Starting phenix.real_space_refine on Fri Aug 22 13:39:33 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8az6_15755/08_2025/8az6_15755.cif Found real_map, /net/cci-nas-00/data/ceres_data/8az6_15755/08_2025/8az6_15755.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8az6_15755/08_2025/8az6_15755.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8az6_15755/08_2025/8az6_15755.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8az6_15755/08_2025/8az6_15755.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8az6_15755/08_2025/8az6_15755.map" } resolution = 3.1 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: 3 Type Number sf(0) Gaussians C 2090 2.51 5 N 630 2.21 5 O 700 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 50 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 3420 Number of models: 1 Model: "" Number of chains: 40 Chain: "A" Number of atoms: 217 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 217 Classifications: {'peptide': 29} Link IDs: {'TRANS': 28} Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 217 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 217 Classifications: {'peptide': 29} Link IDs: {'TRANS': 28} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 123 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 123 Classifications: {'peptide': 17} Link IDs: {'TRANS': 16} Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 123 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 123 Classifications: {'peptide': 17} Link IDs: {'TRANS': 16} Chain: "D" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 217 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 217 Classifications: {'peptide': 29} Link IDs: {'TRANS': 28} Chain: "E" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "F" Number of atoms: 217 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 217 Classifications: {'peptide': 29} Link IDs: {'TRANS': 28} Chain: "F" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "G" Number of atoms: 123 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 123 Classifications: {'peptide': 17} Link IDs: {'TRANS': 16} Chain: "G" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "H" Number of atoms: 123 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 123 Classifications: {'peptide': 17} Link IDs: {'TRANS': 16} Chain: "H" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "I" Number of atoms: 217 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 217 Classifications: {'peptide': 29} Link IDs: {'TRANS': 28} Chain: "I" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "J" Number of atoms: 217 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 217 Classifications: {'peptide': 29} Link IDs: {'TRANS': 28} Chain: "J" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "K" Number of atoms: 123 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 123 Classifications: {'peptide': 17} Link IDs: {'TRANS': 16} Chain: "K" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "L" Number of atoms: 123 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 123 Classifications: {'peptide': 17} Link IDs: {'TRANS': 16} Chain: "L" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "M" Number of atoms: 217 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 217 Classifications: {'peptide': 29} Link IDs: {'TRANS': 28} Chain: "M" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "N" Number of atoms: 217 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 217 Classifications: {'peptide': 29} Link IDs: {'TRANS': 28} Chain: "N" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "O" Number of atoms: 123 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 123 Classifications: {'peptide': 17} Link IDs: {'TRANS': 16} Chain: "O" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "P" Number of atoms: 123 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 123 Classifications: {'peptide': 17} Link IDs: {'TRANS': 16} Chain: "P" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "Q" Number of atoms: 217 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 217 Classifications: {'peptide': 29} Link IDs: {'TRANS': 28} Chain: "Q" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "R" Number of atoms: 217 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 217 Classifications: {'peptide': 29} Link IDs: {'TRANS': 28} Chain: "R" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "S" Number of atoms: 123 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 123 Classifications: {'peptide': 17} Link IDs: {'TRANS': 16} Chain: "S" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "T" Number of atoms: 123 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 123 Classifications: {'peptide': 17} Link IDs: {'TRANS': 16} Chain: "T" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Time building chain proxies: 1.07, per 1000 atoms: 0.31 Number of scatterers: 3420 At special positions: 0 Unit cell: (73.8, 90.9, 52.2, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 3 Type Number sf(0) O 700 8.00 N 630 7.00 C 2090 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=20, symmetry=0 Number of additional bonds: simple=20, symmetry=0 Coordination: Other bonds: Time building additional restraints: 0.25 Conformation dependent library (CDL) restraints added in 118.5 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 820 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 10 sheets defined 0.0% alpha, 52.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.16 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'A' and resid 10 through 22 removed outlier: 7.132A pdb=" N ASN A 21 " --> pdb=" O GLY E 20 " (cutoff:3.500A) removed outlier: 7.129A pdb=" N ASN E 22 " --> pdb=" O ASN A 21 " (cutoff:3.500A) removed outlier: 6.883A pdb=" N ASN E 21 " --> pdb=" O GLY I 20 " (cutoff:3.500A) removed outlier: 6.930A pdb=" N ASN I 22 " --> pdb=" O ASN E 21 " (cutoff:3.500A) removed outlier: 7.085A pdb=" N ASN I 21 " --> pdb=" O GLY M 20 " (cutoff:3.500A) removed outlier: 7.057A pdb=" N ASN M 22 " --> pdb=" O ASN I 21 " (cutoff:3.500A) removed outlier: 7.037A pdb=" N ASN M 21 " --> pdb=" O GLY Q 20 " (cutoff:3.500A) removed outlier: 7.049A 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: 7.013A pdb=" N ASN B 21 " --> pdb=" O GLY F 20 " (cutoff:3.500A) removed outlier: 7.027A pdb=" N ASN F 22 " --> pdb=" O ASN B 21 " (cutoff:3.500A) removed outlier: 7.018A pdb=" N ASN F 21 " --> pdb=" O GLY J 20 " (cutoff:3.500A) removed outlier: 7.053A pdb=" N ASN J 22 " --> pdb=" O ASN F 21 " (cutoff:3.500A) removed outlier: 7.083A pdb=" N ASN J 21 " --> pdb=" O GLY N 20 " (cutoff:3.500A) removed outlier: 7.048A pdb=" N ASN N 22 " --> pdb=" O ASN J 21 " (cutoff:3.500A) removed outlier: 7.027A pdb=" N ASN N 21 " --> pdb=" O GLY R 20 " (cutoff:3.500A) removed outlier: 7.041A 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: 3.528A pdb=" N ASN C 31 " --> pdb=" O THR G 30 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N VAL G 32 " --> pdb=" O ASN C 31 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 35 through 36 removed outlier: 6.735A pdb=" N ASN C 35 " --> pdb=" O THR G 36 " (cutoff:3.500A) removed outlier: 6.711A pdb=" N ASN G 35 " --> pdb=" O THR K 36 " (cutoff:3.500A) removed outlier: 6.629A pdb=" N ASN K 35 " --> pdb=" O THR O 36 " (cutoff:3.500A) removed outlier: 6.539A pdb=" N ASN O 35 " --> pdb=" O THR S 36 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'D' and resid 25 through 32 removed outlier: 3.513A pdb=" N ASN D 31 " --> pdb=" O THR H 30 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N VAL H 32 " --> pdb=" O ASN D 31 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 35 through 36 removed outlier: 6.669A pdb=" N ASN D 35 " --> pdb=" O THR H 36 " (cutoff:3.500A) removed outlier: 6.745A pdb=" N ASN H 35 " --> pdb=" O THR L 36 " (cutoff:3.500A) removed outlier: 6.560A pdb=" N ASN L 35 " --> pdb=" O THR P 36 " (cutoff:3.500A) removed outlier: 6.540A pdb=" N ASN P 35 " --> pdb=" O THR T 36 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 164 hydrogen bonds defined for protein. 492 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: 0.51 Time building geometry restraints manager: 0.35 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.29: 560 1.29 - 1.35: 590 1.35 - 1.42: 416 1.42 - 1.48: 524 1.48 - 1.54: 1350 Bond restraints: 3440 Sorted by residual: bond pdb=" CA ASN E 14 " pdb=" CB ASN E 14 " ideal model delta sigma weight residual 1.534 1.522 0.013 2.47e-02 1.64e+03 2.74e-01 bond pdb=" CA ASN F 14 " pdb=" CB ASN F 14 " ideal model delta sigma weight residual 1.534 1.522 0.013 2.47e-02 1.64e+03 2.65e-01 bond pdb=" CA ASN B 14 " pdb=" CB ASN B 14 " ideal model delta sigma weight residual 1.534 1.522 0.013 2.47e-02 1.64e+03 2.62e-01 bond pdb=" CA ASN A 14 " pdb=" CB ASN A 14 " ideal model delta sigma weight residual 1.534 1.522 0.013 2.47e-02 1.64e+03 2.57e-01 bond pdb=" CA ASN I 14 " pdb=" CB ASN I 14 " ideal model delta sigma weight residual 1.534 1.522 0.012 2.47e-02 1.64e+03 2.43e-01 ... (remaining 3435 not shown) Histogram of bond angle deviations from ideal: 0.00 - 0.55: 3968 0.55 - 1.09: 521 1.09 - 1.64: 131 1.64 - 2.18: 32 2.18 - 2.73: 8 Bond angle restraints: 4660 Sorted by residual: angle pdb=" NE ARG R 11 " pdb=" CZ ARG R 11 " pdb=" NH1 ARG R 11 " ideal model delta sigma weight residual 121.50 120.12 1.38 1.00e+00 1.00e+00 1.92e+00 angle pdb=" NE ARG N 11 " pdb=" CZ ARG N 11 " pdb=" NH1 ARG N 11 " ideal model delta sigma weight residual 121.50 120.14 1.36 1.00e+00 1.00e+00 1.86e+00 angle pdb=" NE ARG M 11 " pdb=" CZ ARG M 11 " pdb=" NH1 ARG M 11 " ideal model delta sigma weight residual 121.50 120.14 1.36 1.00e+00 1.00e+00 1.85e+00 angle pdb=" NE ARG B 11 " pdb=" CZ ARG B 11 " pdb=" NH1 ARG B 11 " ideal model delta sigma weight residual 121.50 120.14 1.36 1.00e+00 1.00e+00 1.84e+00 angle pdb=" NE ARG J 11 " pdb=" CZ ARG J 11 " pdb=" NH1 ARG J 11 " ideal model delta sigma weight residual 121.50 120.16 1.34 1.00e+00 1.00e+00 1.80e+00 ... (remaining 4655 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 9.92: 1744 9.92 - 19.83: 121 19.83 - 29.75: 35 29.75 - 39.66: 20 39.66 - 49.58: 10 Dihedral angle restraints: 1930 sinusoidal: 650 harmonic: 1280 Sorted by residual: dihedral pdb=" CA ASN H 22 " pdb=" C ASN H 22 " pdb=" N PHE H 23 " pdb=" CA PHE H 23 " ideal model delta harmonic sigma weight residual 180.00 169.18 10.82 0 5.00e+00 4.00e-02 4.69e+00 dihedral pdb=" CA ASN L 22 " pdb=" C ASN L 22 " pdb=" N PHE L 23 " pdb=" CA PHE L 23 " ideal model delta harmonic sigma weight residual 180.00 169.19 10.81 0 5.00e+00 4.00e-02 4.67e+00 dihedral pdb=" CA ASN K 22 " pdb=" C ASN K 22 " pdb=" N PHE K 23 " pdb=" CA PHE K 23 " ideal model delta harmonic sigma weight residual 180.00 169.22 10.78 0 5.00e+00 4.00e-02 4.65e+00 ... (remaining 1927 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.028: 341 0.028 - 0.057: 130 0.057 - 0.085: 29 0.085 - 0.113: 29 0.113 - 0.142: 21 Chirality restraints: 550 Sorted by residual: chirality pdb=" CA ILE O 26 " pdb=" N ILE O 26 " pdb=" C ILE O 26 " pdb=" CB ILE O 26 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.14 2.00e-01 2.50e+01 5.02e-01 chirality pdb=" CA ILE P 26 " pdb=" N ILE P 26 " pdb=" C ILE P 26 " pdb=" CB ILE P 26 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.96e-01 chirality pdb=" CA ILE R 26 " pdb=" N ILE R 26 " pdb=" C ILE R 26 " pdb=" CB ILE R 26 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.08e-01 ... (remaining 547 not shown) Planarity restraints: 610 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLY P 33 " 0.003 2.00e-02 2.50e+03 5.38e-03 2.90e-01 pdb=" C GLY P 33 " -0.009 2.00e-02 2.50e+03 pdb=" O GLY P 33 " 0.004 2.00e-02 2.50e+03 pdb=" N SER P 34 " 0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLY O 33 " -0.002 2.00e-02 2.50e+03 4.79e-03 2.29e-01 pdb=" C GLY O 33 " 0.008 2.00e-02 2.50e+03 pdb=" O GLY O 33 " -0.003 2.00e-02 2.50e+03 pdb=" N SER O 34 " -0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB HIS N 18 " 0.004 2.00e-02 2.50e+03 3.78e-03 2.14e-01 pdb=" CG HIS N 18 " -0.008 2.00e-02 2.50e+03 pdb=" ND1 HIS N 18 " 0.002 2.00e-02 2.50e+03 pdb=" CD2 HIS N 18 " 0.001 2.00e-02 2.50e+03 pdb=" CE1 HIS N 18 " -0.000 2.00e-02 2.50e+03 pdb=" NE2 HIS N 18 " 0.002 2.00e-02 2.50e+03 ... (remaining 607 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 180 2.75 - 3.29: 2901 3.29 - 3.82: 5858 3.82 - 4.36: 6099 4.36 - 4.90: 12161 Nonbonded interactions: 27199 Sorted by model distance: nonbonded pdb=" OD1 ASN B 21 " pdb=" ND2 ASN D 35 " model vdw 2.212 3.120 nonbonded pdb=" OD1 ASN R 21 " pdb=" ND2 ASN T 35 " model vdw 2.292 3.120 nonbonded pdb=" OD1 ASN E 21 " pdb=" ND2 ASN G 35 " model vdw 2.296 3.120 nonbonded pdb=" OD1 ASN Q 21 " pdb=" ND2 ASN S 35 " model vdw 2.296 3.120 nonbonded pdb=" OD1 ASN N 21 " pdb=" ND2 ASN P 35 " model vdw 2.301 3.120 ... (remaining 27194 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 '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 'D' selection = chain 'G' selection = chain 'H' selection = chain 'K' selection = chain 'L' selection = chain 'O' selection = chain 'P' selection = chain 'S' selection = chain 'T' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.240 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.070 Check model and map are aligned: 0.010 Set scattering table: 0.030 Process input model: 5.570 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.320 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 9.290 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8138 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 : 0.009 0.103 3460 Z= 0.796 Angle : 0.430 2.730 4660 Z= 0.250 Chirality : 0.043 0.142 550 Planarity : 0.002 0.005 610 Dihedral : 9.460 49.579 1110 Min Nonbonded Distance : 2.212 Molprobity Statistics. All-atom Clashscore : 5.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.76 % Favored : 95.24 % Rotamer: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % 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 aren not related in a simple way. whole: -4.04 (0.19), residues: 420 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.07 (0.14), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 11 TYR 0.005 0.001 TYR M 37 PHE 0.004 0.001 PHE L 23 HIS 0.004 0.002 HIS N 18 Details of bonding type rmsd covalent geometry : bond 0.00374 ( 3440) covalent geometry : angle 0.42987 ( 4660) hydrogen bonds : bond 0.21642 ( 164) hydrogen bonds : angle 6.33773 ( 492) Misc. bond : bond 0.10214 ( 20) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 97 time to evaluate : 0.127 Fit side-chains revert: symmetry clash REVERT: A 11 ARG cc_start: 0.7354 (mtt180) cc_final: 0.7036 (mmp-170) REVERT: B 11 ARG cc_start: 0.7317 (mtt180) cc_final: 0.6790 (mmp-170) REVERT: P 23 PHE cc_start: 0.7101 (m-80) cc_final: 0.6748 (m-80) REVERT: Q 11 ARG cc_start: 0.7631 (mtt180) cc_final: 0.7368 (ptt90) outliers start: 0 outliers final: 0 residues processed: 97 average time/residue: 0.0805 time to fit residues: 9.2882 Evaluate side-chains 65 residues out of total 380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 65 time to evaluate : 0.134 ------------------------------------------------------------------------------- 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: 4.9990 chunk 12 optimal weight: 2.9990 chunk 24 optimal weight: 5.9990 chunk 28 optimal weight: 0.0470 chunk 13 optimal weight: 8.9990 chunk 1 optimal weight: 6.9990 chunk 8 optimal weight: 0.7980 chunk 16 optimal weight: 7.9990 chunk 15 optimal weight: 10.0000 chunk 29 optimal weight: 10.0000 chunk 25 optimal weight: 8.9990 overall best weight: 2.9684 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 35 ASN D 31 ASN E 10 GLN F 10 GLN G 31 ASN G 35 ASN H 31 ASN ** H 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 31 ASN L 31 ASN O 31 ASN O 35 ASN P 21 ASN P 31 ASN Q 10 GLN R 10 GLN S 21 ASN S 31 ASN T 31 ASN T 35 ASN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3894 r_free = 0.3894 target = 0.125159 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.085027 restraints weight = 4341.169| |-----------------------------------------------------------------------------| r_work (start): 0.3354 rms_B_bonded: 2.22 r_work: 0.3233 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.3113 rms_B_bonded: 4.41 restraints_weight: 0.2500 r_work (final): 0.3113 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8386 moved from start: 0.2652 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.020 3460 Z= 0.194 Angle : 0.535 7.415 4660 Z= 0.280 Chirality : 0.042 0.130 550 Planarity : 0.002 0.011 610 Dihedral : 4.568 14.767 470 Min Nonbonded Distance : 2.611 Molprobity Statistics. All-atom Clashscore : 4.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.76 % Favored : 95.24 % Rotamer: Outliers : 5.26 % Allowed : 8.42 % Favored : 86.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.95 (0.21), residues: 420 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.00 (0.16), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 11 TYR 0.003 0.001 TYR S 37 PHE 0.013 0.002 PHE F 15 HIS 0.003 0.001 HIS Q 18 Details of bonding type rmsd covalent geometry : bond 0.00433 ( 3440) covalent geometry : angle 0.53531 ( 4660) hydrogen bonds : bond 0.04157 ( 164) hydrogen bonds : angle 4.69087 ( 492) Misc. bond : bond 0.00059 ( 20) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 85 time to evaluate : 0.133 Fit side-chains REVERT: A 11 ARG cc_start: 0.8008 (mtt180) cc_final: 0.7012 (mmp-170) REVERT: B 10 GLN cc_start: 0.8231 (tt0) cc_final: 0.7847 (tt0) REVERT: B 11 ARG cc_start: 0.7856 (mtt180) cc_final: 0.6839 (mmp-170) REVERT: O 23 PHE cc_start: 0.6560 (m-80) cc_final: 0.6262 (m-80) REVERT: Q 11 ARG cc_start: 0.8101 (mtt180) cc_final: 0.7566 (ptt90) REVERT: S 23 PHE cc_start: 0.6707 (m-80) cc_final: 0.6460 (m-10) REVERT: T 31 ASN cc_start: 0.8530 (t0) cc_final: 0.8214 (t0) outliers start: 20 outliers final: 15 residues processed: 99 average time/residue: 0.0851 time to fit residues: 10.0030 Evaluate side-chains 83 residues out of total 380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 68 time to evaluate : 0.135 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 SER Chi-restraints excluded: chain B residue 34 SER Chi-restraints excluded: chain E residue 34 SER Chi-restraints excluded: chain F residue 34 SER Chi-restraints excluded: chain I residue 34 SER Chi-restraints excluded: chain J residue 34 SER Chi-restraints excluded: chain L residue 28 SER Chi-restraints excluded: chain L residue 30 THR Chi-restraints excluded: chain L residue 32 VAL Chi-restraints excluded: chain M residue 34 SER Chi-restraints excluded: chain O residue 35 ASN Chi-restraints excluded: chain P residue 30 THR Chi-restraints excluded: chain Q residue 34 SER Chi-restraints excluded: chain R residue 34 SER Chi-restraints excluded: chain T residue 35 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 28 optimal weight: 9.9990 chunk 26 optimal weight: 5.9990 chunk 21 optimal weight: 8.9990 chunk 13 optimal weight: 7.9990 chunk 5 optimal weight: 9.9990 chunk 6 optimal weight: 7.9990 chunk 27 optimal weight: 0.8980 chunk 18 optimal weight: 0.9990 chunk 0 optimal weight: 0.7980 chunk 11 optimal weight: 9.9990 chunk 17 optimal weight: 9.9990 overall best weight: 3.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 35 ASN G 21 ASN G 35 ASN K 35 ASN O 21 ASN S 21 ASN T 21 ASN ** T 22 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 35 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3878 r_free = 0.3878 target = 0.124845 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.084443 restraints weight = 4247.205| |-----------------------------------------------------------------------------| r_work (start): 0.3344 rms_B_bonded: 2.25 r_work: 0.3211 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.3083 rms_B_bonded: 4.46 restraints_weight: 0.2500 r_work (final): 0.3083 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8435 moved from start: 0.3302 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.016 3460 Z= 0.209 Angle : 0.552 7.727 4660 Z= 0.286 Chirality : 0.042 0.125 550 Planarity : 0.002 0.010 610 Dihedral : 4.751 16.181 470 Min Nonbonded Distance : 2.566 Molprobity Statistics. All-atom Clashscore : 3.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.29 % Favored : 95.71 % Rotamer: Outliers : 6.05 % Allowed : 11.84 % Favored : 82.11 % 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 aren not related in a simple way. whole: -4.19 (0.21), residues: 420 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.18 (0.16), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 11 TYR 0.003 0.001 TYR B 37 PHE 0.015 0.002 PHE P 23 HIS 0.003 0.002 HIS Q 18 Details of bonding type rmsd covalent geometry : bond 0.00461 ( 3440) covalent geometry : angle 0.55219 ( 4660) hydrogen bonds : bond 0.03835 ( 164) hydrogen bonds : angle 4.57571 ( 492) Misc. bond : bond 0.00069 ( 20) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 74 time to evaluate : 0.138 Fit side-chains REVERT: A 11 ARG cc_start: 0.7936 (mtt180) cc_final: 0.6948 (mmp-170) REVERT: B 10 GLN cc_start: 0.8262 (tt0) cc_final: 0.7874 (tt0) REVERT: B 11 ARG cc_start: 0.7865 (mtt180) cc_final: 0.6844 (mmp-170) REVERT: I 10 GLN cc_start: 0.7817 (tt0) cc_final: 0.7472 (tt0) REVERT: Q 11 ARG cc_start: 0.8181 (mtt180) cc_final: 0.7606 (ptt90) outliers start: 23 outliers final: 20 residues processed: 91 average time/residue: 0.0863 time to fit residues: 9.2866 Evaluate side-chains 89 residues out of total 380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 69 time to evaluate : 0.105 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 SER Chi-restraints excluded: chain B residue 34 SER Chi-restraints excluded: chain C residue 28 SER Chi-restraints excluded: chain C residue 36 THR Chi-restraints excluded: chain D residue 28 SER Chi-restraints excluded: chain E residue 34 SER Chi-restraints excluded: chain F residue 34 SER Chi-restraints excluded: chain H residue 28 SER Chi-restraints excluded: chain I residue 34 SER Chi-restraints excluded: chain J residue 34 SER Chi-restraints excluded: chain K residue 36 THR Chi-restraints excluded: chain L residue 28 SER Chi-restraints excluded: chain L residue 30 THR Chi-restraints excluded: chain M residue 34 SER Chi-restraints excluded: chain N residue 34 SER Chi-restraints excluded: chain P residue 36 THR Chi-restraints excluded: chain Q residue 34 SER Chi-restraints excluded: chain R residue 34 SER Chi-restraints excluded: chain S residue 30 THR Chi-restraints excluded: chain T residue 35 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 22 optimal weight: 20.0000 chunk 28 optimal weight: 1.9990 chunk 17 optimal weight: 20.0000 chunk 14 optimal weight: 8.9990 chunk 25 optimal weight: 4.9990 chunk 15 optimal weight: 1.9990 chunk 8 optimal weight: 0.9990 chunk 5 optimal weight: 9.9990 chunk 0 optimal weight: 8.9990 chunk 26 optimal weight: 4.9990 chunk 20 optimal weight: 0.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 21 ASN ** I 14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 35 ASN ** M 14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 14 ASN P 31 ASN P 35 ASN R 14 ASN S 21 ASN S 31 ASN S 35 ASN T 22 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3904 r_free = 0.3904 target = 0.126813 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.085744 restraints weight = 4153.489| |-----------------------------------------------------------------------------| r_work (start): 0.3370 rms_B_bonded: 2.28 r_work: 0.3239 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.3111 rms_B_bonded: 4.47 restraints_weight: 0.2500 r_work (final): 0.3111 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8403 moved from start: 0.3520 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.011 3460 Z= 0.143 Angle : 0.502 6.747 4660 Z= 0.258 Chirality : 0.041 0.133 550 Planarity : 0.002 0.009 610 Dihedral : 4.462 14.328 470 Min Nonbonded Distance : 2.625 Molprobity Statistics. All-atom Clashscore : 2.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.52 % Favored : 95.48 % Rotamer: Outliers : 5.00 % Allowed : 14.74 % Favored : 80.26 % 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 aren not related in a simple way. whole: -4.33 (0.22), residues: 420 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.30 (0.16), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG F 11 TYR 0.003 0.001 TYR T 37 PHE 0.012 0.002 PHE T 23 HIS 0.003 0.001 HIS R 18 Details of bonding type rmsd covalent geometry : bond 0.00310 ( 3440) covalent geometry : angle 0.50165 ( 4660) hydrogen bonds : bond 0.02983 ( 164) hydrogen bonds : angle 4.34609 ( 492) Misc. bond : bond 0.00056 ( 20) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 68 time to evaluate : 0.133 Fit side-chains REVERT: B 10 GLN cc_start: 0.8273 (tt0) cc_final: 0.7918 (tt0) REVERT: B 11 ARG cc_start: 0.7847 (mtt180) cc_final: 0.6861 (mmp-170) REVERT: K 23 PHE cc_start: 0.7277 (m-80) cc_final: 0.7037 (m-80) REVERT: Q 11 ARG cc_start: 0.8200 (mtt180) cc_final: 0.7642 (ptt90) REVERT: S 22 ASN cc_start: 0.7278 (t0) cc_final: 0.6918 (t0) outliers start: 19 outliers final: 19 residues processed: 84 average time/residue: 0.0888 time to fit residues: 8.8470 Evaluate side-chains 81 residues out of total 380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 62 time to evaluate : 0.166 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 SER Chi-restraints excluded: chain B residue 34 SER Chi-restraints excluded: chain C residue 28 SER Chi-restraints excluded: chain D residue 28 SER Chi-restraints excluded: chain E residue 34 SER Chi-restraints excluded: chain F residue 34 SER Chi-restraints excluded: chain G residue 30 THR Chi-restraints excluded: chain H residue 28 SER Chi-restraints excluded: chain I residue 34 SER Chi-restraints excluded: chain J residue 34 SER Chi-restraints excluded: chain L residue 28 SER Chi-restraints excluded: chain L residue 30 THR Chi-restraints excluded: chain M residue 34 SER Chi-restraints excluded: chain N residue 34 SER Chi-restraints excluded: chain Q residue 34 SER Chi-restraints excluded: chain R residue 34 SER Chi-restraints excluded: chain S residue 30 THR Chi-restraints excluded: chain S residue 31 ASN Chi-restraints excluded: chain T residue 36 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 28 optimal weight: 10.0000 chunk 20 optimal weight: 8.9990 chunk 18 optimal weight: 7.9990 chunk 11 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 chunk 21 optimal weight: 6.9990 chunk 10 optimal weight: 20.0000 chunk 27 optimal weight: 3.9990 chunk 3 optimal weight: 0.5980 chunk 6 optimal weight: 2.9990 chunk 2 optimal weight: 0.7980 overall best weight: 3.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 31 ASN Q 10 GLN T 35 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3885 r_free = 0.3885 target = 0.125232 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.083415 restraints weight = 5173.069| |-----------------------------------------------------------------------------| r_work (start): 0.3331 rms_B_bonded: 2.46 r_work: 0.3196 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work: 0.3063 rms_B_bonded: 4.76 restraints_weight: 0.2500 r_work (final): 0.3063 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8453 moved from start: 0.3657 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.015 3460 Z= 0.193 Angle : 0.527 7.817 4660 Z= 0.276 Chirality : 0.041 0.124 550 Planarity : 0.002 0.009 610 Dihedral : 4.585 14.257 470 Min Nonbonded Distance : 2.619 Molprobity Statistics. All-atom Clashscore : 2.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.76 % Favored : 95.24 % Rotamer: Outliers : 5.26 % Allowed : 16.32 % Favored : 78.42 % 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 aren not related in a simple way. whole: -4.49 (0.22), residues: 420 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.42 (0.17), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG F 11 TYR 0.003 0.001 TYR B 37 PHE 0.012 0.002 PHE A 15 HIS 0.004 0.001 HIS M 18 Details of bonding type rmsd covalent geometry : bond 0.00423 ( 3440) covalent geometry : angle 0.52716 ( 4660) hydrogen bonds : bond 0.03633 ( 164) hydrogen bonds : angle 4.47156 ( 492) Misc. bond : bond 0.00068 ( 20) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 67 time to evaluate : 0.131 Fit side-chains REVERT: A 11 ARG cc_start: 0.7994 (mtt180) cc_final: 0.7016 (mmp-170) REVERT: B 10 GLN cc_start: 0.8342 (tt0) cc_final: 0.8020 (tt0) REVERT: B 11 ARG cc_start: 0.7915 (mtt180) cc_final: 0.6882 (mmp-170) REVERT: I 10 GLN cc_start: 0.7863 (tt0) cc_final: 0.7559 (tt0) REVERT: K 23 PHE cc_start: 0.7228 (m-80) cc_final: 0.6952 (m-80) REVERT: Q 11 ARG cc_start: 0.8299 (mtt180) cc_final: 0.7704 (ptt90) REVERT: S 22 ASN cc_start: 0.7359 (t0) cc_final: 0.7044 (t0) outliers start: 20 outliers final: 20 residues processed: 84 average time/residue: 0.0848 time to fit residues: 8.3755 Evaluate side-chains 84 residues out of total 380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 64 time to evaluate : 0.135 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 SER Chi-restraints excluded: chain B residue 34 SER Chi-restraints excluded: chain C residue 28 SER Chi-restraints excluded: chain D residue 28 SER Chi-restraints excluded: chain D residue 30 THR Chi-restraints excluded: chain E residue 34 SER Chi-restraints excluded: chain F residue 34 SER Chi-restraints excluded: chain G residue 30 THR Chi-restraints excluded: chain H residue 28 SER Chi-restraints excluded: chain I residue 34 SER Chi-restraints excluded: chain J residue 34 SER Chi-restraints excluded: chain L residue 28 SER Chi-restraints excluded: chain L residue 30 THR Chi-restraints excluded: chain M residue 34 SER Chi-restraints excluded: chain N residue 34 SER Chi-restraints excluded: chain O residue 32 VAL Chi-restraints excluded: chain P residue 36 THR Chi-restraints excluded: chain Q residue 34 SER Chi-restraints excluded: chain R residue 34 SER Chi-restraints excluded: chain S residue 31 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 18 optimal weight: 6.9990 chunk 24 optimal weight: 0.9980 chunk 20 optimal weight: 7.9990 chunk 28 optimal weight: 0.9980 chunk 5 optimal weight: 10.0000 chunk 22 optimal weight: 10.0000 chunk 7 optimal weight: 7.9990 chunk 15 optimal weight: 7.9990 chunk 1 optimal weight: 0.6980 chunk 3 optimal weight: 0.0980 chunk 25 optimal weight: 2.9990 overall best weight: 1.1582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 22 ASN D 35 ASN ** I 14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 21 ASN P 31 ASN ** Q 14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3939 r_free = 0.3939 target = 0.129339 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.087529 restraints weight = 5080.624| |-----------------------------------------------------------------------------| r_work (start): 0.3398 rms_B_bonded: 2.47 r_work: 0.3263 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work: 0.3133 rms_B_bonded: 4.78 restraints_weight: 0.2500 r_work (final): 0.3133 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8398 moved from start: 0.3853 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.014 3460 Z= 0.086 Angle : 0.471 7.504 4660 Z= 0.232 Chirality : 0.041 0.125 550 Planarity : 0.001 0.006 610 Dihedral : 4.042 12.499 470 Min Nonbonded Distance : 2.631 Molprobity Statistics. All-atom Clashscore : 1.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.05 % Favored : 95.95 % Rotamer: Outliers : 1.58 % Allowed : 19.47 % Favored : 78.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -4.55 (0.22), residues: 420 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.46 (0.17), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG R 11 TYR 0.003 0.001 TYR S 37 PHE 0.007 0.001 PHE T 23 HIS 0.002 0.001 HIS R 18 Details of bonding type rmsd covalent geometry : bond 0.00181 ( 3440) covalent geometry : angle 0.47079 ( 4660) hydrogen bonds : bond 0.02041 ( 164) hydrogen bonds : angle 4.03086 ( 492) Misc. bond : bond 0.00029 ( 20) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 74 time to evaluate : 0.145 Fit side-chains REVERT: I 10 GLN cc_start: 0.7878 (tt0) cc_final: 0.7560 (tt0) REVERT: K 23 PHE cc_start: 0.7145 (m-80) cc_final: 0.6874 (m-80) REVERT: Q 11 ARG cc_start: 0.8254 (mtt180) cc_final: 0.7744 (ptt90) REVERT: S 22 ASN cc_start: 0.7389 (t0) cc_final: 0.6996 (t0) REVERT: T 31 ASN cc_start: 0.8025 (t0) cc_final: 0.7684 (t0) outliers start: 6 outliers final: 6 residues processed: 80 average time/residue: 0.0798 time to fit residues: 7.5176 Evaluate side-chains 68 residues out of total 380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 62 time to evaluate : 0.106 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 30 THR Chi-restraints excluded: chain G residue 30 THR Chi-restraints excluded: chain L residue 28 SER Chi-restraints excluded: chain M residue 34 SER Chi-restraints excluded: chain O residue 32 VAL Chi-restraints excluded: chain R residue 34 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 18 optimal weight: 9.9990 chunk 6 optimal weight: 8.9990 chunk 15 optimal weight: 9.9990 chunk 2 optimal weight: 3.9990 chunk 8 optimal weight: 1.9990 chunk 7 optimal weight: 6.9990 chunk 24 optimal weight: 2.9990 chunk 22 optimal weight: 7.9990 chunk 25 optimal weight: 7.9990 chunk 11 optimal weight: 10.0000 chunk 27 optimal weight: 1.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 21 ASN C 22 ASN D 31 ASN L 21 ASN O 31 ASN P 21 ASN T 21 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3877 r_free = 0.3877 target = 0.124987 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.082997 restraints weight = 5587.353| |-----------------------------------------------------------------------------| r_work (start): 0.3316 rms_B_bonded: 2.48 r_work: 0.3176 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work: 0.3043 rms_B_bonded: 4.84 restraints_weight: 0.2500 r_work (final): 0.3043 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8466 moved from start: 0.3874 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.017 3460 Z= 0.222 Angle : 0.536 8.365 4660 Z= 0.282 Chirality : 0.042 0.123 550 Planarity : 0.002 0.009 610 Dihedral : 4.577 14.503 470 Min Nonbonded Distance : 2.617 Molprobity Statistics. All-atom Clashscore : 2.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.48 % Favored : 94.52 % Rotamer: Outliers : 5.53 % Allowed : 17.37 % Favored : 77.11 % 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 aren not related in a simple way. whole: -4.65 (0.22), residues: 420 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.54 (0.17), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG F 11 TYR 0.005 0.001 TYR B 37 PHE 0.012 0.002 PHE B 15 HIS 0.004 0.001 HIS R 18 Details of bonding type rmsd covalent geometry : bond 0.00491 ( 3440) covalent geometry : angle 0.53591 ( 4660) hydrogen bonds : bond 0.03797 ( 164) hydrogen bonds : angle 4.52738 ( 492) Misc. bond : bond 0.00101 ( 20) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 62 time to evaluate : 0.139 Fit side-chains REVERT: A 11 ARG cc_start: 0.8040 (mtt180) cc_final: 0.7662 (mtm180) REVERT: B 11 ARG cc_start: 0.7961 (mtt180) cc_final: 0.6945 (mmp-170) REVERT: K 23 PHE cc_start: 0.7282 (m-80) cc_final: 0.6991 (m-80) REVERT: Q 11 ARG cc_start: 0.8327 (mtt180) cc_final: 0.7708 (ptt90) REVERT: S 22 ASN cc_start: 0.7367 (t0) cc_final: 0.7054 (t0) REVERT: S 23 PHE cc_start: 0.6692 (m-10) cc_final: 0.6442 (m-10) outliers start: 21 outliers final: 19 residues processed: 80 average time/residue: 0.0843 time to fit residues: 7.8914 Evaluate side-chains 78 residues out of total 380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 59 time to evaluate : 0.147 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 SER Chi-restraints excluded: chain B residue 34 SER Chi-restraints excluded: chain C residue 28 SER Chi-restraints excluded: chain D residue 28 SER Chi-restraints excluded: chain D residue 30 THR Chi-restraints excluded: chain D residue 36 THR Chi-restraints excluded: chain E residue 34 SER Chi-restraints excluded: chain F residue 34 SER Chi-restraints excluded: chain G residue 30 THR Chi-restraints excluded: chain H residue 28 SER Chi-restraints excluded: chain I residue 34 SER Chi-restraints excluded: chain J residue 34 SER Chi-restraints excluded: chain L residue 28 SER Chi-restraints excluded: chain L residue 30 THR Chi-restraints excluded: chain M residue 34 SER Chi-restraints excluded: chain N residue 34 SER Chi-restraints excluded: chain O residue 32 VAL Chi-restraints excluded: chain Q residue 34 SER Chi-restraints excluded: chain R residue 34 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 28 optimal weight: 9.9990 chunk 10 optimal weight: 10.0000 chunk 1 optimal weight: 0.5980 chunk 11 optimal weight: 4.9990 chunk 3 optimal weight: 1.9990 chunk 17 optimal weight: 5.9990 chunk 6 optimal weight: 1.9990 chunk 15 optimal weight: 6.9990 chunk 0 optimal weight: 0.7980 chunk 4 optimal weight: 0.0050 chunk 9 optimal weight: 0.0870 overall best weight: 0.6974 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 35 ASN P 31 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3943 r_free = 0.3943 target = 0.130444 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.088886 restraints weight = 5049.567| |-----------------------------------------------------------------------------| r_work (start): 0.3420 rms_B_bonded: 2.43 r_work: 0.3281 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work: 0.3152 rms_B_bonded: 4.83 restraints_weight: 0.2500 r_work (final): 0.3152 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8365 moved from start: 0.4060 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.001 0.023 3460 Z= 0.071 Angle : 0.494 8.989 4660 Z= 0.236 Chirality : 0.042 0.123 550 Planarity : 0.001 0.005 610 Dihedral : 3.942 13.700 470 Min Nonbonded Distance : 2.634 Molprobity Statistics. All-atom Clashscore : 1.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 1.84 % Allowed : 21.58 % Favored : 76.58 % 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 aren not related in a simple way. whole: -4.66 (0.22), residues: 420 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.55 (0.17), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG R 11 TYR 0.004 0.001 TYR C 37 PHE 0.010 0.001 PHE T 23 HIS 0.002 0.000 HIS M 18 Details of bonding type rmsd covalent geometry : bond 0.00145 ( 3440) covalent geometry : angle 0.49414 ( 4660) hydrogen bonds : bond 0.01583 ( 164) hydrogen bonds : angle 3.90895 ( 492) Misc. bond : bond 0.00022 ( 20) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 71 time to evaluate : 0.137 Fit side-chains REVERT: K 23 PHE cc_start: 0.7113 (m-80) cc_final: 0.6778 (m-80) REVERT: Q 11 ARG cc_start: 0.8247 (mtt180) cc_final: 0.7767 (ptt90) REVERT: S 23 PHE cc_start: 0.6689 (m-10) cc_final: 0.6441 (m-10) outliers start: 7 outliers final: 7 residues processed: 77 average time/residue: 0.0717 time to fit residues: 6.5921 Evaluate side-chains 74 residues out of total 380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 67 time to evaluate : 0.127 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 30 THR Chi-restraints excluded: chain F residue 34 SER Chi-restraints excluded: chain I residue 34 SER Chi-restraints excluded: chain J residue 34 SER Chi-restraints excluded: chain L residue 28 SER Chi-restraints excluded: chain P residue 30 THR Chi-restraints excluded: chain Q residue 34 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 20 optimal weight: 7.9990 chunk 12 optimal weight: 9.9990 chunk 21 optimal weight: 6.9990 chunk 24 optimal weight: 4.9990 chunk 6 optimal weight: 1.9990 chunk 26 optimal weight: 0.9980 chunk 19 optimal weight: 8.9990 chunk 13 optimal weight: 3.9990 chunk 1 optimal weight: 0.9990 chunk 7 optimal weight: 0.6980 chunk 5 optimal weight: 9.9990 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 22 ASN C 35 ASN D 31 ASN D 35 ASN P 22 ASN P 31 ASN Q 14 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3910 r_free = 0.3910 target = 0.127560 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3337 r_free = 0.3337 target = 0.085537 restraints weight = 5358.696| |-----------------------------------------------------------------------------| r_work (start): 0.3363 rms_B_bonded: 2.47 r_work: 0.3222 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work: 0.3092 rms_B_bonded: 4.83 restraints_weight: 0.2500 r_work (final): 0.3092 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8407 moved from start: 0.3996 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 3460 Z= 0.117 Angle : 0.505 8.223 4660 Z= 0.249 Chirality : 0.042 0.126 550 Planarity : 0.001 0.005 610 Dihedral : 4.054 14.597 470 Min Nonbonded Distance : 2.614 Molprobity Statistics. All-atom Clashscore : 1.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.76 % Favored : 95.24 % Rotamer: Outliers : 3.16 % Allowed : 21.05 % Favored : 75.79 % 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 aren not related in a simple way. whole: -4.67 (0.23), residues: 420 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.55 (0.18), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG R 11 TYR 0.003 0.001 TYR B 37 PHE 0.008 0.001 PHE F 15 HIS 0.003 0.001 HIS R 18 Details of bonding type rmsd covalent geometry : bond 0.00254 ( 3440) covalent geometry : angle 0.50542 ( 4660) hydrogen bonds : bond 0.02572 ( 164) hydrogen bonds : angle 4.10503 ( 492) Misc. bond : bond 0.00049 ( 20) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 64 time to evaluate : 0.117 Fit side-chains REVERT: B 11 ARG cc_start: 0.7806 (mtt180) cc_final: 0.6768 (mmp-170) REVERT: H 23 PHE cc_start: 0.6879 (m-80) cc_final: 0.6586 (m-80) REVERT: K 23 PHE cc_start: 0.7194 (m-80) cc_final: 0.6864 (m-80) REVERT: Q 11 ARG cc_start: 0.8300 (mtt180) cc_final: 0.7731 (ptt90) REVERT: S 23 PHE cc_start: 0.6746 (m-10) cc_final: 0.6491 (m-80) outliers start: 12 outliers final: 12 residues processed: 74 average time/residue: 0.0808 time to fit residues: 7.0594 Evaluate side-chains 73 residues out of total 380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 61 time to evaluate : 0.080 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 SER Chi-restraints excluded: chain C residue 28 SER Chi-restraints excluded: chain D residue 30 THR Chi-restraints excluded: chain E residue 34 SER Chi-restraints excluded: chain F residue 34 SER Chi-restraints excluded: chain G residue 30 THR Chi-restraints excluded: chain I residue 34 SER Chi-restraints excluded: chain J residue 34 SER Chi-restraints excluded: chain L residue 28 SER Chi-restraints excluded: chain N residue 34 SER Chi-restraints excluded: chain P residue 30 THR Chi-restraints excluded: chain Q residue 34 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 6 optimal weight: 7.9990 chunk 11 optimal weight: 10.0000 chunk 14 optimal weight: 5.9990 chunk 5 optimal weight: 5.9990 chunk 25 optimal weight: 0.3980 chunk 26 optimal weight: 1.9990 chunk 20 optimal weight: 4.9990 chunk 19 optimal weight: 0.5980 chunk 15 optimal weight: 7.9990 chunk 29 optimal weight: 6.9990 chunk 17 optimal weight: 6.9990 overall best weight: 2.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 22 ASN D 31 ASN D 35 ASN P 22 ASN P 31 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3878 r_free = 0.3878 target = 0.125532 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.082857 restraints weight = 5296.162| |-----------------------------------------------------------------------------| r_work (start): 0.3326 rms_B_bonded: 2.50 r_work: 0.3181 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work: 0.3051 rms_B_bonded: 4.87 restraints_weight: 0.2500 r_work (final): 0.3051 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8450 moved from start: 0.3970 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.020 3460 Z= 0.174 Angle : 0.532 8.075 4660 Z= 0.273 Chirality : 0.042 0.125 550 Planarity : 0.002 0.009 610 Dihedral : 4.434 16.409 470 Min Nonbonded Distance : 2.613 Molprobity Statistics. All-atom Clashscore : 1.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.00 % Favored : 95.00 % Rotamer: Outliers : 3.42 % Allowed : 21.05 % Favored : 75.53 % 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 aren not related in a simple way. whole: -4.74 (0.23), residues: 420 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.61 (0.17), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG N 11 TYR 0.004 0.001 TYR B 37 PHE 0.012 0.002 PHE L 23 HIS 0.004 0.001 HIS R 18 Details of bonding type rmsd covalent geometry : bond 0.00382 ( 3440) covalent geometry : angle 0.53182 ( 4660) hydrogen bonds : bond 0.03372 ( 164) hydrogen bonds : angle 4.37218 ( 492) Misc. bond : bond 0.00079 ( 20) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 70 residues out of total 380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 57 time to evaluate : 0.098 Fit side-chains REVERT: A 11 ARG cc_start: 0.7996 (mtt180) cc_final: 0.6996 (mmp-170) REVERT: B 11 ARG cc_start: 0.7943 (mtt180) cc_final: 0.6923 (mmp-170) REVERT: K 23 PHE cc_start: 0.7270 (m-80) cc_final: 0.6928 (m-80) REVERT: Q 11 ARG cc_start: 0.8367 (mtt180) cc_final: 0.7730 (ptt90) REVERT: S 23 PHE cc_start: 0.6999 (m-10) cc_final: 0.6747 (m-80) outliers start: 13 outliers final: 13 residues processed: 68 average time/residue: 0.1002 time to fit residues: 7.8391 Evaluate side-chains 70 residues out of total 380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 57 time to evaluate : 0.125 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 SER Chi-restraints excluded: chain B residue 34 SER Chi-restraints excluded: chain C residue 28 SER Chi-restraints excluded: chain D residue 30 THR Chi-restraints excluded: chain E residue 34 SER Chi-restraints excluded: chain F residue 34 SER Chi-restraints excluded: chain G residue 30 THR Chi-restraints excluded: chain I residue 34 SER Chi-restraints excluded: chain J residue 34 SER Chi-restraints excluded: chain L residue 28 SER Chi-restraints excluded: chain N residue 34 SER Chi-restraints excluded: chain P residue 30 THR Chi-restraints excluded: chain Q residue 34 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 28 optimal weight: 10.0000 chunk 6 optimal weight: 8.9990 chunk 11 optimal weight: 9.9990 chunk 20 optimal weight: 8.9990 chunk 27 optimal weight: 0.0870 chunk 16 optimal weight: 9.9990 chunk 1 optimal weight: 1.9990 chunk 4 optimal weight: 10.0000 chunk 9 optimal weight: 7.9990 chunk 18 optimal weight: 1.9990 chunk 5 optimal weight: 5.9990 overall best weight: 3.6166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 22 ASN D 35 ASN P 22 ASN P 31 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3857 r_free = 0.3857 target = 0.123956 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.082311 restraints weight = 5550.877| |-----------------------------------------------------------------------------| r_work (start): 0.3314 rms_B_bonded: 2.48 r_work: 0.3166 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work: 0.3037 rms_B_bonded: 4.87 restraints_weight: 0.2500 r_work (final): 0.3037 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8463 moved from start: 0.4062 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.018 3460 Z= 0.221 Angle : 0.557 7.974 4660 Z= 0.290 Chirality : 0.043 0.124 550 Planarity : 0.002 0.008 610 Dihedral : 4.602 17.753 470 Min Nonbonded Distance : 2.321 Molprobity Statistics. All-atom Clashscore : 2.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.48 % Favored : 94.52 % Rotamer: Outliers : 3.95 % Allowed : 20.26 % Favored : 75.79 % 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 aren not related in a simple way. whole: -4.82 (0.23), residues: 420 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.67 (0.17), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG F 11 TYR 0.006 0.001 TYR B 37 PHE 0.014 0.002 PHE G 23 HIS 0.004 0.001 HIS M 18 Details of bonding type rmsd covalent geometry : bond 0.00488 ( 3440) covalent geometry : angle 0.55704 ( 4660) hydrogen bonds : bond 0.03786 ( 164) hydrogen bonds : angle 4.48032 ( 492) Misc. bond : bond 0.00109 ( 20) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1104.91 seconds wall clock time: 19 minutes 38.55 seconds (1178.55 seconds total)