Starting phenix.real_space_refine on Thu Jul 24 11:56:24 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9opv_70725/07_2025/9opv_70725.cif Found real_map, /net/cci-nas-00/data/ceres_data/9opv_70725/07_2025/9opv_70725.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9opv_70725/07_2025/9opv_70725.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9opv_70725/07_2025/9opv_70725.map" model { file = "/net/cci-nas-00/data/ceres_data/9opv_70725/07_2025/9opv_70725.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9opv_70725/07_2025/9opv_70725.cif" } resolution = 3.4 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= 0.003 sd= 0.042 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 5 5.16 5 C 3740 2.51 5 N 1205 2.21 5 O 1195 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib" Total number of atoms: 6145 Number of models: 1 Model: "" Number of chains: 10 Chain: "M" Number of atoms: 603 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 603 Classifications: {'peptide': 75} Link IDs: {'TRANS': 74} Chain breaks: 2 Chain: "N" Number of atoms: 626 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 626 Classifications: {'peptide': 81} Link IDs: {'TRANS': 80} Chain breaks: 1 Chain: "O" Number of atoms: 603 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 603 Classifications: {'peptide': 75} Link IDs: {'TRANS': 74} Chain breaks: 2 Chain: "P" Number of atoms: 626 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 626 Classifications: {'peptide': 81} Link IDs: {'TRANS': 80} Chain breaks: 1 Chain: "Q" Number of atoms: 603 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 603 Classifications: {'peptide': 75} Link IDs: {'TRANS': 74} Chain breaks: 2 Chain: "R" Number of atoms: 626 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 626 Classifications: {'peptide': 81} Link IDs: {'TRANS': 80} Chain breaks: 1 Chain: "S" Number of atoms: 603 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 603 Classifications: {'peptide': 75} Link IDs: {'TRANS': 74} Chain breaks: 2 Chain: "T" Number of atoms: 626 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 626 Classifications: {'peptide': 81} Link IDs: {'TRANS': 80} Chain breaks: 1 Chain: "U" Number of atoms: 603 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 603 Classifications: {'peptide': 75} Link IDs: {'TRANS': 74} Chain breaks: 2 Chain: "V" Number of atoms: 626 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 626 Classifications: {'peptide': 81} Link IDs: {'TRANS': 80} Chain breaks: 1 Time building chain proxies: 5.65, per 1000 atoms: 0.92 Number of scatterers: 6145 At special positions: 0 Unit cell: (115.5, 117.7, 110, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 5 16.00 O 1195 8.00 N 1205 7.00 C 3740 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: 1.63 Conformation dependent library (CDL) restraints added in 723.2 milliseconds 1460 Ramachandran restraints generated. 730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1450 Finding SS restraints... Secondary structure from input PDB file: 25 helices and 0 sheets defined 96.9% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.46 Creating SS restraints... Processing helix chain 'M' and resid 33 through 44 removed outlier: 3.700A pdb=" N MET M 44 " --> pdb=" O LEU M 40 " (cutoff:3.500A) Processing helix chain 'M' and resid 53 through 62 Processing helix chain 'M' and resid 104 through 154 removed outlier: 4.363A pdb=" N THR M 154 " --> pdb=" O LEU M 150 " (cutoff:3.500A) Processing helix chain 'N' and resid 51 through 65 Processing helix chain 'N' and resid 106 through 169 removed outlier: 3.611A pdb=" N ASN N 123 " --> pdb=" O GLU N 119 " (cutoff:3.500A) Processing helix chain 'O' and resid 34 through 44 removed outlier: 3.728A pdb=" N MET O 44 " --> pdb=" O LEU O 40 " (cutoff:3.500A) Processing helix chain 'O' and resid 53 through 62 Processing helix chain 'O' and resid 104 through 154 removed outlier: 3.824A pdb=" N THR O 154 " --> pdb=" O LEU O 150 " (cutoff:3.500A) Processing helix chain 'P' and resid 51 through 65 Processing helix chain 'P' and resid 106 through 169 Processing helix chain 'Q' and resid 34 through 44 removed outlier: 3.781A pdb=" N MET Q 44 " --> pdb=" O LEU Q 40 " (cutoff:3.500A) Processing helix chain 'Q' and resid 53 through 62 Processing helix chain 'Q' and resid 104 through 154 Processing helix chain 'R' and resid 51 through 65 Processing helix chain 'R' and resid 106 through 169 removed outlier: 3.909A pdb=" N ASN R 123 " --> pdb=" O GLU R 119 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N ASN R 124 " --> pdb=" O GLY R 120 " (cutoff:3.500A) Processing helix chain 'S' and resid 34 through 44 removed outlier: 3.776A pdb=" N MET S 44 " --> pdb=" O LEU S 40 " (cutoff:3.500A) Processing helix chain 'S' and resid 53 through 62 Processing helix chain 'S' and resid 104 through 154 Processing helix chain 'T' and resid 51 through 65 Processing helix chain 'T' and resid 106 through 169 Processing helix chain 'U' and resid 34 through 44 removed outlier: 3.546A pdb=" N MET U 44 " --> pdb=" O LEU U 40 " (cutoff:3.500A) Processing helix chain 'U' and resid 53 through 62 Processing helix chain 'U' and resid 104 through 154 Processing helix chain 'V' and resid 51 through 65 Processing helix chain 'V' and resid 106 through 169 646 hydrogen bonds defined for protein. 1938 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.72 Time building geometry restraints manager: 1.90 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: 1991 1.34 - 1.45: 640 1.45 - 1.57: 3519 1.57 - 1.69: 0 1.69 - 1.81: 10 Bond restraints: 6160 Sorted by residual: bond pdb=" C VAL O 117 " pdb=" O VAL O 117 " ideal model delta sigma weight residual 1.237 1.247 -0.010 1.13e-02 7.83e+03 7.38e-01 bond pdb=" N GLN P 144 " pdb=" CA GLN P 144 " ideal model delta sigma weight residual 1.459 1.469 -0.011 1.28e-02 6.10e+03 6.83e-01 bond pdb=" C LEU P 143 " pdb=" N GLN P 144 " ideal model delta sigma weight residual 1.335 1.346 -0.011 1.38e-02 5.25e+03 6.26e-01 bond pdb=" C GLY N 120 " pdb=" O GLY N 120 " ideal model delta sigma weight residual 1.234 1.243 -0.009 1.19e-02 7.06e+03 5.98e-01 bond pdb=" CG1 ILE Q 122 " pdb=" CD1 ILE Q 122 " ideal model delta sigma weight residual 1.513 1.483 0.030 3.90e-02 6.57e+02 5.73e-01 ... (remaining 6155 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.68: 8136 1.68 - 3.35: 123 3.35 - 5.03: 15 5.03 - 6.71: 9 6.71 - 8.39: 2 Bond angle restraints: 8285 Sorted by residual: angle pdb=" C LEU P 143 " pdb=" N GLN P 144 " pdb=" CA GLN P 144 " ideal model delta sigma weight residual 120.31 114.61 5.70 1.52e+00 4.33e-01 1.41e+01 angle pdb=" N GLN P 144 " pdb=" CA GLN P 144 " pdb=" CB GLN P 144 " ideal model delta sigma weight residual 110.28 115.90 -5.62 1.55e+00 4.16e-01 1.32e+01 angle pdb=" C GLY O 120 " pdb=" N TYR O 121 " pdb=" CA TYR O 121 " ideal model delta sigma weight residual 121.58 114.79 6.79 1.95e+00 2.63e-01 1.21e+01 angle pdb=" N GLU T 159 " pdb=" CA GLU T 159 " pdb=" CB GLU T 159 " ideal model delta sigma weight residual 110.28 114.73 -4.45 1.55e+00 4.16e-01 8.26e+00 angle pdb=" N GLN O 144 " pdb=" CA GLN O 144 " pdb=" CB GLN O 144 " ideal model delta sigma weight residual 110.12 114.32 -4.20 1.47e+00 4.63e-01 8.18e+00 ... (remaining 8280 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.56: 3216 15.56 - 31.12: 444 31.12 - 46.69: 85 46.69 - 62.25: 20 62.25 - 77.81: 10 Dihedral angle restraints: 3775 sinusoidal: 1550 harmonic: 2225 Sorted by residual: dihedral pdb=" CG ARG S 152 " pdb=" CD ARG S 152 " pdb=" NE ARG S 152 " pdb=" CZ ARG S 152 " ideal model delta sinusoidal sigma weight residual 180.00 136.01 43.99 2 1.50e+01 4.44e-03 1.03e+01 dihedral pdb=" CG ARG O 152 " pdb=" CD ARG O 152 " pdb=" NE ARG O 152 " pdb=" CZ ARG O 152 " ideal model delta sinusoidal sigma weight residual -90.00 -133.65 43.65 2 1.50e+01 4.44e-03 1.02e+01 dihedral pdb=" CA ASP U 52 " pdb=" CB ASP U 52 " pdb=" CG ASP U 52 " pdb=" OD1 ASP U 52 " ideal model delta sinusoidal sigma weight residual -30.00 -84.65 54.65 1 2.00e+01 2.50e-03 1.01e+01 ... (remaining 3772 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.031: 704 0.031 - 0.062: 176 0.062 - 0.092: 83 0.092 - 0.123: 11 0.123 - 0.154: 1 Chirality restraints: 975 Sorted by residual: chirality pdb=" CA TYR O 121 " pdb=" N TYR O 121 " pdb=" C TYR O 121 " pdb=" CB TYR O 121 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.15 2.00e-01 2.50e+01 5.93e-01 chirality pdb=" CG LEU Q 132 " pdb=" CB LEU Q 132 " pdb=" CD1 LEU Q 132 " pdb=" CD2 LEU Q 132 " both_signs ideal model delta sigma weight residual False -2.59 -2.48 -0.11 2.00e-01 2.50e+01 3.13e-01 chirality pdb=" CA GLN P 144 " pdb=" N GLN P 144 " pdb=" C GLN P 144 " pdb=" CB GLN P 144 " both_signs ideal model delta sigma weight residual False 2.51 2.40 0.11 2.00e-01 2.50e+01 2.83e-01 ... (remaining 972 not shown) Planarity restraints: 1115 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE O 126 " -0.010 2.00e-02 2.50e+03 1.02e-02 1.80e+00 pdb=" CG PHE O 126 " 0.023 2.00e-02 2.50e+03 pdb=" CD1 PHE O 126 " -0.007 2.00e-02 2.50e+03 pdb=" CD2 PHE O 126 " 0.000 2.00e-02 2.50e+03 pdb=" CE1 PHE O 126 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 PHE O 126 " -0.008 2.00e-02 2.50e+03 pdb=" CZ PHE O 126 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG P 152 " -0.093 9.50e-02 1.11e+02 4.19e-02 1.35e+00 pdb=" NE ARG P 152 " 0.009 2.00e-02 2.50e+03 pdb=" CZ ARG P 152 " -0.008 2.00e-02 2.50e+03 pdb=" NH1 ARG P 152 " 0.004 2.00e-02 2.50e+03 pdb=" NH2 ARG P 152 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA TYR O 121 " -0.006 2.00e-02 2.50e+03 1.11e-02 1.23e+00 pdb=" C TYR O 121 " 0.019 2.00e-02 2.50e+03 pdb=" O TYR O 121 " -0.007 2.00e-02 2.50e+03 pdb=" N ILE O 122 " -0.007 2.00e-02 2.50e+03 ... (remaining 1112 not shown) Histogram of nonbonded interaction distances: 2.39 - 2.89: 2188 2.89 - 3.39: 7414 3.39 - 3.89: 10029 3.89 - 4.40: 10210 4.40 - 4.90: 16321 Nonbonded interactions: 46162 Sorted by model distance: nonbonded pdb=" O ALA P 140 " pdb=" OE1 GLN P 144 " model vdw 2.387 3.040 nonbonded pdb=" O ALA T 155 " pdb=" OE1 GLU T 159 " model vdw 2.458 3.040 nonbonded pdb=" O GLU Q 130 " pdb=" OE1 GLU Q 134 " model vdw 2.490 3.040 nonbonded pdb=" O ALA O 140 " pdb=" OE1 GLN O 144 " model vdw 2.511 3.040 nonbonded pdb=" O ALA R 140 " pdb=" OE1 GLN R 144 " model vdw 2.518 3.040 ... (remaining 46157 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: 0.01 Found NCS groups: ncs_group { reference = chain 'M' selection = chain 'O' selection = chain 'Q' selection = chain 'S' selection = chain 'U' } ncs_group { reference = chain 'N' selection = chain 'P' selection = chain 'R' selection = chain 'T' selection = chain 'V' } 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 individual isotropic 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: 7.770 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.280 Check model and map are aligned: 0.040 Set scattering table: 0.060 Process input model: 19.520 Find NCS groups from input model: 0.260 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.890 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.850 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7097 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 : 0.002 0.030 6160 Z= 0.142 Angle : 0.528 8.387 8285 Z= 0.289 Chirality : 0.034 0.154 975 Planarity : 0.003 0.042 1115 Dihedral : 14.949 77.809 2325 Min Nonbonded Distance : 2.387 Molprobity Statistics. All-atom Clashscore : 8.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % 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: 6.08 (0.27), residues: 730 helix: 4.05 (0.17), residues: 695 sheet: None (None), residues: 0 loop : 0.83 (0.64), residues: 35 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.023 0.001 PHE O 126 TYR 0.018 0.002 TYR M 60 ARG 0.009 0.000 ARG P 152 Details of bonding type rmsd hydrogen bonds : bond 0.07448 ( 646) hydrogen bonds : angle 3.64545 ( 1938) covalent geometry : bond 0.00248 ( 6160) covalent geometry : angle 0.52823 ( 8285) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1460 Ramachandran restraints generated. 730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1460 Ramachandran restraints generated. 730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 283 residues out of total 630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 283 time to evaluate : 0.820 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: N 55 ASP cc_start: 0.8377 (t0) cc_final: 0.7922 (m-30) REVERT: P 56 THR cc_start: 0.9533 (m) cc_final: 0.9305 (p) REVERT: Q 56 THR cc_start: 0.6769 (m) cc_final: 0.4606 (p) REVERT: R 118 LEU cc_start: 0.7504 (tt) cc_final: 0.7220 (mt) REVERT: V 149 GLU cc_start: 0.7271 (pt0) cc_final: 0.6984 (pt0) outliers start: 0 outliers final: 0 residues processed: 283 average time/residue: 0.3263 time to fit residues: 107.3039 Evaluate side-chains 140 residues out of total 630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 140 time to evaluate : 0.710 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 63 optimal weight: 7.9990 chunk 56 optimal weight: 10.0000 chunk 31 optimal weight: 6.9990 chunk 19 optimal weight: 5.9990 chunk 38 optimal weight: 20.0000 chunk 30 optimal weight: 9.9990 chunk 58 optimal weight: 6.9990 chunk 22 optimal weight: 0.0370 chunk 35 optimal weight: 9.9990 chunk 43 optimal weight: 8.9990 chunk 68 optimal weight: 40.0000 overall best weight: 5.6066 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: N 123 ASN P 54 ASN ** P 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 54 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 54 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3993 r_free = 0.3993 target = 0.070150 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3899 r_free = 0.3899 target = 0.065951 restraints weight = 56765.584| |-----------------------------------------------------------------------------| r_work (start): 0.3908 rms_B_bonded: 4.57 r_work (final): 0.3908 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7516 moved from start: 0.4538 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 6160 Z= 0.166 Angle : 0.710 12.504 8285 Z= 0.364 Chirality : 0.037 0.130 975 Planarity : 0.004 0.026 1115 Dihedral : 3.150 14.638 880 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 16.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 4.60 % Allowed : 18.89 % Favored : 76.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 5.49 (0.26), residues: 730 helix: 3.65 (0.16), residues: 700 sheet: None (None), residues: 0 loop : 0.72 (0.89), residues: 30 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.032 0.002 PHE U 126 TYR 0.026 0.002 TYR M 60 ARG 0.006 0.001 ARG N 163 Details of bonding type rmsd hydrogen bonds : bond 0.06307 ( 646) hydrogen bonds : angle 3.89351 ( 1938) covalent geometry : bond 0.00336 ( 6160) covalent geometry : angle 0.71042 ( 8285) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1460 Ramachandran restraints generated. 730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1460 Ramachandran restraints generated. 730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 175 time to evaluate : 0.780 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: N 131 ARG cc_start: 0.8536 (ptp-170) cc_final: 0.8318 (ptp-170) REVERT: O 143 LEU cc_start: 0.9123 (OUTLIER) cc_final: 0.8895 (tp) REVERT: P 56 THR cc_start: 0.9610 (m) cc_final: 0.9364 (p) REVERT: R 118 LEU cc_start: 0.7839 (tt) cc_final: 0.7384 (mt) REVERT: R 150 LEU cc_start: 0.8440 (pp) cc_final: 0.8060 (tp) REVERT: S 143 LEU cc_start: 0.9340 (OUTLIER) cc_final: 0.9123 (tp) REVERT: T 121 TYR cc_start: 0.6289 (OUTLIER) cc_final: 0.4703 (t80) REVERT: V 115 ASN cc_start: 0.7539 (t0) cc_final: 0.7303 (t0) outliers start: 29 outliers final: 15 residues processed: 192 average time/residue: 0.2376 time to fit residues: 55.5087 Evaluate side-chains 148 residues out of total 630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 130 time to evaluate : 0.688 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain M residue 43 ASN Chi-restraints excluded: chain M residue 121 TYR Chi-restraints excluded: chain M residue 143 LEU Chi-restraints excluded: chain N residue 110 VAL Chi-restraints excluded: chain O residue 143 LEU Chi-restraints excluded: chain P residue 144 GLN Chi-restraints excluded: chain Q residue 43 ASN Chi-restraints excluded: chain S residue 54 ASN Chi-restraints excluded: chain S residue 57 VAL Chi-restraints excluded: chain S residue 132 LEU Chi-restraints excluded: chain S residue 143 LEU Chi-restraints excluded: chain T residue 121 TYR Chi-restraints excluded: chain T residue 122 ILE Chi-restraints excluded: chain U residue 37 LEU Chi-restraints excluded: chain U residue 43 ASN Chi-restraints excluded: chain U residue 62 ASP Chi-restraints excluded: chain V residue 136 ASN Chi-restraints excluded: chain V residue 146 ARG Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 12 optimal weight: 10.0000 chunk 70 optimal weight: 9.9990 chunk 30 optimal weight: 3.9990 chunk 61 optimal weight: 7.9990 chunk 27 optimal weight: 8.9990 chunk 46 optimal weight: 20.0000 chunk 49 optimal weight: 7.9990 chunk 21 optimal weight: 7.9990 chunk 43 optimal weight: 8.9990 chunk 37 optimal weight: 6.9990 chunk 54 optimal weight: 8.9990 overall best weight: 6.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** P 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 54 ASN R 144 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3964 r_free = 0.3964 target = 0.068713 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3875 r_free = 0.3875 target = 0.064799 restraints weight = 58608.475| |-----------------------------------------------------------------------------| r_work (start): 0.3867 rms_B_bonded: 4.54 r_work (final): 0.3867 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7566 moved from start: 0.5164 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 6160 Z= 0.171 Angle : 0.691 12.467 8285 Z= 0.363 Chirality : 0.036 0.142 975 Planarity : 0.004 0.022 1115 Dihedral : 3.200 14.564 880 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 16.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 3.81 % Allowed : 23.33 % Favored : 72.86 % 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: 5.07 (0.26), residues: 730 helix: 3.38 (0.17), residues: 700 sheet: None (None), residues: 0 loop : 1.00 (1.02), residues: 30 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.021 0.001 PHE U 126 TYR 0.025 0.002 TYR M 60 ARG 0.005 0.000 ARG P 151 Details of bonding type rmsd hydrogen bonds : bond 0.06658 ( 646) hydrogen bonds : angle 4.00514 ( 1938) covalent geometry : bond 0.00342 ( 6160) covalent geometry : angle 0.69073 ( 8285) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1460 Ramachandran restraints generated. 730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1460 Ramachandran restraints generated. 730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 153 time to evaluate : 0.717 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: N 52 ASP cc_start: 0.6895 (p0) cc_final: 0.6184 (m-30) REVERT: P 56 THR cc_start: 0.9546 (m) cc_final: 0.9310 (p) REVERT: P 130 GLU cc_start: 0.7836 (tp30) cc_final: 0.7604 (tp30) REVERT: R 118 LEU cc_start: 0.7745 (tt) cc_final: 0.7265 (mt) REVERT: S 143 LEU cc_start: 0.9338 (OUTLIER) cc_final: 0.9091 (tp) REVERT: T 121 TYR cc_start: 0.6060 (OUTLIER) cc_final: 0.4515 (t80) REVERT: V 146 ARG cc_start: 0.8109 (OUTLIER) cc_final: 0.7835 (mmt90) outliers start: 24 outliers final: 15 residues processed: 167 average time/residue: 0.2212 time to fit residues: 45.7527 Evaluate side-chains 145 residues out of total 630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 127 time to evaluate : 0.763 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain M residue 43 ASN Chi-restraints excluded: chain M residue 143 LEU Chi-restraints excluded: chain N residue 110 VAL Chi-restraints excluded: chain Q residue 143 LEU Chi-restraints excluded: chain S residue 54 ASN Chi-restraints excluded: chain S residue 57 VAL Chi-restraints excluded: chain S residue 112 ASN Chi-restraints excluded: chain S residue 132 LEU Chi-restraints excluded: chain S residue 143 LEU Chi-restraints excluded: chain T residue 121 TYR Chi-restraints excluded: chain T residue 122 ILE Chi-restraints excluded: chain T residue 134 GLU Chi-restraints excluded: chain U residue 37 LEU Chi-restraints excluded: chain U residue 43 ASN Chi-restraints excluded: chain U residue 62 ASP Chi-restraints excluded: chain V residue 122 ILE Chi-restraints excluded: chain V residue 136 ASN Chi-restraints excluded: chain V residue 146 ARG Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 57 optimal weight: 5.9990 chunk 72 optimal weight: 5.9990 chunk 20 optimal weight: 9.9990 chunk 3 optimal weight: 30.0000 chunk 1 optimal weight: 8.9990 chunk 22 optimal weight: 0.8980 chunk 10 optimal weight: 6.9990 chunk 74 optimal weight: 9.9990 chunk 5 optimal weight: 7.9990 chunk 32 optimal weight: 9.9990 chunk 73 optimal weight: 8.9990 overall best weight: 5.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** P 142 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 = 0.3965 r_free = 0.3965 target = 0.068729 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3879 r_free = 0.3879 target = 0.064881 restraints weight = 60001.639| |-----------------------------------------------------------------------------| r_work (start): 0.3867 rms_B_bonded: 4.58 r_work (final): 0.3867 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7560 moved from start: 0.5469 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 6160 Z= 0.161 Angle : 0.695 11.670 8285 Z= 0.356 Chirality : 0.036 0.207 975 Planarity : 0.003 0.023 1115 Dihedral : 3.154 14.612 880 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 15.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 4.76 % Allowed : 23.97 % Favored : 71.27 % 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: 5.13 (0.27), residues: 730 helix: 3.41 (0.17), residues: 700 sheet: None (None), residues: 0 loop : 1.10 (1.11), residues: 30 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.015 0.001 PHE U 126 TYR 0.017 0.002 TYR M 60 ARG 0.005 0.000 ARG R 160 Details of bonding type rmsd hydrogen bonds : bond 0.06608 ( 646) hydrogen bonds : angle 3.89653 ( 1938) covalent geometry : bond 0.00316 ( 6160) covalent geometry : angle 0.69494 ( 8285) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1460 Ramachandran restraints generated. 730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1460 Ramachandran restraints generated. 730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 147 time to evaluate : 0.785 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: N 52 ASP cc_start: 0.7114 (p0) cc_final: 0.6589 (m-30) REVERT: N 131 ARG cc_start: 0.8568 (ptp-170) cc_final: 0.8179 (ptp-170) REVERT: O 143 LEU cc_start: 0.9267 (OUTLIER) cc_final: 0.8991 (tp) REVERT: P 56 THR cc_start: 0.9542 (m) cc_final: 0.9295 (p) REVERT: P 121 TYR cc_start: 0.7414 (OUTLIER) cc_final: 0.6016 (t80) REVERT: R 118 LEU cc_start: 0.7801 (tt) cc_final: 0.7402 (mt) REVERT: S 143 LEU cc_start: 0.9332 (OUTLIER) cc_final: 0.9086 (tp) REVERT: T 113 ASN cc_start: 0.8346 (m110) cc_final: 0.6857 (m110) REVERT: T 121 TYR cc_start: 0.6020 (OUTLIER) cc_final: 0.4497 (t80) outliers start: 30 outliers final: 19 residues processed: 163 average time/residue: 0.2213 time to fit residues: 44.6452 Evaluate side-chains 150 residues out of total 630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 127 time to evaluate : 0.702 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain M residue 43 ASN Chi-restraints excluded: chain M residue 121 TYR Chi-restraints excluded: chain M residue 143 LEU Chi-restraints excluded: chain N residue 54 ASN Chi-restraints excluded: chain N residue 110 VAL Chi-restraints excluded: chain O residue 143 LEU Chi-restraints excluded: chain P residue 121 TYR Chi-restraints excluded: chain Q residue 43 ASN Chi-restraints excluded: chain Q residue 143 LEU Chi-restraints excluded: chain R residue 122 ILE Chi-restraints excluded: chain S residue 54 ASN Chi-restraints excluded: chain S residue 112 ASN Chi-restraints excluded: chain S residue 132 LEU Chi-restraints excluded: chain S residue 143 LEU Chi-restraints excluded: chain T residue 121 TYR Chi-restraints excluded: chain T residue 122 ILE Chi-restraints excluded: chain T residue 134 GLU Chi-restraints excluded: chain U residue 37 LEU Chi-restraints excluded: chain U residue 43 ASN Chi-restraints excluded: chain U residue 62 ASP Chi-restraints excluded: chain V residue 122 ILE Chi-restraints excluded: chain V residue 136 ASN Chi-restraints excluded: chain V residue 167 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 9 optimal weight: 1.9990 chunk 32 optimal weight: 9.9990 chunk 41 optimal weight: 7.9990 chunk 38 optimal weight: 9.9990 chunk 54 optimal weight: 5.9990 chunk 40 optimal weight: 7.9990 chunk 46 optimal weight: 7.9990 chunk 57 optimal weight: 10.0000 chunk 29 optimal weight: 9.9990 chunk 22 optimal weight: 9.9990 chunk 1 optimal weight: 7.9990 overall best weight: 6.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** P 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 115 ASN R 144 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3950 r_free = 0.3950 target = 0.067920 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3863 r_free = 0.3863 target = 0.064116 restraints weight = 58878.454| |-----------------------------------------------------------------------------| r_work (start): 0.3856 rms_B_bonded: 4.51 r_work (final): 0.3856 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7587 moved from start: 0.5788 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 6160 Z= 0.164 Angle : 0.689 12.093 8285 Z= 0.360 Chirality : 0.036 0.160 975 Planarity : 0.003 0.022 1115 Dihedral : 3.219 15.590 880 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 15.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 4.92 % Allowed : 26.35 % Favored : 68.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 4.96 (0.27), residues: 730 helix: 3.36 (0.17), residues: 695 sheet: None (None), residues: 0 loop : 0.07 (1.05), residues: 35 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.013 0.001 PHE U 126 TYR 0.030 0.002 TYR U 60 ARG 0.005 0.000 ARG R 160 Details of bonding type rmsd hydrogen bonds : bond 0.06739 ( 646) hydrogen bonds : angle 3.99187 ( 1938) covalent geometry : bond 0.00324 ( 6160) covalent geometry : angle 0.68868 ( 8285) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1460 Ramachandran restraints generated. 730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1460 Ramachandran restraints generated. 730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 135 time to evaluate : 0.735 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: N 52 ASP cc_start: 0.7071 (p0) cc_final: 0.6680 (m-30) REVERT: N 131 ARG cc_start: 0.8536 (ptp-170) cc_final: 0.8287 (ptp-170) REVERT: O 121 TYR cc_start: 0.6799 (t80) cc_final: 0.6472 (t80) REVERT: O 143 LEU cc_start: 0.9314 (OUTLIER) cc_final: 0.8890 (tp) REVERT: P 56 THR cc_start: 0.9516 (m) cc_final: 0.9268 (p) REVERT: P 121 TYR cc_start: 0.7622 (OUTLIER) cc_final: 0.6273 (t80) REVERT: T 121 TYR cc_start: 0.6129 (OUTLIER) cc_final: 0.4590 (t80) outliers start: 31 outliers final: 23 residues processed: 155 average time/residue: 0.2312 time to fit residues: 44.1463 Evaluate side-chains 145 residues out of total 630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 119 time to evaluate : 0.760 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain M residue 43 ASN Chi-restraints excluded: chain M residue 112 ASN Chi-restraints excluded: chain M residue 121 TYR Chi-restraints excluded: chain M residue 143 LEU Chi-restraints excluded: chain N residue 54 ASN Chi-restraints excluded: chain N residue 110 VAL Chi-restraints excluded: chain N residue 113 ASN Chi-restraints excluded: chain O residue 143 LEU Chi-restraints excluded: chain P residue 119 GLU Chi-restraints excluded: chain P residue 121 TYR Chi-restraints excluded: chain Q residue 43 ASN Chi-restraints excluded: chain Q residue 143 LEU Chi-restraints excluded: chain R residue 122 ILE Chi-restraints excluded: chain S residue 54 ASN Chi-restraints excluded: chain S residue 61 LEU Chi-restraints excluded: chain S residue 112 ASN Chi-restraints excluded: chain S residue 132 LEU Chi-restraints excluded: chain T residue 121 TYR Chi-restraints excluded: chain T residue 122 ILE Chi-restraints excluded: chain T residue 134 GLU Chi-restraints excluded: chain T residue 167 LEU Chi-restraints excluded: chain U residue 37 LEU Chi-restraints excluded: chain U residue 43 ASN Chi-restraints excluded: chain U residue 62 ASP Chi-restraints excluded: chain V residue 122 ILE Chi-restraints excluded: chain V residue 136 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 2 optimal weight: 7.9990 chunk 40 optimal weight: 7.9990 chunk 22 optimal weight: 5.9990 chunk 55 optimal weight: 6.9990 chunk 48 optimal weight: 8.9990 chunk 67 optimal weight: 20.0000 chunk 35 optimal weight: 5.9990 chunk 27 optimal weight: 7.9990 chunk 28 optimal weight: 8.9990 chunk 64 optimal weight: 10.0000 chunk 0 optimal weight: 40.0000 overall best weight: 6.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** P 142 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 = 0.3943 r_free = 0.3943 target = 0.067657 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3855 r_free = 0.3855 target = 0.063852 restraints weight = 59354.002| |-----------------------------------------------------------------------------| r_work (start): 0.3838 rms_B_bonded: 4.54 r_work (final): 0.3838 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7624 moved from start: 0.6094 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 6160 Z= 0.169 Angle : 0.703 12.174 8285 Z= 0.368 Chirality : 0.036 0.146 975 Planarity : 0.004 0.033 1115 Dihedral : 3.287 14.497 880 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 16.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 5.24 % Allowed : 27.62 % Favored : 67.14 % 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: 4.76 (0.27), residues: 730 helix: 3.23 (0.17), residues: 695 sheet: None (None), residues: 0 loop : 0.12 (1.09), residues: 35 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.011 0.001 PHE U 126 TYR 0.023 0.002 TYR U 60 ARG 0.008 0.000 ARG N 160 Details of bonding type rmsd hydrogen bonds : bond 0.06910 ( 646) hydrogen bonds : angle 4.09005 ( 1938) covalent geometry : bond 0.00333 ( 6160) covalent geometry : angle 0.70279 ( 8285) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1460 Ramachandran restraints generated. 730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1460 Ramachandran restraints generated. 730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 138 time to evaluate : 0.777 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: N 52 ASP cc_start: 0.6975 (p0) cc_final: 0.6679 (m-30) REVERT: O 121 TYR cc_start: 0.6772 (t80) cc_final: 0.6424 (t80) REVERT: P 56 THR cc_start: 0.9561 (m) cc_final: 0.9308 (p) REVERT: R 118 LEU cc_start: 0.7661 (tt) cc_final: 0.7069 (mt) REVERT: T 121 TYR cc_start: 0.6204 (OUTLIER) cc_final: 0.4751 (t80) REVERT: T 166 ASP cc_start: 0.7697 (t0) cc_final: 0.7493 (t0) REVERT: U 60 TYR cc_start: 0.7568 (t80) cc_final: 0.7349 (t80) outliers start: 33 outliers final: 25 residues processed: 158 average time/residue: 0.2428 time to fit residues: 47.1165 Evaluate side-chains 147 residues out of total 630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 121 time to evaluate : 0.746 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain M residue 43 ASN Chi-restraints excluded: chain M residue 121 TYR Chi-restraints excluded: chain M residue 143 LEU Chi-restraints excluded: chain N residue 54 ASN Chi-restraints excluded: chain N residue 110 VAL Chi-restraints excluded: chain N residue 113 ASN Chi-restraints excluded: chain O residue 61 LEU Chi-restraints excluded: chain P residue 119 GLU Chi-restraints excluded: chain Q residue 43 ASN Chi-restraints excluded: chain Q residue 143 LEU Chi-restraints excluded: chain R residue 110 VAL Chi-restraints excluded: chain R residue 122 ILE Chi-restraints excluded: chain S residue 61 LEU Chi-restraints excluded: chain S residue 112 ASN Chi-restraints excluded: chain S residue 132 LEU Chi-restraints excluded: chain T residue 121 TYR Chi-restraints excluded: chain T residue 122 ILE Chi-restraints excluded: chain T residue 134 GLU Chi-restraints excluded: chain T residue 167 LEU Chi-restraints excluded: chain U residue 37 LEU Chi-restraints excluded: chain U residue 43 ASN Chi-restraints excluded: chain U residue 62 ASP Chi-restraints excluded: chain U residue 143 LEU Chi-restraints excluded: chain V residue 122 ILE Chi-restraints excluded: chain V residue 136 ASN Chi-restraints excluded: chain V residue 167 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 71 optimal weight: 5.9990 chunk 57 optimal weight: 10.0000 chunk 23 optimal weight: 6.9990 chunk 11 optimal weight: 5.9990 chunk 10 optimal weight: 8.9990 chunk 62 optimal weight: 9.9990 chunk 29 optimal weight: 9.9990 chunk 12 optimal weight: 6.9990 chunk 63 optimal weight: 8.9990 chunk 32 optimal weight: 6.9990 chunk 26 optimal weight: 5.9990 overall best weight: 6.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 144 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 = 0.3948 r_free = 0.3948 target = 0.067597 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3862 r_free = 0.3862 target = 0.063650 restraints weight = 57078.430| |-----------------------------------------------------------------------------| r_work (start): 0.3851 rms_B_bonded: 4.47 r_work (final): 0.3851 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7592 moved from start: 0.6316 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 6160 Z= 0.167 Angle : 0.702 12.371 8285 Z= 0.373 Chirality : 0.036 0.140 975 Planarity : 0.004 0.078 1115 Dihedral : 3.285 14.211 880 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 15.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 5.87 % Allowed : 28.25 % Favored : 65.87 % 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: 4.62 (0.27), residues: 730 helix: 3.15 (0.17), residues: 695 sheet: None (None), residues: 0 loop : -0.08 (1.08), residues: 35 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.010 0.001 PHE U 126 TYR 0.018 0.002 TYR U 60 ARG 0.014 0.001 ARG Q 58 Details of bonding type rmsd hydrogen bonds : bond 0.06942 ( 646) hydrogen bonds : angle 4.07626 ( 1938) covalent geometry : bond 0.00326 ( 6160) covalent geometry : angle 0.70154 ( 8285) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1460 Ramachandran restraints generated. 730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1460 Ramachandran restraints generated. 730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 136 time to evaluate : 0.826 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: N 52 ASP cc_start: 0.6938 (p0) cc_final: 0.6686 (m-30) REVERT: O 121 TYR cc_start: 0.6561 (t80) cc_final: 0.6188 (t80) REVERT: O 143 LEU cc_start: 0.9345 (OUTLIER) cc_final: 0.8994 (tp) REVERT: P 56 THR cc_start: 0.9521 (m) cc_final: 0.9288 (p) REVERT: P 121 TYR cc_start: 0.7839 (OUTLIER) cc_final: 0.6668 (t80) REVERT: Q 44 MET cc_start: 0.6285 (pmm) cc_final: 0.5485 (pmm) REVERT: T 121 TYR cc_start: 0.6039 (OUTLIER) cc_final: 0.4695 (t80) REVERT: T 166 ASP cc_start: 0.7777 (t0) cc_final: 0.7571 (t0) outliers start: 37 outliers final: 28 residues processed: 159 average time/residue: 0.2246 time to fit residues: 44.1293 Evaluate side-chains 150 residues out of total 630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 119 time to evaluate : 0.690 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain M residue 43 ASN Chi-restraints excluded: chain M residue 112 ASN Chi-restraints excluded: chain M residue 121 TYR Chi-restraints excluded: chain M residue 143 LEU Chi-restraints excluded: chain N residue 54 ASN Chi-restraints excluded: chain N residue 110 VAL Chi-restraints excluded: chain N residue 113 ASN Chi-restraints excluded: chain N residue 167 LEU Chi-restraints excluded: chain O residue 61 LEU Chi-restraints excluded: chain O residue 143 LEU Chi-restraints excluded: chain P residue 119 GLU Chi-restraints excluded: chain P residue 121 TYR Chi-restraints excluded: chain Q residue 43 ASN Chi-restraints excluded: chain Q residue 143 LEU Chi-restraints excluded: chain R residue 110 VAL Chi-restraints excluded: chain R residue 122 ILE Chi-restraints excluded: chain S residue 53 ILE Chi-restraints excluded: chain S residue 54 ASN Chi-restraints excluded: chain S residue 61 LEU Chi-restraints excluded: chain S residue 112 ASN Chi-restraints excluded: chain S residue 132 LEU Chi-restraints excluded: chain T residue 121 TYR Chi-restraints excluded: chain T residue 122 ILE Chi-restraints excluded: chain T residue 134 GLU Chi-restraints excluded: chain T residue 167 LEU Chi-restraints excluded: chain U residue 37 LEU Chi-restraints excluded: chain U residue 43 ASN Chi-restraints excluded: chain U residue 62 ASP Chi-restraints excluded: chain V residue 122 ILE Chi-restraints excluded: chain V residue 136 ASN Chi-restraints excluded: chain V residue 167 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 14 optimal weight: 9.9990 chunk 71 optimal weight: 5.9990 chunk 27 optimal weight: 10.0000 chunk 31 optimal weight: 8.9990 chunk 17 optimal weight: 5.9990 chunk 30 optimal weight: 7.9990 chunk 22 optimal weight: 20.0000 chunk 9 optimal weight: 9.9990 chunk 45 optimal weight: 4.9990 chunk 57 optimal weight: 10.0000 chunk 11 optimal weight: 7.9990 overall best weight: 6.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3947 r_free = 0.3947 target = 0.067455 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3860 r_free = 0.3860 target = 0.063498 restraints weight = 56385.111| |-----------------------------------------------------------------------------| r_work (start): 0.3852 rms_B_bonded: 4.44 r_work (final): 0.3852 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7596 moved from start: 0.6419 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 6160 Z= 0.175 Angle : 0.752 14.276 8285 Z= 0.393 Chirality : 0.037 0.141 975 Planarity : 0.004 0.073 1115 Dihedral : 3.376 14.541 880 Min Nonbonded Distance : 2.361 Molprobity Statistics. All-atom Clashscore : 16.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 5.56 % Allowed : 28.73 % Favored : 65.71 % 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: 4.43 (0.28), residues: 730 helix: 2.97 (0.17), residues: 700 sheet: None (None), residues: 0 loop : 0.88 (1.11), residues: 30 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.009 0.001 PHE U 126 TYR 0.035 0.002 TYR U 60 ARG 0.012 0.001 ARG Q 58 Details of bonding type rmsd hydrogen bonds : bond 0.06998 ( 646) hydrogen bonds : angle 4.17791 ( 1938) covalent geometry : bond 0.00346 ( 6160) covalent geometry : angle 0.75179 ( 8285) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1460 Ramachandran restraints generated. 730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1460 Ramachandran restraints generated. 730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 130 time to evaluate : 0.874 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: N 52 ASP cc_start: 0.7005 (p0) cc_final: 0.6691 (m-30) REVERT: O 121 TYR cc_start: 0.6581 (t80) cc_final: 0.6213 (t80) REVERT: O 143 LEU cc_start: 0.9293 (OUTLIER) cc_final: 0.8934 (tp) REVERT: P 56 THR cc_start: 0.9552 (m) cc_final: 0.9306 (p) REVERT: P 63 GLU cc_start: 0.5956 (OUTLIER) cc_final: 0.5401 (tp30) REVERT: P 121 TYR cc_start: 0.7867 (OUTLIER) cc_final: 0.6744 (t80) REVERT: Q 44 MET cc_start: 0.6296 (pmm) cc_final: 0.5548 (pmm) REVERT: T 121 TYR cc_start: 0.6002 (OUTLIER) cc_final: 0.4645 (t80) outliers start: 35 outliers final: 29 residues processed: 151 average time/residue: 0.2436 time to fit residues: 45.9805 Evaluate side-chains 154 residues out of total 630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 121 time to evaluate : 0.605 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain M residue 43 ASN Chi-restraints excluded: chain M residue 112 ASN Chi-restraints excluded: chain M residue 121 TYR Chi-restraints excluded: chain M residue 143 LEU Chi-restraints excluded: chain N residue 54 ASN Chi-restraints excluded: chain N residue 110 VAL Chi-restraints excluded: chain N residue 113 ASN Chi-restraints excluded: chain N residue 167 LEU Chi-restraints excluded: chain O residue 61 LEU Chi-restraints excluded: chain O residue 143 LEU Chi-restraints excluded: chain P residue 52 ASP Chi-restraints excluded: chain P residue 63 GLU Chi-restraints excluded: chain P residue 119 GLU Chi-restraints excluded: chain P residue 121 TYR Chi-restraints excluded: chain Q residue 43 ASN Chi-restraints excluded: chain Q residue 143 LEU Chi-restraints excluded: chain R residue 110 VAL Chi-restraints excluded: chain R residue 122 ILE Chi-restraints excluded: chain S residue 53 ILE Chi-restraints excluded: chain S residue 61 LEU Chi-restraints excluded: chain S residue 112 ASN Chi-restraints excluded: chain S residue 132 LEU Chi-restraints excluded: chain T residue 54 ASN Chi-restraints excluded: chain T residue 121 TYR Chi-restraints excluded: chain T residue 122 ILE Chi-restraints excluded: chain T residue 134 GLU Chi-restraints excluded: chain T residue 167 LEU Chi-restraints excluded: chain U residue 37 LEU Chi-restraints excluded: chain U residue 43 ASN Chi-restraints excluded: chain U residue 62 ASP Chi-restraints excluded: chain V residue 122 ILE Chi-restraints excluded: chain V residue 136 ASN Chi-restraints excluded: chain V residue 167 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 18 optimal weight: 0.9980 chunk 23 optimal weight: 20.0000 chunk 50 optimal weight: 6.9990 chunk 16 optimal weight: 9.9990 chunk 12 optimal weight: 6.9990 chunk 6 optimal weight: 9.9990 chunk 34 optimal weight: 5.9990 chunk 73 optimal weight: 7.9990 chunk 44 optimal weight: 9.9990 chunk 42 optimal weight: 5.9990 chunk 54 optimal weight: 8.9990 overall best weight: 5.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** Q 115 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 = 0.3958 r_free = 0.3958 target = 0.067881 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3869 r_free = 0.3869 target = 0.063885 restraints weight = 56971.122| |-----------------------------------------------------------------------------| r_work (start): 0.3859 rms_B_bonded: 4.48 r_work (final): 0.3859 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7572 moved from start: 0.6514 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 6160 Z= 0.171 Angle : 0.757 12.925 8285 Z= 0.399 Chirality : 0.037 0.159 975 Planarity : 0.004 0.053 1115 Dihedral : 3.390 15.927 880 Min Nonbonded Distance : 2.377 Molprobity Statistics. All-atom Clashscore : 15.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.27 % Favored : 99.73 % Rotamer: Outliers : 5.24 % Allowed : 29.68 % Favored : 65.08 % 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: 4.52 (0.28), residues: 730 helix: 3.03 (0.17), residues: 700 sheet: None (None), residues: 0 loop : 0.79 (1.12), residues: 30 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.009 0.001 PHE U 126 TYR 0.031 0.002 TYR U 60 ARG 0.010 0.001 ARG Q 58 Details of bonding type rmsd hydrogen bonds : bond 0.06879 ( 646) hydrogen bonds : angle 4.09890 ( 1938) covalent geometry : bond 0.00335 ( 6160) covalent geometry : angle 0.75691 ( 8285) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1460 Ramachandran restraints generated. 730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1460 Ramachandran restraints generated. 730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 131 time to evaluate : 0.799 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: P 56 THR cc_start: 0.9535 (m) cc_final: 0.9294 (p) REVERT: P 63 GLU cc_start: 0.5941 (OUTLIER) cc_final: 0.5386 (tp30) REVERT: P 121 TYR cc_start: 0.7881 (OUTLIER) cc_final: 0.6867 (t80) REVERT: Q 44 MET cc_start: 0.6138 (pmm) cc_final: 0.5451 (pmm) REVERT: T 121 TYR cc_start: 0.5939 (OUTLIER) cc_final: 0.4653 (t80) outliers start: 33 outliers final: 26 residues processed: 151 average time/residue: 0.2473 time to fit residues: 46.4598 Evaluate side-chains 148 residues out of total 630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 119 time to evaluate : 0.717 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain M residue 43 ASN Chi-restraints excluded: chain M residue 112 ASN Chi-restraints excluded: chain M residue 121 TYR Chi-restraints excluded: chain M residue 143 LEU Chi-restraints excluded: chain N residue 110 VAL Chi-restraints excluded: chain N residue 113 ASN Chi-restraints excluded: chain N residue 167 LEU Chi-restraints excluded: chain O residue 61 LEU Chi-restraints excluded: chain P residue 52 ASP Chi-restraints excluded: chain P residue 63 GLU Chi-restraints excluded: chain P residue 121 TYR Chi-restraints excluded: chain Q residue 43 ASN Chi-restraints excluded: chain Q residue 143 LEU Chi-restraints excluded: chain R residue 110 VAL Chi-restraints excluded: chain R residue 122 ILE Chi-restraints excluded: chain S residue 53 ILE Chi-restraints excluded: chain S residue 61 LEU Chi-restraints excluded: chain S residue 112 ASN Chi-restraints excluded: chain S residue 132 LEU Chi-restraints excluded: chain T residue 54 ASN Chi-restraints excluded: chain T residue 121 TYR Chi-restraints excluded: chain T residue 122 ILE Chi-restraints excluded: chain T residue 134 GLU Chi-restraints excluded: chain T residue 167 LEU Chi-restraints excluded: chain U residue 37 LEU Chi-restraints excluded: chain U residue 43 ASN Chi-restraints excluded: chain U residue 62 ASP Chi-restraints excluded: chain V residue 122 ILE Chi-restraints excluded: chain V residue 136 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 67 optimal weight: 6.9990 chunk 14 optimal weight: 10.0000 chunk 48 optimal weight: 6.9990 chunk 54 optimal weight: 8.9990 chunk 44 optimal weight: 9.9990 chunk 22 optimal weight: 0.2980 chunk 49 optimal weight: 6.9990 chunk 53 optimal weight: 20.0000 chunk 31 optimal weight: 7.9990 chunk 71 optimal weight: 8.9990 chunk 42 optimal weight: 8.9990 overall best weight: 5.8588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: P 123 ASN ** P 142 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 = 0.3953 r_free = 0.3953 target = 0.067748 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3866 r_free = 0.3866 target = 0.063675 restraints weight = 57173.366| |-----------------------------------------------------------------------------| r_work (start): 0.3862 rms_B_bonded: 4.58 r_work (final): 0.3862 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7589 moved from start: 0.6603 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 6160 Z= 0.175 Angle : 0.812 14.525 8285 Z= 0.418 Chirality : 0.037 0.163 975 Planarity : 0.004 0.048 1115 Dihedral : 3.380 17.449 880 Min Nonbonded Distance : 2.366 Molprobity Statistics. All-atom Clashscore : 16.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.41 % Favored : 99.59 % Rotamer: Outliers : 4.76 % Allowed : 30.32 % Favored : 64.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 4.42 (0.28), residues: 730 helix: 2.97 (0.17), residues: 700 sheet: None (None), residues: 0 loop : 0.82 (1.12), residues: 30 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.008 0.001 PHE U 126 TYR 0.022 0.002 TYR U 60 ARG 0.009 0.001 ARG Q 58 Details of bonding type rmsd hydrogen bonds : bond 0.06884 ( 646) hydrogen bonds : angle 4.14795 ( 1938) covalent geometry : bond 0.00349 ( 6160) covalent geometry : angle 0.81169 ( 8285) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1460 Ramachandran restraints generated. 730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1460 Ramachandran restraints generated. 730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 123 time to evaluate : 0.768 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: O 143 LEU cc_start: 0.9237 (OUTLIER) cc_final: 0.8947 (tp) REVERT: P 56 THR cc_start: 0.9578 (m) cc_final: 0.9319 (p) REVERT: P 121 TYR cc_start: 0.7843 (OUTLIER) cc_final: 0.6760 (t80) REVERT: Q 44 MET cc_start: 0.6162 (pmm) cc_final: 0.5500 (pmm) REVERT: Q 134 GLU cc_start: 0.8290 (pt0) cc_final: 0.8033 (pm20) REVERT: T 121 TYR cc_start: 0.6110 (OUTLIER) cc_final: 0.4850 (t80) outliers start: 30 outliers final: 26 residues processed: 141 average time/residue: 0.2042 time to fit residues: 36.4345 Evaluate side-chains 146 residues out of total 630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 117 time to evaluate : 0.700 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain M residue 43 ASN Chi-restraints excluded: chain M residue 112 ASN Chi-restraints excluded: chain M residue 121 TYR Chi-restraints excluded: chain M residue 143 LEU Chi-restraints excluded: chain N residue 110 VAL Chi-restraints excluded: chain N residue 113 ASN Chi-restraints excluded: chain N residue 167 LEU Chi-restraints excluded: chain O residue 143 LEU Chi-restraints excluded: chain P residue 52 ASP Chi-restraints excluded: chain P residue 119 GLU Chi-restraints excluded: chain P residue 121 TYR Chi-restraints excluded: chain Q residue 43 ASN Chi-restraints excluded: chain Q residue 143 LEU Chi-restraints excluded: chain R residue 110 VAL Chi-restraints excluded: chain R residue 122 ILE Chi-restraints excluded: chain S residue 53 ILE Chi-restraints excluded: chain S residue 61 LEU Chi-restraints excluded: chain S residue 112 ASN Chi-restraints excluded: chain S residue 132 LEU Chi-restraints excluded: chain T residue 54 ASN Chi-restraints excluded: chain T residue 121 TYR Chi-restraints excluded: chain T residue 122 ILE Chi-restraints excluded: chain T residue 134 GLU Chi-restraints excluded: chain T residue 167 LEU Chi-restraints excluded: chain U residue 37 LEU Chi-restraints excluded: chain U residue 43 ASN Chi-restraints excluded: chain U residue 62 ASP Chi-restraints excluded: chain V residue 122 ILE Chi-restraints excluded: chain V residue 136 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 49 optimal weight: 6.9990 chunk 65 optimal weight: 5.9990 chunk 70 optimal weight: 5.9990 chunk 50 optimal weight: 5.9990 chunk 37 optimal weight: 7.9990 chunk 24 optimal weight: 7.9990 chunk 52 optimal weight: 2.9990 chunk 23 optimal weight: 10.0000 chunk 72 optimal weight: 7.9990 chunk 48 optimal weight: 8.9990 chunk 22 optimal weight: 6.9990 overall best weight: 5.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** P 142 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 = 0.3964 r_free = 0.3964 target = 0.068260 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3873 r_free = 0.3873 target = 0.064106 restraints weight = 57276.117| |-----------------------------------------------------------------------------| r_work (start): 0.3869 rms_B_bonded: 4.65 r_work (final): 0.3869 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7587 moved from start: 0.6719 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 6160 Z= 0.173 Angle : 0.791 13.526 8285 Z= 0.412 Chirality : 0.037 0.160 975 Planarity : 0.004 0.049 1115 Dihedral : 3.349 18.114 880 Min Nonbonded Distance : 2.366 Molprobity Statistics. All-atom Clashscore : 15.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.55 % Favored : 99.45 % Rotamer: Outliers : 4.76 % Allowed : 30.32 % Favored : 64.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 4.46 (0.28), residues: 730 helix: 2.99 (0.17), residues: 700 sheet: None (None), residues: 0 loop : 0.76 (1.10), residues: 30 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.008 0.001 PHE U 126 TYR 0.019 0.002 TYR S 121 ARG 0.010 0.001 ARG R 163 Details of bonding type rmsd hydrogen bonds : bond 0.06829 ( 646) hydrogen bonds : angle 4.11179 ( 1938) covalent geometry : bond 0.00343 ( 6160) covalent geometry : angle 0.79126 ( 8285) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3194.01 seconds wall clock time: 57 minutes 1.57 seconds (3421.57 seconds total)