Starting phenix.real_space_refine on Mon Sep 23 14:51:00 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8az6_15755/09_2024/8az6_15755.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8az6_15755/09_2024/8az6_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8az6_15755/09_2024/8az6_15755.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8az6_15755/09_2024/8az6_15755.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8az6_15755/09_2024/8az6_15755.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8az6_15755/09_2024/8az6_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-5461/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: 2.65, per 1000 atoms: 0.77 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: 1.52 Conformation dependent library (CDL) restraints added in 388.4 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: 0.53 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: 0.92 Time building geometry restraints manager: 1.38 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: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'E' selection = chain 'F' selection = chain 'I' selection = chain 'J' selection = chain 'M' selection = chain 'N' selection = chain 'Q' selection = chain 'R' } ncs_group { reference = chain 'C' selection = chain '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: 1.110 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.140 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 13.660 Find NCS groups from input model: 0.160 Set up NCS constraints: 0.030 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:3.010 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.190 ------------------------------------------------------------------------------- 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 : 0.004 0.014 3440 Z= 0.246 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 *********************** 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 fitting. rotamer outliers: 0 poor density : 97 time to evaluate : 0.375 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: 0.1759 time to fit residues: 20.3155 Evaluate side-chains 65 residues out of total 380 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 65 time to evaluate : 0.424 ------------------------------------------------------------------------------- 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: 8.9990 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: 5.9990 chunk 17 optimal weight: 5.9990 chunk 27 optimal weight: 4.9990 chunk 8 optimal weight: 0.8980 overall best weight: 4.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 31 ASN C 35 ASN D 31 ASN 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 31 ASN R 10 GLN S 21 ASN S 31 ASN T 31 ASN T 35 ASN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8261 moved from start: 0.2967 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.028 3440 Z= 0.437 Angle : 0.600 7.221 4660 Z= 0.321 Chirality : 0.043 0.136 550 Planarity : 0.003 0.009 610 Dihedral : 4.989 16.919 470 Min Nonbonded Distance : 2.618 Molprobity Statistics. All-atom Clashscore : 5.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.76 % Favored : 95.24 % Rotamer: Outliers : 5.79 % Allowed : 6.84 % Favored : 87.37 % 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: -4.15 (0.20), residues: 420 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.16 (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 F 15 TYR 0.005 0.001 TYR B 37 ARG 0.002 0.000 ARG B 11 *********************** 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 111 residues out of total 380 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 89 time to evaluate : 0.374 Fit side-chains REVERT: A 11 ARG cc_start: 0.7275 (mtt180) cc_final: 0.6916 (mmp-170) REVERT: B 10 GLN cc_start: 0.8076 (tt0) cc_final: 0.7656 (tt0) REVERT: B 11 ARG cc_start: 0.7115 (mtt180) cc_final: 0.6758 (mmp-170) REVERT: C 22 ASN cc_start: 0.6636 (t0) cc_final: 0.6398 (t0) REVERT: D 35 ASN cc_start: 0.8692 (t0) cc_final: 0.8395 (t0) REVERT: G 35 ASN cc_start: 0.8737 (OUTLIER) cc_final: 0.8530 (t0) REVERT: I 10 GLN cc_start: 0.7745 (tt0) cc_final: 0.7436 (tt0) REVERT: O 23 PHE cc_start: 0.6848 (m-80) cc_final: 0.6575 (m-80) outliers start: 22 outliers final: 16 residues processed: 105 average time/residue: 0.1707 time to fit residues: 21.3674 Evaluate side-chains 91 residues out of total 380 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 74 time to evaluate : 0.364 ------------------------------------------------------------------------------- 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 G residue 35 ASN 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 32 VAL 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 22 optimal weight: 10.0000 chunk 18 optimal weight: 1.9990 chunk 7 optimal weight: 0.7980 chunk 27 optimal weight: 4.9990 chunk 29 optimal weight: 10.0000 chunk 24 optimal weight: 6.9990 chunk 9 optimal weight: 6.9990 chunk 21 optimal weight: 1.9990 chunk 26 optimal weight: 1.9990 chunk 20 optimal weight: 2.9990 chunk 14 optimal weight: 1.9990 overall best weight: 1.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 21 ASN K 35 ASN L 35 ASN O 21 ASN P 21 ASN P 31 ASN P 35 ASN S 31 ASN S 35 ASN ** T 22 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 31 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8204 moved from start: 0.3502 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.012 3440 Z= 0.169 Angle : 0.516 7.483 4660 Z= 0.257 Chirality : 0.042 0.128 550 Planarity : 0.002 0.007 610 Dihedral : 4.501 15.796 470 Min Nonbonded Distance : 2.625 Molprobity Statistics. All-atom Clashscore : 2.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.05 % Favored : 95.95 % Rotamer: Outliers : 3.68 % Allowed : 14.74 % Favored : 81.58 % 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: -4.23 (0.21), residues: 420 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.22 (0.16), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS Q 18 PHE 0.014 0.002 PHE P 23 TYR 0.003 0.001 TYR O 37 ARG 0.001 0.000 ARG R 11 *********************** 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 91 residues out of total 380 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 77 time to evaluate : 0.555 Fit side-chains REVERT: B 10 GLN cc_start: 0.8032 (tt0) cc_final: 0.7816 (tt0) REVERT: B 11 ARG cc_start: 0.7014 (mtt180) cc_final: 0.6693 (mmp-170) REVERT: D 35 ASN cc_start: 0.8703 (t0) cc_final: 0.8359 (t0) REVERT: I 10 GLN cc_start: 0.7732 (tt0) cc_final: 0.7392 (tt0) outliers start: 14 outliers final: 14 residues processed: 88 average time/residue: 0.1748 time to fit residues: 18.4809 Evaluate side-chains 81 residues out of total 380 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 67 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 D residue 28 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 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 3 optimal weight: 5.9990 chunk 13 optimal weight: 10.0000 chunk 18 optimal weight: 10.0000 chunk 27 optimal weight: 6.9990 chunk 28 optimal weight: 8.9990 chunk 14 optimal weight: 10.0000 chunk 25 optimal weight: 5.9990 chunk 7 optimal weight: 2.9990 chunk 24 optimal weight: 1.9990 chunk 16 optimal weight: 20.0000 chunk 0 optimal weight: 10.0000 overall best weight: 4.7990 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** G 35 ASN M 18 HIS P 31 ASN S 31 ASN ** T 22 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 35 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8274 moved from start: 0.3781 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.022 3440 Z= 0.431 Angle : 0.595 7.351 4660 Z= 0.319 Chirality : 0.043 0.125 550 Planarity : 0.002 0.009 610 Dihedral : 5.054 16.261 470 Min Nonbonded Distance : 2.607 Molprobity Statistics. All-atom Clashscore : 3.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.00 % Favored : 95.00 % Rotamer: Outliers : 5.79 % Allowed : 15.53 % 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: -4.51 (0.21), residues: 420 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.43 (0.16), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.002 HIS R 18 PHE 0.016 0.002 PHE A 15 TYR 0.006 0.001 TYR F 37 ARG 0.001 0.000 ARG F 11 *********************** 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 89 residues out of total 380 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 67 time to evaluate : 0.404 Fit side-chains REVERT: B 10 GLN cc_start: 0.8126 (tt0) cc_final: 0.7832 (tt0) REVERT: B 11 ARG cc_start: 0.7156 (mtt180) cc_final: 0.6852 (mmp-170) REVERT: C 23 PHE cc_start: 0.7455 (m-80) cc_final: 0.7153 (m-80) REVERT: I 10 GLN cc_start: 0.7818 (tt0) cc_final: 0.7486 (tt0) REVERT: K 35 ASN cc_start: 0.8904 (t0) cc_final: 0.8645 (t0) outliers start: 22 outliers final: 22 residues processed: 82 average time/residue: 0.1939 time to fit residues: 18.7131 Evaluate side-chains 84 residues out of total 380 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 62 time to evaluate : 0.389 ------------------------------------------------------------------------------- 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 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 9 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 9 THR Chi-restraints excluded: chain R residue 34 SER 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 21 optimal weight: 5.9990 chunk 11 optimal weight: 9.9990 chunk 24 optimal weight: 1.9990 chunk 20 optimal weight: 3.9990 chunk 0 optimal weight: 8.9990 chunk 14 optimal weight: 0.9980 chunk 26 optimal weight: 2.9990 chunk 7 optimal weight: 3.9990 chunk 9 optimal weight: 4.9990 chunk 5 optimal weight: 0.7980 chunk 17 optimal weight: 20.0000 overall best weight: 2.1586 ------------------------------------------------------------------------------- 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 G 21 ASN O 21 ASN O 31 ASN P 31 ASN T 22 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8228 moved from start: 0.3916 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.019 3440 Z= 0.197 Angle : 0.516 7.135 4660 Z= 0.262 Chirality : 0.042 0.127 550 Planarity : 0.002 0.010 610 Dihedral : 4.467 13.910 470 Min Nonbonded Distance : 2.624 Molprobity Statistics. All-atom Clashscore : 2.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.29 % Favored : 95.71 % 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: -4.67 (0.22), residues: 420 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.55 (0.16), 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 S 37 ARG 0.001 0.000 ARG B 11 *********************** 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 90 residues out of total 380 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 74 time to evaluate : 0.404 Fit side-chains REVERT: A 11 ARG cc_start: 0.7138 (mtm180) cc_final: 0.6916 (mmp-170) REVERT: B 10 GLN cc_start: 0.8125 (tt0) cc_final: 0.7873 (tt0) REVERT: B 11 ARG cc_start: 0.7094 (mtt180) cc_final: 0.6755 (mmp-170) REVERT: D 35 ASN cc_start: 0.8658 (t0) cc_final: 0.8451 (t0) REVERT: K 23 PHE cc_start: 0.7643 (m-80) cc_final: 0.7438 (m-80) outliers start: 16 outliers final: 16 residues processed: 88 average time/residue: 0.1874 time to fit residues: 19.5565 Evaluate side-chains 82 residues out of total 380 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 66 time to evaluate : 0.357 ------------------------------------------------------------------------------- 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 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 31 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 7 optimal weight: 10.0000 chunk 29 optimal weight: 9.9990 chunk 24 optimal weight: 5.9990 chunk 13 optimal weight: 2.9990 chunk 2 optimal weight: 4.9990 chunk 9 optimal weight: 8.9990 chunk 15 optimal weight: 1.9990 chunk 27 optimal weight: 2.9990 chunk 3 optimal weight: 6.9990 chunk 16 optimal weight: 5.9990 chunk 21 optimal weight: 1.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 22 ASN K 35 ASN O 21 ASN O 31 ASN P 31 ASN S 35 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8250 moved from start: 0.4002 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.019 3440 Z= 0.271 Angle : 0.536 7.308 4660 Z= 0.278 Chirality : 0.042 0.126 550 Planarity : 0.002 0.008 610 Dihedral : 4.540 13.445 470 Min Nonbonded Distance : 2.616 Molprobity Statistics. All-atom Clashscore : 2.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.76 % Favored : 95.24 % Rotamer: Outliers : 4.21 % Allowed : 18.95 % Favored : 76.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.76 (0.22), residues: 420 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.62 (0.17), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS R 18 PHE 0.011 0.002 PHE A 15 TYR 0.004 0.001 TYR I 37 ARG 0.001 0.000 ARG A 11 *********************** 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 74 residues out of total 380 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 58 time to evaluate : 0.391 Fit side-chains REVERT: B 10 GLN cc_start: 0.8147 (tt0) cc_final: 0.7884 (tt0) REVERT: B 11 ARG cc_start: 0.7122 (mtt180) cc_final: 0.6798 (mmp-170) outliers start: 16 outliers final: 16 residues processed: 72 average time/residue: 0.2097 time to fit residues: 17.7361 Evaluate side-chains 72 residues out of total 380 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 56 time to evaluate : 0.401 ------------------------------------------------------------------------------- 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 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 16 optimal weight: 20.0000 chunk 24 optimal weight: 0.8980 chunk 28 optimal weight: 8.9990 chunk 18 optimal weight: 0.9990 chunk 17 optimal weight: 20.0000 chunk 13 optimal weight: 5.9990 chunk 11 optimal weight: 7.9990 chunk 8 optimal weight: 3.9990 chunk 5 optimal weight: 6.9990 chunk 19 optimal weight: 0.9980 chunk 14 optimal weight: 0.9980 overall best weight: 1.5784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 22 ASN L 31 ASN L 35 ASN O 31 ASN P 31 ASN S 31 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8207 moved from start: 0.4158 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.018 3440 Z= 0.153 Angle : 0.493 8.082 4660 Z= 0.246 Chirality : 0.042 0.125 550 Planarity : 0.001 0.006 610 Dihedral : 4.169 12.124 470 Min Nonbonded Distance : 2.629 Molprobity Statistics. All-atom Clashscore : 2.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.05 % Favored : 95.95 % Rotamer: Outliers : 4.21 % Allowed : 18.16 % Favored : 77.63 % 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 0.002 0.001 HIS R 18 PHE 0.008 0.001 PHE G 23 TYR 0.003 0.001 TYR P 37 ARG 0.001 0.000 ARG Q 11 *********************** 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 81 residues out of total 380 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 65 time to evaluate : 0.395 Fit side-chains REVERT: B 10 GLN cc_start: 0.8050 (tt0) cc_final: 0.7785 (tt0) REVERT: B 11 ARG cc_start: 0.7040 (mtt180) cc_final: 0.6747 (mmp-170) outliers start: 16 outliers final: 15 residues processed: 80 average time/residue: 0.1857 time to fit residues: 17.5721 Evaluate side-chains 73 residues out of total 380 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 58 time to evaluate : 0.357 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 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 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 2 optimal weight: 5.9990 chunk 22 optimal weight: 10.0000 chunk 26 optimal weight: 7.9990 chunk 27 optimal weight: 6.9990 chunk 25 optimal weight: 7.9990 chunk 16 optimal weight: 9.9990 chunk 11 optimal weight: 20.0000 chunk 21 optimal weight: 2.9990 chunk 8 optimal weight: 2.9990 chunk 24 optimal weight: 2.9990 chunk 17 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: B 14 ASN I 18 HIS O 31 ASN P 31 ASN Q 18 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8268 moved from start: 0.4151 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.021 3440 Z= 0.373 Angle : 0.571 7.719 4660 Z= 0.304 Chirality : 0.042 0.124 550 Planarity : 0.002 0.010 610 Dihedral : 4.675 13.502 470 Min Nonbonded Distance : 2.577 Molprobity Statistics. All-atom Clashscore : 2.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.71 % Favored : 94.29 % Rotamer: Outliers : 5.26 % Allowed : 17.11 % Favored : 77.63 % 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 (0.22), 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 0.004 0.002 HIS R 18 PHE 0.014 0.002 PHE F 15 TYR 0.006 0.001 TYR I 37 ARG 0.001 0.000 ARG N 11 *********************** 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 79 residues out of total 380 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 59 time to evaluate : 0.363 Fit side-chains REVERT: A 11 ARG cc_start: 0.7247 (mtm180) cc_final: 0.6920 (mmt-90) REVERT: B 10 GLN cc_start: 0.8079 (tt0) cc_final: 0.7838 (tt0) REVERT: B 11 ARG cc_start: 0.7173 (mtt180) cc_final: 0.6901 (mmp-170) outliers start: 20 outliers final: 20 residues processed: 75 average time/residue: 0.2074 time to fit residues: 18.2048 Evaluate side-chains 78 residues out of total 380 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 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 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 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 T residue 27 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 28 optimal weight: 9.9990 chunk 17 optimal weight: 20.0000 chunk 13 optimal weight: 1.9990 chunk 19 optimal weight: 1.9990 chunk 29 optimal weight: 10.0000 chunk 27 optimal weight: 3.9990 chunk 23 optimal weight: 6.9990 chunk 2 optimal weight: 2.9990 chunk 18 optimal weight: 3.9990 chunk 14 optimal weight: 0.9980 chunk 25 optimal weight: 0.8980 overall best weight: 1.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** N 14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 31 ASN ** R 14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8219 moved from start: 0.4300 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 3440 Z= 0.171 Angle : 0.518 8.767 4660 Z= 0.256 Chirality : 0.042 0.125 550 Planarity : 0.001 0.007 610 Dihedral : 4.230 12.547 470 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 1.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.52 % Favored : 95.48 % 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: -4.91 (0.22), residues: 420 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.74 (0.17), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS R 18 PHE 0.013 0.001 PHE P 23 TYR 0.003 0.001 TYR I 37 ARG 0.001 0.000 ARG A 11 *********************** 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 78 residues out of total 380 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 61 time to evaluate : 0.389 Fit side-chains REVERT: B 10 GLN cc_start: 0.8054 (tt0) cc_final: 0.7852 (tt0) REVERT: B 11 ARG cc_start: 0.7056 (mtt180) cc_final: 0.6727 (mmp-170) REVERT: S 27 LEU cc_start: 0.7749 (OUTLIER) cc_final: 0.7405 (mt) outliers start: 17 outliers final: 16 residues processed: 76 average time/residue: 0.1908 time to fit residues: 17.1278 Evaluate side-chains 76 residues out of total 380 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 59 time to evaluate : 0.391 ------------------------------------------------------------------------------- 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 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 27 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 7 optimal weight: 7.9990 chunk 21 optimal weight: 7.9990 chunk 3 optimal weight: 6.9990 chunk 6 optimal weight: 0.9990 chunk 23 optimal weight: 20.0000 chunk 9 optimal weight: 0.9980 chunk 24 optimal weight: 0.7980 chunk 4 optimal weight: 7.9990 chunk 20 optimal weight: 3.9990 chunk 1 optimal weight: 1.9990 chunk 17 optimal weight: 5.9990 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** N 14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 31 ASN ** R 14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8217 moved from start: 0.4297 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 3440 Z= 0.169 Angle : 0.504 8.496 4660 Z= 0.252 Chirality : 0.042 0.125 550 Planarity : 0.001 0.006 610 Dihedral : 4.125 13.030 470 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 1.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.76 % Favored : 95.24 % Rotamer: Outliers : 4.47 % Allowed : 18.68 % Favored : 76.84 % 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 : -3.71 (0.18), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS R 18 PHE 0.012 0.001 PHE P 23 TYR 0.003 0.001 TYR K 37 ARG 0.001 0.000 ARG Q 11 ********************** 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 78 residues out of total 380 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 61 time to evaluate : 0.413 Fit side-chains REVERT: B 10 GLN cc_start: 0.8108 (tt0) cc_final: 0.7883 (tt0) REVERT: B 11 ARG cc_start: 0.7039 (mtt180) cc_final: 0.6776 (mmp-170) REVERT: S 27 LEU cc_start: 0.7752 (OUTLIER) cc_final: 0.7410 (mt) outliers start: 17 outliers final: 16 residues processed: 76 average time/residue: 0.1949 time to fit residues: 17.4764 Evaluate side-chains 77 residues out of total 380 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 60 time to evaluate : 0.368 ------------------------------------------------------------------------------- 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 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 27 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 27 optimal weight: 3.9990 chunk 16 optimal weight: 9.9990 chunk 20 optimal weight: 7.9990 chunk 0 optimal weight: 10.0000 chunk 19 optimal weight: 7.9990 chunk 18 optimal weight: 4.9990 chunk 17 optimal weight: 20.0000 chunk 11 optimal weight: 5.9990 chunk 29 optimal weight: 4.9990 chunk 1 optimal weight: 0.6980 chunk 28 optimal weight: 9.9990 overall best weight: 4.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: O 31 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3874 r_free = 0.3874 target = 0.125273 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.084440 restraints weight = 4994.736| |-----------------------------------------------------------------------------| r_work (start): 0.3330 rms_B_bonded: 2.34 r_work: 0.3199 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work: 0.3071 rms_B_bonded: 4.63 restraints_weight: 0.2500 r_work (final): 0.3071 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8455 moved from start: 0.4298 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.019 3440 Z= 0.364 Angle : 0.576 8.487 4660 Z= 0.304 Chirality : 0.043 0.126 550 Planarity : 0.002 0.009 610 Dihedral : 4.664 15.436 470 Min Nonbonded Distance : 2.332 Molprobity Statistics. All-atom Clashscore : 2.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.71 % Favored : 94.29 % Rotamer: Outliers : 4.74 % Allowed : 18.42 % Favored : 76.84 % 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: -4.92 (0.22), residues: 420 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.74 (0.17), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS R 18 PHE 0.018 0.002 PHE P 23 TYR 0.007 0.001 TYR B 37 ARG 0.001 0.000 ARG A 11 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1156.79 seconds wall clock time: 21 minutes 33.24 seconds (1293.24 seconds total)