Starting phenix.real_space_refine on Thu Jul 18 17:29:17 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8az0_15728/07_2024/8az0_15728.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8az0_15728/07_2024/8az0_15728.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8az0_15728/07_2024/8az0_15728.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8az0_15728/07_2024/8az0_15728.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8az0_15728/07_2024/8az0_15728.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8az0_15728/07_2024/8az0_15728.cif" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.003 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 3 Type Number sf(0) Gaussians C 1350 2.51 5 N 420 2.21 5 O 410 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 15": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 23": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 15": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 23": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 15": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 23": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 15": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 23": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 15": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 23": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 15": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 23": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 15": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 23": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 15": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 23": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 15": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 23": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 15": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 23": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/chem_data/mon_lib" Total number of atoms: 2180 Number of models: 1 Model: "" Number of chains: 20 Chain: "A" Number of atoms: 217 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 28, 210 Classifications: {'peptide': 28} Link IDs: {'TRANS': 27} Conformer: "B" Number of residues, atoms: 28, 210 Classifications: {'peptide': 28} Link IDs: {'TRANS': 27} bond proxies already assigned to first conformer: 204 Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 217 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 28, 210 Classifications: {'peptide': 28} Link IDs: {'TRANS': 27} Conformer: "B" Number of residues, atoms: 28, 210 Classifications: {'peptide': 28} Link IDs: {'TRANS': 27} bond proxies already assigned to first conformer: 204 Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 217 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 28, 210 Classifications: {'peptide': 28} Link IDs: {'TRANS': 27} Conformer: "B" Number of residues, atoms: 28, 210 Classifications: {'peptide': 28} Link IDs: {'TRANS': 27} bond proxies already assigned to first conformer: 204 Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 217 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 28, 210 Classifications: {'peptide': 28} Link IDs: {'TRANS': 27} Conformer: "B" Number of residues, atoms: 28, 210 Classifications: {'peptide': 28} Link IDs: {'TRANS': 27} bond proxies already assigned to first conformer: 204 Chain: "D" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 217 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 28, 210 Classifications: {'peptide': 28} Link IDs: {'TRANS': 27} Conformer: "B" Number of residues, atoms: 28, 210 Classifications: {'peptide': 28} Link IDs: {'TRANS': 27} bond proxies already assigned to first conformer: 204 Chain: "E" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "F" Number of atoms: 217 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 28, 210 Classifications: {'peptide': 28} Link IDs: {'TRANS': 27} Conformer: "B" Number of residues, atoms: 28, 210 Classifications: {'peptide': 28} Link IDs: {'TRANS': 27} bond proxies already assigned to first conformer: 204 Chain: "F" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "G" Number of atoms: 217 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 28, 210 Classifications: {'peptide': 28} Link IDs: {'TRANS': 27} Conformer: "B" Number of residues, atoms: 28, 210 Classifications: {'peptide': 28} Link IDs: {'TRANS': 27} bond proxies already assigned to first conformer: 204 Chain: "G" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "H" Number of atoms: 217 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 28, 210 Classifications: {'peptide': 28} Link IDs: {'TRANS': 27} Conformer: "B" Number of residues, atoms: 28, 210 Classifications: {'peptide': 28} Link IDs: {'TRANS': 27} bond proxies already assigned to first conformer: 204 Chain: "H" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "I" Number of atoms: 217 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 28, 210 Classifications: {'peptide': 28} Link IDs: {'TRANS': 27} Conformer: "B" Number of residues, atoms: 28, 210 Classifications: {'peptide': 28} Link IDs: {'TRANS': 27} bond proxies already assigned to first conformer: 204 Chain: "I" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "J" Number of atoms: 217 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 28, 210 Classifications: {'peptide': 28} Link IDs: {'TRANS': 27} Conformer: "B" Number of residues, atoms: 28, 210 Classifications: {'peptide': 28} Link IDs: {'TRANS': 27} bond proxies already assigned to first conformer: 204 Chain: "J" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Time building chain proxies: 3.07, per 1000 atoms: 1.41 Number of scatterers: 2180 At special positions: 0 Unit cell: (63, 73.08, 45.36, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 3 Type Number sf(0) O 410 8.00 N 420 7.00 C 1350 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=10, symmetry=0 Number of additional bonds: simple=10, symmetry=0 Coordination: Other bonds: Time building additional restraints: 0.97 Conformation dependent library (CDL) restraints added in 844.6 milliseconds 540 Ramachandran restraints generated. 270 Oldfield, 0 Emsley, 270 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 520 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 6 sheets defined 0.0% alpha, 53.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.32 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'A' and resid 11 through 22 removed outlier: 6.969A pdb=" N ASN A 21 " --> pdb=" O GLY C 20 " (cutoff:3.500A) removed outlier: 7.017A pdb=" N ASN C 22 " --> pdb=" O ASN A 21 " (cutoff:3.500A) removed outlier: 6.965A pdb=" N ASN C 21 " --> pdb=" O GLY E 20 " (cutoff:3.500A) removed outlier: 7.015A pdb=" N ASN E 22 " --> pdb=" O ASN C 21 " (cutoff:3.500A) removed outlier: 6.940A pdb=" N ASN E 21 " --> pdb=" O GLY G 20 " (cutoff:3.500A) removed outlier: 6.992A pdb=" N ASN G 22 " --> pdb=" O ASN E 21 " (cutoff:3.500A) removed outlier: 6.952A pdb=" N ASN G 21 " --> pdb=" O GLY I 20 " (cutoff:3.500A) removed outlier: 6.999A pdb=" N ASN I 22 " --> pdb=" O ASN G 21 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 25 through 26 Processing sheet with id=AA3, first strand: chain 'A' and resid 29 through 32 removed outlier: 6.413A pdb=" N SER A 29 " --> pdb=" O THR C 30 " (cutoff:3.500A) removed outlier: 8.014A pdb=" N VAL C 32 " --> pdb=" O SER A 29 " (cutoff:3.500A) removed outlier: 6.291A pdb=" N ASN A 31 " --> pdb=" O VAL C 32 " (cutoff:3.500A) removed outlier: 6.408A pdb=" N SER C 29 " --> pdb=" O THR E 30 " (cutoff:3.500A) removed outlier: 8.007A pdb=" N VAL E 32 " --> pdb=" O SER C 29 " (cutoff:3.500A) removed outlier: 6.286A pdb=" N ASN C 31 " --> pdb=" O VAL E 32 " (cutoff:3.500A) removed outlier: 6.447A pdb=" N SER E 29 " --> pdb=" O THR G 30 " (cutoff:3.500A) removed outlier: 8.049A pdb=" N VAL G 32 " --> pdb=" O SER E 29 " (cutoff:3.500A) removed outlier: 6.327A pdb=" N ASN E 31 " --> pdb=" O VAL G 32 " (cutoff:3.500A) removed outlier: 6.396A pdb=" N SER G 29 " --> pdb=" O THR I 30 " (cutoff:3.500A) removed outlier: 7.992A pdb=" N VAL I 32 " --> pdb=" O SER G 29 " (cutoff:3.500A) removed outlier: 6.267A pdb=" N ASN G 31 " --> pdb=" O VAL I 32 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'B' and resid 11 through 22 removed outlier: 6.991A pdb=" N ASN B 21 " --> pdb=" O GLY D 20 " (cutoff:3.500A) removed outlier: 7.030A pdb=" N ASN D 22 " --> pdb=" O ASN B 21 " (cutoff:3.500A) removed outlier: 6.943A pdb=" N ASN D 21 " --> pdb=" O GLY F 20 " (cutoff:3.500A) removed outlier: 7.001A pdb=" N ASN F 22 " --> pdb=" O ASN D 21 " (cutoff:3.500A) removed outlier: 6.937A pdb=" N ASN F 21 " --> pdb=" O GLY H 20 " (cutoff:3.500A) removed outlier: 6.988A pdb=" N ASN H 22 " --> pdb=" O ASN F 21 " (cutoff:3.500A) removed outlier: 6.978A pdb=" N ASN H 21 " --> pdb=" O GLY J 20 " (cutoff:3.500A) removed outlier: 7.022A pdb=" N ASN J 22 " --> pdb=" O ASN H 21 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 25 through 26 Processing sheet with id=AA6, first strand: chain 'B' and resid 29 through 32 removed outlier: 6.397A pdb=" N SER B 29 " --> pdb=" O THR D 30 " (cutoff:3.500A) removed outlier: 7.996A pdb=" N VAL D 32 " --> pdb=" O SER B 29 " (cutoff:3.500A) removed outlier: 6.276A pdb=" N ASN B 31 " --> pdb=" O VAL D 32 " (cutoff:3.500A) removed outlier: 6.446A pdb=" N SER D 29 " --> pdb=" O THR F 30 " (cutoff:3.500A) removed outlier: 8.046A pdb=" N VAL F 32 " --> pdb=" O SER D 29 " (cutoff:3.500A) removed outlier: 6.327A pdb=" N ASN D 31 " --> pdb=" O VAL F 32 " (cutoff:3.500A) removed outlier: 6.410A pdb=" N SER F 29 " --> pdb=" O THR H 30 " (cutoff:3.500A) removed outlier: 8.009A pdb=" N VAL H 32 " --> pdb=" O SER F 29 " (cutoff:3.500A) removed outlier: 6.282A pdb=" N ASN F 31 " --> pdb=" O VAL H 32 " (cutoff:3.500A) removed outlier: 6.393A pdb=" N SER H 29 " --> pdb=" O THR J 30 " (cutoff:3.500A) removed outlier: 7.990A pdb=" N VAL J 32 " --> pdb=" O SER H 29 " (cutoff:3.500A) removed outlier: 6.269A pdb=" N ASN H 31 " --> pdb=" O VAL J 32 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 80 hydrogen bonds defined for protein. 232 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: 0.52 Time building geometry restraints manager: 0.84 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.29: 340 1.29 - 1.35: 400 1.35 - 1.41: 270 1.41 - 1.48: 306 1.48 - 1.54: 904 Bond restraints: 2220 Sorted by residual: bond pdb=" N THR G 36 " pdb=" CA THR G 36 " ideal model delta sigma weight residual 1.457 1.487 -0.030 1.26e-02 6.30e+03 5.76e+00 bond pdb=" N THR J 36 " pdb=" CA THR J 36 " ideal model delta sigma weight residual 1.457 1.487 -0.030 1.26e-02 6.30e+03 5.73e+00 bond pdb=" N THR B 36 " pdb=" CA THR B 36 " ideal model delta sigma weight residual 1.457 1.487 -0.030 1.26e-02 6.30e+03 5.68e+00 bond pdb=" N THR H 36 " pdb=" CA THR H 36 " ideal model delta sigma weight residual 1.457 1.487 -0.030 1.26e-02 6.30e+03 5.62e+00 bond pdb=" N THR E 36 " pdb=" CA THR E 36 " ideal model delta sigma weight residual 1.457 1.487 -0.030 1.26e-02 6.30e+03 5.62e+00 ... (remaining 2215 not shown) Histogram of bond angle deviations from ideal: 106.04 - 111.07: 917 111.07 - 116.10: 470 116.10 - 121.14: 960 121.14 - 126.17: 653 126.17 - 131.20: 20 Bond angle restraints: 3020 Sorted by residual: angle pdb=" CA SER B 34 " pdb=" C SER B 34 " pdb=" O SER B 34 " ideal model delta sigma weight residual 121.28 117.78 3.50 1.19e+00 7.06e-01 8.64e+00 angle pdb=" CA SER A 34 " pdb=" C SER A 34 " pdb=" O SER A 34 " ideal model delta sigma weight residual 121.28 117.80 3.48 1.19e+00 7.06e-01 8.57e+00 angle pdb=" CA SER J 34 " pdb=" C SER J 34 " pdb=" O SER J 34 " ideal model delta sigma weight residual 121.28 117.81 3.47 1.19e+00 7.06e-01 8.49e+00 angle pdb=" CA SER G 34 " pdb=" C SER G 34 " pdb=" O SER G 34 " ideal model delta sigma weight residual 121.28 117.81 3.47 1.19e+00 7.06e-01 8.49e+00 angle pdb=" CA SER D 34 " pdb=" C SER D 34 " pdb=" O SER D 34 " ideal model delta sigma weight residual 121.28 117.83 3.45 1.19e+00 7.06e-01 8.42e+00 ... (remaining 3015 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 5.96: 1022 5.96 - 11.92: 128 11.92 - 17.87: 72 17.87 - 23.83: 28 23.83 - 29.79: 10 Dihedral angle restraints: 1260 sinusoidal: 440 harmonic: 820 Sorted by residual: dihedral pdb=" N HIS J 18 " pdb=" CA AHIS J 18 " pdb=" CB AHIS J 18 " pdb=" CG AHIS J 18 " ideal model delta sinusoidal sigma weight residual -60.00 -83.02 23.02 3 1.50e+01 4.44e-03 3.05e+00 dihedral pdb=" N HIS E 18 " pdb=" CA AHIS E 18 " pdb=" CB AHIS E 18 " pdb=" CG AHIS E 18 " ideal model delta sinusoidal sigma weight residual -60.00 -83.00 23.00 3 1.50e+01 4.44e-03 3.04e+00 dihedral pdb=" N HIS D 18 " pdb=" CA AHIS D 18 " pdb=" CB AHIS D 18 " pdb=" CG AHIS D 18 " ideal model delta sinusoidal sigma weight residual -60.00 -82.99 22.99 3 1.50e+01 4.44e-03 3.04e+00 ... (remaining 1257 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.027: 127 0.027 - 0.054: 149 0.054 - 0.080: 24 0.080 - 0.107: 17 0.107 - 0.134: 23 Chirality restraints: 340 Sorted by residual: chirality pdb=" CA ILE F 26 " pdb=" N ILE F 26 " pdb=" C ILE F 26 " pdb=" CB ILE F 26 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.48e-01 chirality pdb=" CA ILE B 26 " pdb=" N ILE B 26 " pdb=" C ILE B 26 " pdb=" CB ILE B 26 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.28e-01 chirality pdb=" CA ILE I 26 " pdb=" N ILE I 26 " pdb=" C ILE I 26 " pdb=" CB ILE I 26 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.24e-01 ... (remaining 337 not shown) Planarity restraints: 400 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA VAL D 32 " -0.015 2.00e-02 2.50e+03 2.96e-02 8.77e+00 pdb=" C VAL D 32 " 0.051 2.00e-02 2.50e+03 pdb=" O VAL D 32 " -0.019 2.00e-02 2.50e+03 pdb=" N GLY D 33 " -0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL B 32 " -0.015 2.00e-02 2.50e+03 2.96e-02 8.76e+00 pdb=" C VAL B 32 " 0.051 2.00e-02 2.50e+03 pdb=" O VAL B 32 " -0.019 2.00e-02 2.50e+03 pdb=" N GLY B 33 " -0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL I 32 " 0.014 2.00e-02 2.50e+03 2.94e-02 8.67e+00 pdb=" C VAL I 32 " -0.051 2.00e-02 2.50e+03 pdb=" O VAL I 32 " 0.019 2.00e-02 2.50e+03 pdb=" N GLY I 33 " 0.017 2.00e-02 2.50e+03 ... (remaining 397 not shown) Histogram of nonbonded interaction distances: 2.61 - 3.07: 1471 3.07 - 3.53: 1993 3.53 - 3.98: 3105 3.98 - 4.44: 3846 4.44 - 4.90: 7332 Nonbonded interactions: 17747 Sorted by model distance: nonbonded pdb=" O SER B 34 " pdb=" OG SER B 34 " model vdw 2.611 2.440 nonbonded pdb=" O SER J 34 " pdb=" OG SER J 34 " model vdw 2.612 2.440 nonbonded pdb=" O SER F 34 " pdb=" OG SER F 34 " model vdw 2.612 2.440 nonbonded pdb=" O SER H 34 " pdb=" OG SER H 34 " model vdw 2.612 2.440 nonbonded pdb=" O SER D 34 " pdb=" OG SER D 34 " model vdw 2.612 2.440 ... (remaining 17742 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' and (resid 10 through 17 or resid 19 through 37 or resid 38)) selection = (chain 'B' and (resid 10 through 17 or resid 19 through 37 or resid 38)) selection = (chain 'C' and (resid 10 through 17 or resid 19 through 37 or resid 38)) selection = (chain 'D' and (resid 10 through 17 or resid 19 through 37 or resid 38)) selection = (chain 'E' and (resid 10 through 17 or resid 19 through 37 or resid 38)) selection = (chain 'F' and (resid 10 through 17 or resid 19 through 37 or resid 38)) selection = (chain 'G' and (resid 10 through 17 or resid 19 through 37 or resid 38)) selection = (chain 'H' and (resid 10 through 17 or resid 19 through 37 or resid 38)) selection = (chain 'I' and (resid 10 through 17 or resid 19 through 37 or resid 38)) selection = (chain 'J' and (resid 10 through 17 or resid 19 through 37 or resid 38)) } 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=0.50 max=1.00 mean=0.97 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.110 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.090 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 12.800 Find NCS groups from input model: 0.110 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.870 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.030 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8260 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 : 0.006 0.032 2220 Z= 0.392 Angle : 0.742 4.601 3020 Z= 0.491 Chirality : 0.051 0.134 340 Planarity : 0.005 0.030 400 Dihedral : 8.049 29.789 740 Min Nonbonded Distance : 2.611 Molprobity Statistics. All-atom Clashscore : 0.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.69 % Favored : 92.31 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % 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: -4.46 (0.25), residues: 270 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.39 (0.19), residues: 270 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.005 0.001 PHE B 23 TYR 0.003 0.001 TYR E 37 ARG 0.000 0.000 ARG E 11 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 540 Ramachandran restraints generated. 270 Oldfield, 0 Emsley, 270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 540 Ramachandran restraints generated. 270 Oldfield, 0 Emsley, 270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 13 residues out of total 220 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 13 time to evaluate : 0.222 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 13 average time/residue: 0.0699 time to fit residues: 1.4971 Evaluate side-chains 13 residues out of total 220 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 13 time to evaluate : 0.167 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 20 random chunks: chunk 16 optimal weight: 8.9990 chunk 15 optimal weight: 9.9990 chunk 8 optimal weight: 9.9990 chunk 5 optimal weight: 9.9990 chunk 10 optimal weight: 8.9990 chunk 6 optimal weight: 2.9990 chunk 9 optimal weight: 1.9990 chunk 11 optimal weight: 0.9990 chunk 18 optimal weight: 8.9990 chunk 12 optimal weight: 0.9990 chunk 19 optimal weight: 0.9980 overall best weight: 1.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 18 HIS A A 21 ASN B 18 HIS A B 21 ASN C 18 HIS A C 21 ASN D 18 HIS A D 21 ASN E 18 HIS A E 21 ASN F 18 HIS A F 21 ASN G 18 HIS A G 21 ASN H 18 HIS A H 21 ASN I 18 HIS A I 21 ASN J 18 HIS A J 21 ASN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8242 moved from start: 0.1402 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.013 2220 Z= 0.189 Angle : 0.389 2.888 3020 Z= 0.230 Chirality : 0.043 0.124 340 Planarity : 0.002 0.005 400 Dihedral : 3.626 7.558 310 Min Nonbonded Distance : 2.642 Molprobity Statistics. All-atom Clashscore : 0.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Rotamer: Outliers : 0.00 % Allowed : 0.42 % Favored : 99.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.42 (0.27), residues: 270 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.36 (0.21), residues: 270 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.008 0.002 PHE H 15 TYR 0.001 0.000 TYR I 37 ARG 0.001 0.000 ARG J 11 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 540 Ramachandran restraints generated. 270 Oldfield, 0 Emsley, 270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 540 Ramachandran restraints generated. 270 Oldfield, 0 Emsley, 270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 23 residues out of total 220 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 23 time to evaluate : 0.226 Fit side-chains REVERT: G 19 SER cc_start: 0.8612 (t) cc_final: 0.8210 (p) REVERT: H 19 SER cc_start: 0.8591 (t) cc_final: 0.8231 (p) REVERT: I 19 SER cc_start: 0.8813 (t) cc_final: 0.8516 (p) REVERT: J 19 SER cc_start: 0.8936 (t) cc_final: 0.8719 (p) outliers start: 0 outliers final: 0 residues processed: 23 average time/residue: 0.0679 time to fit residues: 2.2990 Evaluate side-chains 23 residues out of total 220 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 23 time to evaluate : 0.206 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 20 random chunks: chunk 16 optimal weight: 0.9980 chunk 18 optimal weight: 8.9990 chunk 6 optimal weight: 10.0000 chunk 14 optimal weight: 6.9990 chunk 17 optimal weight: 7.9990 chunk 13 optimal weight: 0.9980 chunk 9 optimal weight: 5.9990 chunk 2 optimal weight: 6.9990 chunk 8 optimal weight: 9.9990 chunk 12 optimal weight: 0.8980 chunk 19 optimal weight: 3.9990 overall best weight: 2.5784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8271 moved from start: 0.1767 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.017 2220 Z= 0.293 Angle : 0.477 7.129 3020 Z= 0.265 Chirality : 0.044 0.125 340 Planarity : 0.002 0.006 400 Dihedral : 3.935 8.075 310 Min Nonbonded Distance : 2.622 Molprobity Statistics. All-atom Clashscore : 0.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.62 % Favored : 95.38 % Rotamer: Outliers : 0.00 % Allowed : 4.58 % Favored : 95.42 % 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: -4.62 (0.28), residues: 270 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.52 (0.21), residues: 270 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.011 0.002 PHE G 15 TYR 0.004 0.001 TYR A 37 ARG 0.001 0.000 ARG B 11 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 540 Ramachandran restraints generated. 270 Oldfield, 0 Emsley, 270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 540 Ramachandran restraints generated. 270 Oldfield, 0 Emsley, 270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 24 residues out of total 220 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 24 time to evaluate : 0.232 Fit side-chains REVERT: G 19 SER cc_start: 0.8666 (t) cc_final: 0.8199 (p) REVERT: I 19 SER cc_start: 0.8791 (t) cc_final: 0.8495 (p) REVERT: J 19 SER cc_start: 0.8971 (t) cc_final: 0.8706 (p) outliers start: 0 outliers final: 0 residues processed: 24 average time/residue: 0.0717 time to fit residues: 2.5149 Evaluate side-chains 24 residues out of total 220 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 24 time to evaluate : 0.227 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 20 random chunks: chunk 9 optimal weight: 9.9990 chunk 17 optimal weight: 6.9990 chunk 5 optimal weight: 1.9990 chunk 16 optimal weight: 3.9990 chunk 10 optimal weight: 7.9990 chunk 0 optimal weight: 7.9990 chunk 14 optimal weight: 4.9990 chunk 7 optimal weight: 8.9990 chunk 13 optimal weight: 0.8980 chunk 4 optimal weight: 5.9990 chunk 6 optimal weight: 2.9990 overall best weight: 2.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8289 moved from start: 0.2214 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.019 2220 Z= 0.338 Angle : 0.498 5.676 3020 Z= 0.279 Chirality : 0.045 0.126 340 Planarity : 0.002 0.006 400 Dihedral : 4.069 8.421 310 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 0.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.46 % Favored : 96.54 % Rotamer: Outliers : 0.42 % Allowed : 7.50 % Favored : 92.08 % 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 (0.28), residues: 270 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.66 (0.22), residues: 270 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.014 0.003 PHE G 15 TYR 0.010 0.001 TYR G 37 ARG 0.000 0.000 ARG J 11 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 540 Ramachandran restraints generated. 270 Oldfield, 0 Emsley, 270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 540 Ramachandran restraints generated. 270 Oldfield, 0 Emsley, 270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 34 residues out of total 220 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 33 time to evaluate : 0.272 Fit side-chains REVERT: G 19 SER cc_start: 0.8642 (t) cc_final: 0.8172 (p) REVERT: I 19 SER cc_start: 0.8770 (t) cc_final: 0.8398 (p) REVERT: J 19 SER cc_start: 0.8958 (t) cc_final: 0.8565 (p) outliers start: 1 outliers final: 1 residues processed: 33 average time/residue: 0.0542 time to fit residues: 2.6342 Evaluate side-chains 28 residues out of total 220 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 27 time to evaluate : 0.198 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 28 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 20 random chunks: chunk 17 optimal weight: 5.9990 chunk 3 optimal weight: 4.9990 chunk 11 optimal weight: 7.9990 chunk 4 optimal weight: 9.9990 chunk 19 optimal weight: 7.9990 chunk 16 optimal weight: 3.9990 chunk 8 optimal weight: 4.9990 chunk 1 optimal weight: 0.9990 chunk 6 optimal weight: 9.9990 chunk 10 optimal weight: 0.9990 chunk 18 optimal weight: 4.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 35 ASN H 35 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8305 moved from start: 0.2484 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.022 2220 Z= 0.364 Angle : 0.522 5.926 3020 Z= 0.290 Chirality : 0.044 0.126 340 Planarity : 0.003 0.006 400 Dihedral : 4.130 8.787 310 Min Nonbonded Distance : 2.310 Molprobity Statistics. All-atom Clashscore : 0.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.15 % Favored : 88.85 % Rotamer: Outliers : 1.25 % Allowed : 10.42 % Favored : 88.33 % 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: -4.90 (0.29), residues: 270 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.73 (0.22), residues: 270 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.014 0.003 PHE G 15 TYR 0.010 0.001 TYR G 37 ARG 0.000 0.000 ARG E 11 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 540 Ramachandran restraints generated. 270 Oldfield, 0 Emsley, 270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 540 Ramachandran restraints generated. 270 Oldfield, 0 Emsley, 270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 38 residues out of total 220 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 35 time to evaluate : 0.216 Fit side-chains REVERT: G 19 SER cc_start: 0.8649 (t) cc_final: 0.8162 (p) REVERT: I 19 SER cc_start: 0.8767 (t) cc_final: 0.8396 (p) REVERT: J 19 SER cc_start: 0.8919 (t) cc_final: 0.8540 (p) outliers start: 3 outliers final: 3 residues processed: 35 average time/residue: 0.0875 time to fit residues: 3.9640 Evaluate side-chains 35 residues out of total 220 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 32 time to evaluate : 0.184 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 SER Chi-restraints excluded: chain F residue 28 SER Chi-restraints excluded: chain G residue 28 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 20 random chunks: chunk 2 optimal weight: 5.9990 chunk 11 optimal weight: 6.9990 chunk 14 optimal weight: 9.9990 chunk 10 optimal weight: 1.9990 chunk 16 optimal weight: 7.9990 chunk 19 optimal weight: 0.0070 chunk 12 optimal weight: 1.9990 chunk 8 optimal weight: 1.9990 chunk 7 optimal weight: 0.9980 chunk 5 optimal weight: 6.9990 chunk 3 optimal weight: 0.8980 overall best weight: 1.1802 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 35 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8247 moved from start: 0.2679 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 2220 Z= 0.142 Angle : 0.418 5.368 3020 Z= 0.228 Chirality : 0.043 0.123 340 Planarity : 0.003 0.063 400 Dihedral : 3.510 9.629 310 Min Nonbonded Distance : 2.350 Molprobity Statistics. All-atom Clashscore : 0.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 1.67 % Allowed : 10.83 % Favored : 87.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.70 (0.30), residues: 270 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.58 (0.23), residues: 270 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.007 0.001 PHE G 15 TYR 0.007 0.001 TYR G 37 ARG 0.013 0.001 ARG J 11 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 540 Ramachandran restraints generated. 270 Oldfield, 0 Emsley, 270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 540 Ramachandran restraints generated. 270 Oldfield, 0 Emsley, 270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 34 residues out of total 220 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 30 time to evaluate : 0.233 Fit side-chains REVERT: G 19 SER cc_start: 0.8605 (t) cc_final: 0.8212 (p) REVERT: H 19 SER cc_start: 0.8502 (t) cc_final: 0.8132 (p) REVERT: I 19 SER cc_start: 0.8589 (t) cc_final: 0.8380 (p) outliers start: 4 outliers final: 4 residues processed: 32 average time/residue: 0.1191 time to fit residues: 4.7283 Evaluate side-chains 34 residues out of total 220 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 30 time to evaluate : 0.204 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 28 SER Chi-restraints excluded: chain F residue 28 SER Chi-restraints excluded: chain G residue 28 SER Chi-restraints excluded: chain I residue 28 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 20 random chunks: chunk 3 optimal weight: 0.0020 chunk 12 optimal weight: 8.9990 chunk 13 optimal weight: 2.9990 chunk 9 optimal weight: 0.8980 chunk 1 optimal weight: 0.8980 chunk 15 optimal weight: 0.8980 chunk 17 optimal weight: 8.9990 chunk 18 optimal weight: 0.0980 chunk 16 optimal weight: 1.9990 chunk 10 optimal weight: 9.9990 chunk 7 optimal weight: 2.9990 overall best weight: 0.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8211 moved from start: 0.2880 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.001 0.014 2220 Z= 0.081 Angle : 0.373 4.693 3020 Z= 0.204 Chirality : 0.042 0.118 340 Planarity : 0.002 0.027 400 Dihedral : 3.111 7.175 310 Min Nonbonded Distance : 2.407 Molprobity Statistics. All-atom Clashscore : 0.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 1.67 % Allowed : 11.25 % Favored : 87.08 % 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: -4.56 (0.32), residues: 270 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.47 (0.24), residues: 270 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.005 0.001 PHE H 15 TYR 0.004 0.000 TYR G 37 ARG 0.008 0.000 ARG J 11 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 540 Ramachandran restraints generated. 270 Oldfield, 0 Emsley, 270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 540 Ramachandran restraints generated. 270 Oldfield, 0 Emsley, 270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 37 residues out of total 220 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 33 time to evaluate : 0.228 Fit side-chains REVERT: E 19 SER cc_start: 0.8527 (t) cc_final: 0.8148 (p) REVERT: G 19 SER cc_start: 0.8446 (t) cc_final: 0.8187 (p) REVERT: H 19 SER cc_start: 0.8374 (t) cc_final: 0.8144 (p) REVERT: J 11 ARG cc_start: 0.7778 (mtp-110) cc_final: 0.6840 (mtm-85) outliers start: 4 outliers final: 4 residues processed: 34 average time/residue: 0.1191 time to fit residues: 5.0369 Evaluate side-chains 35 residues out of total 220 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 31 time to evaluate : 0.238 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 SER Chi-restraints excluded: chain D residue 28 SER Chi-restraints excluded: chain F residue 28 SER Chi-restraints excluded: chain G residue 28 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 20 random chunks: chunk 14 optimal weight: 9.9990 chunk 5 optimal weight: 9.9990 chunk 16 optimal weight: 7.9990 chunk 17 optimal weight: 5.9990 chunk 11 optimal weight: 8.9990 chunk 18 optimal weight: 2.9990 chunk 9 optimal weight: 0.9980 chunk 13 optimal weight: 0.7980 chunk 19 optimal weight: 5.9990 chunk 15 optimal weight: 0.8980 chunk 1 optimal weight: 0.7980 overall best weight: 1.2982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8245 moved from start: 0.2796 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.015 2220 Z= 0.152 Angle : 0.395 4.583 3020 Z= 0.220 Chirality : 0.042 0.120 340 Planarity : 0.002 0.027 400 Dihedral : 3.375 7.215 310 Min Nonbonded Distance : 2.363 Molprobity Statistics. All-atom Clashscore : 0.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.00 % Favored : 95.00 % Rotamer: Outliers : 2.92 % Allowed : 10.83 % Favored : 86.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.59 (0.32), residues: 270 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.49 (0.24), residues: 270 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.007 0.001 PHE G 15 TYR 0.006 0.001 TYR G 37 ARG 0.007 0.000 ARG J 11 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 540 Ramachandran restraints generated. 270 Oldfield, 0 Emsley, 270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 540 Ramachandran restraints generated. 270 Oldfield, 0 Emsley, 270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 40 residues out of total 220 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 33 time to evaluate : 0.179 Fit side-chains REVERT: G 19 SER cc_start: 0.8512 (t) cc_final: 0.8179 (p) REVERT: H 19 SER cc_start: 0.8505 (t) cc_final: 0.8171 (p) outliers start: 7 outliers final: 7 residues processed: 34 average time/residue: 0.1170 time to fit residues: 4.8995 Evaluate side-chains 40 residues out of total 220 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 33 time to evaluate : 0.210 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 SER Chi-restraints excluded: chain B residue 28 SER Chi-restraints excluded: chain C residue 28 SER Chi-restraints excluded: chain D residue 28 SER Chi-restraints excluded: chain F residue 28 SER Chi-restraints excluded: chain G residue 28 SER Chi-restraints excluded: chain I residue 28 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 20 random chunks: chunk 12 optimal weight: 10.0000 chunk 9 optimal weight: 3.9990 chunk 16 optimal weight: 2.9990 chunk 4 optimal weight: 9.9990 chunk 14 optimal weight: 9.9990 chunk 2 optimal weight: 2.9990 chunk 15 optimal weight: 0.9980 chunk 6 optimal weight: 1.9990 chunk 13 optimal weight: 3.9990 chunk 0 optimal weight: 0.7980 chunk 11 optimal weight: 2.9990 overall best weight: 1.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8272 moved from start: 0.2827 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.016 2220 Z= 0.226 Angle : 0.436 4.567 3020 Z= 0.244 Chirality : 0.042 0.123 340 Planarity : 0.002 0.032 400 Dihedral : 3.621 7.905 310 Min Nonbonded Distance : 2.333 Molprobity Statistics. All-atom Clashscore : 0.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.23 % Favored : 90.77 % Rotamer: Outliers : 2.92 % Allowed : 11.25 % Favored : 85.83 % 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 (0.32), residues: 270 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.54 (0.24), residues: 270 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.010 0.002 PHE G 15 TYR 0.007 0.001 TYR G 37 ARG 0.009 0.000 ARG J 11 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 540 Ramachandran restraints generated. 270 Oldfield, 0 Emsley, 270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 540 Ramachandran restraints generated. 270 Oldfield, 0 Emsley, 270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 40 residues out of total 220 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 33 time to evaluate : 0.246 Fit side-chains REVERT: G 19 SER cc_start: 0.8516 (t) cc_final: 0.8122 (p) REVERT: H 19 SER cc_start: 0.8530 (t) cc_final: 0.8135 (p) outliers start: 7 outliers final: 7 residues processed: 34 average time/residue: 0.1059 time to fit residues: 4.5590 Evaluate side-chains 40 residues out of total 220 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 33 time to evaluate : 0.227 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 SER Chi-restraints excluded: chain B residue 28 SER Chi-restraints excluded: chain C residue 28 SER Chi-restraints excluded: chain D residue 28 SER Chi-restraints excluded: chain F residue 28 SER Chi-restraints excluded: chain G residue 28 SER Chi-restraints excluded: chain I residue 28 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 20 random chunks: chunk 18 optimal weight: 8.9990 chunk 10 optimal weight: 10.0000 chunk 13 optimal weight: 7.9990 chunk 0 optimal weight: 8.9990 chunk 12 optimal weight: 9.9990 chunk 11 optimal weight: 4.9990 chunk 7 optimal weight: 0.9990 chunk 19 optimal weight: 0.7980 chunk 3 optimal weight: 3.9990 chunk 2 optimal weight: 5.9990 chunk 4 optimal weight: 2.9990 overall best weight: 2.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8293 moved from start: 0.2793 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.020 2220 Z= 0.317 Angle : 0.488 4.697 3020 Z= 0.273 Chirality : 0.043 0.124 340 Planarity : 0.003 0.030 400 Dihedral : 3.917 8.259 310 Min Nonbonded Distance : 2.303 Molprobity Statistics. All-atom Clashscore : 0.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.38 % Favored : 89.62 % Rotamer: Outliers : 3.33 % Allowed : 10.83 % Favored : 85.83 % 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 (0.32), residues: 270 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.56 (0.24), residues: 270 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.013 0.003 PHE G 15 TYR 0.008 0.001 TYR G 37 ARG 0.009 0.001 ARG J 11 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 540 Ramachandran restraints generated. 270 Oldfield, 0 Emsley, 270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 540 Ramachandran restraints generated. 270 Oldfield, 0 Emsley, 270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 41 residues out of total 220 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 33 time to evaluate : 0.166 Fit side-chains REVERT: G 19 SER cc_start: 0.8619 (t) cc_final: 0.8152 (p) outliers start: 8 outliers final: 8 residues processed: 33 average time/residue: 0.0870 time to fit residues: 3.5635 Evaluate side-chains 41 residues out of total 220 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 33 time to evaluate : 0.167 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 SER Chi-restraints excluded: chain B residue 28 SER Chi-restraints excluded: chain C residue 28 SER Chi-restraints excluded: chain D residue 28 SER Chi-restraints excluded: chain F residue 28 SER Chi-restraints excluded: chain G residue 28 SER Chi-restraints excluded: chain H residue 28 SER Chi-restraints excluded: chain I residue 28 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 20 random chunks: chunk 16 optimal weight: 0.9980 chunk 18 optimal weight: 0.5980 chunk 0 optimal weight: 7.9990 chunk 8 optimal weight: 8.9990 chunk 2 optimal weight: 6.9990 chunk 5 optimal weight: 0.7980 chunk 4 optimal weight: 1.9990 chunk 12 optimal weight: 0.8980 chunk 7 optimal weight: 7.9990 chunk 3 optimal weight: 0.9990 chunk 10 optimal weight: 10.0000 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3720 r_free = 0.3720 target = 0.110248 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.086050 restraints weight = 18497.922| |-----------------------------------------------------------------------------| r_work (start): 0.3346 rms_B_bonded: 5.53 r_work: 0.3098 rms_B_bonded: 5.37 restraints_weight: 2.0000 r_work (final): 0.3098 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3090 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3090 r_free = 0.3090 target_work(ls_wunit_k1) = 0.068 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3086 r_free = 0.3086 target_work(ls_wunit_k1) = 0.068 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3086 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8132 moved from start: 0.2881 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.018 2220 Z= 0.118 Angle : 0.397 4.727 3020 Z= 0.219 Chirality : 0.042 0.121 340 Planarity : 0.002 0.034 400 Dihedral : 3.397 7.621 310 Min Nonbonded Distance : 2.358 Molprobity Statistics. All-atom Clashscore : 0.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.46 % Favored : 96.54 % Rotamer: Outliers : 2.92 % Allowed : 10.83 % Favored : 86.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.55 (0.32), residues: 270 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.46 (0.25), residues: 270 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.005 0.001 PHE F 15 TYR 0.006 0.001 TYR G 37 ARG 0.009 0.001 ARG J 11 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 913.97 seconds wall clock time: 21 minutes 19.32 seconds (1279.32 seconds total)