Starting phenix.real_space_refine on Sun Mar 10 15:10:28 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yng_33961/03_2024/7yng_33961.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yng_33961/03_2024/7yng_33961.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/7yng_33961/03_2024/7yng_33961.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yng_33961/03_2024/7yng_33961.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yng_33961/03_2024/7yng_33961.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yng_33961/03_2024/7yng_33961.pdb" } 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 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 "A TYR 39": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 46": "OE1" <-> "OE2" Residue "A GLU 57": "OE1" <-> "OE2" Residue "B TYR 39": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 46": "OE1" <-> "OE2" Residue "B GLU 57": "OE1" <-> "OE2" Residue "C TYR 39": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 46": "OE1" <-> "OE2" Residue "C GLU 57": "OE1" <-> "OE2" Residue "D TYR 39": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 46": "OE1" <-> "OE2" Residue "D GLU 57": "OE1" <-> "OE2" Residue "E TYR 39": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 46": "OE1" <-> "OE2" Residue "E GLU 57": "OE1" <-> "OE2" Residue "F TYR 39": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 46": "OE1" <-> "OE2" Residue "F GLU 57": "OE1" <-> "OE2" 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: "A" 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} 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: "F" 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: 1.76, per 1000 atoms: 0.67 Number of scatterers: 2628 At special positions: 0 Unit cell: (115.54, 102.82, 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: 0.92 Conformation dependent library (CDL) restraints added in 513.0 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 12 sheets defined 0.0% alpha, 50.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.34 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'B' and resid 40 through 41 removed outlier: 6.491A pdb=" N VAL A 40 " --> pdb=" O GLY F 41 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 45 through 58 removed outlier: 8.372A pdb=" N GLU A 46 " --> pdb=" O GLY B 47 " (cutoff:3.500A) removed outlier: 7.818A pdb=" N VAL B 49 " --> pdb=" O GLU A 46 " (cutoff:3.500A) removed outlier: 9.203A pdb=" N VAL A 48 " --> pdb=" O VAL B 49 " (cutoff:3.500A) removed outlier: 10.416A pdb=" N GLY B 51 " --> pdb=" O VAL A 48 " (cutoff:3.500A) removed outlier: 6.161A pdb=" N HIS A 50 " --> pdb=" O GLY B 51 " (cutoff:3.500A) removed outlier: 8.608A pdb=" N ALA B 53 " --> pdb=" O HIS A 50 " (cutoff:3.500A) removed outlier: 6.530A pdb=" N VAL A 52 " --> pdb=" O ALA B 53 " (cutoff:3.500A) removed outlier: 7.905A pdb=" N VAL B 55 " --> pdb=" O VAL A 52 " (cutoff:3.500A) removed outlier: 6.531A pdb=" N THR A 54 " --> pdb=" O VAL B 55 " (cutoff:3.500A) removed outlier: 8.250A pdb=" N GLU B 57 " --> pdb=" O THR A 54 " (cutoff:3.500A) removed outlier: 6.480A pdb=" N ALA A 56 " --> pdb=" O GLU B 57 " (cutoff:3.500A) removed outlier: 6.843A pdb=" N VAL F 48 " --> pdb=" O GLY A 47 " (cutoff:3.500A) removed outlier: 6.962A pdb=" N VAL A 49 " --> pdb=" O VAL F 48 " (cutoff:3.500A) removed outlier: 6.922A pdb=" N HIS F 50 " --> pdb=" O VAL A 49 " (cutoff:3.500A) removed outlier: 6.849A pdb=" N GLY A 51 " --> pdb=" O HIS F 50 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 61 through 66 removed outlier: 6.350A pdb=" N GLN A 62 " --> pdb=" O VAL F 63 " (cutoff:3.500A) removed outlier: 7.732A pdb=" N ASN F 65 " --> pdb=" O GLN A 62 " (cutoff:3.500A) removed outlier: 6.252A pdb=" N THR A 64 " --> pdb=" O ASN F 65 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 69 through 71 removed outlier: 6.478A pdb=" N VAL A 70 " --> pdb=" O VAL B 71 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 74 through 82 removed outlier: 6.841A pdb=" N VAL A 77 " --> pdb=" O ALA B 76 " (cutoff:3.500A) removed outlier: 6.950A pdb=" N ALA B 78 " --> pdb=" O VAL A 77 " (cutoff:3.500A) removed outlier: 6.904A pdb=" N GLN A 79 " --> pdb=" O ALA B 78 " (cutoff:3.500A) removed outlier: 6.912A pdb=" N LYS B 80 " --> pdb=" O GLN A 79 " (cutoff:3.500A) removed outlier: 6.916A pdb=" N THR A 81 " --> pdb=" O LYS B 80 " (cutoff:3.500A) removed outlier: 6.867A pdb=" N VAL B 82 " --> pdb=" O THR A 81 " (cutoff:3.500A) removed outlier: 6.288A pdb=" N VAL A 74 " --> pdb=" O THR F 75 " (cutoff:3.500A) removed outlier: 6.145A pdb=" N VAL F 77 " --> pdb=" O VAL A 74 " (cutoff:3.500A) removed outlier: 7.580A pdb=" N ALA A 76 " --> pdb=" O VAL F 77 " (cutoff:3.500A) removed outlier: 10.067A pdb=" N GLN F 79 " --> pdb=" O ALA A 76 " (cutoff:3.500A) removed outlier: 8.989A pdb=" N ALA A 78 " --> pdb=" O GLN F 79 " (cutoff:3.500A) removed outlier: 10.393A pdb=" N THR F 81 " --> pdb=" O ALA A 78 " (cutoff:3.500A) removed outlier: 8.701A pdb=" N LYS A 80 " --> pdb=" O THR F 81 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 89 through 92 removed outlier: 6.707A pdb=" N ALA A 89 " --> pdb=" O ALA F 90 " (cutoff:3.500A) removed outlier: 7.942A pdb=" N THR F 92 " --> pdb=" O ALA A 89 " (cutoff:3.500A) removed outlier: 6.282A pdb=" N ALA A 91 " --> pdb=" O THR F 92 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 40 through 41 removed outlier: 6.490A pdb=" N VAL C 40 " --> pdb=" O GLY D 41 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 45 through 58 removed outlier: 6.840A pdb=" N VAL D 48 " --> pdb=" O GLY C 47 " (cutoff:3.500A) removed outlier: 6.959A pdb=" N VAL C 49 " --> pdb=" O VAL D 48 " (cutoff:3.500A) removed outlier: 6.917A pdb=" N HIS D 50 " --> pdb=" O VAL C 49 " (cutoff:3.500A) removed outlier: 6.844A pdb=" N GLY C 51 " --> pdb=" O HIS D 50 " (cutoff:3.500A) removed outlier: 8.378A pdb=" N GLU C 46 " --> pdb=" O GLY E 47 " (cutoff:3.500A) removed outlier: 7.827A pdb=" N VAL E 49 " --> pdb=" O GLU C 46 " (cutoff:3.500A) removed outlier: 9.214A pdb=" N VAL C 48 " --> pdb=" O VAL E 49 " (cutoff:3.500A) removed outlier: 10.429A pdb=" N GLY E 51 " --> pdb=" O VAL C 48 " (cutoff:3.500A) removed outlier: 6.175A pdb=" N HIS C 50 " --> pdb=" O GLY E 51 " (cutoff:3.500A) removed outlier: 8.625A pdb=" N ALA E 53 " --> pdb=" O HIS C 50 " (cutoff:3.500A) removed outlier: 6.547A pdb=" N VAL C 52 " --> pdb=" O ALA E 53 " (cutoff:3.500A) removed outlier: 7.920A pdb=" N VAL E 55 " --> pdb=" O VAL C 52 " (cutoff:3.500A) removed outlier: 6.549A pdb=" N THR C 54 " --> pdb=" O VAL E 55 " (cutoff:3.500A) removed outlier: 8.267A pdb=" N GLU E 57 " --> pdb=" O THR C 54 " (cutoff:3.500A) removed outlier: 6.498A pdb=" N ALA C 56 " --> pdb=" O GLU E 57 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'D' and resid 61 through 66 removed outlier: 6.354A pdb=" N GLN C 62 " --> pdb=" O VAL D 63 " (cutoff:3.500A) removed outlier: 7.736A pdb=" N ASN D 65 " --> pdb=" O GLN C 62 " (cutoff:3.500A) removed outlier: 6.255A pdb=" N THR C 64 " --> pdb=" O ASN D 65 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 69 through 71 removed outlier: 6.478A pdb=" N VAL C 70 " --> pdb=" O VAL E 71 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 74 through 82 removed outlier: 6.283A pdb=" N VAL C 74 " --> pdb=" O THR D 75 " (cutoff:3.500A) removed outlier: 6.143A pdb=" N VAL D 77 " --> pdb=" O VAL C 74 " (cutoff:3.500A) removed outlier: 7.580A pdb=" N ALA C 76 " --> pdb=" O VAL D 77 " (cutoff:3.500A) removed outlier: 10.068A pdb=" N GLN D 79 " --> pdb=" O ALA C 76 " (cutoff:3.500A) removed outlier: 8.989A pdb=" N ALA C 78 " --> pdb=" O GLN D 79 " (cutoff:3.500A) removed outlier: 10.393A pdb=" N THR D 81 " --> pdb=" O ALA C 78 " (cutoff:3.500A) removed outlier: 8.701A pdb=" N LYS C 80 " --> pdb=" O THR D 81 " (cutoff:3.500A) removed outlier: 6.850A pdb=" N VAL C 77 " --> pdb=" O ALA E 76 " (cutoff:3.500A) removed outlier: 6.956A pdb=" N ALA E 78 " --> pdb=" O VAL C 77 " (cutoff:3.500A) removed outlier: 6.908A pdb=" N GLN C 79 " --> pdb=" O ALA E 78 " (cutoff:3.500A) removed outlier: 6.912A pdb=" N LYS E 80 " --> pdb=" O GLN C 79 " (cutoff:3.500A) removed outlier: 6.915A pdb=" N THR C 81 " --> pdb=" O LYS E 80 " (cutoff:3.500A) removed outlier: 6.863A pdb=" N VAL E 82 " --> pdb=" O THR C 81 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 89 through 92 removed outlier: 6.708A pdb=" N ALA C 89 " --> pdb=" O ALA D 90 " (cutoff:3.500A) removed outlier: 7.943A pdb=" N THR D 92 " --> pdb=" O ALA C 89 " (cutoff:3.500A) removed outlier: 6.282A pdb=" N ALA C 91 " --> pdb=" O THR D 92 " (cutoff:3.500A) 44 hydrogen bonds defined for protein. 132 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: 0.54 Time building geometry restraints manager: 1.02 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.29: 462 1.29 - 1.35: 408 1.35 - 1.42: 108 1.42 - 1.48: 450 1.48 - 1.55: 1212 Bond restraints: 2640 Sorted by residual: bond pdb=" CA SER D 87 " pdb=" C SER D 87 " ideal model delta sigma weight residual 1.528 1.509 0.019 1.35e-02 5.49e+03 2.00e+00 bond pdb=" CA SER A 87 " pdb=" C SER A 87 " ideal model delta sigma weight residual 1.528 1.509 0.019 1.35e-02 5.49e+03 2.00e+00 bond pdb=" CA SER F 87 " pdb=" C SER F 87 " ideal model delta sigma weight residual 1.528 1.509 0.019 1.35e-02 5.49e+03 1.91e+00 bond pdb=" CA SER E 87 " pdb=" C SER E 87 " ideal model delta sigma weight residual 1.528 1.509 0.019 1.35e-02 5.49e+03 1.89e+00 bond pdb=" CA SER B 87 " pdb=" C SER B 87 " ideal model delta sigma weight residual 1.528 1.510 0.018 1.35e-02 5.49e+03 1.83e+00 ... (remaining 2635 not shown) Histogram of bond angle deviations from ideal: 106.16 - 111.15: 1230 111.15 - 116.14: 637 116.14 - 121.13: 893 121.13 - 126.12: 804 126.12 - 131.11: 6 Bond angle restraints: 3570 Sorted by residual: angle pdb=" C THR A 92 " pdb=" N GLY A 93 " pdb=" CA GLY A 93 " ideal model delta sigma weight residual 119.99 123.07 -3.08 1.13e+00 7.83e-01 7.42e+00 angle pdb=" C THR B 92 " pdb=" N GLY B 93 " pdb=" CA GLY B 93 " ideal model delta sigma weight residual 119.99 123.05 -3.06 1.13e+00 7.83e-01 7.34e+00 angle pdb=" C THR D 92 " pdb=" N GLY D 93 " pdb=" CA GLY D 93 " ideal model delta sigma weight residual 119.99 123.05 -3.06 1.13e+00 7.83e-01 7.33e+00 angle pdb=" C THR C 92 " pdb=" N GLY C 93 " pdb=" CA GLY C 93 " ideal model delta sigma weight residual 119.99 123.04 -3.05 1.13e+00 7.83e-01 7.31e+00 angle pdb=" C THR F 92 " pdb=" N GLY F 93 " pdb=" CA GLY F 93 " ideal model delta sigma weight residual 119.99 123.04 -3.05 1.13e+00 7.83e-01 7.28e+00 ... (remaining 3565 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.86: 1368 14.86 - 29.73: 138 29.73 - 44.59: 36 44.59 - 59.46: 0 59.46 - 74.32: 6 Dihedral angle restraints: 1548 sinusoidal: 522 harmonic: 1026 Sorted by residual: dihedral pdb=" CA GLY F 93 " pdb=" C GLY F 93 " pdb=" N PHE F 94 " pdb=" CA PHE F 94 " ideal model delta harmonic sigma weight residual 180.00 160.78 19.22 0 5.00e+00 4.00e-02 1.48e+01 dihedral pdb=" CA GLY A 93 " pdb=" C GLY A 93 " pdb=" N PHE A 94 " pdb=" CA PHE A 94 " ideal model delta harmonic sigma weight residual 180.00 160.79 19.21 0 5.00e+00 4.00e-02 1.48e+01 dihedral pdb=" CA GLY D 93 " pdb=" C GLY D 93 " pdb=" N PHE D 94 " pdb=" CA PHE D 94 " ideal model delta harmonic sigma weight residual 180.00 160.81 19.19 0 5.00e+00 4.00e-02 1.47e+01 ... (remaining 1545 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.025: 156 0.025 - 0.050: 144 0.050 - 0.075: 68 0.075 - 0.100: 59 0.100 - 0.125: 41 Chirality restraints: 468 Sorted by residual: chirality pdb=" CA VAL C 95 " pdb=" N VAL C 95 " pdb=" C VAL C 95 " pdb=" CB VAL C 95 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 3.92e-01 chirality pdb=" CA VAL E 95 " pdb=" N VAL E 95 " pdb=" C VAL E 95 " pdb=" CB VAL E 95 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.12 2.00e-01 2.50e+01 3.86e-01 chirality pdb=" CA VAL A 71 " pdb=" N VAL A 71 " pdb=" C VAL A 71 " pdb=" CB VAL A 71 " both_signs ideal model delta sigma weight residual False 2.44 2.56 -0.12 2.00e-01 2.50e+01 3.83e-01 ... (remaining 465 not shown) Planarity restraints: 444 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLU F 83 " 0.005 2.00e-02 2.50e+03 1.01e-02 1.02e+00 pdb=" C GLU F 83 " -0.017 2.00e-02 2.50e+03 pdb=" O GLU F 83 " 0.007 2.00e-02 2.50e+03 pdb=" N GLY F 84 " 0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU B 83 " 0.005 2.00e-02 2.50e+03 1.00e-02 1.01e+00 pdb=" C GLU B 83 " -0.017 2.00e-02 2.50e+03 pdb=" O GLU B 83 " 0.007 2.00e-02 2.50e+03 pdb=" N GLY B 84 " 0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU C 83 " -0.005 2.00e-02 2.50e+03 1.00e-02 1.00e+00 pdb=" C GLU C 83 " 0.017 2.00e-02 2.50e+03 pdb=" O GLU C 83 " -0.007 2.00e-02 2.50e+03 pdb=" N GLY C 84 " -0.006 2.00e-02 2.50e+03 ... (remaining 441 not shown) Histogram of nonbonded interaction distances: 2.19 - 2.73: 156 2.73 - 3.28: 2535 3.28 - 3.82: 4208 3.82 - 4.36: 4429 4.36 - 4.90: 9232 Nonbonded interactions: 20560 Sorted by model distance: nonbonded pdb=" NZ LYS B 60 " pdb=" OE1 GLN B 62 " model vdw 2.192 2.520 nonbonded pdb=" NZ LYS E 60 " pdb=" OE1 GLN E 62 " model vdw 2.192 2.520 nonbonded pdb=" NZ LYS A 60 " pdb=" OE1 GLN A 62 " model vdw 2.192 2.520 nonbonded pdb=" NZ LYS F 60 " pdb=" OE1 GLN F 62 " model vdw 2.192 2.520 nonbonded pdb=" NZ LYS C 60 " pdb=" OE1 GLN C 62 " model vdw 2.193 2.520 ... (remaining 20555 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: 0.980 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: 4.770 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 12.000 Find NCS groups from input model: 0.180 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:2.870 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.880 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7297 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.042 2640 Z= 0.627 Angle : 0.851 4.552 3570 Z= 0.495 Chirality : 0.057 0.125 468 Planarity : 0.003 0.010 444 Dihedral : 13.706 74.320 900 Min Nonbonded Distance : 2.192 Molprobity Statistics. All-atom Clashscore : 9.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.38 % Favored : 89.62 % Rotamer: Outliers : 0.00 % Allowed : 4.44 % Favored : 95.56 % 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: -4.25 (0.31), residues: 366 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.23 (0.23), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.007 0.004 HIS D 50 PHE 0.011 0.004 PHE D 94 TYR 0.003 0.001 TYR D 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 25 residues out of total 270 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 25 time to evaluate : 0.287 Fit side-chains REVERT: A 45 LYS cc_start: 0.8481 (mtpp) cc_final: 0.8261 (mttt) REVERT: F 45 LYS cc_start: 0.8702 (mtpp) cc_final: 0.8415 (mttm) outliers start: 0 outliers final: 0 residues processed: 25 average time/residue: 0.2658 time to fit residues: 7.6040 Evaluate side-chains 23 residues out of total 270 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 23 time to evaluate : 0.253 ------------------------------------------------------------------------------- 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: 0.3980 chunk 27 optimal weight: 2.9990 chunk 15 optimal weight: 5.9990 chunk 9 optimal weight: 2.9990 chunk 18 optimal weight: 0.0170 chunk 14 optimal weight: 1.9990 chunk 28 optimal weight: 0.9980 chunk 10 optimal weight: 0.9990 chunk 17 optimal weight: 1.9990 chunk 21 optimal weight: 0.9990 chunk 32 optimal weight: 0.0570 overall best weight: 0.4938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 79 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7092 moved from start: 0.1466 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 2640 Z= 0.139 Angle : 0.471 4.494 3570 Z= 0.257 Chirality : 0.052 0.131 468 Planarity : 0.002 0.009 444 Dihedral : 4.482 14.057 378 Min Nonbonded Distance : 2.288 Molprobity Statistics. All-atom Clashscore : 6.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 0.00 % Allowed : 7.41 % Favored : 92.59 % 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: -3.06 (0.37), residues: 366 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.32 (0.28), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS A 50 PHE 0.005 0.001 PHE F 94 TYR 0.003 0.001 TYR B 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 27 residues out of total 270 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 27 time to evaluate : 0.278 Fit side-chains REVERT: B 79 GLN cc_start: 0.8600 (tt0) cc_final: 0.8393 (tt0) REVERT: F 45 LYS cc_start: 0.8484 (mtpp) cc_final: 0.8213 (mttm) outliers start: 0 outliers final: 0 residues processed: 27 average time/residue: 0.2592 time to fit residues: 8.0085 Evaluate side-chains 23 residues out of total 270 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 23 time to evaluate : 0.276 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 18 optimal weight: 0.0170 chunk 10 optimal weight: 5.9990 chunk 27 optimal weight: 7.9990 chunk 22 optimal weight: 1.9990 chunk 9 optimal weight: 8.9990 chunk 32 optimal weight: 0.0010 chunk 35 optimal weight: 0.0570 chunk 29 optimal weight: 9.9990 chunk 11 optimal weight: 2.9990 chunk 26 optimal weight: 6.9990 chunk 24 optimal weight: 7.9990 overall best weight: 1.0146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7108 moved from start: 0.1748 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 2640 Z= 0.164 Angle : 0.434 3.785 3570 Z= 0.241 Chirality : 0.051 0.123 468 Planarity : 0.002 0.009 444 Dihedral : 4.177 13.010 378 Min Nonbonded Distance : 2.292 Molprobity Statistics. All-atom Clashscore : 5.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.64 % Favored : 95.36 % Rotamer: Outliers : 0.00 % Allowed : 8.89 % Favored : 91.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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 0.002 HIS A 50 PHE 0.007 0.002 PHE F 94 TYR 0.006 0.001 TYR C 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 21 residues out of total 270 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 21 time to evaluate : 0.275 Fit side-chains REVERT: F 45 LYS cc_start: 0.8440 (mtpp) cc_final: 0.8182 (mttt) outliers start: 0 outliers final: 0 residues processed: 21 average time/residue: 0.2479 time to fit residues: 6.0767 Evaluate side-chains 18 residues out of total 270 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 18 time to evaluate : 0.267 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 16 optimal weight: 0.1980 chunk 3 optimal weight: 9.9990 chunk 15 optimal weight: 2.9990 chunk 21 optimal weight: 5.9990 chunk 32 optimal weight: 1.9990 chunk 34 optimal weight: 1.9990 chunk 17 optimal weight: 0.8980 chunk 31 optimal weight: 6.9990 chunk 9 optimal weight: 4.9990 chunk 28 optimal weight: 0.8980 chunk 19 optimal weight: 0.9980 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7102 moved from start: 0.2026 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.020 2640 Z= 0.156 Angle : 0.407 3.759 3570 Z= 0.226 Chirality : 0.050 0.123 468 Planarity : 0.001 0.008 444 Dihedral : 3.915 10.882 378 Min Nonbonded Distance : 2.290 Molprobity Statistics. All-atom Clashscore : 6.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.55 % Favored : 96.45 % Rotamer: Outliers : 0.37 % Allowed : 9.63 % Favored : 90.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -2.37 (0.42), residues: 366 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.80 (0.32), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.002 HIS A 50 PHE 0.007 0.002 PHE D 94 TYR 0.006 0.001 TYR C 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 25 residues out of total 270 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 24 time to evaluate : 0.282 Fit side-chains outliers start: 1 outliers final: 1 residues processed: 25 average time/residue: 0.2447 time to fit residues: 7.0505 Evaluate side-chains 19 residues out of total 270 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 18 time to evaluate : 0.284 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 59 THR 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: 6.9990 chunk 14 optimal weight: 9.9990 chunk 29 optimal weight: 0.6980 chunk 24 optimal weight: 7.9990 chunk 17 optimal weight: 2.9990 chunk 31 optimal weight: 3.9990 chunk 8 optimal weight: 6.9990 chunk 11 optimal weight: 0.0870 chunk 6 optimal weight: 5.9990 chunk 20 optimal weight: 0.9980 overall best weight: 1.7562 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7150 moved from start: 0.1950 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.019 2640 Z= 0.235 Angle : 0.453 5.654 3570 Z= 0.252 Chirality : 0.051 0.124 468 Planarity : 0.002 0.007 444 Dihedral : 4.203 11.732 378 Min Nonbonded Distance : 2.279 Molprobity Statistics. All-atom Clashscore : 8.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.74 % Favored : 94.26 % Rotamer: Outliers : 0.00 % Allowed : 9.26 % Favored : 90.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -2.38 (0.42), residues: 366 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.80 (0.32), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.002 HIS A 50 PHE 0.008 0.002 PHE F 94 TYR 0.009 0.002 TYR C 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 19 residues out of total 270 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 19 time to evaluate : 0.258 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 19 average time/residue: 0.2227 time to fit residues: 5.0581 Evaluate side-chains 16 residues out of total 270 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 16 time to evaluate : 0.244 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 8 optimal weight: 6.9990 chunk 34 optimal weight: 7.9990 chunk 28 optimal weight: 5.9990 chunk 16 optimal weight: 1.9990 chunk 2 optimal weight: 3.9990 chunk 11 optimal weight: 10.0000 chunk 18 optimal weight: 0.0370 chunk 33 optimal weight: 7.9990 chunk 3 optimal weight: 1.9990 chunk 19 optimal weight: 4.9990 chunk 25 optimal weight: 1.9990 overall best weight: 2.0066 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7175 moved from start: 0.1978 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.021 2640 Z= 0.261 Angle : 0.485 4.921 3570 Z= 0.268 Chirality : 0.051 0.126 468 Planarity : 0.002 0.007 444 Dihedral : 4.366 12.483 378 Min Nonbonded Distance : 2.246 Molprobity Statistics. All-atom Clashscore : 9.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.74 % Favored : 94.26 % Rotamer: Outliers : 0.00 % Allowed : 10.37 % Favored : 89.63 % 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: -2.39 (0.42), residues: 366 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.82 (0.32), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.003 HIS A 50 PHE 0.007 0.002 PHE F 94 TYR 0.009 0.002 TYR C 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 19 residues out of total 270 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 19 time to evaluate : 0.246 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 19 average time/residue: 0.2307 time to fit residues: 5.2498 Evaluate side-chains 17 residues out of total 270 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 17 time to evaluate : 0.255 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 19 optimal weight: 1.9990 chunk 29 optimal weight: 9.9990 chunk 34 optimal weight: 6.9990 chunk 21 optimal weight: 3.9990 chunk 16 optimal weight: 3.9990 chunk 13 optimal weight: 0.9980 chunk 20 optimal weight: 0.4980 chunk 10 optimal weight: 5.9990 chunk 6 optimal weight: 9.9990 chunk 22 optimal weight: 0.9990 chunk 23 optimal weight: 0.0270 overall best weight: 0.9042 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7109 moved from start: 0.2330 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.016 2640 Z= 0.144 Angle : 0.426 6.300 3570 Z= 0.234 Chirality : 0.050 0.126 468 Planarity : 0.001 0.008 444 Dihedral : 3.876 11.244 378 Min Nonbonded Distance : 2.283 Molprobity Statistics. All-atom Clashscore : 7.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.37 % Favored : 95.63 % Rotamer: Outliers : 0.37 % Allowed : 10.37 % Favored : 89.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.28 (0.43), residues: 366 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.73 (0.33), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS D 50 PHE 0.006 0.002 PHE F 94 TYR 0.005 0.001 TYR C 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 23 residues out of total 270 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 22 time to evaluate : 0.233 Fit side-chains outliers start: 1 outliers final: 1 residues processed: 22 average time/residue: 0.2549 time to fit residues: 6.5132 Evaluate side-chains 21 residues out of total 270 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 20 time to evaluate : 0.281 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 45 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 17 optimal weight: 8.9990 chunk 3 optimal weight: 0.9980 chunk 27 optimal weight: 0.9990 chunk 31 optimal weight: 4.9990 chunk 33 optimal weight: 0.9990 chunk 30 optimal weight: 2.9990 chunk 32 optimal weight: 2.9990 chunk 19 optimal weight: 1.9990 chunk 14 optimal weight: 10.0000 chunk 25 optimal weight: 0.7980 chunk 9 optimal weight: 4.9990 overall best weight: 1.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7123 moved from start: 0.2365 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 2640 Z= 0.176 Angle : 0.491 6.755 3570 Z= 0.266 Chirality : 0.051 0.126 468 Planarity : 0.002 0.024 444 Dihedral : 3.879 10.796 378 Min Nonbonded Distance : 2.289 Molprobity Statistics. All-atom Clashscore : 7.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.92 % Favored : 95.08 % Rotamer: Outliers : 0.37 % Allowed : 11.48 % Favored : 88.15 % 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: -2.22 (0.43), residues: 366 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.68 (0.33), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.002 HIS A 50 PHE 0.006 0.002 PHE F 94 TYR 0.006 0.001 TYR C 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 22 residues out of total 270 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 21 time to evaluate : 0.305 Fit side-chains outliers start: 1 outliers final: 1 residues processed: 21 average time/residue: 0.2685 time to fit residues: 6.6047 Evaluate side-chains 21 residues out of total 270 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 20 time to evaluate : 0.290 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 45 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 29 optimal weight: 1.9990 chunk 30 optimal weight: 6.9990 chunk 32 optimal weight: 1.9990 chunk 21 optimal weight: 10.0000 chunk 34 optimal weight: 1.9990 chunk 20 optimal weight: 0.8980 chunk 16 optimal weight: 3.9990 chunk 23 optimal weight: 8.9990 chunk 35 optimal weight: 0.8980 chunk 33 optimal weight: 5.9990 chunk 28 optimal weight: 4.9990 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 79 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7152 moved from start: 0.2386 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 2640 Z= 0.218 Angle : 0.520 7.138 3570 Z= 0.282 Chirality : 0.051 0.126 468 Planarity : 0.002 0.023 444 Dihedral : 4.074 11.569 378 Min Nonbonded Distance : 2.269 Molprobity Statistics. All-atom Clashscore : 7.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.19 % Favored : 94.81 % Rotamer: Outliers : 0.00 % Allowed : 11.85 % Favored : 88.15 % 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: -2.21 (0.43), residues: 366 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.67 (0.33), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.002 HIS A 50 PHE 0.007 0.002 PHE C 94 TYR 0.007 0.002 TYR C 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 22 residues out of total 270 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 22 time to evaluate : 0.283 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 22 average time/residue: 0.2509 time to fit residues: 6.4526 Evaluate side-chains 21 residues out of total 270 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 21 time to evaluate : 0.301 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 2 optimal weight: 9.9990 chunk 22 optimal weight: 2.9990 chunk 17 optimal weight: 0.9980 chunk 30 optimal weight: 7.9990 chunk 8 optimal weight: 2.9990 chunk 26 optimal weight: 6.9990 chunk 4 optimal weight: 0.8980 chunk 7 optimal weight: 0.6980 chunk 28 optimal weight: 5.9990 chunk 11 optimal weight: 1.9990 chunk 29 optimal weight: 0.0980 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7112 moved from start: 0.2633 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 2640 Z= 0.156 Angle : 0.495 7.625 3570 Z= 0.266 Chirality : 0.050 0.127 468 Planarity : 0.002 0.023 444 Dihedral : 3.774 11.255 378 Min Nonbonded Distance : 2.282 Molprobity Statistics. All-atom Clashscore : 6.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.10 % Favored : 95.90 % Rotamer: Outliers : 0.00 % Allowed : 12.22 % Favored : 87.78 % 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: -2.14 (0.43), residues: 366 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.62 (0.33), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS A 50 PHE 0.006 0.002 PHE F 94 TYR 0.005 0.001 TYR C 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 22 residues out of total 270 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 22 time to evaluate : 0.268 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 22 average time/residue: 0.2497 time to fit residues: 6.3662 Evaluate side-chains 22 residues out of total 270 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 22 time to evaluate : 0.292 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 3 optimal weight: 0.9980 chunk 5 optimal weight: 7.9990 chunk 25 optimal weight: 6.9990 chunk 1 optimal weight: 5.9990 chunk 20 optimal weight: 1.9990 chunk 32 optimal weight: 2.9990 chunk 19 optimal weight: 0.9980 chunk 24 optimal weight: 0.0570 chunk 0 optimal weight: 10.0000 chunk 22 optimal weight: 7.9990 chunk 21 optimal weight: 1.9990 overall best weight: 1.2102 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4885 r_free = 0.4885 target = 0.220656 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4567 r_free = 0.4567 target = 0.185716 restraints weight = 2599.760| |-----------------------------------------------------------------------------| r_work (start): 0.4563 rms_B_bonded: 2.64 r_work: 0.4455 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.4322 rms_B_bonded: 4.83 restraints_weight: 0.2500 r_work (final): 0.4322 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7223 moved from start: 0.2625 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 2640 Z= 0.184 Angle : 0.509 7.778 3570 Z= 0.274 Chirality : 0.050 0.125 468 Planarity : 0.002 0.021 444 Dihedral : 3.856 12.073 378 Min Nonbonded Distance : 2.285 Molprobity Statistics. All-atom Clashscore : 7.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.92 % Favored : 95.08 % Rotamer: Outliers : 0.00 % Allowed : 12.59 % Favored : 87.41 % 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: -2.13 (0.43), residues: 366 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.61 (0.33), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.002 HIS A 50 PHE 0.007 0.002 PHE F 94 TYR 0.006 0.001 TYR C 39 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1117.24 seconds wall clock time: 20 minutes 35.55 seconds (1235.55 seconds total)