Starting phenix.real_space_refine on Tue Feb 3 15:37:20 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8qvp_18671/02_2026/8qvp_18671_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/8qvp_18671/02_2026/8qvp_18671.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.75 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8qvp_18671/02_2026/8qvp_18671.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8qvp_18671/02_2026/8qvp_18671.map" model { file = "/net/cci-nas-00/data/ceres_data/8qvp_18671/02_2026/8qvp_18671_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8qvp_18671/02_2026/8qvp_18671_trim.cif" } resolution = 3.75 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= 0.001 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 C 1400 2.51 5 N 420 2.21 5 O 440 1.98 5 H 2160 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 4420 Number of models: 1 Model: "" Number of chains: 2 Chain: "H" Number of atoms: 441 Number of conformers: 1 Conformer: "" Number of residues, atoms: 30, 441 Classifications: {'peptide': 30} Link IDs: {'PTRANS': 1, 'TRANS': 28} Chain: "H" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Restraints were copied for chains: I, J, K, L, M, N, O, P, Q Time building chain proxies: 0.31, per 1000 atoms: 0.07 Number of scatterers: 4420 At special positions: 0 Unit cell: (51.723, 69.785, 44.334, 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) O 440 8.00 N 420 7.00 C 1400 6.00 H 2160 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=10, symmetry=0 Number of additional bonds: simple=10, symmetry=0 Coordination: Other bonds: Time building additional restraints: 0.43 Conformation dependent library (CDL) restraints added in 102.2 milliseconds 560 Ramachandran restraints generated. 280 Oldfield, 0 Emsley, 280 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 560 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 8 sheets defined 0.0% alpha, 43.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.09 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'L' and resid 9 through 12 removed outlier: 6.822A pdb=" N THR J 9 " --> pdb=" O GLN L 10 " (cutoff:3.500A) removed outlier: 8.303A pdb=" N LEU L 12 " --> pdb=" O THR J 9 " (cutoff:3.500A) removed outlier: 6.529A pdb=" N ARG J 11 " --> pdb=" O LEU L 12 " (cutoff:3.500A) removed outlier: 6.814A pdb=" N THR H 9 " --> pdb=" O GLN J 10 " (cutoff:3.500A) removed outlier: 8.301A pdb=" N LEU J 12 " --> pdb=" O THR H 9 " (cutoff:3.500A) removed outlier: 6.521A pdb=" N ARG H 11 " --> pdb=" O LEU J 12 " (cutoff:3.500A) removed outlier: 6.833A pdb=" N THR N 9 " --> pdb=" O GLN P 10 " (cutoff:3.500A) removed outlier: 8.318A pdb=" N LEU P 12 " --> pdb=" O THR N 9 " (cutoff:3.500A) removed outlier: 6.543A pdb=" N ARG N 11 " --> pdb=" O LEU P 12 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'L' and resid 15 through 17 removed outlier: 6.386A pdb=" N LEU J 16 " --> pdb=" O VAL L 17 " (cutoff:3.500A) removed outlier: 6.399A pdb=" N LEU H 16 " --> pdb=" O VAL J 17 " (cutoff:3.500A) removed outlier: 6.403A pdb=" N LEU N 16 " --> pdb=" O VAL P 17 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'L' and resid 22 through 27 removed outlier: 9.252A pdb=" N PHE J 23 " --> pdb=" O GLY L 24 " (cutoff:3.500A) removed outlier: 9.736A pdb=" N ILE L 26 " --> pdb=" O PHE J 23 " (cutoff:3.500A) removed outlier: 5.905A pdb=" N ALA J 25 " --> pdb=" O ILE L 26 " (cutoff:3.500A) removed outlier: 9.268A pdb=" N PHE H 23 " --> pdb=" O GLY J 24 " (cutoff:3.500A) removed outlier: 9.764A pdb=" N ILE J 26 " --> pdb=" O PHE H 23 " (cutoff:3.500A) removed outlier: 5.908A pdb=" N ALA H 25 " --> pdb=" O ILE J 26 " (cutoff:3.500A) removed outlier: 6.746A pdb=" N PHE P 23 " --> pdb=" O ASN H 22 " (cutoff:3.500A) removed outlier: 6.920A pdb=" N GLY H 24 " --> pdb=" O PHE P 23 " (cutoff:3.500A) removed outlier: 6.851A pdb=" N ALA P 25 " --> pdb=" O GLY H 24 " (cutoff:3.500A) removed outlier: 9.328A pdb=" N PHE N 23 " --> pdb=" O GLY P 24 " (cutoff:3.500A) removed outlier: 9.837A pdb=" N ILE P 26 " --> pdb=" O PHE N 23 " (cutoff:3.500A) removed outlier: 5.995A pdb=" N ALA N 25 " --> pdb=" O ILE P 26 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'L' and resid 30 through 33 removed outlier: 6.299A pdb=" N ASN J 31 " --> pdb=" O VAL L 32 " (cutoff:3.500A) removed outlier: 6.269A pdb=" N ASN H 31 " --> pdb=" O VAL J 32 " (cutoff:3.500A) removed outlier: 6.330A pdb=" N ASN N 31 " --> pdb=" O VAL P 32 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'M' and resid 9 through 12 removed outlier: 6.841A pdb=" N THR K 9 " --> pdb=" O GLN M 10 " (cutoff:3.500A) removed outlier: 8.322A pdb=" N LEU M 12 " --> pdb=" O THR K 9 " (cutoff:3.500A) removed outlier: 6.546A pdb=" N ARG K 11 " --> pdb=" O LEU M 12 " (cutoff:3.500A) removed outlier: 6.764A pdb=" N THR I 9 " --> pdb=" O GLN K 10 " (cutoff:3.500A) removed outlier: 8.241A pdb=" N LEU K 12 " --> pdb=" O THR I 9 " (cutoff:3.500A) removed outlier: 6.458A pdb=" N ARG I 11 " --> pdb=" O LEU K 12 " (cutoff:3.500A) removed outlier: 6.786A pdb=" N THR O 9 " --> pdb=" O GLN Q 10 " (cutoff:3.500A) removed outlier: 8.257A pdb=" N LEU Q 12 " --> pdb=" O THR O 9 " (cutoff:3.500A) removed outlier: 6.475A pdb=" N ARG O 11 " --> pdb=" O LEU Q 12 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'M' and resid 15 through 17 removed outlier: 6.368A pdb=" N LEU K 16 " --> pdb=" O VAL M 17 " (cutoff:3.500A) removed outlier: 6.301A pdb=" N LEU I 16 " --> pdb=" O VAL K 17 " (cutoff:3.500A) removed outlier: 6.316A pdb=" N LEU O 16 " --> pdb=" O VAL Q 17 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'M' and resid 22 through 27 removed outlier: 9.262A pdb=" N PHE K 23 " --> pdb=" O GLY M 24 " (cutoff:3.500A) removed outlier: 9.764A pdb=" N ILE M 26 " --> pdb=" O PHE K 23 " (cutoff:3.500A) removed outlier: 5.942A pdb=" N ALA K 25 " --> pdb=" O ILE M 26 " (cutoff:3.500A) removed outlier: 9.163A pdb=" N PHE I 23 " --> pdb=" O GLY K 24 " (cutoff:3.500A) removed outlier: 9.671A pdb=" N ILE K 26 " --> pdb=" O PHE I 23 " (cutoff:3.500A) removed outlier: 5.921A pdb=" N ALA I 25 " --> pdb=" O ILE K 26 " (cutoff:3.500A) removed outlier: 6.746A pdb=" N PHE Q 23 " --> pdb=" O ASN I 22 " (cutoff:3.500A) removed outlier: 6.981A pdb=" N GLY I 24 " --> pdb=" O PHE Q 23 " (cutoff:3.500A) removed outlier: 6.835A pdb=" N ALA Q 25 " --> pdb=" O GLY I 24 " (cutoff:3.500A) removed outlier: 9.233A pdb=" N PHE O 23 " --> pdb=" O GLY Q 24 " (cutoff:3.500A) removed outlier: 9.753A pdb=" N ILE Q 26 " --> pdb=" O PHE O 23 " (cutoff:3.500A) removed outlier: 6.007A pdb=" N ALA O 25 " --> pdb=" O ILE Q 26 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'M' and resid 30 through 33 removed outlier: 6.322A pdb=" N ASN K 31 " --> pdb=" O VAL M 32 " (cutoff:3.500A) removed outlier: 6.366A pdb=" N ASN I 31 " --> pdb=" O VAL K 32 " (cutoff:3.500A) 23 hydrogen bonds defined for protein. 69 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: 0.62 Time building geometry restraints manager: 0.59 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 0.98: 2160 0.98 - 1.12: 0 1.12 - 1.26: 360 1.26 - 1.40: 620 1.40 - 1.55: 1310 Bond restraints: 4450 Sorted by residual: bond pdb=" N ALA K 8 " pdb=" CA ALA K 8 " ideal model delta sigma weight residual 1.458 1.493 -0.035 1.90e-02 2.77e+03 3.31e+00 bond pdb=" N ALA Q 8 " pdb=" CA ALA Q 8 " ideal model delta sigma weight residual 1.458 1.492 -0.034 1.90e-02 2.77e+03 3.28e+00 bond pdb=" N ALA I 8 " pdb=" CA ALA I 8 " ideal model delta sigma weight residual 1.458 1.492 -0.034 1.90e-02 2.77e+03 3.21e+00 bond pdb=" N ALA N 8 " pdb=" CA ALA N 8 " ideal model delta sigma weight residual 1.458 1.492 -0.034 1.90e-02 2.77e+03 3.20e+00 bond pdb=" N ALA P 8 " pdb=" CA ALA P 8 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 3.03e+00 ... (remaining 4445 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.04: 6774 1.04 - 2.08: 867 2.08 - 3.13: 139 3.13 - 4.17: 100 4.17 - 5.21: 30 Bond angle restraints: 7910 Sorted by residual: angle pdb=" N ASN I 22 " pdb=" CA ASN I 22 " pdb=" C ASN I 22 " ideal model delta sigma weight residual 108.75 112.65 -3.90 1.71e+00 3.42e-01 5.20e+00 angle pdb=" N ASN Q 22 " pdb=" CA ASN Q 22 " pdb=" C ASN Q 22 " ideal model delta sigma weight residual 108.75 112.64 -3.89 1.71e+00 3.42e-01 5.16e+00 angle pdb=" N ASN K 22 " pdb=" CA ASN K 22 " pdb=" C ASN K 22 " ideal model delta sigma weight residual 108.75 112.63 -3.88 1.71e+00 3.42e-01 5.15e+00 angle pdb=" N ASN L 22 " pdb=" CA ASN L 22 " pdb=" C ASN L 22 " ideal model delta sigma weight residual 108.75 112.63 -3.88 1.71e+00 3.42e-01 5.14e+00 angle pdb=" N ASN N 22 " pdb=" CA ASN N 22 " pdb=" C ASN N 22 " ideal model delta sigma weight residual 108.75 112.62 -3.87 1.71e+00 3.42e-01 5.13e+00 ... (remaining 7905 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 13.51: 1898 13.51 - 27.03: 152 27.03 - 40.54: 80 40.54 - 54.06: 0 54.06 - 67.57: 30 Dihedral angle restraints: 2160 sinusoidal: 1130 harmonic: 1030 Sorted by residual: dihedral pdb=" CA SER O 20 " pdb=" C SER O 20 " pdb=" N ASN O 21 " pdb=" CA ASN O 21 " ideal model delta harmonic sigma weight residual 180.00 146.15 33.85 0 5.00e+00 4.00e-02 4.58e+01 dihedral pdb=" CA SER N 20 " pdb=" C SER N 20 " pdb=" N ASN N 21 " pdb=" CA ASN N 21 " ideal model delta harmonic sigma weight residual 180.00 146.20 33.80 0 5.00e+00 4.00e-02 4.57e+01 dihedral pdb=" CA SER J 20 " pdb=" C SER J 20 " pdb=" N ASN J 21 " pdb=" CA ASN J 21 " ideal model delta harmonic sigma weight residual 180.00 146.20 33.80 0 5.00e+00 4.00e-02 4.57e+01 ... (remaining 2157 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.026: 182 0.026 - 0.053: 100 0.053 - 0.079: 28 0.079 - 0.105: 43 0.105 - 0.131: 17 Chirality restraints: 370 Sorted by residual: chirality pdb=" CA ILE K 26 " pdb=" N ILE K 26 " pdb=" C ILE K 26 " pdb=" CB ILE K 26 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.30e-01 chirality pdb=" CA ILE Q 26 " pdb=" N ILE Q 26 " pdb=" C ILE Q 26 " pdb=" CB ILE Q 26 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.27e-01 chirality pdb=" CA ILE N 26 " pdb=" N ILE N 26 " pdb=" C ILE N 26 " pdb=" CB ILE N 26 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.24e-01 ... (remaining 367 not shown) Planarity restraints: 690 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASN O 22 " 0.009 2.00e-02 2.50e+03 1.82e-02 3.30e+00 pdb=" C ASN O 22 " -0.031 2.00e-02 2.50e+03 pdb=" O ASN O 22 " 0.012 2.00e-02 2.50e+03 pdb=" N PHE O 23 " 0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASN P 22 " -0.009 2.00e-02 2.50e+03 1.80e-02 3.26e+00 pdb=" C ASN P 22 " 0.031 2.00e-02 2.50e+03 pdb=" O ASN P 22 " -0.012 2.00e-02 2.50e+03 pdb=" N PHE P 23 " -0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASN L 22 " -0.009 2.00e-02 2.50e+03 1.80e-02 3.23e+00 pdb=" C ASN L 22 " 0.031 2.00e-02 2.50e+03 pdb=" O ASN L 22 " -0.012 2.00e-02 2.50e+03 pdb=" N PHE L 23 " -0.010 2.00e-02 2.50e+03 ... (remaining 687 not shown) Histogram of nonbonded interaction distances: 1.92 - 2.44: 2458 2.44 - 2.95: 9185 2.95 - 3.47: 10695 3.47 - 3.98: 14123 3.98 - 4.50: 19875 Nonbonded interactions: 56336 Sorted by model distance: nonbonded pdb=" H SER I 28 " pdb=" O LEU Q 27 " model vdw 1.924 2.450 nonbonded pdb=" H SER H 28 " pdb=" O LEU P 27 " model vdw 1.932 2.450 nonbonded pdb=" O LEU H 27 " pdb=" H SER J 28 " model vdw 1.935 2.450 nonbonded pdb=" O LEU I 27 " pdb=" H SER K 28 " model vdw 1.948 2.450 nonbonded pdb=" OD1 ASN H 35 " pdb="HD22 ASN L 14 " model vdw 1.983 2.450 ... (remaining 56331 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 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.040 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: 0.020 Extract box with map and model: 0.090 Check model and map are aligned: 0.010 Set scattering table: 0.020 Process input model: 4.810 Find NCS groups from input model: 0.020 Set up NCS constraints: 0.000 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:1.330 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 9.340 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7015 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 0.099 2300 Z= 0.686 Angle : 0.949 4.917 3120 Z= 0.519 Chirality : 0.049 0.131 370 Planarity : 0.004 0.018 410 Dihedral : 12.693 37.047 760 Min Nonbonded Distance : 2.289 Molprobity Statistics. All-atom Clashscore : 6.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 0.00 % Allowed : 16.00 % Favored : 84.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 3.57 % 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: -2.44 (0.31), residues: 280 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.85 (0.24), residues: 280 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG H 11 TYR 0.010 0.003 TYR N 37 PHE 0.003 0.001 PHE K 23 HIS 0.006 0.003 HIS K 18 Details of bonding type rmsd covalent geometry : bond 0.00514 ( 2290) covalent geometry : angle 0.94897 ( 3120) hydrogen bonds : bond 0.21527 ( 23) hydrogen bonds : angle 8.41214 ( 69) Misc. bond : bond 0.09847 ( 10) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 560 Ramachandran restraints generated. 280 Oldfield, 0 Emsley, 280 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 560 Ramachandran restraints generated. 280 Oldfield, 0 Emsley, 280 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 67 residues out of total 250 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 67 time to evaluate : 0.085 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 outliers start: 0 outliers final: 0 residues processed: 67 average time/residue: 0.0285 time to fit residues: 2.8712 Evaluate side-chains 17 residues out of total 250 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 17 time to evaluate : 0.074 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 27 optimal weight: 9.9990 chunk 12 optimal weight: 1.9990 chunk 24 optimal weight: 8.9990 chunk 28 optimal weight: 0.6980 chunk 13 optimal weight: 4.9990 chunk 1 optimal weight: 4.9990 chunk 8 optimal weight: 5.9990 chunk 16 optimal weight: 2.9990 chunk 15 optimal weight: 0.7980 chunk 29 optimal weight: 7.9990 chunk 25 optimal weight: 0.8980 overall best weight: 1.4784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 10 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 14 ASN ** H 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 10 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 14 ASN ** I 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 10 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 14 ASN ** K 10 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 14 ASN ** K 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 10 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 10 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 10 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 14 ASN P 21 ASN ** Q 10 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 14 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4737 r_free = 0.4737 target = 0.197699 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4665 r_free = 0.4665 target = 0.173317 restraints weight = 13072.983| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.4712 r_free = 0.4712 target = 0.179408 restraints weight = 5603.904| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.4739 r_free = 0.4739 target = 0.182887 restraints weight = 2905.751| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.4761 r_free = 0.4761 target = 0.185225 restraints weight = 1718.550| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.4773 r_free = 0.4773 target = 0.186457 restraints weight = 1038.312| |-----------------------------------------------------------------------------| r_work (final): 0.4724 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7231 moved from start: 0.3257 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 2300 Z= 0.127 Angle : 0.594 4.810 3120 Z= 0.323 Chirality : 0.038 0.120 370 Planarity : 0.002 0.009 410 Dihedral : 5.699 23.523 310 Min Nonbonded Distance : 2.346 Molprobity Statistics. All-atom Clashscore : 19.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.07 % Favored : 93.93 % Rotamer: Outliers : 2.00 % Allowed : 25.60 % Favored : 72.40 % 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: -1.75 (0.37), residues: 280 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.33 (0.28), residues: 280 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG L 11 TYR 0.007 0.002 TYR P 37 PHE 0.005 0.001 PHE O 23 HIS 0.004 0.002 HIS H 18 Details of bonding type rmsd covalent geometry : bond 0.00307 ( 2290) covalent geometry : angle 0.59380 ( 3120) hydrogen bonds : bond 0.03387 ( 23) hydrogen bonds : angle 6.21812 ( 69) Misc. bond : bond 0.00010 ( 10) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 560 Ramachandran restraints generated. 280 Oldfield, 0 Emsley, 280 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 560 Ramachandran restraints generated. 280 Oldfield, 0 Emsley, 280 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 25 residues out of total 250 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 20 time to evaluate : 0.127 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 5 outliers final: 3 residues processed: 24 average time/residue: 0.0573 time to fit residues: 2.0272 Evaluate side-chains 13 residues out of total 250 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 10 time to evaluate : 0.125 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain N residue 21 ASN Chi-restraints excluded: chain O residue 21 ASN Chi-restraints excluded: chain Q residue 21 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 29 optimal weight: 10.0000 chunk 23 optimal weight: 8.9990 chunk 5 optimal weight: 2.9990 chunk 3 optimal weight: 10.0000 chunk 4 optimal weight: 0.4980 chunk 8 optimal weight: 9.9990 chunk 12 optimal weight: 0.7980 chunk 16 optimal weight: 3.9990 chunk 28 optimal weight: 0.8980 chunk 20 optimal weight: 4.9990 chunk 13 optimal weight: 0.7980 overall best weight: 1.1982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 10 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 10 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 10 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 10 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 21 ASN ** L 10 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 14 ASN ** M 10 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 14 ASN ** N 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 10 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 21 ASN ** Q 10 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 21 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4761 r_free = 0.4761 target = 0.199975 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4693 r_free = 0.4693 target = 0.174616 restraints weight = 12929.926| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.4743 r_free = 0.4743 target = 0.180586 restraints weight = 5445.728| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.4774 r_free = 0.4774 target = 0.184269 restraints weight = 2868.845| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.4791 r_free = 0.4791 target = 0.186379 restraints weight = 1653.496| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.4802 r_free = 0.4802 target = 0.187715 restraints weight = 1023.835| |-----------------------------------------------------------------------------| r_work (final): 0.4737 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7205 moved from start: 0.3765 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 2300 Z= 0.109 Angle : 0.550 4.417 3120 Z= 0.297 Chirality : 0.038 0.124 370 Planarity : 0.002 0.012 410 Dihedral : 5.505 21.627 310 Min Nonbonded Distance : 2.280 Molprobity Statistics. All-atom Clashscore : 18.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.29 % Favored : 95.71 % Rotamer: Outliers : 3.60 % Allowed : 24.40 % Favored : 72.00 % 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: -1.77 (0.36), residues: 280 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.34 (0.27), residues: 280 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG Q 11 TYR 0.006 0.001 TYR O 37 PHE 0.003 0.001 PHE O 23 HIS 0.003 0.001 HIS H 18 Details of bonding type rmsd covalent geometry : bond 0.00270 ( 2290) covalent geometry : angle 0.55039 ( 3120) hydrogen bonds : bond 0.03344 ( 23) hydrogen bonds : angle 5.30895 ( 69) Misc. bond : bond 0.00004 ( 10) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 560 Ramachandran restraints generated. 280 Oldfield, 0 Emsley, 280 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 560 Ramachandran restraints generated. 280 Oldfield, 0 Emsley, 280 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 19 residues out of total 250 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 10 time to evaluate : 0.128 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 9 outliers final: 6 residues processed: 19 average time/residue: 0.0439 time to fit residues: 1.3963 Evaluate side-chains 15 residues out of total 250 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 9 time to evaluate : 0.129 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 21 ASN Chi-restraints excluded: chain N residue 30 THR Chi-restraints excluded: chain O residue 21 ASN Chi-restraints excluded: chain O residue 30 THR Chi-restraints excluded: chain P residue 21 ASN Chi-restraints excluded: chain Q residue 21 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 23 optimal weight: 7.9990 chunk 19 optimal weight: 5.9990 chunk 26 optimal weight: 10.0000 chunk 12 optimal weight: 8.9990 chunk 6 optimal weight: 3.9990 chunk 10 optimal weight: 5.9990 chunk 28 optimal weight: 6.9990 chunk 0 optimal weight: 6.9990 chunk 1 optimal weight: 0.9990 chunk 3 optimal weight: 3.9990 chunk 16 optimal weight: 0.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 10 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 10 GLN ** J 10 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 21 ASN K 10 GLN ** L 10 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 10 GLN ** M 14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 10 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 10 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4739 r_free = 0.4739 target = 0.201945 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4619 r_free = 0.4619 target = 0.163139 restraints weight = 12761.137| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.4689 r_free = 0.4689 target = 0.169639 restraints weight = 5510.843| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.4718 r_free = 0.4718 target = 0.173451 restraints weight = 2925.343| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.4742 r_free = 0.4742 target = 0.176104 restraints weight = 1773.760| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.4755 r_free = 0.4755 target = 0.177637 restraints weight = 1107.289| |-----------------------------------------------------------------------------| r_work (final): 0.4709 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7341 moved from start: 0.4258 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.033 2300 Z= 0.194 Angle : 0.625 4.704 3120 Z= 0.347 Chirality : 0.038 0.122 370 Planarity : 0.002 0.010 410 Dihedral : 5.529 22.277 310 Min Nonbonded Distance : 2.301 Molprobity Statistics. All-atom Clashscore : 18.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.93 % Favored : 96.07 % Rotamer: Outliers : 3.20 % Allowed : 24.40 % Favored : 72.40 % 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: -1.76 (0.36), residues: 280 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.33 (0.28), residues: 280 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.000 0.000 ARG L 11 TYR 0.013 0.003 TYR O 37 PHE 0.004 0.001 PHE O 23 HIS 0.004 0.002 HIS H 18 Details of bonding type rmsd covalent geometry : bond 0.00457 ( 2290) covalent geometry : angle 0.62518 ( 3120) hydrogen bonds : bond 0.03132 ( 23) hydrogen bonds : angle 5.36619 ( 69) Misc. bond : bond 0.00011 ( 10) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 560 Ramachandran restraints generated. 280 Oldfield, 0 Emsley, 280 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 560 Ramachandran restraints generated. 280 Oldfield, 0 Emsley, 280 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 18 residues out of total 250 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 10 time to evaluate : 0.080 Fit side-chains revert: symmetry clash REVERT: H 21 ASN cc_start: 0.8115 (OUTLIER) cc_final: 0.7891 (m-40) outliers start: 8 outliers final: 5 residues processed: 17 average time/residue: 0.0469 time to fit residues: 1.2707 Evaluate side-chains 13 residues out of total 250 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 7 time to evaluate : 0.143 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 21 ASN Chi-restraints excluded: chain J residue 21 ASN Chi-restraints excluded: chain N residue 21 ASN Chi-restraints excluded: chain N residue 30 THR Chi-restraints excluded: chain O residue 21 ASN Chi-restraints excluded: chain O residue 30 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 9 optimal weight: 7.9990 chunk 19 optimal weight: 3.9990 chunk 6 optimal weight: 6.9990 chunk 27 optimal weight: 8.9990 chunk 7 optimal weight: 1.9990 chunk 2 optimal weight: 8.9990 chunk 20 optimal weight: 6.9990 chunk 8 optimal weight: 2.9990 chunk 17 optimal weight: 10.0000 chunk 28 optimal weight: 0.8980 chunk 0 optimal weight: 0.7980 overall best weight: 2.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 10 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 10 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 21 ASN ** L 10 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 21 ASN ** M 14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 10 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 21 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4735 r_free = 0.4735 target = 0.196037 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4662 r_free = 0.4662 target = 0.166621 restraints weight = 13103.356| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.4714 r_free = 0.4714 target = 0.172709 restraints weight = 5896.170| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.4752 r_free = 0.4752 target = 0.176614 restraints weight = 3205.127| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.4776 r_free = 0.4776 target = 0.178971 restraints weight = 1902.930| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.4790 r_free = 0.4790 target = 0.180479 restraints weight = 1197.781| |-----------------------------------------------------------------------------| r_work (final): 0.4710 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7209 moved from start: 0.4573 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 2300 Z= 0.142 Angle : 0.560 4.421 3120 Z= 0.303 Chirality : 0.037 0.124 370 Planarity : 0.002 0.008 410 Dihedral : 5.461 20.789 310 Min Nonbonded Distance : 2.284 Molprobity Statistics. All-atom Clashscore : 17.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.29 % Favored : 95.71 % Rotamer: Outliers : 4.40 % Allowed : 23.60 % Favored : 72.00 % 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: -1.73 (0.36), residues: 280 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.31 (0.27), residues: 280 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG I 11 TYR 0.010 0.002 TYR O 37 PHE 0.003 0.001 PHE J 23 HIS 0.003 0.002 HIS I 18 Details of bonding type rmsd covalent geometry : bond 0.00343 ( 2290) covalent geometry : angle 0.56014 ( 3120) hydrogen bonds : bond 0.02858 ( 23) hydrogen bonds : angle 5.17580 ( 69) Misc. bond : bond 0.00010 ( 10) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 560 Ramachandran restraints generated. 280 Oldfield, 0 Emsley, 280 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 560 Ramachandran restraints generated. 280 Oldfield, 0 Emsley, 280 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 19 residues out of total 250 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 8 time to evaluate : 0.123 Fit side-chains REVERT: H 21 ASN cc_start: 0.7827 (OUTLIER) cc_final: 0.7496 (m-40) REVERT: J 21 ASN cc_start: 0.7679 (p0) cc_final: 0.7418 (p0) outliers start: 11 outliers final: 7 residues processed: 19 average time/residue: 0.0430 time to fit residues: 1.3277 Evaluate side-chains 15 residues out of total 250 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 7 time to evaluate : 0.078 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 21 ASN Chi-restraints excluded: chain K residue 21 ASN Chi-restraints excluded: chain M residue 22 ASN Chi-restraints excluded: chain N residue 21 ASN Chi-restraints excluded: chain N residue 30 THR Chi-restraints excluded: chain O residue 21 ASN Chi-restraints excluded: chain O residue 30 THR Chi-restraints excluded: chain Q residue 21 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 1 optimal weight: 5.9990 chunk 0 optimal weight: 6.9990 chunk 12 optimal weight: 0.0470 chunk 19 optimal weight: 4.9990 chunk 7 optimal weight: 2.9990 chunk 27 optimal weight: 8.9990 chunk 8 optimal weight: 2.9990 chunk 29 optimal weight: 2.9990 chunk 16 optimal weight: 3.9990 chunk 26 optimal weight: 7.9990 chunk 24 optimal weight: 0.9990 overall best weight: 2.0086 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 10 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 21 ASN ** J 10 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 10 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 10 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4785 r_free = 0.4785 target = 0.202789 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4692 r_free = 0.4692 target = 0.168376 restraints weight = 13051.114| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.4752 r_free = 0.4752 target = 0.174546 restraints weight = 5818.582| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.4782 r_free = 0.4782 target = 0.178191 restraints weight = 3134.698| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.4804 r_free = 0.4804 target = 0.180675 restraints weight = 1883.298| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.4817 r_free = 0.4817 target = 0.182052 restraints weight = 1139.725| |-----------------------------------------------------------------------------| r_work (final): 0.4748 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7212 moved from start: 0.4758 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 2300 Z= 0.137 Angle : 0.550 4.430 3120 Z= 0.297 Chirality : 0.037 0.123 370 Planarity : 0.002 0.009 410 Dihedral : 5.266 19.747 310 Min Nonbonded Distance : 2.391 Molprobity Statistics. All-atom Clashscore : 14.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.00 % Favored : 95.00 % Rotamer: Outliers : 3.60 % Allowed : 24.00 % Favored : 72.40 % 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: -1.64 (0.36), residues: 280 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.24 (0.27), residues: 280 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.000 0.000 ARG L 11 TYR 0.009 0.002 TYR O 37 PHE 0.010 0.001 PHE J 23 HIS 0.003 0.002 HIS Q 18 Details of bonding type rmsd covalent geometry : bond 0.00333 ( 2290) covalent geometry : angle 0.55003 ( 3120) hydrogen bonds : bond 0.02603 ( 23) hydrogen bonds : angle 5.01948 ( 69) Misc. bond : bond 0.00006 ( 10) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 560 Ramachandran restraints generated. 280 Oldfield, 0 Emsley, 280 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 560 Ramachandran restraints generated. 280 Oldfield, 0 Emsley, 280 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 15 residues out of total 250 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 6 time to evaluate : 0.130 Fit side-chains REVERT: H 21 ASN cc_start: 0.7975 (OUTLIER) cc_final: 0.7702 (m110) outliers start: 9 outliers final: 6 residues processed: 15 average time/residue: 0.0298 time to fit residues: 0.8143 Evaluate side-chains 13 residues out of total 250 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 6 time to evaluate : 0.076 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 21 ASN Chi-restraints excluded: chain J residue 22 ASN Chi-restraints excluded: chain L residue 22 ASN Chi-restraints excluded: chain M residue 22 ASN Chi-restraints excluded: chain N residue 21 ASN Chi-restraints excluded: chain N residue 30 THR Chi-restraints excluded: chain O residue 30 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 11 optimal weight: 9.9990 chunk 9 optimal weight: 10.0000 chunk 24 optimal weight: 8.9990 chunk 22 optimal weight: 3.9990 chunk 5 optimal weight: 1.9990 chunk 3 optimal weight: 2.9990 chunk 14 optimal weight: 3.9990 chunk 18 optimal weight: 0.8980 chunk 6 optimal weight: 10.0000 chunk 8 optimal weight: 9.9990 chunk 15 optimal weight: 0.7980 overall best weight: 2.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 10 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 21 ASN ** J 10 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 21 ASN ** L 10 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 14 ASN ** M 14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 10 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 21 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4711 r_free = 0.4711 target = 0.172809 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.4565 r_free = 0.4565 target = 0.153470 restraints weight = 11845.515| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.4625 r_free = 0.4625 target = 0.159514 restraints weight = 5445.042| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.4659 r_free = 0.4659 target = 0.163317 restraints weight = 3069.748| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.4692 r_free = 0.4692 target = 0.166152 restraints weight = 1965.927| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.4708 r_free = 0.4708 target = 0.167923 restraints weight = 1281.124| |-----------------------------------------------------------------------------| r_work (final): 0.4716 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7332 moved from start: 0.4952 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 2300 Z= 0.138 Angle : 0.539 4.378 3120 Z= 0.289 Chirality : 0.037 0.123 370 Planarity : 0.002 0.008 410 Dihedral : 5.282 20.258 310 Min Nonbonded Distance : 2.246 Molprobity Statistics. All-atom Clashscore : 16.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.00 % Favored : 95.00 % Rotamer: Outliers : 4.40 % Allowed : 24.00 % Favored : 71.60 % 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: -1.60 (0.36), residues: 280 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.21 (0.28), residues: 280 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG H 11 TYR 0.009 0.002 TYR O 37 PHE 0.011 0.001 PHE K 23 HIS 0.003 0.002 HIS P 18 Details of bonding type rmsd covalent geometry : bond 0.00335 ( 2290) covalent geometry : angle 0.53899 ( 3120) hydrogen bonds : bond 0.02630 ( 23) hydrogen bonds : angle 4.97797 ( 69) Misc. bond : bond 0.00007 ( 10) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 560 Ramachandran restraints generated. 280 Oldfield, 0 Emsley, 280 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 560 Ramachandran restraints generated. 280 Oldfield, 0 Emsley, 280 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 20 residues out of total 250 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 9 time to evaluate : 0.125 Fit side-chains outliers start: 11 outliers final: 9 residues processed: 19 average time/residue: 0.0461 time to fit residues: 1.4318 Evaluate side-chains 15 residues out of total 250 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 6 time to evaluate : 0.127 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 21 ASN Chi-restraints excluded: chain J residue 22 ASN Chi-restraints excluded: chain K residue 22 ASN Chi-restraints excluded: chain L residue 22 ASN Chi-restraints excluded: chain M residue 22 ASN Chi-restraints excluded: chain N residue 21 ASN Chi-restraints excluded: chain N residue 30 THR Chi-restraints excluded: chain O residue 30 THR Chi-restraints excluded: chain Q residue 21 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 18 optimal weight: 6.9990 chunk 25 optimal weight: 6.9990 chunk 23 optimal weight: 2.9990 chunk 24 optimal weight: 0.7980 chunk 2 optimal weight: 9.9990 chunk 28 optimal weight: 0.9980 chunk 9 optimal weight: 8.9990 chunk 17 optimal weight: 0.7980 chunk 5 optimal weight: 8.9990 chunk 15 optimal weight: 2.9990 chunk 19 optimal weight: 3.9990 overall best weight: 1.7184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 10 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 10 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 21 ASN ** L 10 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 14 ASN ** P 10 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 21 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4791 r_free = 0.4791 target = 0.205778 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4682 r_free = 0.4682 target = 0.164896 restraints weight = 12729.621| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.4743 r_free = 0.4743 target = 0.171315 restraints weight = 5501.610| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.4773 r_free = 0.4773 target = 0.175385 restraints weight = 2953.187| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.4796 r_free = 0.4796 target = 0.178042 restraints weight = 1746.679| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.4810 r_free = 0.4810 target = 0.179515 restraints weight = 1052.642| |-----------------------------------------------------------------------------| r_work (final): 0.4736 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7294 moved from start: 0.5042 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 2300 Z= 0.126 Angle : 0.529 4.334 3120 Z= 0.281 Chirality : 0.037 0.124 370 Planarity : 0.002 0.009 410 Dihedral : 5.162 21.177 310 Min Nonbonded Distance : 2.253 Molprobity Statistics. All-atom Clashscore : 16.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.36 % Favored : 94.64 % Rotamer: Outliers : 4.40 % Allowed : 23.60 % Favored : 72.00 % 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: -1.57 (0.37), residues: 280 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.19 (0.28), residues: 280 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG I 11 TYR 0.007 0.001 TYR O 37 PHE 0.009 0.001 PHE K 23 HIS 0.003 0.001 HIS P 18 Details of bonding type rmsd covalent geometry : bond 0.00303 ( 2290) covalent geometry : angle 0.52929 ( 3120) hydrogen bonds : bond 0.02561 ( 23) hydrogen bonds : angle 4.85184 ( 69) Misc. bond : bond 0.00005 ( 10) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 560 Ramachandran restraints generated. 280 Oldfield, 0 Emsley, 280 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 560 Ramachandran restraints generated. 280 Oldfield, 0 Emsley, 280 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 17 residues out of total 250 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 6 time to evaluate : 0.077 Fit side-chains outliers start: 11 outliers final: 8 residues processed: 16 average time/residue: 0.0286 time to fit residues: 0.7875 Evaluate side-chains 13 residues out of total 250 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 5 time to evaluate : 0.076 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 22 ASN Chi-restraints excluded: chain K residue 21 ASN Chi-restraints excluded: chain K residue 22 ASN Chi-restraints excluded: chain M residue 22 ASN Chi-restraints excluded: chain N residue 21 ASN Chi-restraints excluded: chain N residue 30 THR Chi-restraints excluded: chain O residue 30 THR Chi-restraints excluded: chain P residue 21 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 26 optimal weight: 8.9990 chunk 21 optimal weight: 0.0770 chunk 25 optimal weight: 0.9980 chunk 19 optimal weight: 2.9990 chunk 1 optimal weight: 0.9980 chunk 13 optimal weight: 6.9990 chunk 15 optimal weight: 5.9990 chunk 3 optimal weight: 0.9990 chunk 14 optimal weight: 1.9990 chunk 9 optimal weight: 1.9990 chunk 17 optimal weight: 0.7980 overall best weight: 0.7740 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 10 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 10 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 21 ASN ** L 10 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4765 r_free = 0.4765 target = 0.174836 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4601 r_free = 0.4601 target = 0.157735 restraints weight = 11006.724| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.4652 r_free = 0.4652 target = 0.163199 restraints weight = 5260.587| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.4686 r_free = 0.4686 target = 0.166895 restraints weight = 3019.998| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 45)----------------| | r_work = 0.4718 r_free = 0.4718 target = 0.169369 restraints weight = 1881.392| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.4733 r_free = 0.4733 target = 0.170971 restraints weight = 1223.534| |-----------------------------------------------------------------------------| r_work (final): 0.4767 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7157 moved from start: 0.5094 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.020 2300 Z= 0.093 Angle : 0.509 4.246 3120 Z= 0.269 Chirality : 0.038 0.126 370 Planarity : 0.002 0.010 410 Dihedral : 4.893 19.373 310 Min Nonbonded Distance : 2.254 Molprobity Statistics. All-atom Clashscore : 16.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.64 % Favored : 95.36 % Rotamer: Outliers : 2.40 % Allowed : 24.80 % Favored : 72.80 % 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: -1.49 (0.37), residues: 280 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.12 (0.28), residues: 280 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.000 0.000 ARG H 11 TYR 0.005 0.001 TYR O 37 PHE 0.009 0.001 PHE K 23 HIS 0.002 0.001 HIS Q 18 Details of bonding type rmsd covalent geometry : bond 0.00227 ( 2290) covalent geometry : angle 0.50928 ( 3120) hydrogen bonds : bond 0.02384 ( 23) hydrogen bonds : angle 4.67333 ( 69) Misc. bond : bond 0.00002 ( 10) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 560 Ramachandran restraints generated. 280 Oldfield, 0 Emsley, 280 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 560 Ramachandran restraints generated. 280 Oldfield, 0 Emsley, 280 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 12 residues out of total 250 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 6 time to evaluate : 0.080 Fit side-chains outliers start: 6 outliers final: 4 residues processed: 12 average time/residue: 0.0273 time to fit residues: 0.5990 Evaluate side-chains 9 residues out of total 250 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 5 time to evaluate : 0.079 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 22 ASN Chi-restraints excluded: chain M residue 22 ASN Chi-restraints excluded: chain O residue 30 THR Chi-restraints excluded: chain P residue 22 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 11 optimal weight: 7.9990 chunk 18 optimal weight: 6.9990 chunk 3 optimal weight: 7.9990 chunk 13 optimal weight: 6.9990 chunk 12 optimal weight: 0.9990 chunk 10 optimal weight: 0.7980 chunk 28 optimal weight: 3.9990 chunk 19 optimal weight: 0.9990 chunk 22 optimal weight: 2.9990 chunk 15 optimal weight: 4.9990 chunk 0 optimal weight: 10.0000 overall best weight: 1.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 10 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 10 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 21 ASN ** L 10 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4663 r_free = 0.4663 target = 0.164506 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4467 r_free = 0.4467 target = 0.145073 restraints weight = 11190.621| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.4526 r_free = 0.4526 target = 0.150788 restraints weight = 5308.259| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.4563 r_free = 0.4563 target = 0.154435 restraints weight = 3049.853| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.4591 r_free = 0.4591 target = 0.157358 restraints weight = 1998.243| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.4612 r_free = 0.4612 target = 0.159361 restraints weight = 1345.754| |-----------------------------------------------------------------------------| r_work (final): 0.4631 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7347 moved from start: 0.5301 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 2300 Z= 0.129 Angle : 0.542 4.282 3120 Z= 0.291 Chirality : 0.037 0.125 370 Planarity : 0.002 0.010 410 Dihedral : 5.061 19.445 310 Min Nonbonded Distance : 2.287 Molprobity Statistics. All-atom Clashscore : 16.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.71 % Favored : 94.29 % Rotamer: Outliers : 2.00 % Allowed : 25.20 % Favored : 72.80 % 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: -1.48 (0.37), residues: 280 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.12 (0.29), residues: 280 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG I 11 TYR 0.007 0.002 TYR O 37 PHE 0.006 0.001 PHE K 23 HIS 0.004 0.002 HIS P 18 Details of bonding type rmsd covalent geometry : bond 0.00311 ( 2290) covalent geometry : angle 0.54232 ( 3120) hydrogen bonds : bond 0.02538 ( 23) hydrogen bonds : angle 4.81097 ( 69) Misc. bond : bond 0.00004 ( 10) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 560 Ramachandran restraints generated. 280 Oldfield, 0 Emsley, 280 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 560 Ramachandran restraints generated. 280 Oldfield, 0 Emsley, 280 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 11 residues out of total 250 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 6 time to evaluate : 0.080 Fit side-chains outliers start: 5 outliers final: 4 residues processed: 11 average time/residue: 0.0330 time to fit residues: 0.6542 Evaluate side-chains 9 residues out of total 250 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 5 time to evaluate : 0.077 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 21 ASN Chi-restraints excluded: chain K residue 22 ASN Chi-restraints excluded: chain M residue 22 ASN Chi-restraints excluded: chain O residue 30 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 7 optimal weight: 7.9990 chunk 1 optimal weight: 0.9980 chunk 4 optimal weight: 1.9990 chunk 17 optimal weight: 4.9990 chunk 9 optimal weight: 5.9990 chunk 11 optimal weight: 0.9980 chunk 13 optimal weight: 0.9990 chunk 23 optimal weight: 9.9990 chunk 24 optimal weight: 6.9990 chunk 18 optimal weight: 0.9980 chunk 27 optimal weight: 4.9990 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 10 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 10 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 10 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 21 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 = 0.4668 r_free = 0.4668 target = 0.170522 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4490 r_free = 0.4490 target = 0.150676 restraints weight = 12038.380| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.4560 r_free = 0.4560 target = 0.156759 restraints weight = 5412.936| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.4597 r_free = 0.4597 target = 0.160317 restraints weight = 3052.729| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.4626 r_free = 0.4626 target = 0.163408 restraints weight = 1991.116| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.4645 r_free = 0.4645 target = 0.165271 restraints weight = 1295.866| |-----------------------------------------------------------------------------| r_work (final): 0.4639 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7307 moved from start: 0.5303 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.210 2300 Z= 0.242 Angle : 1.453 59.200 3120 Z= 0.900 Chirality : 0.038 0.132 370 Planarity : 0.002 0.010 410 Dihedral : 5.089 19.077 310 Min Nonbonded Distance : 2.290 Molprobity Statistics. All-atom Clashscore : 18.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.71 % Favored : 94.29 % Rotamer: Outliers : 2.00 % Allowed : 24.40 % Favored : 73.60 % 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: -1.49 (0.37), residues: 280 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.13 (0.29), residues: 280 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG O 11 TYR 0.007 0.001 TYR O 37 PHE 0.006 0.001 PHE J 23 HIS 0.004 0.002 HIS Q 18 Details of bonding type rmsd covalent geometry : bond 0.00557 ( 2290) covalent geometry : angle 1.45255 ( 3120) hydrogen bonds : bond 0.02514 ( 23) hydrogen bonds : angle 4.80011 ( 69) Misc. bond : bond 0.00003 ( 10) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1219.42 seconds wall clock time: 21 minutes 27.66 seconds (1287.66 seconds total)