Starting phenix.real_space_refine (version: dev) on Tue Nov 29 13:05:47 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7soa_25264/11_2022/7soa_25264.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7soa_25264/11_2022/7soa_25264.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7soa_25264/11_2022/7soa_25264.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7soa_25264/11_2022/7soa_25264.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7soa_25264/11_2022/7soa_25264.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7soa_25264/11_2022/7soa_25264.pdb" } resolution = 3.1 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= -0.002 sd= 0.112 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 "L TYR 87": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 106": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ARG 87": "NH1" <-> "NH2" Residue "H TYR 95": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 28": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 235": "NH1" <-> "NH2" Residue "A TYR 264": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4778/modules/chem_data/mon_lib" Total number of atoms: 3850 Number of models: 1 Model: "" Number of chains: 5 Chain: "L" Number of atoms: 832 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 832 Classifications: {'peptide': 107} Link IDs: {'PCIS': 2, 'PTRANS': 5, 'TRANS': 99} Chain: "H" Number of atoms: 940 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 940 Classifications: {'peptide': 121} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 2, 'TRANS': 118} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "A" Number of atoms: 1994 Number of conformers: 1 Conformer: "" Number of residues, atoms: 249, 1994 Classifications: {'peptide': 249} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 14, 'TRANS': 234} Chain breaks: 5 Unresolved non-hydrogen bonds: 35 Unresolved non-hydrogen angles: 44 Unresolved non-hydrogen dihedrals: 31 Planarities with less than four sites: {'GLN:plan1': 2, 'TYR:plan': 1, 'ARG:plan': 2, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 31 Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen chiralities: 4 Time building chain proxies: 2.74, per 1000 atoms: 0.71 Number of scatterers: 3850 At special positions: 0 Unit cell: (63.225, 85.143, 76.713, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 15 16.00 O 739 8.00 N 620 7.00 C 2476 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=5, symmetry=0 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.03 Simple disulfide: pdb=" SG CYS A 15 " - pdb=" SG CYS A 136 " distance=2.03 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 164 " distance=2.03 Simple disulfide: pdb=" SG CYS A 289 " - pdb=" SG CYS A 299 " distance=2.03 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 Links applied BETA1-4 " NAG B 1 " - " NAG B 2 " NAG-ASN " NAG A1301 " - " ASN A 61 " " NAG A1302 " - " ASN A 280 " " NAG A1303 " - " ASN A 163 " " NAG A1304 " - " ASN A 232 " " NAG B 1 " - " ASN A 122 " Time building additional restraints: 1.47 Conformation dependent library (CDL) restraints added in 672.8 milliseconds 922 Ramachandran restraints generated. 461 Oldfield, 0 Emsley, 461 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 888 Finding SS restraints... Secondary structure from input PDB file: 3 helices and 10 sheets defined 4.2% alpha, 55.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.31 Creating SS restraints... Processing helix chain 'H' and resid 28 through 32 Processing helix chain 'H' and resid 87 through 91 Processing helix chain 'A' and resid 292 through 301 Processing sheet with id=AA1, first strand: chain 'L' and resid 4 through 7 removed outlier: 3.970A pdb=" N ASP L 70 " --> pdb=" O SER L 67 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N SER L 67 " --> pdb=" O ASP L 70 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'L' and resid 10 through 13 removed outlier: 6.557A pdb=" N LEU L 11 " --> pdb=" O ASP L 105 " (cutoff:3.500A) removed outlier: 6.353A pdb=" N GLN L 37 " --> pdb=" O LEU L 46 " (cutoff:3.500A) removed outlier: 5.588A pdb=" N LEU L 46 " --> pdb=" O GLN L 37 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'L' and resid 10 through 13 removed outlier: 6.557A pdb=" N LEU L 11 " --> pdb=" O ASP L 105 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N THR L 97 " --> pdb=" O GLN L 90 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'H' and resid 3 through 7 Processing sheet with id=AA5, first strand: chain 'H' and resid 11 through 12 removed outlier: 6.681A pdb=" N MET H 34 " --> pdb=" O PHE H 50 " (cutoff:3.500A) removed outlier: 4.451A pdb=" N PHE H 50 " --> pdb=" O MET H 34 " (cutoff:3.500A) removed outlier: 6.552A pdb=" N TRP H 36 " --> pdb=" O VAL H 48 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'H' and resid 11 through 12 Processing sheet with id=AA7, first strand: chain 'A' and resid 27 through 31 removed outlier: 3.826A pdb=" N SER A 60 " --> pdb=" O SER A 31 " (cutoff:3.500A) removed outlier: 8.688A pdb=" N ASN A 61 " --> pdb=" O TYR A 267 " (cutoff:3.500A) removed outlier: 6.515A pdb=" N TYR A 267 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 6.152A pdb=" N ALA A 262 " --> pdb=" O THR A 95 " (cutoff:3.500A) removed outlier: 4.840A pdb=" N THR A 95 " --> pdb=" O ALA A 262 " (cutoff:3.500A) removed outlier: 6.490A pdb=" N PHE A 199 " --> pdb=" O ASP A 226 " (cutoff:3.500A) removed outlier: 4.809A pdb=" N ASP A 226 " --> pdb=" O PHE A 199 " (cutoff:3.500A) removed outlier: 6.924A pdb=" N ILE A 201 " --> pdb=" O LEU A 224 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 47 through 55 removed outlier: 7.386A pdb=" N THR A 272 " --> pdb=" O ASP A 288 " (cutoff:3.500A) removed outlier: 4.983A pdb=" N ASP A 288 " --> pdb=" O THR A 272 " (cutoff:3.500A) removed outlier: 6.347A pdb=" N LEU A 274 " --> pdb=" O ALA A 286 " (cutoff:3.500A) removed outlier: 4.279A pdb=" N ALA A 286 " --> pdb=" O LEU A 274 " (cutoff:3.500A) removed outlier: 6.940A pdb=" N LYS A 276 " --> pdb=" O THR A 284 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 84 through 85 removed outlier: 6.990A pdb=" N ARG A 235 " --> pdb=" O PHE A 106 " (cutoff:3.500A) removed outlier: 4.683A pdb=" N PHE A 106 " --> pdb=" O ARG A 235 " (cutoff:3.500A) removed outlier: 6.517A pdb=" N GLN A 237 " --> pdb=" O TRP A 104 " (cutoff:3.500A) removed outlier: 4.580A pdb=" N TRP A 104 " --> pdb=" O GLN A 237 " (cutoff:3.500A) removed outlier: 6.799A pdb=" N LEU A 239 " --> pdb=" O ARG A 102 " (cutoff:3.500A) removed outlier: 6.212A pdb=" N ARG A 102 " --> pdb=" O ASN A 121 " (cutoff:3.500A) removed outlier: 6.728A pdb=" N VAL A 126 " --> pdb=" O TYR A 168 " (cutoff:3.500A) removed outlier: 6.745A pdb=" N TYR A 168 " --> pdb=" O VAL A 126 " (cutoff:3.500A) removed outlier: 6.857A pdb=" N ILE A 128 " --> pdb=" O PHE A 166 " (cutoff:3.500A) removed outlier: 6.708A pdb=" N PHE A 166 " --> pdb=" O ILE A 128 " (cutoff:3.500A) removed outlier: 7.202A pdb=" N VAL A 130 " --> pdb=" O CYS A 164 " (cutoff:3.500A) removed outlier: 4.538A pdb=" N CYS A 164 " --> pdb=" O VAL A 130 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N SER A 160 " --> pdb=" O GLN A 134 " (cutoff:3.500A) removed outlier: 5.830A pdb=" N CYS A 136 " --> pdb=" O TYR A 158 " (cutoff:3.500A) removed outlier: 6.694A pdb=" N TYR A 158 " --> pdb=" O CYS A 136 " (cutoff:3.500A) removed outlier: 6.045A pdb=" N ASP A 138 " --> pdb=" O GLY A 156 " (cutoff:3.500A) removed outlier: 7.528A pdb=" N GLY A 156 " --> pdb=" O ASP A 138 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 84 through 85 removed outlier: 13.614A pdb=" N PHE A 236 " --> pdb=" O PHE A 135 " (cutoff:3.500A) removed outlier: 13.010A pdb=" N ASN A 137 " --> pdb=" O PHE A 236 " (cutoff:3.500A) removed outlier: 10.215A pdb=" N THR A 238 " --> pdb=" O ASN A 137 " (cutoff:3.500A) removed outlier: 4.936A pdb=" N LEU A 240 " --> pdb=" O PRO A 139 " (cutoff:3.500A) removed outlier: 6.728A pdb=" N VAL A 126 " --> pdb=" O TYR A 168 " (cutoff:3.500A) removed outlier: 6.745A pdb=" N TYR A 168 " --> pdb=" O VAL A 126 " (cutoff:3.500A) removed outlier: 6.857A pdb=" N ILE A 128 " --> pdb=" O PHE A 166 " (cutoff:3.500A) removed outlier: 6.708A pdb=" N PHE A 166 " --> pdb=" O ILE A 128 " (cutoff:3.500A) removed outlier: 7.202A pdb=" N VAL A 130 " --> pdb=" O CYS A 164 " (cutoff:3.500A) removed outlier: 4.538A pdb=" N CYS A 164 " --> pdb=" O VAL A 130 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N SER A 160 " --> pdb=" O GLN A 134 " (cutoff:3.500A) removed outlier: 5.830A pdb=" N CYS A 136 " --> pdb=" O TYR A 158 " (cutoff:3.500A) removed outlier: 6.694A pdb=" N TYR A 158 " --> pdb=" O CYS A 136 " (cutoff:3.500A) removed outlier: 6.045A pdb=" N ASP A 138 " --> pdb=" O GLY A 156 " (cutoff:3.500A) removed outlier: 7.528A pdb=" N GLY A 156 " --> pdb=" O ASP A 138 " (cutoff:3.500A) 151 hydrogen bonds defined for protein. 369 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.12 Time building geometry restraints manager: 1.59 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 722 1.33 - 1.45: 1076 1.45 - 1.57: 2128 1.57 - 1.70: 2 1.70 - 1.82: 20 Bond restraints: 3948 Sorted by residual: bond pdb=" CA SER A 31 " pdb=" CB SER A 31 " ideal model delta sigma weight residual 1.524 1.469 0.055 1.30e-02 5.92e+03 1.79e+01 bond pdb=" CA SER A 155 " pdb=" CB SER A 155 " ideal model delta sigma weight residual 1.529 1.475 0.054 1.55e-02 4.16e+03 1.22e+01 bond pdb=" C5 NAG A1301 " pdb=" O5 NAG A1301 " ideal model delta sigma weight residual 1.435 1.472 -0.037 1.10e-02 8.26e+03 1.12e+01 bond pdb=" C5 NAG B 1 " pdb=" O5 NAG B 1 " ideal model delta sigma weight residual 1.435 1.471 -0.036 1.10e-02 8.26e+03 1.06e+01 bond pdb=" CB LEU A 242 " pdb=" CG LEU A 242 " ideal model delta sigma weight residual 1.530 1.592 -0.062 2.00e-02 2.50e+03 9.67e+00 ... (remaining 3943 not shown) Histogram of bond angle deviations from ideal: 100.58 - 107.28: 140 107.28 - 113.98: 2096 113.98 - 120.67: 1697 120.67 - 127.37: 1401 127.37 - 134.07: 30 Bond angle restraints: 5364 Sorted by residual: angle pdb=" C LEU A 24 " pdb=" N PRO A 25 " pdb=" CA PRO A 25 " ideal model delta sigma weight residual 119.66 126.12 -6.46 7.20e-01 1.93e+00 8.05e+01 angle pdb=" C ASN A 81 " pdb=" N PRO A 82 " pdb=" CA PRO A 82 " ideal model delta sigma weight residual 120.03 127.67 -7.64 9.90e-01 1.02e+00 5.96e+01 angle pdb=" C LEU A 214 " pdb=" N PRO A 215 " pdb=" CA PRO A 215 " ideal model delta sigma weight residual 120.03 127.11 -7.08 9.90e-01 1.02e+00 5.11e+01 angle pdb=" C PRO A 25 " pdb=" N PRO A 26 " pdb=" CA PRO A 26 " ideal model delta sigma weight residual 119.85 127.00 -7.15 1.01e+00 9.80e-01 5.01e+01 angle pdb=" C ALA L 43 " pdb=" N PRO L 44 " pdb=" CA PRO L 44 " ideal model delta sigma weight residual 119.76 126.92 -7.16 1.03e+00 9.43e-01 4.83e+01 ... (remaining 5359 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.19: 2197 17.19 - 34.39: 73 34.39 - 51.58: 15 51.58 - 68.77: 7 68.77 - 85.96: 2 Dihedral angle restraints: 2294 sinusoidal: 908 harmonic: 1386 Sorted by residual: dihedral pdb=" CB CYS H 22 " pdb=" SG CYS H 22 " pdb=" SG CYS H 96 " pdb=" CB CYS H 96 " ideal model delta sinusoidal sigma weight residual 93.00 47.58 45.42 1 1.00e+01 1.00e-02 2.86e+01 dihedral pdb=" C LYS A 185 " pdb=" N LYS A 185 " pdb=" CA LYS A 185 " pdb=" CB LYS A 185 " ideal model delta harmonic sigma weight residual -122.60 -114.27 -8.33 0 2.50e+00 1.60e-01 1.11e+01 dihedral pdb=" CB GLU A 189 " pdb=" CG GLU A 189 " pdb=" CD GLU A 189 " pdb=" OE1 GLU A 189 " ideal model delta sinusoidal sigma weight residual 0.00 85.96 -85.96 1 3.00e+01 1.11e-03 9.92e+00 ... (remaining 2291 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.095: 485 0.095 - 0.190: 98 0.190 - 0.285: 12 0.285 - 0.380: 8 0.380 - 0.475: 1 Chirality restraints: 604 Sorted by residual: chirality pdb=" C1 NAG B 2 " pdb=" O4 NAG B 1 " pdb=" C2 NAG B 2 " pdb=" O5 NAG B 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.51 0.11 2.00e-02 2.50e+03 2.93e+01 chirality pdb=" C1 NAG A1304 " pdb=" ND2 ASN A 232 " pdb=" C2 NAG A1304 " pdb=" O5 NAG A1304 " both_signs ideal model delta sigma weight residual False -2.40 -1.92 -0.48 2.00e-01 2.50e+01 5.65e+00 chirality pdb=" CA LYS A 185 " pdb=" N LYS A 185 " pdb=" C LYS A 185 " pdb=" CB LYS A 185 " both_signs ideal model delta sigma weight residual False 2.51 2.86 -0.35 2.00e-01 2.50e+01 3.02e+00 ... (remaining 601 not shown) Planarity restraints: 680 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG A1304 " -0.242 2.00e-02 2.50e+03 2.08e-01 5.42e+02 pdb=" C7 NAG A1304 " 0.052 2.00e-02 2.50e+03 pdb=" C8 NAG A1304 " 0.025 2.00e-02 2.50e+03 pdb=" N2 NAG A1304 " 0.348 2.00e-02 2.50e+03 pdb=" O7 NAG A1304 " -0.184 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ARG A 34 " 0.013 2.00e-02 2.50e+03 2.72e-02 7.40e+00 pdb=" C ARG A 34 " -0.047 2.00e-02 2.50e+03 pdb=" O ARG A 34 " 0.017 2.00e-02 2.50e+03 pdb=" N GLY A 35 " 0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR H 104 " -0.031 2.00e-02 2.50e+03 1.70e-02 5.79e+00 pdb=" CG TYR H 104 " 0.011 2.00e-02 2.50e+03 pdb=" CD1 TYR H 104 " 0.012 2.00e-02 2.50e+03 pdb=" CD2 TYR H 104 " 0.014 2.00e-02 2.50e+03 pdb=" CE1 TYR H 104 " 0.010 2.00e-02 2.50e+03 pdb=" CE2 TYR H 104 " 0.009 2.00e-02 2.50e+03 pdb=" CZ TYR H 104 " 0.001 2.00e-02 2.50e+03 pdb=" OH TYR H 104 " -0.026 2.00e-02 2.50e+03 ... (remaining 677 not shown) Histogram of nonbonded interaction distances: 2.19 - 2.73: 205 2.73 - 3.28: 3456 3.28 - 3.82: 6166 3.82 - 4.36: 8061 4.36 - 4.90: 13416 Nonbonded interactions: 31304 Sorted by model distance: nonbonded pdb=" O SER A 31 " pdb=" OG SER A 31 " model vdw 2.194 2.440 nonbonded pdb=" N THR A 29 " pdb=" O THR A 29 " model vdw 2.551 2.496 nonbonded pdb=" N SER A 151 " pdb=" O SER A 151 " model vdw 2.556 2.496 nonbonded pdb=" N GLY A 156 " pdb=" N VAL A 157 " model vdw 2.588 2.560 nonbonded pdb=" O ASP L 92 " pdb=" NH1 ARG H 103 " model vdw 2.595 2.520 ... (remaining 31299 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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: 4 Type Number sf(0) Gaussians S 15 5.16 5 C 2476 2.51 5 N 620 2.21 5 O 739 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: 6.080 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: 26.380 Check model and map are aligned: 0.060 Convert atoms to be neutral: 0.060 Process input model: 18.120 Find NCS groups from input model: 0.100 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Set scattering table: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.770 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 53.600 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8367 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 : 0.010 0.062 3948 Z= 0.671 Angle : 1.258 11.028 5364 Z= 0.886 Chirality : 0.083 0.475 604 Planarity : 0.010 0.208 675 Dihedral : 10.279 85.964 1391 Min Nonbonded Distance : 2.194 Molprobity Statistics. All-atom Clashscore : 1.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer Outliers : 0.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.99 (0.37), residues: 461 helix: 0.55 (1.59), residues: 11 sheet: 1.38 (0.37), residues: 184 loop : 0.20 (0.35), residues: 266 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 922 Ramachandran restraints generated. 461 Oldfield, 0 Emsley, 461 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 922 Ramachandran restraints generated. 461 Oldfield, 0 Emsley, 461 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 420 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 83 time to evaluate : 0.439 Fit side-chains outliers start: 1 outliers final: 0 residues processed: 84 average time/residue: 0.1780 time to fit residues: 18.0984 Evaluate side-chains 56 residues out of total 420 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 56 time to evaluate : 0.403 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.5702 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 46 random chunks: chunk 38 optimal weight: 0.6980 chunk 34 optimal weight: 0.7980 chunk 19 optimal weight: 0.8980 chunk 11 optimal weight: 4.9990 chunk 23 optimal weight: 0.6980 chunk 18 optimal weight: 0.5980 chunk 36 optimal weight: 0.9990 chunk 13 optimal weight: 0.5980 chunk 21 optimal weight: 0.9980 chunk 26 optimal weight: 0.4980 chunk 41 optimal weight: 0.6980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 194 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8632 moved from start: 0.2242 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.104 3948 Z= 0.280 Angle : 0.588 5.217 5364 Z= 0.317 Chirality : 0.047 0.148 604 Planarity : 0.005 0.046 675 Dihedral : 4.868 15.379 551 Min Nonbonded Distance : 2.243 Molprobity Statistics. All-atom Clashscore : 3.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer Outliers : 2.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % 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 (0.38), residues: 461 helix: 2.71 (1.59), residues: 11 sheet: 1.42 (0.36), residues: 193 loop : 0.20 (0.38), residues: 257 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 922 Ramachandran restraints generated. 461 Oldfield, 0 Emsley, 461 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 922 Ramachandran restraints generated. 461 Oldfield, 0 Emsley, 461 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 69 residues out of total 420 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 58 time to evaluate : 0.460 Fit side-chains revert: symmetry clash outliers start: 11 outliers final: 6 residues processed: 64 average time/residue: 0.1529 time to fit residues: 12.5780 Evaluate side-chains 52 residues out of total 420 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 46 time to evaluate : 0.416 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.0439 time to fit residues: 1.0931 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 46 random chunks: chunk 23 optimal weight: 0.9980 chunk 12 optimal weight: 0.0970 chunk 34 optimal weight: 0.7980 chunk 28 optimal weight: 1.9990 chunk 11 optimal weight: 7.9990 chunk 41 optimal weight: 0.0980 chunk 45 optimal weight: 0.8980 chunk 37 optimal weight: 0.5980 chunk 14 optimal weight: 0.0970 chunk 33 optimal weight: 0.5980 chunk 31 optimal weight: 0.5980 overall best weight: 0.2976 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 121 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8628 moved from start: 0.2543 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.019 3948 Z= 0.160 Angle : 0.502 5.235 5364 Z= 0.271 Chirality : 0.043 0.138 604 Planarity : 0.004 0.039 675 Dihedral : 4.590 15.436 551 Min Nonbonded Distance : 2.061 Molprobity Statistics. All-atom Clashscore : 3.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer Outliers : 1.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % 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: 1.17 (0.39), residues: 461 helix: 3.15 (1.69), residues: 11 sheet: 1.47 (0.37), residues: 187 loop : 0.20 (0.38), residues: 263 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 922 Ramachandran restraints generated. 461 Oldfield, 0 Emsley, 461 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 922 Ramachandran restraints generated. 461 Oldfield, 0 Emsley, 461 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 55 residues out of total 420 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 50 time to evaluate : 0.435 Fit side-chains revert: symmetry clash outliers start: 5 outliers final: 3 residues processed: 52 average time/residue: 0.1591 time to fit residues: 10.5285 Evaluate side-chains 48 residues out of total 420 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 45 time to evaluate : 0.396 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.0350 time to fit residues: 0.7188 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 46 random chunks: chunk 21 optimal weight: 0.6980 chunk 4 optimal weight: 0.5980 chunk 19 optimal weight: 0.0980 chunk 28 optimal weight: 0.7980 chunk 41 optimal weight: 0.9980 chunk 44 optimal weight: 0.6980 chunk 39 optimal weight: 0.9990 chunk 11 optimal weight: 3.9990 chunk 37 optimal weight: 0.8980 chunk 25 optimal weight: 1.9990 chunk 0 optimal weight: 1.9990 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 115 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8702 moved from start: 0.3135 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.024 3948 Z= 0.246 Angle : 0.548 9.353 5364 Z= 0.284 Chirality : 0.045 0.146 604 Planarity : 0.004 0.035 675 Dihedral : 4.707 15.619 551 Min Nonbonded Distance : 2.252 Molprobity Statistics. All-atom Clashscore : 3.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer Outliers : 1.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % 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: 1.15 (0.39), residues: 461 helix: 3.05 (1.65), residues: 11 sheet: 1.44 (0.37), residues: 193 loop : 0.17 (0.39), residues: 257 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 922 Ramachandran restraints generated. 461 Oldfield, 0 Emsley, 461 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 922 Ramachandran restraints generated. 461 Oldfield, 0 Emsley, 461 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 55 residues out of total 420 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 48 time to evaluate : 0.395 Fit side-chains revert: symmetry clash outliers start: 7 outliers final: 6 residues processed: 51 average time/residue: 0.1629 time to fit residues: 10.5975 Evaluate side-chains 53 residues out of total 420 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 47 time to evaluate : 0.442 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.0435 time to fit residues: 1.0603 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 46 random chunks: chunk 33 optimal weight: 0.8980 chunk 18 optimal weight: 1.9990 chunk 37 optimal weight: 0.9980 chunk 30 optimal weight: 0.9990 chunk 0 optimal weight: 1.9990 chunk 22 optimal weight: 2.9990 chunk 39 optimal weight: 0.9980 chunk 11 optimal weight: 2.9990 chunk 14 optimal weight: 0.0970 chunk 40 optimal weight: 2.9990 chunk 8 optimal weight: 0.5980 overall best weight: 0.7178 ------------------------------------------------------------------------------- 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: 0.8722 moved from start: 0.3317 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.029 3948 Z= 0.295 Angle : 0.564 10.997 5364 Z= 0.289 Chirality : 0.045 0.143 604 Planarity : 0.004 0.035 675 Dihedral : 4.728 16.041 551 Min Nonbonded Distance : 2.218 Molprobity Statistics. All-atom Clashscore : 3.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer Outliers : 0.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % 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: 1.02 (0.39), residues: 461 helix: 3.07 (1.65), residues: 11 sheet: 1.53 (0.37), residues: 191 loop : -0.07 (0.38), residues: 259 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 922 Ramachandran restraints generated. 461 Oldfield, 0 Emsley, 461 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 922 Ramachandran restraints generated. 461 Oldfield, 0 Emsley, 461 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 52 residues out of total 420 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 50 time to evaluate : 0.420 Fit side-chains outliers start: 2 outliers final: 1 residues processed: 50 average time/residue: 0.1618 time to fit residues: 10.3488 Evaluate side-chains 47 residues out of total 420 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 46 time to evaluate : 0.441 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0633 time to fit residues: 0.6965 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 46 random chunks: chunk 26 optimal weight: 0.8980 chunk 10 optimal weight: 0.9990 chunk 44 optimal weight: 0.9990 chunk 36 optimal weight: 0.6980 chunk 20 optimal weight: 0.9990 chunk 3 optimal weight: 0.9980 chunk 14 optimal weight: 1.9990 chunk 23 optimal weight: 0.0970 chunk 42 optimal weight: 0.5980 chunk 5 optimal weight: 1.9990 chunk 25 optimal weight: 0.9980 overall best weight: 0.6578 ------------------------------------------------------------------------------- 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: 0.8729 moved from start: 0.3521 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.028 3948 Z= 0.274 Angle : 0.548 11.192 5364 Z= 0.281 Chirality : 0.045 0.144 604 Planarity : 0.004 0.036 675 Dihedral : 4.711 16.158 551 Min Nonbonded Distance : 2.225 Molprobity Statistics. All-atom Clashscore : 3.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer Outliers : 1.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.95 (0.39), residues: 461 helix: 2.95 (1.65), residues: 11 sheet: 1.47 (0.38), residues: 191 loop : -0.10 (0.38), residues: 259 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 922 Ramachandran restraints generated. 461 Oldfield, 0 Emsley, 461 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 922 Ramachandran restraints generated. 461 Oldfield, 0 Emsley, 461 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 52 residues out of total 420 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 47 time to evaluate : 0.443 Fit side-chains outliers start: 5 outliers final: 3 residues processed: 50 average time/residue: 0.1520 time to fit residues: 9.8715 Evaluate side-chains 49 residues out of total 420 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 46 time to evaluate : 0.443 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.0390 time to fit residues: 0.8253 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 46 random chunks: chunk 32 optimal weight: 1.9990 chunk 25 optimal weight: 1.9990 chunk 37 optimal weight: 0.9990 chunk 24 optimal weight: 0.9990 chunk 44 optimal weight: 0.3980 chunk 27 optimal weight: 0.0270 chunk 20 optimal weight: 1.9990 chunk 17 optimal weight: 1.9990 chunk 26 optimal weight: 0.8980 chunk 13 optimal weight: 1.9990 chunk 8 optimal weight: 0.9980 overall best weight: 0.6640 ------------------------------------------------------------------------------- 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: 0.8733 moved from start: 0.3688 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.028 3948 Z= 0.274 Angle : 0.555 11.282 5364 Z= 0.286 Chirality : 0.045 0.144 604 Planarity : 0.004 0.036 675 Dihedral : 4.723 16.137 551 Min Nonbonded Distance : 2.214 Molprobity Statistics. All-atom Clashscore : 3.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer Outliers : 1.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.87 (0.39), residues: 461 helix: 3.02 (1.66), residues: 11 sheet: 1.43 (0.38), residues: 191 loop : -0.18 (0.38), residues: 259 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 922 Ramachandran restraints generated. 461 Oldfield, 0 Emsley, 461 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 922 Ramachandran restraints generated. 461 Oldfield, 0 Emsley, 461 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 54 residues out of total 420 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 48 time to evaluate : 0.450 Fit side-chains outliers start: 6 outliers final: 5 residues processed: 52 average time/residue: 0.1384 time to fit residues: 9.4604 Evaluate side-chains 52 residues out of total 420 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 47 time to evaluate : 0.414 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.0430 time to fit residues: 0.9921 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 46 random chunks: chunk 8 optimal weight: 1.9990 chunk 28 optimal weight: 0.7980 chunk 30 optimal weight: 0.9980 chunk 21 optimal weight: 1.9990 chunk 4 optimal weight: 0.6980 chunk 34 optimal weight: 2.9990 chunk 40 optimal weight: 2.9990 chunk 42 optimal weight: 0.5980 chunk 38 optimal weight: 0.6980 chunk 41 optimal weight: 0.9980 chunk 24 optimal weight: 0.5980 overall best weight: 0.6780 ------------------------------------------------------------------------------- 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: 0.8737 moved from start: 0.3817 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.029 3948 Z= 0.280 Angle : 0.562 11.405 5364 Z= 0.287 Chirality : 0.045 0.144 604 Planarity : 0.004 0.036 675 Dihedral : 4.750 16.256 551 Min Nonbonded Distance : 2.213 Molprobity Statistics. All-atom Clashscore : 4.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer Outliers : 0.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.83 (0.39), residues: 461 helix: 2.96 (1.65), residues: 11 sheet: 1.40 (0.38), residues: 191 loop : -0.21 (0.38), residues: 259 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 922 Ramachandran restraints generated. 461 Oldfield, 0 Emsley, 461 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 922 Ramachandran restraints generated. 461 Oldfield, 0 Emsley, 461 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 48 residues out of total 420 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 45 time to evaluate : 0.454 Fit side-chains outliers start: 3 outliers final: 2 residues processed: 47 average time/residue: 0.1559 time to fit residues: 9.5118 Evaluate side-chains 47 residues out of total 420 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 45 time to evaluate : 0.451 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0482 time to fit residues: 0.7656 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 46 random chunks: chunk 17 optimal weight: 0.9980 chunk 32 optimal weight: 1.9990 chunk 12 optimal weight: 0.9990 chunk 37 optimal weight: 0.9980 chunk 39 optimal weight: 0.0000 chunk 41 optimal weight: 0.8980 chunk 27 optimal weight: 1.9990 chunk 43 optimal weight: 0.5980 chunk 26 optimal weight: 0.9980 chunk 20 optimal weight: 0.9980 chunk 30 optimal weight: 0.5980 overall best weight: 0.6184 ------------------------------------------------------------------------------- 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: 0.8732 moved from start: 0.3861 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.031 3948 Z= 0.258 Angle : 0.545 10.913 5364 Z= 0.277 Chirality : 0.045 0.144 604 Planarity : 0.004 0.036 675 Dihedral : 4.692 16.144 551 Min Nonbonded Distance : 2.211 Molprobity Statistics. All-atom Clashscore : 3.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer Outliers : 0.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.86 (0.39), residues: 461 helix: 2.99 (1.66), residues: 11 sheet: 1.42 (0.38), residues: 191 loop : -0.18 (0.38), residues: 259 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 922 Ramachandran restraints generated. 461 Oldfield, 0 Emsley, 461 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 922 Ramachandran restraints generated. 461 Oldfield, 0 Emsley, 461 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 47 residues out of total 420 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 45 time to evaluate : 0.451 Fit side-chains outliers start: 2 outliers final: 2 residues processed: 46 average time/residue: 0.1553 time to fit residues: 9.3256 Evaluate side-chains 44 residues out of total 420 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 42 time to evaluate : 0.445 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0555 time to fit residues: 0.7882 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 46 random chunks: chunk 45 optimal weight: 0.9990 chunk 42 optimal weight: 0.9990 chunk 36 optimal weight: 1.9990 chunk 3 optimal weight: 0.1980 chunk 28 optimal weight: 0.6980 chunk 22 optimal weight: 0.0370 chunk 38 optimal weight: 0.8980 chunk 11 optimal weight: 2.9990 chunk 33 optimal weight: 0.5980 chunk 5 optimal weight: 0.8980 chunk 10 optimal weight: 0.1980 overall best weight: 0.3458 ------------------------------------------------------------------------------- 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: 0.8703 moved from start: 0.3881 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.021 3948 Z= 0.167 Angle : 0.492 8.516 5364 Z= 0.253 Chirality : 0.043 0.139 604 Planarity : 0.004 0.035 675 Dihedral : 4.516 15.545 551 Min Nonbonded Distance : 2.243 Molprobity Statistics. All-atom Clashscore : 3.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.97 (0.40), residues: 461 helix: 3.01 (1.66), residues: 11 sheet: 1.40 (0.38), residues: 196 loop : -0.06 (0.39), residues: 254 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 922 Ramachandran restraints generated. 461 Oldfield, 0 Emsley, 461 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 922 Ramachandran restraints generated. 461 Oldfield, 0 Emsley, 461 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 44 residues out of total 420 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 44 time to evaluate : 0.450 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 44 average time/residue: 0.1660 time to fit residues: 9.4822 Evaluate side-chains 44 residues out of total 420 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 44 time to evaluate : 0.393 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.5559 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 46 random chunks: chunk 36 optimal weight: 1.9990 chunk 15 optimal weight: 0.6980 chunk 37 optimal weight: 0.5980 chunk 4 optimal weight: 0.0970 chunk 6 optimal weight: 1.9990 chunk 32 optimal weight: 1.9990 chunk 2 optimal weight: 0.9980 chunk 26 optimal weight: 0.9980 chunk 41 optimal weight: 0.9980 chunk 24 optimal weight: 0.3980 chunk 31 optimal weight: 0.9980 overall best weight: 0.5578 ------------------------------------------------------------------------------- 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 = 0.3557 r_free = 0.3557 target = 0.138005 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3180 r_free = 0.3180 target = 0.108875 restraints weight = 4022.976| |-----------------------------------------------------------------------------| r_work (start): 0.3050 rms_B_bonded: 2.14 r_work: 0.3021 rms_B_bonded: 1.86 restraints_weight: 0.5000 r_work: 0.3000 rms_B_bonded: 1.88 restraints_weight: 0.2500 r_work: 0.2977 rms_B_bonded: 2.01 restraints_weight: 0.1250 r_work: 0.2949 rms_B_bonded: 2.26 restraints_weight: 0.0625 r_work: 0.2916 rms_B_bonded: 2.62 restraints_weight: 0.0312 r_work: 0.2875 rms_B_bonded: 3.14 restraints_weight: 0.0156 r_work: 0.2824 rms_B_bonded: 3.86 restraints_weight: 0.0078 r_work: 0.2757 rms_B_bonded: 4.88 restraints_weight: 0.0039 r_work (final): 0.2757 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9023 moved from start: 0.3931 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.027 3948 Z= 0.239 Angle : 0.527 9.376 5364 Z= 0.270 Chirality : 0.044 0.142 604 Planarity : 0.004 0.034 675 Dihedral : 4.604 15.760 551 Min Nonbonded Distance : 2.221 Molprobity Statistics. All-atom Clashscore : 4.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer Outliers : 0.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.92 (0.39), residues: 461 helix: 2.94 (1.64), residues: 11 sheet: 1.39 (0.38), residues: 196 loop : -0.09 (0.38), residues: 254 =============================================================================== Job complete usr+sys time: 1492.47 seconds wall clock time: 27 minutes 42.01 seconds (1662.01 seconds total)