Starting phenix.real_space_refine (version: dev) on Fri Feb 17 10:07:07 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7umq_26607/02_2023/7umq_26607.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7umq_26607/02_2023/7umq_26607.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.29 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7umq_26607/02_2023/7umq_26607.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7umq_26607/02_2023/7umq_26607.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7umq_26607/02_2023/7umq_26607.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7umq_26607/02_2023/7umq_26607.pdb" } resolution = 3.29 write_initial_geo_file = False refinement { macro_cycles = 10 } 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 ------------------------------------------------------------------------------- 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= 1.000 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 Process input model Symmetric amino acids flipped None Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/modules/chem_data/mon_lib" Total number of atoms: 4380 Number of models: 1 Model: "" Number of chains: 10 Chain: "J" Number of atoms: 438 Number of conformers: 1 Conformer: "" Number of residues, atoms: 62, 438 Classifications: {'peptide': 62} Link IDs: {'PTRANS': 4, 'TRANS': 57} Chain: "H" Number of atoms: 438 Number of conformers: 1 Conformer: "" Number of residues, atoms: 62, 438 Classifications: {'peptide': 62} Link IDs: {'PTRANS': 4, 'TRANS': 57} Chain: "D" Number of atoms: 438 Number of conformers: 1 Conformer: "" Number of residues, atoms: 62, 438 Classifications: {'peptide': 62} Link IDs: {'PTRANS': 4, 'TRANS': 57} Chain: "B" Number of atoms: 438 Number of conformers: 1 Conformer: "" Number of residues, atoms: 62, 438 Classifications: {'peptide': 62} Link IDs: {'PTRANS': 4, 'TRANS': 57} Chain: "F" Number of atoms: 438 Number of conformers: 1 Conformer: "" Number of residues, atoms: 62, 438 Classifications: {'peptide': 62} Link IDs: {'PTRANS': 4, 'TRANS': 57} Chain: "I" Number of atoms: 438 Number of conformers: 1 Conformer: "" Number of residues, atoms: 62, 438 Classifications: {'peptide': 62} Link IDs: {'PTRANS': 4, 'TRANS': 57} Chain: "G" Number of atoms: 438 Number of conformers: 1 Conformer: "" Number of residues, atoms: 62, 438 Classifications: {'peptide': 62} Link IDs: {'PTRANS': 4, 'TRANS': 57} Chain: "C" Number of atoms: 438 Number of conformers: 1 Conformer: "" Number of residues, atoms: 62, 438 Classifications: {'peptide': 62} Link IDs: {'PTRANS': 4, 'TRANS': 57} Chain: "A" Number of atoms: 438 Number of conformers: 1 Conformer: "" Number of residues, atoms: 62, 438 Classifications: {'peptide': 62} Link IDs: {'PTRANS': 4, 'TRANS': 57} Chain: "E" Number of atoms: 438 Number of conformers: 1 Conformer: "" Number of residues, atoms: 62, 438 Classifications: {'peptide': 62} Link IDs: {'PTRANS': 4, 'TRANS': 57} Time building chain proxies: 2.69, per 1000 atoms: 0.61 Number of scatterers: 4380 At special positions: 0 Unit cell: (89.474, 123.97, 42.042, 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 30 16.00 O 740 8.00 N 850 7.00 C 2760 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: 1.81 Conformation dependent library (CDL) restraints added in 635.4 milliseconds 1200 Ramachandran restraints generated. 600 Oldfield, 0 Emsley, 600 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 940 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 14 sheets defined 0.0% alpha, 29.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.36 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'J' and resid 89 through 91 removed outlier: 6.118A pdb=" N TRP J 89 " --> pdb=" O GLY H 90 " (cutoff:3.500A) removed outlier: 6.118A pdb=" N TRP H 89 " --> pdb=" O GLY F 90 " (cutoff:3.500A) removed outlier: 6.118A pdb=" N TRP D 89 " --> pdb=" O GLY B 90 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'J' and resid 95 through 100 removed outlier: 6.321A pdb=" N THR D 95 " --> pdb=" O HIS F 96 " (cutoff:3.500A) removed outlier: 7.843A pdb=" N GLN F 98 " --> pdb=" O THR D 95 " (cutoff:3.500A) removed outlier: 6.436A pdb=" N SER D 97 " --> pdb=" O GLN F 98 " (cutoff:3.500A) removed outlier: 7.709A pdb=" N ASN F 100 " --> pdb=" O SER D 97 " (cutoff:3.500A) removed outlier: 6.674A pdb=" N TRP D 99 " --> pdb=" O ASN F 100 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'J' and resid 106 through 107 removed outlier: 6.655A pdb=" N LYS D 106 " --> pdb=" O THR F 107 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'J' and resid 115 through 117 removed outlier: 6.522A pdb=" N ALA D 115 " --> pdb=" O ALA F 116 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'J' and resid 120 through 122 removed outlier: 6.965A pdb=" N VAL J 121 " --> pdb=" O VAL H 122 " (cutoff:3.500A) removed outlier: 6.966A pdb=" N VAL H 121 " --> pdb=" O VAL F 122 " (cutoff:3.500A) removed outlier: 6.965A pdb=" N VAL D 121 " --> pdb=" O VAL B 122 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'J' and resid 125 through 130 removed outlier: 6.891A pdb=" N GLY J 126 " --> pdb=" O LEU H 125 " (cutoff:3.500A) removed outlier: 6.859A pdb=" N GLY H 127 " --> pdb=" O GLY J 126 " (cutoff:3.500A) removed outlier: 6.759A pdb=" N TYR J 128 " --> pdb=" O GLY H 127 " (cutoff:3.500A) removed outlier: 6.890A pdb=" N GLY H 126 " --> pdb=" O LEU F 125 " (cutoff:3.500A) removed outlier: 6.861A pdb=" N GLY F 127 " --> pdb=" O GLY H 126 " (cutoff:3.500A) removed outlier: 6.760A pdb=" N TYR H 128 " --> pdb=" O GLY F 127 " (cutoff:3.500A) removed outlier: 9.074A pdb=" N LEU D 125 " --> pdb=" O GLY F 126 " (cutoff:3.500A) removed outlier: 10.541A pdb=" N TYR F 128 " --> pdb=" O LEU D 125 " (cutoff:3.500A) removed outlier: 5.178A pdb=" N GLY D 127 " --> pdb=" O TYR F 128 " (cutoff:3.500A) removed outlier: 8.193A pdb=" N LEU F 130 " --> pdb=" O GLY D 127 " (cutoff:3.500A) removed outlier: 6.343A pdb=" N VAL D 129 " --> pdb=" O LEU F 130 " (cutoff:3.500A) removed outlier: 6.891A pdb=" N GLY D 126 " --> pdb=" O LEU B 125 " (cutoff:3.500A) removed outlier: 6.859A pdb=" N GLY B 127 " --> pdb=" O GLY D 126 " (cutoff:3.500A) removed outlier: 6.760A pdb=" N TYR D 128 " --> pdb=" O GLY B 127 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'J' and resid 138 through 139 removed outlier: 6.539A pdb=" N ILE J 138 " --> pdb=" O ILE H 139 " (cutoff:3.500A) removed outlier: 6.539A pdb=" N ILE H 138 " --> pdb=" O ILE F 139 " (cutoff:3.500A) removed outlier: 6.539A pdb=" N ILE D 138 " --> pdb=" O ILE B 139 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'I' and resid 89 through 91 removed outlier: 6.118A pdb=" N TRP I 89 " --> pdb=" O GLY G 90 " (cutoff:3.500A) removed outlier: 6.118A pdb=" N TRP G 89 " --> pdb=" O GLY E 90 " (cutoff:3.500A) removed outlier: 6.119A pdb=" N TRP C 89 " --> pdb=" O GLY A 90 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'I' and resid 95 through 100 removed outlier: 6.322A pdb=" N THR C 95 " --> pdb=" O HIS E 96 " (cutoff:3.500A) removed outlier: 7.842A pdb=" N GLN E 98 " --> pdb=" O THR C 95 " (cutoff:3.500A) removed outlier: 6.436A pdb=" N SER C 97 " --> pdb=" O GLN E 98 " (cutoff:3.500A) removed outlier: 7.708A pdb=" N ASN E 100 " --> pdb=" O SER C 97 " (cutoff:3.500A) removed outlier: 6.673A pdb=" N TRP C 99 " --> pdb=" O ASN E 100 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'I' and resid 106 through 107 removed outlier: 6.654A pdb=" N LYS C 106 " --> pdb=" O THR E 107 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'I' and resid 115 through 117 removed outlier: 6.522A pdb=" N ALA C 115 " --> pdb=" O ALA E 116 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'I' and resid 120 through 122 removed outlier: 6.965A pdb=" N VAL I 121 " --> pdb=" O VAL G 122 " (cutoff:3.500A) removed outlier: 6.966A pdb=" N VAL G 121 " --> pdb=" O VAL E 122 " (cutoff:3.500A) removed outlier: 6.965A pdb=" N VAL C 121 " --> pdb=" O VAL A 122 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'I' and resid 125 through 130 removed outlier: 6.891A pdb=" N GLY I 126 " --> pdb=" O LEU G 125 " (cutoff:3.500A) removed outlier: 6.859A pdb=" N GLY G 127 " --> pdb=" O GLY I 126 " (cutoff:3.500A) removed outlier: 6.758A pdb=" N TYR I 128 " --> pdb=" O GLY G 127 " (cutoff:3.500A) removed outlier: 6.890A pdb=" N GLY G 126 " --> pdb=" O LEU E 125 " (cutoff:3.500A) removed outlier: 6.861A pdb=" N GLY E 127 " --> pdb=" O GLY G 126 " (cutoff:3.500A) removed outlier: 6.759A pdb=" N TYR G 128 " --> pdb=" O GLY E 127 " (cutoff:3.500A) removed outlier: 9.075A pdb=" N LEU C 125 " --> pdb=" O GLY E 126 " (cutoff:3.500A) removed outlier: 10.541A pdb=" N TYR E 128 " --> pdb=" O LEU C 125 " (cutoff:3.500A) removed outlier: 5.177A pdb=" N GLY C 127 " --> pdb=" O TYR E 128 " (cutoff:3.500A) removed outlier: 8.193A pdb=" N LEU E 130 " --> pdb=" O GLY C 127 " (cutoff:3.500A) removed outlier: 6.344A pdb=" N VAL C 129 " --> pdb=" O LEU E 130 " (cutoff:3.500A) removed outlier: 6.890A pdb=" N GLY C 126 " --> pdb=" O LEU A 125 " (cutoff:3.500A) removed outlier: 6.860A pdb=" N GLY A 127 " --> pdb=" O GLY C 126 " (cutoff:3.500A) removed outlier: 6.760A pdb=" N TYR C 128 " --> pdb=" O GLY A 127 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'I' and resid 138 through 139 removed outlier: 6.539A pdb=" N ILE I 138 " --> pdb=" O ILE G 139 " (cutoff:3.500A) removed outlier: 6.539A pdb=" N ILE G 138 " --> pdb=" O ILE E 139 " (cutoff:3.500A) removed outlier: 6.539A pdb=" N ILE C 138 " --> pdb=" O ILE A 139 " (cutoff:3.500A) 70 hydrogen bonds defined for protein. 210 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: 1.09 Time building geometry restraints manager: 1.86 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 1403 1.33 - 1.45: 1147 1.45 - 1.57: 1910 1.57 - 1.69: 10 1.69 - 1.81: 60 Bond restraints: 4530 Sorted by residual: bond pdb=" CG HIS D 111 " pdb=" CD2 HIS D 111 " ideal model delta sigma weight residual 1.354 1.271 0.083 1.10e-02 8.26e+03 5.63e+01 bond pdb=" CG HIS I 111 " pdb=" CD2 HIS I 111 " ideal model delta sigma weight residual 1.354 1.272 0.082 1.10e-02 8.26e+03 5.61e+01 bond pdb=" CG HIS F 111 " pdb=" CD2 HIS F 111 " ideal model delta sigma weight residual 1.354 1.272 0.082 1.10e-02 8.26e+03 5.60e+01 bond pdb=" CG HIS J 111 " pdb=" CD2 HIS J 111 " ideal model delta sigma weight residual 1.354 1.272 0.082 1.10e-02 8.26e+03 5.59e+01 bond pdb=" CG HIS B 111 " pdb=" CD2 HIS B 111 " ideal model delta sigma weight residual 1.354 1.272 0.082 1.10e-02 8.26e+03 5.59e+01 ... (remaining 4525 not shown) Histogram of bond angle deviations from ideal: 98.29 - 105.45: 190 105.45 - 112.62: 2086 112.62 - 119.78: 1831 119.78 - 126.95: 1863 126.95 - 134.11: 140 Bond angle restraints: 6110 Sorted by residual: angle pdb=" C ARG E 136 " pdb=" N PRO E 137 " pdb=" CA PRO E 137 " ideal model delta sigma weight residual 119.85 126.78 -6.93 1.01e+00 9.80e-01 4.71e+01 angle pdb=" C ARG I 136 " pdb=" N PRO I 137 " pdb=" CA PRO I 137 " ideal model delta sigma weight residual 119.85 126.75 -6.90 1.01e+00 9.80e-01 4.66e+01 angle pdb=" C ARG J 136 " pdb=" N PRO J 137 " pdb=" CA PRO J 137 " ideal model delta sigma weight residual 119.85 126.74 -6.89 1.01e+00 9.80e-01 4.66e+01 angle pdb=" C ARG F 136 " pdb=" N PRO F 137 " pdb=" CA PRO F 137 " ideal model delta sigma weight residual 119.85 126.73 -6.88 1.01e+00 9.80e-01 4.64e+01 angle pdb=" C ARG B 136 " pdb=" N PRO B 137 " pdb=" CA PRO B 137 " ideal model delta sigma weight residual 119.85 126.73 -6.88 1.01e+00 9.80e-01 4.64e+01 ... (remaining 6105 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 10.45: 2240 10.45 - 20.91: 110 20.91 - 31.36: 90 31.36 - 41.81: 10 41.81 - 52.26: 10 Dihedral angle restraints: 2460 sinusoidal: 900 harmonic: 1560 Sorted by residual: dihedral pdb=" C TRP A 89 " pdb=" N TRP A 89 " pdb=" CA TRP A 89 " pdb=" CB TRP A 89 " ideal model delta harmonic sigma weight residual -122.60 -129.47 6.87 0 2.50e+00 1.60e-01 7.56e+00 dihedral pdb=" C TRP B 89 " pdb=" N TRP B 89 " pdb=" CA TRP B 89 " pdb=" CB TRP B 89 " ideal model delta harmonic sigma weight residual -122.60 -129.46 6.86 0 2.50e+00 1.60e-01 7.52e+00 dihedral pdb=" C TRP E 89 " pdb=" N TRP E 89 " pdb=" CA TRP E 89 " pdb=" CB TRP E 89 " ideal model delta harmonic sigma weight residual -122.60 -129.45 6.85 0 2.50e+00 1.60e-01 7.50e+00 ... (remaining 2457 not shown) Histogram of chiral volume deviations from ideal: 0.002 - 0.066: 309 0.066 - 0.129: 147 0.129 - 0.192: 64 0.192 - 0.255: 22 0.255 - 0.319: 18 Chirality restraints: 560 Sorted by residual: chirality pdb=" CA TRP D 89 " pdb=" N TRP D 89 " pdb=" C TRP D 89 " pdb=" CB TRP D 89 " both_signs ideal model delta sigma weight residual False 2.51 2.19 0.32 2.00e-01 2.50e+01 2.54e+00 chirality pdb=" CA TRP E 89 " pdb=" N TRP E 89 " pdb=" C TRP E 89 " pdb=" CB TRP E 89 " both_signs ideal model delta sigma weight residual False 2.51 2.19 0.32 2.00e-01 2.50e+01 2.53e+00 chirality pdb=" CA TRP J 89 " pdb=" N TRP J 89 " pdb=" C TRP J 89 " pdb=" CB TRP J 89 " both_signs ideal model delta sigma weight residual False 2.51 2.19 0.32 2.00e-01 2.50e+01 2.52e+00 ... (remaining 557 not shown) Planarity restraints: 800 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP F 81 " -0.032 2.00e-02 2.50e+03 1.63e-02 6.62e+00 pdb=" CG TRP F 81 " 0.009 2.00e-02 2.50e+03 pdb=" CD1 TRP F 81 " 0.005 2.00e-02 2.50e+03 pdb=" CD2 TRP F 81 " 0.017 2.00e-02 2.50e+03 pdb=" NE1 TRP F 81 " 0.005 2.00e-02 2.50e+03 pdb=" CE2 TRP F 81 " 0.004 2.00e-02 2.50e+03 pdb=" CE3 TRP F 81 " 0.024 2.00e-02 2.50e+03 pdb=" CZ2 TRP F 81 " -0.013 2.00e-02 2.50e+03 pdb=" CZ3 TRP F 81 " 0.002 2.00e-02 2.50e+03 pdb=" CH2 TRP F 81 " -0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP E 81 " 0.032 2.00e-02 2.50e+03 1.62e-02 6.59e+00 pdb=" CG TRP E 81 " -0.009 2.00e-02 2.50e+03 pdb=" CD1 TRP E 81 " -0.005 2.00e-02 2.50e+03 pdb=" CD2 TRP E 81 " -0.017 2.00e-02 2.50e+03 pdb=" NE1 TRP E 81 " -0.005 2.00e-02 2.50e+03 pdb=" CE2 TRP E 81 " -0.004 2.00e-02 2.50e+03 pdb=" CE3 TRP E 81 " -0.024 2.00e-02 2.50e+03 pdb=" CZ2 TRP E 81 " 0.013 2.00e-02 2.50e+03 pdb=" CZ3 TRP E 81 " -0.001 2.00e-02 2.50e+03 pdb=" CH2 TRP E 81 " 0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP I 81 " 0.032 2.00e-02 2.50e+03 1.62e-02 6.54e+00 pdb=" CG TRP I 81 " -0.009 2.00e-02 2.50e+03 pdb=" CD1 TRP I 81 " -0.005 2.00e-02 2.50e+03 pdb=" CD2 TRP I 81 " -0.016 2.00e-02 2.50e+03 pdb=" NE1 TRP I 81 " -0.005 2.00e-02 2.50e+03 pdb=" CE2 TRP I 81 " -0.004 2.00e-02 2.50e+03 pdb=" CE3 TRP I 81 " -0.024 2.00e-02 2.50e+03 pdb=" CZ2 TRP I 81 " 0.013 2.00e-02 2.50e+03 pdb=" CZ3 TRP I 81 " -0.002 2.00e-02 2.50e+03 pdb=" CH2 TRP I 81 " 0.021 2.00e-02 2.50e+03 ... (remaining 797 not shown) Histogram of nonbonded interaction distances: 2.54 - 3.01: 2414 3.01 - 3.48: 4106 3.48 - 3.96: 6913 3.96 - 4.43: 8233 4.43 - 4.90: 15076 Nonbonded interactions: 36742 Sorted by model distance: nonbonded pdb=" N GLY G 93 " pdb=" O GLY G 93 " model vdw 2.540 2.496 nonbonded pdb=" N GLY E 93 " pdb=" O GLY E 93 " model vdw 2.541 2.496 nonbonded pdb=" N GLY H 93 " pdb=" O GLY H 93 " model vdw 2.541 2.496 nonbonded pdb=" N GLY F 93 " pdb=" O GLY F 93 " model vdw 2.541 2.496 nonbonded pdb=" N GLY D 93 " pdb=" O GLY D 93 " model vdw 2.541 2.496 ... (remaining 36737 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' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 30 5.16 5 C 2760 2.51 5 N 850 2.21 5 O 740 1.98 5 sf(0) = scattering factor at diffraction angle 0. Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.870 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: 3.270 Check model and map are aligned: 0.060 Process input model: 15.490 Find NCS groups from input model: 0.280 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Set scattering table: 0.040 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:2.660 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.690 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7397 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 : 0.023 0.101 4530 Z= 1.595 Angle : 2.110 7.226 6110 Z= 1.387 Chirality : 0.102 0.319 560 Planarity : 0.009 0.024 800 Dihedral : 9.850 52.261 1520 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 2.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.00 % Favored : 90.00 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.35 (0.24), residues: 600 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.54 (0.19), residues: 600 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1200 Ramachandran restraints generated. 600 Oldfield, 0 Emsley, 600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1200 Ramachandran restraints generated. 600 Oldfield, 0 Emsley, 600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 171 time to evaluate : 0.476 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 171 average time/residue: 0.1505 time to fit residues: 32.4193 Evaluate side-chains 110 residues out of total 390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 110 time to evaluate : 0.517 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.6570 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 50 optimal weight: 5.9990 chunk 45 optimal weight: 5.9990 chunk 25 optimal weight: 6.9990 chunk 15 optimal weight: 5.9990 chunk 30 optimal weight: 1.9990 chunk 24 optimal weight: 6.9990 chunk 47 optimal weight: 4.9990 chunk 18 optimal weight: 7.9990 chunk 28 optimal weight: 5.9990 chunk 35 optimal weight: 6.9990 chunk 54 optimal weight: 5.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 100 ASN ** D 85 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 100 ASN ** C 85 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7541 moved from start: 0.4404 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.037 4530 Z= 0.366 Angle : 0.788 4.593 6110 Z= 0.408 Chirality : 0.045 0.165 560 Planarity : 0.004 0.057 800 Dihedral : 5.145 13.819 630 Min Nonbonded Distance : 2.238 Molprobity Statistics. All-atom Clashscore : 18.16 Ramachandran Plot: Outliers : 0.17 % Allowed : 7.50 % Favored : 92.33 % Rotamer Outliers : 4.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.90 (0.22), residues: 600 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.96 (0.17), residues: 600 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1200 Ramachandran restraints generated. 600 Oldfield, 0 Emsley, 600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1200 Ramachandran restraints generated. 600 Oldfield, 0 Emsley, 600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 133 time to evaluate : 0.462 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 19 outliers final: 13 residues processed: 135 average time/residue: 0.0972 time to fit residues: 18.6113 Evaluate side-chains 129 residues out of total 390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 116 time to evaluate : 0.474 Switching outliers to nearest non-outliers outliers start: 13 outliers final: 0 residues processed: 13 average time/residue: 0.0429 time to fit residues: 1.6139 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 30 optimal weight: 10.0000 chunk 16 optimal weight: 10.0000 chunk 45 optimal weight: 30.0000 chunk 37 optimal weight: 20.0000 chunk 15 optimal weight: 30.0000 chunk 54 optimal weight: 9.9990 chunk 58 optimal weight: 0.9980 chunk 48 optimal weight: 10.0000 chunk 18 optimal weight: 5.9990 chunk 43 optimal weight: 20.0000 chunk 53 optimal weight: 5.9990 overall best weight: 6.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 85 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 140 HIS ** C 85 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 140 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7626 moved from start: 0.5406 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.037 4530 Z= 0.430 Angle : 0.797 5.585 6110 Z= 0.407 Chirality : 0.045 0.164 560 Planarity : 0.004 0.033 800 Dihedral : 5.237 14.934 630 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 17.69 Ramachandran Plot: Outliers : 0.17 % Allowed : 12.00 % Favored : 87.83 % Rotamer Outliers : 3.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.24 (0.23), residues: 600 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.23 (0.17), residues: 600 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1200 Ramachandran restraints generated. 600 Oldfield, 0 Emsley, 600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1200 Ramachandran restraints generated. 600 Oldfield, 0 Emsley, 600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 127 time to evaluate : 0.495 Fit side-chains outliers start: 14 outliers final: 6 residues processed: 129 average time/residue: 0.1231 time to fit residues: 21.2683 Evaluate side-chains 115 residues out of total 390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 109 time to evaluate : 0.458 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.0507 time to fit residues: 1.1161 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 41 optimal weight: 5.9990 chunk 28 optimal weight: 9.9990 chunk 6 optimal weight: 9.9990 chunk 26 optimal weight: 5.9990 chunk 36 optimal weight: 4.9990 chunk 54 optimal weight: 10.0000 chunk 57 optimal weight: 7.9990 chunk 51 optimal weight: 10.0000 chunk 15 optimal weight: 30.0000 chunk 48 optimal weight: 9.9990 chunk 32 optimal weight: 9.9990 overall best weight: 6.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** J 111 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 140 HIS ** H 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 140 HIS ** D 85 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 140 HIS ** B 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 140 HIS F 140 HIS ** I 111 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 140 HIS ** G 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 85 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 140 HIS ** A 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 140 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7669 moved from start: 0.6073 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.041 4530 Z= 0.446 Angle : 0.810 5.859 6110 Z= 0.415 Chirality : 0.046 0.155 560 Planarity : 0.004 0.022 800 Dihedral : 5.307 15.716 630 Min Nonbonded Distance : 2.207 Molprobity Statistics. All-atom Clashscore : 20.37 Ramachandran Plot: Outliers : 0.17 % Allowed : 11.67 % Favored : 88.17 % Rotamer Outliers : 4.36 % 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: -4.48 (0.22), residues: 600 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.41 (0.17), residues: 600 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1200 Ramachandran restraints generated. 600 Oldfield, 0 Emsley, 600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1200 Ramachandran restraints generated. 600 Oldfield, 0 Emsley, 600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 110 time to evaluate : 0.504 Fit side-chains outliers start: 17 outliers final: 13 residues processed: 115 average time/residue: 0.1009 time to fit residues: 16.5106 Evaluate side-chains 115 residues out of total 390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 102 time to evaluate : 0.483 Switching outliers to nearest non-outliers outliers start: 13 outliers final: 0 residues processed: 13 average time/residue: 0.0436 time to fit residues: 1.6436 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 0 optimal weight: 10.0000 chunk 43 optimal weight: 10.0000 chunk 23 optimal weight: 3.9990 chunk 49 optimal weight: 10.0000 chunk 40 optimal weight: 9.9990 chunk 29 optimal weight: 6.9990 chunk 52 optimal weight: 3.9990 chunk 14 optimal weight: 7.9990 chunk 19 optimal weight: 0.7980 chunk 11 optimal weight: 3.9990 chunk 34 optimal weight: 8.9990 overall best weight: 3.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 85 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 85 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7620 moved from start: 0.6286 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.033 4530 Z= 0.282 Angle : 0.686 6.110 6110 Z= 0.345 Chirality : 0.043 0.149 560 Planarity : 0.003 0.024 800 Dihedral : 4.743 13.482 630 Min Nonbonded Distance : 2.232 Molprobity Statistics. All-atom Clashscore : 18.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.17 % Favored : 88.83 % Rotamer Outliers : 1.28 % 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 (0.22), residues: 600 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.47 (0.16), residues: 600 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1200 Ramachandran restraints generated. 600 Oldfield, 0 Emsley, 600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1200 Ramachandran restraints generated. 600 Oldfield, 0 Emsley, 600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 105 time to evaluate : 0.449 Fit side-chains outliers start: 5 outliers final: 4 residues processed: 105 average time/residue: 0.1007 time to fit residues: 14.9396 Evaluate side-chains 104 residues out of total 390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 100 time to evaluate : 0.441 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.0444 time to fit residues: 0.8773 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 14 optimal weight: 9.9990 chunk 58 optimal weight: 20.0000 chunk 48 optimal weight: 0.4980 chunk 26 optimal weight: 9.9990 chunk 4 optimal weight: 9.9990 chunk 19 optimal weight: 20.0000 chunk 30 optimal weight: 10.0000 chunk 55 optimal weight: 20.0000 chunk 6 optimal weight: 10.0000 chunk 33 optimal weight: 20.0000 chunk 42 optimal weight: 0.7980 overall best weight: 6.2586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** J 111 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 85 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 111 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 85 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7673 moved from start: 0.6473 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.042 4530 Z= 0.407 Angle : 0.768 6.514 6110 Z= 0.391 Chirality : 0.046 0.165 560 Planarity : 0.004 0.023 800 Dihedral : 5.018 14.415 630 Min Nonbonded Distance : 2.224 Molprobity Statistics. All-atom Clashscore : 21.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.00 % Favored : 87.00 % Rotamer Outliers : 3.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.81 (0.21), residues: 600 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.66 (0.16), residues: 600 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1200 Ramachandran restraints generated. 600 Oldfield, 0 Emsley, 600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1200 Ramachandran restraints generated. 600 Oldfield, 0 Emsley, 600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 106 time to evaluate : 0.456 Fit side-chains outliers start: 14 outliers final: 7 residues processed: 109 average time/residue: 0.1158 time to fit residues: 17.4094 Evaluate side-chains 108 residues out of total 390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 101 time to evaluate : 0.477 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.0423 time to fit residues: 1.1583 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 32 optimal weight: 9.9990 chunk 48 optimal weight: 0.9980 chunk 57 optimal weight: 30.0000 chunk 36 optimal weight: 9.9990 chunk 35 optimal weight: 9.9990 chunk 26 optimal weight: 2.9990 chunk 23 optimal weight: 3.9990 chunk 34 optimal weight: 0.8980 chunk 17 optimal weight: 5.9990 chunk 11 optimal weight: 6.9990 chunk 39 optimal weight: 8.9990 overall best weight: 2.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 85 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 111 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 85 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7590 moved from start: 0.6631 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.035 4530 Z= 0.248 Angle : 0.662 6.211 6110 Z= 0.329 Chirality : 0.045 0.172 560 Planarity : 0.004 0.028 800 Dihedral : 4.518 13.033 630 Min Nonbonded Distance : 2.275 Molprobity Statistics. All-atom Clashscore : 17.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.50 % Favored : 90.50 % Rotamer Outliers : 1.54 % 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: -4.79 (0.21), residues: 600 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.64 (0.16), residues: 600 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1200 Ramachandran restraints generated. 600 Oldfield, 0 Emsley, 600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1200 Ramachandran restraints generated. 600 Oldfield, 0 Emsley, 600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 104 time to evaluate : 0.412 Fit side-chains outliers start: 6 outliers final: 3 residues processed: 107 average time/residue: 0.1159 time to fit residues: 17.3266 Evaluate side-chains 101 residues out of total 390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 98 time to evaluate : 0.476 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.0432 time to fit residues: 0.9643 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 28 optimal weight: 9.9990 chunk 5 optimal weight: 0.9980 chunk 45 optimal weight: 20.0000 chunk 52 optimal weight: 10.0000 chunk 55 optimal weight: 9.9990 chunk 50 optimal weight: 10.0000 chunk 53 optimal weight: 10.0000 chunk 32 optimal weight: 0.0270 chunk 23 optimal weight: 7.9990 chunk 42 optimal weight: 20.0000 chunk 16 optimal weight: 3.9990 overall best weight: 4.6044 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** J 111 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 85 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 85 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7642 moved from start: 0.6658 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.035 4530 Z= 0.314 Angle : 0.704 6.931 6110 Z= 0.353 Chirality : 0.045 0.152 560 Planarity : 0.004 0.026 800 Dihedral : 4.628 13.706 630 Min Nonbonded Distance : 2.275 Molprobity Statistics. All-atom Clashscore : 19.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.17 % Favored : 87.83 % Rotamer Outliers : 1.54 % 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: -4.90 (0.20), residues: 600 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.72 (0.16), residues: 600 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1200 Ramachandran restraints generated. 600 Oldfield, 0 Emsley, 600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1200 Ramachandran restraints generated. 600 Oldfield, 0 Emsley, 600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 100 time to evaluate : 0.512 Fit side-chains outliers start: 6 outliers final: 6 residues processed: 100 average time/residue: 0.1150 time to fit residues: 15.7714 Evaluate side-chains 102 residues out of total 390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 96 time to evaluate : 0.491 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.0427 time to fit residues: 1.0769 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 48 optimal weight: 0.7980 chunk 50 optimal weight: 20.0000 chunk 53 optimal weight: 5.9990 chunk 35 optimal weight: 0.9980 chunk 56 optimal weight: 10.0000 chunk 34 optimal weight: 6.9990 chunk 27 optimal weight: 20.0000 chunk 39 optimal weight: 5.9990 chunk 59 optimal weight: 5.9990 chunk 55 optimal weight: 20.0000 chunk 47 optimal weight: 3.9990 overall best weight: 3.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** J 111 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 85 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 85 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7609 moved from start: 0.6732 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.032 4530 Z= 0.262 Angle : 0.672 6.782 6110 Z= 0.334 Chirality : 0.045 0.147 560 Planarity : 0.004 0.028 800 Dihedral : 4.466 13.460 630 Min Nonbonded Distance : 2.303 Molprobity Statistics. All-atom Clashscore : 18.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.33 % Favored : 89.67 % Rotamer Outliers : 0.51 % 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: -4.91 (0.21), residues: 600 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.74 (0.16), residues: 600 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1200 Ramachandran restraints generated. 600 Oldfield, 0 Emsley, 600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1200 Ramachandran restraints generated. 600 Oldfield, 0 Emsley, 600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 100 time to evaluate : 0.451 Fit side-chains outliers start: 2 outliers final: 2 residues processed: 102 average time/residue: 0.1134 time to fit residues: 15.8933 Evaluate side-chains 99 residues out of total 390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 97 time to evaluate : 0.477 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0432 time to fit residues: 0.7691 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 4 optimal weight: 6.9990 chunk 36 optimal weight: 6.9990 chunk 29 optimal weight: 10.0000 chunk 37 optimal weight: 20.0000 chunk 50 optimal weight: 4.9990 chunk 14 optimal weight: 5.9990 chunk 43 optimal weight: 20.0000 chunk 7 optimal weight: 20.0000 chunk 13 optimal weight: 9.9990 chunk 47 optimal weight: 10.0000 chunk 19 optimal weight: 9.9990 overall best weight: 6.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** J 111 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 85 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 85 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7688 moved from start: 0.6726 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.041 4530 Z= 0.443 Angle : 0.794 6.446 6110 Z= 0.404 Chirality : 0.047 0.158 560 Planarity : 0.004 0.026 800 Dihedral : 4.959 15.121 630 Min Nonbonded Distance : 2.300 Molprobity Statistics. All-atom Clashscore : 22.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.83 % Favored : 85.17 % Rotamer Outliers : 0.77 % 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: 600 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.82 (0.16), residues: 600 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1200 Ramachandran restraints generated. 600 Oldfield, 0 Emsley, 600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1200 Ramachandran restraints generated. 600 Oldfield, 0 Emsley, 600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 95 time to evaluate : 0.447 Fit side-chains outliers start: 3 outliers final: 3 residues processed: 96 average time/residue: 0.1133 time to fit residues: 14.9527 Evaluate side-chains 96 residues out of total 390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 93 time to evaluate : 0.507 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.0467 time to fit residues: 0.8599 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 48 optimal weight: 0.0030 chunk 6 optimal weight: 5.9990 chunk 8 optimal weight: 8.9990 chunk 41 optimal weight: 5.9990 chunk 2 optimal weight: 5.9990 chunk 34 optimal weight: 9.9990 chunk 54 optimal weight: 8.9990 chunk 32 optimal weight: 2.9990 chunk 40 optimal weight: 4.9990 chunk 1 optimal weight: 0.9990 chunk 38 optimal weight: 5.9990 overall best weight: 2.9998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 85 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 85 HIS ** 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 = 0.4566 r_free = 0.4566 target = 0.155600 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4479 r_free = 0.4479 target = 0.146800 restraints weight = 8647.281| |-----------------------------------------------------------------------------| r_work (start): 0.4482 rms_B_bonded: 3.19 r_work: 0.4383 rms_B_bonded: 3.66 restraints_weight: 0.5000 r_work (final): 0.4383 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7495 moved from start: 0.6850 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.040 4530 Z= 0.248 Angle : 0.679 10.215 6110 Z= 0.333 Chirality : 0.045 0.146 560 Planarity : 0.004 0.030 800 Dihedral : 4.487 13.251 630 Min Nonbonded Distance : 2.328 Molprobity Statistics. All-atom Clashscore : 17.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.00 % Favored : 90.00 % Rotamer Outliers : 0.77 % 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 (0.21), residues: 600 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.78 (0.16), residues: 600 =============================================================================== Job complete usr+sys time: 1063.24 seconds wall clock time: 20 minutes 13.13 seconds (1213.13 seconds total)