Starting phenix.real_space_refine on Thu Oct 22 20:58:55 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/29hp_57188/10_2026/29hp_57188_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/29hp_57188/10_2026/29hp_57188.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/29hp_57188/10_2026/29hp_57188_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/29hp_57188/10_2026/29hp_57188_trim.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/29hp_57188/10_2026/29hp_57188.map" default_real_map = "/net/cci-nas-00/data/ceres_data/29hp_57188/10_2026/29hp_57188.map" } resolution = 3.6 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= 0.002 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 1715 2.51 5 N 520 2.21 5 O 565 1.98 5 H 2635 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 10 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.3rc1-6221/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 5435 Number of models: 1 Model: "" Number of chains: 15 Chain: "A" Number of atoms: 425 Number of conformers: 1 Conformer: "" Number of residues, atoms: 30, 425 Unusual residues: {'NH2': 1} Classifications: {'peptide': 29, 'undetermined': 1} Link IDs: {'NH2_CTERM': 1, 'TRANS': 28} Chain: "B" Number of atoms: 425 Number of conformers: 1 Conformer: "" Number of residues, atoms: 30, 425 Unusual residues: {'NH2': 1} Classifications: {'peptide': 29, 'undetermined': 1} Link IDs: {'NH2_CTERM': 1, 'TRANS': 28} Chain: "C" Number of atoms: 237 Number of conformers: 1 Conformer: "" Number of residues, atoms: 18, 237 Unusual residues: {'NH2': 1} Classifications: {'peptide': 17, 'undetermined': 1} Link IDs: {'NH2_CTERM': 1, 'TRANS': 16} Chain: "E" Number of atoms: 425 Number of conformers: 1 Conformer: "" Number of residues, atoms: 30, 425 Unusual residues: {'NH2': 1} Classifications: {'peptide': 29, 'undetermined': 1} Link IDs: {'NH2_CTERM': 1, 'TRANS': 28} Chain: "F" Number of atoms: 425 Number of conformers: 1 Conformer: "" Number of residues, atoms: 30, 425 Unusual residues: {'NH2': 1} Classifications: {'peptide': 29, 'undetermined': 1} Link IDs: {'NH2_CTERM': 1, 'TRANS': 28} Chain: "G" Number of atoms: 237 Number of conformers: 1 Conformer: "" Number of residues, atoms: 18, 237 Unusual residues: {'NH2': 1} Classifications: {'peptide': 17, 'undetermined': 1} Link IDs: {'NH2_CTERM': 1, 'TRANS': 16} Chain: "I" Number of atoms: 425 Number of conformers: 1 Conformer: "" Number of residues, atoms: 30, 425 Unusual residues: {'NH2': 1} Classifications: {'peptide': 29, 'undetermined': 1} Link IDs: {'NH2_CTERM': 1, 'TRANS': 28} Chain: "J" Number of atoms: 425 Number of conformers: 1 Conformer: "" Number of residues, atoms: 30, 425 Unusual residues: {'NH2': 1} Classifications: {'peptide': 29, 'undetermined': 1} Link IDs: {'NH2_CTERM': 1, 'TRANS': 28} Chain: "K" Number of atoms: 237 Number of conformers: 1 Conformer: "" Number of residues, atoms: 18, 237 Unusual residues: {'NH2': 1} Classifications: {'peptide': 17, 'undetermined': 1} Link IDs: {'NH2_CTERM': 1, 'TRANS': 16} Chain: "M" Number of atoms: 425 Number of conformers: 1 Conformer: "" Number of residues, atoms: 30, 425 Unusual residues: {'NH2': 1} Classifications: {'peptide': 29, 'undetermined': 1} Link IDs: {'NH2_CTERM': 1, 'TRANS': 28} Chain: "N" Number of atoms: 425 Number of conformers: 1 Conformer: "" Number of residues, atoms: 30, 425 Unusual residues: {'NH2': 1} Classifications: {'peptide': 29, 'undetermined': 1} Link IDs: {'NH2_CTERM': 1, 'TRANS': 28} Chain: "O" Number of atoms: 237 Number of conformers: 1 Conformer: "" Number of residues, atoms: 18, 237 Unusual residues: {'NH2': 1} Classifications: {'peptide': 17, 'undetermined': 1} Link IDs: {'NH2_CTERM': 1, 'TRANS': 16} Chain: "Q" Number of atoms: 425 Number of conformers: 1 Conformer: "" Number of residues, atoms: 30, 425 Unusual residues: {'NH2': 1} Classifications: {'peptide': 29, 'undetermined': 1} Link IDs: {'NH2_CTERM': 1, 'TRANS': 28} Chain: "R" Number of atoms: 425 Number of conformers: 1 Conformer: "" Number of residues, atoms: 30, 425 Unusual residues: {'NH2': 1} Classifications: {'peptide': 29, 'undetermined': 1} Link IDs: {'NH2_CTERM': 1, 'TRANS': 28} Chain: "S" Number of atoms: 237 Number of conformers: 1 Conformer: "" Number of residues, atoms: 18, 237 Unusual residues: {'NH2': 1} Classifications: {'peptide': 17, 'undetermined': 1} Link IDs: {'NH2_CTERM': 1, 'TRANS': 16} Time building chain proxies: 1.02, per 1000 atoms: 0.19 Number of scatterers: 5435 At special positions: 0 Unit cell: (75.9, 92.4, 55, 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 565 8.00 N 520 7.00 C 1715 6.00 H 2635 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.38 Conformation dependent library (CDL) restraints added in 103.6 milliseconds 690 Ramachandran restraints generated. 345 Oldfield, 0 Emsley, 345 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 670 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 8 sheets defined 0.0% alpha, 53.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.07 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'A' and resid 10 through 22 removed outlier: 6.892A pdb=" N ASN A 21 " --> pdb=" O GLY E 20 " (cutoff:3.500A) removed outlier: 6.971A pdb=" N ASN E 22 " --> pdb=" O ASN A 21 " (cutoff:3.500A) removed outlier: 6.898A pdb=" N ASN E 21 " --> pdb=" O GLY I 20 " (cutoff:3.500A) removed outlier: 6.901A pdb=" N ASN I 22 " --> pdb=" O ASN E 21 " (cutoff:3.500A) removed outlier: 6.869A pdb=" N ASN I 21 " --> pdb=" O GLY M 20 " (cutoff:3.500A) removed outlier: 6.906A pdb=" N ASN M 22 " --> pdb=" O ASN I 21 " (cutoff:3.500A) removed outlier: 6.871A pdb=" N ASN M 21 " --> pdb=" O GLY Q 20 " (cutoff:3.500A) removed outlier: 6.963A pdb=" N ASN Q 22 " --> pdb=" O ASN M 21 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 25 through 26 Processing sheet with id=AA3, first strand: chain 'A' and resid 29 through 32 Processing sheet with id=AA4, first strand: chain 'B' and resid 10 through 22 removed outlier: 6.875A pdb=" N ASN B 21 " --> pdb=" O GLY F 20 " (cutoff:3.500A) removed outlier: 6.922A pdb=" N ASN F 22 " --> pdb=" O ASN B 21 " (cutoff:3.500A) removed outlier: 6.885A pdb=" N ASN F 21 " --> pdb=" O GLY J 20 " (cutoff:3.500A) removed outlier: 6.953A pdb=" N ASN J 22 " --> pdb=" O ASN F 21 " (cutoff:3.500A) removed outlier: 6.920A pdb=" N ASN J 21 " --> pdb=" O GLY N 20 " (cutoff:3.500A) removed outlier: 7.013A pdb=" N ASN N 22 " --> pdb=" O ASN J 21 " (cutoff:3.500A) removed outlier: 6.953A pdb=" N ASN N 21 " --> pdb=" O GLY R 20 " (cutoff:3.500A) removed outlier: 6.977A pdb=" N ASN R 22 " --> pdb=" O ASN N 21 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 25 through 26 Processing sheet with id=AA6, first strand: chain 'B' and resid 29 through 32 Processing sheet with id=AA7, first strand: chain 'C' and resid 25 through 32 removed outlier: 6.606A pdb=" N ALA C 25 " --> pdb=" O ILE G 26 " (cutoff:3.500A) removed outlier: 8.006A pdb=" N SER G 28 " --> pdb=" O ALA C 25 " (cutoff:3.500A) removed outlier: 6.514A pdb=" N LEU C 27 " --> pdb=" O SER G 28 " (cutoff:3.500A) removed outlier: 8.268A pdb=" N THR G 30 " --> pdb=" O LEU C 27 " (cutoff:3.500A) removed outlier: 6.504A pdb=" N SER C 29 " --> pdb=" O THR G 30 " (cutoff:3.500A) removed outlier: 8.306A pdb=" N VAL G 32 " --> pdb=" O SER C 29 " (cutoff:3.500A) removed outlier: 6.881A pdb=" N ASN C 31 " --> pdb=" O VAL G 32 " (cutoff:3.500A) removed outlier: 6.610A pdb=" N ALA G 25 " --> pdb=" O ILE K 26 " (cutoff:3.500A) removed outlier: 8.007A pdb=" N SER K 28 " --> pdb=" O ALA G 25 " (cutoff:3.500A) removed outlier: 6.477A pdb=" N LEU G 27 " --> pdb=" O SER K 28 " (cutoff:3.500A) removed outlier: 8.204A pdb=" N THR K 30 " --> pdb=" O LEU G 27 " (cutoff:3.500A) removed outlier: 6.446A pdb=" N SER G 29 " --> pdb=" O THR K 30 " (cutoff:3.500A) removed outlier: 8.285A pdb=" N VAL K 32 " --> pdb=" O SER G 29 " (cutoff:3.500A) removed outlier: 6.989A pdb=" N ASN G 31 " --> pdb=" O VAL K 32 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 35 through 36 removed outlier: 6.477A pdb=" N ASN C 35 " --> pdb=" O THR G 36 " (cutoff:3.500A) removed outlier: 6.624A pdb=" N ASN G 35 " --> pdb=" O THR K 36 " (cutoff:3.500A) removed outlier: 6.568A pdb=" N ASN K 35 " --> pdb=" O THR O 36 " (cutoff:3.500A) removed outlier: 6.544A pdb=" N ASN O 35 " --> pdb=" O THR S 36 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 126 hydrogen bonds defined for protein. 378 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: 1.09 Time building geometry restraints manager: 0.47 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.95 - 1.07: 705 1.07 - 1.19: 1930 1.19 - 1.31: 535 1.31 - 1.43: 805 1.43 - 1.55: 1495 Bond restraints: 5470 Sorted by residual: bond pdb=" ND2 ASN Q 35 " pdb="HD22 ASN Q 35 " ideal model delta sigma weight residual 0.860 1.010 -0.150 2.00e-02 2.50e+03 5.66e+01 bond pdb=" N LEU G 27 " pdb=" H LEU G 27 " ideal model delta sigma weight residual 0.860 1.010 -0.150 2.00e-02 2.50e+03 5.66e+01 bond pdb=" N ALA O 25 " pdb=" H ALA O 25 " ideal model delta sigma weight residual 0.860 1.010 -0.150 2.00e-02 2.50e+03 5.66e+01 bond pdb=" ND2 ASN A 22 " pdb="HD21 ASN A 22 " ideal model delta sigma weight residual 0.860 1.010 -0.150 2.00e-02 2.50e+03 5.66e+01 bond pdb=" CE1 HIS F 18 " pdb=" HE1 HIS F 18 " ideal model delta sigma weight residual 0.930 1.080 -0.150 2.00e-02 2.50e+03 5.66e+01 ... (remaining 5465 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.40: 6120 1.40 - 2.81: 2280 2.81 - 4.21: 666 4.21 - 5.61: 401 5.61 - 7.02: 193 Bond angle restraints: 9660 Sorted by residual: angle pdb=" CB HIS A 18 " pdb=" CG HIS A 18 " pdb=" CD2 HIS A 18 " ideal model delta sigma weight residual 131.20 125.46 5.74 1.30e+00 5.92e-01 1.95e+01 angle pdb=" CB HIS I 18 " pdb=" CG HIS I 18 " pdb=" CD2 HIS I 18 " ideal model delta sigma weight residual 131.20 125.77 5.43 1.30e+00 5.92e-01 1.74e+01 angle pdb=" CB HIS B 18 " pdb=" CG HIS B 18 " pdb=" CD2 HIS B 18 " ideal model delta sigma weight residual 131.20 125.78 5.42 1.30e+00 5.92e-01 1.74e+01 angle pdb=" CB HIS R 18 " pdb=" CG HIS R 18 " pdb=" CD2 HIS R 18 " ideal model delta sigma weight residual 131.20 125.79 5.41 1.30e+00 5.92e-01 1.73e+01 angle pdb=" CB HIS Q 18 " pdb=" CG HIS Q 18 " pdb=" CD2 HIS Q 18 " ideal model delta sigma weight residual 131.20 125.80 5.40 1.30e+00 5.92e-01 1.72e+01 ... (remaining 9655 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 13.93: 2402 13.93 - 27.86: 94 27.86 - 41.79: 77 41.79 - 55.71: 22 55.71 - 69.64: 35 Dihedral angle restraints: 2630 sinusoidal: 1370 harmonic: 1260 Sorted by residual: dihedral pdb=" CA THR O 36 " pdb=" C THR O 36 " pdb=" N TYR O 37 " pdb=" CA TYR O 37 " ideal model delta harmonic sigma weight residual 180.00 157.54 22.46 0 5.00e+00 4.00e-02 2.02e+01 dihedral pdb=" CA THR C 36 " pdb=" C THR C 36 " pdb=" N TYR C 37 " pdb=" CA TYR C 37 " ideal model delta harmonic sigma weight residual 180.00 157.97 22.03 0 5.00e+00 4.00e-02 1.94e+01 dihedral pdb=" CA THR G 36 " pdb=" C THR G 36 " pdb=" N TYR G 37 " pdb=" CA TYR G 37 " ideal model delta harmonic sigma weight residual 180.00 158.43 21.57 0 5.00e+00 4.00e-02 1.86e+01 ... (remaining 2627 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.046: 226 0.046 - 0.091: 120 0.091 - 0.136: 58 0.136 - 0.182: 34 0.182 - 0.227: 12 Chirality restraints: 450 Sorted by residual: chirality pdb=" CA SER A 34 " pdb=" N SER A 34 " pdb=" C SER A 34 " pdb=" CB SER A 34 " both_signs ideal model delta sigma weight residual False 2.51 2.28 0.23 2.00e-01 2.50e+01 1.29e+00 chirality pdb=" CG LEU Q 12 " pdb=" CB LEU Q 12 " pdb=" CD1 LEU Q 12 " pdb=" CD2 LEU Q 12 " both_signs ideal model delta sigma weight residual False -2.59 -2.81 0.22 2.00e-01 2.50e+01 1.20e+00 chirality pdb=" CA SER J 34 " pdb=" N SER J 34 " pdb=" C SER J 34 " pdb=" CB SER J 34 " both_signs ideal model delta sigma weight residual False 2.51 2.29 0.22 2.00e-01 2.50e+01 1.19e+00 ... (remaining 447 not shown) Planarity restraints: 875 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN Q 35 " -0.016 2.00e-02 2.50e+03 3.86e-02 2.23e+01 pdb=" CG ASN Q 35 " -0.018 2.00e-02 2.50e+03 pdb=" OD1 ASN Q 35 " 0.042 2.00e-02 2.50e+03 pdb=" ND2 ASN Q 35 " -0.052 2.00e-02 2.50e+03 pdb="HD21 ASN Q 35 " 0.060 2.00e-02 2.50e+03 pdb="HD22 ASN Q 35 " -0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN E 21 " -0.043 2.00e-02 2.50e+03 3.64e-02 1.99e+01 pdb=" CG ASN E 21 " 0.024 2.00e-02 2.50e+03 pdb=" OD1 ASN E 21 " 0.026 2.00e-02 2.50e+03 pdb=" ND2 ASN E 21 " 0.005 2.00e-02 2.50e+03 pdb="HD21 ASN E 21 " 0.042 2.00e-02 2.50e+03 pdb="HD22 ASN E 21 " -0.055 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN M 21 " -0.043 2.00e-02 2.50e+03 3.62e-02 1.97e+01 pdb=" CG ASN M 21 " 0.024 2.00e-02 2.50e+03 pdb=" OD1 ASN M 21 " 0.026 2.00e-02 2.50e+03 pdb=" ND2 ASN M 21 " 0.009 2.00e-02 2.50e+03 pdb="HD21 ASN M 21 " 0.040 2.00e-02 2.50e+03 pdb="HD22 ASN M 21 " -0.056 2.00e-02 2.50e+03 ... (remaining 872 not shown) Histogram of nonbonded interaction distances: 1.69 - 2.25: 674 2.25 - 2.81: 9388 2.81 - 3.37: 12125 3.37 - 3.94: 19110 3.94 - 4.50: 24218 Nonbonded interactions: 65515 Sorted by model distance: nonbonded pdb=" O ILE E 26 " pdb=" HG SER E 28 " model vdw 1.686 2.450 nonbonded pdb=" O ILE M 26 " pdb=" HG SER M 28 " model vdw 1.691 2.450 nonbonded pdb=" O ILE A 26 " pdb=" HG SER A 28 " model vdw 1.694 2.450 nonbonded pdb=" O ILE J 26 " pdb=" HG SER J 28 " model vdw 1.702 2.450 nonbonded pdb=" O ILE Q 26 " pdb=" HG SER Q 28 " model vdw 1.708 2.450 ... (remaining 65510 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'E' selection = chain 'F' selection = chain 'I' selection = chain 'J' selection = chain 'M' selection = chain 'N' selection = chain 'Q' selection = chain 'R' } ncs_group { reference = chain 'C' selection = chain 'G' selection = chain 'K' selection = chain 'O' selection = chain 'S' } 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: 2.370 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.090 Check model and map are aligned: 0.020 Set scattering table: 0.010 Process input model: 6.540 Find NCS groups from input model: 0.070 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:1.110 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 10.230 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: -0.0750 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 : 0.011 0.033 2835 Z= 0.682 Angle : 1.732 5.795 3850 Z= 1.181 Chirality : 0.079 0.227 450 Planarity : 0.008 0.037 515 Dihedral : 10.315 34.661 915 Min Nonbonded Distance : 2.644 Molprobity Statistics. All-atom Clashscore : 0.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.70 % Favored : 91.30 % Rotamer: Outliers : 1.29 % Allowed : 0.97 % Favored : 97.74 % 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: -2.19 (0.36), residues: 345 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.66 (0.28), residues: 345 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG Q 11 TYR 0.058 0.010 TYR N 37 PHE 0.029 0.007 PHE A 15 HIS 0.007 0.003 HIS M 18 Details of bonding type rmsd/Z covalent geometry : bond 0.01127 / 0.68 ( 2835) covalent geometry : angle 1.73181 / 1.18 ( 3850) hydrogen bonds : bond 0.11397 / 7.89 ( 126) hydrogen bonds : angle 7.31316 / 4.96 ( 378) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 690 Ramachandran restraints generated. 345 Oldfield, 0 Emsley, 345 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 690 Ramachandran restraints generated. 345 Oldfield, 0 Emsley, 345 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 38 residues out of total 310 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 34 time to evaluate : 0.086 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 4 outliers final: 2 residues processed: 38 average time/residue: 0.0553 time to fit residues: 3.1247 Evaluate side-chains 11 residues out of total 310 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 9 time to evaluate : 0.140 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 31 ASN Chi-restraints excluded: chain O residue 31 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 35 random chunks: [24, 26, 2, 16, 32, 31, 25, 19, 30, 22, 13] chunk 24 optimal weight: 5.9990 chunk 26 optimal weight: 5.9990 chunk 2 optimal weight: 2.9990 chunk 16 optimal weight: 3.9990 chunk 32 optimal weight: 0.9980 chunk 31 optimal weight: 1.9990 chunk 25 optimal weight: 9.9990 chunk 19 optimal weight: 5.9990 chunk 30 optimal weight: 1.9990 chunk 22 optimal weight: 5.9990 chunk 13 optimal weight: 9.9990 overall best weight: 2.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 35 ASN ** C 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 35 ASN F 35 ASN ** G 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 35 ASN M 35 ASN O 22 ASN ** Q 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 35 ASN R 22 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4910 r_free = 0.4910 target = 0.227111 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4697 r_free = 0.4697 target = 0.205592 restraints weight = 8650.988| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.4753 r_free = 0.4753 target = 0.213464 restraints weight = 3526.111| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.4792 r_free = 0.4792 target = 0.218301 restraints weight = 1806.741| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.4817 r_free = 0.4817 target = 0.221161 restraints weight = 1049.117| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.4837 r_free = 0.4837 target = 0.222979 restraints weight = 661.519| |-----------------------------------------------------------------------------| r_work (final): 0.4892 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3035 moved from start: 1.0410 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.039 2835 Z= 0.373 Angle : 1.117 10.726 3850 Z= 0.600 Chirality : 0.059 0.208 450 Planarity : 0.007 0.038 515 Dihedral : 7.888 35.604 389 Min Nonbonded Distance : 2.306 Molprobity Statistics. All-atom Clashscore : 17.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 3.23 % Allowed : 3.23 % Favored : 93.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.06 (0.24), residues: 345 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.09 (0.18), residues: 345 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.002 ARG F 11 TYR 0.026 0.006 TYR A 37 PHE 0.030 0.004 PHE I 15 HIS 0.012 0.002 HIS F 18 Details of bonding type rmsd/Z covalent geometry : bond 0.00736 / 0.37 ( 2835) covalent geometry : angle 1.11688 / 0.60 ( 3850) hydrogen bonds : bond 0.05886 / 3.79 ( 126) hydrogen bonds : angle 6.32789 / 4.36 ( 378) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 690 Ramachandran restraints generated. 345 Oldfield, 0 Emsley, 345 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 690 Ramachandran restraints generated. 345 Oldfield, 0 Emsley, 345 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 67 residues out of total 310 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 57 time to evaluate : 0.154 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 21 ASN cc_start: 0.6451 (m-40) cc_final: 0.6116 (m-40) REVERT: B 23 PHE cc_start: 0.6742 (m-80) cc_final: 0.6338 (p90) REVERT: E 37 TYR cc_start: 0.4133 (m-80) cc_final: 0.3848 (m-80) REVERT: J 14 ASN cc_start: 0.6598 (OUTLIER) cc_final: 0.6318 (m-40) REVERT: N 12 LEU cc_start: 0.5041 (OUTLIER) cc_final: 0.4693 (pp) outliers start: 10 outliers final: 3 residues processed: 66 average time/residue: 0.0575 time to fit residues: 5.5571 Evaluate side-chains 46 residues out of total 310 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 41 time to evaluate : 0.108 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 14 ASN Chi-restraints excluded: chain J residue 9 THR Chi-restraints excluded: chain J residue 14 ASN Chi-restraints excluded: chain N residue 12 LEU Chi-restraints excluded: chain O residue 31 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 35 random chunks: [31, 18, 21, 5, 13, 2, 25, 16, 32, 14, 4] chunk 31 optimal weight: 6.9990 chunk 18 optimal weight: 5.9990 chunk 21 optimal weight: 5.9990 chunk 5 optimal weight: 2.9990 chunk 13 optimal weight: 0.6980 chunk 2 optimal weight: 0.4980 chunk 25 optimal weight: 0.9990 chunk 16 optimal weight: 3.9990 chunk 32 optimal weight: 0.9980 chunk 14 optimal weight: 0.9990 chunk 4 optimal weight: 0.0870 overall best weight: 0.6560 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 35 ASN E 35 ASN I 35 ASN M 35 ASN Q 21 ASN ** R 22 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4712 r_free = 0.4712 target = 0.192004 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4478 r_free = 0.4478 target = 0.166832 restraints weight = 8699.057| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.4535 r_free = 0.4535 target = 0.174073 restraints weight = 3700.749| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.4575 r_free = 0.4575 target = 0.178989 restraints weight = 2041.355| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.4604 r_free = 0.4604 target = 0.182300 restraints weight = 1295.558| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.4624 r_free = 0.4624 target = 0.184536 restraints weight = 895.968| |-----------------------------------------------------------------------------| r_work (final): 0.4660 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3317 moved from start: 1.1230 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 2835 Z= 0.123 Angle : 0.506 3.808 3850 Z= 0.283 Chirality : 0.045 0.142 450 Planarity : 0.002 0.018 515 Dihedral : 4.935 36.980 387 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 3.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Rotamer: Outliers : 1.29 % Allowed : 12.90 % Favored : 85.81 % 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: -3.63 (0.26), residues: 345 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.76 (0.20), residues: 345 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG R 11 TYR 0.012 0.002 TYR Q 37 PHE 0.013 0.002 PHE Q 15 HIS 0.003 0.001 HIS M 18 Details of bonding type rmsd/Z covalent geometry : bond 0.00261 / 0.12 ( 2835) covalent geometry : angle 0.50621 / 0.28 ( 3850) hydrogen bonds : bond 0.02941 / 1.98 ( 126) hydrogen bonds : angle 4.99102 / 3.47 ( 378) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 690 Ramachandran restraints generated. 345 Oldfield, 0 Emsley, 345 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 690 Ramachandran restraints generated. 345 Oldfield, 0 Emsley, 345 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 48 residues out of total 310 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 44 time to evaluate : 0.129 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 21 ASN cc_start: 0.6176 (m-40) cc_final: 0.5903 (m-40) REVERT: B 23 PHE cc_start: 0.7015 (m-80) cc_final: 0.6155 (p90) REVERT: J 21 ASN cc_start: 0.7046 (m110) cc_final: 0.6768 (m-40) outliers start: 4 outliers final: 4 residues processed: 48 average time/residue: 0.0536 time to fit residues: 3.7359 Evaluate side-chains 41 residues out of total 310 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 37 time to evaluate : 0.101 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 34 SER Chi-restraints excluded: chain F residue 14 ASN Chi-restraints excluded: chain J residue 9 THR Chi-restraints excluded: chain O residue 31 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 35 random chunks: [6, 31, 9, 27, 0, 22, 11, 30, 21, 17, 13] chunk 6 optimal weight: 0.8980 chunk 31 optimal weight: 6.9990 chunk 9 optimal weight: 5.9990 chunk 27 optimal weight: 9.9990 chunk 0 optimal weight: 4.9990 chunk 22 optimal weight: 6.9990 chunk 11 optimal weight: 7.9990 chunk 30 optimal weight: 0.8980 chunk 21 optimal weight: 2.9990 chunk 17 optimal weight: 10.0000 chunk 13 optimal weight: 1.9990 overall best weight: 2.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 35 ASN C 35 ASN F 35 ASN G 31 ASN G 35 ASN K 35 ASN M 35 ASN N 18 HIS O 35 ASN R 18 HIS ** R 22 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4700 r_free = 0.4700 target = 0.189430 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4403 r_free = 0.4403 target = 0.159680 restraints weight = 9062.859| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.4463 r_free = 0.4463 target = 0.166599 restraints weight = 4406.825| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.4508 r_free = 0.4508 target = 0.171327 restraints weight = 2616.457| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.4537 r_free = 0.4537 target = 0.174447 restraints weight = 1789.558| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.4561 r_free = 0.4561 target = 0.176826 restraints weight = 1346.923| |-----------------------------------------------------------------------------| r_work (final): 0.4584 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5348 moved from start: 1.6786 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.103 2835 Z= 0.299 Angle : 0.838 9.030 3850 Z= 0.465 Chirality : 0.052 0.191 450 Planarity : 0.005 0.028 515 Dihedral : 6.616 54.316 387 Min Nonbonded Distance : 2.283 Molprobity Statistics. All-atom Clashscore : 11.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.67 % Favored : 93.33 % Rotamer: Outliers : 2.58 % Allowed : 17.42 % Favored : 80.00 % 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: -4.07 (0.26), residues: 345 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.09 (0.20), residues: 345 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG E 11 TYR 0.018 0.003 TYR R 37 PHE 0.029 0.005 PHE A 15 HIS 0.005 0.002 HIS B 18 Details of bonding type rmsd/Z covalent geometry : bond 0.00622 / 0.30 ( 2835) covalent geometry : angle 0.83788 / 0.46 ( 3850) hydrogen bonds : bond 0.04642 / 3.12 ( 126) hydrogen bonds : angle 5.54438 / 3.80 ( 378) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 690 Ramachandran restraints generated. 345 Oldfield, 0 Emsley, 345 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 690 Ramachandran restraints generated. 345 Oldfield, 0 Emsley, 345 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 67 residues out of total 310 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 59 time to evaluate : 0.148 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 9 THR cc_start: 0.7853 (m) cc_final: 0.7505 (p) REVERT: B 11 ARG cc_start: 0.6046 (mtt180) cc_final: 0.5797 (mmt180) REVERT: I 35 ASN cc_start: 0.7511 (m-40) cc_final: 0.7305 (m-40) REVERT: J 21 ASN cc_start: 0.6796 (m110) cc_final: 0.6571 (m-40) REVERT: R 9 THR cc_start: 0.7314 (m) cc_final: 0.7086 (p) outliers start: 8 outliers final: 2 residues processed: 66 average time/residue: 0.0623 time to fit residues: 5.8006 Evaluate side-chains 58 residues out of total 310 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 56 time to evaluate : 0.143 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 27 LEU Chi-restraints excluded: chain R residue 31 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 35 random chunks: [26, 17, 10, 32, 3, 20, 19, 9, 18, 34, 22] chunk 26 optimal weight: 6.9990 chunk 17 optimal weight: 5.9990 chunk 10 optimal weight: 0.8980 chunk 32 optimal weight: 4.9990 chunk 3 optimal weight: 1.9990 chunk 20 optimal weight: 0.8980 chunk 19 optimal weight: 0.7980 chunk 9 optimal weight: 0.9990 chunk 18 optimal weight: 3.9990 chunk 34 optimal weight: 6.9990 chunk 22 optimal weight: 4.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... G 31 ASN ** K 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 22 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 = 0.4685 r_free = 0.4685 target = 0.178075 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4358 r_free = 0.4358 target = 0.147136 restraints weight = 9093.821| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.4418 r_free = 0.4418 target = 0.153871 restraints weight = 4145.299| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.4469 r_free = 0.4469 target = 0.158680 restraints weight = 2440.588| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.4498 r_free = 0.4498 target = 0.161788 restraints weight = 1676.502| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.4522 r_free = 0.4522 target = 0.164137 restraints weight = 1282.633| |-----------------------------------------------------------------------------| r_work (final): 0.4547 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5540 moved from start: 1.7624 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 2835 Z= 0.123 Angle : 0.486 3.590 3850 Z= 0.277 Chirality : 0.043 0.136 450 Planarity : 0.002 0.013 515 Dihedral : 4.400 14.754 385 Min Nonbonded Distance : 2.344 Molprobity Statistics. All-atom Clashscore : 5.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Rotamer: Outliers : 1.61 % Allowed : 20.97 % Favored : 77.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.76 (0.27), residues: 345 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.86 (0.21), residues: 345 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG N 11 TYR 0.006 0.001 TYR R 37 PHE 0.009 0.001 PHE B 23 HIS 0.003 0.001 HIS I 18 Details of bonding type rmsd/Z covalent geometry : bond 0.00257 / 0.12 ( 2835) covalent geometry : angle 0.48569 / 0.28 ( 3850) hydrogen bonds : bond 0.02523 / 1.69 ( 126) hydrogen bonds : angle 4.39758 / 3.03 ( 378) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 690 Ramachandran restraints generated. 345 Oldfield, 0 Emsley, 345 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 690 Ramachandran restraints generated. 345 Oldfield, 0 Emsley, 345 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 310 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 66 time to evaluate : 0.169 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 9 THR cc_start: 0.7935 (m) cc_final: 0.7489 (p) REVERT: E 31 ASN cc_start: 0.7456 (m-40) cc_final: 0.7252 (m-40) REVERT: F 9 THR cc_start: 0.7125 (m) cc_final: 0.6655 (p) REVERT: J 9 THR cc_start: 0.7290 (m) cc_final: 0.6797 (p) REVERT: S 26 ILE cc_start: 0.6479 (mt) cc_final: 0.6098 (mt) outliers start: 5 outliers final: 5 residues processed: 69 average time/residue: 0.0633 time to fit residues: 6.0813 Evaluate side-chains 65 residues out of total 310 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 60 time to evaluate : 0.152 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 30 THR Chi-restraints excluded: chain J residue 14 ASN Chi-restraints excluded: chain N residue 14 ASN Chi-restraints excluded: chain O residue 30 THR Chi-restraints excluded: chain R residue 12 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 35 random chunks: [19, 34, 7, 3, 17, 4, 10, 15, 30, 8, 22] chunk 19 optimal weight: 1.9990 chunk 34 optimal weight: 1.9990 chunk 7 optimal weight: 2.9990 chunk 3 optimal weight: 2.9990 chunk 17 optimal weight: 4.9990 chunk 4 optimal weight: 3.9990 chunk 10 optimal weight: 0.9980 chunk 15 optimal weight: 4.9990 chunk 30 optimal weight: 1.9990 chunk 8 optimal weight: 0.6980 chunk 22 optimal weight: 0.8980 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 14 ASN G 35 ASN ** I 14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 21 ASN K 35 ASN ** M 14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 21 ASN O 35 ASN ** R 22 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4817 r_free = 0.4817 target = 0.184878 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4486 r_free = 0.4486 target = 0.156438 restraints weight = 8896.593| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.4547 r_free = 0.4547 target = 0.162887 restraints weight = 3881.670| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.4593 r_free = 0.4593 target = 0.167290 restraints weight = 2275.727| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.4621 r_free = 0.4621 target = 0.170087 restraints weight = 1576.417| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.4644 r_free = 0.4644 target = 0.172082 restraints weight = 1219.697| |-----------------------------------------------------------------------------| r_work (final): 0.4684 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6143 moved from start: 1.9299 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 2835 Z= 0.171 Angle : 0.571 7.323 3850 Z= 0.317 Chirality : 0.046 0.154 450 Planarity : 0.003 0.014 515 Dihedral : 4.786 16.646 385 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 9.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.83 % Favored : 92.17 % Rotamer: Outliers : 1.61 % Allowed : 23.87 % Favored : 74.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.90 (0.28), residues: 345 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.97 (0.22), residues: 345 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.001 ARG A 11 TYR 0.022 0.002 TYR K 37 PHE 0.011 0.002 PHE Q 23 HIS 0.002 0.001 HIS R 18 Details of bonding type rmsd/Z covalent geometry : bond 0.00368 / 0.17 ( 2835) covalent geometry : angle 0.57075 / 0.32 ( 3850) hydrogen bonds : bond 0.02634 / 1.85 ( 126) hydrogen bonds : angle 4.06138 / 2.77 ( 378) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 690 Ramachandran restraints generated. 345 Oldfield, 0 Emsley, 345 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 690 Ramachandran restraints generated. 345 Oldfield, 0 Emsley, 345 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 310 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 68 time to evaluate : 0.186 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 9 THR cc_start: 0.7926 (m) cc_final: 0.7480 (p) REVERT: J 9 THR cc_start: 0.7756 (m) cc_final: 0.7188 (p) REVERT: M 22 ASN cc_start: 0.8024 (t0) cc_final: 0.7598 (t0) REVERT: N 36 THR cc_start: 0.6897 (p) cc_final: 0.6658 (t) REVERT: S 26 ILE cc_start: 0.6762 (mt) cc_final: 0.6453 (mt) outliers start: 5 outliers final: 3 residues processed: 72 average time/residue: 0.0789 time to fit residues: 7.3434 Evaluate side-chains 67 residues out of total 310 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 64 time to evaluate : 0.151 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 30 THR Chi-restraints excluded: chain J residue 14 ASN Chi-restraints excluded: chain N residue 14 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 35 random chunks: [7, 6, 1, 32, 2, 23, 5, 27, 12, 25, 10] chunk 7 optimal weight: 4.9990 chunk 6 optimal weight: 5.9990 chunk 1 optimal weight: 2.9990 chunk 32 optimal weight: 4.9990 chunk 2 optimal weight: 3.9990 chunk 23 optimal weight: 5.9990 chunk 5 optimal weight: 0.5980 chunk 27 optimal weight: 9.9990 chunk 12 optimal weight: 0.6980 chunk 25 optimal weight: 3.9990 chunk 10 optimal weight: 8.9990 overall best weight: 2.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 31 ASN B 35 ASN ** C 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 35 ASN G 22 ASN ** I 14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 35 ASN K 31 ASN ** M 14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 22 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4550 r_free = 0.4550 target = 0.154627 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4168 r_free = 0.4168 target = 0.125055 restraints weight = 9872.698| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.4228 r_free = 0.4228 target = 0.130056 restraints weight = 4657.857| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4267 r_free = 0.4267 target = 0.133364 restraints weight = 2937.543| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.4299 r_free = 0.4299 target = 0.135758 restraints weight = 2189.559| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.4318 r_free = 0.4318 target = 0.137257 restraints weight = 1780.626| |-----------------------------------------------------------------------------| r_work (final): 0.4350 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7034 moved from start: 2.3123 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 2835 Z= 0.254 Angle : 0.724 7.938 3850 Z= 0.390 Chirality : 0.050 0.218 450 Planarity : 0.005 0.055 515 Dihedral : 5.680 18.351 385 Min Nonbonded Distance : 2.408 Molprobity Statistics. All-atom Clashscore : 15.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.67 % Favored : 93.33 % Rotamer: Outliers : 3.55 % Allowed : 23.23 % Favored : 73.23 % 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: -4.58 (0.24), residues: 345 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.49 (0.18), residues: 345 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG F 11 TYR 0.012 0.003 TYR K 37 PHE 0.021 0.003 PHE E 15 HIS 0.007 0.002 HIS A 18 Details of bonding type rmsd/Z covalent geometry : bond 0.00534 / 0.25 ( 2835) covalent geometry : angle 0.72413 / 0.39 ( 3850) hydrogen bonds : bond 0.03329 / 2.28 ( 126) hydrogen bonds : angle 4.98095 / 3.40 ( 378) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 690 Ramachandran restraints generated. 345 Oldfield, 0 Emsley, 345 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 690 Ramachandran restraints generated. 345 Oldfield, 0 Emsley, 345 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 310 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 84 time to evaluate : 0.153 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 9 THR cc_start: 0.7996 (m) cc_final: 0.7427 (p) REVERT: C 26 ILE cc_start: 0.6873 (mt) cc_final: 0.6505 (mt) REVERT: C 32 VAL cc_start: 0.7907 (t) cc_final: 0.7598 (p) REVERT: J 9 THR cc_start: 0.8149 (m) cc_final: 0.7604 (p) REVERT: J 32 VAL cc_start: 0.8877 (t) cc_final: 0.8638 (t) REVERT: M 22 ASN cc_start: 0.8713 (t0) cc_final: 0.8460 (t0) REVERT: N 9 THR cc_start: 0.7522 (m) cc_final: 0.6958 (p) outliers start: 11 outliers final: 6 residues processed: 90 average time/residue: 0.0814 time to fit residues: 9.3297 Evaluate side-chains 82 residues out of total 310 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 76 time to evaluate : 0.152 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 30 THR Chi-restraints excluded: chain E residue 31 ASN Chi-restraints excluded: chain J residue 14 ASN Chi-restraints excluded: chain J residue 36 THR Chi-restraints excluded: chain K residue 32 VAL Chi-restraints excluded: chain O residue 32 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 35 random chunks: [14, 5, 16, 4, 13, 27, 28, 22, 1, 8, 3] chunk 14 optimal weight: 5.9990 chunk 5 optimal weight: 3.9990 chunk 16 optimal weight: 4.9990 chunk 4 optimal weight: 3.9990 chunk 13 optimal weight: 10.0000 chunk 27 optimal weight: 6.9990 chunk 28 optimal weight: 3.9990 chunk 22 optimal weight: 2.9990 chunk 1 optimal weight: 1.9990 chunk 8 optimal weight: 0.8980 chunk 3 optimal weight: 1.9990 overall best weight: 2.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... F 21 ASN ** I 14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 35 ASN ** M 14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 22 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4514 r_free = 0.4514 target = 0.151125 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4137 r_free = 0.4137 target = 0.121813 restraints weight = 9780.325| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.4198 r_free = 0.4198 target = 0.126912 restraints weight = 4604.984| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.4239 r_free = 0.4239 target = 0.130288 restraints weight = 2907.916| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.4266 r_free = 0.4266 target = 0.132475 restraints weight = 2160.632| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.4282 r_free = 0.4282 target = 0.133838 restraints weight = 1778.884| |-----------------------------------------------------------------------------| r_work (final): 0.4305 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7240 moved from start: 2.4385 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 2835 Z= 0.201 Angle : 0.597 6.989 3850 Z= 0.324 Chirality : 0.045 0.143 450 Planarity : 0.003 0.022 515 Dihedral : 5.080 15.609 385 Min Nonbonded Distance : 2.396 Molprobity Statistics. All-atom Clashscore : 12.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.54 % Favored : 92.46 % Rotamer: Outliers : 1.94 % Allowed : 25.48 % Favored : 72.58 % 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: -4.56 (0.25), residues: 345 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.47 (0.19), residues: 345 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG I 11 TYR 0.009 0.001 TYR G 37 PHE 0.011 0.002 PHE E 15 HIS 0.002 0.001 HIS B 18 Details of bonding type rmsd/Z covalent geometry : bond 0.00421 / 0.20 ( 2835) covalent geometry : angle 0.59745 / 0.32 ( 3850) hydrogen bonds : bond 0.02536 / 1.76 ( 126) hydrogen bonds : angle 4.61189 / 3.11 ( 378) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 690 Ramachandran restraints generated. 345 Oldfield, 0 Emsley, 345 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 690 Ramachandran restraints generated. 345 Oldfield, 0 Emsley, 345 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 310 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 69 time to evaluate : 0.125 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 11 ARG cc_start: 0.4123 (mmp-170) cc_final: 0.3804 (mmm160) REVERT: J 32 VAL cc_start: 0.8881 (t) cc_final: 0.8672 (t) REVERT: N 9 THR cc_start: 0.8014 (m) cc_final: 0.7592 (p) outliers start: 6 outliers final: 5 residues processed: 73 average time/residue: 0.1031 time to fit residues: 9.2121 Evaluate side-chains 67 residues out of total 310 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 62 time to evaluate : 0.154 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 30 THR Chi-restraints excluded: chain E residue 9 THR Chi-restraints excluded: chain I residue 28 SER Chi-restraints excluded: chain J residue 14 ASN Chi-restraints excluded: chain N residue 14 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 35 random chunks: [2, 31, 33, 6, 14, 30, 13, 9, 7, 0, 10] chunk 2 optimal weight: 2.9990 chunk 31 optimal weight: 2.9990 chunk 33 optimal weight: 2.9990 chunk 6 optimal weight: 0.2980 chunk 14 optimal weight: 4.9990 chunk 30 optimal weight: 3.9990 chunk 13 optimal weight: 5.9990 chunk 9 optimal weight: 3.9990 chunk 7 optimal weight: 0.6980 chunk 0 optimal weight: 0.9990 chunk 10 optimal weight: 6.9990 overall best weight: 1.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 35 ASN ** I 14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 22 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 = 0.4493 r_free = 0.4493 target = 0.148657 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4114 r_free = 0.4114 target = 0.119748 restraints weight = 10034.687| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.4173 r_free = 0.4173 target = 0.124802 restraints weight = 4606.500| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.4216 r_free = 0.4216 target = 0.128182 restraints weight = 2876.082| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.4239 r_free = 0.4239 target = 0.130202 restraints weight = 2132.462| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.4262 r_free = 0.4262 target = 0.131816 restraints weight = 1771.429| |-----------------------------------------------------------------------------| r_work (final): 0.4282 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7295 moved from start: 2.5169 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 2835 Z= 0.147 Angle : 0.495 5.032 3850 Z= 0.276 Chirality : 0.043 0.138 450 Planarity : 0.002 0.015 515 Dihedral : 4.507 14.043 385 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 10.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.96 % Favored : 93.04 % Rotamer: Outliers : 0.97 % Allowed : 26.13 % Favored : 72.90 % 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: -4.43 (0.26), residues: 345 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.37 (0.20), residues: 345 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG J 11 TYR 0.005 0.001 TYR N 37 PHE 0.013 0.001 PHE E 15 HIS 0.001 0.001 HIS I 18 Details of bonding type rmsd/Z covalent geometry : bond 0.00310 / 0.15 ( 2835) covalent geometry : angle 0.49535 / 0.28 ( 3850) hydrogen bonds : bond 0.01928 / 1.33 ( 126) hydrogen bonds : angle 4.17725 / 2.84 ( 378) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 690 Ramachandran restraints generated. 345 Oldfield, 0 Emsley, 345 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 690 Ramachandran restraints generated. 345 Oldfield, 0 Emsley, 345 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 310 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 63 time to evaluate : 0.101 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: I 12 LEU cc_start: 0.8208 (mp) cc_final: 0.7923 (tp) REVERT: N 9 THR cc_start: 0.8020 (m) cc_final: 0.7592 (p) REVERT: S 23 PHE cc_start: 0.7280 (m-80) cc_final: 0.6079 (p90) outliers start: 3 outliers final: 2 residues processed: 64 average time/residue: 0.0958 time to fit residues: 7.6243 Evaluate side-chains 63 residues out of total 310 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 61 time to evaluate : 0.156 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 30 THR Chi-restraints excluded: chain E residue 9 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 35 random chunks: [2, 13, 8, 33, 19, 14, 20, 1, 34, 6, 24] chunk 2 optimal weight: 3.9990 chunk 13 optimal weight: 7.9990 chunk 8 optimal weight: 2.9990 chunk 33 optimal weight: 2.9990 chunk 19 optimal weight: 7.9990 chunk 14 optimal weight: 3.9990 chunk 20 optimal weight: 1.9990 chunk 1 optimal weight: 0.2980 chunk 34 optimal weight: 3.9990 chunk 6 optimal weight: 1.9990 chunk 24 optimal weight: 7.9990 overall best weight: 2.0588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** I 14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 22 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 = 0.4368 r_free = 0.4368 target = 0.136119 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4008 r_free = 0.4008 target = 0.108689 restraints weight = 10511.696| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.4063 r_free = 0.4063 target = 0.113006 restraints weight = 5064.755| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.4102 r_free = 0.4102 target = 0.115997 restraints weight = 3301.782| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.4124 r_free = 0.4124 target = 0.117813 restraints weight = 2497.170| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.4145 r_free = 0.4145 target = 0.119248 restraints weight = 2092.676| |-----------------------------------------------------------------------------| r_work (final): 0.4162 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7504 moved from start: 2.6250 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 2835 Z= 0.190 Angle : 0.558 5.867 3850 Z= 0.305 Chirality : 0.045 0.152 450 Planarity : 0.004 0.074 515 Dihedral : 4.845 14.463 385 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 10.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.99 % Favored : 91.01 % Rotamer: Outliers : 1.29 % Allowed : 26.45 % Favored : 72.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.37 (0.27), residues: 345 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.32 (0.21), residues: 345 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG F 11 TYR 0.010 0.001 TYR M 37 PHE 0.015 0.002 PHE B 23 HIS 0.002 0.001 HIS J 18 Details of bonding type rmsd/Z covalent geometry : bond 0.00401 / 0.19 ( 2835) covalent geometry : angle 0.55818 / 0.31 ( 3850) hydrogen bonds : bond 0.02424 / 1.77 ( 126) hydrogen bonds : angle 4.27576 / 2.89 ( 378) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 690 Ramachandran restraints generated. 345 Oldfield, 0 Emsley, 345 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 690 Ramachandran restraints generated. 345 Oldfield, 0 Emsley, 345 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 57 residues out of total 310 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 53 time to evaluate : 0.156 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: I 10 GLN cc_start: 0.6568 (mp10) cc_final: 0.6269 (mp10) REVERT: N 9 THR cc_start: 0.8116 (m) cc_final: 0.7653 (p) REVERT: N 27 LEU cc_start: 0.8462 (OUTLIER) cc_final: 0.8174 (mp) outliers start: 4 outliers final: 2 residues processed: 56 average time/residue: 0.1144 time to fit residues: 7.9243 Evaluate side-chains 52 residues out of total 310 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 49 time to evaluate : 0.157 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 9 THR Chi-restraints excluded: chain I residue 28 SER Chi-restraints excluded: chain N residue 27 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 35 random chunks: [28, 33, 3, 31, 2, 15, 9, 29, 1, 30, 25] chunk 28 optimal weight: 0.8980 chunk 33 optimal weight: 3.9990 chunk 3 optimal weight: 0.0980 chunk 31 optimal weight: 0.0970 chunk 2 optimal weight: 3.9990 chunk 15 optimal weight: 3.9990 chunk 9 optimal weight: 1.9990 chunk 29 optimal weight: 3.9990 chunk 1 optimal weight: 0.9980 chunk 30 optimal weight: 4.9990 chunk 25 optimal weight: 4.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** I 14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 22 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 = 0.4394 r_free = 0.4394 target = 0.138872 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4041 r_free = 0.4041 target = 0.111138 restraints weight = 10284.857| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.4100 r_free = 0.4100 target = 0.115529 restraints weight = 4960.575| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.4138 r_free = 0.4138 target = 0.118626 restraints weight = 3235.721| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.4164 r_free = 0.4164 target = 0.120644 restraints weight = 2434.940| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.4180 r_free = 0.4180 target = 0.121983 restraints weight = 2013.517| |-----------------------------------------------------------------------------| r_work (final): 0.4196 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7455 moved from start: 2.6559 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 2835 Z= 0.096 Angle : 0.485 5.605 3850 Z= 0.265 Chirality : 0.043 0.129 450 Planarity : 0.001 0.014 515 Dihedral : 4.256 12.248 385 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 8.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.22 % Favored : 94.78 % Rotamer: Outliers : 0.65 % Allowed : 28.06 % Favored : 71.29 % 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: -4.19 (0.29), residues: 345 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.18 (0.22), residues: 345 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG J 11 TYR 0.006 0.001 TYR C 37 PHE 0.013 0.001 PHE E 15 HIS 0.001 0.000 HIS J 18 Details of bonding type rmsd/Z covalent geometry : bond 0.00211 / 0.10 ( 2835) covalent geometry : angle 0.48538 / 0.26 ( 3850) hydrogen bonds : bond 0.01671 / 1.18 ( 126) hydrogen bonds : angle 3.96260 / 2.68 ( 378) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1353.83 seconds wall clock time: 23 minutes 44.73 seconds (1424.73 seconds total)