Starting phenix.real_space_refine on Tue Feb 13 06:35:34 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8qx9_18715/02_2024/8qx9_18715.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8qx9_18715/02_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_18715/02_2024/8qx9_18715.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8qx9_18715/02_2024/8qx9_18715.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8qx9_18715/02_2024/8qx9_18715.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8qx9_18715/02_2024/8qx9_18715.pdb" } 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-5238/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: 2.08, per 1000 atoms: 0.56 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: 1.30 Conformation dependent library (CDL) restraints added in 736.0 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: 0.41 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: 0.80 Time building geometry restraints manager: 1.40 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 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: 0.600 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: 2.340 Check model and map are aligned: 0.060 Set scattering table: 0.040 Process input model: 14.140 Find NCS groups from input model: 0.280 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.750 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.240 ------------------------------------------------------------------------------- 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 : 0.461 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: 0.1258 time to fit residues: 27.3068 Evaluate side-chains 160 residues out of total 348 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 160 time to evaluate : 0.378 ------------------------------------------------------------------------------- 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: 4.9990 chunk 36 optimal weight: 6.9990 chunk 20 optimal weight: 1.9990 chunk 12 optimal weight: 5.9990 chunk 24 optimal weight: 4.9990 chunk 19 optimal weight: 0.8980 chunk 37 optimal weight: 0.6980 chunk 14 optimal weight: 0.8980 chunk 22 optimal weight: 2.9990 chunk 28 optimal weight: 0.9980 chunk 43 optimal weight: 2.9990 overall best weight: 1.0982 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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** K 319 ASN K 327 GLN L 319 ASN L 327 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6933 moved from start: 0.4175 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 3744 Z= 0.221 Angle : 0.659 7.129 4980 Z= 0.338 Chirality : 0.038 0.109 480 Planarity : 0.003 0.017 684 Dihedral : 5.861 22.113 528 Min Nonbonded Distance : 2.244 Molprobity Statistics. All-atom Clashscore : 14.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.55 % Favored : 98.45 % Rotamer: Outliers : 1.15 % Allowed : 26.15 % Favored : 72.70 % 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: -4.58 (0.17), residues: 516 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.48 (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 160 residues out of total 348 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 156 time to evaluate : 0.404 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 336 MET cc_start: 0.7737 (OUTLIER) cc_final: 0.7415 (tmm) REVERT: C 346 GLN cc_start: 0.5959 (mm-40) cc_final: 0.5671 (mm-40) REVERT: D 336 MET cc_start: 0.7741 (OUTLIER) cc_final: 0.7419 (tmm) REVERT: D 346 GLN cc_start: 0.5967 (mm-40) cc_final: 0.5674 (mm-40) REVERT: I 336 MET cc_start: 0.8032 (tmm) cc_final: 0.7614 (tmm) REVERT: I 337 MET cc_start: 0.7836 (mtp) cc_final: 0.7505 (mtp) REVERT: J 336 MET cc_start: 0.8020 (tmm) cc_final: 0.7625 (tmm) REVERT: J 337 MET cc_start: 0.7841 (mtp) cc_final: 0.7512 (mtp) outliers start: 4 outliers final: 0 residues processed: 156 average time/residue: 0.1212 time to fit residues: 23.9976 Evaluate side-chains 144 residues out of total 348 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 142 time to evaluate : 0.387 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 336 MET Chi-restraints excluded: chain D residue 336 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 24 optimal weight: 0.4980 chunk 13 optimal weight: 6.9990 chunk 36 optimal weight: 8.9990 chunk 29 optimal weight: 5.9990 chunk 12 optimal weight: 10.0000 chunk 43 optimal weight: 4.9990 chunk 47 optimal weight: 4.9990 chunk 38 optimal weight: 5.9990 chunk 14 optimal weight: 7.9990 chunk 35 optimal weight: 4.9990 chunk 32 optimal weight: 6.9990 overall best weight: 4.2988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 319 ASN B 319 ASN ** C 346 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 319 ASN H 319 ASN K 327 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7302 moved from start: 0.5716 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.058 3744 Z= 0.581 Angle : 0.917 8.070 4980 Z= 0.487 Chirality : 0.045 0.142 480 Planarity : 0.005 0.021 684 Dihedral : 7.265 29.509 528 Min Nonbonded Distance : 2.240 Molprobity Statistics. All-atom Clashscore : 21.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % Rotamer: Outliers : 6.90 % Allowed : 24.71 % Favored : 68.39 % 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: -4.66 (0.18), residues: 516 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.54 (0.14), residues: 516 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.043 0.007 TRP D 334 PHE 0.015 0.003 PHE G 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 176 residues out of total 348 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 152 time to evaluate : 0.403 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: I 307 MET cc_start: 0.8485 (ttm) cc_final: 0.8260 (ttp) REVERT: I 337 MET cc_start: 0.8286 (mtp) cc_final: 0.7908 (mtp) REVERT: J 307 MET cc_start: 0.8475 (ttm) cc_final: 0.8252 (ttp) REVERT: J 337 MET cc_start: 0.8301 (mtp) cc_final: 0.7911 (mtp) outliers start: 24 outliers final: 16 residues processed: 152 average time/residue: 0.1291 time to fit residues: 24.8378 Evaluate side-chains 160 residues out of total 348 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 144 time to evaluate : 0.408 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 345 ASN Chi-restraints excluded: chain B residue 345 ASN Chi-restraints excluded: chain C residue 336 MET Chi-restraints excluded: chain C residue 345 ASN Chi-restraints excluded: chain D residue 336 MET Chi-restraints excluded: chain D residue 345 ASN Chi-restraints excluded: chain E residue 345 ASN Chi-restraints excluded: chain F residue 345 ASN 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 Chi-restraints excluded: chain I residue 345 ASN Chi-restraints excluded: chain J residue 345 ASN Chi-restraints excluded: chain K residue 323 MET Chi-restraints excluded: chain L residue 323 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 22 optimal weight: 6.9990 chunk 4 optimal weight: 10.0000 chunk 20 optimal weight: 5.9990 chunk 29 optimal weight: 0.3980 chunk 43 optimal weight: 2.9990 chunk 46 optimal weight: 7.9990 chunk 41 optimal weight: 1.9990 chunk 12 optimal weight: 9.9990 chunk 38 optimal weight: 0.9980 chunk 26 optimal weight: 0.9980 chunk 0 optimal weight: 10.0000 overall best weight: 1.4784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 346 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 346 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7155 moved from start: 0.5961 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.020 3744 Z= 0.258 Angle : 0.719 7.680 4980 Z= 0.362 Chirality : 0.039 0.104 480 Planarity : 0.003 0.018 684 Dihedral : 6.218 22.664 528 Min Nonbonded Distance : 2.302 Molprobity Statistics. All-atom Clashscore : 17.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.16 % Favored : 98.84 % Rotamer: Outliers : 2.87 % Allowed : 32.18 % Favored : 64.94 % 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: -4.68 (0.19), residues: 516 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.56 (0.14), residues: 516 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.005 TRP C 334 PHE 0.015 0.002 PHE G 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 160 residues out of total 348 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 150 time to evaluate : 0.399 Fit side-chains REVERT: I 337 MET cc_start: 0.7999 (mtp) cc_final: 0.7716 (mtt) REVERT: J 337 MET cc_start: 0.8002 (mtp) cc_final: 0.7716 (mtt) outliers start: 10 outliers final: 3 residues processed: 150 average time/residue: 0.1204 time to fit residues: 23.0483 Evaluate side-chains 145 residues out of total 348 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 142 time to evaluate : 0.389 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 323 MET Chi-restraints excluded: chain I residue 323 MET Chi-restraints excluded: chain J residue 323 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 34 optimal weight: 10.0000 chunk 19 optimal weight: 0.2980 chunk 39 optimal weight: 4.9990 chunk 32 optimal weight: 0.0980 chunk 0 optimal weight: 10.0000 chunk 23 optimal weight: 0.7980 chunk 41 optimal weight: 1.9990 chunk 11 optimal weight: 2.9990 chunk 15 optimal weight: 2.9990 chunk 9 optimal weight: 2.9990 chunk 27 optimal weight: 2.9990 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 327 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7128 moved from start: 0.6242 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 3744 Z= 0.229 Angle : 0.648 6.883 4980 Z= 0.332 Chirality : 0.039 0.107 480 Planarity : 0.002 0.015 684 Dihedral : 5.986 21.747 528 Min Nonbonded Distance : 2.278 Molprobity Statistics. All-atom Clashscore : 18.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % Rotamer: Outliers : 2.30 % Allowed : 35.06 % 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: -4.68 (0.19), residues: 516 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.56 (0.14), residues: 516 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.004 TRP C 334 PHE 0.013 0.002 PHE H 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 158 residues out of total 348 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 150 time to evaluate : 0.388 Fit side-chains REVERT: C 322 MET cc_start: 0.6741 (mtt) cc_final: 0.6411 (mtt) REVERT: D 322 MET cc_start: 0.6722 (mtt) cc_final: 0.6462 (mtt) REVERT: I 337 MET cc_start: 0.8066 (mtp) cc_final: 0.7525 (mtt) REVERT: J 337 MET cc_start: 0.8069 (mtp) cc_final: 0.7526 (mtt) REVERT: K 312 ASN cc_start: 0.7279 (t0) cc_final: 0.6850 (t0) REVERT: L 312 ASN cc_start: 0.7284 (t0) cc_final: 0.6857 (t0) outliers start: 8 outliers final: 2 residues processed: 150 average time/residue: 0.1136 time to fit residues: 21.6978 Evaluate side-chains 150 residues out of total 348 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 148 time to evaluate : 0.346 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 345 ASN Chi-restraints excluded: chain B residue 345 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 11 optimal weight: 6.9990 chunk 46 optimal weight: 7.9990 chunk 38 optimal weight: 5.9990 chunk 21 optimal weight: 3.9990 chunk 3 optimal weight: 0.6980 chunk 15 optimal weight: 3.9990 chunk 24 optimal weight: 0.7980 chunk 44 optimal weight: 0.0970 chunk 5 optimal weight: 4.9990 chunk 26 optimal weight: 8.9990 chunk 33 optimal weight: 1.9990 overall best weight: 1.5182 ------------------------------------------------------------------------------- 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 ** D 346 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 331 GLN ** G 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 331 GLN ** G 346 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 331 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7151 moved from start: 0.6520 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 3744 Z= 0.265 Angle : 0.671 7.444 4980 Z= 0.343 Chirality : 0.038 0.109 480 Planarity : 0.002 0.014 684 Dihedral : 5.912 21.137 528 Min Nonbonded Distance : 2.213 Molprobity Statistics. All-atom Clashscore : 20.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.94 % Favored : 98.06 % Rotamer: Outliers : 4.31 % Allowed : 31.90 % Favored : 63.79 % 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: -4.71 (0.19), residues: 516 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.58 (0.15), residues: 516 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.004 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 161 residues out of total 348 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 146 time to evaluate : 0.385 Fit side-chains REVERT: I 337 MET cc_start: 0.7918 (mtp) cc_final: 0.7696 (mtt) REVERT: J 337 MET cc_start: 0.7923 (mtp) cc_final: 0.7683 (mtt) outliers start: 15 outliers final: 8 residues processed: 146 average time/residue: 0.1175 time to fit residues: 21.9415 Evaluate side-chains 154 residues out of total 348 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 146 time to evaluate : 0.353 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 344 GLN Chi-restraints excluded: chain H residue 323 MET Chi-restraints excluded: chain H residue 344 GLN Chi-restraints excluded: chain I residue 323 MET Chi-restraints excluded: chain I residue 346 GLN Chi-restraints excluded: chain J residue 346 GLN Chi-restraints excluded: chain K residue 323 MET Chi-restraints excluded: chain L residue 323 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 26 optimal weight: 8.9990 chunk 39 optimal weight: 0.9990 chunk 25 optimal weight: 4.9990 chunk 46 optimal weight: 10.0000 chunk 28 optimal weight: 5.9990 chunk 21 optimal weight: 4.9990 chunk 18 optimal weight: 0.7980 chunk 27 optimal weight: 4.9990 chunk 13 optimal weight: 0.6980 chunk 9 optimal weight: 5.9990 chunk 8 optimal weight: 10.0000 overall best weight: 2.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 346 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7256 moved from start: 0.6821 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.030 3744 Z= 0.378 Angle : 0.744 8.034 4980 Z= 0.385 Chirality : 0.040 0.110 480 Planarity : 0.003 0.020 684 Dihedral : 6.340 23.335 528 Min Nonbonded Distance : 2.189 Molprobity Statistics. All-atom Clashscore : 21.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.04 % Favored : 94.96 % Rotamer: Outliers : 3.74 % Allowed : 34.20 % Favored : 62.07 % 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: -4.97 (0.20), residues: 516 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.78 (0.15), residues: 516 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.005 TRP G 334 PHE 0.010 0.002 PHE G 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 160 residues out of total 348 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 147 time to evaluate : 0.391 Fit side-chains REVERT: A 336 MET cc_start: 0.7676 (OUTLIER) cc_final: 0.7082 (tmt) REVERT: B 336 MET cc_start: 0.7749 (OUTLIER) cc_final: 0.7114 (tmt) REVERT: I 337 MET cc_start: 0.8090 (mtp) cc_final: 0.7866 (mtt) REVERT: J 337 MET cc_start: 0.8088 (mtp) cc_final: 0.7850 (mtt) outliers start: 13 outliers final: 9 residues processed: 147 average time/residue: 0.1212 time to fit residues: 22.9467 Evaluate side-chains 157 residues out of total 348 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 146 time to evaluate : 0.349 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 336 MET Chi-restraints excluded: chain B residue 336 MET Chi-restraints excluded: chain G residue 323 MET Chi-restraints excluded: chain G residue 344 GLN Chi-restraints excluded: chain H residue 323 MET Chi-restraints excluded: chain H residue 344 GLN Chi-restraints excluded: chain I residue 323 MET Chi-restraints excluded: chain I residue 346 GLN Chi-restraints excluded: chain J residue 346 GLN Chi-restraints excluded: chain K residue 323 MET Chi-restraints excluded: chain L residue 323 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 29 optimal weight: 2.9990 chunk 31 optimal weight: 0.8980 chunk 22 optimal weight: 1.9990 chunk 4 optimal weight: 10.0000 chunk 36 optimal weight: 8.9990 chunk 42 optimal weight: 7.9990 chunk 44 optimal weight: 6.9990 chunk 40 optimal weight: 0.6980 chunk 43 optimal weight: 0.9990 chunk 25 optimal weight: 5.9990 chunk 18 optimal weight: 5.9990 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 346 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7198 moved from start: 0.6936 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 3744 Z= 0.272 Angle : 0.701 8.108 4980 Z= 0.358 Chirality : 0.039 0.107 480 Planarity : 0.002 0.017 684 Dihedral : 6.004 21.217 528 Min Nonbonded Distance : 2.207 Molprobity Statistics. All-atom Clashscore : 19.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer: Outliers : 4.31 % Allowed : 37.36 % Favored : 58.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -5.02 (0.20), residues: 516 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.82 (0.15), residues: 516 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.004 TRP G 334 PHE 0.012 0.002 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: 15 poor density : 148 time to evaluate : 0.381 Fit side-chains REVERT: A 336 MET cc_start: 0.7430 (OUTLIER) cc_final: 0.6957 (tmt) REVERT: B 336 MET cc_start: 0.7517 (OUTLIER) cc_final: 0.6980 (tmt) outliers start: 15 outliers final: 9 residues processed: 148 average time/residue: 0.1147 time to fit residues: 21.6485 Evaluate side-chains 157 residues out of total 348 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 146 time to evaluate : 0.354 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 336 MET Chi-restraints excluded: chain B residue 336 MET Chi-restraints excluded: chain G residue 323 MET Chi-restraints excluded: chain G residue 344 GLN Chi-restraints excluded: chain H residue 323 MET Chi-restraints excluded: chain H residue 344 GLN Chi-restraints excluded: chain I residue 346 GLN Chi-restraints excluded: chain J residue 323 MET Chi-restraints excluded: chain J residue 346 GLN Chi-restraints excluded: chain K residue 323 MET Chi-restraints excluded: chain L residue 323 MET 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: 0.7980 chunk 38 optimal weight: 0.9990 chunk 40 optimal weight: 4.9990 chunk 42 optimal weight: 3.9990 chunk 28 optimal weight: 10.0000 chunk 45 optimal weight: 0.7980 chunk 27 optimal weight: 0.8980 chunk 21 optimal weight: 0.8980 chunk 31 optimal weight: 4.9990 chunk 47 optimal weight: 0.7980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7112 moved from start: 0.7057 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 3744 Z= 0.204 Angle : 0.663 7.691 4980 Z= 0.338 Chirality : 0.038 0.105 480 Planarity : 0.002 0.013 684 Dihedral : 5.655 20.744 528 Min Nonbonded Distance : 2.257 Molprobity Statistics. All-atom Clashscore : 18.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 2.87 % Allowed : 39.37 % Favored : 57.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.88 (0.20), residues: 516 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.72 (0.15), residues: 516 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.003 TRP D 334 PHE 0.012 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 161 residues out of total 348 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 151 time to evaluate : 0.381 Fit side-chains REVERT: C 336 MET cc_start: 0.6997 (tmm) cc_final: 0.6745 (tmm) outliers start: 10 outliers final: 7 residues processed: 151 average time/residue: 0.1195 time to fit residues: 22.9129 Evaluate side-chains 153 residues out of total 348 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 146 time to evaluate : 0.390 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 323 MET Chi-restraints excluded: chain G residue 344 GLN Chi-restraints excluded: chain H residue 323 MET Chi-restraints excluded: chain H residue 344 GLN Chi-restraints excluded: chain I residue 346 GLN Chi-restraints excluded: chain J residue 346 GLN Chi-restraints excluded: chain K residue 323 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 44 optimal weight: 0.0030 chunk 38 optimal weight: 0.7980 chunk 3 optimal weight: 4.9990 chunk 29 optimal weight: 0.9980 chunk 23 optimal weight: 0.9980 chunk 30 optimal weight: 3.9990 chunk 40 optimal weight: 7.9990 chunk 11 optimal weight: 0.4980 chunk 35 optimal weight: 1.9990 chunk 5 optimal weight: 4.9990 chunk 10 optimal weight: 6.9990 overall best weight: 0.6590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 344 GLN ** C 346 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 344 GLN ** D 346 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7085 moved from start: 0.7145 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 3744 Z= 0.201 Angle : 0.710 11.038 4980 Z= 0.356 Chirality : 0.039 0.108 480 Planarity : 0.002 0.014 684 Dihedral : 5.740 24.911 528 Min Nonbonded Distance : 2.265 Molprobity Statistics. All-atom Clashscore : 19.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 2.59 % Allowed : 40.52 % Favored : 56.90 % 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 0.011 0.002 TRP C 334 PHE 0.010 0.002 PHE G 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 157 residues out of total 348 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 148 time to evaluate : 0.395 Fit side-chains REVERT: C 336 MET cc_start: 0.6933 (tmm) cc_final: 0.6567 (tmm) outliers start: 9 outliers final: 5 residues processed: 148 average time/residue: 0.1216 time to fit residues: 22.7929 Evaluate side-chains 151 residues out of total 348 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 146 time to evaluate : 0.448 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 323 MET Chi-restraints excluded: chain G residue 344 GLN Chi-restraints excluded: chain H residue 323 MET Chi-restraints excluded: chain H residue 344 GLN Chi-restraints excluded: chain J residue 346 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 38 optimal weight: 9.9990 chunk 15 optimal weight: 3.9990 chunk 39 optimal weight: 1.9990 chunk 4 optimal weight: 10.0000 chunk 7 optimal weight: 0.9990 chunk 33 optimal weight: 2.9990 chunk 2 optimal weight: 7.9990 chunk 27 optimal weight: 4.9990 chunk 43 optimal weight: 0.9990 chunk 25 optimal weight: 0.6980 chunk 32 optimal weight: 5.9990 overall best weight: 1.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 346 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 331 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 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5212 r_free = 0.5212 target = 0.382861 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 90)----------------| | r_work = 0.5701 r_free = 0.5701 target = 0.262341 restraints weight = 5291.703| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 22)----------------| | r_work = 0.5701 r_free = 0.5701 target = 0.262341 restraints weight = 4777.862| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.5701 r_free = 0.5701 target = 0.262341 restraints weight = 4777.862| |-----------------------------------------------------------------------------| r_work (final): 0.5033 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7392 moved from start: 0.7214 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= 0.271 Angle : 0.719 9.481 4980 Z= 0.364 Chirality : 0.039 0.108 480 Planarity : 0.002 0.013 684 Dihedral : 5.957 24.563 528 Min Nonbonded Distance : 2.230 Molprobity Statistics. All-atom Clashscore : 20.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.68 % Favored : 96.32 % Rotamer: Outliers : 2.30 % Allowed : 39.94 % Favored : 57.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.87 (0.20), residues: 516 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.71 (0.15), residues: 516 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.004 TRP D 334 PHE 0.008 0.002 PHE G 313 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1219.07 seconds wall clock time: 22 minutes 25.73 seconds (1345.73 seconds total)