Starting phenix.real_space_refine (version: dev) on Sat May 14 03:03:58 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nju_12423/05_2022/7nju_12423.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nju_12423/05_2022/7nju_12423.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.74 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nju_12423/05_2022/7nju_12423.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nju_12423/05_2022/7nju_12423.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nju_12423/05_2022/7nju_12423.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nju_12423/05_2022/7nju_12423.pdb" } resolution = 3.74 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.001 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 "S GLU 65": "OE1" <-> "OE2" Residue "S TYR 68": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "a TYR 145": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4597/modules/chem_data/mon_lib" Total number of atoms: 16438 Number of models: 1 Model: "" Number of chains: 12 Chain: "L" Number of atoms: 1192 Number of conformers: 1 Conformer: "" Number of residues, atoms: 84, 1192 Classifications: {'peptide': 84} Link IDs: {'PTRANS': 4, 'TRANS': 79} Chain: "M" Number of atoms: 1192 Number of conformers: 1 Conformer: "" Number of residues, atoms: 84, 1192 Classifications: {'peptide': 84} Link IDs: {'PTRANS': 4, 'TRANS': 79} Chain: "N" Number of atoms: 1192 Number of conformers: 1 Conformer: "" Number of residues, atoms: 84, 1192 Classifications: {'peptide': 84} Link IDs: {'PTRANS': 4, 'TRANS': 79} Chain: "O" Number of atoms: 1192 Number of conformers: 1 Conformer: "" Number of residues, atoms: 84, 1192 Classifications: {'peptide': 84} Link IDs: {'PTRANS': 4, 'TRANS': 79} Chain: "P" Number of atoms: 1192 Number of conformers: 1 Conformer: "" Number of residues, atoms: 84, 1192 Classifications: {'peptide': 84} Link IDs: {'PTRANS': 4, 'TRANS': 79} Chain: "Q" Number of atoms: 1192 Number of conformers: 1 Conformer: "" Number of residues, atoms: 84, 1192 Classifications: {'peptide': 84} Link IDs: {'PTRANS': 4, 'TRANS': 79} Chain: "R" Number of atoms: 1192 Number of conformers: 1 Conformer: "" Number of residues, atoms: 84, 1192 Classifications: {'peptide': 84} Link IDs: {'PTRANS': 4, 'TRANS': 79} Chain: "S" Number of atoms: 1192 Number of conformers: 1 Conformer: "" Number of residues, atoms: 84, 1192 Classifications: {'peptide': 84} Link IDs: {'PTRANS': 4, 'TRANS': 79} Chain: "T" Number of atoms: 1204 Number of conformers: 1 Conformer: "" Number of residues, atoms: 85, 1204 Classifications: {'peptide': 85} Link IDs: {'PTRANS': 4, 'TRANS': 80} Chain: "a" Number of atoms: 3767 Number of conformers: 1 Conformer: "" Number of residues, atoms: 238, 3767 Classifications: {'peptide': 238} Link IDs: {'PTRANS': 10, 'TRANS': 227} Chain: "b" Number of atoms: 979 Number of conformers: 1 Conformer: "" Number of residues, atoms: 63, 979 Classifications: {'peptide': 63} Link IDs: {'PTRANS': 3, 'TRANS': 59} Chain: "d" Number of atoms: 952 Number of conformers: 1 Conformer: "" Number of residues, atoms: 61, 952 Classifications: {'peptide': 61} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 2, 'TRANS': 58} Time building chain proxies: 8.09, per 1000 atoms: 0.49 Number of scatterers: 16438 At special positions: 0 Unit cell: (92.96, 78.02, 120.35, 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 28 16.00 O 1402 8.00 N 1317 7.00 C 5350 6.00 H 8341 1.00 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: 15.49 Conformation dependent library (CDL) restraints added in 1.6 seconds 2190 Ramachandran restraints generated. 1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1906 Finding SS restraints... Secondary structure from input PDB file: 32 helices and 2 sheets defined 87.5% alpha, 0.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.22 Creating SS restraints... Processing helix chain 'L' and resid 4 through 46 removed outlier: 3.574A pdb=" N ILE L 8 " --> pdb=" O ASP L 4 " (cutoff:3.500A) Processing helix chain 'L' and resid 49 through 81 removed outlier: 4.323A pdb=" N THR L 55 " --> pdb=" O GLY L 51 " (cutoff:3.500A) Proline residue: L 56 - end of helix removed outlier: 4.177A pdb=" N ALA L 67 " --> pdb=" O LEU L 63 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N TYR L 68 " --> pdb=" O VAL L 64 " (cutoff:3.500A) Processing helix chain 'M' and resid 4 through 46 removed outlier: 3.631A pdb=" N ILE M 8 " --> pdb=" O ASP M 4 " (cutoff:3.500A) Processing helix chain 'M' and resid 49 through 80 removed outlier: 3.669A pdb=" N PHE M 54 " --> pdb=" O GLN M 50 " (cutoff:3.500A) removed outlier: 4.689A pdb=" N THR M 55 " --> pdb=" O GLY M 51 " (cutoff:3.500A) Proline residue: M 56 - end of helix removed outlier: 3.568A pdb=" N ILE M 59 " --> pdb=" O THR M 55 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N TYR M 68 " --> pdb=" O VAL M 64 " (cutoff:3.500A) Processing helix chain 'N' and resid 4 through 46 removed outlier: 3.911A pdb=" N ILE N 8 " --> pdb=" O ASP N 4 " (cutoff:3.500A) Processing helix chain 'N' and resid 49 through 80 removed outlier: 3.903A pdb=" N PHE N 54 " --> pdb=" O GLN N 50 " (cutoff:3.500A) removed outlier: 4.476A pdb=" N THR N 55 " --> pdb=" O GLY N 51 " (cutoff:3.500A) Proline residue: N 56 - end of helix removed outlier: 3.637A pdb=" N ILE N 59 " --> pdb=" O THR N 55 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N LEU N 63 " --> pdb=" O ILE N 59 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N ALA N 67 " --> pdb=" O LEU N 63 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N TYR N 68 " --> pdb=" O VAL N 64 " (cutoff:3.500A) Processing helix chain 'O' and resid 4 through 46 removed outlier: 3.646A pdb=" N ILE O 8 " --> pdb=" O ASP O 4 " (cutoff:3.500A) Processing helix chain 'O' and resid 49 through 80 removed outlier: 4.555A pdb=" N THR O 55 " --> pdb=" O GLY O 51 " (cutoff:3.500A) Proline residue: O 56 - end of helix removed outlier: 3.530A pdb=" N ILE O 59 " --> pdb=" O THR O 55 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N ALA O 67 " --> pdb=" O LEU O 63 " (cutoff:3.500A) Processing helix chain 'P' and resid 4 through 46 removed outlier: 3.695A pdb=" N ILE P 8 " --> pdb=" O ASP P 4 " (cutoff:3.500A) Processing helix chain 'P' and resid 49 through 80 removed outlier: 3.802A pdb=" N PHE P 54 " --> pdb=" O GLN P 50 " (cutoff:3.500A) removed outlier: 4.448A pdb=" N THR P 55 " --> pdb=" O GLY P 51 " (cutoff:3.500A) Proline residue: P 56 - end of helix removed outlier: 3.555A pdb=" N LEU P 63 " --> pdb=" O ILE P 59 " (cutoff:3.500A) Processing helix chain 'Q' and resid 4 through 46 removed outlier: 3.640A pdb=" N ILE Q 8 " --> pdb=" O ASP Q 4 " (cutoff:3.500A) Processing helix chain 'Q' and resid 49 through 80 removed outlier: 3.865A pdb=" N THR Q 55 " --> pdb=" O GLY Q 51 " (cutoff:3.500A) Proline residue: Q 56 - end of helix removed outlier: 3.661A pdb=" N LEU Q 63 " --> pdb=" O ILE Q 59 " (cutoff:3.500A) Processing helix chain 'R' and resid 4 through 46 removed outlier: 3.785A pdb=" N ILE R 8 " --> pdb=" O ASP R 4 " (cutoff:3.500A) Processing helix chain 'R' and resid 49 through 80 removed outlier: 4.973A pdb=" N THR R 55 " --> pdb=" O GLY R 51 " (cutoff:3.500A) Proline residue: R 56 - end of helix removed outlier: 3.771A pdb=" N ILE R 59 " --> pdb=" O THR R 55 " (cutoff:3.500A) Processing helix chain 'S' and resid 4 through 46 Processing helix chain 'S' and resid 49 through 80 removed outlier: 4.699A pdb=" N THR S 55 " --> pdb=" O GLY S 51 " (cutoff:3.500A) Proline residue: S 56 - end of helix removed outlier: 3.629A pdb=" N ILE S 59 " --> pdb=" O THR S 55 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ALA S 66 " --> pdb=" O GLY S 62 " (cutoff:3.500A) removed outlier: 4.731A pdb=" N ALA S 67 " --> pdb=" O LEU S 63 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N ALA S 73 " --> pdb=" O PHE S 69 " (cutoff:3.500A) Processing helix chain 'T' and resid 4 through 46 removed outlier: 3.680A pdb=" N ILE T 8 " --> pdb=" O ASP T 4 " (cutoff:3.500A) Processing helix chain 'T' and resid 49 through 81 removed outlier: 3.880A pdb=" N THR T 55 " --> pdb=" O GLY T 51 " (cutoff:3.500A) Proline residue: T 56 - end of helix removed outlier: 3.602A pdb=" N ALA T 66 " --> pdb=" O GLY T 62 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N ALA T 67 " --> pdb=" O LEU T 63 " (cutoff:3.500A) Processing helix chain 'a' and resid 28 through 52 Processing helix chain 'a' and resid 60 through 81 Processing helix chain 'a' and resid 88 through 106 removed outlier: 3.770A pdb=" N LEU a 92 " --> pdb=" O PHE a 88 " (cutoff:3.500A) Processing helix chain 'a' and resid 107 through 109 No H-bonds generated for 'chain 'a' and resid 107 through 109' Processing helix chain 'a' and resid 126 through 129 Processing helix chain 'a' and resid 130 through 154 removed outlier: 3.804A pdb=" N VAL a 134 " --> pdb=" O ASP a 130 " (cutoff:3.500A) Processing helix chain 'a' and resid 156 through 165 removed outlier: 3.513A pdb=" N ILE a 160 " --> pdb=" O VAL a 156 " (cutoff:3.500A) Processing helix chain 'a' and resid 167 through 169 No H-bonds generated for 'chain 'a' and resid 167 through 169' Processing helix chain 'a' and resid 170 through 204 Proline residue: a 182 - end of helix removed outlier: 3.763A pdb=" N ARG a 188 " --> pdb=" O SER a 184 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N LEU a 189 " --> pdb=" O LEU a 185 " (cutoff:3.500A) removed outlier: 4.370A pdb=" N GLY a 196 " --> pdb=" O ASN a 192 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N ALA a 201 " --> pdb=" O GLY a 197 " (cutoff:3.500A) Processing helix chain 'a' and resid 207 through 245 removed outlier: 3.963A pdb=" N TRP a 212 " --> pdb=" O TRP a 208 " (cutoff:3.500A) removed outlier: 6.088A pdb=" N PHE a 213 " --> pdb=" O TYR a 209 " (cutoff:3.500A) Proline residue: a 214 - end of helix Processing helix chain 'b' and resid 29 through 48 removed outlier: 3.754A pdb=" N ALA b 33 " --> pdb=" O GLY b 29 " (cutoff:3.500A) Processing helix chain 'b' and resid 49 through 84 Processing helix chain 'd' and resid 2 through 22 Processing helix chain 'd' and resid 22 through 61 Processing sheet with id=AA1, first strand: chain 'a' and resid 20 through 22 Processing sheet with id=AA2, first strand: chain 'a' and resid 112 through 114 778 hydrogen bonds defined for protein. 2325 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 6.35 Time building geometry restraints manager: 15.77 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 8340 1.03 - 1.23: 8 1.23 - 1.42: 3356 1.42 - 1.62: 4847 1.62 - 1.81: 55 Bond restraints: 16606 Sorted by residual: bond pdb=" N ILE a 96 " pdb=" CA ILE a 96 " ideal model delta sigma weight residual 1.463 1.454 0.009 1.14e-02 7.69e+03 6.55e-01 bond pdb=" C THR a 220 " pdb=" O THR a 220 " ideal model delta sigma weight residual 1.236 1.245 -0.008 1.15e-02 7.56e+03 5.06e-01 bond pdb=" CG LEU L 19 " pdb=" CD1 LEU L 19 " ideal model delta sigma weight residual 1.521 1.498 0.023 3.30e-02 9.18e+02 4.99e-01 bond pdb=" CG LEU M 19 " pdb=" CD2 LEU M 19 " ideal model delta sigma weight residual 1.521 1.498 0.023 3.30e-02 9.18e+02 4.90e-01 bond pdb=" N PRO R 47 " pdb=" CA PRO R 47 " ideal model delta sigma weight residual 1.469 1.477 -0.009 1.28e-02 6.10e+03 4.72e-01 ... (remaining 16601 not shown) Histogram of bond angle deviations from ideal: 100.06 - 106.84: 259 106.84 - 113.62: 19743 113.62 - 120.40: 5864 120.40 - 127.18: 4198 127.18 - 133.96: 73 Bond angle restraints: 30137 Sorted by residual: angle pdb=" C CYS a 144 " pdb=" N TYR a 145 " pdb=" CA TYR a 145 " ideal model delta sigma weight residual 120.68 116.24 4.44 1.70e+00 3.46e-01 6.81e+00 angle pdb=" N TYR a 145 " pdb=" CA TYR a 145 " pdb=" CB TYR a 145 " ideal model delta sigma weight residual 110.30 113.78 -3.48 1.54e+00 4.22e-01 5.12e+00 angle pdb=" CA TYR a 145 " pdb=" CB TYR a 145 " pdb=" CG TYR a 145 " ideal model delta sigma weight residual 113.90 117.89 -3.99 1.80e+00 3.09e-01 4.91e+00 angle pdb=" N ILE a 96 " pdb=" CA ILE a 96 " pdb=" C ILE a 96 " ideal model delta sigma weight residual 110.23 107.93 2.30 1.04e+00 9.25e-01 4.89e+00 angle pdb=" CB MET N 21 " pdb=" CG MET N 21 " pdb=" SD MET N 21 " ideal model delta sigma weight residual 112.70 118.72 -6.02 3.00e+00 1.11e-01 4.03e+00 ... (remaining 30132 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.08: 5696 17.08 - 34.16: 610 34.16 - 51.24: 92 51.24 - 68.32: 11 68.32 - 85.40: 9 Dihedral angle restraints: 6418 sinusoidal: 2806 harmonic: 3612 Sorted by residual: dihedral pdb=" CA GLN R 46 " pdb=" C GLN R 46 " pdb=" N PRO R 47 " pdb=" CA PRO R 47 " ideal model delta harmonic sigma weight residual -180.00 -163.79 -16.21 0 5.00e+00 4.00e-02 1.05e+01 dihedral pdb=" CB GLU R 65 " pdb=" CG GLU R 65 " pdb=" CD GLU R 65 " pdb=" OE1 GLU R 65 " ideal model delta sinusoidal sigma weight residual 0.00 -85.40 85.40 1 3.00e+01 1.11e-03 9.81e+00 dihedral pdb=" CB MET a 25 " pdb=" CG MET a 25 " pdb=" SD MET a 25 " pdb=" CE MET a 25 " ideal model delta sinusoidal sigma weight residual 180.00 128.16 51.84 3 1.50e+01 4.44e-03 9.06e+00 ... (remaining 6415 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.029: 854 0.029 - 0.057: 248 0.057 - 0.086: 171 0.086 - 0.114: 45 0.114 - 0.143: 5 Chirality restraints: 1323 Sorted by residual: chirality pdb=" CA ILE b 26 " pdb=" N ILE b 26 " pdb=" C ILE b 26 " pdb=" CB ILE b 26 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.14 2.00e-01 2.50e+01 5.08e-01 chirality pdb=" CA PRO R 47 " pdb=" N PRO R 47 " pdb=" C PRO R 47 " pdb=" CB PRO R 47 " both_signs ideal model delta sigma weight residual False 2.72 2.59 0.13 2.00e-01 2.50e+01 4.20e-01 chirality pdb=" CA VAL a 58 " pdb=" N VAL a 58 " pdb=" C VAL a 58 " pdb=" CB VAL a 58 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 4.18e-01 ... (remaining 1320 not shown) Planarity restraints: 2498 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA PHE a 99 " 0.009 2.00e-02 2.50e+03 1.79e-02 3.19e+00 pdb=" C PHE a 99 " -0.031 2.00e-02 2.50e+03 pdb=" O PHE a 99 " 0.012 2.00e-02 2.50e+03 pdb=" N ILE a 100 " 0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PHE a 97 " 0.007 2.00e-02 2.50e+03 1.49e-02 2.22e+00 pdb=" C PHE a 97 " -0.026 2.00e-02 2.50e+03 pdb=" O PHE a 97 " 0.010 2.00e-02 2.50e+03 pdb=" N VAL a 98 " 0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLY a 191 " -0.007 2.00e-02 2.50e+03 1.41e-02 1.98e+00 pdb=" C GLY a 191 " 0.024 2.00e-02 2.50e+03 pdb=" O GLY a 191 " -0.009 2.00e-02 2.50e+03 pdb=" N ASN a 192 " -0.008 2.00e-02 2.50e+03 ... (remaining 2495 not shown) Histogram of nonbonded interaction distances: 1.64 - 2.23: 1638 2.23 - 2.83: 37492 2.83 - 3.42: 47377 3.42 - 4.01: 62369 4.01 - 4.60: 97235 Nonbonded interactions: 246111 Sorted by model distance: nonbonded pdb=" O PHE M 78 " pdb=" HG1 THR M 82 " model vdw 1.643 1.850 nonbonded pdb=" O PHE Q 78 " pdb=" HG1 THR Q 82 " model vdw 1.658 1.850 nonbonded pdb=" O PHE T 78 " pdb=" HG1 THR T 82 " model vdw 1.695 1.850 nonbonded pdb=" OD1 ASN a 132 " pdb=" H ASN b 28 " model vdw 1.695 1.850 nonbonded pdb=" O PHE S 78 " pdb=" HG1 THR S 82 " model vdw 1.700 1.850 ... (remaining 246106 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 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = (chain 'T' and ((resid 3 and (name N or name CA or name C or name O or name CB o \ r name CG or name CD1 or name CD2 or name HA or name HB2 or name HB3 or name HG \ or name HD11 or name HD12 or name HD13 or name HD21 or name HD22 or name HD23)) \ or resid 4 through 86)) } 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 S 28 5.16 5 C 5350 2.51 5 N 1317 2.21 5 O 1402 1.98 5 H 8341 0.53 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 group one per residue 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: 10.770 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 24.710 Check model and map are aligned: 0.250 Convert atoms to be neutral: 0.150 Process input model: 57.860 Find NCS groups from input model: 0.670 Set up NCS constraints: 0.080 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:2.990 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 97.490 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8295 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.023 8265 Z= 0.184 Angle : 0.468 6.173 11229 Z= 0.255 Chirality : 0.038 0.143 1323 Planarity : 0.004 0.031 1442 Dihedral : 14.405 85.401 2792 Min Nonbonded Distance : 2.064 Molprobity Statistics. All-atom Clashscore : 6.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.02 % Favored : 95.98 % 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: 2.44 (0.27), residues: 1095 helix: 1.71 (0.18), residues: 894 sheet: None (None), residues: 0 loop : 1.54 (0.52), residues: 201 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2190 Ramachandran restraints generated. 1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2190 Ramachandran restraints generated. 1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 68 residues out of total 773 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 68 time to evaluate : 1.366 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 68 average time/residue: 0.3670 time to fit residues: 37.2466 Evaluate side-chains 58 residues out of total 773 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 58 time to evaluate : 1.299 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.5099 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 90 optimal weight: 2.9990 chunk 81 optimal weight: 1.9990 chunk 45 optimal weight: 0.7980 chunk 27 optimal weight: 0.9980 chunk 54 optimal weight: 1.9990 chunk 43 optimal weight: 0.9980 chunk 83 optimal weight: 0.7980 chunk 32 optimal weight: 1.9990 chunk 50 optimal weight: 1.9990 chunk 62 optimal weight: 1.9990 chunk 97 optimal weight: 1.9990 overall best weight: 1.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** a 192 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8320 moved from start: 0.0749 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.034 8265 Z= 0.263 Angle : 0.517 5.463 11229 Z= 0.283 Chirality : 0.039 0.143 1323 Planarity : 0.004 0.038 1442 Dihedral : 3.478 14.513 1150 Min Nonbonded Distance : 2.072 Molprobity Statistics. All-atom Clashscore : 6.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Rotamer Outliers : 0.39 % 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: 3.51 (0.26), residues: 1095 helix: 2.49 (0.17), residues: 904 sheet: None (None), residues: 0 loop : 1.66 (0.53), residues: 191 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2190 Ramachandran restraints generated. 1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2190 Ramachandran restraints generated. 1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 59 residues out of total 773 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 56 time to evaluate : 1.449 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 3 outliers final: 2 residues processed: 58 average time/residue: 0.3617 time to fit residues: 31.5553 Evaluate side-chains 57 residues out of total 773 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 55 time to evaluate : 1.171 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.1703 time to fit residues: 1.9526 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 54 optimal weight: 1.9990 chunk 30 optimal weight: 1.9990 chunk 80 optimal weight: 0.9980 chunk 66 optimal weight: 0.7980 chunk 26 optimal weight: 1.9990 chunk 97 optimal weight: 0.3980 chunk 105 optimal weight: 1.9990 chunk 86 optimal weight: 0.7980 chunk 96 optimal weight: 1.9990 chunk 33 optimal weight: 1.9990 chunk 78 optimal weight: 0.7980 overall best weight: 0.7580 ------------------------------------------------------------------------------- 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: 0.8302 moved from start: 0.1025 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.029 8265 Z= 0.196 Angle : 0.479 5.198 11229 Z= 0.258 Chirality : 0.038 0.140 1323 Planarity : 0.004 0.040 1442 Dihedral : 3.474 12.931 1150 Min Nonbonded Distance : 2.143 Molprobity Statistics. All-atom Clashscore : 5.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer Outliers : 0.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 4.21 (0.26), residues: 1095 helix: 2.98 (0.17), residues: 906 sheet: None (None), residues: 0 loop : 1.81 (0.54), residues: 189 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2190 Ramachandran restraints generated. 1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2190 Ramachandran restraints generated. 1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 67 residues out of total 773 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 65 time to evaluate : 1.292 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 2 outliers final: 1 residues processed: 65 average time/residue: 0.3641 time to fit residues: 35.5436 Evaluate side-chains 57 residues out of total 773 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 56 time to evaluate : 1.341 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.2546 time to fit residues: 2.0312 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 96 optimal weight: 1.9990 chunk 73 optimal weight: 2.9990 chunk 50 optimal weight: 2.9990 chunk 10 optimal weight: 1.9990 chunk 46 optimal weight: 0.9990 chunk 65 optimal weight: 1.9990 chunk 97 optimal weight: 0.8980 chunk 103 optimal weight: 1.9990 chunk 51 optimal weight: 0.9990 chunk 92 optimal weight: 0.3980 chunk 27 optimal weight: 0.9980 overall best weight: 0.8584 ------------------------------------------------------------------------------- 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: 0.8304 moved from start: 0.1213 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.032 8265 Z= 0.218 Angle : 0.482 5.232 11229 Z= 0.260 Chirality : 0.038 0.138 1323 Planarity : 0.004 0.039 1442 Dihedral : 3.506 13.178 1150 Min Nonbonded Distance : 2.141 Molprobity Statistics. All-atom Clashscore : 6.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Rotamer Outliers : 0.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 4.30 (0.25), residues: 1095 helix: 3.08 (0.16), residues: 904 sheet: None (None), residues: 0 loop : 1.66 (0.53), residues: 191 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2190 Ramachandran restraints generated. 1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2190 Ramachandran restraints generated. 1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 60 residues out of total 773 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 58 time to evaluate : 1.361 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 2 outliers final: 2 residues processed: 59 average time/residue: 0.3668 time to fit residues: 32.5498 Evaluate side-chains 58 residues out of total 773 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 56 time to evaluate : 1.418 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.2135 time to fit residues: 2.2159 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 86 optimal weight: 1.9990 chunk 58 optimal weight: 2.9990 chunk 1 optimal weight: 2.9990 chunk 77 optimal weight: 1.9990 chunk 42 optimal weight: 2.9990 chunk 88 optimal weight: 0.9980 chunk 71 optimal weight: 1.9990 chunk 0 optimal weight: 1.9990 chunk 52 optimal weight: 0.9990 chunk 92 optimal weight: 1.9990 chunk 26 optimal weight: 2.9990 overall best weight: 1.5988 ------------------------------------------------------------------------------- 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: 0.8359 moved from start: 0.1516 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.043 8265 Z= 0.355 Angle : 0.541 5.415 11229 Z= 0.300 Chirality : 0.039 0.144 1323 Planarity : 0.004 0.037 1442 Dihedral : 3.692 13.275 1150 Min Nonbonded Distance : 2.135 Molprobity Statistics. All-atom Clashscore : 6.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer Outliers : 0.26 % 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: 3.76 (0.25), residues: 1095 helix: 2.71 (0.16), residues: 908 sheet: None (None), residues: 0 loop : 1.44 (0.53), residues: 187 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2190 Ramachandran restraints generated. 1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2190 Ramachandran restraints generated. 1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 58 residues out of total 773 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 56 time to evaluate : 1.329 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 2 outliers final: 2 residues processed: 57 average time/residue: 0.3893 time to fit residues: 33.3569 Evaluate side-chains 57 residues out of total 773 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 55 time to evaluate : 1.300 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.2332 time to fit residues: 2.3830 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 34 optimal weight: 0.9990 chunk 93 optimal weight: 1.9990 chunk 20 optimal weight: 1.9990 chunk 60 optimal weight: 0.8980 chunk 25 optimal weight: 1.9990 chunk 103 optimal weight: 0.5980 chunk 85 optimal weight: 1.9990 chunk 47 optimal weight: 0.1980 chunk 8 optimal weight: 2.9990 chunk 54 optimal weight: 1.9990 chunk 99 optimal weight: 1.9990 overall best weight: 0.9384 ------------------------------------------------------------------------------- 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: 0.8328 moved from start: 0.1527 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.033 8265 Z= 0.226 Angle : 0.486 5.162 11229 Z= 0.263 Chirality : 0.038 0.139 1323 Planarity : 0.004 0.035 1442 Dihedral : 3.611 12.997 1150 Min Nonbonded Distance : 2.168 Molprobity Statistics. All-atom Clashscore : 5.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer Outliers : 0.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 4.06 (0.25), residues: 1095 helix: 2.91 (0.16), residues: 908 sheet: None (None), residues: 0 loop : 1.59 (0.53), residues: 187 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2190 Ramachandran restraints generated. 1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2190 Ramachandran restraints generated. 1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 58 residues out of total 773 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 57 time to evaluate : 1.605 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 58 average time/residue: 0.3624 time to fit residues: 31.6922 Evaluate side-chains 57 residues out of total 773 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 57 time to evaluate : 1.305 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.5121 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 11 optimal weight: 1.9990 chunk 58 optimal weight: 2.9990 chunk 75 optimal weight: 1.9990 chunk 87 optimal weight: 0.1980 chunk 57 optimal weight: 1.9990 chunk 103 optimal weight: 0.1980 chunk 64 optimal weight: 1.9990 chunk 62 optimal weight: 0.9980 chunk 47 optimal weight: 0.4980 chunk 63 optimal weight: 0.5980 chunk 41 optimal weight: 1.9990 overall best weight: 0.4980 ------------------------------------------------------------------------------- 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: 0.8292 moved from start: 0.1558 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.034 8265 Z= 0.161 Angle : 0.460 5.078 11229 Z= 0.243 Chirality : 0.038 0.142 1323 Planarity : 0.003 0.031 1442 Dihedral : 3.483 12.614 1150 Min Nonbonded Distance : 2.107 Molprobity Statistics. All-atom Clashscore : 5.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Rotamer Outliers : 0.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 4.59 (0.25), residues: 1095 helix: 3.27 (0.17), residues: 906 sheet: None (None), residues: 0 loop : 1.82 (0.54), residues: 189 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2190 Ramachandran restraints generated. 1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2190 Ramachandran restraints generated. 1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 68 residues out of total 773 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 65 time to evaluate : 1.318 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 3 outliers final: 2 residues processed: 65 average time/residue: 0.3677 time to fit residues: 36.1518 Evaluate side-chains 64 residues out of total 773 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 62 time to evaluate : 1.565 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.2206 time to fit residues: 2.3542 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 61 optimal weight: 0.8980 chunk 31 optimal weight: 0.7980 chunk 20 optimal weight: 1.9990 chunk 19 optimal weight: 0.5980 chunk 65 optimal weight: 1.9990 chunk 70 optimal weight: 1.9990 chunk 50 optimal weight: 1.9990 chunk 9 optimal weight: 1.9990 chunk 81 optimal weight: 1.9990 chunk 93 optimal weight: 0.9990 chunk 98 optimal weight: 0.6980 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** a 192 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8307 moved from start: 0.1629 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.032 8265 Z= 0.204 Angle : 0.478 5.173 11229 Z= 0.255 Chirality : 0.038 0.139 1323 Planarity : 0.003 0.031 1442 Dihedral : 3.494 14.779 1150 Min Nonbonded Distance : 2.264 Molprobity Statistics. All-atom Clashscore : 6.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % Rotamer Outliers : 0.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 4.51 (0.25), residues: 1095 helix: 3.22 (0.16), residues: 906 sheet: None (None), residues: 0 loop : 1.75 (0.53), residues: 189 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2190 Ramachandran restraints generated. 1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2190 Ramachandran restraints generated. 1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 63 residues out of total 773 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 61 time to evaluate : 1.329 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 2 outliers final: 0 residues processed: 61 average time/residue: 0.3569 time to fit residues: 32.9582 Evaluate side-chains 61 residues out of total 773 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 61 time to evaluate : 1.213 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.3404 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 90 optimal weight: 1.9990 chunk 96 optimal weight: 0.3980 chunk 98 optimal weight: 0.0980 chunk 57 optimal weight: 2.9990 chunk 41 optimal weight: 1.9990 chunk 75 optimal weight: 1.9990 chunk 29 optimal weight: 0.3980 chunk 86 optimal weight: 2.9990 chunk 95 optimal weight: 0.8980 chunk 63 optimal weight: 0.6980 chunk 101 optimal weight: 2.9990 overall best weight: 0.4980 ------------------------------------------------------------------------------- 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: 0.8285 moved from start: 0.1678 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.027 8265 Z= 0.158 Angle : 0.463 5.548 11229 Z= 0.243 Chirality : 0.038 0.142 1323 Planarity : 0.003 0.032 1442 Dihedral : 3.426 14.706 1150 Min Nonbonded Distance : 2.274 Molprobity Statistics. All-atom Clashscore : 6.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.10 % Favored : 97.90 % Rotamer Outliers : 0.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 4.76 (0.25), residues: 1095 helix: 3.38 (0.16), residues: 906 sheet: None (None), residues: 0 loop : 1.88 (0.53), residues: 189 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2190 Ramachandran restraints generated. 1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2190 Ramachandran restraints generated. 1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 773 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 65 time to evaluate : 1.336 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 65 average time/residue: 0.3886 time to fit residues: 38.2285 Evaluate side-chains 59 residues out of total 773 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 59 time to evaluate : 1.327 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.5161 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 62 optimal weight: 0.8980 chunk 48 optimal weight: 1.9990 chunk 70 optimal weight: 1.9990 chunk 106 optimal weight: 1.9990 chunk 98 optimal weight: 0.2980 chunk 84 optimal weight: 0.6980 chunk 8 optimal weight: 1.9990 chunk 65 optimal weight: 1.9990 chunk 52 optimal weight: 0.6980 chunk 67 optimal weight: 0.8980 chunk 90 optimal weight: 0.3980 overall best weight: 0.5980 ------------------------------------------------------------------------------- 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: 0.8288 moved from start: 0.1732 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.029 8265 Z= 0.173 Angle : 0.472 6.057 11229 Z= 0.247 Chirality : 0.038 0.140 1323 Planarity : 0.003 0.033 1442 Dihedral : 3.407 14.692 1150 Min Nonbonded Distance : 2.088 Molprobity Statistics. All-atom Clashscore : 6.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % 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: 4.77 (0.25), residues: 1095 helix: 3.40 (0.16), residues: 906 sheet: None (None), residues: 0 loop : 1.85 (0.53), residues: 189 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2190 Ramachandran restraints generated. 1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2190 Ramachandran restraints generated. 1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 59 residues out of total 773 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 59 time to evaluate : 1.308 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 59 average time/residue: 0.3645 time to fit residues: 32.4990 Evaluate side-chains 58 residues out of total 773 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 58 time to evaluate : 1.364 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.4913 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 26 optimal weight: 1.9990 chunk 78 optimal weight: 0.9980 chunk 12 optimal weight: 0.4980 chunk 23 optimal weight: 0.8980 chunk 85 optimal weight: 0.9980 chunk 35 optimal weight: 0.9980 chunk 87 optimal weight: 0.7980 chunk 10 optimal weight: 1.9990 chunk 15 optimal weight: 0.5980 chunk 74 optimal weight: 2.9990 chunk 4 optimal weight: 0.0980 overall best weight: 0.5780 ------------------------------------------------------------------------------- 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 = 0.3551 r_free = 0.3551 target = 0.082029 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.074774 restraints weight = 75119.034| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.076895 restraints weight = 27819.961| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.078068 restraints weight = 13577.088| |-----------------------------------------------------------------------------| r_work (final): 0.3474 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8275 moved from start: 0.1778 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.029 8265 Z= 0.170 Angle : 0.469 5.876 11229 Z= 0.245 Chirality : 0.038 0.141 1323 Planarity : 0.003 0.034 1442 Dihedral : 3.381 14.660 1150 Min Nonbonded Distance : 2.105 Molprobity Statistics. All-atom Clashscore : 7.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % 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: 4.85 (0.25), residues: 1095 helix: 3.45 (0.16), residues: 906 sheet: None (None), residues: 0 loop : 1.88 (0.53), residues: 189 =============================================================================== Job complete usr+sys time: 3107.95 seconds wall clock time: 59 minutes 21.83 seconds (3561.83 seconds total)