Starting phenix.real_space_refine on Tue Aug 4 16:22:51 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9vmd_65185/08_2026/9vmd_65185.cif Found real_map, /net/cci-nas-00/data/ceres_data/9vmd_65185/08_2026/9vmd_65185.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.38 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9vmd_65185/08_2026/9vmd_65185.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9vmd_65185/08_2026/9vmd_65185.map" model { file = "/net/cci-nas-00/data/ceres_data/9vmd_65185/08_2026/9vmd_65185.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9vmd_65185/08_2026/9vmd_65185.cif" } resolution = 4.38 write_initial_geo_file = False refinement { macro_cycles = 10 } 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= 0.007 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 P 75 5.49 5 S 15 5.16 5 C 2692 2.51 5 N 816 2.21 5 O 1145 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 4 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 4743 Number of models: 1 Model: "" Number of chains: 4 Chain: "O" Number of atoms: 1391 Number of conformers: 1 Conformer: "" Number of residues, atoms: 180, 1391 Classifications: {'peptide': 180} Link IDs: {'PTRANS': 5, 'TRANS': 174} Chain: "P" Number of atoms: 973 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 973 Classifications: {'peptide': 127} Link IDs: {'PTRANS': 2, 'TRANS': 124} Chain: "Q" Number of atoms: 792 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 792 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 7, 'TRANS': 99} Chain: "R" Number of atoms: 1587 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 1587 Classifications: {'RNA': 75} Modifications used: {'rna2p_pur': 3, 'rna2p_pyr': 5, 'rna3p_pur': 30, 'rna3p_pyr': 36} Link IDs: {'rna2p': 8, 'rna3p': 66} Chain breaks: 1 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 0.93, per 1000 atoms: 0.20 Number of scatterers: 4743 At special positions: 0 Unit cell: (76.8, 87.36, 96, 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 15 16.00 P 75 15.00 O 1145 8.00 N 816 7.00 C 2692 6.00 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: 0.23 Conformation dependent library (CDL) restraints added in 76.1 milliseconds 816 Ramachandran restraints generated. 408 Oldfield, 0 Emsley, 408 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 734 Finding SS restraints... Secondary structure from input PDB file: 6 helices and 8 sheets defined 8.9% alpha, 44.2% beta 26 base pairs and 46 stacking pairs defined. Time for finding SS restraints: 0.55 Creating SS restraints... Processing helix chain 'O' and resid 3 through 14 Processing helix chain 'O' and resid 38 through 42 Processing helix chain 'O' and resid 86 through 90 removed outlier: 3.881A pdb=" N ILE O 90 " --> pdb=" O ARG O 87 " (cutoff:3.500A) Processing helix chain 'P' and resid 89 through 93 removed outlier: 3.791A pdb=" N THR P 93 " --> pdb=" O ALA P 90 " (cutoff:3.500A) Processing helix chain 'Q' and resid 26 through 30 removed outlier: 3.837A pdb=" N ASP Q 29 " --> pdb=" O LYS Q 26 " (cutoff:3.500A) Processing helix chain 'Q' and resid 78 through 82 removed outlier: 4.019A pdb=" N GLU Q 82 " --> pdb=" O ALA Q 79 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'O' and resid 15 through 20 removed outlier: 6.956A pdb=" N VAL O 34 " --> pdb=" O ILE O 30 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N ILE O 68 " --> pdb=" O ASP O 64 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N LEU O 70 " --> pdb=" O LEU O 62 " (cutoff:3.500A) removed outlier: 7.273A pdb=" N LEU O 62 " --> pdb=" O LEU O 70 " (cutoff:3.500A) removed outlier: 7.064A pdb=" N LEU O 72 " --> pdb=" O TYR O 60 " (cutoff:3.500A) removed outlier: 7.034A pdb=" N TYR O 60 " --> pdb=" O LEU O 72 " (cutoff:3.500A) removed outlier: 7.000A pdb=" N VAL O 74 " --> pdb=" O ASP O 58 " (cutoff:3.500A) removed outlier: 6.900A pdb=" N ASP O 58 " --> pdb=" O VAL O 74 " (cutoff:3.500A) removed outlier: 7.553A pdb=" N THR O 76 " --> pdb=" O VAL O 56 " (cutoff:3.500A) removed outlier: 5.600A pdb=" N VAL O 56 " --> pdb=" O THR O 76 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'O' and resid 119 through 120 removed outlier: 3.747A pdb=" N THR O 119 " --> pdb=" O ARG O 136 " (cutoff:3.500A) removed outlier: 5.687A pdb=" N ALA O 171 " --> pdb=" O HIS O 160 " (cutoff:3.500A) removed outlier: 5.575A pdb=" N HIS O 160 " --> pdb=" O ALA O 171 " (cutoff:3.500A) removed outlier: 4.941A pdb=" N ILE O 156 " --> pdb=" O ALA O 152 " (cutoff:3.500A) removed outlier: 6.512A pdb=" N ALA O 152 " --> pdb=" O ILE O 156 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N GLY O 158 " --> pdb=" O LEU O 150 " (cutoff:3.500A) removed outlier: 6.377A pdb=" N SER O 105 " --> pdb=" O THR O 109 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N THR O 109 " --> pdb=" O SER O 105 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'O' and resid 123 through 126 removed outlier: 3.752A pdb=" N ILE O 124 " --> pdb=" O THR O 131 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N THR O 131 " --> pdb=" O ILE O 124 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'P' and resid 5 through 10 Processing sheet with id=AA5, first strand: chain 'P' and resid 12 through 14 removed outlier: 3.660A pdb=" N GLY P 12 " --> pdb=" O THR P 123 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N THR P 125 " --> pdb=" O GLY P 12 " (cutoff:3.500A) removed outlier: 6.727A pdb=" N MET P 36 " --> pdb=" O VAL P 52 " (cutoff:3.500A) removed outlier: 4.518A pdb=" N VAL P 52 " --> pdb=" O MET P 36 " (cutoff:3.500A) removed outlier: 6.724A pdb=" N TRP P 38 " --> pdb=" O VAL P 50 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'Q' and resid 4 through 5 Processing sheet with id=AA7, first strand: chain 'Q' and resid 9 through 11 removed outlier: 3.682A pdb=" N THR Q 104 " --> pdb=" O VAL Q 10 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N TYR Q 31 " --> pdb=" O TRP Q 90 " (cutoff:3.500A) removed outlier: 7.034A pdb=" N TRP Q 34 " --> pdb=" O VAL Q 46 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'Q' and resid 9 through 11 removed outlier: 3.682A pdb=" N THR Q 104 " --> pdb=" O VAL Q 10 " (cutoff:3.500A) 122 hydrogen bonds defined for protein. 297 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 67 hydrogen bonds 122 hydrogen bond angles 0 basepair planarities 26 basepair parallelities 46 stacking parallelities Total time for adding SS restraints: 0.54 Time building geometry restraints manager: 0.31 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: 1237 1.34 - 1.46: 1540 1.46 - 1.58: 2040 1.58 - 1.70: 148 1.70 - 1.82: 22 Bond restraints: 4987 Sorted by residual: bond pdb=" C VAL Q 3 " pdb=" O VAL Q 3 " ideal model delta sigma weight residual 1.236 1.275 -0.039 1.04e-02 9.25e+03 1.41e+01 bond pdb=" CA PRO Q 7 " pdb=" C PRO Q 7 " ideal model delta sigma weight residual 1.514 1.495 0.020 5.50e-03 3.31e+04 1.29e+01 bond pdb=" C TYR Q 2 " pdb=" O TYR Q 2 " ideal model delta sigma weight residual 1.234 1.278 -0.044 1.27e-02 6.20e+03 1.19e+01 bond pdb=" CA SER Q 11 " pdb=" CB SER Q 11 " ideal model delta sigma weight residual 1.534 1.482 0.052 1.76e-02 3.23e+03 8.62e+00 bond pdb=" N GLN P 8 " pdb=" CA GLN P 8 " ideal model delta sigma weight residual 1.454 1.488 -0.034 1.18e-02 7.18e+03 8.31e+00 ... (remaining 4982 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.08: 6641 2.08 - 4.16: 348 4.16 - 6.24: 109 6.24 - 8.32: 6 8.32 - 10.40: 2 Bond angle restraints: 7106 Sorted by residual: angle pdb=" N TYR P 97 " pdb=" CA TYR P 97 " pdb=" C TYR P 97 " ideal model delta sigma weight residual 110.42 116.35 -5.93 1.55e+00 4.16e-01 1.46e+01 angle pdb=" O4' U R 38 " pdb=" C4' U R 38 " pdb=" C3' U R 38 " ideal model delta sigma weight residual 106.10 103.27 2.83 8.00e-01 1.56e+00 1.25e+01 angle pdb=" N TYR P 96 " pdb=" CA TYR P 96 " pdb=" C TYR P 96 " ideal model delta sigma weight residual 108.90 114.59 -5.69 1.63e+00 3.76e-01 1.22e+01 angle pdb=" CB MET Q 80 " pdb=" CG MET Q 80 " pdb=" SD MET Q 80 " ideal model delta sigma weight residual 112.70 123.10 -10.40 3.00e+00 1.11e-01 1.20e+01 angle pdb=" C3' C R 7 " pdb=" C2' C R 7 " pdb=" C1' C R 7 " ideal model delta sigma weight residual 101.30 103.69 -2.39 7.00e-01 2.04e+00 1.16e+01 ... (remaining 7101 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.96: 2431 17.96 - 35.91: 352 35.91 - 53.87: 142 53.87 - 71.82: 117 71.82 - 89.78: 29 Dihedral angle restraints: 3071 sinusoidal: 1907 harmonic: 1164 Sorted by residual: dihedral pdb=" C3' U R 38 " pdb=" C4' U R 38 " pdb=" O4' U R 38 " pdb=" C1' U R 38 " ideal model delta sinusoidal sigma weight residual -2.00 -26.68 24.68 1 8.00e+00 1.56e-02 1.37e+01 dihedral pdb=" C4' U R 38 " pdb=" O4' U R 38 " pdb=" C1' U R 38 " pdb=" C2' U R 38 " ideal model delta sinusoidal sigma weight residual -21.00 2.95 -23.95 1 8.00e+00 1.56e-02 1.29e+01 dihedral pdb=" C4' C R 7 " pdb=" O4' C R 7 " pdb=" C1' C R 7 " pdb=" C2' C R 7 " ideal model delta sinusoidal sigma weight residual 3.00 -20.91 23.91 1 8.00e+00 1.56e-02 1.29e+01 ... (remaining 3068 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.116: 700 0.116 - 0.231: 111 0.231 - 0.346: 4 0.346 - 0.462: 29 0.462 - 0.577: 16 Chirality restraints: 860 Sorted by residual: chirality pdb=" P C R 25 " pdb=" OP1 C R 25 " pdb=" OP2 C R 25 " pdb=" O5' C R 25 " both_signs ideal model delta sigma weight residual True 2.41 -2.99 -0.58 2.00e-01 2.50e+01 8.34e+00 chirality pdb=" P G R 1 " pdb=" OP1 G R 1 " pdb=" OP2 G R 1 " pdb=" O5' G R 1 " both_signs ideal model delta sigma weight residual True 2.41 -2.98 -0.57 2.00e-01 2.50e+01 8.16e+00 chirality pdb=" P U R 42 " pdb=" OP1 U R 42 " pdb=" OP2 U R 42 " pdb=" O5' U R 42 " both_signs ideal model delta sigma weight residual True 2.41 -2.94 -0.53 2.00e-01 2.50e+01 6.91e+00 ... (remaining 857 not shown) Planarity restraints: 635 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE O 37 " -0.034 5.00e-02 4.00e+02 5.20e-02 4.32e+00 pdb=" N PRO O 38 " 0.090 5.00e-02 4.00e+02 pdb=" CA PRO O 38 " -0.027 5.00e-02 4.00e+02 pdb=" CD PRO O 38 " -0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CD ARG O 79 " -0.161 9.50e-02 1.11e+02 7.21e-02 3.19e+00 pdb=" NE ARG O 79 " 0.010 2.00e-02 2.50e+03 pdb=" CZ ARG O 79 " 0.002 2.00e-02 2.50e+03 pdb=" NH1 ARG O 79 " 0.001 2.00e-02 2.50e+03 pdb=" NH2 ARG O 79 " -0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU P 7 " -0.008 2.00e-02 2.50e+03 1.52e-02 2.32e+00 pdb=" C LEU P 7 " 0.026 2.00e-02 2.50e+03 pdb=" O LEU P 7 " -0.010 2.00e-02 2.50e+03 pdb=" N GLN P 8 " -0.009 2.00e-02 2.50e+03 ... (remaining 632 not shown) Histogram of nonbonded interaction distances: 1.95 - 2.54: 31 2.54 - 3.13: 3425 3.13 - 3.72: 8029 3.72 - 4.31: 10879 4.31 - 4.90: 16137 Nonbonded interactions: 38501 Sorted by model distance: nonbonded pdb=" OD1 ASP O 64 " pdb=" CD PRO O 65 " model vdw 1.946 3.440 nonbonded pdb=" O ASP O 93 " pdb=" OD1 ASP O 93 " model vdw 2.202 3.040 nonbonded pdb=" OG1 THR O 26 " pdb=" OG SER O 105 " model vdw 2.241 3.040 nonbonded pdb=" OG SER P 19 " pdb=" OE1 GLN P 84 " model vdw 2.249 3.040 nonbonded pdb=" OD2 ASP P 75 " pdb=" NZ LYS P 78 " model vdw 2.257 3.120 ... (remaining 38496 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 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.420 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.070 Check model and map are aligned: 0.010 Set scattering table: 0.000 Process input model: 5.170 Find NCS groups from input model: 0.010 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:0.960 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 7.660 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4018 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 : 0.008 0.052 4987 Z= 0.537 Angle : 1.124 10.396 7106 Z= 0.640 Chirality : 0.131 0.577 860 Planarity : 0.005 0.072 635 Dihedral : 22.707 89.776 2337 Min Nonbonded Distance : 1.946 Molprobity Statistics. All-atom Clashscore : 12.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.66 % Favored : 95.34 % Rotamer: Outliers : 0.00 % Allowed : 25.22 % Favored : 74.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.35 (0.44), residues: 408 helix: 0.39 (1.52), residues: 12 sheet: 0.04 (0.42), residues: 171 loop : -0.40 (0.43), residues: 225 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG O 84 TYR 0.022 0.002 TYR O 60 PHE 0.008 0.001 PHE O 178 TRP 0.009 0.002 TRP Q 90 HIS 0.006 0.001 HIS O 40 Details of bonding type rmsd/Z covalent geometry : bond 0.00794 / 0.54 ( 4987) covalent geometry : angle 1.12361 / 0.64 ( 7106) hydrogen bonds : bond 0.16790 / 10.59 ( 186) hydrogen bonds : angle 8.42412 / 6.57 ( 419) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 816 Ramachandran restraints generated. 408 Oldfield, 0 Emsley, 408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 816 Ramachandran restraints generated. 408 Oldfield, 0 Emsley, 408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 65 residues out of total 345 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 65 time to evaluate : 0.133 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: O 110 ASN cc_start: 0.7303 (m110) cc_final: 0.6339 (m-40) outliers start: 0 outliers final: 0 residues processed: 65 average time/residue: 0.1044 time to fit residues: 8.0156 Evaluate side-chains 27 residues out of total 345 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 27 time to evaluate : 0.135 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 47 random chunks: chunk 24 optimal weight: 2.9990 chunk 26 optimal weight: 7.9990 chunk 2 optimal weight: 7.9990 chunk 16 optimal weight: 1.9990 chunk 32 optimal weight: 5.9990 chunk 31 skipped: trial refinement blew up (Bond distance > max_reasonable_bond_distance: 69.3272 > 50:) chunk 25 optimal weight: 7.9990 chunk 19 optimal weight: 3.9990 chunk 30 optimal weight: 0.9980 chunk 22 optimal weight: 2.9990 chunk 37 optimal weight: 10.0000 overall best weight: 2.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... O 80 ASN ** O 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 8 GLN P 15 GLN Q 49 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4390 r_free = 0.4390 target = 0.120347 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.4146 r_free = 0.4146 target = 0.092070 restraints weight = 48572.762| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 20)----------------| | r_work = 0.4146 r_free = 0.4146 target = 0.092070 restraints weight = 44839.798| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.4146 r_free = 0.4146 target = 0.092070 restraints weight = 44840.001| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.4146 r_free = 0.4146 target = 0.092070 restraints weight = 44840.001| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.4146 r_free = 0.4146 target = 0.092070 restraints weight = 44840.001| |-----------------------------------------------------------------------------| r_work (final): 0.4142 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6081 moved from start: 0.2948 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 4987 Z= 0.190 Angle : 0.731 7.614 7106 Z= 0.389 Chirality : 0.049 0.227 860 Planarity : 0.007 0.095 635 Dihedral : 23.070 85.246 1625 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 17.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.66 % Favored : 95.34 % Rotamer: Outliers : 0.29 % Allowed : 6.09 % Favored : 93.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.16 (0.43), residues: 408 helix: 0.86 (1.37), residues: 12 sheet: 0.57 (0.44), residues: 154 loop : -0.60 (0.42), residues: 242 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.019 0.002 ARG O 33 TYR 0.009 0.002 TYR P 96 PHE 0.017 0.003 PHE O 83 TRP 0.010 0.002 TRP P 38 HIS 0.004 0.002 HIS O 40 Details of bonding type rmsd/Z covalent geometry : bond 0.00374 / 0.19 ( 4987) covalent geometry : angle 0.73075 / 0.39 ( 7106) hydrogen bonds : bond 0.07423 / 4.88 ( 186) hydrogen bonds : angle 5.12413 / 3.89 ( 419) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 816 Ramachandran restraints generated. 408 Oldfield, 0 Emsley, 408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 816 Ramachandran restraints generated. 408 Oldfield, 0 Emsley, 408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 33 residues out of total 345 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 32 time to evaluate : 0.137 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: O 134 MET cc_start: -0.1004 (mpp) cc_final: -0.1244 (mtt) REVERT: P 108 PHE cc_start: 0.6386 (p90) cc_final: 0.6077 (p90) outliers start: 1 outliers final: 0 residues processed: 33 average time/residue: 0.1168 time to fit residues: 4.5771 Evaluate side-chains 26 residues out of total 345 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 26 time to evaluate : 0.138 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 47 random chunks: chunk 7 optimal weight: 4.9990 chunk 3 optimal weight: 9.9990 chunk 29 optimal weight: 4.9990 chunk 33 optimal weight: 5.9990 chunk 35 optimal weight: 2.9990 chunk 39 optimal weight: 0.9990 chunk 36 optimal weight: 0.9980 chunk 34 optimal weight: 50.0000 chunk 42 optimal weight: 20.0000 chunk 24 optimal weight: 5.9990 chunk 26 optimal weight: 6.9990 overall best weight: 2.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... O 14 ASN O 104 HIS O 110 ASN ** O 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 167 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 36 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4325 r_free = 0.4325 target = 0.115895 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4045 r_free = 0.4045 target = 0.087622 restraints weight = 44019.466| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 22)----------------| | r_work = 0.4045 r_free = 0.4045 target = 0.087622 restraints weight = 43157.930| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.4045 r_free = 0.4045 target = 0.087622 restraints weight = 43157.930| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.4045 r_free = 0.4045 target = 0.087622 restraints weight = 43157.930| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.4045 r_free = 0.4045 target = 0.087622 restraints weight = 43157.930| |-----------------------------------------------------------------------------| r_work (final): 0.4017 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6512 moved from start: 0.4417 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 4987 Z= 0.208 Angle : 0.697 7.998 7106 Z= 0.382 Chirality : 0.044 0.168 860 Planarity : 0.007 0.068 635 Dihedral : 23.353 93.818 1625 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 22.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.41 % Favored : 95.59 % Rotamer: Outliers : 0.29 % Allowed : 3.77 % Favored : 95.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.50 (0.41), residues: 408 helix: 1.54 (1.45), residues: 12 sheet: 0.21 (0.41), residues: 155 loop : -0.79 (0.39), residues: 241 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.026 0.002 ARG O 87 TYR 0.016 0.002 TYR P 55 PHE 0.016 0.002 PHE Q 61 TRP 0.018 0.002 TRP P 118 HIS 0.002 0.001 HIS O 160 Details of bonding type rmsd/Z covalent geometry : bond 0.00421 / 0.21 ( 4987) covalent geometry : angle 0.69724 / 0.38 ( 7106) hydrogen bonds : bond 0.08688 / 5.55 ( 186) hydrogen bonds : angle 5.18235 / 3.92 ( 419) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 816 Ramachandran restraints generated. 408 Oldfield, 0 Emsley, 408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 816 Ramachandran restraints generated. 408 Oldfield, 0 Emsley, 408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 35 residues out of total 345 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 34 time to evaluate : 0.142 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 outliers start: 1 outliers final: 0 residues processed: 35 average time/residue: 0.1355 time to fit residues: 5.5916 Evaluate side-chains 29 residues out of total 345 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 29 time to evaluate : 0.094 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 47 random chunks: chunk 16 optimal weight: 10.0000 chunk 1 optimal weight: 5.9990 chunk 17 optimal weight: 7.9990 chunk 3 optimal weight: 0.9980 chunk 42 optimal weight: 20.0000 chunk 2 optimal weight: 3.9990 chunk 25 optimal weight: 9.9990 chunk 22 optimal weight: 0.6980 chunk 0 optimal weight: 20.0000 chunk 30 optimal weight: 1.9990 chunk 36 optimal weight: 10.0000 overall best weight: 2.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... O 104 HIS ** O 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 36 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4311 r_free = 0.4311 target = 0.115911 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4049 r_free = 0.4049 target = 0.088361 restraints weight = 44495.932| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.4043 r_free = 0.4043 target = 0.088604 restraints weight = 42363.424| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.4043 r_free = 0.4043 target = 0.088604 restraints weight = 41353.118| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.4043 r_free = 0.4043 target = 0.088604 restraints weight = 41353.118| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.4043 r_free = 0.4043 target = 0.088604 restraints weight = 41353.118| |-----------------------------------------------------------------------------| r_work (final): 0.3987 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6317 moved from start: 0.5103 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 4987 Z= 0.195 Angle : 0.661 8.568 7106 Z= 0.367 Chirality : 0.043 0.171 860 Planarity : 0.007 0.069 635 Dihedral : 23.316 94.130 1625 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 19.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.66 % Favored : 95.34 % Rotamer: Outliers : 0.00 % Allowed : 3.48 % Favored : 96.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.68 (0.40), residues: 408 helix: 1.70 (1.39), residues: 12 sheet: 0.09 (0.41), residues: 149 loop : -0.91 (0.39), residues: 247 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG P 18 TYR 0.016 0.002 TYR P 55 PHE 0.008 0.001 PHE O 178 TRP 0.014 0.002 TRP P 118 HIS 0.002 0.001 HIS O 160 Details of bonding type rmsd/Z covalent geometry : bond 0.00378 / 0.20 ( 4987) covalent geometry : angle 0.66124 / 0.37 ( 7106) hydrogen bonds : bond 0.07442 / 4.74 ( 186) hydrogen bonds : angle 5.26096 / 3.92 ( 419) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 816 Ramachandran restraints generated. 408 Oldfield, 0 Emsley, 408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 816 Ramachandran restraints generated. 408 Oldfield, 0 Emsley, 408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 31 residues out of total 345 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 31 time to evaluate : 0.141 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: P 108 PHE cc_start: 0.6767 (p90) cc_final: 0.6496 (p90) REVERT: P 109 TRP cc_start: 0.8845 (t60) cc_final: 0.8505 (t60) outliers start: 0 outliers final: 0 residues processed: 31 average time/residue: 0.1157 time to fit residues: 4.3896 Evaluate side-chains 26 residues out of total 345 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 26 time to evaluate : 0.138 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 47 random chunks: chunk 13 optimal weight: 1.9990 chunk 19 optimal weight: 3.9990 chunk 42 optimal weight: 20.0000 chunk 24 optimal weight: 3.9990 chunk 9 optimal weight: 7.9990 chunk 10 optimal weight: 6.9990 chunk 40 optimal weight: 20.0000 chunk 3 optimal weight: 5.9990 chunk 12 optimal weight: 5.9990 chunk 7 optimal weight: 1.9990 chunk 4 optimal weight: 10.0000 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** O 104 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 167 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 15 GLN Q 36 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4199 r_free = 0.4199 target = 0.105958 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3918 r_free = 0.3918 target = 0.079023 restraints weight = 45679.323| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3918 r_free = 0.3918 target = 0.078972 restraints weight = 46723.224| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.3918 r_free = 0.3918 target = 0.078972 restraints weight = 46686.080| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.3918 r_free = 0.3918 target = 0.078972 restraints weight = 46685.056| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3918 r_free = 0.3918 target = 0.078972 restraints weight = 46685.056| |-----------------------------------------------------------------------------| r_work (final): 0.3862 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6147 moved from start: 0.6556 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.076 4987 Z= 0.248 Angle : 0.760 6.930 7106 Z= 0.426 Chirality : 0.049 0.204 860 Planarity : 0.008 0.110 635 Dihedral : 23.584 95.787 1625 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 32.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.37 % Favored : 93.63 % Rotamer: Outliers : 0.29 % Allowed : 4.64 % Favored : 95.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.17 (0.39), residues: 408 helix: 1.81 (1.44), residues: 12 sheet: -0.42 (0.38), residues: 155 loop : -1.16 (0.39), residues: 241 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.002 ARG O 33 TYR 0.020 0.003 TYR P 96 PHE 0.020 0.003 PHE O 83 TRP 0.022 0.003 TRP P 118 HIS 0.002 0.001 HIS O 104 Details of bonding type rmsd/Z covalent geometry : bond 0.00504 / 0.25 ( 4987) covalent geometry : angle 0.75975 / 0.43 ( 7106) hydrogen bonds : bond 0.10563 / 6.78 ( 186) hydrogen bonds : angle 5.83249 / 4.35 ( 419) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 816 Ramachandran restraints generated. 408 Oldfield, 0 Emsley, 408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 816 Ramachandran restraints generated. 408 Oldfield, 0 Emsley, 408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 30 residues out of total 345 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 29 time to evaluate : 0.137 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 outliers start: 1 outliers final: 1 residues processed: 30 average time/residue: 0.1063 time to fit residues: 3.9140 Evaluate side-chains 23 residues out of total 345 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 22 time to evaluate : 0.086 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 47 random chunks: chunk 7 optimal weight: 2.9990 chunk 3 optimal weight: 3.9990 chunk 16 optimal weight: 8.9990 chunk 22 optimal weight: 2.9990 chunk 33 optimal weight: 5.9990 chunk 38 optimal weight: 1.9990 chunk 42 optimal weight: 30.0000 chunk 23 optimal weight: 0.9980 chunk 6 optimal weight: 0.2980 chunk 4 optimal weight: 3.9990 chunk 14 optimal weight: 9.9990 overall best weight: 1.8586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** O 104 HIS ** 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 = 0.4237 r_free = 0.4237 target = 0.106905 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3962 r_free = 0.3962 target = 0.079530 restraints weight = 46573.320| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 14)----------------| | r_work = 0.3962 r_free = 0.3962 target = 0.079531 restraints weight = 46039.235| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.3962 r_free = 0.3962 target = 0.079530 restraints weight = 46047.218| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.3962 r_free = 0.3962 target = 0.079530 restraints weight = 46049.584| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3962 r_free = 0.3962 target = 0.079530 restraints weight = 46049.583| |-----------------------------------------------------------------------------| r_work (final): 0.3912 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6733 moved from start: 0.6622 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 4987 Z= 0.148 Angle : 0.628 6.377 7106 Z= 0.347 Chirality : 0.043 0.195 860 Planarity : 0.006 0.053 635 Dihedral : 23.364 95.438 1625 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 19.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.17 % Favored : 95.83 % Rotamer: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.00 (0.40), residues: 408 helix: 2.20 (1.49), residues: 12 sheet: -0.45 (0.38), residues: 164 loop : -0.95 (0.39), residues: 232 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG P 18 TYR 0.016 0.002 TYR P 55 PHE 0.015 0.002 PHE O 169 TRP 0.012 0.002 TRP P 118 HIS 0.003 0.001 HIS O 104 Details of bonding type rmsd/Z covalent geometry : bond 0.00299 / 0.15 ( 4987) covalent geometry : angle 0.62843 / 0.35 ( 7106) hydrogen bonds : bond 0.07083 / 4.28 ( 186) hydrogen bonds : angle 5.41436 / 3.97 ( 419) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 816 Ramachandran restraints generated. 408 Oldfield, 0 Emsley, 408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 816 Ramachandran restraints generated. 408 Oldfield, 0 Emsley, 408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 28 residues out of total 345 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 28 time to evaluate : 0.137 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: P 109 TRP cc_start: 0.8901 (t60) cc_final: 0.8455 (t60) outliers start: 0 outliers final: 0 residues processed: 28 average time/residue: 0.1024 time to fit residues: 3.5356 Evaluate side-chains 23 residues out of total 345 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 23 time to evaluate : 0.155 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 47 random chunks: chunk 16 optimal weight: 4.9990 chunk 39 optimal weight: 7.9990 chunk 21 optimal weight: 0.9980 chunk 46 optimal weight: 30.0000 chunk 26 optimal weight: 7.9990 chunk 9 optimal weight: 30.0000 chunk 23 optimal weight: 6.9990 chunk 42 optimal weight: 20.0000 chunk 5 optimal weight: 0.0570 chunk 33 optimal weight: 5.9990 chunk 27 optimal weight: 2.9990 overall best weight: 3.0104 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** O 145 GLN ** 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 = 0.4176 r_free = 0.4176 target = 0.102429 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3873 r_free = 0.3873 target = 0.075280 restraints weight = 43279.557| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3873 r_free = 0.3873 target = 0.075260 restraints weight = 43441.955| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.3873 r_free = 0.3873 target = 0.075260 restraints weight = 43608.080| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.3873 r_free = 0.3873 target = 0.075260 restraints weight = 43607.844| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3873 r_free = 0.3873 target = 0.075260 restraints weight = 43607.844| |-----------------------------------------------------------------------------| r_work (final): 0.3851 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6775 moved from start: 0.7499 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 4987 Z= 0.213 Angle : 0.689 6.462 7106 Z= 0.382 Chirality : 0.045 0.230 860 Planarity : 0.006 0.050 635 Dihedral : 23.347 93.321 1625 Min Nonbonded Distance : 2.383 Molprobity Statistics. All-atom Clashscore : 28.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.60 % Favored : 92.40 % Rotamer: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.23 (0.39), residues: 408 helix: 1.88 (1.48), residues: 12 sheet: -0.54 (0.40), residues: 154 loop : -1.14 (0.38), residues: 242 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG O 33 TYR 0.014 0.002 TYR P 55 PHE 0.009 0.002 PHE P 29 TRP 0.016 0.002 TRP P 38 HIS 0.006 0.002 HIS P 37 Details of bonding type rmsd/Z covalent geometry : bond 0.00427 / 0.21 ( 4987) covalent geometry : angle 0.68934 / 0.38 ( 7106) hydrogen bonds : bond 0.09857 / 6.27 ( 186) hydrogen bonds : angle 5.75120 / 4.20 ( 419) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 816 Ramachandran restraints generated. 408 Oldfield, 0 Emsley, 408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 816 Ramachandran restraints generated. 408 Oldfield, 0 Emsley, 408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 29 residues out of total 345 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 29 time to evaluate : 0.141 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: P 109 TRP cc_start: 0.8922 (t60) cc_final: 0.8412 (t60) outliers start: 0 outliers final: 0 residues processed: 29 average time/residue: 0.0794 time to fit residues: 2.8414 Evaluate side-chains 23 residues out of total 345 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 23 time to evaluate : 0.080 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 47 random chunks: chunk 10 optimal weight: 3.9990 chunk 32 optimal weight: 7.9990 chunk 5 optimal weight: 6.9990 chunk 34 optimal weight: 8.9990 chunk 26 optimal weight: 4.9990 chunk 17 optimal weight: 0.0980 chunk 24 optimal weight: 7.9990 chunk 42 optimal weight: 20.0000 chunk 3 optimal weight: 0.9990 chunk 6 optimal weight: 0.0570 chunk 9 optimal weight: 9.9990 overall best weight: 2.0304 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4192 r_free = 0.4192 target = 0.103389 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3904 r_free = 0.3904 target = 0.076055 restraints weight = 44926.860| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 12)----------------| | r_work = 0.3904 r_free = 0.3904 target = 0.076054 restraints weight = 44338.426| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 17)----------------| | r_work = 0.3904 r_free = 0.3904 target = 0.076054 restraints weight = 44335.084| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.3904 r_free = 0.3904 target = 0.076054 restraints weight = 44335.081| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3904 r_free = 0.3904 target = 0.076054 restraints weight = 44332.068| |-----------------------------------------------------------------------------| r_work (final): 0.3850 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6769 moved from start: 0.7747 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 4987 Z= 0.149 Angle : 0.617 7.311 7106 Z= 0.338 Chirality : 0.041 0.206 860 Planarity : 0.006 0.051 635 Dihedral : 23.260 93.940 1625 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 21.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.64 % Favored : 94.36 % Rotamer: Outliers : 0.00 % Allowed : 1.45 % Favored : 98.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.14 (0.40), residues: 408 helix: 2.41 (1.42), residues: 11 sheet: -0.61 (0.40), residues: 162 loop : -0.99 (0.39), residues: 235 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG P 69 TYR 0.013 0.001 TYR P 55 PHE 0.010 0.002 PHE P 29 TRP 0.014 0.001 TRP P 38 HIS 0.005 0.001 HIS P 37 Details of bonding type rmsd/Z covalent geometry : bond 0.00300 / 0.15 ( 4987) covalent geometry : angle 0.61732 / 0.34 ( 7106) hydrogen bonds : bond 0.07277 / 4.38 ( 186) hydrogen bonds : angle 5.50229 / 4.00 ( 419) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 816 Ramachandran restraints generated. 408 Oldfield, 0 Emsley, 408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 816 Ramachandran restraints generated. 408 Oldfield, 0 Emsley, 408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 27 residues out of total 345 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 27 time to evaluate : 0.143 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: P 109 TRP cc_start: 0.8982 (t60) cc_final: 0.8487 (t60) outliers start: 0 outliers final: 0 residues processed: 27 average time/residue: 0.0825 time to fit residues: 2.9341 Evaluate side-chains 22 residues out of total 345 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 22 time to evaluate : 0.137 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 47 random chunks: chunk 25 optimal weight: 3.9990 chunk 34 optimal weight: 6.9990 chunk 16 optimal weight: 0.0870 chunk 3 optimal weight: 3.9990 chunk 45 optimal weight: 9.9990 chunk 26 optimal weight: 4.9990 chunk 39 optimal weight: 10.0000 chunk 20 optimal weight: 2.9990 chunk 40 optimal weight: 20.0000 chunk 19 optimal weight: 10.0000 chunk 28 optimal weight: 0.7980 overall best weight: 2.3764 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** O 145 GLN ** 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 = 0.4169 r_free = 0.4169 target = 0.099674 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3867 r_free = 0.3867 target = 0.072456 restraints weight = 47698.989| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 22)----------------| | r_work = 0.3867 r_free = 0.3867 target = 0.072456 restraints weight = 48101.101| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.3867 r_free = 0.3867 target = 0.072456 restraints weight = 48101.101| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.3867 r_free = 0.3867 target = 0.072456 restraints weight = 48101.101| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3867 r_free = 0.3867 target = 0.072456 restraints weight = 48101.101| |-----------------------------------------------------------------------------| r_work (final): 0.3815 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6838 moved from start: 0.8095 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 4987 Z= 0.170 Angle : 0.649 6.570 7106 Z= 0.356 Chirality : 0.043 0.216 860 Planarity : 0.007 0.078 635 Dihedral : 23.207 92.891 1625 Min Nonbonded Distance : 2.384 Molprobity Statistics. All-atom Clashscore : 23.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.62 % Favored : 93.38 % Rotamer: Outliers : 0.00 % Allowed : 1.45 % Favored : 98.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.23 (0.40), residues: 408 helix: 1.91 (1.58), residues: 10 sheet: -0.67 (0.39), residues: 158 loop : -1.02 (0.39), residues: 240 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG P 18 TYR 0.012 0.002 TYR P 55 PHE 0.009 0.002 PHE O 83 TRP 0.014 0.001 TRP P 38 HIS 0.004 0.002 HIS P 37 Details of bonding type rmsd/Z covalent geometry : bond 0.00344 / 0.17 ( 4987) covalent geometry : angle 0.64869 / 0.36 ( 7106) hydrogen bonds : bond 0.08045 / 4.93 ( 186) hydrogen bonds : angle 5.48218 / 3.99 ( 419) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 816 Ramachandran restraints generated. 408 Oldfield, 0 Emsley, 408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 816 Ramachandran restraints generated. 408 Oldfield, 0 Emsley, 408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 25 residues out of total 345 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 25 time to evaluate : 0.146 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: P 109 TRP cc_start: 0.9068 (t60) cc_final: 0.8593 (t60) outliers start: 0 outliers final: 0 residues processed: 25 average time/residue: 0.0731 time to fit residues: 2.5156 Evaluate side-chains 20 residues out of total 345 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 20 time to evaluate : 0.142 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 47 random chunks: chunk 44 optimal weight: 20.0000 chunk 4 optimal weight: 0.9980 chunk 19 optimal weight: 5.9990 chunk 1 optimal weight: 6.9990 chunk 23 optimal weight: 4.9990 chunk 14 optimal weight: 10.0000 chunk 39 optimal weight: 9.9990 chunk 32 optimal weight: 8.9990 chunk 21 optimal weight: 5.9990 chunk 45 optimal weight: 9.9990 chunk 29 optimal weight: 0.9990 overall best weight: 3.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... O 167 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4089 r_free = 0.4089 target = 0.099065 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3725 r_free = 0.3725 target = 0.070580 restraints weight = 39171.596| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3726 r_free = 0.3726 target = 0.070703 restraints weight = 38915.323| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3726 r_free = 0.3726 target = 0.070730 restraints weight = 38436.152| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.3726 r_free = 0.3726 target = 0.070730 restraints weight = 38260.402| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3726 r_free = 0.3726 target = 0.070730 restraints weight = 38260.402| |-----------------------------------------------------------------------------| r_work (final): 0.3680 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6051 moved from start: 0.9397 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.072 4987 Z= 0.262 Angle : 0.818 6.625 7106 Z= 0.454 Chirality : 0.053 0.277 860 Planarity : 0.009 0.131 635 Dihedral : 23.647 92.581 1625 Min Nonbonded Distance : 2.284 Molprobity Statistics. All-atom Clashscore : 35.91 Ramachandran Plot: Outliers : 0.25 % Allowed : 8.82 % Favored : 90.93 % Rotamer: Outliers : 0.00 % Allowed : 0.58 % Favored : 99.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.80 (0.40), residues: 408 helix: 0.91 (1.50), residues: 10 sheet: -0.92 (0.42), residues: 133 loop : -1.48 (0.37), residues: 265 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.019 0.002 ARG O 55 TYR 0.020 0.003 TYR P 55 PHE 0.014 0.003 PHE P 29 TRP 0.024 0.003 TRP P 118 HIS 0.013 0.004 HIS O 104 Details of bonding type rmsd/Z covalent geometry : bond 0.00514 / 0.26 ( 4987) covalent geometry : angle 0.81769 / 0.45 ( 7106) hydrogen bonds : bond 0.11069 / 7.16 ( 186) hydrogen bonds : angle 6.20090 / 4.51 ( 419) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 816 Ramachandran restraints generated. 408 Oldfield, 0 Emsley, 408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 816 Ramachandran restraints generated. 408 Oldfield, 0 Emsley, 408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 22 residues out of total 345 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 22 time to evaluate : 0.146 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: O 134 MET cc_start: 0.2032 (mtt) cc_final: 0.1753 (mtt) REVERT: P 109 TRP cc_start: 0.8857 (t60) cc_final: 0.8572 (t60) outliers start: 0 outliers final: 0 residues processed: 22 average time/residue: 0.0736 time to fit residues: 2.1853 Evaluate side-chains 17 residues out of total 345 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 17 time to evaluate : 0.143 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 47 random chunks: chunk 0 optimal weight: 20.0000 chunk 28 optimal weight: 4.9990 chunk 22 optimal weight: 9.9990 chunk 27 optimal weight: 1.9990 chunk 30 optimal weight: 0.0870 chunk 18 optimal weight: 0.9980 chunk 37 optimal weight: 10.0000 chunk 9 optimal weight: 0.0570 chunk 34 optimal weight: 3.9990 chunk 4 optimal weight: 4.9990 chunk 20 optimal weight: 5.9990 overall best weight: 1.4280 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... O 167 GLN ** P 8 GLN ** 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 = 0.4136 r_free = 0.4136 target = 0.098194 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3806 r_free = 0.3806 target = 0.070441 restraints weight = 45567.952| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 22)----------------| | r_work = 0.3806 r_free = 0.3806 target = 0.070441 restraints weight = 46318.266| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.3806 r_free = 0.3806 target = 0.070441 restraints weight = 46318.266| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.3806 r_free = 0.3806 target = 0.070441 restraints weight = 46318.266| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3806 r_free = 0.3806 target = 0.070441 restraints weight = 46318.266| |-----------------------------------------------------------------------------| r_work (final): 0.3764 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6802 moved from start: 0.9266 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 4987 Z= 0.143 Angle : 0.641 6.850 7106 Z= 0.352 Chirality : 0.043 0.197 860 Planarity : 0.006 0.059 635 Dihedral : 23.409 94.085 1625 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 21.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.62 % Favored : 93.38 % Rotamer: Outliers : 0.00 % Allowed : 0.29 % Favored : 99.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.53 (0.40), residues: 408 helix: 1.43 (1.49), residues: 10 sheet: -1.00 (0.41), residues: 144 loop : -1.11 (0.39), residues: 254 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG O 55 TYR 0.011 0.002 TYR P 55 PHE 0.012 0.002 PHE P 29 TRP 0.013 0.002 TRP P 118 HIS 0.005 0.002 HIS P 37 Details of bonding type rmsd/Z covalent geometry : bond 0.00291 / 0.14 ( 4987) covalent geometry : angle 0.64112 / 0.35 ( 7106) hydrogen bonds : bond 0.07649 / 4.58 ( 186) hydrogen bonds : angle 5.69809 / 4.10 ( 419) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1197.27 seconds wall clock time: 21 minutes 16.18 seconds (1276.18 seconds total)