Starting phenix.real_space_refine on Fri May 9 18:33:34 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8az6_15755/05_2025/8az6_15755.cif Found real_map, /net/cci-nas-00/data/ceres_data/8az6_15755/05_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8az6_15755/05_2025/8az6_15755.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8az6_15755/05_2025/8az6_15755.map" model { file = "/net/cci-nas-00/data/ceres_data/8az6_15755/05_2025/8az6_15755.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8az6_15755/05_2025/8az6_15755.cif" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 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): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/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: 2.56, per 1000 atoms: 0.75 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: 0.87 Conformation dependent library (CDL) restraints added in 406.9 milliseconds 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: 0.55 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: 0.86 Time building geometry restraints manager: 1.03 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: 0.04 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: 1.120 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: 0.140 Check model and map are aligned: 0.020 Set scattering table: 0.040 Process input model: 12.860 Find NCS groups from input model: 0.080 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.610 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.890 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.04 (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 HIS 0.004 0.002 HIS N 18 PHE 0.004 0.001 PHE L 23 TYR 0.005 0.001 TYR M 37 ARG 0.002 0.000 ARG B 11 Details of bonding type rmsd hydrogen bonds : bond 0.21642 ( 164) hydrogen bonds : angle 6.33773 ( 492) covalent geometry : bond 0.00374 ( 3440) covalent geometry : angle 0.42987 ( 4660) 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 : 0.368 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: 0.1718 time to fit residues: 19.7109 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 : 0.519 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 25 optimal weight: 5.9990 chunk 22 optimal weight: 8.9990 chunk 12 optimal weight: 2.9990 chunk 7 optimal weight: 8.9990 chunk 15 optimal weight: 10.0000 chunk 23 optimal weight: 20.0000 chunk 9 optimal weight: 7.9990 chunk 14 optimal weight: 0.9980 chunk 17 optimal weight: 5.9990 chunk 27 optimal weight: 4.9990 chunk 8 optimal weight: 0.8980 overall best weight: 3.1786 ------------------------------------------------------------------------------- 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 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: 18 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3889 r_free = 0.3889 target = 0.124797 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.084941 restraints weight = 4280.870| |-----------------------------------------------------------------------------| r_work (start): 0.3352 rms_B_bonded: 2.20 r_work: 0.3229 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.3111 rms_B_bonded: 4.38 restraints_weight: 0.2500 r_work (final): 0.3111 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8391 moved from start: 0.2766 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.022 3460 Z= 0.204 Angle : 0.546 7.360 4660 Z= 0.284 Chirality : 0.042 0.131 550 Planarity : 0.002 0.008 610 Dihedral : 4.656 15.338 470 Min Nonbonded Distance : 2.618 Molprobity Statistics. All-atom Clashscore : 4.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.76 % Favored : 95.24 % Rotamer: Outliers : 5.53 % Allowed : 7.89 % Favored : 86.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.99 (0.21), residues: 420 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.03 (0.16), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS Q 18 PHE 0.014 0.002 PHE F 15 TYR 0.003 0.001 TYR L 37 ARG 0.001 0.000 ARG B 11 Details of bonding type rmsd hydrogen bonds : bond 0.04004 ( 164) hydrogen bonds : angle 4.60082 ( 492) covalent geometry : bond 0.00457 ( 3440) covalent geometry : angle 0.54570 ( 4660) Misc. bond : bond 0.00071 ( 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 108 residues out of total 380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 87 time to evaluate : 0.359 Fit side-chains REVERT: A 11 ARG cc_start: 0.7995 (mtt180) cc_final: 0.7008 (mmp-170) REVERT: B 10 GLN cc_start: 0.8187 (tt0) cc_final: 0.7741 (tt0) REVERT: B 11 ARG cc_start: 0.7868 (mtt180) cc_final: 0.6836 (mmp-170) REVERT: D 35 ASN cc_start: 0.8670 (t0) cc_final: 0.8452 (t0) REVERT: O 23 PHE cc_start: 0.6594 (m-80) cc_final: 0.6289 (m-80) REVERT: Q 11 ARG cc_start: 0.8123 (mtt180) cc_final: 0.7560 (ptt90) REVERT: T 31 ASN cc_start: 0.8533 (t0) cc_final: 0.8188 (t0) outliers start: 21 outliers final: 15 residues processed: 102 average time/residue: 0.1664 time to fit residues: 20.2006 Evaluate side-chains 85 residues out of total 380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 70 time to evaluate : 0.352 ------------------------------------------------------------------------------- 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 16 optimal weight: 20.0000 chunk 23 optimal weight: 10.0000 chunk 26 optimal weight: 0.9990 chunk 18 optimal weight: 10.0000 chunk 19 optimal weight: 7.9990 chunk 17 optimal weight: 9.9990 chunk 0 optimal weight: 8.9990 chunk 12 optimal weight: 2.9990 chunk 2 optimal weight: 2.9990 chunk 28 optimal weight: 8.9990 chunk 24 optimal weight: 5.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 21 ASN G 21 ASN G 35 ASN K 35 ASN O 21 ASN O 35 ASN ** P 22 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 10 GLN T 35 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3886 r_free = 0.3886 target = 0.124886 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.085152 restraints weight = 4109.402| |-----------------------------------------------------------------------------| r_work (start): 0.3351 rms_B_bonded: 2.23 r_work: 0.3221 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.3094 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.3094 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8438 moved from start: 0.3417 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.020 3460 Z= 0.258 Angle : 0.585 7.128 4660 Z= 0.306 Chirality : 0.042 0.126 550 Planarity : 0.002 0.010 610 Dihedral : 4.921 16.354 470 Min Nonbonded Distance : 2.561 Molprobity Statistics. All-atom Clashscore : 4.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.52 % Favored : 95.48 % Rotamer: Outliers : 5.79 % Allowed : 13.95 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.30 (0.21), residues: 420 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.27 (0.16), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.002 HIS Q 18 PHE 0.017 0.002 PHE P 23 TYR 0.005 0.001 TYR B 37 ARG 0.001 0.000 ARG B 11 Details of bonding type rmsd hydrogen bonds : bond 0.04373 ( 164) hydrogen bonds : angle 4.69207 ( 492) covalent geometry : bond 0.00573 ( 3440) covalent geometry : angle 0.58510 ( 4660) Misc. bond : bond 0.00093 ( 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 96 residues out of total 380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 74 time to evaluate : 0.384 Fit side-chains REVERT: A 11 ARG cc_start: 0.7911 (mtt180) cc_final: 0.7548 (mtm180) REVERT: B 10 GLN cc_start: 0.8257 (tt0) cc_final: 0.7881 (tt0) REVERT: B 11 ARG cc_start: 0.7848 (mtt180) cc_final: 0.6833 (mmp-170) REVERT: I 10 GLN cc_start: 0.7776 (tt0) cc_final: 0.7399 (tt0) REVERT: Q 11 ARG cc_start: 0.8239 (mtt180) cc_final: 0.7617 (ptt90) outliers start: 22 outliers final: 21 residues processed: 90 average time/residue: 0.1863 time to fit residues: 20.0198 Evaluate side-chains 91 residues out of total 380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 70 time to evaluate : 0.351 ------------------------------------------------------------------------------- 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 21 ASN 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 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 O residue 35 ASN 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 17 optimal weight: 20.0000 chunk 28 optimal weight: 10.0000 chunk 21 optimal weight: 6.9990 chunk 19 optimal weight: 7.9990 chunk 8 optimal weight: 7.9990 chunk 26 optimal weight: 0.7980 chunk 0 optimal weight: 8.9990 chunk 25 optimal weight: 0.9990 chunk 2 optimal weight: 1.9990 chunk 5 optimal weight: 0.0570 chunk 16 optimal weight: 10.0000 overall best weight: 2.1704 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 31 ASN D 35 ASN L 35 ASN P 31 ASN P 35 ASN S 31 ASN S 35 ASN T 21 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3916 r_free = 0.3916 target = 0.127039 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.087146 restraints weight = 4219.857| |-----------------------------------------------------------------------------| r_work (start): 0.3385 rms_B_bonded: 2.25 r_work: 0.3256 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.3129 rms_B_bonded: 4.39 restraints_weight: 0.2500 r_work (final): 0.3129 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8406 moved from start: 0.3559 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.013 3460 Z= 0.142 Angle : 0.509 6.539 4660 Z= 0.261 Chirality : 0.042 0.128 550 Planarity : 0.002 0.007 610 Dihedral : 4.562 15.045 470 Min Nonbonded Distance : 2.622 Molprobity Statistics. All-atom Clashscore : 3.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.76 % Favored : 95.24 % Rotamer: Outliers : 4.21 % Allowed : 17.37 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.41 (0.21), residues: 420 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.36 (0.16), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS R 18 PHE 0.011 0.002 PHE T 23 TYR 0.003 0.001 TYR S 37 ARG 0.001 0.000 ARG F 11 Details of bonding type rmsd hydrogen bonds : bond 0.03053 ( 164) hydrogen bonds : angle 4.38162 ( 492) covalent geometry : bond 0.00308 ( 3440) covalent geometry : angle 0.50919 ( 4660) Misc. bond : bond 0.00057 ( 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 86 residues out of total 380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 70 time to evaluate : 0.431 Fit side-chains REVERT: B 10 GLN cc_start: 0.8243 (tt0) cc_final: 0.7893 (tt0) REVERT: B 11 ARG cc_start: 0.7812 (mtt180) cc_final: 0.6828 (mmp-170) REVERT: D 35 ASN cc_start: 0.8637 (t0) cc_final: 0.8329 (t0) REVERT: Q 11 ARG cc_start: 0.8169 (mtt180) cc_final: 0.7673 (ptt90) outliers start: 16 outliers final: 16 residues processed: 83 average time/residue: 0.1884 time to fit residues: 18.7911 Evaluate side-chains 78 residues out of total 380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 62 time to evaluate : 0.410 ------------------------------------------------------------------------------- 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 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 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 Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 2 optimal weight: 0.8980 chunk 12 optimal weight: 8.9990 chunk 14 optimal weight: 10.0000 chunk 11 optimal weight: 10.0000 chunk 21 optimal weight: 7.9990 chunk 8 optimal weight: 1.9990 chunk 3 optimal weight: 0.9990 chunk 4 optimal weight: 10.0000 chunk 9 optimal weight: 2.9990 chunk 17 optimal weight: 5.9990 chunk 20 optimal weight: 5.9990 overall best weight: 2.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** T 22 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 35 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3912 r_free = 0.3912 target = 0.126760 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.086116 restraints weight = 4737.957| |-----------------------------------------------------------------------------| r_work (start): 0.3371 rms_B_bonded: 2.36 r_work: 0.3237 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.3103 rms_B_bonded: 4.60 restraints_weight: 0.2500 r_work (final): 0.3103 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8428 moved from start: 0.3641 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= 0.164 Angle : 0.503 5.941 4660 Z= 0.265 Chirality : 0.041 0.123 550 Planarity : 0.002 0.006 610 Dihedral : 4.471 14.042 470 Min Nonbonded Distance : 2.622 Molprobity Statistics. All-atom Clashscore : 2.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.76 % Favored : 95.24 % Rotamer: Outliers : 5.00 % Allowed : 16.58 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.53 (0.22), residues: 420 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.44 (0.17), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS M 18 PHE 0.010 0.002 PHE A 15 TYR 0.004 0.001 TYR I 37 ARG 0.001 0.000 ARG F 11 Details of bonding type rmsd hydrogen bonds : bond 0.03275 ( 164) hydrogen bonds : angle 4.35532 ( 492) covalent geometry : bond 0.00359 ( 3440) covalent geometry : angle 0.50288 ( 4660) Misc. bond : bond 0.00060 ( 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 82 residues out of total 380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 63 time to evaluate : 0.344 Fit side-chains REVERT: A 11 ARG cc_start: 0.7892 (mtt180) cc_final: 0.6905 (mmp-170) REVERT: B 10 GLN cc_start: 0.8321 (tt0) cc_final: 0.7967 (tt0) REVERT: B 11 ARG cc_start: 0.7807 (mtt180) cc_final: 0.6834 (mmp-170) REVERT: Q 11 ARG cc_start: 0.8242 (mtt180) cc_final: 0.7679 (ptt90) outliers start: 19 outliers final: 18 residues processed: 80 average time/residue: 0.1870 time to fit residues: 17.5728 Evaluate side-chains 79 residues out of total 380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 61 time to evaluate : 0.388 ------------------------------------------------------------------------------- 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 O residue 32 VAL 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 24 optimal weight: 4.9990 chunk 4 optimal weight: 10.0000 chunk 14 optimal weight: 9.9990 chunk 17 optimal weight: 6.9990 chunk 22 optimal weight: 9.9990 chunk 7 optimal weight: 7.9990 chunk 8 optimal weight: 0.9990 chunk 25 optimal weight: 5.9990 chunk 12 optimal weight: 3.9990 chunk 5 optimal weight: 10.0000 chunk 27 optimal weight: 3.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- 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 G 21 ASN O 21 ASN P 31 ASN T 21 ASN ** T 22 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3878 r_free = 0.3878 target = 0.124692 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.084207 restraints weight = 5007.933| |-----------------------------------------------------------------------------| r_work (start): 0.3334 rms_B_bonded: 2.34 r_work: 0.3203 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work: 0.3075 rms_B_bonded: 4.64 restraints_weight: 0.2500 r_work (final): 0.3075 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8462 moved from start: 0.3862 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.019 3460 Z= 0.246 Angle : 0.549 5.938 4660 Z= 0.295 Chirality : 0.042 0.123 550 Planarity : 0.002 0.008 610 Dihedral : 4.761 14.187 470 Min Nonbonded Distance : 2.602 Molprobity Statistics. All-atom Clashscore : 3.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.24 % Favored : 94.76 % Rotamer: Outliers : 6.05 % Allowed : 15.26 % Favored : 78.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.69 (0.22), residues: 420 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.57 (0.17), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.002 HIS R 18 PHE 0.013 0.002 PHE B 15 TYR 0.006 0.001 TYR I 37 ARG 0.001 0.000 ARG E 11 Details of bonding type rmsd hydrogen bonds : bond 0.04094 ( 164) hydrogen bonds : angle 4.58734 ( 492) covalent geometry : bond 0.00545 ( 3440) covalent geometry : angle 0.54875 ( 4660) Misc. bond : bond 0.00112 ( 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 79 residues out of total 380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 56 time to evaluate : 0.362 Fit side-chains REVERT: A 11 ARG cc_start: 0.7962 (mtt180) cc_final: 0.6974 (mmp-170) REVERT: B 10 GLN cc_start: 0.8297 (tt0) cc_final: 0.7970 (tt0) REVERT: B 11 ARG cc_start: 0.7916 (mtt180) cc_final: 0.6925 (mmp-170) REVERT: K 23 PHE cc_start: 0.7344 (m-80) cc_final: 0.7073 (m-80) REVERT: Q 11 ARG cc_start: 0.8329 (mtt180) cc_final: 0.7652 (ptt90) outliers start: 23 outliers final: 22 residues processed: 74 average time/residue: 0.2038 time to fit residues: 17.5802 Evaluate side-chains 76 residues out of total 380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 54 time to evaluate : 0.367 ------------------------------------------------------------------------------- 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 30 THR Chi-restraints excluded: chain D residue 28 SER 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 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 O residue 32 VAL Chi-restraints excluded: chain P residue 30 THR Chi-restraints excluded: chain P residue 36 THR Chi-restraints excluded: chain Q residue 34 SER 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 10 optimal weight: 9.9990 chunk 15 optimal weight: 6.9990 chunk 11 optimal weight: 0.9990 chunk 19 optimal weight: 4.9990 chunk 9 optimal weight: 1.9990 chunk 20 optimal weight: 3.9990 chunk 12 optimal weight: 7.9990 chunk 2 optimal weight: 0.9990 chunk 7 optimal weight: 4.9990 chunk 21 optimal weight: 0.9980 chunk 27 optimal weight: 3.9990 overall best weight: 1.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 22 ASN R 14 ASN ** T 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 = 0.3921 r_free = 0.3921 target = 0.128034 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.087325 restraints weight = 5062.700| |-----------------------------------------------------------------------------| r_work (start): 0.3389 rms_B_bonded: 2.38 r_work: 0.3258 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work: 0.3129 rms_B_bonded: 4.72 restraints_weight: 0.2500 r_work (final): 0.3129 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8416 moved from start: 0.3936 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.015 3460 Z= 0.119 Angle : 0.482 6.404 4660 Z= 0.246 Chirality : 0.042 0.126 550 Planarity : 0.001 0.006 610 Dihedral : 4.223 12.248 470 Min Nonbonded Distance : 2.574 Molprobity Statistics. All-atom Clashscore : 1.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.29 % Favored : 95.71 % Rotamer: Outliers : 3.95 % Allowed : 16.84 % Favored : 79.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.78 (0.22), residues: 420 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.63 (0.17), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS M 18 PHE 0.008 0.001 PHE F 15 TYR 0.003 0.001 TYR N 37 ARG 0.000 0.000 ARG R 11 Details of bonding type rmsd hydrogen bonds : bond 0.02590 ( 164) hydrogen bonds : angle 4.13197 ( 492) covalent geometry : bond 0.00256 ( 3440) covalent geometry : angle 0.48197 ( 4660) Misc. bond : bond 0.00053 ( 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 78 residues out of total 380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 63 time to evaluate : 0.388 Fit side-chains REVERT: B 10 GLN cc_start: 0.8289 (tt0) cc_final: 0.7980 (tt0) REVERT: B 11 ARG cc_start: 0.7809 (mtt180) cc_final: 0.6867 (mmp-170) REVERT: Q 11 ARG cc_start: 0.8309 (mtt180) cc_final: 0.7695 (ptt90) outliers start: 15 outliers final: 15 residues processed: 77 average time/residue: 0.1918 time to fit residues: 17.5636 Evaluate side-chains 69 residues out of total 380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 54 time to evaluate : 0.386 ------------------------------------------------------------------------------- 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 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 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 10 optimal weight: 20.0000 chunk 27 optimal weight: 3.9990 chunk 16 optimal weight: 5.9990 chunk 7 optimal weight: 7.9990 chunk 22 optimal weight: 6.9990 chunk 1 optimal weight: 1.9990 chunk 9 optimal weight: 10.0000 chunk 18 optimal weight: 3.9990 chunk 17 optimal weight: 20.0000 chunk 23 optimal weight: 6.9990 chunk 3 optimal weight: 0.8980 overall best weight: 3.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 31 ASN O 21 ASN P 31 ASN Q 18 HIS ** T 22 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 = 0.3895 r_free = 0.3895 target = 0.126024 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.084679 restraints weight = 5288.799| |-----------------------------------------------------------------------------| r_work (start): 0.3342 rms_B_bonded: 2.41 r_work: 0.3206 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work: 0.3074 rms_B_bonded: 4.73 restraints_weight: 0.2500 r_work (final): 0.3074 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8455 moved from start: 0.3972 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= 0.207 Angle : 0.537 8.198 4660 Z= 0.283 Chirality : 0.042 0.124 550 Planarity : 0.002 0.008 610 Dihedral : 4.541 13.161 470 Min Nonbonded Distance : 2.351 Molprobity Statistics. All-atom Clashscore : 2.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.24 % Favored : 94.76 % Rotamer: Outliers : 4.74 % Allowed : 17.11 % Favored : 78.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.81 (0.22), residues: 420 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.66 (0.17), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS R 18 PHE 0.012 0.002 PHE A 15 TYR 0.005 0.001 TYR I 37 ARG 0.000 0.000 ARG R 11 Details of bonding type rmsd hydrogen bonds : bond 0.03725 ( 164) hydrogen bonds : angle 4.46069 ( 492) covalent geometry : bond 0.00457 ( 3440) covalent geometry : angle 0.53684 ( 4660) Misc. bond : bond 0.00098 ( 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 73 residues out of total 380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 55 time to evaluate : 0.392 Fit side-chains REVERT: A 11 ARG cc_start: 0.7963 (mtt180) cc_final: 0.6981 (mmp-170) REVERT: B 10 GLN cc_start: 0.8333 (tt0) cc_final: 0.8008 (tt0) REVERT: B 11 ARG cc_start: 0.7871 (mtt180) cc_final: 0.6911 (mmp-170) REVERT: Q 11 ARG cc_start: 0.8348 (mtt180) cc_final: 0.7700 (ptt90) outliers start: 18 outliers final: 18 residues processed: 71 average time/residue: 0.2108 time to fit residues: 17.4416 Evaluate side-chains 71 residues out of total 380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 53 time to evaluate : 0.355 ------------------------------------------------------------------------------- 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 P residue 30 THR Chi-restraints excluded: chain P residue 36 THR Chi-restraints excluded: chain Q residue 34 SER Chi-restraints excluded: chain R residue 34 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 25 optimal weight: 7.9990 chunk 26 optimal weight: 7.9990 chunk 7 optimal weight: 4.9990 chunk 0 optimal weight: 8.9990 chunk 18 optimal weight: 1.9990 chunk 14 optimal weight: 6.9990 chunk 12 optimal weight: 1.9990 chunk 27 optimal weight: 7.9990 chunk 24 optimal weight: 0.9980 chunk 11 optimal weight: 9.9990 chunk 1 optimal weight: 0.7980 overall best weight: 2.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** T 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 = 0.3909 r_free = 0.3909 target = 0.127931 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.086403 restraints weight = 5221.153| |-----------------------------------------------------------------------------| r_work (start): 0.3368 rms_B_bonded: 2.43 r_work: 0.3229 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work: 0.3101 rms_B_bonded: 4.74 restraints_weight: 0.2500 r_work (final): 0.3101 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8429 moved from start: 0.4063 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.018 3460 Z= 0.137 Angle : 0.502 7.578 4660 Z= 0.257 Chirality : 0.042 0.126 550 Planarity : 0.001 0.006 610 Dihedral : 4.275 12.740 470 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 1.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.52 % Favored : 95.48 % Rotamer: Outliers : 4.47 % Allowed : 17.63 % Favored : 77.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.87 (0.23), residues: 420 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.71 (0.17), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS R 18 PHE 0.009 0.001 PHE F 15 TYR 0.003 0.001 TYR N 37 ARG 0.000 0.000 ARG R 11 Details of bonding type rmsd hydrogen bonds : bond 0.02867 ( 164) hydrogen bonds : angle 4.19999 ( 492) covalent geometry : bond 0.00298 ( 3440) covalent geometry : angle 0.50170 ( 4660) Misc. bond : bond 0.00069 ( 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 77 residues out of total 380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 60 time to evaluate : 0.420 Fit side-chains REVERT: B 10 GLN cc_start: 0.8315 (tt0) cc_final: 0.8010 (tt0) REVERT: B 11 ARG cc_start: 0.7809 (mtt180) cc_final: 0.6868 (mmp-170) REVERT: Q 11 ARG cc_start: 0.8351 (mtt180) cc_final: 0.7752 (ptt90) outliers start: 17 outliers final: 17 residues processed: 75 average time/residue: 0.1982 time to fit residues: 17.5638 Evaluate side-chains 75 residues out of total 380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 58 time to evaluate : 0.399 ------------------------------------------------------------------------------- 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 30 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 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 11 optimal weight: 9.9990 chunk 10 optimal weight: 20.0000 chunk 16 optimal weight: 6.9990 chunk 25 optimal weight: 5.9990 chunk 29 optimal weight: 0.0670 chunk 0 optimal weight: 8.9990 chunk 23 optimal weight: 9.9990 chunk 14 optimal weight: 1.9990 chunk 8 optimal weight: 3.9990 chunk 20 optimal weight: 1.9990 chunk 4 optimal weight: 2.9990 overall best weight: 2.2126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 35 ASN P 31 ASN S 35 ASN ** T 22 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3912 r_free = 0.3912 target = 0.127980 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.086607 restraints weight = 5094.585| |-----------------------------------------------------------------------------| r_work (start): 0.3369 rms_B_bonded: 2.41 r_work: 0.3233 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work: 0.3103 rms_B_bonded: 4.74 restraints_weight: 0.2500 r_work (final): 0.3103 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8433 moved from start: 0.4100 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.018 3460 Z= 0.141 Angle : 0.513 7.863 4660 Z= 0.260 Chirality : 0.042 0.125 550 Planarity : 0.001 0.006 610 Dihedral : 4.253 13.475 470 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 2.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.76 % Favored : 95.24 % Rotamer: Outliers : 4.21 % Allowed : 18.42 % Favored : 77.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.87 (0.23), residues: 420 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.70 (0.17), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS R 18 PHE 0.011 0.002 PHE H 23 TYR 0.003 0.001 TYR N 37 ARG 0.001 0.000 ARG F 11 Details of bonding type rmsd hydrogen bonds : bond 0.02978 ( 164) hydrogen bonds : angle 4.22102 ( 492) covalent geometry : bond 0.00307 ( 3440) covalent geometry : angle 0.51300 ( 4660) Misc. bond : bond 0.00071 ( 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: 16 poor density : 54 time to evaluate : 0.407 Fit side-chains REVERT: B 10 GLN cc_start: 0.8335 (tt0) cc_final: 0.8039 (tt0) REVERT: B 11 ARG cc_start: 0.7838 (mtt180) cc_final: 0.6889 (mmp-170) REVERT: Q 11 ARG cc_start: 0.8340 (mtt180) cc_final: 0.7727 (ptt90) outliers start: 16 outliers final: 16 residues processed: 68 average time/residue: 0.2035 time to fit residues: 16.3442 Evaluate side-chains 68 residues out of total 380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 52 time to evaluate : 0.397 ------------------------------------------------------------------------------- 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 30 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 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 23 optimal weight: 20.0000 chunk 0 optimal weight: 10.0000 chunk 14 optimal weight: 4.9990 chunk 17 optimal weight: 6.9990 chunk 19 optimal weight: 7.9990 chunk 1 optimal weight: 0.1980 chunk 6 optimal weight: 2.9990 chunk 2 optimal weight: 0.8980 chunk 28 optimal weight: 6.9990 chunk 10 optimal weight: 6.9990 chunk 24 optimal weight: 4.9990 overall best weight: 2.8186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 31 ASN ** T 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 = 0.3896 r_free = 0.3896 target = 0.126897 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.085986 restraints weight = 4730.882| |-----------------------------------------------------------------------------| r_work (start): 0.3357 rms_B_bonded: 2.33 r_work: 0.3222 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work: 0.3094 rms_B_bonded: 4.61 restraints_weight: 0.2500 r_work (final): 0.3094 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8442 moved from start: 0.4120 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.017 3460 Z= 0.175 Angle : 0.530 7.675 4660 Z= 0.273 Chirality : 0.042 0.124 550 Planarity : 0.002 0.007 610 Dihedral : 4.392 14.186 470 Min Nonbonded Distance : 2.282 Molprobity Statistics. All-atom Clashscore : 2.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.00 % Favored : 95.00 % Rotamer: Outliers : 4.47 % Allowed : 18.16 % Favored : 77.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.88 (0.23), residues: 420 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.72 (0.17), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS R 18 PHE 0.012 0.002 PHE P 23 TYR 0.004 0.001 TYR I 37 ARG 0.001 0.000 ARG F 11 Details of bonding type rmsd hydrogen bonds : bond 0.03387 ( 164) hydrogen bonds : angle 4.32398 ( 492) covalent geometry : bond 0.00386 ( 3440) covalent geometry : angle 0.53023 ( 4660) Misc. bond : bond 0.00094 ( 20) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2136.32 seconds wall clock time: 37 minutes 42.68 seconds (2262.68 seconds total)