Starting phenix.real_space_refine on Fri Aug 2 16:47:32 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8qx9_18715/08_2024/8qx9_18715.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8qx9_18715/08_2024/8qx9_18715.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.76 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8qx9_18715/08_2024/8qx9_18715.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8qx9_18715/08_2024/8qx9_18715.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8qx9_18715/08_2024/8qx9_18715.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8qx9_18715/08_2024/8qx9_18715.cif" } resolution = 3.76 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: 4 Type Number sf(0) Gaussians S 84 5.16 5 C 2232 2.51 5 N 660 2.21 5 O 720 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 313": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 313": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 313": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 313": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 313": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 313": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 313": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 313": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 313": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 313": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 313": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 313": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/chem_data/mon_lib" Total number of atoms: 3696 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 308 Number of conformers: 1 Conformer: "" Number of residues, atoms: 45, 308 Classifications: {'peptide': 45} Link IDs: {'PTRANS': 1, 'TRANS': 43} Chain: "B" Number of atoms: 308 Number of conformers: 1 Conformer: "" Number of residues, atoms: 45, 308 Classifications: {'peptide': 45} Link IDs: {'PTRANS': 1, 'TRANS': 43} Chain: "C" Number of atoms: 308 Number of conformers: 1 Conformer: "" Number of residues, atoms: 45, 308 Classifications: {'peptide': 45} Link IDs: {'PTRANS': 1, 'TRANS': 43} Chain: "D" Number of atoms: 308 Number of conformers: 1 Conformer: "" Number of residues, atoms: 45, 308 Classifications: {'peptide': 45} Link IDs: {'PTRANS': 1, 'TRANS': 43} Chain: "E" Number of atoms: 308 Number of conformers: 1 Conformer: "" Number of residues, atoms: 45, 308 Classifications: {'peptide': 45} Link IDs: {'PTRANS': 1, 'TRANS': 43} Chain: "F" Number of atoms: 308 Number of conformers: 1 Conformer: "" Number of residues, atoms: 45, 308 Classifications: {'peptide': 45} Link IDs: {'PTRANS': 1, 'TRANS': 43} Chain: "G" Number of atoms: 308 Number of conformers: 1 Conformer: "" Number of residues, atoms: 45, 308 Classifications: {'peptide': 45} Link IDs: {'PTRANS': 1, 'TRANS': 43} Chain: "H" Number of atoms: 308 Number of conformers: 1 Conformer: "" Number of residues, atoms: 45, 308 Classifications: {'peptide': 45} Link IDs: {'PTRANS': 1, 'TRANS': 43} Chain: "I" Number of atoms: 308 Number of conformers: 1 Conformer: "" Number of residues, atoms: 45, 308 Classifications: {'peptide': 45} Link IDs: {'PTRANS': 1, 'TRANS': 43} Chain: "J" Number of atoms: 308 Number of conformers: 1 Conformer: "" Number of residues, atoms: 45, 308 Classifications: {'peptide': 45} Link IDs: {'PTRANS': 1, 'TRANS': 43} Chain: "K" Number of atoms: 308 Number of conformers: 1 Conformer: "" Number of residues, atoms: 45, 308 Classifications: {'peptide': 45} Link IDs: {'PTRANS': 1, 'TRANS': 43} Chain: "L" Number of atoms: 308 Number of conformers: 1 Conformer: "" Number of residues, atoms: 45, 308 Classifications: {'peptide': 45} Link IDs: {'PTRANS': 1, 'TRANS': 43} Time building chain proxies: 2.39, per 1000 atoms: 0.65 Number of scatterers: 3696 At special positions: 0 Unit cell: (102.96, 84.24, 46.8, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 84 16.00 O 720 8.00 N 660 7.00 C 2232 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: 1.31 Conformation dependent library (CDL) restraints added in 602.4 milliseconds 1032 Ramachandran restraints generated. 516 Oldfield, 0 Emsley, 516 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 888 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 6 sheets defined 0.0% alpha, 20.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.47 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'A' and resid 311 through 312 Processing sheet with id=AA2, first strand: chain 'A' and resid 321 through 323 Processing sheet with id=AA3, first strand: chain 'A' and resid 328 through 334 removed outlier: 6.592A pdb=" N ALA A 329 " --> pdb=" O LEU C 330 " (cutoff:3.500A) removed outlier: 8.381A pdb=" N SER C 332 " --> pdb=" O ALA A 329 " (cutoff:3.500A) removed outlier: 6.755A pdb=" N GLN A 331 " --> pdb=" O SER C 332 " (cutoff:3.500A) removed outlier: 8.204A pdb=" N TRP C 334 " --> pdb=" O GLN A 331 " (cutoff:3.500A) removed outlier: 6.760A pdb=" N SER A 333 " --> pdb=" O TRP C 334 " (cutoff:3.500A) removed outlier: 6.592A pdb=" N ALA C 329 " --> pdb=" O LEU E 330 " (cutoff:3.500A) removed outlier: 8.381A pdb=" N SER E 332 " --> pdb=" O ALA C 329 " (cutoff:3.500A) removed outlier: 6.755A pdb=" N GLN C 331 " --> pdb=" O SER E 332 " (cutoff:3.500A) removed outlier: 8.203A pdb=" N TRP E 334 " --> pdb=" O GLN C 331 " (cutoff:3.500A) removed outlier: 6.761A pdb=" N SER C 333 " --> pdb=" O TRP E 334 " (cutoff:3.500A) removed outlier: 6.592A pdb=" N ALA E 329 " --> pdb=" O LEU G 330 " (cutoff:3.500A) removed outlier: 8.381A pdb=" N SER G 332 " --> pdb=" O ALA E 329 " (cutoff:3.500A) removed outlier: 6.755A pdb=" N GLN E 331 " --> pdb=" O SER G 332 " (cutoff:3.500A) removed outlier: 8.204A pdb=" N TRP G 334 " --> pdb=" O GLN E 331 " (cutoff:3.500A) removed outlier: 6.760A pdb=" N SER E 333 " --> pdb=" O TRP G 334 " (cutoff:3.500A) removed outlier: 6.592A pdb=" N ALA G 329 " --> pdb=" O LEU I 330 " (cutoff:3.500A) removed outlier: 8.381A pdb=" N SER I 332 " --> pdb=" O ALA G 329 " (cutoff:3.500A) removed outlier: 6.755A pdb=" N GLN G 331 " --> pdb=" O SER I 332 " (cutoff:3.500A) removed outlier: 8.204A pdb=" N TRP I 334 " --> pdb=" O GLN G 331 " (cutoff:3.500A) removed outlier: 6.761A pdb=" N SER G 333 " --> pdb=" O TRP I 334 " (cutoff:3.500A) removed outlier: 6.592A pdb=" N ALA I 329 " --> pdb=" O LEU K 330 " (cutoff:3.500A) removed outlier: 8.381A pdb=" N SER K 332 " --> pdb=" O ALA I 329 " (cutoff:3.500A) removed outlier: 6.755A pdb=" N GLN I 331 " --> pdb=" O SER K 332 " (cutoff:3.500A) removed outlier: 8.204A pdb=" N TRP K 334 " --> pdb=" O GLN I 331 " (cutoff:3.500A) removed outlier: 6.761A pdb=" N SER I 333 " --> pdb=" O TRP K 334 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'B' and resid 311 through 312 Processing sheet with id=AA5, first strand: chain 'B' and resid 321 through 323 Processing sheet with id=AA6, first strand: chain 'B' and resid 328 through 334 removed outlier: 6.592A pdb=" N ALA B 329 " --> pdb=" O LEU D 330 " (cutoff:3.500A) removed outlier: 8.381A pdb=" N SER D 332 " --> pdb=" O ALA B 329 " (cutoff:3.500A) removed outlier: 6.755A pdb=" N GLN B 331 " --> pdb=" O SER D 332 " (cutoff:3.500A) removed outlier: 8.204A pdb=" N TRP D 334 " --> pdb=" O GLN B 331 " (cutoff:3.500A) removed outlier: 6.760A pdb=" N SER B 333 " --> pdb=" O TRP D 334 " (cutoff:3.500A) removed outlier: 6.592A pdb=" N ALA D 329 " --> pdb=" O LEU F 330 " (cutoff:3.500A) removed outlier: 8.381A pdb=" N SER F 332 " --> pdb=" O ALA D 329 " (cutoff:3.500A) removed outlier: 6.755A pdb=" N GLN D 331 " --> pdb=" O SER F 332 " (cutoff:3.500A) removed outlier: 8.203A pdb=" N TRP F 334 " --> pdb=" O GLN D 331 " (cutoff:3.500A) removed outlier: 6.761A pdb=" N SER D 333 " --> pdb=" O TRP F 334 " (cutoff:3.500A) removed outlier: 6.592A pdb=" N ALA F 329 " --> pdb=" O LEU H 330 " (cutoff:3.500A) removed outlier: 8.381A pdb=" N SER H 332 " --> pdb=" O ALA F 329 " (cutoff:3.500A) removed outlier: 6.755A pdb=" N GLN F 331 " --> pdb=" O SER H 332 " (cutoff:3.500A) removed outlier: 8.204A pdb=" N TRP H 334 " --> pdb=" O GLN F 331 " (cutoff:3.500A) removed outlier: 6.760A pdb=" N SER F 333 " --> pdb=" O TRP H 334 " (cutoff:3.500A) removed outlier: 6.592A pdb=" N ALA H 329 " --> pdb=" O LEU J 330 " (cutoff:3.500A) removed outlier: 8.381A pdb=" N SER J 332 " --> pdb=" O ALA H 329 " (cutoff:3.500A) removed outlier: 6.755A pdb=" N GLN H 331 " --> pdb=" O SER J 332 " (cutoff:3.500A) removed outlier: 8.204A pdb=" N TRP J 334 " --> pdb=" O GLN H 331 " (cutoff:3.500A) removed outlier: 6.761A pdb=" N SER H 333 " --> pdb=" O TRP J 334 " (cutoff:3.500A) removed outlier: 6.592A pdb=" N ALA J 329 " --> pdb=" O LEU L 330 " (cutoff:3.500A) removed outlier: 8.381A pdb=" N SER L 332 " --> pdb=" O ALA J 329 " (cutoff:3.500A) removed outlier: 6.755A pdb=" N GLN J 331 " --> pdb=" O SER L 332 " (cutoff:3.500A) removed outlier: 8.204A pdb=" N TRP L 334 " --> pdb=" O GLN J 331 " (cutoff:3.500A) removed outlier: 6.761A pdb=" N SER J 333 " --> pdb=" O TRP L 334 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 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: 0.84 Time building geometry restraints manager: 1.47 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.31: 648 1.31 - 1.44: 972 1.44 - 1.56: 1956 1.56 - 1.69: 0 1.69 - 1.81: 168 Bond restraints: 3744 Sorted by residual: bond pdb=" C PRO E 320 " pdb=" O PRO E 320 " ideal model delta sigma weight residual 1.233 1.189 0.044 1.16e-02 7.43e+03 1.42e+01 bond pdb=" C PRO F 320 " pdb=" O PRO F 320 " ideal model delta sigma weight residual 1.233 1.189 0.044 1.16e-02 7.43e+03 1.42e+01 bond pdb=" C PRO D 320 " pdb=" O PRO D 320 " ideal model delta sigma weight residual 1.233 1.189 0.044 1.16e-02 7.43e+03 1.42e+01 bond pdb=" C PRO C 320 " pdb=" O PRO C 320 " ideal model delta sigma weight residual 1.233 1.189 0.044 1.16e-02 7.43e+03 1.42e+01 bond pdb=" C PRO J 320 " pdb=" O PRO J 320 " ideal model delta sigma weight residual 1.233 1.189 0.044 1.16e-02 7.43e+03 1.41e+01 ... (remaining 3739 not shown) Histogram of bond angle deviations from ideal: 99.20 - 106.20: 236 106.20 - 113.21: 1624 113.21 - 120.21: 1596 120.21 - 127.22: 1488 127.22 - 134.22: 36 Bond angle restraints: 4980 Sorted by residual: angle pdb=" N GLN E 327 " pdb=" CA GLN E 327 " pdb=" C GLN E 327 " ideal model delta sigma weight residual 111.36 105.16 6.20 1.09e+00 8.42e-01 3.24e+01 angle pdb=" N GLN I 327 " pdb=" CA GLN I 327 " pdb=" C GLN I 327 " ideal model delta sigma weight residual 111.36 105.16 6.20 1.09e+00 8.42e-01 3.23e+01 angle pdb=" N GLN J 327 " pdb=" CA GLN J 327 " pdb=" C GLN J 327 " ideal model delta sigma weight residual 111.36 105.16 6.20 1.09e+00 8.42e-01 3.23e+01 angle pdb=" N GLN K 327 " pdb=" CA GLN K 327 " pdb=" C GLN K 327 " ideal model delta sigma weight residual 111.36 105.17 6.19 1.09e+00 8.42e-01 3.23e+01 angle pdb=" N GLN L 327 " pdb=" CA GLN L 327 " pdb=" C GLN L 327 " ideal model delta sigma weight residual 111.36 105.17 6.19 1.09e+00 8.42e-01 3.23e+01 ... (remaining 4975 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.26: 1858 16.26 - 32.51: 218 32.51 - 48.76: 84 48.76 - 65.02: 12 65.02 - 81.27: 24 Dihedral angle restraints: 2196 sinusoidal: 780 harmonic: 1416 Sorted by residual: dihedral pdb=" C PHE K 316 " pdb=" N PHE K 316 " pdb=" CA PHE K 316 " pdb=" CB PHE K 316 " ideal model delta harmonic sigma weight residual -122.60 -114.64 -7.96 0 2.50e+00 1.60e-01 1.01e+01 dihedral pdb=" C PHE L 316 " pdb=" N PHE L 316 " pdb=" CA PHE L 316 " pdb=" CB PHE L 316 " ideal model delta harmonic sigma weight residual -122.60 -114.64 -7.96 0 2.50e+00 1.60e-01 1.01e+01 dihedral pdb=" C PHE G 316 " pdb=" N PHE G 316 " pdb=" CA PHE G 316 " pdb=" CB PHE G 316 " ideal model delta harmonic sigma weight residual -122.60 -114.65 -7.95 0 2.50e+00 1.60e-01 1.01e+01 ... (remaining 2193 not shown) Histogram of chiral volume deviations from ideal: 0.004 - 0.056: 182 0.056 - 0.107: 142 0.107 - 0.159: 84 0.159 - 0.210: 58 0.210 - 0.262: 14 Chirality restraints: 480 Sorted by residual: chirality pdb=" CA TRP A 334 " pdb=" N TRP A 334 " pdb=" C TRP A 334 " pdb=" CB TRP A 334 " both_signs ideal model delta sigma weight residual False 2.51 2.25 0.26 2.00e-01 2.50e+01 1.72e+00 chirality pdb=" CA TRP B 334 " pdb=" N TRP B 334 " pdb=" C TRP B 334 " pdb=" CB TRP B 334 " both_signs ideal model delta sigma weight residual False 2.51 2.25 0.26 2.00e-01 2.50e+01 1.72e+00 chirality pdb=" CA TRP G 334 " pdb=" N TRP G 334 " pdb=" C TRP G 334 " pdb=" CB TRP G 334 " both_signs ideal model delta sigma weight residual False 2.51 2.25 0.26 2.00e-01 2.50e+01 1.70e+00 ... (remaining 477 not shown) Planarity restraints: 684 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP C 334 " 0.028 2.00e-02 2.50e+03 1.75e-02 7.63e+00 pdb=" CG TRP C 334 " -0.046 2.00e-02 2.50e+03 pdb=" CD1 TRP C 334 " 0.007 2.00e-02 2.50e+03 pdb=" CD2 TRP C 334 " 0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP C 334 " 0.003 2.00e-02 2.50e+03 pdb=" CE2 TRP C 334 " 0.003 2.00e-02 2.50e+03 pdb=" CE3 TRP C 334 " -0.004 2.00e-02 2.50e+03 pdb=" CZ2 TRP C 334 " 0.006 2.00e-02 2.50e+03 pdb=" CZ3 TRP C 334 " 0.001 2.00e-02 2.50e+03 pdb=" CH2 TRP C 334 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP D 334 " 0.028 2.00e-02 2.50e+03 1.75e-02 7.63e+00 pdb=" CG TRP D 334 " -0.046 2.00e-02 2.50e+03 pdb=" CD1 TRP D 334 " 0.007 2.00e-02 2.50e+03 pdb=" CD2 TRP D 334 " 0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP D 334 " 0.003 2.00e-02 2.50e+03 pdb=" CE2 TRP D 334 " 0.003 2.00e-02 2.50e+03 pdb=" CE3 TRP D 334 " -0.004 2.00e-02 2.50e+03 pdb=" CZ2 TRP D 334 " 0.006 2.00e-02 2.50e+03 pdb=" CZ3 TRP D 334 " 0.001 2.00e-02 2.50e+03 pdb=" CH2 TRP D 334 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP L 334 " 0.028 2.00e-02 2.50e+03 1.75e-02 7.63e+00 pdb=" CG TRP L 334 " -0.046 2.00e-02 2.50e+03 pdb=" CD1 TRP L 334 " 0.007 2.00e-02 2.50e+03 pdb=" CD2 TRP L 334 " 0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP L 334 " 0.003 2.00e-02 2.50e+03 pdb=" CE2 TRP L 334 " 0.003 2.00e-02 2.50e+03 pdb=" CE3 TRP L 334 " -0.004 2.00e-02 2.50e+03 pdb=" CZ2 TRP L 334 " 0.006 2.00e-02 2.50e+03 pdb=" CZ3 TRP L 334 " 0.001 2.00e-02 2.50e+03 pdb=" CH2 TRP L 334 " 0.001 2.00e-02 2.50e+03 ... (remaining 681 not shown) Histogram of nonbonded interaction distances: 2.50 - 2.98: 1576 2.98 - 3.46: 3594 3.46 - 3.94: 6298 3.94 - 4.42: 6843 4.42 - 4.90: 13577 Nonbonded interactions: 31888 Sorted by model distance: nonbonded pdb=" N ILE A 318 " pdb=" O ILE A 318 " model vdw 2.496 2.496 nonbonded pdb=" N ILE B 318 " pdb=" O ILE B 318 " model vdw 2.496 2.496 nonbonded pdb=" N ILE J 318 " pdb=" O ILE J 318 " model vdw 2.496 2.496 nonbonded pdb=" N ILE I 318 " pdb=" O ILE I 318 " model vdw 2.496 2.496 nonbonded pdb=" N ILE H 318 " pdb=" O ILE H 318 " model vdw 2.496 2.496 ... (remaining 31883 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' } 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 group one per residue 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: 0.610 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.140 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 14.560 Find NCS groups from input model: 0.150 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.750 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.290 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6797 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 : 0.014 0.044 3744 Z= 0.915 Angle : 2.173 7.720 4980 Z= 1.625 Chirality : 0.110 0.262 480 Planarity : 0.010 0.025 684 Dihedral : 18.791 81.271 1308 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 2.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 0.00 % Allowed : 27.59 % Favored : 72.41 % 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: -4.75 (0.17), residues: 516 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.61 (0.13), residues: 516 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.046 0.010 TRP C 334 PHE 0.012 0.003 PHE L 316 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1032 Ramachandran restraints generated. 516 Oldfield, 0 Emsley, 516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1032 Ramachandran restraints generated. 516 Oldfield, 0 Emsley, 516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 348 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 172 time to evaluate : 0.372 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: I 337 MET cc_start: 0.7608 (mtp) cc_final: 0.6965 (mtp) REVERT: J 337 MET cc_start: 0.7626 (mtp) cc_final: 0.6969 (mtp) outliers start: 0 outliers final: 0 residues processed: 172 average time/residue: 0.1231 time to fit residues: 26.5977 Evaluate side-chains 160 residues out of total 348 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 160 time to evaluate : 0.374 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 40 optimal weight: 5.9990 chunk 36 optimal weight: 3.9990 chunk 20 optimal weight: 1.9990 chunk 12 optimal weight: 2.9990 chunk 24 optimal weight: 6.9990 chunk 19 optimal weight: 0.8980 chunk 37 optimal weight: 0.6980 chunk 14 optimal weight: 0.8980 chunk 22 optimal weight: 0.9990 chunk 28 optimal weight: 2.9990 chunk 43 optimal weight: 1.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 331 GLN B 331 GLN ** C 346 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 346 GLN ** E 346 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 346 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 331 GLN ** G 346 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 331 GLN ** H 346 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 346 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 346 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 319 ASN K 327 GLN L 319 ASN L 327 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6932 moved from start: 0.4226 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 3744 Z= 0.224 Angle : 0.668 7.421 4980 Z= 0.345 Chirality : 0.039 0.111 480 Planarity : 0.003 0.018 684 Dihedral : 5.850 22.376 528 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 12.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.55 % Favored : 98.45 % Rotamer: Outliers : 2.01 % Allowed : 26.72 % Favored : 71.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.57 (0.17), residues: 516 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.47 (0.13), residues: 516 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.004 TRP D 334 PHE 0.009 0.003 PHE G 313 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1032 Ramachandran restraints generated. 516 Oldfield, 0 Emsley, 516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1032 Ramachandran restraints generated. 516 Oldfield, 0 Emsley, 516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 348 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 158 time to evaluate : 0.375 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 322 MET cc_start: 0.7040 (mtt) cc_final: 0.6741 (mtt) REVERT: H 322 MET cc_start: 0.7006 (mtt) cc_final: 0.6716 (mtt) REVERT: I 336 MET cc_start: 0.7956 (tmm) cc_final: 0.7544 (tmm) REVERT: I 337 MET cc_start: 0.7852 (mtp) cc_final: 0.7520 (mtp) REVERT: J 336 MET cc_start: 0.7945 (tmm) cc_final: 0.7558 (tmm) REVERT: J 337 MET cc_start: 0.7855 (mtp) cc_final: 0.7530 (mtp) outliers start: 7 outliers final: 5 residues processed: 158 average time/residue: 0.1218 time to fit residues: 24.3580 Evaluate side-chains 145 residues out of total 348 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 140 time to evaluate : 0.352 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 336 MET Chi-restraints excluded: chain D residue 336 MET Chi-restraints excluded: chain D residue 346 GLN Chi-restraints excluded: chain I residue 345 ASN Chi-restraints excluded: chain J residue 345 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 24 optimal weight: 7.9990 chunk 13 optimal weight: 1.9990 chunk 36 optimal weight: 10.0000 chunk 29 optimal weight: 0.9980 chunk 12 optimal weight: 10.0000 chunk 43 optimal weight: 0.5980 chunk 47 optimal weight: 0.9980 chunk 38 optimal weight: 4.9990 chunk 14 optimal weight: 9.9990 chunk 35 optimal weight: 5.9990 chunk 32 optimal weight: 0.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 346 GLN D 346 GLN ** E 346 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 346 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 346 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 346 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 346 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6978 moved from start: 0.4836 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 3744 Z= 0.222 Angle : 0.687 7.622 4980 Z= 0.346 Chirality : 0.040 0.108 480 Planarity : 0.002 0.012 684 Dihedral : 5.704 20.972 528 Min Nonbonded Distance : 2.601 Molprobity Statistics. All-atom Clashscore : 11.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 2.30 % Allowed : 28.45 % Favored : 69.25 % 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: -4.42 (0.18), residues: 516 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.36 (0.14), residues: 516 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.004 TRP C 334 PHE 0.013 0.002 PHE H 313 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1032 Ramachandran restraints generated. 516 Oldfield, 0 Emsley, 516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1032 Ramachandran restraints generated. 516 Oldfield, 0 Emsley, 516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 348 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 150 time to evaluate : 0.317 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: I 307 MET cc_start: 0.8342 (ttm) cc_final: 0.8011 (ttp) REVERT: I 337 MET cc_start: 0.7766 (mtp) cc_final: 0.7318 (mtp) REVERT: J 307 MET cc_start: 0.8333 (ttm) cc_final: 0.8005 (ttp) REVERT: J 337 MET cc_start: 0.7777 (mtp) cc_final: 0.7327 (mtp) outliers start: 8 outliers final: 3 residues processed: 150 average time/residue: 0.1203 time to fit residues: 23.0052 Evaluate side-chains 143 residues out of total 348 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 140 time to evaluate : 0.375 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 345 ASN Chi-restraints excluded: chain C residue 346 GLN Chi-restraints excluded: chain D residue 345 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 22 optimal weight: 8.9990 chunk 4 optimal weight: 10.0000 chunk 20 optimal weight: 0.8980 chunk 29 optimal weight: 0.5980 chunk 43 optimal weight: 0.0040 chunk 46 optimal weight: 9.9990 chunk 41 optimal weight: 0.2980 chunk 12 optimal weight: 10.0000 chunk 38 optimal weight: 1.9990 chunk 26 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 overall best weight: 0.7594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 346 GLN E 327 GLN E 346 GLN F 346 GLN G 327 GLN G 346 GLN H 327 GLN H 346 GLN ** I 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6942 moved from start: 0.5335 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 3744 Z= 0.202 Angle : 0.659 7.525 4980 Z= 0.339 Chirality : 0.039 0.111 480 Planarity : 0.002 0.007 684 Dihedral : 5.558 22.704 528 Min Nonbonded Distance : 2.558 Molprobity Statistics. All-atom Clashscore : 11.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 6.03 % Allowed : 24.43 % Favored : 69.54 % 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: -4.37 (0.18), residues: 516 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.33 (0.14), residues: 516 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.003 TRP D 334 PHE 0.012 0.002 PHE H 313 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1032 Ramachandran restraints generated. 516 Oldfield, 0 Emsley, 516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1032 Ramachandran restraints generated. 516 Oldfield, 0 Emsley, 516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 348 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 146 time to evaluate : 0.367 Fit side-chains REVERT: C 322 MET cc_start: 0.6427 (mtt) cc_final: 0.6043 (mtt) REVERT: C 336 MET cc_start: 0.7180 (tmm) cc_final: 0.6736 (tmm) REVERT: D 322 MET cc_start: 0.6453 (mtt) cc_final: 0.6171 (mtt) REVERT: D 336 MET cc_start: 0.7192 (tmm) cc_final: 0.6747 (tmm) REVERT: I 307 MET cc_start: 0.8323 (ttm) cc_final: 0.7967 (ttp) REVERT: J 307 MET cc_start: 0.8316 (ttm) cc_final: 0.7961 (ttp) outliers start: 21 outliers final: 9 residues processed: 146 average time/residue: 0.1234 time to fit residues: 22.9007 Evaluate side-chains 149 residues out of total 348 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 140 time to evaluate : 0.338 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 345 ASN Chi-restraints excluded: chain E residue 327 GLN Chi-restraints excluded: chain E residue 346 GLN Chi-restraints excluded: chain F residue 346 GLN Chi-restraints excluded: chain G residue 323 MET Chi-restraints excluded: chain G residue 327 GLN Chi-restraints excluded: chain G residue 346 GLN Chi-restraints excluded: chain H residue 327 GLN Chi-restraints excluded: chain H residue 346 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 34 optimal weight: 4.9990 chunk 19 optimal weight: 5.9990 chunk 39 optimal weight: 4.9990 chunk 32 optimal weight: 0.0370 chunk 0 optimal weight: 10.0000 chunk 23 optimal weight: 4.9990 chunk 41 optimal weight: 2.9990 chunk 11 optimal weight: 3.9990 chunk 15 optimal weight: 0.9980 chunk 9 optimal weight: 3.9990 chunk 27 optimal weight: 0.9980 overall best weight: 1.8062 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 331 GLN B 331 GLN D 346 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7055 moved from start: 0.5677 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 3744 Z= 0.289 Angle : 0.707 7.650 4980 Z= 0.371 Chirality : 0.040 0.105 480 Planarity : 0.002 0.012 684 Dihedral : 5.677 20.765 528 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 13.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 3.45 % Allowed : 27.59 % Favored : 68.97 % 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: -4.54 (0.17), residues: 516 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.45 (0.13), residues: 516 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.004 TRP D 334 PHE 0.012 0.002 PHE G 313 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1032 Ramachandran restraints generated. 516 Oldfield, 0 Emsley, 516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1032 Ramachandran restraints generated. 516 Oldfield, 0 Emsley, 516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 348 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 148 time to evaluate : 0.345 Fit side-chains REVERT: I 336 MET cc_start: 0.7868 (tmm) cc_final: 0.7304 (tmm) REVERT: J 336 MET cc_start: 0.7864 (tmm) cc_final: 0.7298 (tmm) REVERT: K 322 MET cc_start: 0.7371 (mpp) cc_final: 0.7108 (mtt) REVERT: L 322 MET cc_start: 0.7387 (mpp) cc_final: 0.7128 (mtt) outliers start: 12 outliers final: 10 residues processed: 148 average time/residue: 0.1175 time to fit residues: 22.1675 Evaluate side-chains 154 residues out of total 348 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 144 time to evaluate : 0.403 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 323 MET Chi-restraints excluded: chain D residue 345 ASN Chi-restraints excluded: chain D residue 346 GLN Chi-restraints excluded: chain F residue 346 GLN Chi-restraints excluded: chain G residue 323 MET Chi-restraints excluded: chain G residue 345 ASN Chi-restraints excluded: chain G residue 346 GLN Chi-restraints excluded: chain H residue 323 MET Chi-restraints excluded: chain H residue 345 ASN Chi-restraints excluded: chain H residue 346 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 11 optimal weight: 4.9990 chunk 46 optimal weight: 0.0970 chunk 38 optimal weight: 2.9990 chunk 21 optimal weight: 4.9990 chunk 3 optimal weight: 1.9990 chunk 15 optimal weight: 3.9990 chunk 24 optimal weight: 10.0000 chunk 44 optimal weight: 0.0040 chunk 5 optimal weight: 3.9990 chunk 26 optimal weight: 10.0000 chunk 33 optimal weight: 0.6980 overall best weight: 1.1594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 331 GLN B 331 GLN C 331 GLN D 331 GLN E 331 GLN F 331 GLN G 331 GLN H 331 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7019 moved from start: 0.6105 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 3744 Z= 0.229 Angle : 0.682 7.166 4980 Z= 0.356 Chirality : 0.039 0.104 480 Planarity : 0.002 0.012 684 Dihedral : 5.645 20.052 528 Min Nonbonded Distance : 2.561 Molprobity Statistics. All-atom Clashscore : 14.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.39 % Favored : 99.61 % Rotamer: Outliers : 3.16 % Allowed : 33.33 % Favored : 63.51 % 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: -4.57 (0.18), residues: 516 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.48 (0.14), residues: 516 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.003 TRP D 334 PHE 0.012 0.002 PHE G 313 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1032 Ramachandran restraints generated. 516 Oldfield, 0 Emsley, 516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1032 Ramachandran restraints generated. 516 Oldfield, 0 Emsley, 516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 348 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 154 time to evaluate : 0.378 Fit side-chains REVERT: I 336 MET cc_start: 0.7627 (tmm) cc_final: 0.7122 (tmm) REVERT: J 336 MET cc_start: 0.7625 (tmm) cc_final: 0.7102 (tmm) outliers start: 11 outliers final: 4 residues processed: 154 average time/residue: 0.1254 time to fit residues: 24.4776 Evaluate side-chains 152 residues out of total 348 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 148 time to evaluate : 0.376 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 323 MET Chi-restraints excluded: chain G residue 345 ASN Chi-restraints excluded: chain H residue 323 MET Chi-restraints excluded: chain H residue 345 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 26 optimal weight: 4.9990 chunk 39 optimal weight: 5.9990 chunk 25 optimal weight: 8.9990 chunk 46 optimal weight: 0.0970 chunk 28 optimal weight: 9.9990 chunk 21 optimal weight: 4.9990 chunk 18 optimal weight: 0.7980 chunk 27 optimal weight: 2.9990 chunk 13 optimal weight: 1.9990 chunk 9 optimal weight: 4.9990 chunk 8 optimal weight: 3.9990 overall best weight: 1.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 327 GLN D 346 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7105 moved from start: 0.6463 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.030 3744 Z= 0.325 Angle : 0.783 7.627 4980 Z= 0.406 Chirality : 0.040 0.105 480 Planarity : 0.002 0.009 684 Dihedral : 5.952 22.249 528 Min Nonbonded Distance : 2.579 Molprobity Statistics. All-atom Clashscore : 13.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 4.02 % Allowed : 34.20 % Favored : 61.78 % 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: -4.70 (0.18), residues: 516 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.58 (0.14), residues: 516 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.004 TRP D 334 PHE 0.013 0.002 PHE H 313 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1032 Ramachandran restraints generated. 516 Oldfield, 0 Emsley, 516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1032 Ramachandran restraints generated. 516 Oldfield, 0 Emsley, 516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 348 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 150 time to evaluate : 0.397 Fit side-chains REVERT: D 327 GLN cc_start: 0.5652 (OUTLIER) cc_final: 0.5418 (mt0) REVERT: I 336 MET cc_start: 0.7775 (tmm) cc_final: 0.7464 (tmm) REVERT: J 336 MET cc_start: 0.7759 (tmm) cc_final: 0.7454 (tmm) outliers start: 14 outliers final: 5 residues processed: 150 average time/residue: 0.1326 time to fit residues: 25.2410 Evaluate side-chains 152 residues out of total 348 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 146 time to evaluate : 0.346 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 345 ASN Chi-restraints excluded: chain D residue 327 GLN Chi-restraints excluded: chain G residue 323 MET Chi-restraints excluded: chain G residue 345 ASN Chi-restraints excluded: chain H residue 323 MET Chi-restraints excluded: chain H residue 344 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 29 optimal weight: 4.9990 chunk 31 optimal weight: 0.8980 chunk 22 optimal weight: 5.9990 chunk 4 optimal weight: 10.0000 chunk 36 optimal weight: 20.0000 chunk 42 optimal weight: 10.0000 chunk 44 optimal weight: 6.9990 chunk 40 optimal weight: 3.9990 chunk 43 optimal weight: 0.4980 chunk 25 optimal weight: 0.9980 chunk 18 optimal weight: 5.9990 overall best weight: 2.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 331 GLN E 331 GLN G 331 GLN ** I 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7149 moved from start: 0.6716 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.031 3744 Z= 0.368 Angle : 0.844 7.926 4980 Z= 0.439 Chirality : 0.041 0.103 480 Planarity : 0.003 0.011 684 Dihedral : 6.336 22.825 528 Min Nonbonded Distance : 2.560 Molprobity Statistics. All-atom Clashscore : 14.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 2.87 % Allowed : 35.63 % Favored : 61.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.78 (0.19), residues: 516 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.64 (0.14), residues: 516 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.005 TRP D 334 PHE 0.013 0.003 PHE G 313 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1032 Ramachandran restraints generated. 516 Oldfield, 0 Emsley, 516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1032 Ramachandran restraints generated. 516 Oldfield, 0 Emsley, 516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 348 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 153 time to evaluate : 0.368 Fit side-chains REVERT: I 307 MET cc_start: 0.8331 (ttm) cc_final: 0.8011 (ttm) REVERT: I 336 MET cc_start: 0.7933 (tmm) cc_final: 0.7557 (tmm) REVERT: J 336 MET cc_start: 0.7898 (tmm) cc_final: 0.7502 (tmm) outliers start: 10 outliers final: 7 residues processed: 153 average time/residue: 0.1193 time to fit residues: 23.2307 Evaluate side-chains 156 residues out of total 348 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 149 time to evaluate : 0.433 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 337 MET Chi-restraints excluded: chain C residue 345 ASN Chi-restraints excluded: chain G residue 323 MET Chi-restraints excluded: chain G residue 344 GLN Chi-restraints excluded: chain G residue 345 ASN Chi-restraints excluded: chain H residue 323 MET Chi-restraints excluded: chain H residue 344 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 33 optimal weight: 2.9990 chunk 13 optimal weight: 1.9990 chunk 38 optimal weight: 8.9990 chunk 40 optimal weight: 7.9990 chunk 42 optimal weight: 9.9990 chunk 28 optimal weight: 6.9990 chunk 45 optimal weight: 1.9990 chunk 27 optimal weight: 0.8980 chunk 21 optimal weight: 0.9980 chunk 31 optimal weight: 1.9990 chunk 47 optimal weight: 2.9990 overall best weight: 1.5786 ------------------------------------------------------------------------------- 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: 0.7110 moved from start: 0.6951 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 3744 Z= 0.294 Angle : 0.810 7.881 4980 Z= 0.419 Chirality : 0.041 0.105 480 Planarity : 0.002 0.010 684 Dihedral : 6.159 22.331 528 Min Nonbonded Distance : 2.570 Molprobity Statistics. All-atom Clashscore : 14.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.26 % Favored : 95.74 % Rotamer: Outliers : 3.16 % Allowed : 33.62 % Favored : 63.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.76 (0.19), residues: 516 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.62 (0.15), residues: 516 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.004 TRP D 334 PHE 0.015 0.002 PHE G 313 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1032 Ramachandran restraints generated. 516 Oldfield, 0 Emsley, 516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1032 Ramachandran restraints generated. 516 Oldfield, 0 Emsley, 516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 348 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 153 time to evaluate : 0.356 Fit side-chains outliers start: 11 outliers final: 7 residues processed: 153 average time/residue: 0.1130 time to fit residues: 22.0649 Evaluate side-chains 155 residues out of total 348 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 148 time to evaluate : 0.338 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 345 ASN Chi-restraints excluded: chain G residue 323 MET Chi-restraints excluded: chain G residue 337 MET Chi-restraints excluded: chain G residue 344 GLN Chi-restraints excluded: chain G residue 345 ASN Chi-restraints excluded: chain H residue 323 MET Chi-restraints excluded: chain H residue 344 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 44 optimal weight: 1.9990 chunk 38 optimal weight: 8.9990 chunk 3 optimal weight: 4.9990 chunk 29 optimal weight: 3.9990 chunk 23 optimal weight: 2.9990 chunk 30 optimal weight: 5.9990 chunk 40 optimal weight: 3.9990 chunk 11 optimal weight: 0.9980 chunk 35 optimal weight: 1.9990 chunk 5 optimal weight: 4.9990 chunk 10 optimal weight: 3.9990 overall best weight: 2.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 344 GLN ** E 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 344 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7183 moved from start: 0.7107 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.032 3744 Z= 0.393 Angle : 0.919 9.854 4980 Z= 0.473 Chirality : 0.043 0.120 480 Planarity : 0.003 0.012 684 Dihedral : 6.427 23.911 528 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 16.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.62 % Favored : 94.38 % Rotamer: Outliers : 3.16 % Allowed : 33.62 % Favored : 63.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.92 (0.20), residues: 516 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.74 (0.15), residues: 516 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.005 TRP D 334 PHE 0.014 0.003 PHE H 313 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1032 Ramachandran restraints generated. 516 Oldfield, 0 Emsley, 516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1032 Ramachandran restraints generated. 516 Oldfield, 0 Emsley, 516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 348 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 151 time to evaluate : 0.394 Fit side-chains outliers start: 11 outliers final: 9 residues processed: 151 average time/residue: 0.1178 time to fit residues: 22.7234 Evaluate side-chains 157 residues out of total 348 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 148 time to evaluate : 0.376 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 337 MET Chi-restraints excluded: chain B residue 337 MET Chi-restraints excluded: chain C residue 323 MET Chi-restraints excluded: chain C residue 345 ASN Chi-restraints excluded: chain G residue 323 MET Chi-restraints excluded: chain G residue 344 GLN Chi-restraints excluded: chain G residue 345 ASN Chi-restraints excluded: chain H residue 323 MET Chi-restraints excluded: chain H residue 344 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 38 optimal weight: 0.4980 chunk 15 optimal weight: 4.9990 chunk 39 optimal weight: 0.7980 chunk 4 optimal weight: 10.0000 chunk 7 optimal weight: 0.6980 chunk 33 optimal weight: 2.9990 chunk 2 optimal weight: 2.9990 chunk 27 optimal weight: 0.9990 chunk 43 optimal weight: 0.8980 chunk 25 optimal weight: 0.7980 chunk 32 optimal weight: 5.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 331 GLN C 331 GLN C 346 GLN E 331 GLN G 331 GLN G 346 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5306 r_free = 0.5306 target = 0.413002 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 79)----------------| | r_work = 0.5887 r_free = 0.5887 target = 0.295311 restraints weight = 5586.854| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.5889 r_free = 0.5889 target = 0.295969 restraints weight = 4992.697| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.5889 r_free = 0.5889 target = 0.296010 restraints weight = 4687.321| |-----------------------------------------------------------------------------| r_work (final): 0.5108 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7274 moved from start: 0.7389 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 3744 Z= 0.243 Angle : 0.820 9.294 4980 Z= 0.414 Chirality : 0.040 0.105 480 Planarity : 0.002 0.011 684 Dihedral : 6.008 22.989 528 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 16.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % Rotamer: Outliers : 3.16 % Allowed : 34.20 % Favored : 62.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.81 (0.20), residues: 516 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.66 (0.15), residues: 516 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.003 TRP H 334 PHE 0.015 0.002 PHE H 313 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1250.17 seconds wall clock time: 22 minutes 49.75 seconds (1369.75 seconds total)