Starting phenix.real_space_refine on Mon Jun 24 20:48:08 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8rrr_19462/06_2024/8rrr_19462.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8rrr_19462/06_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_19462/06_2024/8rrr_19462.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8rrr_19462/06_2024/8rrr_19462.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8rrr_19462/06_2024/8rrr_19462.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8rrr_19462/06_2024/8rrr_19462.pdb" } 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-5370/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: 3.65, per 1000 atoms: 0.74 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: 1.88 Conformation dependent library (CDL) restraints added in 1.1 seconds 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: 0.78 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: 1.27 Time building geometry restraints manager: 2.04 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 2.440 nonbonded pdb=" N GLN F 24 " pdb=" OE1 GLN F 24 " model vdw 2.341 2.520 nonbonded pdb=" O THR H 72 " pdb=" OG1 THR H 72 " model vdw 2.342 2.440 nonbonded pdb=" NZ LYS I 45 " pdb=" OE1 GLU I 46 " model vdw 2.359 2.520 nonbonded pdb=" N GLN A 24 " pdb=" OE1 GLN A 24 " model vdw 2.369 2.520 ... (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 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: 4.400 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: 6.860 Check model and map are aligned: 0.040 Set scattering table: 0.050 Process input model: 18.640 Find NCS groups from input model: 0.410 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:2.860 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.290 ------------------------------------------------------------------------------- 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 : 1.021 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: 0.1611 time to fit residues: 15.1963 Evaluate side-chains 59 residues out of total 495 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 57 time to evaluate : 0.558 ------------------------------------------------------------------------------- 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: 10.0000 chunk 53 optimal weight: 4.9990 chunk 29 optimal weight: 0.0000 chunk 18 optimal weight: 1.9990 chunk 35 optimal weight: 20.0000 chunk 28 optimal weight: 5.9990 chunk 54 optimal weight: 4.9990 chunk 21 optimal weight: 10.0000 chunk 33 optimal weight: 10.0000 chunk 40 optimal weight: 3.9990 chunk 63 optimal weight: 7.9990 overall best weight: 3.1992 ------------------------------------------------------------------------------- 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** H 79 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7600 moved from start: 0.0801 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 4935 Z= 0.277 Angle : 0.638 7.353 6665 Z= 0.359 Chirality : 0.053 0.122 875 Planarity : 0.002 0.010 835 Dihedral : 6.717 31.362 729 Min Nonbonded Distance : 2.279 Molprobity Statistics. All-atom Clashscore : 9.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.49 % Favored : 91.51 % Rotamer: Outliers : 2.34 % Allowed : 16.60 % Favored : 81.06 % 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: -4.18 (0.26), residues: 695 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.18 (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 67 residues out of total 495 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 56 time to evaluate : 0.578 Fit side-chains REVERT: B 61 GLU cc_start: 0.8542 (mp0) cc_final: 0.8194 (mp0) REVERT: B 83 GLU cc_start: 0.8262 (OUTLIER) cc_final: 0.7058 (mp0) REVERT: C 24 GLN cc_start: 0.6869 (mm110) cc_final: 0.5978 (pm20) REVERT: C 57 GLU cc_start: 0.7843 (OUTLIER) cc_final: 0.6903 (pm20) REVERT: D 57 GLU cc_start: 0.7768 (mt-10) cc_final: 0.7550 (tt0) REVERT: F 80 LYS cc_start: 0.7850 (mtmt) cc_final: 0.7438 (mttm) outliers start: 11 outliers final: 6 residues processed: 62 average time/residue: 0.1419 time to fit residues: 12.4297 Evaluate side-chains 59 residues out of total 495 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 51 time to evaluate : 0.496 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 THR Chi-restraints excluded: chain B residue 72 THR Chi-restraints excluded: chain B residue 83 GLU Chi-restraints excluded: chain C residue 57 GLU Chi-restraints excluded: chain E residue 22 THR Chi-restraints excluded: chain F residue 44 THR Chi-restraints excluded: chain F residue 72 THR 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: 8.9990 chunk 52 optimal weight: 6.9990 chunk 43 optimal weight: 9.9990 chunk 17 optimal weight: 0.0370 chunk 63 optimal weight: 3.9990 chunk 68 optimal weight: 10.0000 chunk 56 optimal weight: 10.0000 chunk 21 optimal weight: 9.9990 chunk 51 optimal weight: 10.0000 chunk 62 optimal weight: 9.9990 overall best weight: 6.0066 ------------------------------------------------------------------------------- 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** F 50 HIS ** H 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7660 moved from start: 0.1167 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.045 4935 Z= 0.482 Angle : 0.744 6.969 6665 Z= 0.422 Chirality : 0.056 0.123 875 Planarity : 0.003 0.011 835 Dihedral : 7.385 43.450 728 Min Nonbonded Distance : 2.201 Molprobity Statistics. All-atom Clashscore : 10.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.22 % Favored : 89.78 % Rotamer: Outliers : 5.11 % Allowed : 16.60 % Favored : 78.30 % 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: -4.32 (0.25), residues: 695 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.29 (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 0.021 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 79 residues out of total 495 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 55 time to evaluate : 0.528 Fit side-chains REVERT: B 46 GLU cc_start: 0.8245 (tt0) cc_final: 0.8034 (tt0) REVERT: B 83 GLU cc_start: 0.8188 (OUTLIER) cc_final: 0.6787 (mp0) REVERT: D 57 GLU cc_start: 0.7706 (mt-10) cc_final: 0.7484 (tt0) REVERT: E 80 LYS cc_start: 0.8189 (mttt) cc_final: 0.7819 (mttm) REVERT: F 61 GLU cc_start: 0.8529 (mp0) cc_final: 0.8296 (mp0) REVERT: F 80 LYS cc_start: 0.7948 (mtmt) cc_final: 0.6792 (mttm) REVERT: F 83 GLU cc_start: 0.8232 (OUTLIER) cc_final: 0.6912 (mp0) outliers start: 24 outliers final: 16 residues processed: 70 average time/residue: 0.1266 time to fit residues: 12.2908 Evaluate side-chains 72 residues out of total 495 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 54 time to evaluate : 0.546 ------------------------------------------------------------------------------- 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 72 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 E residue 92 THR Chi-restraints excluded: chain F residue 44 THR Chi-restraints excluded: chain F residue 72 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 74 VAL 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: 6.9990 chunk 7 optimal weight: 20.0000 chunk 30 optimal weight: 0.7980 chunk 42 optimal weight: 20.0000 chunk 63 optimal weight: 9.9990 chunk 67 optimal weight: 1.9990 chunk 60 optimal weight: 5.9990 chunk 18 optimal weight: 3.9990 chunk 56 optimal weight: 5.9990 chunk 38 optimal weight: 3.9990 overall best weight: 3.3588 ------------------------------------------------------------------------------- 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 65 ASN ** H 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7616 moved from start: 0.1272 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 4935 Z= 0.287 Angle : 0.630 6.918 6665 Z= 0.356 Chirality : 0.053 0.121 875 Planarity : 0.002 0.010 835 Dihedral : 6.781 45.626 728 Min Nonbonded Distance : 2.276 Molprobity Statistics. All-atom Clashscore : 9.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.91 % Favored : 92.09 % Rotamer: Outliers : 3.83 % Allowed : 17.23 % Favored : 78.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.17 (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 0.000 HIS C 50 PHE 0.008 0.001 PHE G 94 TYR 0.014 0.003 TYR B 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 74 residues out of total 495 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 56 time to evaluate : 0.583 Fit side-chains REVERT: B 80 LYS cc_start: 0.8057 (mttp) cc_final: 0.7194 (mttp) REVERT: B 83 GLU cc_start: 0.8155 (OUTLIER) cc_final: 0.6817 (mp0) REVERT: C 57 GLU cc_start: 0.7933 (OUTLIER) cc_final: 0.6877 (pm20) REVERT: D 57 GLU cc_start: 0.7733 (mt-10) cc_final: 0.7497 (tt0) REVERT: D 83 GLU cc_start: 0.8036 (OUTLIER) cc_final: 0.6732 (mp0) REVERT: F 61 GLU cc_start: 0.8606 (mp0) cc_final: 0.8206 (mp0) REVERT: F 80 LYS cc_start: 0.7887 (mtmt) cc_final: 0.7137 (mtmt) REVERT: F 83 GLU cc_start: 0.8218 (OUTLIER) cc_final: 0.7034 (mp0) outliers start: 18 outliers final: 14 residues processed: 68 average time/residue: 0.1359 time to fit residues: 12.9151 Evaluate side-chains 70 residues out of total 495 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 52 time to evaluate : 0.559 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 THR Chi-restraints excluded: chain A residue 59 THR Chi-restraints excluded: chain B residue 22 THR Chi-restraints excluded: chain B residue 72 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 22 THR Chi-restraints excluded: chain D residue 83 GLU Chi-restraints excluded: chain E residue 22 THR Chi-restraints excluded: chain E residue 38 LEU Chi-restraints excluded: chain E residue 92 THR Chi-restraints excluded: chain F residue 44 THR Chi-restraints excluded: chain F residue 72 THR Chi-restraints excluded: chain F residue 83 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 0 optimal weight: 20.0000 chunk 50 optimal weight: 10.0000 chunk 27 optimal weight: 7.9990 chunk 57 optimal weight: 10.0000 chunk 46 optimal weight: 9.9990 chunk 34 optimal weight: 3.9990 chunk 60 optimal weight: 0.9990 chunk 17 optimal weight: 10.0000 chunk 22 optimal weight: 10.0000 chunk 13 optimal weight: 8.9990 chunk 39 optimal weight: 1.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- 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** ** 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: 0.7646 moved from start: 0.1404 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= 0.393 Angle : 0.682 6.675 6665 Z= 0.386 Chirality : 0.055 0.122 875 Planarity : 0.002 0.009 835 Dihedral : 7.061 47.990 728 Min Nonbonded Distance : 2.238 Molprobity Statistics. All-atom Clashscore : 10.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.64 % Favored : 90.36 % Rotamer: Outliers : 4.47 % Allowed : 17.45 % Favored : 78.09 % 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: -4.23 (0.26), residues: 695 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.22 (0.20), residues: 695 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS C 50 PHE 0.007 0.001 PHE A 94 TYR 0.017 0.004 TYR C 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 77 residues out of total 495 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 56 time to evaluate : 0.562 Fit side-chains REVERT: B 61 GLU cc_start: 0.8642 (mp0) cc_final: 0.8211 (mp0) REVERT: B 80 LYS cc_start: 0.8157 (mttp) cc_final: 0.7313 (mttp) REVERT: B 83 GLU cc_start: 0.8215 (OUTLIER) cc_final: 0.6834 (mp0) REVERT: D 57 GLU cc_start: 0.7829 (mt-10) cc_final: 0.7517 (tt0) REVERT: D 83 GLU cc_start: 0.8185 (OUTLIER) cc_final: 0.6760 (mp0) REVERT: E 80 LYS cc_start: 0.8168 (mttt) cc_final: 0.7786 (mttm) REVERT: F 80 LYS cc_start: 0.7953 (mtmt) cc_final: 0.7124 (mtmt) REVERT: F 83 GLU cc_start: 0.8313 (OUTLIER) cc_final: 0.7069 (mp0) outliers start: 21 outliers final: 17 residues processed: 71 average time/residue: 0.1317 time to fit residues: 12.8071 Evaluate side-chains 75 residues out of total 495 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 55 time to evaluate : 0.527 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 THR Chi-restraints excluded: chain A residue 59 THR Chi-restraints excluded: chain B residue 22 THR Chi-restraints excluded: chain B residue 72 THR Chi-restraints excluded: chain B residue 83 GLU Chi-restraints excluded: chain C residue 44 THR Chi-restraints excluded: chain C residue 57 GLU Chi-restraints excluded: chain C residue 92 THR Chi-restraints excluded: chain D residue 22 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 44 THR Chi-restraints excluded: chain F residue 72 THR Chi-restraints excluded: chain F residue 83 GLU Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 92 THR Chi-restraints excluded: chain J residue 38 LEU Chi-restraints excluded: chain J residue 59 THR Chi-restraints excluded: chain J residue 92 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 16 optimal weight: 3.9990 chunk 67 optimal weight: 4.9990 chunk 56 optimal weight: 20.0000 chunk 31 optimal weight: 0.0020 chunk 5 optimal weight: 2.9990 chunk 22 optimal weight: 3.9990 chunk 35 optimal weight: 20.0000 chunk 65 optimal weight: 3.9990 chunk 7 optimal weight: 20.0000 chunk 38 optimal weight: 9.9990 chunk 49 optimal weight: 5.9990 overall best weight: 2.9996 ------------------------------------------------------------------------------- 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** ** 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: 0.7608 moved from start: 0.1521 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 4935 Z= 0.259 Angle : 0.614 6.888 6665 Z= 0.344 Chirality : 0.053 0.120 875 Planarity : 0.002 0.010 835 Dihedral : 6.639 50.199 728 Min Nonbonded Distance : 2.291 Molprobity Statistics. All-atom Clashscore : 8.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.34 % Favored : 92.66 % Rotamer: Outliers : 4.47 % Allowed : 18.09 % Favored : 77.45 % 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: -4.13 (0.27), residues: 695 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.14 (0.20), residues: 695 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS C 50 PHE 0.007 0.001 PHE G 94 TYR 0.012 0.003 TYR B 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 75 residues out of total 495 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 54 time to evaluate : 0.548 Fit side-chains REVERT: B 61 GLU cc_start: 0.8670 (mp0) cc_final: 0.8200 (mp0) REVERT: B 80 LYS cc_start: 0.8055 (mttp) cc_final: 0.7146 (mttp) REVERT: B 83 GLU cc_start: 0.8264 (OUTLIER) cc_final: 0.6978 (mp0) REVERT: D 57 GLU cc_start: 0.7714 (mt-10) cc_final: 0.7472 (tt0) REVERT: D 83 GLU cc_start: 0.8034 (OUTLIER) cc_final: 0.6705 (mp0) REVERT: E 61 GLU cc_start: 0.8482 (mp0) cc_final: 0.8266 (mp0) REVERT: F 61 GLU cc_start: 0.8630 (mp0) cc_final: 0.8287 (mp0) REVERT: F 80 LYS cc_start: 0.7874 (mtmt) cc_final: 0.7128 (mtmt) REVERT: F 83 GLU cc_start: 0.8376 (OUTLIER) cc_final: 0.7167 (mp0) REVERT: G 57 GLU cc_start: 0.8072 (OUTLIER) cc_final: 0.7652 (tt0) REVERT: I 83 GLU cc_start: 0.8211 (OUTLIER) cc_final: 0.6910 (mp0) REVERT: J 61 GLU cc_start: 0.8345 (mp0) cc_final: 0.8061 (mp0) outliers start: 21 outliers final: 14 residues processed: 69 average time/residue: 0.1302 time to fit residues: 12.5080 Evaluate side-chains 70 residues out of total 495 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 51 time to evaluate : 0.597 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 THR Chi-restraints excluded: chain A residue 59 THR Chi-restraints excluded: chain B residue 22 THR Chi-restraints excluded: chain B residue 72 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 22 THR Chi-restraints excluded: chain D residue 83 GLU Chi-restraints excluded: chain E residue 22 THR Chi-restraints excluded: chain F residue 44 THR Chi-restraints excluded: chain F residue 72 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 I residue 83 GLU Chi-restraints excluded: chain J residue 22 THR Chi-restraints excluded: chain J residue 38 LEU Chi-restraints excluded: chain J residue 59 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 38 optimal weight: 9.9990 chunk 57 optimal weight: 1.9990 chunk 37 optimal weight: 9.9990 chunk 67 optimal weight: 9.9990 chunk 42 optimal weight: 20.0000 chunk 41 optimal weight: 9.9990 chunk 31 optimal weight: 5.9990 chunk 26 optimal weight: 10.0000 chunk 40 optimal weight: 8.9990 chunk 20 optimal weight: 0.0980 chunk 13 optimal weight: 10.0000 overall best weight: 5.4188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 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: 0.7653 moved from start: 0.1623 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.049 4935 Z= 0.436 Angle : 0.699 6.688 6665 Z= 0.396 Chirality : 0.055 0.124 875 Planarity : 0.002 0.009 835 Dihedral : 7.142 52.157 728 Min Nonbonded Distance : 2.218 Molprobity Statistics. All-atom Clashscore : 10.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.79 % Favored : 89.21 % Rotamer: Outliers : 4.89 % Allowed : 17.23 % Favored : 77.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.25 (0.26), residues: 695 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.23 (0.20), residues: 695 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS C 50 PHE 0.005 0.001 PHE A 94 TYR 0.017 0.004 TYR G 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 74 residues out of total 495 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 51 time to evaluate : 0.790 Fit side-chains REVERT: B 61 GLU cc_start: 0.8555 (mp0) cc_final: 0.8150 (mp0) REVERT: B 80 LYS cc_start: 0.8141 (mttp) cc_final: 0.7288 (mttp) REVERT: B 83 GLU cc_start: 0.8260 (OUTLIER) cc_final: 0.6884 (mp0) REVERT: D 57 GLU cc_start: 0.7853 (mt-10) cc_final: 0.7549 (tt0) REVERT: D 83 GLU cc_start: 0.8257 (OUTLIER) cc_final: 0.6836 (mp0) REVERT: E 80 LYS cc_start: 0.8196 (mttt) cc_final: 0.7779 (mttm) REVERT: F 61 GLU cc_start: 0.8616 (mp0) cc_final: 0.8108 (mp0) REVERT: F 80 LYS cc_start: 0.7962 (mtmt) cc_final: 0.7038 (mtmt) REVERT: F 83 GLU cc_start: 0.8373 (OUTLIER) cc_final: 0.7091 (mp0) REVERT: G 57 GLU cc_start: 0.8087 (OUTLIER) cc_final: 0.7621 (tt0) REVERT: I 83 GLU cc_start: 0.8316 (OUTLIER) cc_final: 0.6927 (mp0) outliers start: 23 outliers final: 18 residues processed: 68 average time/residue: 0.1469 time to fit residues: 13.6928 Evaluate side-chains 73 residues out of total 495 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 50 time to evaluate : 0.626 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 THR Chi-restraints excluded: chain A residue 59 THR Chi-restraints excluded: chain B residue 22 THR Chi-restraints excluded: chain B residue 59 THR Chi-restraints excluded: chain B residue 72 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 22 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 44 THR Chi-restraints excluded: chain F residue 72 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 22 THR Chi-restraints excluded: chain J residue 38 LEU Chi-restraints excluded: chain J residue 59 THR 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: 8.9990 chunk 42 optimal weight: 20.0000 chunk 45 optimal weight: 9.9990 chunk 33 optimal weight: 6.9990 chunk 6 optimal weight: 5.9990 chunk 53 optimal weight: 0.9980 chunk 61 optimal weight: 10.0000 chunk 64 optimal weight: 9.9990 chunk 58 optimal weight: 9.9990 chunk 62 optimal weight: 5.9990 chunk 37 optimal weight: 4.9990 overall best weight: 4.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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: 0.7648 moved from start: 0.1721 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.044 4935 Z= 0.400 Angle : 0.681 6.779 6665 Z= 0.385 Chirality : 0.055 0.122 875 Planarity : 0.002 0.010 835 Dihedral : 7.087 54.562 728 Min Nonbonded Distance : 2.260 Molprobity Statistics. All-atom Clashscore : 10.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.92 % Favored : 91.08 % Rotamer: Outliers : 5.11 % Allowed : 17.02 % Favored : 77.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.28 (0.26), 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 0.002 0.001 HIS C 50 PHE 0.006 0.001 PHE A 94 TYR 0.016 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 75 residues out of total 495 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 51 time to evaluate : 0.546 Fit side-chains REVERT: B 61 GLU cc_start: 0.8625 (mp0) cc_final: 0.8134 (mp0) REVERT: B 80 LYS cc_start: 0.8142 (mttp) cc_final: 0.7293 (mttp) REVERT: B 83 GLU cc_start: 0.8325 (OUTLIER) cc_final: 0.6963 (mp0) REVERT: D 57 GLU cc_start: 0.7913 (mt-10) cc_final: 0.7599 (tt0) REVERT: D 83 GLU cc_start: 0.8248 (OUTLIER) cc_final: 0.6830 (mp0) REVERT: E 80 LYS cc_start: 0.8137 (mttt) cc_final: 0.7785 (mttm) REVERT: F 61 GLU cc_start: 0.8608 (mp0) cc_final: 0.8103 (mp0) REVERT: F 80 LYS cc_start: 0.7955 (mtmt) cc_final: 0.7033 (mtmt) REVERT: F 83 GLU cc_start: 0.8349 (OUTLIER) cc_final: 0.7078 (mp0) REVERT: G 57 GLU cc_start: 0.8083 (OUTLIER) cc_final: 0.7668 (tt0) REVERT: I 83 GLU cc_start: 0.8302 (OUTLIER) cc_final: 0.6935 (mp0) REVERT: J 83 GLU cc_start: 0.8298 (OUTLIER) cc_final: 0.7325 (mp0) outliers start: 24 outliers final: 18 residues processed: 69 average time/residue: 0.1337 time to fit residues: 12.7676 Evaluate side-chains 72 residues out of total 495 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 48 time to evaluate : 0.600 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 THR Chi-restraints excluded: chain A residue 59 THR Chi-restraints excluded: chain B residue 22 THR Chi-restraints excluded: chain B residue 72 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 22 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 44 THR Chi-restraints excluded: chain F residue 72 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 22 THR Chi-restraints excluded: chain I residue 83 GLU Chi-restraints excluded: chain J residue 22 THR 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: 7.9990 chunk 49 optimal weight: 8.9990 chunk 19 optimal weight: 3.9990 chunk 56 optimal weight: 20.0000 chunk 59 optimal weight: 0.9990 chunk 62 optimal weight: 7.9990 chunk 41 optimal weight: 6.9990 chunk 66 optimal weight: 10.0000 chunk 40 optimal weight: 8.9990 chunk 31 optimal weight: 8.9990 chunk 46 optimal weight: 4.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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: 0.7649 moved from start: 0.1779 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.049 4935 Z= 0.401 Angle : 0.687 6.827 6665 Z= 0.388 Chirality : 0.055 0.166 875 Planarity : 0.002 0.009 835 Dihedral : 7.166 56.290 728 Min Nonbonded Distance : 2.235 Molprobity Statistics. All-atom Clashscore : 11.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.50 % Favored : 89.50 % Rotamer: Outliers : 5.32 % Allowed : 17.02 % Favored : 77.66 % 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 0.006 0.001 PHE A 94 TYR 0.016 0.003 TYR F 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 74 residues out of total 495 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 49 time to evaluate : 0.549 Fit side-chains REVERT: B 61 GLU cc_start: 0.8524 (mp0) cc_final: 0.8096 (mp0) REVERT: B 80 LYS cc_start: 0.8153 (mttp) cc_final: 0.7310 (mttp) REVERT: B 83 GLU cc_start: 0.8299 (OUTLIER) cc_final: 0.6910 (mp0) REVERT: D 57 GLU cc_start: 0.7908 (mt-10) cc_final: 0.7593 (tt0) REVERT: D 83 GLU cc_start: 0.8335 (OUTLIER) cc_final: 0.6909 (mp0) REVERT: E 80 LYS cc_start: 0.8151 (mttt) cc_final: 0.7757 (mttm) REVERT: F 61 GLU cc_start: 0.8616 (mp0) cc_final: 0.8076 (mp0) REVERT: F 80 LYS cc_start: 0.7953 (mtmt) cc_final: 0.7034 (mtmt) REVERT: F 83 GLU cc_start: 0.8367 (OUTLIER) cc_final: 0.7096 (mp0) REVERT: G 57 GLU cc_start: 0.8082 (OUTLIER) cc_final: 0.7612 (tt0) REVERT: I 83 GLU cc_start: 0.8294 (OUTLIER) cc_final: 0.6915 (mp0) REVERT: J 83 GLU cc_start: 0.8301 (OUTLIER) cc_final: 0.7320 (mp0) outliers start: 25 outliers final: 18 residues processed: 68 average time/residue: 0.1264 time to fit residues: 11.9230 Evaluate side-chains 73 residues out of total 495 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 49 time to evaluate : 0.495 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 THR Chi-restraints excluded: chain A residue 59 THR Chi-restraints excluded: chain B residue 22 THR Chi-restraints excluded: chain B residue 72 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 22 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 44 THR Chi-restraints excluded: chain F residue 72 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 22 THR Chi-restraints excluded: chain I residue 83 GLU Chi-restraints excluded: chain J residue 22 THR 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 69 optimal weight: 5.9990 chunk 64 optimal weight: 9.9990 chunk 55 optimal weight: 10.0000 chunk 5 optimal weight: 6.9990 chunk 42 optimal weight: 0.0670 chunk 34 optimal weight: 10.0000 chunk 44 optimal weight: 2.9990 chunk 59 optimal weight: 5.9990 chunk 17 optimal weight: 10.0000 chunk 51 optimal weight: 0.0470 chunk 8 optimal weight: 9.9990 overall best weight: 3.0222 ------------------------------------------------------------------------------- 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** ** 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: 0.7617 moved from start: 0.1828 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 4935 Z= 0.265 Angle : 0.615 6.724 6665 Z= 0.345 Chirality : 0.053 0.122 875 Planarity : 0.002 0.015 835 Dihedral : 6.734 56.903 728 Min Nonbonded Distance : 2.288 Molprobity Statistics. All-atom Clashscore : 9.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.48 % Favored : 92.52 % Rotamer: Outliers : 4.68 % Allowed : 17.23 % Favored : 78.09 % 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: -4.16 (0.26), residues: 695 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.16 (0.20), residues: 695 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS E 50 PHE 0.007 0.001 PHE A 94 TYR 0.012 0.002 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 75 residues out of total 495 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 53 time to evaluate : 0.536 Fit side-chains REVERT: B 61 GLU cc_start: 0.8664 (mp0) cc_final: 0.8143 (mp0) REVERT: B 80 LYS cc_start: 0.8124 (mttp) cc_final: 0.7230 (mttp) REVERT: B 83 GLU cc_start: 0.8350 (OUTLIER) cc_final: 0.7030 (mp0) REVERT: D 57 GLU cc_start: 0.7716 (mt-10) cc_final: 0.7468 (tt0) REVERT: D 83 GLU cc_start: 0.8319 (OUTLIER) cc_final: 0.6957 (mp0) REVERT: F 61 GLU cc_start: 0.8590 (mp0) cc_final: 0.8078 (mp0) REVERT: F 80 LYS cc_start: 0.7911 (mtmt) cc_final: 0.7003 (mtmt) REVERT: F 83 GLU cc_start: 0.8366 (OUTLIER) cc_final: 0.7102 (mp0) REVERT: G 57 GLU cc_start: 0.8069 (OUTLIER) cc_final: 0.7664 (tt0) REVERT: H 20 GLU cc_start: 0.7470 (mp0) cc_final: 0.7164 (mp0) REVERT: I 83 GLU cc_start: 0.8294 (OUTLIER) cc_final: 0.6953 (mp0) REVERT: J 61 GLU cc_start: 0.8547 (mp0) cc_final: 0.8222 (mp0) REVERT: J 83 GLU cc_start: 0.8315 (OUTLIER) cc_final: 0.7389 (mp0) outliers start: 22 outliers final: 16 residues processed: 69 average time/residue: 0.1300 time to fit residues: 12.4161 Evaluate side-chains 71 residues out of total 495 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 49 time to evaluate : 0.528 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 THR Chi-restraints excluded: chain A residue 59 THR Chi-restraints excluded: chain B residue 22 THR Chi-restraints excluded: chain B residue 72 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 22 THR Chi-restraints excluded: chain D residue 83 GLU Chi-restraints excluded: chain E residue 22 THR Chi-restraints excluded: chain F residue 44 THR Chi-restraints excluded: chain F residue 72 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 22 THR Chi-restraints excluded: chain I residue 83 GLU Chi-restraints excluded: chain J residue 22 THR Chi-restraints excluded: chain J residue 38 LEU Chi-restraints excluded: chain J residue 59 THR Chi-restraints excluded: chain J residue 83 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 15 optimal weight: 10.0000 chunk 55 optimal weight: 8.9990 chunk 23 optimal weight: 10.0000 chunk 57 optimal weight: 8.9990 chunk 7 optimal weight: 10.0000 chunk 10 optimal weight: 0.8980 chunk 48 optimal weight: 6.9990 chunk 3 optimal weight: 1.9990 chunk 40 optimal weight: 9.9990 chunk 63 optimal weight: 20.0000 chunk 37 optimal weight: 10.0000 overall best weight: 5.5788 ------------------------------------------------------------------------------- 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** ** C 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 79 GLN ** H 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4315 r_free = 0.4315 target = 0.132728 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4104 r_free = 0.4104 target = 0.114872 restraints weight = 7522.097| |-----------------------------------------------------------------------------| r_work (start): 0.4110 rms_B_bonded: 2.77 r_work: 0.3994 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work (final): 0.3994 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7559 moved from start: 0.1893 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.045 4935 Z= 0.442 Angle : 0.706 6.887 6665 Z= 0.398 Chirality : 0.055 0.122 875 Planarity : 0.002 0.014 835 Dihedral : 7.201 56.537 728 Min Nonbonded Distance : 2.223 Molprobity Statistics. All-atom Clashscore : 11.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.08 % Favored : 88.92 % Rotamer: Outliers : 5.11 % Allowed : 17.45 % Favored : 77.45 % 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 (0.26), residues: 695 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.26 (0.20), residues: 695 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS C 50 PHE 0.005 0.001 PHE F 94 TYR 0.016 0.004 TYR F 39 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1249.09 seconds wall clock time: 23 minutes 25.89 seconds (1405.89 seconds total)