Starting phenix.real_space_refine (version: dev) on Mon Feb 20 07:15:23 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7r5r_14334/02_2023/7r5r_14334.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7r5r_14334/02_2023/7r5r_14334.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.44 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7r5r_14334/02_2023/7r5r_14334.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7r5r_14334/02_2023/7r5r_14334.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7r5r_14334/02_2023/7r5r_14334.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7r5r_14334/02_2023/7r5r_14334.pdb" } resolution = 2.44 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= -0.001 sd= 0.049 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 Process input model Symmetric amino acids flipped Residue "A GLU 50": "OE1" <-> "OE2" Residue "A GLU 99": "OE1" <-> "OE2" Residue "A GLU 107": "OE1" <-> "OE2" Residue "A GLU 136": "OE1" <-> "OE2" Residue "C ARG 81": "NH1" <-> "NH2" Residue "D GLU 71": "OE1" <-> "OE2" Residue "D GLU 76": "OE1" <-> "OE2" Residue "D GLU 93": "OE1" <-> "OE2" Residue "E GLU 99": "OE1" <-> "OE2" Residue "F GLU 52": "OE1" <-> "OE2" Residue "F ARG 92": "NH1" <-> "NH2" Residue "G GLU 41": "OE1" <-> "OE2" Residue "G GLU 64": "OE1" <-> "OE2" Residue "H GLU 35": "OE1" <-> "OE2" Residue "H GLU 105": "OE1" <-> "OE2" Residue "L ARG 526": "NH1" <-> "NH2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/modules/chem_data/mon_lib" Total number of atoms: 11625 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 799 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 799 Classifications: {'peptide': 99} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 2, 'TRANS': 96} Unresolved non-hydrogen bonds: 19 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 16 Planarities with less than four sites: {'ARG:plan': 3} Unresolved non-hydrogen planarities: 15 Chain: "B" Number of atoms: 622 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 622 Classifications: {'peptide': 78} Link IDs: {'PTRANS': 1, 'TRANS': 76} Chain: "C" Number of atoms: 755 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 755 Classifications: {'peptide': 98} Link IDs: {'PTRANS': 4, 'TRANS': 93} Chain: "D" Number of atoms: 719 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 719 Classifications: {'peptide': 92} Link IDs: {'PTRANS': 2, 'TRANS': 89} Chain: "E" Number of atoms: 770 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 770 Classifications: {'peptide': 94} Link IDs: {'PTRANS': 2, 'TRANS': 91} Chain: "F" Number of atoms: 641 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 641 Classifications: {'peptide': 80} Link IDs: {'PTRANS': 1, 'TRANS': 78} Chain: "G" Number of atoms: 784 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 784 Classifications: {'peptide': 103} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 5, 'TRANS': 97} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 8 Unresolved non-hydrogen chiralities: 3 Chain: "H" Number of atoms: 719 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 719 Classifications: {'peptide': 92} Link IDs: {'PTRANS': 2, 'TRANS': 89} Chain: "I" Number of atoms: 2729 Number of conformers: 1 Conformer: "" Number of residues, atoms: 133, 2729 Classifications: {'DNA': 133} Link IDs: {'rna3p': 132} Chain: "J" Number of atoms: 2724 Number of conformers: 1 Conformer: "" Number of residues, atoms: 133, 2724 Classifications: {'DNA': 133} Link IDs: {'rna3p': 132} Chain breaks: 1 Chain: "K" Number of atoms: 178 Number of conformers: 1 Conformer: "" Number of residues, atoms: 21, 178 Classifications: {'peptide': 21} Link IDs: {'PTRANS': 1, 'TRANS': 19} Chain: "L" Number of atoms: 185 Number of conformers: 1 Conformer: "" Number of residues, atoms: 22, 185 Classifications: {'peptide': 22} Link IDs: {'PTRANS': 1, 'TRANS': 20} Time building chain proxies: 6.78, per 1000 atoms: 0.58 Number of scatterers: 11625 At special positions: 0 Unit cell: (81.888, 116.861, 119.42, 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 8 16.00 P 266 15.00 O 2678 8.00 N 2145 7.00 C 6528 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: 5.61 Conformation dependent library (CDL) restraints added in 1.1 seconds 1518 Ramachandran restraints generated. 759 Oldfield, 0 Emsley, 759 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1450 Finding SS restraints... Secondary structure from input PDB file: 34 helices and 11 sheets defined 68.5% alpha, 2.8% beta 124 base pairs and 236 stacking pairs defined. Time for finding SS restraints: 4.59 Creating SS restraints... Processing helix chain 'A' and resid 45 through 55 removed outlier: 4.293A pdb=" N LYS A 49 " --> pdb=" O GLN A 45 " (cutoff:3.500A) Processing helix chain 'A' and resid 63 through 79 removed outlier: 3.751A pdb=" N PHE A 67 " --> pdb=" O ARG A 63 " (cutoff:3.500A) Processing helix chain 'A' and resid 87 through 116 Processing helix chain 'A' and resid 122 through 134 removed outlier: 3.703A pdb=" N VAL A 126 " --> pdb=" O PHE A 122 " (cutoff:3.500A) Processing helix chain 'B' and resid 24 through 29 removed outlier: 3.666A pdb=" N ILE B 29 " --> pdb=" O ILE B 26 " (cutoff:3.500A) Processing helix chain 'B' and resid 30 through 41 Processing helix chain 'B' and resid 49 through 76 removed outlier: 4.063A pdb=" N GLU B 53 " --> pdb=" O LEU B 49 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N ALA B 76 " --> pdb=" O TYR B 72 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 92 removed outlier: 3.515A pdb=" N VAL B 86 " --> pdb=" O THR B 82 " (cutoff:3.500A) Processing helix chain 'C' and resid 16 through 21 Processing helix chain 'C' and resid 27 through 36 Processing helix chain 'C' and resid 46 through 72 removed outlier: 3.640A pdb=" N LEU C 65 " --> pdb=" O GLU C 61 " (cutoff:3.500A) Processing helix chain 'C' and resid 79 through 89 Processing helix chain 'C' and resid 90 through 97 Processing helix chain 'D' and resid 37 through 49 Processing helix chain 'D' and resid 55 through 84 removed outlier: 3.687A pdb=" N MET D 59 " --> pdb=" O SER D 55 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ASN D 84 " --> pdb=" O LEU D 80 " (cutoff:3.500A) Processing helix chain 'D' and resid 90 through 102 Processing helix chain 'D' and resid 103 through 123 Processing helix chain 'E' and resid 47 through 55 Processing helix chain 'E' and resid 63 through 79 removed outlier: 3.851A pdb=" N PHE E 67 " --> pdb=" O ARG E 63 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N PHE E 78 " --> pdb=" O ILE E 74 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N THR E 79 " --> pdb=" O CYS E 75 " (cutoff:3.500A) Processing helix chain 'E' and resid 87 through 117 Processing helix chain 'E' and resid 122 through 134 removed outlier: 3.656A pdb=" N VAL E 126 " --> pdb=" O PHE E 122 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N GLY E 134 " --> pdb=" O ARG E 130 " (cutoff:3.500A) Processing helix chain 'F' and resid 24 through 29 removed outlier: 3.646A pdb=" N ILE F 29 " --> pdb=" O ILE F 26 " (cutoff:3.500A) Processing helix chain 'F' and resid 30 through 41 Processing helix chain 'F' and resid 49 through 76 removed outlier: 3.944A pdb=" N GLU F 53 " --> pdb=" O LEU F 49 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N ALA F 76 " --> pdb=" O TYR F 72 " (cutoff:3.500A) Processing helix chain 'F' and resid 82 through 93 Processing helix chain 'G' and resid 16 through 21 Processing helix chain 'G' and resid 27 through 36 Processing helix chain 'G' and resid 46 through 73 Processing helix chain 'G' and resid 79 through 89 Processing helix chain 'G' and resid 90 through 97 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 103 through 122 Processing sheet with id=AA1, first strand: chain 'A' and resid 85 through 86 removed outlier: 6.853A pdb=" N ASN A 85 " --> pdb=" O VAL B 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 120 through 121 Processing sheet with id=AA3, first strand: chain 'B' and resid 96 through 97 removed outlier: 6.437A pdb=" N THR B 96 " --> pdb=" O THR G 101 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'C' and resid 42 through 43 removed outlier: 7.319A pdb=" N ARG C 42 " --> pdb=" O ILE D 89 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'C' and resid 77 through 78 Processing sheet with id=AA6, first strand: chain 'C' and resid 100 through 101 Processing sheet with id=AA7, first strand: chain 'E' and resid 85 through 86 removed outlier: 6.925A pdb=" N ASN E 85 " --> pdb=" O VAL F 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'E' and resid 120 through 121 Processing sheet with id=AA9, first strand: chain 'G' and resid 42 through 43 removed outlier: 7.306A pdb=" N ARG G 42 " --> pdb=" O ILE H 89 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'G' and resid 77 through 78 Processing sheet with id=AB2, first strand: chain 'L' and resid 516 through 517 389 hydrogen bonds defined for protein. 1152 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 286 hydrogen bonds 572 hydrogen bond angles 0 basepair planarities 124 basepair parallelities 236 stacking parallelities Total time for adding SS restraints: 4.63 Time building geometry restraints manager: 5.99 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2058 1.33 - 1.45: 4086 1.45 - 1.57: 5694 1.57 - 1.69: 527 1.69 - 1.81: 14 Bond restraints: 12379 Sorted by residual: bond pdb=" O3' DA I 20 " pdb=" P DC I 21 " ideal model delta sigma weight residual 1.607 1.683 -0.076 1.50e-02 4.44e+03 2.54e+01 bond pdb=" O3' DA I 17 " pdb=" P DT I 18 " ideal model delta sigma weight residual 1.607 1.548 0.059 1.50e-02 4.44e+03 1.57e+01 bond pdb=" C1' DG J 34 " pdb=" N9 DG J 34 " ideal model delta sigma weight residual 1.460 1.388 0.072 2.00e-02 2.50e+03 1.28e+01 bond pdb=" C1' DG I -20 " pdb=" N9 DG I -20 " ideal model delta sigma weight residual 1.460 1.394 0.066 2.00e-02 2.50e+03 1.08e+01 bond pdb=" O3' DG J -16 " pdb=" P DT J -15 " ideal model delta sigma weight residual 1.607 1.654 -0.047 1.50e-02 4.44e+03 9.87e+00 ... (remaining 12374 not shown) Histogram of bond angle deviations from ideal: 94.07 - 102.24: 285 102.24 - 110.41: 4901 110.41 - 118.58: 5794 118.58 - 126.75: 5998 126.75 - 134.92: 882 Bond angle restraints: 17860 Sorted by residual: angle pdb=" C4' DA J -18 " pdb=" C3' DA J -18 " pdb=" O3' DA J -18 " ideal model delta sigma weight residual 110.00 94.07 15.93 1.50e+00 4.44e-01 1.13e+02 angle pdb=" C3' DA I 17 " pdb=" O3' DA I 17 " pdb=" P DT I 18 " ideal model delta sigma weight residual 120.20 134.92 -14.72 1.50e+00 4.44e-01 9.64e+01 angle pdb=" O3' DT I 18 " pdb=" C3' DT I 18 " pdb=" C2' DT I 18 " ideal model delta sigma weight residual 111.50 98.04 13.46 1.50e+00 4.44e-01 8.05e+01 angle pdb=" O3' DA J -18 " pdb=" C3' DA J -18 " pdb=" C2' DA J -18 " ideal model delta sigma weight residual 111.50 100.12 11.38 1.50e+00 4.44e-01 5.76e+01 angle pdb=" C4' DT I 18 " pdb=" C3' DT I 18 " pdb=" O3' DT I 18 " ideal model delta sigma weight residual 110.00 99.69 10.31 1.50e+00 4.44e-01 4.73e+01 ... (remaining 17855 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.80: 5286 35.80 - 71.60: 1169 71.60 - 107.40: 19 107.40 - 143.19: 0 143.19 - 178.99: 2 Dihedral angle restraints: 6476 sinusoidal: 4231 harmonic: 2245 Sorted by residual: dihedral pdb=" C4' DA J -49 " pdb=" C3' DA J -49 " pdb=" O3' DA J -49 " pdb=" P DG J -48 " ideal model delta sinusoidal sigma weight residual 220.00 41.01 178.99 1 3.50e+01 8.16e-04 1.57e+01 dihedral pdb=" C4' DG J -16 " pdb=" C3' DG J -16 " pdb=" O3' DG J -16 " pdb=" P DT J -15 " ideal model delta sinusoidal sigma weight residual -140.00 30.40 -170.40 1 3.50e+01 8.16e-04 1.56e+01 dihedral pdb=" CA GLY E 134 " pdb=" C GLY E 134 " pdb=" N LEU E 135 " pdb=" CA LEU E 135 " ideal model delta harmonic sigma weight residual 180.00 161.08 18.92 0 5.00e+00 4.00e-02 1.43e+01 ... (remaining 6473 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.098: 1975 0.098 - 0.196: 47 0.196 - 0.295: 8 0.295 - 0.393: 2 0.393 - 0.491: 1 Chirality restraints: 2033 Sorted by residual: chirality pdb=" C3' DA J -18 " pdb=" C4' DA J -18 " pdb=" O3' DA J -18 " pdb=" C2' DA J -18 " both_signs ideal model delta sigma weight residual False -2.66 -3.15 0.49 2.00e-01 2.50e+01 6.03e+00 chirality pdb=" C3' DT I 18 " pdb=" C4' DT I 18 " pdb=" O3' DT I 18 " pdb=" C2' DT I 18 " both_signs ideal model delta sigma weight residual False -2.66 -3.04 0.38 2.00e-01 2.50e+01 3.67e+00 chirality pdb=" C3' DT J -15 " pdb=" C4' DT J -15 " pdb=" O3' DT J -15 " pdb=" C2' DT J -15 " both_signs ideal model delta sigma weight residual False -2.66 -2.96 0.30 2.00e-01 2.50e+01 2.22e+00 ... (remaining 2030 not shown) Planarity restraints: 1328 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' DG J -16 " -0.019 2.00e-02 2.50e+03 2.08e-02 1.29e+01 pdb=" N9 DG J -16 " 0.045 2.00e-02 2.50e+03 pdb=" C8 DG J -16 " -0.025 2.00e-02 2.50e+03 pdb=" N7 DG J -16 " 0.007 2.00e-02 2.50e+03 pdb=" C5 DG J -16 " 0.001 2.00e-02 2.50e+03 pdb=" C6 DG J -16 " -0.000 2.00e-02 2.50e+03 pdb=" O6 DG J -16 " 0.000 2.00e-02 2.50e+03 pdb=" N1 DG J -16 " 0.003 2.00e-02 2.50e+03 pdb=" C2 DG J -16 " -0.041 2.00e-02 2.50e+03 pdb=" N2 DG J -16 " 0.015 2.00e-02 2.50e+03 pdb=" N3 DG J -16 " 0.014 2.00e-02 2.50e+03 pdb=" C4 DG J -16 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DG J -19 " 0.015 2.00e-02 2.50e+03 1.93e-02 1.11e+01 pdb=" N9 DG J -19 " 0.002 2.00e-02 2.50e+03 pdb=" C8 DG J -19 " -0.027 2.00e-02 2.50e+03 pdb=" N7 DG J -19 " -0.005 2.00e-02 2.50e+03 pdb=" C5 DG J -19 " 0.030 2.00e-02 2.50e+03 pdb=" C6 DG J -19 " 0.042 2.00e-02 2.50e+03 pdb=" O6 DG J -19 " -0.019 2.00e-02 2.50e+03 pdb=" N1 DG J -19 " -0.014 2.00e-02 2.50e+03 pdb=" C2 DG J -19 " -0.009 2.00e-02 2.50e+03 pdb=" N2 DG J -19 " 0.001 2.00e-02 2.50e+03 pdb=" N3 DG J -19 " -0.008 2.00e-02 2.50e+03 pdb=" C4 DG J -19 " -0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DA I 20 " 0.013 2.00e-02 2.50e+03 1.94e-02 1.03e+01 pdb=" N9 DA I 20 " -0.031 2.00e-02 2.50e+03 pdb=" C8 DA I 20 " 0.024 2.00e-02 2.50e+03 pdb=" N7 DA I 20 " 0.001 2.00e-02 2.50e+03 pdb=" C5 DA I 20 " -0.044 2.00e-02 2.50e+03 pdb=" C6 DA I 20 " -0.001 2.00e-02 2.50e+03 pdb=" N6 DA I 20 " 0.015 2.00e-02 2.50e+03 pdb=" N1 DA I 20 " 0.003 2.00e-02 2.50e+03 pdb=" C2 DA I 20 " 0.001 2.00e-02 2.50e+03 pdb=" N3 DA I 20 " 0.003 2.00e-02 2.50e+03 pdb=" C4 DA I 20 " 0.015 2.00e-02 2.50e+03 ... (remaining 1325 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.76: 1514 2.76 - 3.30: 9716 3.30 - 3.83: 21549 3.83 - 4.37: 25862 4.37 - 4.90: 37546 Nonbonded interactions: 96187 Sorted by model distance: nonbonded pdb=" OH TYR C 39 " pdb=" OE2 GLU D 71 " model vdw 2.226 2.440 nonbonded pdb=" OG1 THR A 113 " pdb=" OD2 ASP A 125 " model vdw 2.259 2.440 nonbonded pdb=" OG SER G 18 " pdb=" O PHE G 25 " model vdw 2.273 2.440 nonbonded pdb=" O TYR G 39 " pdb=" OG SER H 78 " model vdw 2.283 2.440 nonbonded pdb=" OG1 THR E 113 " pdb=" OD2 ASP E 125 " model vdw 2.334 2.440 ... (remaining 96182 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 46 through 139) selection = chain 'E' } ncs_group { reference = chain 'B' selection = (chain 'F' and resid 24 through 101) } ncs_group { reference = (chain 'C' and resid 15 through 111) selection = (chain 'G' and resid 15 through 111) } ncs_group { reference = chain 'D' selection = chain 'H' } ncs_group { reference = chain 'K' selection = (chain 'L' and resid 515 through 535) } 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 266 5.49 5 S 8 5.16 5 C 6528 2.51 5 N 2145 2.21 5 O 2678 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=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: 2.370 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: 10.680 Check model and map are aligned: 0.190 Process input model: 37.870 Find NCS groups from input model: 0.460 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Set scattering table: 0.100 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:11.990 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 63.710 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3945 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 : 0.004 0.076 12379 Z= 0.187 Angle : 0.656 15.927 17860 Z= 0.422 Chirality : 0.040 0.491 2033 Planarity : 0.004 0.041 1328 Dihedral : 27.142 178.993 5026 Min Nonbonded Distance : 2.226 Molprobity Statistics. All-atom Clashscore : 6.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer Outliers : 0.31 % 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: -0.10 (0.27), residues: 759 helix: 1.05 (0.20), residues: 533 sheet: None (None), residues: 0 loop : -2.86 (0.29), residues: 226 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1518 Ramachandran restraints generated. 759 Oldfield, 0 Emsley, 759 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1518 Ramachandran restraints generated. 759 Oldfield, 0 Emsley, 759 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 651 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 133 time to evaluate : 0.995 Fit side-chains outliers start: 2 outliers final: 1 residues processed: 134 average time/residue: 2.3058 time to fit residues: 322.6263 Evaluate side-chains 114 residues out of total 651 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 113 time to evaluate : 0.979 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 1 residues processed: 1 average time/residue: 0.3343 time to fit residues: 1.6035 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 84 optimal weight: 10.0000 chunk 75 optimal weight: 4.9990 chunk 42 optimal weight: 3.9990 chunk 25 optimal weight: 0.0870 chunk 51 optimal weight: 0.0170 chunk 40 optimal weight: 0.5980 chunk 78 optimal weight: 5.9990 chunk 30 optimal weight: 0.8980 chunk 47 optimal weight: 3.9990 chunk 58 optimal weight: 1.9990 chunk 90 optimal weight: 3.9990 overall best weight: 0.7198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 45 GLN B 93 GLN C 94 ASN E 87 GLN F 93 GLN G 73 ASN G 94 ASN H 84 ASN H 95 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3958 moved from start: 0.1066 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.036 12379 Z= 0.176 Angle : 0.559 7.046 17860 Z= 0.336 Chirality : 0.033 0.127 2033 Planarity : 0.004 0.037 1328 Dihedral : 30.920 179.294 3527 Min Nonbonded Distance : 2.204 Molprobity Statistics. All-atom Clashscore : 5.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Rotamer Outliers : 2.02 % 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: 1.51 (0.29), residues: 759 helix: 2.27 (0.21), residues: 533 sheet: None (None), residues: 0 loop : -2.32 (0.31), residues: 226 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1518 Ramachandran restraints generated. 759 Oldfield, 0 Emsley, 759 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1518 Ramachandran restraints generated. 759 Oldfield, 0 Emsley, 759 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 651 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 118 time to evaluate : 0.981 Fit side-chains outliers start: 13 outliers final: 7 residues processed: 126 average time/residue: 2.1395 time to fit residues: 282.3411 Evaluate side-chains 122 residues out of total 651 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 115 time to evaluate : 0.923 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 5 residues processed: 3 average time/residue: 1.4683 time to fit residues: 5.8279 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 50 optimal weight: 3.9990 chunk 28 optimal weight: 2.9990 chunk 75 optimal weight: 4.9990 chunk 61 optimal weight: 0.4980 chunk 25 optimal weight: 0.9980 chunk 90 optimal weight: 3.9990 chunk 98 optimal weight: 8.9990 chunk 81 optimal weight: 8.9990 chunk 31 optimal weight: 0.0980 chunk 72 optimal weight: 3.9990 chunk 89 optimal weight: 2.9990 overall best weight: 1.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 75 HIS G 73 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4006 moved from start: 0.1701 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.036 12379 Z= 0.264 Angle : 0.613 8.355 17860 Z= 0.363 Chirality : 0.036 0.127 2033 Planarity : 0.005 0.042 1328 Dihedral : 31.125 178.741 3527 Min Nonbonded Distance : 2.189 Molprobity Statistics. All-atom Clashscore : 5.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer Outliers : 2.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.68 (0.29), residues: 759 helix: 2.35 (0.21), residues: 533 sheet: None (None), residues: 0 loop : -2.12 (0.32), residues: 226 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1518 Ramachandran restraints generated. 759 Oldfield, 0 Emsley, 759 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1518 Ramachandran restraints generated. 759 Oldfield, 0 Emsley, 759 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 651 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 121 time to evaluate : 0.985 Fit side-chains outliers start: 17 outliers final: 9 residues processed: 132 average time/residue: 2.1148 time to fit residues: 292.4739 Evaluate side-chains 121 residues out of total 651 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 112 time to evaluate : 0.941 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 8 residues processed: 1 average time/residue: 1.6504 time to fit residues: 2.8708 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 68 optimal weight: 2.9990 chunk 47 optimal weight: 2.9990 chunk 10 optimal weight: 0.9980 chunk 43 optimal weight: 2.9990 chunk 61 optimal weight: 1.9990 chunk 91 optimal weight: 4.9990 chunk 96 optimal weight: 0.9980 chunk 86 optimal weight: 4.9990 chunk 26 optimal weight: 0.2980 chunk 80 optimal weight: 3.9990 chunk 54 optimal weight: 0.6980 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 73 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3997 moved from start: 0.1722 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.036 12379 Z= 0.205 Angle : 0.593 8.025 17860 Z= 0.353 Chirality : 0.035 0.128 2033 Planarity : 0.004 0.045 1328 Dihedral : 31.120 178.842 3527 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 5.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer Outliers : 2.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.92 (0.30), residues: 759 helix: 2.52 (0.21), residues: 533 sheet: None (None), residues: 0 loop : -1.98 (0.33), residues: 226 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1518 Ramachandran restraints generated. 759 Oldfield, 0 Emsley, 759 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1518 Ramachandran restraints generated. 759 Oldfield, 0 Emsley, 759 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 651 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 115 time to evaluate : 0.940 Fit side-chains outliers start: 17 outliers final: 14 residues processed: 127 average time/residue: 2.0078 time to fit residues: 267.8389 Evaluate side-chains 128 residues out of total 651 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 114 time to evaluate : 0.954 Switching outliers to nearest non-outliers outliers start: 14 outliers final: 10 residues processed: 4 average time/residue: 1.5574 time to fit residues: 7.6974 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 1 optimal weight: 0.8980 chunk 71 optimal weight: 5.9990 chunk 39 optimal weight: 1.9990 chunk 82 optimal weight: 20.0000 chunk 66 optimal weight: 3.9990 chunk 0 optimal weight: 6.9990 chunk 49 optimal weight: 0.9990 chunk 86 optimal weight: 4.9990 chunk 24 optimal weight: 0.9980 chunk 32 optimal weight: 0.7980 chunk 87 optimal weight: 4.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 73 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3990 moved from start: 0.1853 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.036 12379 Z= 0.216 Angle : 0.584 8.005 17860 Z= 0.348 Chirality : 0.034 0.127 2033 Planarity : 0.004 0.039 1328 Dihedral : 31.059 178.290 3527 Min Nonbonded Distance : 2.193 Molprobity Statistics. All-atom Clashscore : 5.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Rotamer Outliers : 2.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.11 (0.30), residues: 759 helix: 2.64 (0.21), residues: 533 sheet: None (None), residues: 0 loop : -1.85 (0.34), residues: 226 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1518 Ramachandran restraints generated. 759 Oldfield, 0 Emsley, 759 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1518 Ramachandran restraints generated. 759 Oldfield, 0 Emsley, 759 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 651 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 119 time to evaluate : 1.076 Fit side-chains outliers start: 17 outliers final: 13 residues processed: 130 average time/residue: 2.0350 time to fit residues: 277.9558 Evaluate side-chains 128 residues out of total 651 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 115 time to evaluate : 0.963 Switching outliers to nearest non-outliers outliers start: 13 outliers final: 10 residues processed: 3 average time/residue: 1.6683 time to fit residues: 6.4226 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 19 optimal weight: 2.9990 chunk 56 optimal weight: 1.9990 chunk 23 optimal weight: 0.5980 chunk 96 optimal weight: 7.9990 chunk 80 optimal weight: 4.9990 chunk 44 optimal weight: 3.9990 chunk 8 optimal weight: 1.9990 chunk 32 optimal weight: 0.5980 chunk 50 optimal weight: 1.9990 chunk 93 optimal weight: 3.9990 chunk 10 optimal weight: 0.4980 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 73 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3996 moved from start: 0.1990 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.037 12379 Z= 0.219 Angle : 0.592 8.095 17860 Z= 0.352 Chirality : 0.035 0.129 2033 Planarity : 0.004 0.043 1328 Dihedral : 31.072 178.249 3527 Min Nonbonded Distance : 2.191 Molprobity Statistics. All-atom Clashscore : 5.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Rotamer Outliers : 2.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.18 (0.30), residues: 759 helix: 2.68 (0.21), residues: 533 sheet: None (None), residues: 0 loop : -1.78 (0.34), residues: 226 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1518 Ramachandran restraints generated. 759 Oldfield, 0 Emsley, 759 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1518 Ramachandran restraints generated. 759 Oldfield, 0 Emsley, 759 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 651 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 119 time to evaluate : 0.998 Fit side-chains outliers start: 17 outliers final: 12 residues processed: 131 average time/residue: 2.1062 time to fit residues: 289.2429 Evaluate side-chains 127 residues out of total 651 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 115 time to evaluate : 0.993 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 9 residues processed: 3 average time/residue: 1.3227 time to fit residues: 5.5350 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 55 optimal weight: 2.9990 chunk 70 optimal weight: 10.0000 chunk 54 optimal weight: 0.5980 chunk 81 optimal weight: 8.9990 chunk 96 optimal weight: 6.9990 chunk 60 optimal weight: 0.3980 chunk 58 optimal weight: 0.9980 chunk 44 optimal weight: 3.9990 chunk 59 optimal weight: 0.9980 chunk 38 optimal weight: 0.9980 chunk 57 optimal weight: 1.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3992 moved from start: 0.1988 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.037 12379 Z= 0.191 Angle : 0.587 7.738 17860 Z= 0.350 Chirality : 0.034 0.130 2033 Planarity : 0.005 0.069 1328 Dihedral : 31.071 178.268 3527 Min Nonbonded Distance : 2.202 Molprobity Statistics. All-atom Clashscore : 6.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer Outliers : 2.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.26 (0.30), residues: 759 helix: 2.74 (0.21), residues: 533 sheet: None (None), residues: 0 loop : -1.76 (0.34), residues: 226 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1518 Ramachandran restraints generated. 759 Oldfield, 0 Emsley, 759 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1518 Ramachandran restraints generated. 759 Oldfield, 0 Emsley, 759 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 651 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 115 time to evaluate : 0.960 Fit side-chains outliers start: 14 outliers final: 11 residues processed: 127 average time/residue: 2.1543 time to fit residues: 286.9478 Evaluate side-chains 125 residues out of total 651 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 114 time to evaluate : 0.943 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 10 residues processed: 1 average time/residue: 1.6053 time to fit residues: 2.7777 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 29 optimal weight: 0.9980 chunk 18 optimal weight: 0.4980 chunk 61 optimal weight: 0.9990 chunk 65 optimal weight: 2.9990 chunk 47 optimal weight: 2.9990 chunk 8 optimal weight: 1.9990 chunk 75 optimal weight: 4.9990 chunk 87 optimal weight: 4.9990 chunk 92 optimal weight: 4.9990 chunk 84 optimal weight: 10.0000 chunk 89 optimal weight: 2.9990 overall best weight: 1.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4013 moved from start: 0.2227 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.036 12379 Z= 0.261 Angle : 0.623 7.990 17860 Z= 0.368 Chirality : 0.036 0.130 2033 Planarity : 0.005 0.045 1328 Dihedral : 31.167 177.913 3527 Min Nonbonded Distance : 2.165 Molprobity Statistics. All-atom Clashscore : 5.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Rotamer Outliers : 1.87 % 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: 2.09 (0.30), residues: 759 helix: 2.59 (0.21), residues: 533 sheet: None (None), residues: 0 loop : -1.77 (0.34), residues: 226 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1518 Ramachandran restraints generated. 759 Oldfield, 0 Emsley, 759 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1518 Ramachandran restraints generated. 759 Oldfield, 0 Emsley, 759 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 651 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 116 time to evaluate : 1.081 Fit side-chains outliers start: 12 outliers final: 11 residues processed: 126 average time/residue: 2.1046 time to fit residues: 278.0995 Evaluate side-chains 125 residues out of total 651 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 114 time to evaluate : 0.961 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 9 residues processed: 2 average time/residue: 1.8250 time to fit residues: 4.9973 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 92 optimal weight: 4.9990 chunk 54 optimal weight: 1.9990 chunk 39 optimal weight: 0.6980 chunk 70 optimal weight: 10.0000 chunk 27 optimal weight: 0.9990 chunk 81 optimal weight: 8.9990 chunk 84 optimal weight: 10.0000 chunk 89 optimal weight: 2.9990 chunk 58 optimal weight: 2.9990 chunk 94 optimal weight: 3.9990 chunk 57 optimal weight: 0.7980 overall best weight: 1.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4010 moved from start: 0.2232 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.036 12379 Z= 0.263 Angle : 0.626 9.362 17860 Z= 0.369 Chirality : 0.036 0.130 2033 Planarity : 0.005 0.044 1328 Dihedral : 31.163 177.728 3527 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 5.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer Outliers : 1.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.08 (0.29), residues: 759 helix: 2.58 (0.21), residues: 533 sheet: None (None), residues: 0 loop : -1.75 (0.34), residues: 226 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1518 Ramachandran restraints generated. 759 Oldfield, 0 Emsley, 759 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1518 Ramachandran restraints generated. 759 Oldfield, 0 Emsley, 759 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 651 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 117 time to evaluate : 0.960 Fit side-chains outliers start: 10 outliers final: 9 residues processed: 126 average time/residue: 2.1918 time to fit residues: 289.7462 Evaluate side-chains 125 residues out of total 651 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 116 time to evaluate : 0.973 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 9 residues processed: 0 time to fit residues: 1.2107 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 45 optimal weight: 2.9990 chunk 66 optimal weight: 2.9990 chunk 99 optimal weight: 0.7980 chunk 91 optimal weight: 4.9990 chunk 79 optimal weight: 5.9990 chunk 8 optimal weight: 0.9990 chunk 61 optimal weight: 0.9990 chunk 48 optimal weight: 0.8980 chunk 63 optimal weight: 1.9990 chunk 84 optimal weight: 10.0000 chunk 24 optimal weight: 0.8980 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4005 moved from start: 0.2220 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.037 12379 Z= 0.209 Angle : 0.616 11.625 17860 Z= 0.364 Chirality : 0.035 0.130 2033 Planarity : 0.004 0.046 1328 Dihedral : 31.167 177.790 3527 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 6.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer Outliers : 1.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.16 (0.30), residues: 759 helix: 2.64 (0.21), residues: 533 sheet: None (None), residues: 0 loop : -1.72 (0.34), residues: 226 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1518 Ramachandran restraints generated. 759 Oldfield, 0 Emsley, 759 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1518 Ramachandran restraints generated. 759 Oldfield, 0 Emsley, 759 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 651 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 116 time to evaluate : 1.093 Fit side-chains outliers start: 9 outliers final: 9 residues processed: 125 average time/residue: 2.0756 time to fit residues: 272.0888 Evaluate side-chains 123 residues out of total 651 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 114 time to evaluate : 0.889 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 9 residues processed: 0 time to fit residues: 1.0136 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 73 optimal weight: 5.9990 chunk 11 optimal weight: 2.9990 chunk 22 optimal weight: 2.9990 chunk 79 optimal weight: 5.9990 chunk 33 optimal weight: 2.9990 chunk 81 optimal weight: 8.9990 chunk 10 optimal weight: 2.9990 chunk 14 optimal weight: 4.9990 chunk 69 optimal weight: 3.9990 chunk 4 optimal weight: 1.9990 chunk 57 optimal weight: 0.7980 overall best weight: 2.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 38 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3968 r_free = 0.3968 target = 0.145972 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.096540 restraints weight = 15959.555| |-----------------------------------------------------------------------------| r_work (start): 0.3258 rms_B_bonded: 1.39 r_work: 0.3084 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work: 0.2963 rms_B_bonded: 4.85 restraints_weight: 0.2500 r_work (final): 0.2963 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8690 moved from start: 0.2553 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.042 12379 Z= 0.372 Angle : 0.693 11.386 17860 Z= 0.404 Chirality : 0.041 0.143 2033 Planarity : 0.005 0.048 1328 Dihedral : 31.361 177.515 3527 Min Nonbonded Distance : 2.131 Molprobity Statistics. All-atom Clashscore : 5.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer Outliers : 1.56 % 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: 1.78 (0.29), residues: 759 helix: 2.33 (0.21), residues: 533 sheet: None (None), residues: 0 loop : -1.79 (0.34), residues: 226 =============================================================================== Job complete usr+sys time: 4903.08 seconds wall clock time: 87 minutes 21.83 seconds (5241.83 seconds total)