Starting phenix.real_space_refine (version: dev) on Fri Jun 3 21:32:57 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xd0_33131/06_2022/7xd0_33131.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xd0_33131/06_2022/7xd0_33131.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.48 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xd0_33131/06_2022/7xd0_33131.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xd0_33131/06_2022/7xd0_33131.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xd0_33131/06_2022/7xd0_33131.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xd0_33131/06_2022/7xd0_33131.pdb" } resolution = 3.48 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 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 Convert atoms to be neutral Process input model Symmetric amino acids flipped Residue "G TYR 50": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 35": "OE1" <-> "OE2" Residue "H GLU 113": "OE1" <-> "OE2" Residue "E TYR 54": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 97": "OE1" <-> "OE2" Residue "E ASP 123": "OD1" <-> "OD2" Residue "E GLU 133": "OE1" <-> "OE2" Residue "A TYR 54": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 73": "OE1" <-> "OE2" Residue "D TYR 42": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 76": "OE1" <-> "OE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4617/modules/chem_data/mon_lib" Total number of atoms: 13222 Number of models: 1 Model: "" Number of chains: 12 Chain: "L" Number of atoms: 602 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 602 Classifications: {'peptide': 76} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 72} Chain: "F" Number of atoms: 657 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 657 Classifications: {'peptide': 83} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 1, 'CIS': 1, 'TRANS': 80} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "G" Number of atoms: 831 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 831 Classifications: {'peptide': 108} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 5, 'TRANS': 102} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "H" Number of atoms: 718 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 718 Classifications: {'peptide': 92} Link IDs: {'PTRANS': 2, 'TRANS': 89} Chain: "E" Number of atoms: 805 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 805 Classifications: {'peptide': 98} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 4, 'TRANS': 93} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "A" Number of atoms: 811 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 811 Classifications: {'peptide': 99} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 4, 'TRANS': 94} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "D" Number of atoms: 718 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 718 Classifications: {'peptide': 92} Link IDs: {'PTRANS': 2, 'TRANS': 89} Chain: "C" Number of atoms: 835 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 835 Classifications: {'peptide': 108} Link IDs: {'PTRANS': 5, 'TRANS': 102} Chain: "B" Number of atoms: 657 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 657 Classifications: {'peptide': 83} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 1, 'TRANS': 81} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "I" Number of atoms: 2975 Number of conformers: 1 Conformer: "" Number of residues, atoms: 146, 2975 Classifications: {'DNA': 146} Link IDs: {'rna3p': 145} Chain: "J" Number of atoms: 3011 Number of conformers: 1 Conformer: "" Number of residues, atoms: 146, 3011 Classifications: {'DNA': 146} Link IDs: {'rna3p': 145} Chain: "K" Number of atoms: 602 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 602 Classifications: {'peptide': 76} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 72} Residues with excluded nonbonded symmetry interactions: 8 residue: pdb=" N LEU L 73 " occ=0.45 ... (6 atoms not shown) pdb=" CD2 LEU L 73 " occ=0.45 residue: pdb=" N ARG L 74 " occ=0.45 ... (9 atoms not shown) pdb=" NH2 ARG L 74 " occ=0.45 residue: pdb=" N GLY L 75 " occ=0.25 ... (2 atoms not shown) pdb=" O GLY L 75 " occ=0.25 residue: pdb=" N GLY L 76 " occ=0.25 ... (3 atoms not shown) pdb=" OXT GLY L 76 " occ=0.25 residue: pdb=" N LEU K 73 " occ=0.45 ... (6 atoms not shown) pdb=" CD2 LEU K 73 " occ=0.45 residue: pdb=" N ARG K 74 " occ=0.45 ... (9 atoms not shown) pdb=" NH2 ARG K 74 " occ=0.45 residue: pdb=" N GLY K 75 " occ=0.25 ... (2 atoms not shown) pdb=" O GLY K 75 " occ=0.25 residue: pdb=" N GLY K 76 " occ=0.25 ... (3 atoms not shown) pdb=" OXT GLY K 76 " occ=0.25 Time building chain proxies: 7.87, per 1000 atoms: 0.60 Number of scatterers: 13222 At special positions: 0 Unit cell: (131.028, 135.324, 93.438, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 14 16.00 P 292 15.00 O 3052 8.00 N 2466 7.00 C 7398 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: 6.44 Conformation dependent library (CDL) restraints added in 1.1 seconds 1790 Ramachandran restraints generated. 895 Oldfield, 0 Emsley, 895 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1706 Finding SS restraints... Secondary structure from input PDB file: 40 helices and 10 sheets defined 60.4% alpha, 5.4% beta 141 base pairs and 244 stacking pairs defined. Time for finding SS restraints: 5.03 Creating SS restraints... Processing helix chain 'L' and resid 22 through 35 removed outlier: 3.507A pdb=" N LYS L 27 " --> pdb=" O ILE L 23 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N GLN L 31 " --> pdb=" O LYS L 27 " (cutoff:3.500A) Processing helix chain 'L' and resid 37 through 39 No H-bonds generated for 'chain 'L' and resid 37 through 39' Processing helix chain 'F' and resid 30 through 35 Processing helix chain 'F' and resid 37 through 42 Processing helix chain 'F' and resid 49 through 57 removed outlier: 3.753A pdb=" N GLU F 53 " --> pdb=" O LEU F 49 " (cutoff:3.500A) Processing helix chain 'F' and resid 82 through 87 removed outlier: 3.533A pdb=" N VAL F 86 " --> pdb=" O THR F 82 " (cutoff:3.500A) Processing helix chain 'G' and resid 16 through 21 Processing helix chain 'G' and resid 26 through 36 Processing helix chain 'G' and resid 45 through 73 removed outlier: 4.467A pdb=" N VAL G 49 " --> pdb=" O ALA G 45 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N LEU G 65 " --> pdb=" O GLU G 61 " (cutoff:3.500A) Processing helix chain 'G' and resid 79 through 90 Processing helix chain 'G' and resid 90 through 97 removed outlier: 3.660A pdb=" N LEU G 96 " --> pdb=" O GLU G 92 " (cutoff:3.500A) Processing helix chain 'G' and resid 112 through 116 Processing helix chain 'H' and resid 37 through 49 Processing helix chain 'H' and resid 55 through 84 Processing helix chain 'H' and resid 90 through 102 Processing helix chain 'H' and resid 104 through 124 removed outlier: 3.834A pdb=" N LYS H 108 " --> pdb=" O GLY H 104 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ALA H 124 " --> pdb=" O LYS H 120 " (cutoff:3.500A) Processing helix chain 'E' and resid 44 through 55 removed outlier: 3.863A pdb=" N LEU E 48 " --> pdb=" O GLY E 44 " (cutoff:3.500A) Processing helix chain 'E' and resid 63 through 76 Processing helix chain 'E' and resid 85 through 114 Processing helix chain 'E' and resid 120 through 131 removed outlier: 3.565A pdb=" N ILE E 124 " --> pdb=" O MET E 120 " (cutoff:3.500A) Processing helix chain 'A' and resid 44 through 55 Processing helix chain 'A' and resid 63 through 76 Processing helix chain 'A' and resid 85 through 114 Processing helix chain 'A' and resid 120 through 132 Processing helix chain 'D' and resid 37 through 49 Processing helix chain 'D' and resid 55 through 84 Processing helix chain 'D' and resid 90 through 102 Processing helix chain 'D' and resid 103 through 124 Processing helix chain 'C' and resid 16 through 22 Processing helix chain 'C' and resid 26 through 36 Processing helix chain 'C' and resid 45 through 73 removed outlier: 4.384A pdb=" N VAL C 49 " --> pdb=" O ALA C 45 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N LEU C 65 " --> pdb=" O GLU C 61 " (cutoff:3.500A) Processing helix chain 'C' and resid 79 through 90 Processing helix chain 'C' and resid 90 through 97 Processing helix chain 'B' and resid 24 through 29 removed outlier: 3.525A pdb=" N ILE B 29 " --> pdb=" O ILE B 26 " (cutoff:3.500A) Processing helix chain 'B' and resid 30 through 42 Processing helix chain 'B' and resid 49 through 76 removed outlier: 3.933A pdb=" N GLU B 53 " --> pdb=" O LEU B 49 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 92 removed outlier: 3.651A pdb=" N VAL B 86 " --> pdb=" O THR B 82 " (cutoff:3.500A) Processing helix chain 'K' and resid 22 through 32 removed outlier: 4.222A pdb=" N GLN K 31 " --> pdb=" O LYS K 27 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N ASP K 32 " --> pdb=" O ALA K 28 " (cutoff:3.500A) Processing helix chain 'K' and resid 37 through 41 Processing helix chain 'K' and resid 55 through 59 Processing sheet with id=AA1, first strand: chain 'L' and resid 12 through 16 removed outlier: 3.598A pdb=" N PHE L 45 " --> pdb=" O LYS L 48 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'F' and resid 45 through 46 removed outlier: 7.530A pdb=" N ARG F 45 " --> pdb=" O ILE E 119 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'F' and resid 96 through 98 removed outlier: 5.985A pdb=" N THR F 96 " --> pdb=" O THR C 101 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'G' and resid 42 through 43 removed outlier: 7.489A pdb=" N ARG G 42 " --> pdb=" O ILE H 89 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'G' and resid 77 through 78 Processing sheet with id=AA6, first strand: chain 'G' and resid 100 through 102 Processing sheet with id=AA7, first strand: chain 'D' and resid 53 through 54 removed outlier: 7.731A pdb=" N GLY D 53 " --> pdb=" O ILE C 78 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'D' and resid 88 through 89 Processing sheet with id=AA9, first strand: chain 'K' and resid 12 through 16 Processing sheet with id=AB1, first strand: chain 'K' and resid 44 through 45 404 hydrogen bonds defined for protein. 1182 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 360 hydrogen bonds 712 hydrogen bond angles 0 basepair planarities 141 basepair parallelities 244 stacking parallelities Total time for adding SS restraints: 4.33 Time building geometry restraints manager: 6.73 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.33: 2880 1.33 - 1.45: 4181 1.45 - 1.57: 6373 1.57 - 1.69: 582 1.69 - 1.81: 26 Bond restraints: 14042 Sorted by residual: bond pdb=" C3' DC J 126 " pdb=" O3' DC J 126 " ideal model delta sigma weight residual 1.422 1.466 -0.044 3.00e-02 1.11e+03 2.18e+00 bond pdb=" C3' DT J 15 " pdb=" O3' DT J 15 " ideal model delta sigma weight residual 1.422 1.465 -0.043 3.00e-02 1.11e+03 2.06e+00 bond pdb=" N THR F 71 " pdb=" CA THR F 71 " ideal model delta sigma weight residual 1.456 1.471 -0.015 1.23e-02 6.61e+03 1.47e+00 bond pdb=" N ILE F 29 " pdb=" CA ILE F 29 " ideal model delta sigma weight residual 1.474 1.457 0.018 1.57e-02 4.06e+03 1.27e+00 bond pdb=" CA ASP H 51 " pdb=" C ASP H 51 " ideal model delta sigma weight residual 1.526 1.538 -0.011 1.03e-02 9.43e+03 1.17e+00 ... (remaining 14037 not shown) Histogram of bond angle deviations from ideal: 98.32 - 105.19: 1262 105.19 - 112.06: 7751 112.06 - 118.94: 3609 118.94 - 125.81: 6610 125.81 - 132.68: 981 Bond angle restraints: 20213 Sorted by residual: angle pdb=" N ASP F 68 " pdb=" CA ASP F 68 " pdb=" C ASP F 68 " ideal model delta sigma weight residual 112.93 108.08 4.85 1.33e+00 5.65e-01 1.33e+01 angle pdb=" C VAL F 70 " pdb=" N THR F 71 " pdb=" CA THR F 71 " ideal model delta sigma weight residual 126.45 132.68 -6.23 1.77e+00 3.19e-01 1.24e+01 angle pdb=" OG1 THR F 71 " pdb=" CB THR F 71 " pdb=" CG2 THR F 71 " ideal model delta sigma weight residual 109.30 102.73 6.57 2.00e+00 2.50e-01 1.08e+01 angle pdb=" CA ARG F 67 " pdb=" C ARG F 67 " pdb=" N ASP F 68 " ideal model delta sigma weight residual 118.87 115.37 3.50 1.18e+00 7.18e-01 8.82e+00 angle pdb=" N PHE F 100 " pdb=" CA PHE F 100 " pdb=" C PHE F 100 " ideal model delta sigma weight residual 110.80 116.73 -5.93 2.13e+00 2.20e-01 7.75e+00 ... (remaining 20208 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.47: 6043 34.47 - 68.93: 1392 68.93 - 103.40: 30 103.40 - 137.87: 0 137.87 - 172.33: 3 Dihedral angle restraints: 7468 sinusoidal: 4825 harmonic: 2643 Sorted by residual: dihedral pdb=" CA THR F 71 " pdb=" C THR F 71 " pdb=" N TYR F 72 " pdb=" CA TYR F 72 " ideal model delta harmonic sigma weight residual 180.00 152.64 27.36 0 5.00e+00 4.00e-02 2.99e+01 dihedral pdb=" CA ALA F 89 " pdb=" C ALA F 89 " pdb=" N LEU F 90 " pdb=" CA LEU F 90 " ideal model delta harmonic sigma weight residual 180.00 152.90 27.10 0 5.00e+00 4.00e-02 2.94e+01 dihedral pdb=" CA ALA F 69 " pdb=" C ALA F 69 " pdb=" N VAL F 70 " pdb=" CA VAL F 70 " ideal model delta harmonic sigma weight residual 180.00 157.59 22.41 0 5.00e+00 4.00e-02 2.01e+01 ... (remaining 7465 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.036: 1761 0.036 - 0.072: 425 0.072 - 0.109: 95 0.109 - 0.145: 28 0.145 - 0.181: 2 Chirality restraints: 2311 Sorted by residual: chirality pdb=" CB THR F 71 " pdb=" CA THR F 71 " pdb=" OG1 THR F 71 " pdb=" CG2 THR F 71 " both_signs ideal model delta sigma weight residual False 2.55 2.73 -0.18 2.00e-01 2.50e+01 8.18e-01 chirality pdb=" CA PHE F 100 " pdb=" N PHE F 100 " pdb=" C PHE F 100 " pdb=" CB PHE F 100 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.15 2.00e-01 2.50e+01 5.58e-01 chirality pdb=" CA ILE C 79 " pdb=" N ILE C 79 " pdb=" C ILE C 79 " pdb=" CB ILE C 79 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.54e-01 ... (remaining 2308 not shown) Planarity restraints: 1552 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LEU F 62 " 0.015 2.00e-02 2.50e+03 3.04e-02 9.23e+00 pdb=" C LEU F 62 " -0.053 2.00e-02 2.50e+03 pdb=" O LEU F 62 " 0.020 2.00e-02 2.50e+03 pdb=" N GLU F 63 " 0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ILE C 79 " 0.030 5.00e-02 4.00e+02 4.56e-02 3.32e+00 pdb=" N PRO C 80 " -0.079 5.00e-02 4.00e+02 pdb=" CA PRO C 80 " 0.023 5.00e-02 4.00e+02 pdb=" CD PRO C 80 " 0.025 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C1' DA I 91 " -0.018 2.00e-02 2.50e+03 8.14e-03 1.82e+00 pdb=" N9 DA I 91 " 0.018 2.00e-02 2.50e+03 pdb=" C8 DA I 91 " 0.000 2.00e-02 2.50e+03 pdb=" N7 DA I 91 " 0.004 2.00e-02 2.50e+03 pdb=" C5 DA I 91 " -0.003 2.00e-02 2.50e+03 pdb=" C6 DA I 91 " -0.004 2.00e-02 2.50e+03 pdb=" N6 DA I 91 " -0.006 2.00e-02 2.50e+03 pdb=" N1 DA I 91 " 0.001 2.00e-02 2.50e+03 pdb=" C2 DA I 91 " 0.002 2.00e-02 2.50e+03 pdb=" N3 DA I 91 " 0.004 2.00e-02 2.50e+03 pdb=" C4 DA I 91 " 0.001 2.00e-02 2.50e+03 ... (remaining 1549 not shown) Histogram of nonbonded interaction distances: 2.13 - 2.69: 410 2.69 - 3.24: 11577 3.24 - 3.79: 24561 3.79 - 4.35: 31338 4.35 - 4.90: 44601 Nonbonded interactions: 112487 Sorted by model distance: nonbonded pdb=" O GLN L 62 " pdb=" OG SER L 65 " model vdw 2.132 2.440 nonbonded pdb=" O2 DC I 74 " pdb=" N2 DG J 74 " model vdw 2.183 2.496 nonbonded pdb=" OG1 THR D 90 " pdb=" OE1 GLU D 93 " model vdw 2.223 2.440 nonbonded pdb=" OG1 THR H 90 " pdb=" OE1 GLU H 93 " model vdw 2.238 2.440 nonbonded pdb=" OE1 GLU D 71 " pdb=" OH TYR C 39 " model vdw 2.240 2.440 ... (remaining 112482 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 37 through 134) selection = chain 'E' } ncs_group { reference = chain 'B' selection = chain 'F' } ncs_group { reference = (chain 'C' and (resid 11 through 117 or (resid 118 and (name N or name CA or nam \ e C or name O or name CB )))) selection = chain 'G' } ncs_group { reference = chain 'D' selection = chain 'H' } ncs_group { reference = chain 'K' selection = chain 'L' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 292 5.49 5 S 14 5.16 5 C 7398 2.51 5 N 2466 2.21 5 O 3052 1.98 5 sf(0) = scattering factor at diffraction angle 0. Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.25 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.620 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.130 Construct map_model_manager: 0.010 Extract box with map and model: 4.620 Check model and map are aligned: 0.180 Convert atoms to be neutral: 0.100 Process input model: 40.430 Find NCS groups from input model: 0.480 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Set scattering table: 0.020 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:2.780 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 49.430 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8090 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.044 14042 Z= 0.180 Angle : 0.568 6.573 20213 Z= 0.343 Chirality : 0.036 0.181 2311 Planarity : 0.004 0.046 1552 Dihedral : 27.188 172.333 5762 Min Nonbonded Distance : 2.132 Molprobity Statistics. All-atom Clashscore : 10.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer Outliers : 0.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.11 % 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: 1.23 (0.29), residues: 895 helix: 1.48 (0.23), residues: 562 sheet: -0.93 (0.76), residues: 50 loop : -0.06 (0.38), residues: 283 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1790 Ramachandran restraints generated. 895 Oldfield, 0 Emsley, 895 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1790 Ramachandran restraints generated. 895 Oldfield, 0 Emsley, 895 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 770 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 140 time to evaluate : 1.074 Fit side-chains outliers start: 1 outliers final: 0 residues processed: 140 average time/residue: 0.2595 time to fit residues: 52.0380 Evaluate side-chains 122 residues out of total 770 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 122 time to evaluate : 1.116 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.2993 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 96 optimal weight: 5.9990 chunk 86 optimal weight: 5.9990 chunk 47 optimal weight: 4.9990 chunk 29 optimal weight: 1.9990 chunk 58 optimal weight: 0.5980 chunk 46 optimal weight: 0.2980 chunk 89 optimal weight: 5.9990 chunk 34 optimal weight: 4.9990 chunk 54 optimal weight: 5.9990 chunk 66 optimal weight: 5.9990 chunk 103 optimal weight: 5.9990 overall best weight: 2.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 73 ASN G 84 GLN A 108 ASN D 63 ASN C 38 ASN ** C 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8172 moved from start: 0.1197 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.050 14042 Z= 0.361 Angle : 0.655 9.913 20213 Z= 0.378 Chirality : 0.040 0.162 2311 Planarity : 0.005 0.043 1552 Dihedral : 30.983 172.442 3946 Min Nonbonded Distance : 2.129 Molprobity Statistics. All-atom Clashscore : 10.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.25 % Favored : 95.75 % Rotamer Outliers : 2.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.11 % Twisted Proline : 0.00 % Twisted General : 0.11 % 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: 1.14 (0.29), residues: 895 helix: 1.41 (0.22), residues: 573 sheet: -0.94 (0.73), residues: 50 loop : -0.16 (0.37), residues: 272 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1790 Ramachandran restraints generated. 895 Oldfield, 0 Emsley, 895 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1790 Ramachandran restraints generated. 895 Oldfield, 0 Emsley, 895 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 770 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 123 time to evaluate : 1.055 Fit side-chains outliers start: 16 outliers final: 11 residues processed: 133 average time/residue: 0.2582 time to fit residues: 49.1860 Evaluate side-chains 127 residues out of total 770 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 116 time to evaluate : 0.952 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 0 residues processed: 11 average time/residue: 0.1100 time to fit residues: 3.4998 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 57 optimal weight: 0.0870 chunk 32 optimal weight: 0.9990 chunk 86 optimal weight: 4.9990 chunk 70 optimal weight: 4.9990 chunk 28 optimal weight: 1.9990 chunk 103 optimal weight: 4.9990 chunk 112 optimal weight: 1.9990 chunk 92 optimal weight: 8.9990 chunk 102 optimal weight: 4.9990 chunk 35 optimal weight: 0.8980 chunk 83 optimal weight: 4.9990 overall best weight: 1.1964 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 73 ASN G 84 GLN H 84 ASN ** B 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8142 moved from start: 0.1125 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.044 14042 Z= 0.209 Angle : 0.568 10.657 20213 Z= 0.337 Chirality : 0.036 0.132 2311 Planarity : 0.004 0.039 1552 Dihedral : 30.891 172.307 3946 Min Nonbonded Distance : 2.165 Molprobity Statistics. All-atom Clashscore : 9.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer Outliers : 1.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.11 % Twisted Proline : 0.00 % Twisted General : 0.11 % 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: 1.53 (0.29), residues: 895 helix: 1.74 (0.23), residues: 571 sheet: -0.97 (0.72), residues: 50 loop : -0.02 (0.38), residues: 274 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1790 Ramachandran restraints generated. 895 Oldfield, 0 Emsley, 895 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1790 Ramachandran restraints generated. 895 Oldfield, 0 Emsley, 895 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 770 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 127 time to evaluate : 1.079 Fit side-chains outliers start: 8 outliers final: 3 residues processed: 131 average time/residue: 0.2626 time to fit residues: 49.6846 Evaluate side-chains 121 residues out of total 770 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 118 time to evaluate : 1.081 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.2257 time to fit residues: 2.2686 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 102 optimal weight: 5.9990 chunk 77 optimal weight: 5.9990 chunk 53 optimal weight: 4.9990 chunk 11 optimal weight: 1.9990 chunk 49 optimal weight: 3.9990 chunk 69 optimal weight: 4.9990 chunk 104 optimal weight: 5.9990 chunk 110 optimal weight: 3.9990 chunk 54 optimal weight: 0.8980 chunk 98 optimal weight: 5.9990 chunk 29 optimal weight: 0.7980 overall best weight: 2.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 73 ASN G 84 GLN A 125 GLN D 63 ASN C 38 ASN C 73 ASN ** K 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8179 moved from start: 0.1533 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.047 14042 Z= 0.331 Angle : 0.635 10.425 20213 Z= 0.369 Chirality : 0.039 0.158 2311 Planarity : 0.004 0.038 1552 Dihedral : 31.188 172.432 3946 Min Nonbonded Distance : 2.163 Molprobity Statistics. All-atom Clashscore : 10.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.69 % Favored : 95.31 % Rotamer Outliers : 2.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.11 % Twisted Proline : 0.00 % Twisted General : 0.11 % 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: 1.27 (0.29), residues: 895 helix: 1.55 (0.23), residues: 571 sheet: -1.03 (0.73), residues: 50 loop : -0.18 (0.37), residues: 274 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1790 Ramachandran restraints generated. 895 Oldfield, 0 Emsley, 895 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1790 Ramachandran restraints generated. 895 Oldfield, 0 Emsley, 895 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 770 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 116 time to evaluate : 1.184 Fit side-chains outliers start: 19 outliers final: 14 residues processed: 122 average time/residue: 0.2693 time to fit residues: 46.8772 Evaluate side-chains 126 residues out of total 770 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 112 time to evaluate : 1.215 Switching outliers to nearest non-outliers outliers start: 14 outliers final: 0 residues processed: 14 average time/residue: 0.1149 time to fit residues: 4.2566 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 91 optimal weight: 5.9990 chunk 62 optimal weight: 3.9990 chunk 1 optimal weight: 9.9990 chunk 82 optimal weight: 6.9990 chunk 45 optimal weight: 1.9990 chunk 94 optimal weight: 6.9990 chunk 76 optimal weight: 2.9990 chunk 0 optimal weight: 9.9990 chunk 56 optimal weight: 1.9990 chunk 98 optimal weight: 5.9990 chunk 27 optimal weight: 3.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 25 ASN G 73 ASN G 84 GLN A 108 ASN A 125 GLN D 63 ASN C 73 ASN B 64 ASN ** K 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8199 moved from start: 0.1915 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.007 0.047 14042 Z= 0.402 Angle : 0.685 10.499 20213 Z= 0.394 Chirality : 0.042 0.167 2311 Planarity : 0.005 0.042 1552 Dihedral : 31.447 172.599 3946 Min Nonbonded Distance : 2.138 Molprobity Statistics. All-atom Clashscore : 11.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.47 % Favored : 95.53 % Rotamer Outliers : 1.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.11 % Twisted Proline : 0.00 % Twisted General : 0.11 % 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: 0.89 (0.28), residues: 895 helix: 1.29 (0.22), residues: 571 sheet: -1.20 (0.71), residues: 51 loop : -0.40 (0.36), residues: 273 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1790 Ramachandran restraints generated. 895 Oldfield, 0 Emsley, 895 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1790 Ramachandran restraints generated. 895 Oldfield, 0 Emsley, 895 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 770 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 111 time to evaluate : 1.016 Fit side-chains outliers start: 12 outliers final: 5 residues processed: 118 average time/residue: 0.2904 time to fit residues: 48.3544 Evaluate side-chains 107 residues out of total 770 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 102 time to evaluate : 1.080 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.1172 time to fit residues: 2.3848 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 37 optimal weight: 0.5980 chunk 99 optimal weight: 3.9990 chunk 21 optimal weight: 1.9990 chunk 64 optimal weight: 0.5980 chunk 27 optimal weight: 0.9980 chunk 110 optimal weight: 6.9990 chunk 91 optimal weight: 5.9990 chunk 51 optimal weight: 2.9990 chunk 9 optimal weight: 0.5980 chunk 36 optimal weight: 0.8980 chunk 57 optimal weight: 3.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 25 ASN G 73 ASN G 84 GLN A 125 GLN D 63 ASN C 73 ASN B 64 ASN ** K 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8125 moved from start: 0.1561 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.045 14042 Z= 0.170 Angle : 0.557 11.228 20213 Z= 0.332 Chirality : 0.035 0.133 2311 Planarity : 0.003 0.037 1552 Dihedral : 30.883 172.005 3946 Min Nonbonded Distance : 2.170 Molprobity Statistics. All-atom Clashscore : 10.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.13 % Favored : 96.87 % Rotamer Outliers : 1.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.11 % 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: 1.68 (0.29), residues: 895 helix: 1.90 (0.23), residues: 570 sheet: -0.78 (0.75), residues: 50 loop : -0.10 (0.38), residues: 275 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1790 Ramachandran restraints generated. 895 Oldfield, 0 Emsley, 895 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1790 Ramachandran restraints generated. 895 Oldfield, 0 Emsley, 895 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 770 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 127 time to evaluate : 1.096 Fit side-chains outliers start: 8 outliers final: 4 residues processed: 130 average time/residue: 0.2519 time to fit residues: 48.0942 Evaluate side-chains 119 residues out of total 770 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 115 time to evaluate : 1.060 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.1322 time to fit residues: 2.2212 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 106 optimal weight: 8.9990 chunk 12 optimal weight: 4.9990 chunk 62 optimal weight: 4.9990 chunk 80 optimal weight: 6.9990 chunk 92 optimal weight: 9.9990 chunk 61 optimal weight: 3.9990 chunk 109 optimal weight: 0.8980 chunk 68 optimal weight: 2.9990 chunk 66 optimal weight: 2.9990 chunk 50 optimal weight: 0.8980 chunk 67 optimal weight: 1.9990 overall best weight: 1.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 73 ASN H 84 ASN A 125 GLN D 84 ASN C 38 ASN C 73 ASN ** K 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8165 moved from start: 0.1750 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.043 14042 Z= 0.287 Angle : 0.614 10.795 20213 Z= 0.357 Chirality : 0.038 0.157 2311 Planarity : 0.004 0.037 1552 Dihedral : 31.123 172.480 3946 Min Nonbonded Distance : 2.167 Molprobity Statistics. All-atom Clashscore : 10.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.91 % Favored : 96.09 % Rotamer Outliers : 1.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.11 % Twisted Proline : 0.00 % Twisted General : 0.11 % 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: 1.55 (0.29), residues: 895 helix: 1.80 (0.23), residues: 571 sheet: -0.74 (0.74), residues: 51 loop : -0.18 (0.37), residues: 273 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1790 Ramachandran restraints generated. 895 Oldfield, 0 Emsley, 895 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1790 Ramachandran restraints generated. 895 Oldfield, 0 Emsley, 895 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 770 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 112 time to evaluate : 1.150 Fit side-chains outliers start: 10 outliers final: 7 residues processed: 115 average time/residue: 0.2501 time to fit residues: 42.4133 Evaluate side-chains 116 residues out of total 770 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 109 time to evaluate : 0.962 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.1117 time to fit residues: 2.6020 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 43 optimal weight: 0.6980 chunk 65 optimal weight: 0.7980 chunk 33 optimal weight: 0.9990 chunk 21 optimal weight: 3.9990 chunk 69 optimal weight: 2.9990 chunk 74 optimal weight: 0.9980 chunk 54 optimal weight: 1.9990 chunk 10 optimal weight: 0.8980 chunk 86 optimal weight: 4.9990 chunk 99 optimal weight: 4.9990 chunk 105 optimal weight: 7.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 73 ASN H 84 ASN A 108 ASN A 125 GLN D 84 ASN C 73 ASN ** K 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8130 moved from start: 0.1651 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.044 14042 Z= 0.180 Angle : 0.566 11.039 20213 Z= 0.333 Chirality : 0.036 0.139 2311 Planarity : 0.003 0.037 1552 Dihedral : 30.924 172.270 3946 Min Nonbonded Distance : 2.162 Molprobity Statistics. All-atom Clashscore : 10.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer Outliers : 0.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.11 % 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: 1.79 (0.29), residues: 895 helix: 1.96 (0.23), residues: 572 sheet: -0.53 (0.75), residues: 51 loop : -0.05 (0.38), residues: 272 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1790 Ramachandran restraints generated. 895 Oldfield, 0 Emsley, 895 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1790 Ramachandran restraints generated. 895 Oldfield, 0 Emsley, 895 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 770 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 126 time to evaluate : 0.991 Fit side-chains outliers start: 5 outliers final: 2 residues processed: 127 average time/residue: 0.2497 time to fit residues: 46.8864 Evaluate side-chains 122 residues out of total 770 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 120 time to evaluate : 0.997 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.1095 time to fit residues: 1.6397 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 96 optimal weight: 5.9990 chunk 102 optimal weight: 5.9990 chunk 105 optimal weight: 7.9990 chunk 61 optimal weight: 3.9990 chunk 44 optimal weight: 3.9990 chunk 80 optimal weight: 7.9990 chunk 31 optimal weight: 0.9980 chunk 92 optimal weight: 8.9990 chunk 67 optimal weight: 0.9990 chunk 108 optimal weight: 3.9990 chunk 66 optimal weight: 2.9990 overall best weight: 2.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 73 ASN H 84 ASN A 108 ASN A 125 GLN D 84 ASN C 38 ASN C 73 ASN ** K 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8182 moved from start: 0.1964 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.043 14042 Z= 0.356 Angle : 0.660 10.483 20213 Z= 0.378 Chirality : 0.040 0.161 2311 Planarity : 0.005 0.037 1552 Dihedral : 31.285 172.626 3946 Min Nonbonded Distance : 2.160 Molprobity Statistics. All-atom Clashscore : 11.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.47 % Favored : 95.53 % Rotamer Outliers : 0.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.11 % Twisted Proline : 0.00 % Twisted General : 0.11 % 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: 1.36 (0.29), residues: 895 helix: 1.64 (0.23), residues: 571 sheet: -0.56 (0.75), residues: 51 loop : -0.30 (0.37), residues: 273 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1790 Ramachandran restraints generated. 895 Oldfield, 0 Emsley, 895 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1790 Ramachandran restraints generated. 895 Oldfield, 0 Emsley, 895 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 770 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 109 time to evaluate : 1.105 Fit side-chains outliers start: 7 outliers final: 4 residues processed: 112 average time/residue: 0.2549 time to fit residues: 41.7156 Evaluate side-chains 111 residues out of total 770 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 107 time to evaluate : 1.046 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.1117 time to fit residues: 2.1069 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 51 optimal weight: 1.9990 chunk 75 optimal weight: 0.9990 chunk 113 optimal weight: 9.9990 chunk 104 optimal weight: 5.9990 chunk 90 optimal weight: 5.9990 chunk 9 optimal weight: 0.5980 chunk 69 optimal weight: 0.8980 chunk 55 optimal weight: 0.9990 chunk 71 optimal weight: 1.9990 chunk 96 optimal weight: 4.9990 chunk 27 optimal weight: 0.9990 overall best weight: 0.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 73 ASN H 84 ASN A 108 ASN D 84 ASN ** C 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8129 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 : 0.003 0.045 14042 Z= 0.186 Angle : 0.573 11.134 20213 Z= 0.336 Chirality : 0.036 0.145 2311 Planarity : 0.004 0.038 1552 Dihedral : 30.897 172.044 3946 Min Nonbonded Distance : 2.138 Molprobity Statistics. All-atom Clashscore : 10.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer Outliers : 0.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.11 % 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: 1.77 (0.29), residues: 895 helix: 1.95 (0.23), residues: 572 sheet: -0.36 (0.77), residues: 51 loop : -0.10 (0.38), residues: 272 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1790 Ramachandran restraints generated. 895 Oldfield, 0 Emsley, 895 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1790 Ramachandran restraints generated. 895 Oldfield, 0 Emsley, 895 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 770 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 124 time to evaluate : 1.069 Fit side-chains outliers start: 5 outliers final: 3 residues processed: 125 average time/residue: 0.2584 time to fit residues: 47.3893 Evaluate side-chains 120 residues out of total 770 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 117 time to evaluate : 1.132 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.1299 time to fit residues: 1.9833 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 83 optimal weight: 6.9990 chunk 13 optimal weight: 2.9990 chunk 25 optimal weight: 2.9990 chunk 90 optimal weight: 5.9990 chunk 37 optimal weight: 2.9990 chunk 93 optimal weight: 7.9990 chunk 11 optimal weight: 1.9990 chunk 16 optimal weight: 1.9990 chunk 79 optimal weight: 8.9990 chunk 5 optimal weight: 10.0000 chunk 65 optimal weight: 2.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 73 ASN H 84 ASN A 108 ASN A 125 GLN D 84 ASN ** C 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 73 ASN ** K 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3652 r_free = 0.3652 target = 0.106350 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3022 r_free = 0.3022 target = 0.071056 restraints weight = 31566.057| |-----------------------------------------------------------------------------| r_work (start): 0.2988 rms_B_bonded: 2.60 r_work: 0.2972 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.2959 rms_B_bonded: 2.50 restraints_weight: 0.2500 r_work: 0.2945 rms_B_bonded: 2.57 restraints_weight: 0.1250 r_work: 0.2931 rms_B_bonded: 2.68 restraints_weight: 0.0625 r_work: 0.2914 rms_B_bonded: 2.84 restraints_weight: 0.0312 r_work: 0.2896 rms_B_bonded: 3.05 restraints_weight: 0.0156 r_work: 0.2876 rms_B_bonded: 3.33 restraints_weight: 0.0078 r_work: 0.2853 rms_B_bonded: 3.69 restraints_weight: 0.0039 r_work: 0.2826 rms_B_bonded: 4.14 restraints_weight: 0.0020 r_work: 0.2796 rms_B_bonded: 4.70 restraints_weight: 0.0010 r_work (final): 0.2796 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3652 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3652 r_free = 0.3652 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3651 r_free = 0.3651 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3651 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8342 moved from start: 0.2015 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.043 14042 Z= 0.358 Angle : 0.666 11.165 20213 Z= 0.381 Chirality : 0.040 0.164 2311 Planarity : 0.004 0.038 1552 Dihedral : 31.278 172.609 3946 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 11.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.58 % Favored : 95.42 % Rotamer Outliers : 0.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.11 % Twisted Proline : 0.00 % Twisted General : 0.11 % 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: 1.36 (0.29), residues: 895 helix: 1.65 (0.23), residues: 571 sheet: -0.52 (0.76), residues: 51 loop : -0.33 (0.37), residues: 273 =============================================================================== Job complete usr+sys time: 1910.13 seconds wall clock time: 35 minutes 39.26 seconds (2139.26 seconds total)