Starting phenix.real_space_refine on Fri Aug 2 20:06:05 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8rrr_19462/08_2024/8rrr_19462.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8rrr_19462/08_2024/8rrr_19462.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/8rrr_19462/08_2024/8rrr_19462.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8rrr_19462/08_2024/8rrr_19462.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8rrr_19462/08_2024/8rrr_19462.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8rrr_19462/08_2024/8rrr_19462.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= 0.001 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 3065 2.51 5 N 865 2.21 5 O 995 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 46": "OE1" <-> "OE2" Residue "A GLU 57": "OE1" <-> "OE2" Residue "B GLU 46": "OE1" <-> "OE2" Residue "B GLU 57": "OE1" <-> "OE2" Residue "C GLU 20": "OE1" <-> "OE2" Residue "C GLU 57": "OE1" <-> "OE2" Residue "C GLU 61": "OE1" <-> "OE2" Residue "C GLU 83": "OE1" <-> "OE2" Residue "C PHE 94": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 46": "OE1" <-> "OE2" Residue "D GLU 57": "OE1" <-> "OE2" Residue "D GLU 83": "OE1" <-> "OE2" Residue "E GLU 61": "OE1" <-> "OE2" Residue "E PHE 94": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 46": "OE1" <-> "OE2" Residue "F GLU 61": "OE1" <-> "OE2" Residue "G GLU 46": "OE1" <-> "OE2" Residue "G GLU 61": "OE1" <-> "OE2" Residue "G GLU 83": "OE1" <-> "OE2" Residue "H GLU 46": "OE1" <-> "OE2" Residue "H GLU 57": "OE1" <-> "OE2" Residue "H GLU 83": "OE1" <-> "OE2" Residue "H PHE 94": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I GLU 57": "OE1" <-> "OE2" Residue "I GLU 83": "OE1" <-> "OE2" Residue "I PHE 94": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J GLU 61": "OE1" <-> "OE2" Residue "J GLU 83": "OE1" <-> "OE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/chem_data/mon_lib" Total number of atoms: 4925 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 495 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 495 Classifications: {'peptide': 74} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'TRANS': 73} Chain breaks: 1 Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 495 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 495 Classifications: {'peptide': 74} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'TRANS': 73} Chain breaks: 1 Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 1 Chain: "C" Number of atoms: 495 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 495 Classifications: {'peptide': 74} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'TRANS': 73} Chain breaks: 1 Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 1 Chain: "D" Number of atoms: 495 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 495 Classifications: {'peptide': 74} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'TRANS': 73} Chain breaks: 1 Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 1 Chain: "E" Number of atoms: 495 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 495 Classifications: {'peptide': 74} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'TRANS': 73} Chain breaks: 1 Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 1 Chain: "F" Number of atoms: 490 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 490 Classifications: {'peptide': 73} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'TRANS': 72} Chain breaks: 1 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Unresolved non-hydrogen chiralities: 1 Chain: "G" Number of atoms: 490 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 490 Classifications: {'peptide': 73} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'TRANS': 72} Chain breaks: 1 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Unresolved non-hydrogen chiralities: 1 Chain: "H" Number of atoms: 490 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 490 Classifications: {'peptide': 73} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'TRANS': 72} Chain breaks: 1 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Unresolved non-hydrogen chiralities: 1 Chain: "I" Number of atoms: 490 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 490 Classifications: {'peptide': 73} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'TRANS': 72} Chain breaks: 1 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Unresolved non-hydrogen chiralities: 1 Chain: "J" Number of atoms: 490 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 490 Classifications: {'peptide': 73} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'TRANS': 72} Chain breaks: 1 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 3.61, per 1000 atoms: 0.73 Number of scatterers: 4925 At special positions: 0 Unit cell: (82.95, 113.4, 42, 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 995 8.00 N 865 7.00 C 3065 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.71 Conformation dependent library (CDL) restraints added in 914.0 milliseconds 1390 Ramachandran restraints generated. 695 Oldfield, 0 Emsley, 695 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1230 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 18 sheets defined 0.0% alpha, 42.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.92 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'C' and resid 15 through 20 removed outlier: 6.104A pdb=" N VAL D 15 " --> pdb=" O VAL E 16 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 15 through 20 removed outlier: 8.728A pdb=" N GLU D 20 " --> pdb=" O ALA A 17 " (cutoff:3.500A) removed outlier: 6.677A pdb=" N ALA A 19 " --> pdb=" O GLU D 20 " (cutoff:3.500A) removed outlier: 6.468A pdb=" N ALA D 19 " --> pdb=" O GLU E 20 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 40 through 41 removed outlier: 6.074A pdb=" N LEU A 38 " --> pdb=" O TYR D 39 " (cutoff:3.500A) removed outlier: 7.253A pdb=" N GLY D 41 " --> pdb=" O LEU A 38 " (cutoff:3.500A) removed outlier: 6.316A pdb=" N VAL A 40 " --> pdb=" O GLY D 41 " (cutoff:3.500A) removed outlier: 6.412A pdb=" N LEU D 38 " --> pdb=" O TYR E 39 " (cutoff:3.500A) removed outlier: 7.594A pdb=" N GLY E 41 " --> pdb=" O LEU D 38 " (cutoff:3.500A) removed outlier: 6.504A pdb=" N VAL D 40 " --> pdb=" O GLY E 41 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 47 through 50 removed outlier: 6.383A pdb=" N VAL B 48 " --> pdb=" O VAL C 49 " (cutoff:3.500A) removed outlier: 6.425A pdb=" N VAL A 48 " --> pdb=" O VAL B 49 " (cutoff:3.500A) removed outlier: 6.335A pdb=" N GLY A 47 " --> pdb=" O VAL D 48 " (cutoff:3.500A) removed outlier: 8.029A pdb=" N HIS D 50 " --> pdb=" O GLY A 47 " (cutoff:3.500A) removed outlier: 6.444A pdb=" N VAL A 49 " --> pdb=" O HIS D 50 " (cutoff:3.500A) removed outlier: 6.328A pdb=" N GLY D 47 " --> pdb=" O VAL E 48 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'A' and resid 53 through 55 removed outlier: 5.893A pdb=" N THR A 54 " --> pdb=" O VAL D 55 " (cutoff:3.500A) removed outlier: 6.080A pdb=" N THR D 54 " --> pdb=" O VAL E 55 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'C' and resid 61 through 66 removed outlier: 6.982A pdb=" N GLU B 61 " --> pdb=" O GLN C 62 " (cutoff:3.500A) removed outlier: 8.193A pdb=" N THR C 64 " --> pdb=" O GLU B 61 " (cutoff:3.500A) removed outlier: 6.796A pdb=" N VAL B 63 " --> pdb=" O THR C 64 " (cutoff:3.500A) removed outlier: 7.830A pdb=" N VAL C 66 " --> pdb=" O VAL B 63 " (cutoff:3.500A) removed outlier: 6.683A pdb=" N ASN B 65 " --> pdb=" O VAL C 66 " (cutoff:3.500A) removed outlier: 6.887A pdb=" N GLU A 61 " --> pdb=" O GLN B 62 " (cutoff:3.500A) removed outlier: 8.054A pdb=" N THR B 64 " --> pdb=" O GLU A 61 " (cutoff:3.500A) removed outlier: 6.626A pdb=" N VAL A 63 " --> pdb=" O THR B 64 " (cutoff:3.500A) removed outlier: 7.847A pdb=" N VAL B 66 " --> pdb=" O VAL A 63 " (cutoff:3.500A) removed outlier: 6.756A pdb=" N ASN A 65 " --> pdb=" O VAL B 66 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 69 through 71 removed outlier: 6.903A pdb=" N ALA B 69 " --> pdb=" O VAL C 70 " (cutoff:3.500A) removed outlier: 7.067A pdb=" N ALA A 69 " --> pdb=" O VAL B 70 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 75 through 79 removed outlier: 6.386A pdb=" N ALA B 76 " --> pdb=" O VAL C 77 " (cutoff:3.500A) removed outlier: 8.190A pdb=" N GLN C 79 " --> pdb=" O ALA B 76 " (cutoff:3.500A) removed outlier: 6.490A pdb=" N ALA B 78 " --> pdb=" O GLN C 79 " (cutoff:3.500A) removed outlier: 6.441A pdb=" N ALA A 76 " --> pdb=" O VAL B 77 " (cutoff:3.500A) removed outlier: 8.128A pdb=" N GLN B 79 " --> pdb=" O ALA A 76 " (cutoff:3.500A) removed outlier: 6.444A pdb=" N ALA A 78 " --> pdb=" O GLN B 79 " (cutoff:3.500A) removed outlier: 6.198A pdb=" N THR A 75 " --> pdb=" O ALA D 76 " (cutoff:3.500A) removed outlier: 7.809A pdb=" N ALA D 78 " --> pdb=" O THR A 75 " (cutoff:3.500A) removed outlier: 6.462A pdb=" N VAL A 77 " --> pdb=" O ALA D 78 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 88 through 93 removed outlier: 6.323A pdb=" N SER A 87 " --> pdb=" O ILE D 88 " (cutoff:3.500A) removed outlier: 7.862A pdb=" N ALA D 90 " --> pdb=" O SER A 87 " (cutoff:3.500A) removed outlier: 6.255A pdb=" N ALA A 89 " --> pdb=" O ALA D 90 " (cutoff:3.500A) removed outlier: 7.795A pdb=" N THR D 92 " --> pdb=" O ALA A 89 " (cutoff:3.500A) removed outlier: 6.467A pdb=" N ALA A 91 " --> pdb=" O THR D 92 " (cutoff:3.500A) removed outlier: 6.380A pdb=" N SER D 87 " --> pdb=" O ILE E 88 " (cutoff:3.500A) removed outlier: 7.903A pdb=" N ALA E 90 " --> pdb=" O SER D 87 " (cutoff:3.500A) removed outlier: 6.290A pdb=" N ALA D 89 " --> pdb=" O ALA E 90 " (cutoff:3.500A) removed outlier: 7.845A pdb=" N THR E 92 " --> pdb=" O ALA D 89 " (cutoff:3.500A) removed outlier: 6.322A pdb=" N ALA D 91 " --> pdb=" O THR E 92 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 53 through 55 Processing sheet with id=AB2, first strand: chain 'H' and resid 19 through 20 removed outlier: 6.251A pdb=" N ALA F 17 " --> pdb=" O ALA G 18 " (cutoff:3.500A) removed outlier: 8.460A pdb=" N GLU G 20 " --> pdb=" O ALA F 17 " (cutoff:3.500A) removed outlier: 6.442A pdb=" N ALA F 19 " --> pdb=" O GLU G 20 " (cutoff:3.500A) removed outlier: 6.362A pdb=" N ALA G 17 " --> pdb=" O ALA I 18 " (cutoff:3.500A) removed outlier: 8.332A pdb=" N GLU I 20 " --> pdb=" O ALA G 17 " (cutoff:3.500A) removed outlier: 6.631A pdb=" N ALA G 19 " --> pdb=" O GLU I 20 " (cutoff:3.500A) removed outlier: 6.113A pdb=" N VAL I 15 " --> pdb=" O VAL J 16 " (cutoff:3.500A) removed outlier: 7.818A pdb=" N ALA J 18 " --> pdb=" O VAL I 15 " (cutoff:3.500A) removed outlier: 6.236A pdb=" N ALA I 17 " --> pdb=" O ALA J 18 " (cutoff:3.500A) removed outlier: 8.162A pdb=" N GLU J 20 " --> pdb=" O ALA I 17 " (cutoff:3.500A) removed outlier: 6.585A pdb=" N ALA I 19 " --> pdb=" O GLU J 20 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'H' and resid 37 through 41 removed outlier: 6.177A pdb=" N LEU F 38 " --> pdb=" O TYR G 39 " (cutoff:3.500A) removed outlier: 7.614A pdb=" N GLY G 41 " --> pdb=" O LEU F 38 " (cutoff:3.500A) removed outlier: 6.576A pdb=" N VAL F 40 " --> pdb=" O GLY G 41 " (cutoff:3.500A) removed outlier: 6.106A pdb=" N LEU G 38 " --> pdb=" O TYR I 39 " (cutoff:3.500A) removed outlier: 7.535A pdb=" N GLY I 41 " --> pdb=" O LEU G 38 " (cutoff:3.500A) removed outlier: 6.459A pdb=" N VAL G 40 " --> pdb=" O GLY I 41 " (cutoff:3.500A) removed outlier: 6.509A pdb=" N LEU I 38 " --> pdb=" O TYR J 39 " (cutoff:3.500A) removed outlier: 7.653A pdb=" N GLY J 41 " --> pdb=" O LEU I 38 " (cutoff:3.500A) removed outlier: 6.694A pdb=" N VAL I 40 " --> pdb=" O GLY J 41 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'H' and resid 47 through 50 removed outlier: 6.362A pdb=" N VAL F 48 " --> pdb=" O VAL H 49 " (cutoff:3.500A) removed outlier: 6.425A pdb=" N GLY I 47 " --> pdb=" O VAL J 48 " (cutoff:3.500A) removed outlier: 8.083A pdb=" N HIS J 50 " --> pdb=" O GLY I 47 " (cutoff:3.500A) removed outlier: 6.454A pdb=" N VAL I 49 " --> pdb=" O HIS J 50 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'H' and resid 53 through 55 removed outlier: 6.077A pdb=" N THR F 54 " --> pdb=" O VAL G 55 " (cutoff:3.500A) removed outlier: 5.974A pdb=" N THR G 54 " --> pdb=" O VAL I 55 " (cutoff:3.500A) removed outlier: 6.198A pdb=" N THR I 54 " --> pdb=" O VAL J 55 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'H' and resid 61 through 66 removed outlier: 6.754A pdb=" N GLU F 61 " --> pdb=" O GLN H 62 " (cutoff:3.500A) removed outlier: 8.315A pdb=" N THR H 64 " --> pdb=" O GLU F 61 " (cutoff:3.500A) removed outlier: 6.842A pdb=" N VAL F 63 " --> pdb=" O THR H 64 " (cutoff:3.500A) removed outlier: 7.911A pdb=" N VAL H 66 " --> pdb=" O VAL F 63 " (cutoff:3.500A) removed outlier: 6.750A pdb=" N ASN F 65 " --> pdb=" O VAL H 66 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'H' and resid 69 through 71 removed outlier: 7.054A pdb=" N ALA F 69 " --> pdb=" O VAL H 70 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'H' and resid 75 through 79 removed outlier: 6.544A pdb=" N ALA F 76 " --> pdb=" O VAL H 77 " (cutoff:3.500A) removed outlier: 8.212A pdb=" N GLN H 79 " --> pdb=" O ALA F 76 " (cutoff:3.500A) removed outlier: 6.462A pdb=" N ALA F 78 " --> pdb=" O GLN H 79 " (cutoff:3.500A) removed outlier: 6.145A pdb=" N THR G 75 " --> pdb=" O ALA I 76 " (cutoff:3.500A) removed outlier: 7.791A pdb=" N ALA I 78 " --> pdb=" O THR G 75 " (cutoff:3.500A) removed outlier: 6.386A pdb=" N VAL G 77 " --> pdb=" O ALA I 78 " (cutoff:3.500A) removed outlier: 6.125A pdb=" N THR I 75 " --> pdb=" O ALA J 76 " (cutoff:3.500A) removed outlier: 7.743A pdb=" N ALA J 78 " --> pdb=" O THR I 75 " (cutoff:3.500A) removed outlier: 6.414A pdb=" N VAL I 77 " --> pdb=" O ALA J 78 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'H' and resid 88 through 93 removed outlier: 6.421A pdb=" N SER F 87 " --> pdb=" O ILE G 88 " (cutoff:3.500A) removed outlier: 7.882A pdb=" N ALA G 90 " --> pdb=" O SER F 87 " (cutoff:3.500A) removed outlier: 6.229A pdb=" N ALA F 89 " --> pdb=" O ALA G 90 " (cutoff:3.500A) removed outlier: 7.866A pdb=" N THR G 92 " --> pdb=" O ALA F 89 " (cutoff:3.500A) removed outlier: 6.236A pdb=" N ALA F 91 " --> pdb=" O THR G 92 " (cutoff:3.500A) removed outlier: 6.418A pdb=" N SER G 87 " --> pdb=" O ILE I 88 " (cutoff:3.500A) removed outlier: 7.845A pdb=" N ALA I 90 " --> pdb=" O SER G 87 " (cutoff:3.500A) removed outlier: 6.210A pdb=" N ALA G 89 " --> pdb=" O ALA I 90 " (cutoff:3.500A) removed outlier: 7.736A pdb=" N THR I 92 " --> pdb=" O ALA G 89 " (cutoff:3.500A) removed outlier: 6.309A pdb=" N ALA G 91 " --> pdb=" O THR I 92 " (cutoff:3.500A) removed outlier: 6.517A pdb=" N SER I 87 " --> pdb=" O ILE J 88 " (cutoff:3.500A) removed outlier: 7.852A pdb=" N ALA J 90 " --> pdb=" O SER I 87 " (cutoff:3.500A) removed outlier: 6.146A pdb=" N ALA I 89 " --> pdb=" O ALA J 90 " (cutoff:3.500A) removed outlier: 7.687A pdb=" N THR J 92 " --> pdb=" O ALA I 89 " (cutoff:3.500A) removed outlier: 6.315A pdb=" N ALA I 91 " --> pdb=" O THR J 92 " (cutoff:3.500A) 104 hydrogen bonds defined for protein. 306 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.18 Time building geometry restraints manager: 1.89 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: 875 1.28 - 1.35: 775 1.35 - 1.42: 180 1.42 - 1.48: 835 1.48 - 1.55: 2270 Bond restraints: 4935 Sorted by residual: bond pdb=" CA GLY D 93 " pdb=" C GLY D 93 " ideal model delta sigma weight residual 1.530 1.512 0.019 1.04e-02 9.25e+03 3.23e+00 bond pdb=" C ALA I 85 " pdb=" N GLY I 86 " ideal model delta sigma weight residual 1.331 1.319 0.012 6.60e-03 2.30e+04 3.19e+00 bond pdb=" N GLY D 93 " pdb=" CA GLY D 93 " ideal model delta sigma weight residual 1.464 1.446 0.018 1.12e-02 7.97e+03 2.59e+00 bond pdb=" CG LEU A 38 " pdb=" CD1 LEU A 38 " ideal model delta sigma weight residual 1.521 1.470 0.051 3.30e-02 9.18e+02 2.38e+00 bond pdb=" C THR J 59 " pdb=" N LYS J 60 " ideal model delta sigma weight residual 1.333 1.311 0.021 1.45e-02 4.76e+03 2.14e+00 ... (remaining 4930 not shown) Histogram of bond angle deviations from ideal: 103.70 - 109.20: 511 109.20 - 114.70: 2733 114.70 - 120.20: 1243 120.20 - 125.70: 2166 125.70 - 131.20: 12 Bond angle restraints: 6665 Sorted by residual: angle pdb=" C GLU J 83 " pdb=" CA GLU J 83 " pdb=" CB GLU J 83 " ideal model delta sigma weight residual 111.45 105.31 6.14 1.72e+00 3.38e-01 1.27e+01 angle pdb=" C GLU H 83 " pdb=" CA GLU H 83 " pdb=" CB GLU H 83 " ideal model delta sigma weight residual 111.45 105.63 5.82 1.72e+00 3.38e-01 1.14e+01 angle pdb=" C GLU C 83 " pdb=" N GLY C 84 " pdb=" CA GLY C 84 " ideal model delta sigma weight residual 121.41 114.90 6.51 1.96e+00 2.60e-01 1.10e+01 angle pdb=" C GLU C 83 " pdb=" CA GLU C 83 " pdb=" CB GLU C 83 " ideal model delta sigma weight residual 111.28 106.21 5.07 1.58e+00 4.01e-01 1.03e+01 angle pdb=" C GLU E 83 " pdb=" N GLY E 84 " pdb=" CA GLY E 84 " ideal model delta sigma weight residual 121.41 115.19 6.22 1.96e+00 2.60e-01 1.01e+01 ... (remaining 6660 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.89: 2506 15.89 - 31.78: 265 31.78 - 47.67: 62 47.67 - 63.56: 17 63.56 - 79.45: 5 Dihedral angle restraints: 2855 sinusoidal: 900 harmonic: 1955 Sorted by residual: dihedral pdb=" CA GLY A 84 " pdb=" C GLY A 84 " pdb=" N ALA A 85 " pdb=" CA ALA A 85 " ideal model delta harmonic sigma weight residual 180.00 152.67 27.33 0 5.00e+00 4.00e-02 2.99e+01 dihedral pdb=" CA GLY G 73 " pdb=" C GLY G 73 " pdb=" N VAL G 74 " pdb=" CA VAL G 74 " ideal model delta harmonic sigma weight residual 180.00 153.28 26.72 0 5.00e+00 4.00e-02 2.86e+01 dihedral pdb=" CA GLY A 73 " pdb=" C GLY A 73 " pdb=" N VAL A 74 " pdb=" CA VAL A 74 " ideal model delta harmonic sigma weight residual 180.00 153.72 26.28 0 5.00e+00 4.00e-02 2.76e+01 ... (remaining 2852 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.033: 442 0.033 - 0.066: 237 0.066 - 0.099: 92 0.099 - 0.131: 101 0.131 - 0.164: 3 Chirality restraints: 875 Sorted by residual: chirality pdb=" CG LEU C 38 " pdb=" CB LEU C 38 " pdb=" CD1 LEU C 38 " pdb=" CD2 LEU C 38 " both_signs ideal model delta sigma weight residual False -2.59 -2.75 0.16 2.00e-01 2.50e+01 6.75e-01 chirality pdb=" CG LEU G 38 " pdb=" CB LEU G 38 " pdb=" CD1 LEU G 38 " pdb=" CD2 LEU G 38 " both_signs ideal model delta sigma weight residual False -2.59 -2.74 0.15 2.00e-01 2.50e+01 5.67e-01 chirality pdb=" CG LEU F 38 " pdb=" CB LEU F 38 " pdb=" CD1 LEU F 38 " pdb=" CD2 LEU F 38 " both_signs ideal model delta sigma weight residual False -2.59 -2.73 0.14 2.00e-01 2.50e+01 5.16e-01 ... (remaining 872 not shown) Planarity restraints: 835 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CG GLU E 61 " -0.008 2.00e-02 2.50e+03 1.57e-02 2.46e+00 pdb=" CD GLU E 61 " 0.027 2.00e-02 2.50e+03 pdb=" OE1 GLU E 61 " -0.010 2.00e-02 2.50e+03 pdb=" OE2 GLU E 61 " -0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLU J 61 " 0.008 2.00e-02 2.50e+03 1.55e-02 2.40e+00 pdb=" CD GLU J 61 " -0.027 2.00e-02 2.50e+03 pdb=" OE1 GLU J 61 " 0.010 2.00e-02 2.50e+03 pdb=" OE2 GLU J 61 " 0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLU F 61 " 0.007 2.00e-02 2.50e+03 1.47e-02 2.16e+00 pdb=" CD GLU F 61 " -0.025 2.00e-02 2.50e+03 pdb=" OE1 GLU F 61 " 0.009 2.00e-02 2.50e+03 pdb=" OE2 GLU F 61 " 0.009 2.00e-02 2.50e+03 ... (remaining 832 not shown) Histogram of nonbonded interaction distances: 2.32 - 2.83: 1622 2.83 - 3.35: 4131 3.35 - 3.87: 8146 3.87 - 4.38: 8663 4.38 - 4.90: 17468 Nonbonded interactions: 40030 Sorted by model distance: nonbonded pdb=" O THR B 72 " pdb=" OG1 THR B 72 " model vdw 2.315 3.040 nonbonded pdb=" N GLN F 24 " pdb=" OE1 GLN F 24 " model vdw 2.341 3.120 nonbonded pdb=" O THR H 72 " pdb=" OG1 THR H 72 " model vdw 2.342 3.040 nonbonded pdb=" NZ LYS I 45 " pdb=" OE1 GLU I 46 " model vdw 2.359 3.120 nonbonded pdb=" N GLN A 24 " pdb=" OE1 GLN A 24 " model vdw 2.369 3.120 ... (remaining 40025 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and resid 14 through 96) selection = (chain 'B' and resid 14 through 96) selection = (chain 'C' and resid 14 through 96) selection = (chain 'D' and resid 14 through 96) selection = (chain 'E' and resid 14 through 96) selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators 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: 3.090 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: 0.210 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 18.090 Find NCS groups from input model: 0.250 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:2.740 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.480 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7619 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 0.051 4935 Z= 0.400 Angle : 0.833 7.448 6665 Z= 0.486 Chirality : 0.055 0.164 875 Planarity : 0.002 0.016 835 Dihedral : 15.099 79.447 1625 Min Nonbonded Distance : 2.315 Molprobity Statistics. All-atom Clashscore : 9.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.35 % Favored : 90.65 % Rotamer: Outliers : 0.64 % Allowed : 17.23 % Favored : 82.13 % 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: -4.20 (0.26), residues: 695 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.20 (0.20), residues: 695 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS D 50 PHE 0.011 0.002 PHE A 94 TYR 0.020 0.004 TYR G 39 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1390 Ramachandran restraints generated. 695 Oldfield, 0 Emsley, 695 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1390 Ramachandran restraints generated. 695 Oldfield, 0 Emsley, 695 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 67 residues out of total 495 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 64 time to evaluate : 0.535 Fit side-chains REVERT: C 24 GLN cc_start: 0.7034 (mm110) cc_final: 0.6114 (pm20) REVERT: C 57 GLU cc_start: 0.7919 (OUTLIER) cc_final: 0.6943 (pm20) REVERT: D 57 GLU cc_start: 0.7707 (mt-10) cc_final: 0.7491 (tt0) REVERT: E 80 LYS cc_start: 0.8114 (mttt) cc_final: 0.7696 (mttm) REVERT: F 80 LYS cc_start: 0.7969 (mtmt) cc_final: 0.7714 (mttp) outliers start: 3 outliers final: 1 residues processed: 65 average time/residue: 0.1414 time to fit residues: 12.5009 Evaluate side-chains 59 residues out of total 495 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 57 time to evaluate : 0.532 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 57 GLU Chi-restraints excluded: chain J residue 59 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 59 optimal weight: 8.9990 chunk 53 optimal weight: 6.9990 chunk 29 optimal weight: 0.0770 chunk 18 optimal weight: 3.9990 chunk 35 optimal weight: 20.0000 chunk 28 optimal weight: 7.9990 chunk 54 optimal weight: 6.9990 chunk 21 optimal weight: 9.9990 chunk 33 optimal weight: 10.0000 chunk 40 optimal weight: 2.9990 chunk 63 optimal weight: 1.9990 overall best weight: 3.2146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 24 GLN H 79 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7603 moved from start: 0.0880 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 4935 Z= 0.280 Angle : 0.647 7.293 6665 Z= 0.364 Chirality : 0.053 0.122 875 Planarity : 0.002 0.010 835 Dihedral : 6.794 33.123 729 Min Nonbonded Distance : 2.562 Molprobity Statistics. All-atom Clashscore : 7.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.63 % Favored : 91.37 % Rotamer: Outliers : 1.70 % Allowed : 15.32 % Favored : 82.98 % 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: -4.17 (0.26), residues: 695 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.17 (0.20), residues: 695 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS C 50 PHE 0.010 0.001 PHE A 94 TYR 0.015 0.003 TYR C 39 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1390 Ramachandran restraints generated. 695 Oldfield, 0 Emsley, 695 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1390 Ramachandran restraints generated. 695 Oldfield, 0 Emsley, 695 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 495 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 58 time to evaluate : 0.484 Fit side-chains REVERT: B 61 GLU cc_start: 0.8496 (mp0) cc_final: 0.8191 (mp0) REVERT: B 83 GLU cc_start: 0.8255 (OUTLIER) cc_final: 0.7073 (mp0) REVERT: C 24 GLN cc_start: 0.6845 (mm110) cc_final: 0.5982 (pm20) REVERT: C 57 GLU cc_start: 0.7778 (OUTLIER) cc_final: 0.6816 (pm20) REVERT: D 57 GLU cc_start: 0.7736 (mt-10) cc_final: 0.7532 (tt0) REVERT: F 80 LYS cc_start: 0.7906 (mtmt) cc_final: 0.7505 (mttm) REVERT: I 24 GLN cc_start: 0.7577 (mp10) cc_final: 0.7241 (mp10) outliers start: 8 outliers final: 2 residues processed: 62 average time/residue: 0.1266 time to fit residues: 10.9406 Evaluate side-chains 55 residues out of total 495 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 51 time to evaluate : 0.504 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 THR Chi-restraints excluded: chain B residue 83 GLU Chi-restraints excluded: chain C residue 57 GLU Chi-restraints excluded: chain H residue 37 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 35 optimal weight: 20.0000 chunk 19 optimal weight: 7.9990 chunk 52 optimal weight: 0.0570 chunk 43 optimal weight: 10.0000 chunk 17 optimal weight: 10.0000 chunk 63 optimal weight: 0.0040 chunk 68 optimal weight: 9.9990 chunk 56 optimal weight: 6.9990 chunk 21 optimal weight: 20.0000 chunk 51 optimal weight: 7.9990 chunk 62 optimal weight: 10.0000 overall best weight: 4.6116 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7637 moved from start: 0.1108 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 4935 Z= 0.379 Angle : 0.685 6.909 6665 Z= 0.387 Chirality : 0.055 0.124 875 Planarity : 0.002 0.010 835 Dihedral : 7.027 39.363 728 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 7.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.06 % Favored : 90.94 % Rotamer: Outliers : 3.19 % Allowed : 16.17 % Favored : 80.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.19 (0.26), residues: 695 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.19 (0.20), residues: 695 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS C 50 PHE 0.009 0.001 PHE A 94 TYR 0.018 0.004 TYR C 39 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1390 Ramachandran restraints generated. 695 Oldfield, 0 Emsley, 695 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1390 Ramachandran restraints generated. 695 Oldfield, 0 Emsley, 695 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 495 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 57 time to evaluate : 0.532 Fit side-chains REVERT: B 83 GLU cc_start: 0.8155 (OUTLIER) cc_final: 0.6820 (mp0) REVERT: C 57 GLU cc_start: 0.7846 (OUTLIER) cc_final: 0.6741 (pm20) REVERT: D 57 GLU cc_start: 0.7771 (mt-10) cc_final: 0.7517 (tt0) REVERT: F 80 LYS cc_start: 0.8002 (mtmt) cc_final: 0.6840 (mttm) REVERT: F 83 GLU cc_start: 0.8196 (OUTLIER) cc_final: 0.7005 (mp0) outliers start: 15 outliers final: 9 residues processed: 64 average time/residue: 0.1371 time to fit residues: 12.2410 Evaluate side-chains 63 residues out of total 495 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 51 time to evaluate : 0.475 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 GLU Chi-restraints excluded: chain A residue 59 THR Chi-restraints excluded: chain B residue 83 GLU Chi-restraints excluded: chain C residue 57 GLU Chi-restraints excluded: chain C residue 92 THR Chi-restraints excluded: chain E residue 22 THR Chi-restraints excluded: chain E residue 38 LEU Chi-restraints excluded: chain F residue 83 GLU Chi-restraints excluded: chain G residue 57 GLU Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 92 THR Chi-restraints excluded: chain J residue 59 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 47 optimal weight: 10.0000 chunk 33 optimal weight: 10.0000 chunk 7 optimal weight: 20.0000 chunk 30 optimal weight: 10.0000 chunk 42 optimal weight: 20.0000 chunk 63 optimal weight: 0.8980 chunk 67 optimal weight: 6.9990 chunk 60 optimal weight: 6.9990 chunk 18 optimal weight: 5.9990 chunk 56 optimal weight: 7.9990 chunk 38 optimal weight: 9.9990 overall best weight: 5.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 50 HIS H 24 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7660 moved from start: 0.1416 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.050 4935 Z= 0.458 Angle : 0.727 6.791 6665 Z= 0.414 Chirality : 0.056 0.145 875 Planarity : 0.002 0.010 835 Dihedral : 7.293 45.264 728 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 7.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.36 % Favored : 89.64 % Rotamer: Outliers : 3.62 % Allowed : 16.81 % Favored : 79.57 % 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: -4.28 (0.25), residues: 695 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.26 (0.19), residues: 695 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS C 50 PHE 0.009 0.001 PHE A 94 TYR 0.018 0.004 TYR G 39 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1390 Ramachandran restraints generated. 695 Oldfield, 0 Emsley, 695 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1390 Ramachandran restraints generated. 695 Oldfield, 0 Emsley, 695 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 495 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 58 time to evaluate : 0.535 Fit side-chains REVERT: A 57 GLU cc_start: 0.8071 (OUTLIER) cc_final: 0.7592 (tt0) REVERT: B 61 GLU cc_start: 0.8638 (mp0) cc_final: 0.8214 (mp0) REVERT: B 83 GLU cc_start: 0.8257 (OUTLIER) cc_final: 0.6871 (mp0) REVERT: C 57 GLU cc_start: 0.7994 (OUTLIER) cc_final: 0.6767 (pm20) REVERT: D 57 GLU cc_start: 0.7891 (mt-10) cc_final: 0.7589 (tt0) REVERT: D 83 GLU cc_start: 0.8097 (OUTLIER) cc_final: 0.6673 (mp0) REVERT: E 80 LYS cc_start: 0.8172 (mttt) cc_final: 0.7780 (mttm) REVERT: F 80 LYS cc_start: 0.7963 (mtmt) cc_final: 0.7046 (mtmt) REVERT: F 83 GLU cc_start: 0.8240 (OUTLIER) cc_final: 0.7000 (mp0) REVERT: J 24 GLN cc_start: 0.6808 (mp10) cc_final: 0.6375 (mp10) outliers start: 17 outliers final: 10 residues processed: 68 average time/residue: 0.1286 time to fit residues: 12.0854 Evaluate side-chains 63 residues out of total 495 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 48 time to evaluate : 0.496 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 GLU Chi-restraints excluded: chain A residue 59 THR Chi-restraints excluded: chain B residue 22 THR Chi-restraints excluded: chain B residue 83 GLU Chi-restraints excluded: chain C residue 57 GLU Chi-restraints excluded: chain C residue 92 THR Chi-restraints excluded: chain D residue 83 GLU Chi-restraints excluded: chain E residue 22 THR Chi-restraints excluded: chain E residue 92 THR Chi-restraints excluded: chain F residue 83 GLU Chi-restraints excluded: chain G residue 57 GLU Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 92 THR Chi-restraints excluded: chain J residue 59 THR Chi-restraints excluded: chain J residue 92 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 0 optimal weight: 20.0000 chunk 50 optimal weight: 9.9990 chunk 27 optimal weight: 9.9990 chunk 57 optimal weight: 10.0000 chunk 46 optimal weight: 1.9990 chunk 34 optimal weight: 5.9990 chunk 60 optimal weight: 5.9990 chunk 17 optimal weight: 10.0000 chunk 22 optimal weight: 5.9990 chunk 13 optimal weight: 9.9990 chunk 39 optimal weight: 2.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 24 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7644 moved from start: 0.1550 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 4935 Z= 0.373 Angle : 0.688 6.868 6665 Z= 0.389 Chirality : 0.055 0.141 875 Planarity : 0.002 0.012 835 Dihedral : 7.079 47.079 728 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 7.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.21 % Favored : 90.79 % Rotamer: Outliers : 3.40 % Allowed : 17.23 % Favored : 79.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.24 (0.25), residues: 695 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.22 (0.19), residues: 695 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS C 50 PHE 0.008 0.001 PHE A 94 TYR 0.016 0.004 TYR F 39 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1390 Ramachandran restraints generated. 695 Oldfield, 0 Emsley, 695 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1390 Ramachandran restraints generated. 695 Oldfield, 0 Emsley, 695 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 495 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 56 time to evaluate : 0.600 Fit side-chains REVERT: B 61 GLU cc_start: 0.8613 (mp0) cc_final: 0.8157 (mp0) REVERT: B 83 GLU cc_start: 0.8229 (OUTLIER) cc_final: 0.6880 (mp0) REVERT: C 57 GLU cc_start: 0.7924 (OUTLIER) cc_final: 0.6745 (pm20) REVERT: D 57 GLU cc_start: 0.7901 (mt-10) cc_final: 0.7592 (tt0) REVERT: D 83 GLU cc_start: 0.8128 (OUTLIER) cc_final: 0.6775 (mp0) REVERT: E 57 GLU cc_start: 0.7544 (tt0) cc_final: 0.7239 (tm-30) REVERT: F 80 LYS cc_start: 0.7966 (mtmt) cc_final: 0.7171 (mtmt) REVERT: F 83 GLU cc_start: 0.8232 (OUTLIER) cc_final: 0.7113 (mp0) REVERT: I 83 GLU cc_start: 0.8156 (OUTLIER) cc_final: 0.6862 (mp0) outliers start: 16 outliers final: 10 residues processed: 65 average time/residue: 0.1311 time to fit residues: 12.0307 Evaluate side-chains 66 residues out of total 495 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 51 time to evaluate : 0.537 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 THR Chi-restraints excluded: chain B residue 22 THR Chi-restraints excluded: chain B residue 83 GLU Chi-restraints excluded: chain C residue 57 GLU Chi-restraints excluded: chain C residue 92 THR Chi-restraints excluded: chain D residue 83 GLU Chi-restraints excluded: chain E residue 22 THR Chi-restraints excluded: chain E residue 92 THR Chi-restraints excluded: chain F residue 83 GLU Chi-restraints excluded: chain G residue 57 GLU Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 92 THR Chi-restraints excluded: chain I residue 83 GLU Chi-restraints excluded: chain J residue 38 LEU Chi-restraints excluded: chain J residue 59 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 16 optimal weight: 9.9990 chunk 67 optimal weight: 0.9990 chunk 56 optimal weight: 10.0000 chunk 31 optimal weight: 0.3980 chunk 5 optimal weight: 7.9990 chunk 22 optimal weight: 3.9990 chunk 35 optimal weight: 20.0000 chunk 65 optimal weight: 9.9990 chunk 7 optimal weight: 20.0000 chunk 38 optimal weight: 7.9990 chunk 49 optimal weight: 10.0000 overall best weight: 4.2788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7640 moved from start: 0.1647 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 4935 Z= 0.353 Angle : 0.681 6.841 6665 Z= 0.384 Chirality : 0.055 0.125 875 Planarity : 0.002 0.013 835 Dihedral : 6.982 47.715 728 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 7.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.78 % Favored : 91.22 % Rotamer: Outliers : 4.04 % Allowed : 16.60 % Favored : 79.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.24 (0.25), residues: 695 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.22 (0.19), residues: 695 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS C 50 PHE 0.008 0.001 PHE A 94 TYR 0.015 0.003 TYR F 39 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1390 Ramachandran restraints generated. 695 Oldfield, 0 Emsley, 695 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1390 Ramachandran restraints generated. 695 Oldfield, 0 Emsley, 695 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 495 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 54 time to evaluate : 0.516 Fit side-chains REVERT: B 61 GLU cc_start: 0.8593 (mp0) cc_final: 0.8150 (mp0) REVERT: B 83 GLU cc_start: 0.8254 (OUTLIER) cc_final: 0.6921 (mp0) REVERT: C 57 GLU cc_start: 0.7936 (OUTLIER) cc_final: 0.6726 (pm20) REVERT: D 57 GLU cc_start: 0.7923 (mt-10) cc_final: 0.7635 (tt0) REVERT: D 83 GLU cc_start: 0.8053 (OUTLIER) cc_final: 0.6732 (mp0) REVERT: E 57 GLU cc_start: 0.7574 (tt0) cc_final: 0.7264 (tm-30) REVERT: F 61 GLU cc_start: 0.8632 (mp0) cc_final: 0.8417 (mp0) REVERT: F 80 LYS cc_start: 0.7954 (mtmt) cc_final: 0.7146 (mtmt) REVERT: F 83 GLU cc_start: 0.8245 (OUTLIER) cc_final: 0.7079 (mp0) REVERT: I 83 GLU cc_start: 0.8126 (OUTLIER) cc_final: 0.6849 (mp0) REVERT: J 83 GLU cc_start: 0.8266 (OUTLIER) cc_final: 0.7321 (mp0) outliers start: 19 outliers final: 11 residues processed: 66 average time/residue: 0.1204 time to fit residues: 11.2589 Evaluate side-chains 65 residues out of total 495 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 48 time to evaluate : 0.515 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 THR Chi-restraints excluded: chain B residue 22 THR Chi-restraints excluded: chain B residue 83 GLU Chi-restraints excluded: chain C residue 57 GLU Chi-restraints excluded: chain C residue 92 THR Chi-restraints excluded: chain D residue 83 GLU Chi-restraints excluded: chain E residue 22 THR Chi-restraints excluded: chain E residue 92 THR Chi-restraints excluded: chain F residue 83 GLU Chi-restraints excluded: chain G residue 57 GLU Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 92 THR Chi-restraints excluded: chain I residue 83 GLU Chi-restraints excluded: chain J residue 38 LEU Chi-restraints excluded: chain J residue 59 THR Chi-restraints excluded: chain J residue 83 GLU Chi-restraints excluded: chain J residue 92 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 38 optimal weight: 5.9990 chunk 57 optimal weight: 5.9990 chunk 37 optimal weight: 6.9990 chunk 67 optimal weight: 7.9990 chunk 42 optimal weight: 20.0000 chunk 41 optimal weight: 10.0000 chunk 31 optimal weight: 1.9990 chunk 26 optimal weight: 10.0000 chunk 40 optimal weight: 6.9990 chunk 20 optimal weight: 10.0000 chunk 13 optimal weight: 10.0000 overall best weight: 5.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7665 moved from start: 0.1754 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.052 4935 Z= 0.446 Angle : 0.730 6.723 6665 Z= 0.415 Chirality : 0.056 0.126 875 Planarity : 0.002 0.010 835 Dihedral : 7.269 49.067 728 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 8.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.07 % Favored : 89.93 % Rotamer: Outliers : 4.26 % Allowed : 16.17 % Favored : 79.57 % 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: -4.31 (0.25), residues: 695 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.28 (0.19), residues: 695 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS C 50 PHE 0.007 0.001 PHE A 94 TYR 0.017 0.004 TYR C 39 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1390 Ramachandran restraints generated. 695 Oldfield, 0 Emsley, 695 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1390 Ramachandran restraints generated. 695 Oldfield, 0 Emsley, 695 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 69 residues out of total 495 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 49 time to evaluate : 0.524 Fit side-chains REVERT: B 83 GLU cc_start: 0.8317 (OUTLIER) cc_final: 0.6962 (mp0) REVERT: C 57 GLU cc_start: 0.8002 (OUTLIER) cc_final: 0.6758 (pm20) REVERT: D 57 GLU cc_start: 0.7897 (mt-10) cc_final: 0.7581 (tt0) REVERT: D 83 GLU cc_start: 0.8105 (OUTLIER) cc_final: 0.6703 (mp0) REVERT: E 80 LYS cc_start: 0.8185 (mttt) cc_final: 0.7797 (mttm) REVERT: E 83 GLU cc_start: 0.8304 (OUTLIER) cc_final: 0.7505 (mp0) REVERT: F 61 GLU cc_start: 0.8545 (mp0) cc_final: 0.8191 (mp0) REVERT: F 80 LYS cc_start: 0.7947 (mtmt) cc_final: 0.7136 (mtmt) REVERT: F 83 GLU cc_start: 0.8280 (OUTLIER) cc_final: 0.7056 (mp0) REVERT: I 83 GLU cc_start: 0.8189 (OUTLIER) cc_final: 0.6824 (mp0) REVERT: J 83 GLU cc_start: 0.8271 (OUTLIER) cc_final: 0.7319 (mp0) outliers start: 20 outliers final: 10 residues processed: 61 average time/residue: 0.1329 time to fit residues: 11.2579 Evaluate side-chains 62 residues out of total 495 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 45 time to evaluate : 0.597 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 THR Chi-restraints excluded: chain B residue 22 THR Chi-restraints excluded: chain B residue 83 GLU Chi-restraints excluded: chain C residue 57 GLU Chi-restraints excluded: chain C residue 92 THR Chi-restraints excluded: chain D residue 83 GLU Chi-restraints excluded: chain E residue 22 THR Chi-restraints excluded: chain E residue 83 GLU Chi-restraints excluded: chain E residue 92 THR Chi-restraints excluded: chain F residue 83 GLU Chi-restraints excluded: chain G residue 57 GLU Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 92 THR Chi-restraints excluded: chain I residue 83 GLU Chi-restraints excluded: chain J residue 59 THR Chi-restraints excluded: chain J residue 83 GLU Chi-restraints excluded: chain J residue 92 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 13 optimal weight: 10.0000 chunk 42 optimal weight: 10.0000 chunk 45 optimal weight: 6.9990 chunk 33 optimal weight: 0.8980 chunk 6 optimal weight: 8.9990 chunk 53 optimal weight: 2.9990 chunk 61 optimal weight: 10.0000 chunk 64 optimal weight: 8.9990 chunk 58 optimal weight: 6.9990 chunk 62 optimal weight: 6.9990 chunk 37 optimal weight: 5.9990 overall best weight: 4.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7651 moved from start: 0.1827 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.047 4935 Z= 0.384 Angle : 0.697 6.890 6665 Z= 0.394 Chirality : 0.055 0.125 875 Planarity : 0.002 0.010 835 Dihedral : 7.103 49.894 728 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 8.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.21 % Favored : 90.79 % Rotamer: Outliers : 4.47 % Allowed : 16.17 % Favored : 79.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.30 (0.25), residues: 695 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.27 (0.19), residues: 695 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS C 50 PHE 0.008 0.001 PHE A 94 TYR 0.015 0.003 TYR F 39 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1390 Ramachandran restraints generated. 695 Oldfield, 0 Emsley, 695 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1390 Ramachandran restraints generated. 695 Oldfield, 0 Emsley, 695 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 74 residues out of total 495 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 53 time to evaluate : 0.511 Fit side-chains REVERT: A 83 GLU cc_start: 0.8337 (OUTLIER) cc_final: 0.6814 (mp0) REVERT: B 83 GLU cc_start: 0.8318 (OUTLIER) cc_final: 0.6928 (mp0) REVERT: C 57 GLU cc_start: 0.7989 (OUTLIER) cc_final: 0.6767 (pm20) REVERT: D 57 GLU cc_start: 0.7901 (mt-10) cc_final: 0.7570 (tt0) REVERT: D 83 GLU cc_start: 0.8120 (OUTLIER) cc_final: 0.6660 (mp0) REVERT: E 61 GLU cc_start: 0.8477 (mp0) cc_final: 0.8269 (mp0) REVERT: E 83 GLU cc_start: 0.8215 (OUTLIER) cc_final: 0.7447 (mp0) REVERT: F 80 LYS cc_start: 0.7943 (mtmt) cc_final: 0.7131 (mtmt) REVERT: F 83 GLU cc_start: 0.8325 (OUTLIER) cc_final: 0.7123 (mp0) REVERT: I 83 GLU cc_start: 0.8181 (OUTLIER) cc_final: 0.6833 (mp0) REVERT: J 61 GLU cc_start: 0.8330 (mp0) cc_final: 0.8065 (mp0) REVERT: J 83 GLU cc_start: 0.8274 (OUTLIER) cc_final: 0.7290 (mp0) outliers start: 21 outliers final: 12 residues processed: 67 average time/residue: 0.1328 time to fit residues: 12.5550 Evaluate side-chains 67 residues out of total 495 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 47 time to evaluate : 0.579 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 GLU Chi-restraints excluded: chain A residue 59 THR Chi-restraints excluded: chain A residue 83 GLU Chi-restraints excluded: chain B residue 22 THR Chi-restraints excluded: chain B residue 83 GLU Chi-restraints excluded: chain C residue 57 GLU Chi-restraints excluded: chain C residue 92 THR Chi-restraints excluded: chain D residue 83 GLU Chi-restraints excluded: chain E residue 22 THR Chi-restraints excluded: chain E residue 83 GLU Chi-restraints excluded: chain E residue 92 THR Chi-restraints excluded: chain F residue 83 GLU Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 44 THR Chi-restraints excluded: chain H residue 92 THR Chi-restraints excluded: chain I residue 83 GLU Chi-restraints excluded: chain J residue 38 LEU Chi-restraints excluded: chain J residue 59 THR Chi-restraints excluded: chain J residue 83 GLU Chi-restraints excluded: chain J residue 92 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 27 optimal weight: 8.9990 chunk 49 optimal weight: 4.9990 chunk 19 optimal weight: 7.9990 chunk 56 optimal weight: 9.9990 chunk 59 optimal weight: 10.0000 chunk 62 optimal weight: 9.9990 chunk 41 optimal weight: 10.0000 chunk 66 optimal weight: 7.9990 chunk 40 optimal weight: 7.9990 chunk 31 optimal weight: 10.0000 chunk 46 optimal weight: 0.9990 overall best weight: 5.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7671 moved from start: 0.1912 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.064 4935 Z= 0.475 Angle : 0.755 6.862 6665 Z= 0.427 Chirality : 0.057 0.167 875 Planarity : 0.002 0.010 835 Dihedral : 7.376 50.944 728 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 9.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.93 % Favored : 90.07 % Rotamer: Outliers : 4.47 % Allowed : 16.38 % Favored : 79.15 % 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: -4.41 (0.24), residues: 695 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.35 (0.19), residues: 695 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS C 50 PHE 0.007 0.001 PHE A 94 TYR 0.019 0.004 TYR C 39 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1390 Ramachandran restraints generated. 695 Oldfield, 0 Emsley, 695 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1390 Ramachandran restraints generated. 695 Oldfield, 0 Emsley, 695 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 68 residues out of total 495 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 47 time to evaluate : 0.548 Fit side-chains REVERT: A 83 GLU cc_start: 0.8275 (OUTLIER) cc_final: 0.6679 (mp0) REVERT: B 83 GLU cc_start: 0.8323 (OUTLIER) cc_final: 0.6908 (mp0) REVERT: C 57 GLU cc_start: 0.8011 (OUTLIER) cc_final: 0.6867 (pm20) REVERT: D 57 GLU cc_start: 0.7909 (mt-10) cc_final: 0.7573 (tt0) REVERT: D 83 GLU cc_start: 0.8183 (OUTLIER) cc_final: 0.6771 (mp0) REVERT: E 80 LYS cc_start: 0.8193 (mttt) cc_final: 0.7836 (mttm) REVERT: E 83 GLU cc_start: 0.8227 (OUTLIER) cc_final: 0.7461 (mp0) REVERT: F 61 GLU cc_start: 0.8493 (mp0) cc_final: 0.8199 (mp0) REVERT: F 80 LYS cc_start: 0.7956 (mtmt) cc_final: 0.7136 (mtmt) REVERT: F 83 GLU cc_start: 0.8344 (OUTLIER) cc_final: 0.7123 (mp0) REVERT: I 83 GLU cc_start: 0.8289 (OUTLIER) cc_final: 0.6924 (mp0) REVERT: J 83 GLU cc_start: 0.8363 (OUTLIER) cc_final: 0.7352 (mp0) outliers start: 21 outliers final: 11 residues processed: 60 average time/residue: 0.1368 time to fit residues: 11.4577 Evaluate side-chains 65 residues out of total 495 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 46 time to evaluate : 0.521 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 GLU Chi-restraints excluded: chain A residue 59 THR Chi-restraints excluded: chain A residue 83 GLU Chi-restraints excluded: chain B residue 22 THR Chi-restraints excluded: chain B residue 83 GLU Chi-restraints excluded: chain C residue 57 GLU Chi-restraints excluded: chain C residue 92 THR Chi-restraints excluded: chain D residue 83 GLU Chi-restraints excluded: chain E residue 22 THR Chi-restraints excluded: chain E residue 83 GLU Chi-restraints excluded: chain E residue 92 THR Chi-restraints excluded: chain F residue 83 GLU Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 44 THR Chi-restraints excluded: chain H residue 92 THR Chi-restraints excluded: chain I residue 83 GLU Chi-restraints excluded: chain J residue 59 THR Chi-restraints excluded: chain J residue 83 GLU Chi-restraints excluded: chain J residue 92 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 69 optimal weight: 10.0000 chunk 64 optimal weight: 6.9990 chunk 55 optimal weight: 4.9990 chunk 5 optimal weight: 3.9990 chunk 42 optimal weight: 10.0000 chunk 34 optimal weight: 0.8980 chunk 44 optimal weight: 4.9990 chunk 59 optimal weight: 6.9990 chunk 17 optimal weight: 4.9990 chunk 51 optimal weight: 7.9990 chunk 8 optimal weight: 7.9990 overall best weight: 3.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7637 moved from start: 0.1936 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 4935 Z= 0.336 Angle : 0.679 6.870 6665 Z= 0.382 Chirality : 0.055 0.127 875 Planarity : 0.002 0.023 835 Dihedral : 7.010 50.649 728 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 8.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.35 % Favored : 91.65 % Rotamer: Outliers : 4.26 % Allowed : 16.60 % Favored : 79.15 % 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: -4.30 (0.25), residues: 695 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.27 (0.19), residues: 695 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS H 50 PHE 0.008 0.001 PHE A 94 TYR 0.014 0.003 TYR F 39 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1390 Ramachandran restraints generated. 695 Oldfield, 0 Emsley, 695 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1390 Ramachandran restraints generated. 695 Oldfield, 0 Emsley, 695 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 495 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 51 time to evaluate : 0.537 Fit side-chains REVERT: A 83 GLU cc_start: 0.8334 (OUTLIER) cc_final: 0.6780 (mp0) REVERT: B 83 GLU cc_start: 0.8399 (OUTLIER) cc_final: 0.7035 (mp0) REVERT: C 57 GLU cc_start: 0.7962 (OUTLIER) cc_final: 0.6837 (pm20) REVERT: D 57 GLU cc_start: 0.7931 (mt-10) cc_final: 0.7603 (tt0) REVERT: D 83 GLU cc_start: 0.8109 (OUTLIER) cc_final: 0.6710 (mp0) REVERT: E 83 GLU cc_start: 0.8228 (OUTLIER) cc_final: 0.7506 (mp0) REVERT: F 61 GLU cc_start: 0.8569 (mp0) cc_final: 0.8273 (mp0) REVERT: F 80 LYS cc_start: 0.7951 (mtmt) cc_final: 0.7024 (mtmt) REVERT: F 83 GLU cc_start: 0.8367 (OUTLIER) cc_final: 0.7171 (mp0) REVERT: I 83 GLU cc_start: 0.8248 (OUTLIER) cc_final: 0.6907 (mp0) REVERT: J 83 GLU cc_start: 0.8274 (OUTLIER) cc_final: 0.7290 (mp0) outliers start: 20 outliers final: 11 residues processed: 64 average time/residue: 0.1230 time to fit residues: 11.1073 Evaluate side-chains 68 residues out of total 495 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 49 time to evaluate : 0.521 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 GLU Chi-restraints excluded: chain A residue 59 THR Chi-restraints excluded: chain A residue 83 GLU Chi-restraints excluded: chain B residue 22 THR Chi-restraints excluded: chain B residue 83 GLU Chi-restraints excluded: chain C residue 57 GLU Chi-restraints excluded: chain C residue 92 THR Chi-restraints excluded: chain D residue 83 GLU Chi-restraints excluded: chain E residue 22 THR Chi-restraints excluded: chain E residue 83 GLU Chi-restraints excluded: chain E residue 92 THR Chi-restraints excluded: chain F residue 83 GLU Chi-restraints excluded: chain G residue 57 GLU Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 92 THR Chi-restraints excluded: chain I residue 83 GLU Chi-restraints excluded: chain J residue 59 THR Chi-restraints excluded: chain J residue 83 GLU Chi-restraints excluded: chain J residue 92 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 15 optimal weight: 7.9990 chunk 55 optimal weight: 0.0050 chunk 23 optimal weight: 10.0000 chunk 57 optimal weight: 10.0000 chunk 7 optimal weight: 20.0000 chunk 10 optimal weight: 10.0000 chunk 48 optimal weight: 7.9990 chunk 3 optimal weight: 2.9990 chunk 40 optimal weight: 8.9990 chunk 63 optimal weight: 7.9990 chunk 37 optimal weight: 10.0000 overall best weight: 5.4002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4399 r_free = 0.4399 target = 0.143381 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4213 r_free = 0.4213 target = 0.127131 restraints weight = 7033.133| |-----------------------------------------------------------------------------| r_work (start): 0.4222 rms_B_bonded: 2.63 r_work: 0.4119 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work (final): 0.4119 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7522 moved from start: 0.2013 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.060 4935 Z= 0.433 Angle : 0.732 6.893 6665 Z= 0.413 Chirality : 0.056 0.181 875 Planarity : 0.003 0.028 835 Dihedral : 7.257 50.741 728 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 8.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.64 % Favored : 90.36 % Rotamer: Outliers : 4.04 % Allowed : 16.81 % Favored : 79.15 % 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: -4.36 (0.25), residues: 695 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.32 (0.19), residues: 695 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS C 50 PHE 0.007 0.001 PHE A 94 TYR 0.017 0.004 TYR B 39 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1171.15 seconds wall clock time: 22 minutes 7.89 seconds (1327.89 seconds total)