Starting phenix.real_space_refine (version: dev) on Fri Sep 2 12:08:43 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7y7i_33666/09_2022/7y7i_33666.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7y7i_33666/09_2022/7y7i_33666.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.42 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7y7i_33666/09_2022/7y7i_33666.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7y7i_33666/09_2022/7y7i_33666.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7y7i_33666/09_2022/7y7i_33666.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7y7i_33666/09_2022/7y7i_33666.pdb" } resolution = 3.42 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= 0.010 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 "D GLU 71": "OE1" <-> "OE2" Residue "D TYR 83": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 59": "OE1" <-> "OE2" Residue "F ASP 68": "OD1" <-> "OD2" Residue "G GLU 42": "OE1" <-> "OE2" Residue "G GLU 57": "OE1" <-> "OE2" Residue "G GLU 92": "OE1" <-> "OE2" Residue "G GLU 93": "OE1" <-> "OE2" Residue "H TYR 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 522": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4709/modules/chem_data/mon_lib" Total number of atoms: 12445 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 845 Number of conformers: 1 Conformer: "" Number of residues, atoms: 102, 845 Classifications: {'peptide': 102} Link IDs: {'PTRANS': 3, 'TRANS': 98} Chain: "B" Number of atoms: 638 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 638 Classifications: {'peptide': 80} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 78} Chain: "C" Number of atoms: 826 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 826 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 5, 'TRANS': 101} Chain: "D" Number of atoms: 740 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 740 Classifications: {'peptide': 94} Link IDs: {'PTRANS': 2, 'TRANS': 91} Chain: "E" Number of atoms: 811 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 811 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 3, 'TRANS': 93} Chain: "F" Number of atoms: 619 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 619 Classifications: {'peptide': 78} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 76} Chain: "G" Number of atoms: 810 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 810 Classifications: {'peptide': 105} Link IDs: {'PTRANS': 5, 'TRANS': 99} Chain: "H" Number of atoms: 731 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 731 Classifications: {'peptide': 93} Link IDs: {'PTRANS': 2, 'TRANS': 90} Chain: "I" Number of atoms: 2915 Number of conformers: 1 Conformer: "" Number of residues, atoms: 143, 2915 Classifications: {'DNA': 143} Link IDs: {'rna3p': 142} Chain: "J" Number of atoms: 2948 Number of conformers: 1 Conformer: "" Number of residues, atoms: 143, 2948 Classifications: {'DNA': 143} Link IDs: {'rna3p': 142} Chain: "K" Number of atoms: 281 Number of conformers: 1 Conformer: "" Number of residues, atoms: 34, 281 Classifications: {'peptide': 34} Link IDs: {'PTRANS': 2, 'TRANS': 31} Chain: "L" Number of atoms: 281 Number of conformers: 1 Conformer: "" Number of residues, atoms: 34, 281 Classifications: {'peptide': 34} Link IDs: {'PTRANS': 2, 'TRANS': 31} Time building chain proxies: 7.10, per 1000 atoms: 0.57 Number of scatterers: 12445 At special positions: 0 Unit cell: (117.6, 111.72, 116.62, 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 286 15.00 O 2861 8.00 N 2341 7.00 C 6943 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: 6.45 Conformation dependent library (CDL) restraints added in 958.9 milliseconds 1608 Ramachandran restraints generated. 804 Oldfield, 0 Emsley, 804 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1528 Finding SS restraints... Secondary structure from input PDB file: 37 helices and 12 sheets defined 67.8% alpha, 3.6% beta 136 base pairs and 228 stacking pairs defined. Time for finding SS restraints: 5.31 Creating SS restraints... Processing helix chain 'A' and resid 44 through 55 removed outlier: 4.057A pdb=" N ARG A 49 " --> pdb=" O THR A 45 " (cutoff:3.500A) Processing helix chain 'A' and resid 63 through 80 Processing helix chain 'A' and resid 87 through 116 removed outlier: 3.684A pdb=" N LEU A 91 " --> pdb=" O GLN A 87 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N LEU A 92 " --> pdb=" O ALA A 88 " (cutoff:3.500A) Processing helix chain 'A' and resid 122 through 133 removed outlier: 3.629A pdb=" N LEU A 126 " --> pdb=" O TYR A 122 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N ARG A 133 " --> pdb=" O ALA A 129 " (cutoff:3.500A) Processing helix chain 'A' and resid 134 through 139 removed outlier: 3.901A pdb=" N GLY A 139 " --> pdb=" O LEU A 135 " (cutoff:3.500A) Processing helix chain 'B' and resid 24 through 29 removed outlier: 3.684A 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: 4.058A pdb=" N GLU B 53 " --> pdb=" O LEU B 49 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 94 removed outlier: 3.694A pdb=" N VAL B 86 " --> pdb=" O THR B 82 " (cutoff:3.500A) Processing helix chain 'C' and resid 17 through 23 Processing helix chain 'C' and resid 28 through 38 Processing helix chain 'C' and resid 47 through 74 Processing helix chain 'C' and resid 80 through 90 removed outlier: 3.607A pdb=" N ASN C 90 " --> pdb=" O LEU C 86 " (cutoff:3.500A) Processing helix chain 'C' and resid 91 through 98 removed outlier: 3.987A pdb=" N LYS C 96 " --> pdb=" O GLU C 92 " (cutoff:3.500A) Processing helix chain 'D' and resid 37 through 49 removed outlier: 3.707A pdb=" N GLN D 47 " --> pdb=" O LYS D 43 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N VAL D 48 " --> pdb=" O VAL D 44 " (cutoff:3.500A) Processing helix chain 'D' and resid 55 through 84 removed outlier: 3.558A pdb=" N MET D 59 " --> pdb=" O SER D 55 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N ASN D 84 " --> pdb=" O LEU D 80 " (cutoff:3.500A) Processing helix chain 'D' and resid 90 through 102 removed outlier: 3.553A pdb=" N ILE D 94 " --> pdb=" O THR D 90 " (cutoff:3.500A) Processing helix chain 'D' and resid 104 through 123 removed outlier: 3.691A pdb=" N SER D 123 " --> pdb=" O THR D 119 " (cutoff:3.500A) Processing helix chain 'E' and resid 44 through 57 removed outlier: 3.978A pdb=" N ARG E 49 " --> pdb=" O THR E 45 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N SER E 57 " --> pdb=" O ARG E 53 " (cutoff:3.500A) Processing helix chain 'E' and resid 63 through 80 removed outlier: 3.546A pdb=" N PHE E 67 " --> pdb=" O ARG E 63 " (cutoff:3.500A) Processing helix chain 'E' and resid 87 through 116 removed outlier: 3.694A pdb=" N LEU E 91 " --> pdb=" O GLN E 87 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N LEU E 92 " --> pdb=" O ALA E 88 " (cutoff:3.500A) Processing helix chain 'E' and resid 122 through 133 removed outlier: 3.794A pdb=" N LEU E 126 " --> pdb=" O TYR E 122 " (cutoff:3.500A) Processing helix chain 'F' and resid 25 through 29 removed outlier: 3.615A 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: 3.812A pdb=" N GLU F 53 " --> pdb=" O LEU F 49 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N ALA F 76 " --> pdb=" O TYR F 72 " (cutoff:3.500A) Processing helix chain 'F' and resid 82 through 94 removed outlier: 3.504A pdb=" N VAL F 86 " --> pdb=" O THR F 82 " (cutoff:3.500A) Processing helix chain 'G' and resid 17 through 22 removed outlier: 3.836A pdb=" N ALA G 22 " --> pdb=" O ARG G 18 " (cutoff:3.500A) Processing helix chain 'G' and resid 28 through 38 Processing helix chain 'G' and resid 46 through 74 removed outlier: 4.410A pdb=" N VAL G 50 " --> pdb=" O ALA G 46 " (cutoff:3.500A) Processing helix chain 'G' and resid 80 through 89 Processing helix chain 'G' and resid 91 through 98 removed outlier: 4.103A pdb=" N LEU G 97 " --> pdb=" O GLU G 93 " (cutoff:3.500A) Processing helix chain 'H' and resid 38 through 49 Processing helix chain 'H' and resid 55 through 84 removed outlier: 3.605A pdb=" N ASN H 84 " --> pdb=" O LEU H 80 " (cutoff:3.500A) Processing helix chain 'H' and resid 90 through 102 removed outlier: 3.793A pdb=" N ILE H 94 " --> pdb=" O THR H 90 " (cutoff:3.500A) Processing helix chain 'H' and resid 104 through 123 Processing helix chain 'K' and resid 534 through 538 Processing helix chain 'L' and resid 534 through 538 Processing sheet with id=AA1, first strand: chain 'A' and resid 85 through 86 removed outlier: 6.594A pdb=" N ARG 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 98 removed outlier: 6.559A pdb=" N THR B 96 " --> pdb=" O THR G 102 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'C' and resid 43 through 44 removed outlier: 7.636A pdb=" N ARG C 43 " --> 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 78 through 79 removed outlier: 3.560A pdb=" N ILE C 79 " --> pdb=" O GLY D 53 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'C' and resid 101 through 102 Processing sheet with id=AA7, first strand: chain 'E' and resid 85 through 86 removed outlier: 6.818A pdb=" N ARG 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 43 through 44 removed outlier: 7.584A pdb=" N ARG G 43 " --> 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 78 through 79 Processing sheet with id=AB2, first strand: chain 'K' and resid 541 through 543 Processing sheet with id=AB3, first strand: chain 'L' and resid 540 through 542 393 hydrogen bonds defined for protein. 1152 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 351 hydrogen bonds 702 hydrogen bond angles 0 basepair planarities 136 basepair parallelities 228 stacking parallelities Total time for adding SS restraints: 5.18 Time building geometry restraints manager: 6.83 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: 2513 1.33 - 1.45: 4151 1.45 - 1.57: 6002 1.57 - 1.69: 570 1.69 - 1.81: 22 Bond restraints: 13258 Sorted by residual: bond pdb=" CB MET H 59 " pdb=" CG MET H 59 " ideal model delta sigma weight residual 1.520 1.482 0.038 3.00e-02 1.11e+03 1.62e+00 bond pdb=" C3' DC J 192 " pdb=" O3' DC J 192 " ideal model delta sigma weight residual 1.422 1.460 -0.038 3.00e-02 1.11e+03 1.59e+00 bond pdb=" C3' DC J 178 " pdb=" O3' DC J 178 " ideal model delta sigma weight residual 1.422 1.459 -0.037 3.00e-02 1.11e+03 1.50e+00 bond pdb=" C1' DT I 103 " pdb=" N1 DT I 103 " ideal model delta sigma weight residual 1.490 1.525 -0.035 3.00e-02 1.11e+03 1.37e+00 bond pdb=" C3' DC J 242 " pdb=" C2' DC J 242 " ideal model delta sigma weight residual 1.525 1.546 -0.021 2.00e-02 2.50e+03 1.09e+00 ... (remaining 13253 not shown) Histogram of bond angle deviations from ideal: 96.94 - 104.34: 1086 104.34 - 111.75: 7152 111.75 - 119.15: 3913 119.15 - 126.56: 6121 126.56 - 133.96: 863 Bond angle restraints: 19135 Sorted by residual: angle pdb=" C3' DC J 190 " pdb=" C2' DC J 190 " pdb=" C1' DC J 190 " ideal model delta sigma weight residual 101.60 96.94 4.66 1.50e+00 4.44e-01 9.65e+00 angle pdb=" CB MET H 59 " pdb=" CG MET H 59 " pdb=" SD MET H 59 " ideal model delta sigma weight residual 112.70 104.82 7.88 3.00e+00 1.11e-01 6.90e+00 angle pdb=" C ASN G 111 " pdb=" CA ASN G 111 " pdb=" CB ASN G 111 " ideal model delta sigma weight residual 109.68 114.86 -5.18 1.98e+00 2.55e-01 6.84e+00 angle pdb=" C3' DC J 192 " pdb=" O3' DC J 192 " pdb=" P DC J 193 " ideal model delta sigma weight residual 120.20 123.84 -3.64 1.50e+00 4.44e-01 5.89e+00 angle pdb=" C4' DG I 66 " pdb=" C3' DG I 66 " pdb=" C2' DG I 66 " ideal model delta sigma weight residual 102.40 98.79 3.61 1.50e+00 4.44e-01 5.81e+00 ... (remaining 19130 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 25.68: 5013 25.68 - 51.37: 1455 51.37 - 77.05: 464 77.05 - 102.73: 26 102.73 - 128.41: 2 Dihedral angle restraints: 6960 sinusoidal: 4582 harmonic: 2378 Sorted by residual: dihedral pdb=" C4' DC J 178 " pdb=" C3' DC J 178 " pdb=" O3' DC J 178 " pdb=" P DT J 179 " ideal model delta sinusoidal sigma weight residual -140.00 -11.59 -128.41 1 3.50e+01 8.16e-04 1.27e+01 dihedral pdb=" C4' DC J 192 " pdb=" C3' DC J 192 " pdb=" O3' DC J 192 " pdb=" P DC J 193 " ideal model delta sinusoidal sigma weight residual -140.00 -13.98 -126.02 1 3.50e+01 8.16e-04 1.24e+01 dihedral pdb=" CA ARG E 80 " pdb=" C ARG E 80 " pdb=" N GLY E 81 " pdb=" CA GLY E 81 " ideal model delta harmonic sigma weight residual 180.00 163.25 16.75 0 5.00e+00 4.00e-02 1.12e+01 ... (remaining 6957 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.032: 1519 0.032 - 0.064: 478 0.064 - 0.095: 117 0.095 - 0.127: 46 0.127 - 0.159: 5 Chirality restraints: 2165 Sorted by residual: chirality pdb=" C3' DC J 191 " pdb=" C4' DC J 191 " pdb=" O3' DC J 191 " pdb=" C2' DC J 191 " both_signs ideal model delta sigma weight residual False -2.66 -2.82 0.16 2.00e-01 2.50e+01 6.32e-01 chirality pdb=" C3' DC J 190 " pdb=" C4' DC J 190 " pdb=" O3' DC J 190 " pdb=" C2' DC J 190 " both_signs ideal model delta sigma weight residual False -2.66 -2.82 0.16 2.00e-01 2.50e+01 6.24e-01 chirality pdb=" CA ILE G 112 " pdb=" N ILE G 112 " pdb=" C ILE G 112 " pdb=" CB ILE G 112 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.44e-01 ... (remaining 2162 not shown) Planarity restraints: 1429 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' DG J 162 " -0.016 2.00e-02 2.50e+03 1.52e-02 6.92e+00 pdb=" N9 DG J 162 " 0.022 2.00e-02 2.50e+03 pdb=" C8 DG J 162 " 0.001 2.00e-02 2.50e+03 pdb=" N7 DG J 162 " 0.004 2.00e-02 2.50e+03 pdb=" C5 DG J 162 " 0.000 2.00e-02 2.50e+03 pdb=" C6 DG J 162 " -0.013 2.00e-02 2.50e+03 pdb=" O6 DG J 162 " 0.004 2.00e-02 2.50e+03 pdb=" N1 DG J 162 " 0.001 2.00e-02 2.50e+03 pdb=" C2 DG J 162 " -0.034 2.00e-02 2.50e+03 pdb=" N2 DG J 162 " 0.026 2.00e-02 2.50e+03 pdb=" N3 DG J 162 " 0.001 2.00e-02 2.50e+03 pdb=" C4 DG J 162 " 0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LYS K 530 " -0.039 5.00e-02 4.00e+02 5.95e-02 5.67e+00 pdb=" N PRO K 531 " 0.103 5.00e-02 4.00e+02 pdb=" CA PRO K 531 " -0.031 5.00e-02 4.00e+02 pdb=" CD PRO K 531 " -0.033 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C1' DC I 63 " -0.006 2.00e-02 2.50e+03 1.30e-02 3.80e+00 pdb=" N1 DC I 63 " 0.008 2.00e-02 2.50e+03 pdb=" C2 DC I 63 " -0.031 2.00e-02 2.50e+03 pdb=" O2 DC I 63 " 0.021 2.00e-02 2.50e+03 pdb=" N3 DC I 63 " 0.001 2.00e-02 2.50e+03 pdb=" C4 DC I 63 " -0.003 2.00e-02 2.50e+03 pdb=" N4 DC I 63 " 0.001 2.00e-02 2.50e+03 pdb=" C5 DC I 63 " 0.004 2.00e-02 2.50e+03 pdb=" C6 DC I 63 " 0.004 2.00e-02 2.50e+03 ... (remaining 1426 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.77: 1936 2.77 - 3.30: 11063 3.30 - 3.83: 23605 3.83 - 4.37: 26505 4.37 - 4.90: 40152 Nonbonded interactions: 103261 Sorted by model distance: nonbonded pdb=" OG1 THR L 523 " pdb=" OG SER L 525 " model vdw 2.234 2.440 nonbonded pdb=" NH2 ARG A 40 " pdb=" O2 DT J 227 " model vdw 2.242 2.520 nonbonded pdb=" O TYR C 40 " pdb=" OG SER D 78 " model vdw 2.261 2.440 nonbonded pdb=" OH TYR C 40 " pdb=" OE1 GLU D 71 " model vdw 2.296 2.440 nonbonded pdb=" N2 DG I 127 " pdb=" N3 DC J 164 " model vdw 2.305 2.600 ... (remaining 103256 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 38 through 134) selection = chain 'E' } ncs_group { reference = (chain 'B' and resid 25 through 102) selection = chain 'F' } ncs_group { reference = (chain 'C' and resid 14 through 118) selection = chain 'G' } ncs_group { reference = (chain 'D' and resid 31 through 123) 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 286 5.49 5 S 14 5.16 5 C 6943 2.51 5 N 2341 2.21 5 O 2861 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: 0.490 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: 2.830 Check model and map are aligned: 0.200 Convert atoms to be neutral: 0.100 Process input model: 40.060 Find NCS groups from input model: 0.490 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Set scattering table: 0.010 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:2.730 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 46.980 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7705 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 0.038 13258 Z= 0.193 Angle : 0.571 7.878 19135 Z= 0.342 Chirality : 0.036 0.159 2165 Planarity : 0.004 0.060 1429 Dihedral : 28.775 128.413 5432 Min Nonbonded Distance : 2.234 Molprobity Statistics. All-atom Clashscore : 9.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Rotamer Outliers : 0.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.18 (0.30), residues: 804 helix: 2.59 (0.23), residues: 511 sheet: -2.85 (0.88), residues: 26 loop : -0.40 (0.38), residues: 267 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1608 Ramachandran restraints generated. 804 Oldfield, 0 Emsley, 804 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1608 Ramachandran restraints generated. 804 Oldfield, 0 Emsley, 804 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 687 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 159 time to evaluate : 1.024 Fit side-chains outliers start: 1 outliers final: 0 residues processed: 160 average time/residue: 0.4371 time to fit residues: 87.1418 Evaluate side-chains 92 residues out of total 687 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 92 time to evaluate : 0.994 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.1943 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 89 optimal weight: 5.9990 chunk 80 optimal weight: 10.0000 chunk 44 optimal weight: 3.9990 chunk 27 optimal weight: 0.9980 chunk 54 optimal weight: 2.9990 chunk 42 optimal weight: 3.9990 chunk 83 optimal weight: 7.9990 chunk 32 optimal weight: 2.9990 chunk 50 optimal weight: 2.9990 chunk 61 optimal weight: 0.5980 chunk 96 optimal weight: 10.0000 overall best weight: 2.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 25 ASN C 25 GLN ** L 548 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7878 moved from start: 0.2626 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.040 13258 Z= 0.241 Angle : 0.619 8.075 19135 Z= 0.366 Chirality : 0.039 0.159 2165 Planarity : 0.005 0.055 1429 Dihedral : 31.885 128.233 3804 Min Nonbonded Distance : 2.114 Molprobity Statistics. All-atom Clashscore : 8.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.24 % Favored : 97.76 % 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: 2.20 (0.30), residues: 804 helix: 2.46 (0.22), residues: 532 sheet: -2.42 (1.21), residues: 20 loop : -0.43 (0.37), residues: 252 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1608 Ramachandran restraints generated. 804 Oldfield, 0 Emsley, 804 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1608 Ramachandran restraints generated. 804 Oldfield, 0 Emsley, 804 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 687 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 95 time to evaluate : 0.978 Fit side-chains outliers start: 15 outliers final: 7 residues processed: 106 average time/residue: 0.3056 time to fit residues: 43.6464 Evaluate side-chains 89 residues out of total 687 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 82 time to evaluate : 1.114 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.1053 time to fit residues: 2.5061 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 53 optimal weight: 10.0000 chunk 29 optimal weight: 1.9990 chunk 80 optimal weight: 10.0000 chunk 65 optimal weight: 8.9990 chunk 26 optimal weight: 1.9990 chunk 96 optimal weight: 10.0000 chunk 104 optimal weight: 9.9990 chunk 85 optimal weight: 10.0000 chunk 95 optimal weight: 10.0000 chunk 32 optimal weight: 1.9990 chunk 77 optimal weight: 6.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- 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: 0.7998 moved from start: 0.4053 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.007 0.073 13258 Z= 0.396 Angle : 0.724 8.758 19135 Z= 0.427 Chirality : 0.045 0.233 2165 Planarity : 0.006 0.058 1429 Dihedral : 32.246 118.692 3804 Min Nonbonded Distance : 2.118 Molprobity Statistics. All-atom Clashscore : 9.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer Outliers : 2.77 % 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: 1.67 (0.29), residues: 804 helix: 2.13 (0.22), residues: 520 sheet: -2.40 (1.24), residues: 20 loop : -0.71 (0.35), residues: 264 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1608 Ramachandran restraints generated. 804 Oldfield, 0 Emsley, 804 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1608 Ramachandran restraints generated. 804 Oldfield, 0 Emsley, 804 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 687 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 89 time to evaluate : 1.006 Fit side-chains outliers start: 19 outliers final: 11 residues processed: 104 average time/residue: 0.3501 time to fit residues: 47.5936 Evaluate side-chains 94 residues out of total 687 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 83 time to evaluate : 0.967 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 0 residues processed: 11 average time/residue: 0.1338 time to fit residues: 3.6388 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 95 optimal weight: 10.0000 chunk 72 optimal weight: 10.0000 chunk 50 optimal weight: 0.5980 chunk 10 optimal weight: 0.9980 chunk 46 optimal weight: 8.9990 chunk 64 optimal weight: 2.9990 chunk 96 optimal weight: 10.0000 chunk 102 optimal weight: 10.0000 chunk 91 optimal weight: 10.0000 chunk 27 optimal weight: 7.9990 chunk 85 optimal weight: 10.0000 overall best weight: 4.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 25 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8003 moved from start: 0.4342 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.064 13258 Z= 0.374 Angle : 0.689 7.189 19135 Z= 0.410 Chirality : 0.044 0.215 2165 Planarity : 0.006 0.054 1429 Dihedral : 32.232 117.582 3804 Min Nonbonded Distance : 2.093 Molprobity Statistics. All-atom Clashscore : 8.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer Outliers : 2.04 % 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: 1.60 (0.29), residues: 804 helix: 2.07 (0.22), residues: 523 sheet: -2.60 (1.21), residues: 20 loop : -0.75 (0.36), residues: 261 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1608 Ramachandran restraints generated. 804 Oldfield, 0 Emsley, 804 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1608 Ramachandran restraints generated. 804 Oldfield, 0 Emsley, 804 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 687 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 83 time to evaluate : 0.930 Fit side-chains outliers start: 14 outliers final: 12 residues processed: 92 average time/residue: 0.3371 time to fit residues: 41.1330 Evaluate side-chains 93 residues out of total 687 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 81 time to evaluate : 0.955 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 0 residues processed: 12 average time/residue: 0.1098 time to fit residues: 3.5893 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 58 optimal weight: 4.9990 chunk 1 optimal weight: 3.9990 chunk 76 optimal weight: 10.0000 chunk 42 optimal weight: 0.9980 chunk 87 optimal weight: 6.9990 chunk 70 optimal weight: 0.8980 chunk 0 optimal weight: 8.9990 chunk 52 optimal weight: 4.9990 chunk 91 optimal weight: 10.0000 chunk 25 optimal weight: 4.9990 chunk 34 optimal weight: 0.9990 overall best weight: 2.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 25 GLN D 47 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7955 moved from start: 0.4338 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.046 13258 Z= 0.252 Angle : 0.603 6.691 19135 Z= 0.363 Chirality : 0.039 0.167 2165 Planarity : 0.004 0.050 1429 Dihedral : 31.953 121.775 3804 Min Nonbonded Distance : 2.098 Molprobity Statistics. All-atom Clashscore : 8.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Rotamer Outliers : 0.44 % 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: 1.98 (0.30), residues: 804 helix: 2.43 (0.22), residues: 522 sheet: -2.60 (1.21), residues: 20 loop : -0.70 (0.36), residues: 262 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1608 Ramachandran restraints generated. 804 Oldfield, 0 Emsley, 804 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1608 Ramachandran restraints generated. 804 Oldfield, 0 Emsley, 804 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 687 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 85 time to evaluate : 1.001 Fit side-chains outliers start: 3 outliers final: 2 residues processed: 85 average time/residue: 0.4024 time to fit residues: 44.4726 Evaluate side-chains 82 residues out of total 687 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 80 time to evaluate : 1.030 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.1089 time to fit residues: 1.7592 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 92 optimal weight: 10.0000 chunk 20 optimal weight: 0.9990 chunk 60 optimal weight: 0.6980 chunk 25 optimal weight: 0.8980 chunk 102 optimal weight: 0.9990 chunk 85 optimal weight: 10.0000 chunk 47 optimal weight: 7.9990 chunk 8 optimal weight: 4.9990 chunk 33 optimal weight: 5.9990 chunk 53 optimal weight: 9.9990 chunk 98 optimal weight: 10.0000 overall best weight: 1.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7942 moved from start: 0.4349 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.049 13258 Z= 0.211 Angle : 0.583 6.100 19135 Z= 0.353 Chirality : 0.038 0.167 2165 Planarity : 0.004 0.048 1429 Dihedral : 31.912 123.182 3804 Min Nonbonded Distance : 2.226 Molprobity Statistics. All-atom Clashscore : 8.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.24 % Favored : 97.76 % Rotamer Outliers : 0.44 % 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: 2.15 (0.30), residues: 804 helix: 2.57 (0.22), residues: 522 sheet: -2.55 (1.22), residues: 20 loop : -0.66 (0.36), residues: 262 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1608 Ramachandran restraints generated. 804 Oldfield, 0 Emsley, 804 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1608 Ramachandran restraints generated. 804 Oldfield, 0 Emsley, 804 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 687 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 79 time to evaluate : 1.305 Fit side-chains outliers start: 3 outliers final: 3 residues processed: 82 average time/residue: 0.3756 time to fit residues: 40.6076 Evaluate side-chains 79 residues out of total 687 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 76 time to evaluate : 0.972 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.1124 time to fit residues: 1.8750 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 11 optimal weight: 3.9990 chunk 58 optimal weight: 0.9990 chunk 74 optimal weight: 10.0000 chunk 86 optimal weight: 10.0000 chunk 57 optimal weight: 0.9990 chunk 102 optimal weight: 8.9990 chunk 63 optimal weight: 7.9990 chunk 62 optimal weight: 4.9990 chunk 47 optimal weight: 8.9990 chunk 40 optimal weight: 3.9990 chunk 61 optimal weight: 0.7980 overall best weight: 2.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 49 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7950 moved from start: 0.4442 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.050 13258 Z= 0.236 Angle : 0.589 6.000 19135 Z= 0.356 Chirality : 0.038 0.163 2165 Planarity : 0.004 0.046 1429 Dihedral : 31.857 125.243 3804 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 8.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % Rotamer Outliers : 1.02 % 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: 2.13 (0.30), residues: 804 helix: 2.54 (0.22), residues: 524 sheet: -2.56 (1.24), residues: 20 loop : -0.67 (0.36), residues: 260 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1608 Ramachandran restraints generated. 804 Oldfield, 0 Emsley, 804 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1608 Ramachandran restraints generated. 804 Oldfield, 0 Emsley, 804 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 687 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 76 time to evaluate : 1.174 Fit side-chains outliers start: 7 outliers final: 4 residues processed: 79 average time/residue: 0.4245 time to fit residues: 45.1875 Evaluate side-chains 79 residues out of total 687 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 75 time to evaluate : 0.998 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.1127 time to fit residues: 2.1505 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 30 optimal weight: 7.9990 chunk 20 optimal weight: 1.9990 chunk 19 optimal weight: 0.8980 chunk 64 optimal weight: 8.9990 chunk 69 optimal weight: 2.9990 chunk 50 optimal weight: 0.8980 chunk 9 optimal weight: 4.9990 chunk 80 optimal weight: 10.0000 chunk 92 optimal weight: 10.0000 chunk 97 optimal weight: 10.0000 chunk 89 optimal weight: 5.9990 overall best weight: 2.3586 ------------------------------------------------------------------------------- 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: 0.7952 moved from start: 0.4577 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.051 13258 Z= 0.245 Angle : 0.595 7.002 19135 Z= 0.358 Chirality : 0.039 0.161 2165 Planarity : 0.004 0.046 1429 Dihedral : 31.782 124.645 3804 Min Nonbonded Distance : 2.170 Molprobity Statistics. All-atom Clashscore : 8.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer Outliers : 0.29 % 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: 804 helix: 2.54 (0.22), residues: 523 sheet: -2.60 (1.19), residues: 20 loop : -0.70 (0.36), residues: 261 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1608 Ramachandran restraints generated. 804 Oldfield, 0 Emsley, 804 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1608 Ramachandran restraints generated. 804 Oldfield, 0 Emsley, 804 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 687 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 75 time to evaluate : 0.976 Fit side-chains outliers start: 2 outliers final: 0 residues processed: 77 average time/residue: 0.3675 time to fit residues: 37.3815 Evaluate side-chains 75 residues out of total 687 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 75 time to evaluate : 0.985 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.1436 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 95 optimal weight: 10.0000 chunk 97 optimal weight: 10.0000 chunk 57 optimal weight: 7.9990 chunk 41 optimal weight: 8.9990 chunk 74 optimal weight: 10.0000 chunk 29 optimal weight: 0.9990 chunk 86 optimal weight: 10.0000 chunk 90 optimal weight: 8.9990 chunk 94 optimal weight: 10.0000 chunk 62 optimal weight: 5.9990 chunk 100 optimal weight: 9.9990 overall best weight: 6.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 548 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8042 moved from start: 0.5063 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.009 0.096 13258 Z= 0.528 Angle : 0.794 7.579 19135 Z= 0.464 Chirality : 0.050 0.260 2165 Planarity : 0.007 0.054 1429 Dihedral : 32.423 119.254 3804 Min Nonbonded Distance : 1.999 Molprobity Statistics. All-atom Clashscore : 8.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer Outliers : 0.58 % 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: 1.14 (0.29), residues: 804 helix: 1.76 (0.22), residues: 524 sheet: -3.39 (1.07), residues: 24 loop : -0.92 (0.36), residues: 256 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1608 Ramachandran restraints generated. 804 Oldfield, 0 Emsley, 804 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1608 Ramachandran restraints generated. 804 Oldfield, 0 Emsley, 804 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 687 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 80 time to evaluate : 0.842 Fit side-chains outliers start: 4 outliers final: 4 residues processed: 81 average time/residue: 0.3678 time to fit residues: 39.1353 Evaluate side-chains 81 residues out of total 687 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 77 time to evaluate : 0.962 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.1087 time to fit residues: 2.0593 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 61 optimal weight: 0.9980 chunk 47 optimal weight: 3.9990 chunk 69 optimal weight: 3.9990 chunk 105 optimal weight: 6.9990 chunk 97 optimal weight: 10.0000 chunk 84 optimal weight: 7.9990 chunk 8 optimal weight: 1.9990 chunk 64 optimal weight: 0.8980 chunk 51 optimal weight: 6.9990 chunk 66 optimal weight: 0.8980 chunk 89 optimal weight: 4.9990 overall best weight: 1.7584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 47 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7950 moved from start: 0.4830 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.058 13258 Z= 0.216 Angle : 0.599 6.908 19135 Z= 0.362 Chirality : 0.039 0.169 2165 Planarity : 0.004 0.047 1429 Dihedral : 31.972 120.283 3804 Min Nonbonded Distance : 2.109 Molprobity Statistics. All-atom Clashscore : 9.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.24 % Favored : 97.76 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.91 (0.30), residues: 804 helix: 2.41 (0.22), residues: 522 sheet: -2.27 (1.21), residues: 20 loop : -0.87 (0.35), residues: 262 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1608 Ramachandran restraints generated. 804 Oldfield, 0 Emsley, 804 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1608 Ramachandran restraints generated. 804 Oldfield, 0 Emsley, 804 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 687 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 78 time to evaluate : 0.978 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 78 average time/residue: 0.3537 time to fit residues: 36.5548 Evaluate side-chains 73 residues out of total 687 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 73 time to evaluate : 0.987 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.2225 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 25 optimal weight: 0.8980 chunk 77 optimal weight: 5.9990 chunk 12 optimal weight: 0.2980 chunk 23 optimal weight: 1.9990 chunk 84 optimal weight: 10.0000 chunk 35 optimal weight: 1.9990 chunk 86 optimal weight: 10.0000 chunk 10 optimal weight: 0.8980 chunk 15 optimal weight: 0.5980 chunk 73 optimal weight: 10.0000 chunk 4 optimal weight: 8.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3954 r_free = 0.3954 target = 0.178289 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3586 r_free = 0.3586 target = 0.146005 restraints weight = 15137.985| |-----------------------------------------------------------------------------| r_work (start): 0.3512 rms_B_bonded: 0.70 r_work: 0.3446 rms_B_bonded: 1.68 restraints_weight: 0.5000 r_work: 0.3303 rms_B_bonded: 4.74 restraints_weight: 0.2500 r_work (final): 0.3303 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7992 moved from start: 0.4819 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.057 13258 Z= 0.184 Angle : 0.585 7.163 19135 Z= 0.355 Chirality : 0.038 0.171 2165 Planarity : 0.004 0.047 1429 Dihedral : 31.937 121.146 3804 Min Nonbonded Distance : 2.184 Molprobity Statistics. All-atom Clashscore : 9.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.24 % Favored : 97.76 % Rotamer Outliers : 0.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.25 (0.30), residues: 804 helix: 2.70 (0.22), residues: 522 sheet: -2.09 (1.22), residues: 20 loop : -0.80 (0.35), residues: 262 =============================================================================== Job complete usr+sys time: 1630.39 seconds wall clock time: 31 minutes 13.53 seconds (1873.53 seconds total)