Starting phenix.real_space_refine on Sun Mar 10 15:06:20 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uak_26427/03_2024/7uak_26427.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uak_26427/03_2024/7uak_26427.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.38 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uak_26427/03_2024/7uak_26427.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uak_26427/03_2024/7uak_26427.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uak_26427/03_2024/7uak_26427.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uak_26427/03_2024/7uak_26427.pdb" } resolution = 3.38 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= 0.004 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 1614 2.51 5 N 450 2.21 5 O 522 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 57": "OE1" <-> "OE2" Residue "B GLU 57": "OE1" <-> "OE2" Residue "C GLU 57": "OE1" <-> "OE2" Residue "D GLU 57": "OE1" <-> "OE2" Residue "E GLU 57": "OE1" <-> "OE2" Residue "F GLU 57": "OE1" <-> "OE2" Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 2586 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 431 Number of conformers: 1 Conformer: "" Number of residues, atoms: 62, 431 Classifications: {'peptide': 62} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'TRANS': 61} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "B" Number of atoms: 431 Number of conformers: 1 Conformer: "" Number of residues, atoms: 62, 431 Classifications: {'peptide': 62} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'TRANS': 61} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "C" Number of atoms: 431 Number of conformers: 1 Conformer: "" Number of residues, atoms: 62, 431 Classifications: {'peptide': 62} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'TRANS': 61} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "D" Number of atoms: 431 Number of conformers: 1 Conformer: "" Number of residues, atoms: 62, 431 Classifications: {'peptide': 62} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'TRANS': 61} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "E" Number of atoms: 431 Number of conformers: 1 Conformer: "" Number of residues, atoms: 62, 431 Classifications: {'peptide': 62} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'TRANS': 61} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "F" Number of atoms: 431 Number of conformers: 1 Conformer: "" Number of residues, atoms: 62, 431 Classifications: {'peptide': 62} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'TRANS': 61} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Time building chain proxies: 1.72, per 1000 atoms: 0.67 Number of scatterers: 2586 At special positions: 0 Unit cell: (95.23, 112.35, 34.24, 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 522 8.00 N 450 7.00 C 1614 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.91 Conformation dependent library (CDL) restraints added in 480.4 milliseconds 720 Ramachandran restraints generated. 360 Oldfield, 0 Emsley, 360 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 636 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 13 sheets defined 0.0% alpha, 37.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.35 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'A' and resid 48 through 56 removed outlier: 8.984A pdb=" N VAL A 49 " --> pdb=" O HIS C 50 " (cutoff:3.500A) removed outlier: 8.809A pdb=" N VAL C 52 " --> pdb=" O VAL A 49 " (cutoff:3.500A) removed outlier: 6.511A pdb=" N GLY A 51 " --> pdb=" O VAL C 52 " (cutoff:3.500A) removed outlier: 7.432A pdb=" N THR C 54 " --> pdb=" O GLY A 51 " (cutoff:3.500A) removed outlier: 6.606A pdb=" N GLU A 53 " --> pdb=" O THR C 54 " (cutoff:3.500A) removed outlier: 8.171A pdb=" N ALA C 56 " --> pdb=" O GLU A 53 " (cutoff:3.500A) removed outlier: 6.376A pdb=" N VAL A 55 " --> pdb=" O ALA C 56 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 48 through 56 removed outlier: 8.984A pdb=" N VAL A 49 " --> pdb=" O HIS C 50 " (cutoff:3.500A) removed outlier: 8.809A pdb=" N VAL C 52 " --> pdb=" O VAL A 49 " (cutoff:3.500A) removed outlier: 6.511A pdb=" N GLY A 51 " --> pdb=" O VAL C 52 " (cutoff:3.500A) removed outlier: 7.432A pdb=" N THR C 54 " --> pdb=" O GLY A 51 " (cutoff:3.500A) removed outlier: 6.606A pdb=" N GLU A 53 " --> pdb=" O THR C 54 " (cutoff:3.500A) removed outlier: 8.171A pdb=" N ALA C 56 " --> pdb=" O GLU A 53 " (cutoff:3.500A) removed outlier: 6.376A pdb=" N VAL A 55 " --> pdb=" O ALA C 56 " (cutoff:3.500A) removed outlier: 8.707A pdb=" N VAL E 52 " --> pdb=" O VAL C 49 " (cutoff:3.500A) removed outlier: 6.275A pdb=" N GLY C 51 " --> pdb=" O VAL E 52 " (cutoff:3.500A) removed outlier: 7.229A pdb=" N THR E 54 " --> pdb=" O GLY C 51 " (cutoff:3.500A) removed outlier: 6.421A pdb=" N GLU C 53 " --> pdb=" O THR E 54 " (cutoff:3.500A) removed outlier: 7.988A pdb=" N ALA E 56 " --> pdb=" O GLU C 53 " (cutoff:3.500A) removed outlier: 6.137A pdb=" N VAL C 55 " --> pdb=" O ALA E 56 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 63 through 64 Processing sheet with id=AA4, first strand: chain 'A' and resid 69 through 71 removed outlier: 6.204A pdb=" N ALA A 69 " --> pdb=" O VAL C 70 " (cutoff:3.500A) removed outlier: 7.694A pdb=" N THR C 72 " --> pdb=" O ALA A 69 " (cutoff:3.500A) removed outlier: 5.754A pdb=" N VAL A 71 " --> pdb=" O THR C 72 " (cutoff:3.500A) removed outlier: 6.480A pdb=" N ALA C 69 " --> pdb=" O VAL E 70 " (cutoff:3.500A) removed outlier: 7.975A pdb=" N THR E 72 " --> pdb=" O ALA C 69 " (cutoff:3.500A) removed outlier: 5.990A pdb=" N VAL C 71 " --> pdb=" O THR E 72 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'A' and resid 75 through 76 removed outlier: 6.410A pdb=" N THR A 75 " --> pdb=" O ALA C 76 " (cutoff:3.500A) removed outlier: 6.436A pdb=" N THR C 75 " --> pdb=" O ALA E 76 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'A' and resid 81 through 82 Processing sheet with id=AA7, first strand: chain 'A' and resid 88 through 94 removed outlier: 8.104A pdb=" N ALA A 89 " --> pdb=" O ALA C 90 " (cutoff:3.500A) removed outlier: 7.652A pdb=" N THR C 92 " --> pdb=" O ALA A 89 " (cutoff:3.500A) removed outlier: 9.118A pdb=" N ALA A 91 " --> pdb=" O THR C 92 " (cutoff:3.500A) removed outlier: 8.471A pdb=" N PHE C 94 " --> pdb=" O ALA A 91 " (cutoff:3.500A) removed outlier: 6.589A pdb=" N GLY A 93 " --> pdb=" O PHE C 94 " (cutoff:3.500A) removed outlier: 7.789A pdb=" N LYS C 96 " --> pdb=" O GLY A 93 " (cutoff:3.500A) removed outlier: 7.067A pdb=" N ALA E 89 " --> pdb=" O ILE C 88 " (cutoff:3.500A) removed outlier: 7.059A pdb=" N ALA C 90 " --> pdb=" O ALA E 89 " (cutoff:3.500A) removed outlier: 7.034A pdb=" N PHE C 94 " --> pdb=" O GLY E 93 " (cutoff:3.500A) removed outlier: 6.978A pdb=" N VAL E 95 " --> pdb=" O PHE C 94 " (cutoff:3.500A) removed outlier: 7.065A pdb=" N LYS C 96 " --> pdb=" O VAL E 95 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 49 through 56 removed outlier: 8.787A pdb=" N VAL B 49 " --> pdb=" O HIS D 50 " (cutoff:3.500A) removed outlier: 8.520A pdb=" N VAL D 52 " --> pdb=" O VAL B 49 " (cutoff:3.500A) removed outlier: 6.097A pdb=" N GLY B 51 " --> pdb=" O VAL D 52 " (cutoff:3.500A) removed outlier: 6.991A pdb=" N THR D 54 " --> pdb=" O GLY B 51 " (cutoff:3.500A) removed outlier: 6.147A pdb=" N GLU B 53 " --> pdb=" O THR D 54 " (cutoff:3.500A) removed outlier: 7.717A pdb=" N ALA D 56 " --> pdb=" O GLU B 53 " (cutoff:3.500A) removed outlier: 5.878A pdb=" N VAL B 55 " --> pdb=" O ALA D 56 " (cutoff:3.500A) removed outlier: 6.947A pdb=" N VAL D 52 " --> pdb=" O GLY F 51 " (cutoff:3.500A) removed outlier: 7.056A pdb=" N GLU F 53 " --> pdb=" O VAL D 52 " (cutoff:3.500A) removed outlier: 7.014A pdb=" N THR D 54 " --> pdb=" O GLU F 53 " (cutoff:3.500A) removed outlier: 7.069A pdb=" N VAL F 55 " --> pdb=" O THR D 54 " (cutoff:3.500A) removed outlier: 7.122A pdb=" N ALA D 56 " --> pdb=" O VAL F 55 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 63 through 64 Processing sheet with id=AB1, first strand: chain 'B' and resid 69 through 71 removed outlier: 6.349A pdb=" N ALA B 69 " --> pdb=" O VAL D 70 " (cutoff:3.500A) removed outlier: 6.312A pdb=" N ALA D 69 " --> pdb=" O VAL F 70 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'B' and resid 75 through 76 removed outlier: 6.679A pdb=" N THR B 75 " --> pdb=" O ALA D 76 " (cutoff:3.500A) removed outlier: 6.437A pdb=" N THR D 75 " --> pdb=" O ALA F 76 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'B' and resid 81 through 82 Processing sheet with id=AB4, first strand: chain 'B' and resid 88 through 96 removed outlier: 8.156A pdb=" N ALA B 89 " --> pdb=" O ALA D 90 " (cutoff:3.500A) removed outlier: 7.602A pdb=" N THR D 92 " --> pdb=" O ALA B 89 " (cutoff:3.500A) removed outlier: 9.125A pdb=" N ALA B 91 " --> pdb=" O THR D 92 " (cutoff:3.500A) removed outlier: 8.484A pdb=" N PHE D 94 " --> pdb=" O ALA B 91 " (cutoff:3.500A) removed outlier: 6.577A pdb=" N GLY B 93 " --> pdb=" O PHE D 94 " (cutoff:3.500A) removed outlier: 7.755A pdb=" N LYS D 96 " --> pdb=" O GLY B 93 " (cutoff:3.500A) removed outlier: 6.585A pdb=" N VAL B 95 " --> pdb=" O LYS D 96 " (cutoff:3.500A) removed outlier: 8.158A pdb=" N ALA D 89 " --> pdb=" O ALA F 90 " (cutoff:3.500A) removed outlier: 7.641A pdb=" N THR F 92 " --> pdb=" O ALA D 89 " (cutoff:3.500A) removed outlier: 9.154A pdb=" N ALA D 91 " --> pdb=" O THR F 92 " (cutoff:3.500A) removed outlier: 8.512A pdb=" N PHE F 94 " --> pdb=" O ALA D 91 " (cutoff:3.500A) removed outlier: 6.612A pdb=" N GLY D 93 " --> pdb=" O PHE F 94 " (cutoff:3.500A) removed outlier: 7.793A pdb=" N LYS F 96 " --> pdb=" O GLY D 93 " (cutoff:3.500A) removed outlier: 6.585A pdb=" N VAL D 95 " --> pdb=" O LYS F 96 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB4 16 hydrogen bonds defined for protein. 48 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: 0.53 Time building geometry restraints manager: 0.99 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.28: 456 1.28 - 1.35: 402 1.35 - 1.41: 96 1.41 - 1.48: 438 1.48 - 1.55: 1206 Bond restraints: 2598 Sorted by residual: bond pdb=" N GLU B 46 " pdb=" CA GLU B 46 " ideal model delta sigma weight residual 1.456 1.479 -0.023 1.25e-02 6.40e+03 3.39e+00 bond pdb=" N GLU A 46 " pdb=" CA GLU A 46 " ideal model delta sigma weight residual 1.456 1.479 -0.023 1.25e-02 6.40e+03 3.36e+00 bond pdb=" N GLU D 46 " pdb=" CA GLU D 46 " ideal model delta sigma weight residual 1.456 1.478 -0.023 1.25e-02 6.40e+03 3.31e+00 bond pdb=" N GLU E 46 " pdb=" CA GLU E 46 " ideal model delta sigma weight residual 1.456 1.478 -0.022 1.25e-02 6.40e+03 3.16e+00 bond pdb=" N GLU F 46 " pdb=" CA GLU F 46 " ideal model delta sigma weight residual 1.456 1.478 -0.022 1.25e-02 6.40e+03 3.15e+00 ... (remaining 2593 not shown) Histogram of bond angle deviations from ideal: 106.08 - 111.11: 1086 111.11 - 116.13: 777 116.13 - 121.15: 796 121.15 - 126.18: 845 126.18 - 131.20: 6 Bond angle restraints: 3510 Sorted by residual: angle pdb=" C GLU E 46 " pdb=" CA GLU E 46 " pdb=" CB GLU E 46 " ideal model delta sigma weight residual 109.64 115.00 -5.36 1.77e+00 3.19e-01 9.19e+00 angle pdb=" C GLU B 46 " pdb=" CA GLU B 46 " pdb=" CB GLU B 46 " ideal model delta sigma weight residual 109.64 115.00 -5.36 1.77e+00 3.19e-01 9.16e+00 angle pdb=" C GLU D 46 " pdb=" CA GLU D 46 " pdb=" CB GLU D 46 " ideal model delta sigma weight residual 109.64 114.99 -5.35 1.77e+00 3.19e-01 9.12e+00 angle pdb=" C GLU F 46 " pdb=" CA GLU F 46 " pdb=" CB GLU F 46 " ideal model delta sigma weight residual 109.64 114.97 -5.33 1.77e+00 3.19e-01 9.08e+00 angle pdb=" C GLU A 46 " pdb=" CA GLU A 46 " pdb=" CB GLU A 46 " ideal model delta sigma weight residual 109.64 114.97 -5.33 1.77e+00 3.19e-01 9.06e+00 ... (remaining 3505 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 10.04: 1206 10.04 - 20.08: 204 20.08 - 30.12: 72 30.12 - 40.16: 24 40.16 - 50.20: 18 Dihedral angle restraints: 1524 sinusoidal: 516 harmonic: 1008 Sorted by residual: dihedral pdb=" CA GLU D 46 " pdb=" C GLU D 46 " pdb=" N GLY D 47 " pdb=" CA GLY D 47 " ideal model delta harmonic sigma weight residual -180.00 -156.27 -23.73 0 5.00e+00 4.00e-02 2.25e+01 dihedral pdb=" CA GLU C 46 " pdb=" C GLU C 46 " pdb=" N GLY C 47 " pdb=" CA GLY C 47 " ideal model delta harmonic sigma weight residual -180.00 -156.28 -23.72 0 5.00e+00 4.00e-02 2.25e+01 dihedral pdb=" CA GLU A 46 " pdb=" C GLU A 46 " pdb=" N GLY A 47 " pdb=" CA GLY A 47 " ideal model delta harmonic sigma weight residual -180.00 -156.28 -23.72 0 5.00e+00 4.00e-02 2.25e+01 ... (remaining 1521 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.035: 310 0.035 - 0.071: 54 0.071 - 0.106: 48 0.106 - 0.141: 38 0.141 - 0.177: 6 Chirality restraints: 456 Sorted by residual: chirality pdb=" CB VAL E 77 " pdb=" CA VAL E 77 " pdb=" CG1 VAL E 77 " pdb=" CG2 VAL E 77 " both_signs ideal model delta sigma weight residual False -2.63 -2.45 -0.18 2.00e-01 2.50e+01 7.80e-01 chirality pdb=" CB VAL D 77 " pdb=" CA VAL D 77 " pdb=" CG1 VAL D 77 " pdb=" CG2 VAL D 77 " both_signs ideal model delta sigma weight residual False -2.63 -2.45 -0.18 2.00e-01 2.50e+01 7.76e-01 chirality pdb=" CB VAL C 77 " pdb=" CA VAL C 77 " pdb=" CG1 VAL C 77 " pdb=" CG2 VAL C 77 " both_signs ideal model delta sigma weight residual False -2.63 -2.45 -0.18 2.00e-01 2.50e+01 7.72e-01 ... (remaining 453 not shown) Planarity restraints: 438 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE E 94 " 0.000 2.00e-02 2.50e+03 9.16e-03 1.47e+00 pdb=" CG PHE E 94 " 0.014 2.00e-02 2.50e+03 pdb=" CD1 PHE E 94 " -0.015 2.00e-02 2.50e+03 pdb=" CD2 PHE E 94 " -0.009 2.00e-02 2.50e+03 pdb=" CE1 PHE E 94 " 0.008 2.00e-02 2.50e+03 pdb=" CE2 PHE E 94 " 0.003 2.00e-02 2.50e+03 pdb=" CZ PHE E 94 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 94 " 0.000 2.00e-02 2.50e+03 9.03e-03 1.43e+00 pdb=" CG PHE A 94 " 0.014 2.00e-02 2.50e+03 pdb=" CD1 PHE A 94 " -0.014 2.00e-02 2.50e+03 pdb=" CD2 PHE A 94 " -0.009 2.00e-02 2.50e+03 pdb=" CE1 PHE A 94 " 0.008 2.00e-02 2.50e+03 pdb=" CE2 PHE A 94 " 0.003 2.00e-02 2.50e+03 pdb=" CZ PHE A 94 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE B 94 " -0.001 2.00e-02 2.50e+03 8.95e-03 1.40e+00 pdb=" CG PHE B 94 " -0.014 2.00e-02 2.50e+03 pdb=" CD1 PHE B 94 " 0.014 2.00e-02 2.50e+03 pdb=" CD2 PHE B 94 " 0.009 2.00e-02 2.50e+03 pdb=" CE1 PHE B 94 " -0.008 2.00e-02 2.50e+03 pdb=" CE2 PHE B 94 " -0.003 2.00e-02 2.50e+03 pdb=" CZ PHE B 94 " 0.002 2.00e-02 2.50e+03 ... (remaining 435 not shown) Histogram of nonbonded interaction distances: 2.41 - 2.91: 1110 2.91 - 3.40: 2293 3.40 - 3.90: 4080 3.90 - 4.40: 3915 4.40 - 4.90: 8123 Nonbonded interactions: 19521 Sorted by model distance: nonbonded pdb=" N ASP B 98 " pdb=" OD1 ASP B 98 " model vdw 2.407 2.520 nonbonded pdb=" N ASP C 98 " pdb=" OD1 ASP C 98 " model vdw 2.407 2.520 nonbonded pdb=" N ASP D 98 " pdb=" OD1 ASP D 98 " model vdw 2.407 2.520 nonbonded pdb=" N ASP E 98 " pdb=" OD1 ASP E 98 " model vdw 2.407 2.520 nonbonded pdb=" N ASP F 98 " pdb=" OD1 ASP F 98 " model vdw 2.407 2.520 ... (remaining 19516 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.100 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: 0.010 Extract box with map and model: 5.390 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 11.720 Find NCS groups from input model: 0.180 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.810 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.300 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6421 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 : 0.003 0.042 2598 Z= 0.234 Angle : 0.696 6.133 3510 Z= 0.404 Chirality : 0.053 0.177 456 Planarity : 0.002 0.010 438 Dihedral : 13.749 50.196 888 Min Nonbonded Distance : 2.407 Molprobity Statistics. All-atom Clashscore : 13.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.44 % Favored : 85.56 % 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: -2.82 (0.41), residues: 360 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.14 (0.31), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS B 50 PHE 0.015 0.007 PHE E 94 TYR 0.001 0.000 TYR E 39 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 720 Ramachandran restraints generated. 360 Oldfield, 0 Emsley, 360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 720 Ramachandran restraints generated. 360 Oldfield, 0 Emsley, 360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 19 residues out of total 270 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 19 time to evaluate : 0.287 Fit side-chains REVERT: E 79 GLN cc_start: 0.8009 (mp10) cc_final: 0.7802 (mp10) REVERT: F 57 GLU cc_start: 0.7570 (mp0) cc_final: 0.6840 (tm-30) outliers start: 0 outliers final: 0 residues processed: 19 average time/residue: 0.1501 time to fit residues: 3.7109 Evaluate side-chains 16 residues out of total 270 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 16 time to evaluate : 0.278 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 30 optimal weight: 9.9990 chunk 27 optimal weight: 5.9990 chunk 15 optimal weight: 2.9990 chunk 9 optimal weight: 7.9990 chunk 18 optimal weight: 1.9990 chunk 14 optimal weight: 0.7980 chunk 28 optimal weight: 2.9990 chunk 10 optimal weight: 2.9990 chunk 17 optimal weight: 3.9990 chunk 21 optimal weight: 1.9990 chunk 32 optimal weight: 0.7980 overall best weight: 1.7186 ------------------------------------------------------------------------------- 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: 0.6790 moved from start: 0.2751 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.026 2598 Z= 0.281 Angle : 0.626 5.364 3510 Z= 0.345 Chirality : 0.050 0.129 456 Planarity : 0.003 0.010 438 Dihedral : 6.314 26.375 372 Min Nonbonded Distance : 2.322 Molprobity Statistics. All-atom Clashscore : 9.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 18.61 % Favored : 81.39 % Rotamer: Outliers : 3.03 % Allowed : 6.44 % Favored : 90.53 % 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: -3.17 (0.38), residues: 360 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.41 (0.29), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.007 0.003 HIS D 50 PHE 0.011 0.003 PHE D 94 TYR 0.003 0.001 TYR F 39 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 720 Ramachandran restraints generated. 360 Oldfield, 0 Emsley, 360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 720 Ramachandran restraints generated. 360 Oldfield, 0 Emsley, 360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 30 residues out of total 270 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 22 time to evaluate : 0.261 Fit side-chains REVERT: A 57 GLU cc_start: 0.7627 (mp0) cc_final: 0.7373 (mp0) REVERT: E 58 LYS cc_start: 0.7329 (ptpt) cc_final: 0.7127 (ptpt) REVERT: F 58 LYS cc_start: 0.7354 (ptpt) cc_final: 0.6899 (ptpt) outliers start: 8 outliers final: 6 residues processed: 27 average time/residue: 0.1715 time to fit residues: 5.6158 Evaluate side-chains 25 residues out of total 270 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 19 time to evaluate : 0.288 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 VAL Chi-restraints excluded: chain D residue 59 THR Chi-restraints excluded: chain D residue 77 VAL Chi-restraints excluded: chain E residue 59 THR Chi-restraints excluded: chain E residue 77 VAL Chi-restraints excluded: chain F residue 59 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 18 optimal weight: 9.9990 chunk 10 optimal weight: 0.2980 chunk 27 optimal weight: 0.9980 chunk 22 optimal weight: 0.9990 chunk 9 optimal weight: 8.9990 chunk 32 optimal weight: 3.9990 chunk 35 optimal weight: 4.9990 chunk 29 optimal weight: 3.9990 chunk 11 optimal weight: 0.8980 chunk 26 optimal weight: 0.6980 chunk 24 optimal weight: 7.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- 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: 0.6754 moved from start: 0.2735 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.014 2598 Z= 0.143 Angle : 0.522 4.920 3510 Z= 0.285 Chirality : 0.049 0.134 456 Planarity : 0.002 0.007 438 Dihedral : 5.798 26.538 372 Min Nonbonded Distance : 2.335 Molprobity Statistics. All-atom Clashscore : 7.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.61 % Favored : 86.39 % Rotamer: Outliers : 1.89 % Allowed : 13.26 % Favored : 84.85 % 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: -3.12 (0.39), residues: 360 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.37 (0.30), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS D 50 PHE 0.009 0.002 PHE A 94 TYR 0.004 0.001 TYR B 39 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 720 Ramachandran restraints generated. 360 Oldfield, 0 Emsley, 360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 720 Ramachandran restraints generated. 360 Oldfield, 0 Emsley, 360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 21 residues out of total 270 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 16 time to evaluate : 0.288 Fit side-chains REVERT: A 57 GLU cc_start: 0.7550 (mp0) cc_final: 0.6839 (mp0) REVERT: A 58 LYS cc_start: 0.7302 (OUTLIER) cc_final: 0.7019 (ptpt) REVERT: E 58 LYS cc_start: 0.7404 (ptpt) cc_final: 0.7046 (ptpt) outliers start: 5 outliers final: 2 residues processed: 19 average time/residue: 0.2343 time to fit residues: 5.3469 Evaluate side-chains 19 residues out of total 270 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 16 time to evaluate : 0.419 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 LYS Chi-restraints excluded: chain B residue 65 ASN Chi-restraints excluded: chain D residue 77 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 16 optimal weight: 4.9990 chunk 3 optimal weight: 0.8980 chunk 15 optimal weight: 2.9990 chunk 21 optimal weight: 5.9990 chunk 32 optimal weight: 1.9990 chunk 34 optimal weight: 5.9990 chunk 17 optimal weight: 2.9990 chunk 31 optimal weight: 4.9990 chunk 9 optimal weight: 6.9990 chunk 28 optimal weight: 6.9990 chunk 19 optimal weight: 2.9990 overall best weight: 2.3788 ------------------------------------------------------------------------------- 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: 0.6905 moved from start: 0.3609 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.027 2598 Z= 0.354 Angle : 0.654 4.921 3510 Z= 0.363 Chirality : 0.052 0.134 456 Planarity : 0.003 0.009 438 Dihedral : 6.693 26.937 372 Min Nonbonded Distance : 2.298 Molprobity Statistics. All-atom Clashscore : 7.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 17.22 % Favored : 82.78 % Rotamer: Outliers : 6.06 % Allowed : 12.12 % Favored : 81.82 % 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: -3.49 (0.37), residues: 360 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.65 (0.28), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.004 HIS F 50 PHE 0.005 0.002 PHE C 94 TYR 0.003 0.001 TYR D 39 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 720 Ramachandran restraints generated. 360 Oldfield, 0 Emsley, 360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 720 Ramachandran restraints generated. 360 Oldfield, 0 Emsley, 360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 42 residues out of total 270 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 26 time to evaluate : 0.294 Fit side-chains REVERT: A 58 LYS cc_start: 0.7520 (mttt) cc_final: 0.7303 (ptpt) REVERT: E 58 LYS cc_start: 0.7356 (ptpt) cc_final: 0.7101 (ptpt) REVERT: F 58 LYS cc_start: 0.7330 (ptpt) cc_final: 0.6904 (ptpt) outliers start: 16 outliers final: 12 residues processed: 38 average time/residue: 0.2057 time to fit residues: 9.0700 Evaluate side-chains 30 residues out of total 270 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 18 time to evaluate : 0.301 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 VAL Chi-restraints excluded: chain B residue 65 ASN Chi-restraints excluded: chain B residue 77 VAL Chi-restraints excluded: chain C residue 65 ASN Chi-restraints excluded: chain C residue 77 VAL Chi-restraints excluded: chain D residue 59 THR Chi-restraints excluded: chain D residue 77 VAL Chi-restraints excluded: chain E residue 59 THR Chi-restraints excluded: chain E residue 77 VAL Chi-restraints excluded: chain F residue 59 THR Chi-restraints excluded: chain F residue 65 ASN Chi-restraints excluded: chain F residue 77 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 0 optimal weight: 10.0000 chunk 25 optimal weight: 5.9990 chunk 14 optimal weight: 6.9990 chunk 29 optimal weight: 0.5980 chunk 24 optimal weight: 7.9990 chunk 17 optimal weight: 0.9980 chunk 31 optimal weight: 5.9990 chunk 8 optimal weight: 3.9990 chunk 11 optimal weight: 0.3980 chunk 6 optimal weight: 9.9990 chunk 20 optimal weight: 0.8980 overall best weight: 1.3782 ------------------------------------------------------------------------------- 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: 0.6876 moved from start: 0.3700 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 2598 Z= 0.214 Angle : 0.566 4.714 3510 Z= 0.312 Chirality : 0.049 0.137 456 Planarity : 0.002 0.007 438 Dihedral : 6.189 25.870 372 Min Nonbonded Distance : 2.308 Molprobity Statistics. All-atom Clashscore : 6.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 15.83 % Favored : 84.17 % Rotamer: Outliers : 4.92 % Allowed : 15.91 % Favored : 79.17 % 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: -3.46 (0.37), residues: 360 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.63 (0.28), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.002 HIS D 50 PHE 0.005 0.001 PHE D 94 TYR 0.002 0.001 TYR D 39 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 720 Ramachandran restraints generated. 360 Oldfield, 0 Emsley, 360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 720 Ramachandran restraints generated. 360 Oldfield, 0 Emsley, 360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 35 residues out of total 270 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 22 time to evaluate : 0.267 Fit side-chains REVERT: A 38 LEU cc_start: 0.4806 (OUTLIER) cc_final: 0.4465 (tt) REVERT: E 38 LEU cc_start: 0.4133 (OUTLIER) cc_final: 0.3790 (tt) REVERT: E 58 LYS cc_start: 0.7312 (ptpt) cc_final: 0.7022 (ptpt) REVERT: F 58 LYS cc_start: 0.7372 (ptpt) cc_final: 0.6908 (ptpt) outliers start: 13 outliers final: 9 residues processed: 35 average time/residue: 0.1976 time to fit residues: 8.1073 Evaluate side-chains 32 residues out of total 270 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 21 time to evaluate : 0.293 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 LEU Chi-restraints excluded: chain A residue 59 THR Chi-restraints excluded: chain A residue 77 VAL Chi-restraints excluded: chain B residue 65 ASN Chi-restraints excluded: chain C residue 38 LEU Chi-restraints excluded: chain D residue 59 THR Chi-restraints excluded: chain D residue 77 VAL Chi-restraints excluded: chain E residue 38 LEU Chi-restraints excluded: chain E residue 59 THR Chi-restraints excluded: chain F residue 59 THR Chi-restraints excluded: chain F residue 65 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 8 optimal weight: 0.4980 chunk 34 optimal weight: 4.9990 chunk 28 optimal weight: 4.9990 chunk 16 optimal weight: 4.9990 chunk 2 optimal weight: 0.9990 chunk 11 optimal weight: 0.0570 chunk 18 optimal weight: 9.9990 chunk 33 optimal weight: 4.9990 chunk 3 optimal weight: 4.9990 chunk 19 optimal weight: 0.9990 chunk 25 optimal weight: 1.9990 overall best weight: 0.9104 ------------------------------------------------------------------------------- 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: 0.6843 moved from start: 0.3724 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.015 2598 Z= 0.151 Angle : 0.530 4.442 3510 Z= 0.290 Chirality : 0.048 0.129 456 Planarity : 0.002 0.008 438 Dihedral : 5.638 24.122 372 Min Nonbonded Distance : 2.312 Molprobity Statistics. All-atom Clashscore : 5.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 15.56 % Favored : 84.44 % Rotamer: Outliers : 4.17 % Allowed : 18.94 % Favored : 76.89 % 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: -3.31 (0.39), residues: 360 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.51 (0.30), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.002 HIS E 50 PHE 0.004 0.001 PHE D 94 TYR 0.002 0.000 TYR B 39 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 720 Ramachandran restraints generated. 360 Oldfield, 0 Emsley, 360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 720 Ramachandran restraints generated. 360 Oldfield, 0 Emsley, 360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 32 residues out of total 270 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 21 time to evaluate : 0.274 Fit side-chains REVERT: B 38 LEU cc_start: 0.4582 (OUTLIER) cc_final: 0.3968 (tt) REVERT: C 57 GLU cc_start: 0.7633 (mp0) cc_final: 0.7424 (mp0) REVERT: C 58 LYS cc_start: 0.7063 (pttt) cc_final: 0.6736 (ptpt) REVERT: D 98 ASP cc_start: 0.6633 (OUTLIER) cc_final: 0.6276 (p0) REVERT: E 58 LYS cc_start: 0.7446 (ptpt) cc_final: 0.7070 (ptpt) REVERT: E 98 ASP cc_start: 0.7175 (OUTLIER) cc_final: 0.6952 (p0) REVERT: F 38 LEU cc_start: 0.4808 (OUTLIER) cc_final: 0.4294 (tt) REVERT: F 57 GLU cc_start: 0.7825 (mp0) cc_final: 0.7524 (mp0) REVERT: F 58 LYS cc_start: 0.7325 (ptpt) cc_final: 0.6903 (ptpt) outliers start: 11 outliers final: 4 residues processed: 30 average time/residue: 0.2090 time to fit residues: 7.3631 Evaluate side-chains 29 residues out of total 270 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 21 time to evaluate : 0.274 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 38 LEU Chi-restraints excluded: chain B residue 65 ASN Chi-restraints excluded: chain C residue 38 LEU Chi-restraints excluded: chain D residue 77 VAL Chi-restraints excluded: chain D residue 98 ASP Chi-restraints excluded: chain E residue 98 ASP Chi-restraints excluded: chain F residue 38 LEU Chi-restraints excluded: chain F residue 59 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 19 optimal weight: 7.9990 chunk 29 optimal weight: 5.9990 chunk 34 optimal weight: 0.9980 chunk 21 optimal weight: 5.9990 chunk 16 optimal weight: 5.9990 chunk 13 optimal weight: 8.9990 chunk 20 optimal weight: 5.9990 chunk 10 optimal weight: 5.9990 chunk 6 optimal weight: 9.9990 chunk 22 optimal weight: 1.9990 chunk 23 optimal weight: 0.8980 overall best weight: 3.1786 ------------------------------------------------------------------------------- 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: 0.6993 moved from start: 0.4317 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.038 2598 Z= 0.458 Angle : 0.722 5.224 3510 Z= 0.403 Chirality : 0.055 0.159 456 Planarity : 0.003 0.009 438 Dihedral : 6.984 24.984 372 Min Nonbonded Distance : 2.277 Molprobity Statistics. All-atom Clashscore : 8.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 19.17 % Favored : 80.83 % Rotamer: Outliers : 8.71 % Allowed : 16.29 % Favored : 75.00 % 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: -3.72 (0.35), residues: 360 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.83 (0.27), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.007 0.004 HIS F 50 PHE 0.007 0.002 PHE D 94 TYR 0.003 0.001 TYR B 39 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 720 Ramachandran restraints generated. 360 Oldfield, 0 Emsley, 360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 720 Ramachandran restraints generated. 360 Oldfield, 0 Emsley, 360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 56 residues out of total 270 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 33 time to evaluate : 0.291 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 58 LYS cc_start: 0.7538 (ptpt) cc_final: 0.7291 (ptpt) REVERT: B 38 LEU cc_start: 0.4466 (OUTLIER) cc_final: 0.3771 (tt) REVERT: C 79 GLN cc_start: 0.8411 (mp10) cc_final: 0.8198 (mp10) REVERT: D 98 ASP cc_start: 0.6725 (OUTLIER) cc_final: 0.6413 (p0) REVERT: E 38 LEU cc_start: 0.4436 (OUTLIER) cc_final: 0.3936 (tt) REVERT: E 57 GLU cc_start: 0.7994 (mp0) cc_final: 0.7628 (mp0) REVERT: E 58 LYS cc_start: 0.7456 (ptpt) cc_final: 0.7141 (ptpt) REVERT: E 98 ASP cc_start: 0.7456 (OUTLIER) cc_final: 0.7140 (p0) REVERT: F 38 LEU cc_start: 0.5259 (OUTLIER) cc_final: 0.4933 (tt) REVERT: F 58 LYS cc_start: 0.7417 (ptpt) cc_final: 0.6797 (ptpt) outliers start: 23 outliers final: 13 residues processed: 52 average time/residue: 0.1943 time to fit residues: 11.6304 Evaluate side-chains 47 residues out of total 270 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 29 time to evaluate : 0.287 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 THR Chi-restraints excluded: chain A residue 77 VAL Chi-restraints excluded: chain B residue 38 LEU Chi-restraints excluded: chain B residue 65 ASN Chi-restraints excluded: chain B residue 77 VAL Chi-restraints excluded: chain C residue 65 ASN Chi-restraints excluded: chain C residue 77 VAL Chi-restraints excluded: chain D residue 59 THR Chi-restraints excluded: chain D residue 77 VAL Chi-restraints excluded: chain D residue 98 ASP Chi-restraints excluded: chain E residue 38 LEU Chi-restraints excluded: chain E residue 59 THR Chi-restraints excluded: chain E residue 77 VAL Chi-restraints excluded: chain E residue 98 ASP Chi-restraints excluded: chain F residue 38 LEU Chi-restraints excluded: chain F residue 59 THR Chi-restraints excluded: chain F residue 65 ASN Chi-restraints excluded: chain F residue 77 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 17 optimal weight: 1.9990 chunk 3 optimal weight: 0.8980 chunk 27 optimal weight: 1.9990 chunk 31 optimal weight: 3.9990 chunk 33 optimal weight: 1.9990 chunk 30 optimal weight: 4.9990 chunk 32 optimal weight: 1.9990 chunk 19 optimal weight: 3.9990 chunk 14 optimal weight: 0.9980 chunk 25 optimal weight: 2.9990 chunk 9 optimal weight: 0.8980 overall best weight: 1.3584 ------------------------------------------------------------------------------- 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: 0.6920 moved from start: 0.4212 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 2598 Z= 0.209 Angle : 0.583 4.223 3510 Z= 0.320 Chirality : 0.049 0.131 456 Planarity : 0.002 0.007 438 Dihedral : 6.167 24.231 372 Min Nonbonded Distance : 2.307 Molprobity Statistics. All-atom Clashscore : 6.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 16.67 % Favored : 83.33 % Rotamer: Outliers : 6.82 % Allowed : 18.56 % Favored : 74.62 % 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: -3.54 (0.37), residues: 360 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.69 (0.29), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.002 HIS C 50 PHE 0.005 0.001 PHE D 94 TYR 0.002 0.000 TYR D 39 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 720 Ramachandran restraints generated. 360 Oldfield, 0 Emsley, 360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 720 Ramachandran restraints generated. 360 Oldfield, 0 Emsley, 360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 42 residues out of total 270 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 24 time to evaluate : 0.322 Fit side-chains REVERT: A 58 LYS cc_start: 0.7591 (ptpt) cc_final: 0.7335 (ptpt) REVERT: B 38 LEU cc_start: 0.4217 (OUTLIER) cc_final: 0.3432 (tt) REVERT: E 38 LEU cc_start: 0.4153 (OUTLIER) cc_final: 0.3691 (tt) REVERT: E 58 LYS cc_start: 0.7326 (ptpt) cc_final: 0.7099 (ptpt) REVERT: E 98 ASP cc_start: 0.7371 (OUTLIER) cc_final: 0.6462 (p0) REVERT: F 38 LEU cc_start: 0.4375 (OUTLIER) cc_final: 0.3849 (tt) outliers start: 18 outliers final: 11 residues processed: 38 average time/residue: 0.1928 time to fit residues: 8.6102 Evaluate side-chains 39 residues out of total 270 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 24 time to evaluate : 0.320 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 THR Chi-restraints excluded: chain B residue 38 LEU Chi-restraints excluded: chain B residue 65 ASN Chi-restraints excluded: chain B residue 92 THR Chi-restraints excluded: chain C residue 38 LEU Chi-restraints excluded: chain C residue 65 ASN Chi-restraints excluded: chain D residue 58 LYS Chi-restraints excluded: chain D residue 59 THR Chi-restraints excluded: chain D residue 77 VAL Chi-restraints excluded: chain E residue 38 LEU Chi-restraints excluded: chain E residue 59 THR Chi-restraints excluded: chain E residue 98 ASP Chi-restraints excluded: chain F residue 38 LEU Chi-restraints excluded: chain F residue 59 THR Chi-restraints excluded: chain F residue 65 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 29 optimal weight: 0.0670 chunk 30 optimal weight: 7.9990 chunk 32 optimal weight: 4.9990 chunk 21 optimal weight: 0.4980 chunk 34 optimal weight: 3.9990 chunk 20 optimal weight: 1.9990 chunk 16 optimal weight: 7.9990 chunk 23 optimal weight: 4.9990 chunk 35 optimal weight: 0.9990 chunk 33 optimal weight: 3.9990 chunk 28 optimal weight: 4.9990 overall best weight: 1.5124 ------------------------------------------------------------------------------- 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: 0.6932 moved from start: 0.4292 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 2598 Z= 0.234 Angle : 0.597 4.434 3510 Z= 0.327 Chirality : 0.049 0.128 456 Planarity : 0.002 0.008 438 Dihedral : 6.061 23.259 372 Min Nonbonded Distance : 2.305 Molprobity Statistics. All-atom Clashscore : 6.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 20.28 % Favored : 79.72 % Rotamer: Outliers : 6.06 % Allowed : 18.56 % Favored : 75.38 % 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: -3.53 (0.38), residues: 360 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.68 (0.29), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.002 HIS D 50 PHE 0.006 0.001 PHE D 94 TYR 0.002 0.000 TYR D 39 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 720 Ramachandran restraints generated. 360 Oldfield, 0 Emsley, 360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 720 Ramachandran restraints generated. 360 Oldfield, 0 Emsley, 360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 45 residues out of total 270 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 29 time to evaluate : 0.287 Fit side-chains revert: symmetry clash REVERT: A 58 LYS cc_start: 0.7561 (ptpt) cc_final: 0.7293 (ptpt) REVERT: B 38 LEU cc_start: 0.4345 (OUTLIER) cc_final: 0.3525 (tt) REVERT: E 38 LEU cc_start: 0.4115 (OUTLIER) cc_final: 0.3683 (tt) REVERT: E 58 LYS cc_start: 0.7310 (ptpt) cc_final: 0.6942 (ptpt) REVERT: E 98 ASP cc_start: 0.7543 (OUTLIER) cc_final: 0.6682 (p0) REVERT: F 38 LEU cc_start: 0.4571 (OUTLIER) cc_final: 0.3986 (tt) REVERT: F 57 GLU cc_start: 0.7790 (mp0) cc_final: 0.7571 (mp0) outliers start: 16 outliers final: 11 residues processed: 42 average time/residue: 0.2190 time to fit residues: 10.5112 Evaluate side-chains 44 residues out of total 270 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 29 time to evaluate : 0.290 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 THR Chi-restraints excluded: chain B residue 38 LEU Chi-restraints excluded: chain B residue 58 LYS Chi-restraints excluded: chain B residue 65 ASN Chi-restraints excluded: chain B residue 92 THR Chi-restraints excluded: chain C residue 38 LEU Chi-restraints excluded: chain C residue 65 ASN Chi-restraints excluded: chain D residue 59 THR Chi-restraints excluded: chain D residue 77 VAL Chi-restraints excluded: chain E residue 38 LEU Chi-restraints excluded: chain E residue 59 THR Chi-restraints excluded: chain E residue 98 ASP Chi-restraints excluded: chain F residue 38 LEU Chi-restraints excluded: chain F residue 59 THR Chi-restraints excluded: chain F residue 65 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 2 optimal weight: 0.7980 chunk 22 optimal weight: 0.9980 chunk 17 optimal weight: 0.6980 chunk 30 optimal weight: 7.9990 chunk 8 optimal weight: 0.9990 chunk 26 optimal weight: 0.9990 chunk 4 optimal weight: 4.9990 chunk 7 optimal weight: 2.9990 chunk 28 optimal weight: 3.9990 chunk 11 optimal weight: 3.9990 chunk 29 optimal weight: 0.0970 overall best weight: 0.7180 ------------------------------------------------------------------------------- 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: 0.6866 moved from start: 0.4228 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.020 2598 Z= 0.141 Angle : 0.549 4.056 3510 Z= 0.300 Chirality : 0.048 0.125 456 Planarity : 0.002 0.011 438 Dihedral : 5.622 22.307 372 Min Nonbonded Distance : 2.291 Molprobity Statistics. All-atom Clashscore : 4.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.72 % Favored : 85.28 % Rotamer: Outliers : 4.55 % Allowed : 21.97 % Favored : 73.48 % 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: -3.33 (0.40), residues: 360 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.53 (0.30), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS C 50 PHE 0.004 0.001 PHE D 94 TYR 0.002 0.000 TYR B 39 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 720 Ramachandran restraints generated. 360 Oldfield, 0 Emsley, 360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 720 Ramachandran restraints generated. 360 Oldfield, 0 Emsley, 360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 36 residues out of total 270 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 24 time to evaluate : 0.278 Fit side-chains REVERT: A 57 GLU cc_start: 0.7548 (mp0) cc_final: 0.7204 (mp0) REVERT: B 38 LEU cc_start: 0.4269 (OUTLIER) cc_final: 0.3531 (tt) REVERT: B 57 GLU cc_start: 0.7718 (mp0) cc_final: 0.7410 (mp0) REVERT: E 38 LEU cc_start: 0.3959 (OUTLIER) cc_final: 0.3602 (tt) REVERT: E 57 GLU cc_start: 0.7708 (mp0) cc_final: 0.7425 (mp0) REVERT: E 98 ASP cc_start: 0.7533 (OUTLIER) cc_final: 0.7326 (p0) REVERT: F 38 LEU cc_start: 0.4190 (OUTLIER) cc_final: 0.3484 (tt) REVERT: F 57 GLU cc_start: 0.7736 (mp0) cc_final: 0.7514 (mp0) outliers start: 12 outliers final: 6 residues processed: 34 average time/residue: 0.2148 time to fit residues: 8.4398 Evaluate side-chains 34 residues out of total 270 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 24 time to evaluate : 0.286 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 38 LEU Chi-restraints excluded: chain B residue 65 ASN Chi-restraints excluded: chain B residue 92 THR Chi-restraints excluded: chain C residue 38 LEU Chi-restraints excluded: chain D residue 77 VAL Chi-restraints excluded: chain E residue 38 LEU Chi-restraints excluded: chain E residue 59 THR Chi-restraints excluded: chain E residue 98 ASP Chi-restraints excluded: chain F residue 38 LEU Chi-restraints excluded: chain F residue 59 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 3 optimal weight: 9.9990 chunk 5 optimal weight: 1.9990 chunk 25 optimal weight: 7.9990 chunk 1 optimal weight: 2.9990 chunk 20 optimal weight: 5.9990 chunk 32 optimal weight: 0.8980 chunk 19 optimal weight: 7.9990 chunk 24 optimal weight: 0.0670 chunk 0 optimal weight: 6.9990 chunk 22 optimal weight: 6.9990 chunk 21 optimal weight: 2.9990 overall best weight: 1.7924 ------------------------------------------------------------------------------- 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 = 0.4194 r_free = 0.4194 target = 0.128316 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3820 r_free = 0.3820 target = 0.092091 restraints weight = 3016.361| |-----------------------------------------------------------------------------| r_work (start): 0.3891 rms_B_bonded: 2.98 r_work: 0.3757 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.3757 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7306 moved from start: 0.4421 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.026 2598 Z= 0.272 Angle : 0.614 4.481 3510 Z= 0.337 Chirality : 0.050 0.125 456 Planarity : 0.002 0.009 438 Dihedral : 6.137 22.530 372 Min Nonbonded Distance : 2.292 Molprobity Statistics. All-atom Clashscore : 6.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 19.17 % Favored : 80.83 % Rotamer: Outliers : 4.92 % Allowed : 20.08 % Favored : 75.00 % 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: -3.49 (0.39), residues: 360 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.65 (0.29), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.003 HIS B 50 PHE 0.005 0.001 PHE D 94 TYR 0.002 0.001 TYR D 39 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1078.99 seconds wall clock time: 20 minutes 0.63 seconds (1200.63 seconds total)