chain F residue 182 THR Chi-restraints excluded: chain F residue 233 LEU Chi-restraints excluded: chain F residue 268 GLU Chi-restraints excluded: chain F residue 351 THR Chi-restraints excluded: chain F residue 361 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 65 optimal weight: 0.6980 chunk 57 optimal weight: 9.9990 chunk 25 optimal weight: 2.9990 chunk 36 optimal weight: 3.9990 chunk 47 optimal weight: 1.9990 chunk 19 optimal weight: 0.9990 chunk 61 optimal weight: 0.6980 chunk 14 optimal weight: 0.4980 chunk 67 optimal weight: 0.6980 chunk 54 optimal weight: 2.9990 chunk 87 optimal weight: 0.6980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 43 HIS ** A 252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 252 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 = 0.4185 r_free = 0.4185 target = 0.180398 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3635 r_free = 0.3635 target = 0.128878 restraints weight = 23303.919| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3664 r_free = 0.3664 target = 0.132547 restraints weight = 14818.635| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3683 r_free = 0.3683 target = 0.134206 restraints weight = 11238.576| |-----------------------------------------------------------------------------| r_work (final): 0.3659 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7718 moved from start: 0.2523 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 7680 Z= 0.169 Angle : 0.564 9.260 10412 Z= 0.300 Chirality : 0.057 0.429 1174 Planarity : 0.003 0.035 1332 Dihedral : 4.267 41.849 1006 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 4.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 3.05 % Allowed : 26.34 % Favored : 70.61 % 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: 1.26 (0.30), residues: 934 helix: 3.38 (0.27), residues: 344 sheet: -0.49 (0.27), residues: 388 loop : -0.85 (0.46), residues: 202 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP E 32 HIS 0.010 0.001 HIS C 43 PHE 0.010 0.001 PHE A 116 TYR 0.006 0.001 TYR A 307 ARG 0.001 0.000 ARG A 310 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1868 Ramachandran restraints generated. 934 Oldfield, 0 Emsley, 934 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1868 Ramachandran restraints generated. 934 Oldfield, 0 Emsley, 934 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 166 time to evaluate : 1.190 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 128 LYS cc_start: 0.8382 (ttpt) cc_final: 0.8150 (ttpt) REVERT: E 49 ASN cc_start: 0.7725 (p0) cc_final: 0.7518 (p0) REVERT: G 128 LYS cc_start: 0.8342 (ttpt) cc_final: 0.8112 (ttpt) REVERT: F 94 MET cc_start: 0.8098 (tpp) cc_final: 0.7665 (tpp) outliers start: 25 outliers final: 24 residues processed: 184 average time/residue: 0.3771 time to fit residues: 98.2530 Evaluate side-chains 186 residues out of total 820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 162 time to evaluate : 1.195 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 95 SER Chi-restraints excluded: chain B residue 105 THR Chi-restraints excluded: chain B residue 124 ILE Chi-restraints excluded: chain C residue 15 ARG Chi-restraints excluded: chain C residue 17 HIS Chi-restraints excluded: chain A residue 76 LEU Chi-restraints excluded: chain A residue 101 SER Chi-restraints excluded: chain A residue 108 SER Chi-restraints excluded: chain A residue 150 ILE Chi-restraints excluded: chain A residue 182 THR Chi-restraints excluded: chain A residue 233 LEU Chi-restraints excluded: chain A residue 268 GLU Chi-restraints excluded: chain A residue 361 THR Chi-restraints excluded: chain G residue 105 THR Chi-restraints excluded: chain G residue 124 ILE Chi-restraints excluded: chain H residue 15 ARG Chi-restraints excluded: chain F residue 76 LEU Chi-restraints excluded: chain F residue 101 SER Chi-restraints excluded: chain F residue 108 SER Chi-restraints excluded: chain F residue 136 SER Chi-restraints excluded: chain F residue 182 THR Chi-restraints excluded: chain F residue 233 LEU Chi-restraints excluded: chain F residue 268 GLU Chi-restraints excluded: chain F residue 361 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 26 optimal weight: 2.9990 chunk 67 optimal weight: 1.9990 chunk 6 optimal weight: 0.9980 chunk 8 optimal weight: 3.9990 chunk 14 optimal weight: 0.8980 chunk 38 optimal weight: 2.9990 chunk 4 optimal weight: 1.9990 chunk 75 optimal weight: 3.9990 chunk 52 optimal weight: 0.9990 chunk 35 optimal weight: 0.8980 chunk 60 optimal weight: 0.7980 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 43 HIS ** A 252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 252 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 = 0.4178 r_free = 0.4178 target = 0.179684 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 75)----------------| | r_work = 0.3619 r_free = 0.3619 target = 0.127659 restraints weight = 23187.359| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.3674 r_free = 0.3674 target = 0.132164 restraints weight = 14144.103| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3701 r_free = 0.3701 target = 0.134738 restraints weight = 10619.606| |-----------------------------------------------------------------------------| r_work (final): 0.3675 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7739 moved from start: 0.2609 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 7680 Z= 0.197 Angle : 0.573 9.277 10412 Z= 0.305 Chirality : 0.057 0.431 1174 Planarity : 0.003 0.035 1332 Dihedral : 4.241 40.694 1006 Min Nonbonded Distance : 2.304 Molprobity Statistics. All-atom Clashscore : 4.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 3.66 % Allowed : 26.46 % Favored : 69.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.26 (0.29), residues: 934 helix: 3.37 (0.27), residues: 344 sheet: -0.48 (0.27), residues: 388 loop : -0.84 (0.46), residues: 202 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP E 32 HIS 0.014 0.001 HIS C 43 PHE 0.010 0.001 PHE A 116 TYR 0.007 0.001 TYR J 38 ARG 0.001 0.000 ARG F 310 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5026.59 seconds wall clock time: 89 minutes 48.97 seconds (5388.97 seconds total)