Starting phenix.real_space_refine on Sun Mar 10 15:10:18 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yk2_33884/03_2024/7yk2_33884.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yk2_33884/03_2024/7yk2_33884.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yk2_33884/03_2024/7yk2_33884.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yk2_33884/03_2024/7yk2_33884.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yk2_33884/03_2024/7yk2_33884.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yk2_33884/03_2024/7yk2_33884.pdb" } resolution = 2.8 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= 0.003 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 1644 2.51 5 N 456 2.21 5 O 528 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "C PHE 94": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 94": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 94": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 94": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 94": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 94": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 2628 Number of models: 1 Model: "" Number of chains: 6 Chain: "C" Number of atoms: 438 Number of conformers: 1 Conformer: "" Number of residues, atoms: 63, 438 Classifications: {'peptide': 63} Link IDs: {'TRANS': 62} Chain: "D" Number of atoms: 438 Number of conformers: 1 Conformer: "" Number of residues, atoms: 63, 438 Classifications: {'peptide': 63} Link IDs: {'TRANS': 62} Chain: "E" Number of atoms: 438 Number of conformers: 1 Conformer: "" Number of residues, atoms: 63, 438 Classifications: {'peptide': 63} Link IDs: {'TRANS': 62} Chain: "A" Number of atoms: 438 Number of conformers: 1 Conformer: "" Number of residues, atoms: 63, 438 Classifications: {'peptide': 63} Link IDs: {'TRANS': 62} Chain: "F" Number of atoms: 438 Number of conformers: 1 Conformer: "" Number of residues, atoms: 63, 438 Classifications: {'peptide': 63} Link IDs: {'TRANS': 62} Chain: "B" Number of atoms: 438 Number of conformers: 1 Conformer: "" Number of residues, atoms: 63, 438 Classifications: {'peptide': 63} Link IDs: {'TRANS': 62} Time building chain proxies: 2.00, per 1000 atoms: 0.76 Number of scatterers: 2628 At special positions: 0 Unit cell: (98.58, 117.66, 31.8, 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 528 8.00 N 456 7.00 C 1644 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 - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.01 Conformation dependent library (CDL) restraints added in 554.4 milliseconds 732 Ramachandran restraints generated. 366 Oldfield, 0 Emsley, 366 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 648 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 8 sheets defined 0.0% alpha, 42.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.30 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'C' and resid 46 through 58 removed outlier: 8.665A pdb=" N GLU C 46 " --> pdb=" O GLY F 47 " (cutoff:3.500A) removed outlier: 8.307A pdb=" N VAL F 49 " --> pdb=" O GLU C 46 " (cutoff:3.500A) removed outlier: 9.163A pdb=" N VAL C 48 " --> pdb=" O VAL F 49 " (cutoff:3.500A) removed outlier: 10.541A pdb=" N GLY F 51 " --> pdb=" O VAL C 48 " (cutoff:3.500A) removed outlier: 6.126A pdb=" N HIS C 50 " --> pdb=" O GLY F 51 " (cutoff:3.500A) removed outlier: 8.834A pdb=" N ALA F 53 " --> pdb=" O HIS C 50 " (cutoff:3.500A) removed outlier: 6.287A pdb=" N VAL C 52 " --> pdb=" O ALA F 53 " (cutoff:3.500A) removed outlier: 8.215A pdb=" N VAL F 55 " --> pdb=" O VAL C 52 " (cutoff:3.500A) removed outlier: 6.480A pdb=" N THR C 54 " --> pdb=" O VAL F 55 " (cutoff:3.500A) removed outlier: 8.210A pdb=" N GLU F 57 " --> pdb=" O THR C 54 " (cutoff:3.500A) removed outlier: 6.822A pdb=" N ALA C 56 " --> pdb=" O GLU F 57 " (cutoff:3.500A) removed outlier: 6.870A pdb=" N VAL F 48 " --> pdb=" O GLY E 47 " (cutoff:3.500A) removed outlier: 6.941A pdb=" N VAL E 49 " --> pdb=" O VAL F 48 " (cutoff:3.500A) removed outlier: 6.889A pdb=" N HIS F 50 " --> pdb=" O VAL E 49 " (cutoff:3.500A) removed outlier: 6.848A pdb=" N GLY E 51 " --> pdb=" O HIS F 50 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 62 through 65 removed outlier: 6.908A pdb=" N GLN E 62 " --> pdb=" O VAL F 63 " (cutoff:3.500A) removed outlier: 8.121A pdb=" N ASN F 65 " --> pdb=" O GLN E 62 " (cutoff:3.500A) removed outlier: 6.416A pdb=" N THR E 64 " --> pdb=" O ASN F 65 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 71 through 82 removed outlier: 8.999A pdb=" N VAL C 71 " --> pdb=" O THR F 72 " (cutoff:3.500A) removed outlier: 9.394A pdb=" N VAL F 74 " --> pdb=" O VAL C 71 " (cutoff:3.500A) removed outlier: 6.797A pdb=" N GLY C 73 " --> pdb=" O VAL F 74 " (cutoff:3.500A) removed outlier: 7.842A pdb=" N ALA F 76 " --> pdb=" O GLY C 73 " (cutoff:3.500A) removed outlier: 8.630A pdb=" N THR C 75 " --> pdb=" O ALA F 76 " (cutoff:3.500A) removed outlier: 7.975A pdb=" N ALA F 78 " --> pdb=" O THR C 75 " (cutoff:3.500A) removed outlier: 9.108A pdb=" N VAL C 77 " --> pdb=" O ALA F 78 " (cutoff:3.500A) removed outlier: 10.641A pdb=" N LYS F 80 " --> pdb=" O VAL C 77 " (cutoff:3.500A) removed outlier: 9.094A pdb=" N GLN C 79 " --> pdb=" O LYS F 80 " (cutoff:3.500A) removed outlier: 10.364A pdb=" N VAL F 82 " --> pdb=" O GLN C 79 " (cutoff:3.500A) removed outlier: 8.922A pdb=" N THR C 81 " --> pdb=" O VAL F 82 " (cutoff:3.500A) removed outlier: 6.945A pdb=" N THR E 72 " --> pdb=" O VAL F 71 " (cutoff:3.500A) removed outlier: 6.805A pdb=" N GLY F 73 " --> pdb=" O THR E 72 " (cutoff:3.500A) removed outlier: 6.809A pdb=" N VAL F 77 " --> pdb=" O ALA E 76 " (cutoff:3.500A) removed outlier: 6.972A pdb=" N ALA E 78 " --> pdb=" O VAL F 77 " (cutoff:3.500A) removed outlier: 6.829A pdb=" N GLN F 79 " --> pdb=" O ALA E 78 " (cutoff:3.500A) removed outlier: 6.896A pdb=" N LYS E 80 " --> pdb=" O GLN F 79 " (cutoff:3.500A) removed outlier: 6.949A pdb=" N THR F 81 " --> pdb=" O LYS E 80 " (cutoff:3.500A) removed outlier: 6.969A pdb=" N VAL E 82 " --> pdb=" O THR F 81 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 86 through 87 removed outlier: 6.238A pdb=" N GLY E 86 " --> pdb=" O SER F 87 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'D' and resid 46 through 58 removed outlier: 8.658A pdb=" N GLU D 46 " --> pdb=" O GLY B 47 " (cutoff:3.500A) removed outlier: 8.306A pdb=" N VAL B 49 " --> pdb=" O GLU D 46 " (cutoff:3.500A) removed outlier: 9.164A pdb=" N VAL D 48 " --> pdb=" O VAL B 49 " (cutoff:3.500A) removed outlier: 10.542A pdb=" N GLY B 51 " --> pdb=" O VAL D 48 " (cutoff:3.500A) removed outlier: 6.125A pdb=" N HIS D 50 " --> pdb=" O GLY B 51 " (cutoff:3.500A) removed outlier: 8.823A pdb=" N ALA B 53 " --> pdb=" O HIS D 50 " (cutoff:3.500A) removed outlier: 6.275A pdb=" N VAL D 52 " --> pdb=" O ALA B 53 " (cutoff:3.500A) removed outlier: 8.203A pdb=" N VAL B 55 " --> pdb=" O VAL D 52 " (cutoff:3.500A) removed outlier: 6.466A pdb=" N THR D 54 " --> pdb=" O VAL B 55 " (cutoff:3.500A) removed outlier: 8.196A pdb=" N GLU B 57 " --> pdb=" O THR D 54 " (cutoff:3.500A) removed outlier: 6.808A pdb=" N ALA D 56 " --> pdb=" O GLU B 57 " (cutoff:3.500A) removed outlier: 6.859A pdb=" N VAL B 48 " --> pdb=" O GLY A 47 " (cutoff:3.500A) removed outlier: 6.932A pdb=" N VAL A 49 " --> pdb=" O VAL B 48 " (cutoff:3.500A) removed outlier: 6.884A pdb=" N HIS B 50 " --> pdb=" O VAL A 49 " (cutoff:3.500A) removed outlier: 6.841A pdb=" N GLY A 51 " --> pdb=" O HIS B 50 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'D' and resid 62 through 65 removed outlier: 6.271A pdb=" N VAL D 63 " --> pdb=" O THR B 64 " (cutoff:3.500A) removed outlier: 6.901A pdb=" N GLN A 62 " --> pdb=" O VAL B 63 " (cutoff:3.500A) removed outlier: 8.115A pdb=" N ASN B 65 " --> pdb=" O GLN A 62 " (cutoff:3.500A) removed outlier: 6.409A pdb=" N THR A 64 " --> pdb=" O ASN B 65 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'D' and resid 71 through 82 removed outlier: 6.919A pdb=" N THR B 72 " --> pdb=" O VAL D 71 " (cutoff:3.500A) removed outlier: 6.779A pdb=" N GLY D 73 " --> pdb=" O THR B 72 " (cutoff:3.500A) removed outlier: 6.786A pdb=" N VAL D 77 " --> pdb=" O ALA B 76 " (cutoff:3.500A) removed outlier: 6.951A pdb=" N ALA B 78 " --> pdb=" O VAL D 77 " (cutoff:3.500A) removed outlier: 6.810A pdb=" N GLN D 79 " --> pdb=" O ALA B 78 " (cutoff:3.500A) removed outlier: 6.879A pdb=" N LYS B 80 " --> pdb=" O GLN D 79 " (cutoff:3.500A) removed outlier: 6.938A pdb=" N THR D 81 " --> pdb=" O LYS B 80 " (cutoff:3.500A) removed outlier: 6.958A pdb=" N VAL B 82 " --> pdb=" O THR D 81 " (cutoff:3.500A) removed outlier: 6.937A pdb=" N THR A 72 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 6.800A pdb=" N GLY B 73 " --> pdb=" O THR A 72 " (cutoff:3.500A) removed outlier: 6.800A pdb=" N VAL B 77 " --> pdb=" O ALA A 76 " (cutoff:3.500A) removed outlier: 6.961A pdb=" N ALA A 78 " --> pdb=" O VAL B 77 " (cutoff:3.500A) removed outlier: 6.817A pdb=" N GLN B 79 " --> pdb=" O ALA A 78 " (cutoff:3.500A) removed outlier: 6.883A pdb=" N LYS A 80 " --> pdb=" O GLN B 79 " (cutoff:3.500A) removed outlier: 6.931A pdb=" N THR B 81 " --> pdb=" O LYS A 80 " (cutoff:3.500A) removed outlier: 6.952A pdb=" N VAL A 82 " --> pdb=" O THR B 81 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 86 through 87 removed outlier: 6.234A pdb=" N GLY A 86 " --> pdb=" O SER B 87 " (cutoff:3.500A) 30 hydrogen bonds defined for protein. 90 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: 0.53 Time building geometry restraints manager: 1.08 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: 462 1.29 - 1.35: 414 1.35 - 1.42: 102 1.42 - 1.48: 426 1.48 - 1.55: 1236 Bond restraints: 2640 Sorted by residual: bond pdb=" CG LEU D 38 " pdb=" CD1 LEU D 38 " ideal model delta sigma weight residual 1.521 1.485 0.036 3.30e-02 9.18e+02 1.21e+00 bond pdb=" CG LEU A 38 " pdb=" CD1 LEU A 38 " ideal model delta sigma weight residual 1.521 1.485 0.036 3.30e-02 9.18e+02 1.20e+00 bond pdb=" CG LEU F 38 " pdb=" CD1 LEU F 38 " ideal model delta sigma weight residual 1.521 1.485 0.036 3.30e-02 9.18e+02 1.20e+00 bond pdb=" CG LEU B 38 " pdb=" CD1 LEU B 38 " ideal model delta sigma weight residual 1.521 1.485 0.036 3.30e-02 9.18e+02 1.19e+00 bond pdb=" CG LEU C 38 " pdb=" CD1 LEU C 38 " ideal model delta sigma weight residual 1.521 1.485 0.036 3.30e-02 9.18e+02 1.18e+00 ... (remaining 2635 not shown) Histogram of bond angle deviations from ideal: 106.08 - 111.09: 1157 111.09 - 116.11: 741 116.11 - 121.12: 851 121.12 - 126.14: 815 126.14 - 131.15: 6 Bond angle restraints: 3570 Sorted by residual: angle pdb=" CA ILE B 88 " pdb=" C ILE B 88 " pdb=" N ALA B 89 " ideal model delta sigma weight residual 117.15 119.77 -2.62 7.80e-01 1.64e+00 1.13e+01 angle pdb=" CA ILE A 88 " pdb=" C ILE A 88 " pdb=" N ALA A 89 " ideal model delta sigma weight residual 117.15 119.75 -2.60 7.80e-01 1.64e+00 1.11e+01 angle pdb=" CA ILE C 88 " pdb=" C ILE C 88 " pdb=" N ALA C 89 " ideal model delta sigma weight residual 117.15 119.75 -2.60 7.80e-01 1.64e+00 1.11e+01 angle pdb=" CA ILE F 88 " pdb=" C ILE F 88 " pdb=" N ALA F 89 " ideal model delta sigma weight residual 117.15 119.74 -2.59 7.80e-01 1.64e+00 1.11e+01 angle pdb=" CA ILE D 88 " pdb=" C ILE D 88 " pdb=" N ALA D 89 " ideal model delta sigma weight residual 117.15 119.74 -2.59 7.80e-01 1.64e+00 1.10e+01 ... (remaining 3565 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 10.30: 1308 10.30 - 20.60: 162 20.60 - 30.90: 54 30.90 - 41.20: 18 41.20 - 51.50: 6 Dihedral angle restraints: 1548 sinusoidal: 522 harmonic: 1026 Sorted by residual: dihedral pdb=" CA TYR E 39 " pdb=" CB TYR E 39 " pdb=" CG TYR E 39 " pdb=" CD1 TYR E 39 " ideal model delta sinusoidal sigma weight residual -20.00 31.50 -51.50 2 2.00e+01 2.50e-03 7.35e+00 dihedral pdb=" CA TYR F 39 " pdb=" CB TYR F 39 " pdb=" CG TYR F 39 " pdb=" CD1 TYR F 39 " ideal model delta sinusoidal sigma weight residual -20.00 31.42 -51.42 2 2.00e+01 2.50e-03 7.33e+00 dihedral pdb=" CA TYR B 39 " pdb=" CB TYR B 39 " pdb=" CG TYR B 39 " pdb=" CD1 TYR B 39 " ideal model delta sinusoidal sigma weight residual -20.00 31.40 -51.40 2 2.00e+01 2.50e-03 7.33e+00 ... (remaining 1545 not shown) Histogram of chiral volume deviations from ideal: 0.001 - 0.027: 232 0.027 - 0.053: 120 0.053 - 0.080: 48 0.080 - 0.106: 39 0.106 - 0.132: 29 Chirality restraints: 468 Sorted by residual: chirality pdb=" CA VAL A 70 " pdb=" N VAL A 70 " pdb=" C VAL A 70 " pdb=" CB VAL A 70 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 4.38e-01 chirality pdb=" CA VAL E 70 " pdb=" N VAL E 70 " pdb=" C VAL E 70 " pdb=" CB VAL E 70 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 4.31e-01 chirality pdb=" CA VAL F 70 " pdb=" N VAL F 70 " pdb=" C VAL F 70 " pdb=" CB VAL F 70 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 4.25e-01 ... (remaining 465 not shown) Planarity restraints: 444 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLU B 83 " -0.006 2.00e-02 2.50e+03 1.15e-02 1.32e+00 pdb=" C GLU B 83 " 0.020 2.00e-02 2.50e+03 pdb=" O GLU B 83 " -0.008 2.00e-02 2.50e+03 pdb=" N GLY B 84 " -0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU A 83 " -0.006 2.00e-02 2.50e+03 1.14e-02 1.31e+00 pdb=" C GLU A 83 " 0.020 2.00e-02 2.50e+03 pdb=" O GLU A 83 " -0.008 2.00e-02 2.50e+03 pdb=" N GLY A 84 " -0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU D 83 " -0.006 2.00e-02 2.50e+03 1.14e-02 1.31e+00 pdb=" C GLU D 83 " 0.020 2.00e-02 2.50e+03 pdb=" O GLU D 83 " -0.008 2.00e-02 2.50e+03 pdb=" N GLY D 84 " -0.007 2.00e-02 2.50e+03 ... (remaining 441 not shown) Histogram of nonbonded interaction distances: 2.42 - 2.92: 1092 2.92 - 3.41: 2311 3.41 - 3.91: 3902 3.91 - 4.40: 4330 4.40 - 4.90: 8827 Nonbonded interactions: 20462 Sorted by model distance: nonbonded pdb=" NE2 GLN F 62 " pdb=" OG1 THR F 64 " model vdw 2.424 2.520 nonbonded pdb=" NE2 GLN E 62 " pdb=" OG1 THR E 64 " model vdw 2.424 2.520 nonbonded pdb=" NE2 GLN B 62 " pdb=" OG1 THR B 64 " model vdw 2.424 2.520 nonbonded pdb=" NE2 GLN A 62 " pdb=" OG1 THR A 64 " model vdw 2.425 2.520 nonbonded pdb=" NE2 GLN C 62 " pdb=" OG1 THR C 64 " model vdw 2.425 2.520 ... (remaining 20457 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' } 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: 1.000 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: 4.840 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 12.530 Find NCS groups from input model: 0.170 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:11.670 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.290 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7534 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 : 0.005 0.036 2640 Z= 0.347 Angle : 0.816 4.432 3570 Z= 0.547 Chirality : 0.051 0.132 468 Planarity : 0.002 0.011 444 Dihedral : 11.384 51.497 900 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 12.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.48 % Favored : 88.52 % Rotamer: Outliers : 0.00 % Allowed : 6.67 % Favored : 93.33 % 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: -3.89 (0.35), residues: 366 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.96 (0.27), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.004 HIS D 50 PHE 0.013 0.004 PHE B 94 TYR 0.007 0.002 TYR C 39 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 732 Ramachandran restraints generated. 366 Oldfield, 0 Emsley, 366 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 732 Ramachandran restraints generated. 366 Oldfield, 0 Emsley, 366 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 51 residues out of total 270 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 51 time to evaluate : 0.296 Fit side-chains REVERT: C 80 LYS cc_start: 0.8084 (tttm) cc_final: 0.7741 (tttp) REVERT: F 83 GLU cc_start: 0.6983 (tm-30) cc_final: 0.6714 (tm-30) outliers start: 0 outliers final: 0 residues processed: 51 average time/residue: 1.3965 time to fit residues: 72.7532 Evaluate side-chains 43 residues out of total 270 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 43 time to evaluate : 0.295 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 30 optimal weight: 9.9990 chunk 27 optimal weight: 4.9990 chunk 15 optimal weight: 0.9980 chunk 9 optimal weight: 0.0980 chunk 18 optimal weight: 7.9990 chunk 14 optimal weight: 5.9990 chunk 28 optimal weight: 6.9990 chunk 10 optimal weight: 6.9990 chunk 17 optimal weight: 2.9990 chunk 21 optimal weight: 2.9990 chunk 32 optimal weight: 5.9990 overall best weight: 2.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 65 ASN D 65 ASN ** D 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 65 ASN E 79 GLN A 65 ASN F 65 ASN F 79 GLN B 65 ASN B 79 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7504 moved from start: 0.1312 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.026 2640 Z= 0.278 Angle : 0.593 3.517 3570 Z= 0.336 Chirality : 0.051 0.136 468 Planarity : 0.002 0.007 444 Dihedral : 5.056 14.738 378 Min Nonbonded Distance : 2.212 Molprobity Statistics. All-atom Clashscore : 9.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.20 % Favored : 91.80 % Rotamer: Outliers : 3.70 % Allowed : 13.33 % Favored : 82.96 % 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: -3.19 (0.38), residues: 366 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.42 (0.29), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.003 HIS F 50 PHE 0.016 0.004 PHE D 94 TYR 0.005 0.002 TYR F 39 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 732 Ramachandran restraints generated. 366 Oldfield, 0 Emsley, 366 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 732 Ramachandran restraints generated. 366 Oldfield, 0 Emsley, 366 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 60 residues out of total 270 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 50 time to evaluate : 0.299 Fit side-chains REVERT: F 62 GLN cc_start: 0.6256 (OUTLIER) cc_final: 0.5651 (tp40) REVERT: F 83 GLU cc_start: 0.6837 (tm-30) cc_final: 0.6607 (tm-30) outliers start: 10 outliers final: 6 residues processed: 50 average time/residue: 1.3346 time to fit residues: 68.2155 Evaluate side-chains 52 residues out of total 270 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 45 time to evaluate : 0.272 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 46 GLU Chi-restraints excluded: chain E residue 66 VAL Chi-restraints excluded: chain A residue 62 GLN Chi-restraints excluded: chain F residue 62 GLN Chi-restraints excluded: chain F residue 66 VAL Chi-restraints excluded: chain B residue 46 GLU Chi-restraints excluded: chain B residue 66 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 18 optimal weight: 10.0000 chunk 10 optimal weight: 6.9990 chunk 27 optimal weight: 6.9990 chunk 22 optimal weight: 9.9990 chunk 9 optimal weight: 3.9990 chunk 32 optimal weight: 8.9990 chunk 35 optimal weight: 4.9990 chunk 29 optimal weight: 8.9990 chunk 11 optimal weight: 2.9990 chunk 26 optimal weight: 6.9990 chunk 24 optimal weight: 0.0970 overall best weight: 3.8186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 79 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7564 moved from start: 0.1907 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.030 2640 Z= 0.422 Angle : 0.692 4.091 3570 Z= 0.399 Chirality : 0.054 0.131 468 Planarity : 0.003 0.009 444 Dihedral : 5.564 15.605 378 Min Nonbonded Distance : 2.216 Molprobity Statistics. All-atom Clashscore : 11.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 16.67 % Favored : 83.33 % Rotamer: Outliers : 6.67 % Allowed : 15.93 % Favored : 77.41 % 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: -2.96 (0.38), residues: 366 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.25 (0.29), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.008 0.005 HIS D 50 PHE 0.021 0.006 PHE B 94 TYR 0.007 0.002 TYR B 39 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 732 Ramachandran restraints generated. 366 Oldfield, 0 Emsley, 366 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 732 Ramachandran restraints generated. 366 Oldfield, 0 Emsley, 366 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 63 residues out of total 270 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 45 time to evaluate : 0.299 Fit side-chains REVERT: D 60 LYS cc_start: 0.7775 (OUTLIER) cc_final: 0.7310 (tttp) REVERT: F 83 GLU cc_start: 0.6909 (tm-30) cc_final: 0.6668 (tm-30) outliers start: 18 outliers final: 11 residues processed: 55 average time/residue: 1.3060 time to fit residues: 73.4037 Evaluate side-chains 54 residues out of total 270 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 42 time to evaluate : 0.290 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 40 VAL Chi-restraints excluded: chain C residue 46 GLU Chi-restraints excluded: chain D residue 40 VAL Chi-restraints excluded: chain D residue 60 LYS Chi-restraints excluded: chain E residue 66 VAL Chi-restraints excluded: chain A residue 46 GLU Chi-restraints excluded: chain A residue 62 GLN Chi-restraints excluded: chain F residue 40 VAL Chi-restraints excluded: chain F residue 46 GLU Chi-restraints excluded: chain F residue 66 VAL Chi-restraints excluded: chain B residue 46 GLU Chi-restraints excluded: chain B residue 66 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 16 optimal weight: 7.9990 chunk 3 optimal weight: 0.0470 chunk 15 optimal weight: 0.5980 chunk 21 optimal weight: 0.9980 chunk 32 optimal weight: 2.9990 chunk 34 optimal weight: 5.9990 chunk 17 optimal weight: 5.9990 chunk 31 optimal weight: 4.9990 chunk 9 optimal weight: 2.9990 chunk 28 optimal weight: 4.9990 chunk 19 optimal weight: 0.6980 overall best weight: 1.0680 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 79 GLN F 79 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7463 moved from start: 0.2130 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.019 2640 Z= 0.154 Angle : 0.479 3.187 3570 Z= 0.272 Chirality : 0.049 0.130 468 Planarity : 0.002 0.008 444 Dihedral : 4.609 15.136 378 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 6.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.83 % Favored : 93.17 % Rotamer: Outliers : 5.19 % Allowed : 17.04 % Favored : 77.78 % 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: -2.79 (0.39), residues: 366 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.12 (0.30), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.002 HIS B 50 PHE 0.009 0.003 PHE F 94 TYR 0.003 0.001 TYR E 39 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 732 Ramachandran restraints generated. 366 Oldfield, 0 Emsley, 366 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 732 Ramachandran restraints generated. 366 Oldfield, 0 Emsley, 366 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 54 residues out of total 270 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 40 time to evaluate : 0.302 Fit side-chains REVERT: D 46 GLU cc_start: 0.7764 (pt0) cc_final: 0.7441 (pt0) REVERT: D 60 LYS cc_start: 0.7775 (OUTLIER) cc_final: 0.7268 (tttp) REVERT: F 62 GLN cc_start: 0.6135 (OUTLIER) cc_final: 0.5637 (tp40) REVERT: F 83 GLU cc_start: 0.6859 (tm-30) cc_final: 0.6610 (tm-30) outliers start: 14 outliers final: 5 residues processed: 48 average time/residue: 1.1152 time to fit residues: 54.9810 Evaluate side-chains 46 residues out of total 270 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 39 time to evaluate : 0.259 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 40 VAL Chi-restraints excluded: chain D residue 40 VAL Chi-restraints excluded: chain D residue 60 LYS Chi-restraints excluded: chain A residue 46 GLU Chi-restraints excluded: chain F residue 46 GLU Chi-restraints excluded: chain F residue 62 GLN Chi-restraints excluded: chain B residue 46 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 0 optimal weight: 10.0000 chunk 25 optimal weight: 7.9990 chunk 14 optimal weight: 4.9990 chunk 29 optimal weight: 9.9990 chunk 24 optimal weight: 0.0570 chunk 17 optimal weight: 7.9990 chunk 31 optimal weight: 6.9990 chunk 8 optimal weight: 0.0270 chunk 11 optimal weight: 0.0370 chunk 6 optimal weight: 10.0000 chunk 20 optimal weight: 4.9990 overall best weight: 2.0238 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 79 GLN A 62 GLN F 79 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7504 moved from start: 0.2240 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 2640 Z= 0.237 Angle : 0.522 3.472 3570 Z= 0.300 Chirality : 0.050 0.130 468 Planarity : 0.002 0.007 444 Dihedral : 4.954 15.542 378 Min Nonbonded Distance : 2.279 Molprobity Statistics. All-atom Clashscore : 7.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.20 % Favored : 88.80 % Rotamer: Outliers : 4.44 % Allowed : 19.26 % Favored : 76.30 % 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: -2.79 (0.39), residues: 366 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.12 (0.30), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.003 HIS B 50 PHE 0.014 0.004 PHE F 94 TYR 0.003 0.001 TYR E 39 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 732 Ramachandran restraints generated. 366 Oldfield, 0 Emsley, 366 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 732 Ramachandran restraints generated. 366 Oldfield, 0 Emsley, 366 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 59 residues out of total 270 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 47 time to evaluate : 0.311 Fit side-chains REVERT: D 60 LYS cc_start: 0.7817 (OUTLIER) cc_final: 0.7308 (tttp) REVERT: F 62 GLN cc_start: 0.6201 (OUTLIER) cc_final: 0.5751 (tp40) REVERT: F 83 GLU cc_start: 0.6881 (tm-30) cc_final: 0.6679 (tm-30) outliers start: 12 outliers final: 6 residues processed: 54 average time/residue: 1.2383 time to fit residues: 68.4958 Evaluate side-chains 54 residues out of total 270 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 46 time to evaluate : 0.301 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 40 VAL Chi-restraints excluded: chain D residue 40 VAL Chi-restraints excluded: chain D residue 60 LYS Chi-restraints excluded: chain E residue 66 VAL Chi-restraints excluded: chain A residue 46 GLU Chi-restraints excluded: chain F residue 46 GLU Chi-restraints excluded: chain F residue 62 GLN Chi-restraints excluded: chain B residue 46 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 8 optimal weight: 0.9980 chunk 34 optimal weight: 0.8980 chunk 28 optimal weight: 4.9990 chunk 16 optimal weight: 1.9990 chunk 2 optimal weight: 1.9990 chunk 11 optimal weight: 4.9990 chunk 18 optimal weight: 10.0000 chunk 33 optimal weight: 7.9990 chunk 3 optimal weight: 0.6980 chunk 19 optimal weight: 2.9990 chunk 25 optimal weight: 3.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 79 GLN F 79 GLN B 62 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7465 moved from start: 0.2426 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 2640 Z= 0.176 Angle : 0.481 3.259 3570 Z= 0.275 Chirality : 0.049 0.130 468 Planarity : 0.002 0.006 444 Dihedral : 4.630 15.095 378 Min Nonbonded Distance : 2.314 Molprobity Statistics. All-atom Clashscore : 6.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.56 % Favored : 93.44 % Rotamer: Outliers : 4.44 % Allowed : 18.52 % Favored : 77.04 % 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: -2.73 (0.39), residues: 366 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.07 (0.30), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.002 HIS B 50 PHE 0.012 0.003 PHE B 94 TYR 0.003 0.001 TYR B 39 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 732 Ramachandran restraints generated. 366 Oldfield, 0 Emsley, 366 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 732 Ramachandran restraints generated. 366 Oldfield, 0 Emsley, 366 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 53 residues out of total 270 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 41 time to evaluate : 0.302 Fit side-chains REVERT: C 46 GLU cc_start: 0.7616 (OUTLIER) cc_final: 0.7361 (pt0) REVERT: D 46 GLU cc_start: 0.7763 (pt0) cc_final: 0.7423 (pt0) REVERT: D 60 LYS cc_start: 0.7774 (OUTLIER) cc_final: 0.7285 (tttp) REVERT: F 62 GLN cc_start: 0.6111 (OUTLIER) cc_final: 0.5790 (tp40) REVERT: F 83 GLU cc_start: 0.6878 (tm-30) cc_final: 0.6621 (tm-30) REVERT: B 43 LYS cc_start: 0.7237 (mtmm) cc_final: 0.6790 (mptp) outliers start: 12 outliers final: 6 residues processed: 47 average time/residue: 1.2124 time to fit residues: 58.4295 Evaluate side-chains 50 residues out of total 270 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 41 time to evaluate : 0.293 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 40 VAL Chi-restraints excluded: chain C residue 46 GLU Chi-restraints excluded: chain D residue 40 VAL Chi-restraints excluded: chain D residue 60 LYS Chi-restraints excluded: chain E residue 66 VAL Chi-restraints excluded: chain A residue 46 GLU Chi-restraints excluded: chain F residue 46 GLU Chi-restraints excluded: chain F residue 62 GLN Chi-restraints excluded: chain B residue 46 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 19 optimal weight: 7.9990 chunk 29 optimal weight: 10.0000 chunk 34 optimal weight: 7.9990 chunk 21 optimal weight: 0.6980 chunk 16 optimal weight: 0.0970 chunk 13 optimal weight: 0.8980 chunk 20 optimal weight: 2.9990 chunk 10 optimal weight: 1.9990 chunk 6 optimal weight: 10.0000 chunk 22 optimal weight: 0.0970 chunk 23 optimal weight: 0.9990 overall best weight: 0.5578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 62 GLN F 79 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7405 moved from start: 0.2645 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.018 2640 Z= 0.111 Angle : 0.424 3.467 3570 Z= 0.240 Chirality : 0.049 0.128 468 Planarity : 0.001 0.005 444 Dihedral : 4.129 13.511 378 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 5.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.19 % Favored : 94.81 % Rotamer: Outliers : 3.33 % Allowed : 20.74 % Favored : 75.93 % 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: -2.59 (0.41), residues: 366 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.96 (0.31), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS B 50 PHE 0.008 0.002 PHE F 94 TYR 0.001 0.000 TYR B 39 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 732 Ramachandran restraints generated. 366 Oldfield, 0 Emsley, 366 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 732 Ramachandran restraints generated. 366 Oldfield, 0 Emsley, 366 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 51 residues out of total 270 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 42 time to evaluate : 0.314 Fit side-chains REVERT: D 60 LYS cc_start: 0.7804 (OUTLIER) cc_final: 0.7293 (tttp) REVERT: E 62 GLN cc_start: 0.6499 (tt0) cc_final: 0.6230 (tt0) REVERT: F 62 GLN cc_start: 0.6073 (OUTLIER) cc_final: 0.5661 (tp40) REVERT: F 83 GLU cc_start: 0.6841 (tm-30) cc_final: 0.6597 (tm-30) REVERT: B 62 GLN cc_start: 0.6847 (tm-30) cc_final: 0.6422 (tm-30) outliers start: 9 outliers final: 4 residues processed: 48 average time/residue: 1.1411 time to fit residues: 56.2703 Evaluate side-chains 48 residues out of total 270 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 42 time to evaluate : 0.307 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 40 VAL Chi-restraints excluded: chain D residue 40 VAL Chi-restraints excluded: chain D residue 60 LYS Chi-restraints excluded: chain A residue 46 GLU Chi-restraints excluded: chain F residue 46 GLU Chi-restraints excluded: chain F residue 62 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 17 optimal weight: 9.9990 chunk 3 optimal weight: 4.9990 chunk 27 optimal weight: 2.9990 chunk 31 optimal weight: 7.9990 chunk 33 optimal weight: 3.9990 chunk 30 optimal weight: 0.8980 chunk 32 optimal weight: 8.9990 chunk 19 optimal weight: 0.7980 chunk 14 optimal weight: 0.9980 chunk 25 optimal weight: 5.9990 chunk 9 optimal weight: 3.9990 overall best weight: 1.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 79 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7492 moved from start: 0.2509 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 2640 Z= 0.233 Angle : 0.510 3.898 3570 Z= 0.293 Chirality : 0.050 0.131 468 Planarity : 0.002 0.006 444 Dihedral : 4.801 15.226 378 Min Nonbonded Distance : 2.286 Molprobity Statistics. All-atom Clashscore : 7.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.20 % Favored : 91.80 % Rotamer: Outliers : 3.70 % Allowed : 19.63 % Favored : 76.67 % 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: -2.63 (0.40), residues: 366 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.00 (0.31), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.003 HIS D 50 PHE 0.014 0.004 PHE B 94 TYR 0.003 0.001 TYR B 39 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 732 Ramachandran restraints generated. 366 Oldfield, 0 Emsley, 366 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 732 Ramachandran restraints generated. 366 Oldfield, 0 Emsley, 366 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 58 residues out of total 270 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 48 time to evaluate : 0.295 Fit side-chains REVERT: D 60 LYS cc_start: 0.7791 (OUTLIER) cc_final: 0.7275 (tttp) REVERT: F 62 GLN cc_start: 0.6104 (OUTLIER) cc_final: 0.5770 (tp40) REVERT: F 83 GLU cc_start: 0.6903 (tm-30) cc_final: 0.6640 (tm-30) REVERT: B 57 GLU cc_start: 0.8029 (mt-10) cc_final: 0.7819 (mt-10) REVERT: B 62 GLN cc_start: 0.6860 (tm-30) cc_final: 0.6431 (tm-30) outliers start: 10 outliers final: 6 residues processed: 54 average time/residue: 1.3889 time to fit residues: 76.5770 Evaluate side-chains 56 residues out of total 270 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 48 time to evaluate : 0.291 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 40 VAL Chi-restraints excluded: chain D residue 40 VAL Chi-restraints excluded: chain D residue 60 LYS Chi-restraints excluded: chain E residue 66 VAL Chi-restraints excluded: chain A residue 46 GLU Chi-restraints excluded: chain F residue 46 GLU Chi-restraints excluded: chain F residue 62 GLN Chi-restraints excluded: chain B residue 46 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 29 optimal weight: 8.9990 chunk 30 optimal weight: 9.9990 chunk 32 optimal weight: 8.9990 chunk 21 optimal weight: 0.6980 chunk 34 optimal weight: 4.9990 chunk 20 optimal weight: 0.9990 chunk 16 optimal weight: 8.9990 chunk 23 optimal weight: 4.9990 chunk 35 optimal weight: 0.9980 chunk 33 optimal weight: 0.9980 chunk 28 optimal weight: 2.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 79 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7465 moved from start: 0.2630 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 2640 Z= 0.175 Angle : 0.482 3.973 3570 Z= 0.275 Chirality : 0.049 0.131 468 Planarity : 0.002 0.009 444 Dihedral : 4.586 14.442 378 Min Nonbonded Distance : 2.306 Molprobity Statistics. All-atom Clashscore : 6.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.01 % Favored : 93.99 % Rotamer: Outliers : 4.07 % Allowed : 19.26 % Favored : 76.67 % 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: -2.63 (0.40), residues: 366 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.99 (0.31), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.003 HIS B 50 PHE 0.011 0.003 PHE B 94 TYR 0.003 0.001 TYR B 39 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 732 Ramachandran restraints generated. 366 Oldfield, 0 Emsley, 366 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 732 Ramachandran restraints generated. 366 Oldfield, 0 Emsley, 366 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 53 residues out of total 270 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 42 time to evaluate : 0.298 Fit side-chains REVERT: D 60 LYS cc_start: 0.7795 (OUTLIER) cc_final: 0.7272 (tttp) REVERT: F 62 GLN cc_start: 0.6058 (OUTLIER) cc_final: 0.5757 (tp40) REVERT: F 83 GLU cc_start: 0.6910 (tm-30) cc_final: 0.6649 (tm-30) REVERT: B 62 GLN cc_start: 0.6940 (tm-30) cc_final: 0.6536 (tm-30) outliers start: 11 outliers final: 7 residues processed: 48 average time/residue: 1.2838 time to fit residues: 63.0787 Evaluate side-chains 50 residues out of total 270 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 41 time to evaluate : 0.291 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 40 VAL Chi-restraints excluded: chain D residue 40 VAL Chi-restraints excluded: chain D residue 60 LYS Chi-restraints excluded: chain E residue 66 VAL Chi-restraints excluded: chain A residue 46 GLU Chi-restraints excluded: chain F residue 46 GLU Chi-restraints excluded: chain F residue 62 GLN Chi-restraints excluded: chain F residue 66 VAL Chi-restraints excluded: chain B residue 46 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 2 optimal weight: 0.5980 chunk 22 optimal weight: 9.9990 chunk 17 optimal weight: 8.9990 chunk 30 optimal weight: 3.9990 chunk 8 optimal weight: 3.9990 chunk 26 optimal weight: 7.9990 chunk 4 optimal weight: 6.9990 chunk 7 optimal weight: 3.9990 chunk 28 optimal weight: 2.9990 chunk 11 optimal weight: 9.9990 chunk 29 optimal weight: 2.9990 overall best weight: 2.9188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 79 GLN ** B 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7537 moved from start: 0.2634 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.029 2640 Z= 0.334 Angle : 0.623 4.781 3570 Z= 0.357 Chirality : 0.052 0.130 468 Planarity : 0.002 0.010 444 Dihedral : 5.356 15.940 378 Min Nonbonded Distance : 2.205 Molprobity Statistics. All-atom Clashscore : 7.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.66 % Favored : 86.34 % Rotamer: Outliers : 3.70 % Allowed : 20.00 % Favored : 76.30 % 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: -2.73 (0.40), residues: 366 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.07 (0.30), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.008 0.005 HIS C 50 PHE 0.018 0.005 PHE B 94 TYR 0.004 0.001 TYR B 39 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 732 Ramachandran restraints generated. 366 Oldfield, 0 Emsley, 366 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 732 Ramachandran restraints generated. 366 Oldfield, 0 Emsley, 366 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 59 residues out of total 270 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 49 time to evaluate : 0.273 Fit side-chains REVERT: D 60 LYS cc_start: 0.7824 (OUTLIER) cc_final: 0.7309 (tttp) REVERT: F 62 GLN cc_start: 0.6144 (OUTLIER) cc_final: 0.5531 (tp40) REVERT: F 83 GLU cc_start: 0.6947 (tm-30) cc_final: 0.6668 (tm-30) REVERT: B 57 GLU cc_start: 0.8067 (mt-10) cc_final: 0.7840 (mt-10) REVERT: B 62 GLN cc_start: 0.6879 (tm-30) cc_final: 0.6461 (tm-30) outliers start: 10 outliers final: 7 residues processed: 53 average time/residue: 1.3446 time to fit residues: 72.8923 Evaluate side-chains 58 residues out of total 270 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 49 time to evaluate : 0.323 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 40 VAL Chi-restraints excluded: chain D residue 40 VAL Chi-restraints excluded: chain D residue 60 LYS Chi-restraints excluded: chain E residue 66 VAL Chi-restraints excluded: chain A residue 46 GLU Chi-restraints excluded: chain F residue 46 GLU Chi-restraints excluded: chain F residue 62 GLN Chi-restraints excluded: chain F residue 66 VAL Chi-restraints excluded: chain B residue 46 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 3 optimal weight: 0.0670 chunk 5 optimal weight: 0.5980 chunk 25 optimal weight: 3.9990 chunk 1 optimal weight: 0.7980 chunk 20 optimal weight: 1.9990 chunk 32 optimal weight: 0.7980 chunk 19 optimal weight: 5.9990 chunk 24 optimal weight: 10.0000 chunk 0 optimal weight: 0.9980 chunk 22 optimal weight: 0.7980 chunk 21 optimal weight: 4.9990 overall best weight: 0.6118 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 79 GLN F 79 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4889 r_free = 0.4889 target = 0.221967 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.4484 r_free = 0.4484 target = 0.174758 restraints weight = 2570.506| |-----------------------------------------------------------------------------| r_work (start): 0.4479 rms_B_bonded: 2.45 r_work: 0.4364 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.4242 rms_B_bonded: 4.81 restraints_weight: 0.2500 r_work (final): 0.4242 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7604 moved from start: 0.2888 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 2640 Z= 0.129 Angle : 0.480 6.018 3570 Z= 0.269 Chirality : 0.049 0.129 468 Planarity : 0.001 0.009 444 Dihedral : 4.371 13.556 378 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 5.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.74 % Favored : 94.26 % Rotamer: Outliers : 2.96 % Allowed : 21.11 % Favored : 75.93 % 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: -2.63 (0.41), residues: 366 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.99 (0.31), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.002 HIS B 50 PHE 0.008 0.002 PHE F 94 TYR 0.002 0.000 TYR B 39 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1716.87 seconds wall clock time: 30 minutes 59.74 seconds (1859.74 seconds total)