Starting phenix.real_space_refine on Sat Apr 6 06:31:04 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8w5k_37295/04_2024/8w5k_37295_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8w5k_37295/04_2024/8w5k_37295.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8w5k_37295/04_2024/8w5k_37295.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8w5k_37295/04_2024/8w5k_37295.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8w5k_37295/04_2024/8w5k_37295_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8w5k_37295/04_2024/8w5k_37295_updated.pdb" } resolution = 3.6 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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 Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- 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= 0.003 sd= 0.070 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 Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 1 5.49 5 S 22 5.16 5 C 4741 2.51 5 N 1225 2.21 5 O 1390 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B GLU 120": "OE1" <-> "OE2" Residue "C GLU 19": "OE1" <-> "OE2" Residue "D PHE 48": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 55": "OD1" <-> "OD2" Residue "E PHE 35": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 41": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 69": "OE1" <-> "OE2" Residue "F TYR 79": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 104": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 170": "OD1" <-> "OD2" Residue "F PHE 245": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 314": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 327": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 120": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ASP 134": "OD1" <-> "OD2" Residue "I TYR 143": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ASP 146": "OD1" <-> "OD2" Residue "I TYR 217": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 245": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 307": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 359": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 7379 Number of models: 1 Model: "" Number of chains: 11 Chain: "B" Number of atoms: 387 Number of conformers: 1 Conformer: "" Number of residues, atoms: 50, 387 Classifications: {'peptide': 50} Link IDs: {'PTRANS': 1, 'TRANS': 48} Chain: "C" Number of atoms: 303 Number of conformers: 1 Conformer: "" Number of residues, atoms: 37, 303 Classifications: {'peptide': 37} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 1, 'TRANS': 35} Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 12 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "D" Number of atoms: 267 Number of conformers: 1 Conformer: "" Number of residues, atoms: 35, 267 Classifications: {'peptide': 35} Link IDs: {'PTRANS': 3, 'TRANS': 31} Chain: "E" Number of atoms: 342 Number of conformers: 1 Conformer: "" Number of residues, atoms: 42, 342 Classifications: {'peptide': 42} Link IDs: {'PTRANS': 4, 'TRANS': 37} Chain: "J" Number of atoms: 387 Number of conformers: 1 Conformer: "" Number of residues, atoms: 50, 387 Classifications: {'peptide': 50} Link IDs: {'PTRANS': 1, 'TRANS': 48} Chain: "K" Number of atoms: 303 Number of conformers: 1 Conformer: "" Number of residues, atoms: 37, 303 Classifications: {'peptide': 37} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 1, 'TRANS': 35} Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 12 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "L" Number of atoms: 267 Number of conformers: 1 Conformer: "" Number of residues, atoms: 35, 267 Classifications: {'peptide': 35} Link IDs: {'PTRANS': 3, 'TRANS': 31} Chain: "M" Number of atoms: 342 Number of conformers: 1 Conformer: "" Number of residues, atoms: 42, 342 Classifications: {'peptide': 42} Link IDs: {'PTRANS': 4, 'TRANS': 37} Chain: "F" Number of atoms: 2369 Number of conformers: 1 Conformer: "" Number of residues, atoms: 307, 2369 Classifications: {'peptide': 307} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 9, 'TRANS': 297} Chain breaks: 1 Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'GLN:plan1': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "I" Number of atoms: 2369 Number of conformers: 1 Conformer: "" Number of residues, atoms: 307, 2369 Classifications: {'peptide': 307} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 9, 'TRANS': 297} Chain breaks: 1 Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'GLN:plan1': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "I" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'46E': 1} Classifications: {'undetermined': 1} Time building chain proxies: 4.31, per 1000 atoms: 0.58 Number of scatterers: 7379 At special positions: 0 Unit cell: (94.8024, 104.498, 142.204, 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 22 16.00 P 1 15.00 O 1390 8.00 N 1225 7.00 C 4741 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.69 Conformation dependent library (CDL) restraints added in 1.2 seconds 1836 Ramachandran restraints generated. 918 Oldfield, 0 Emsley, 918 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1760 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 20 helices and 2 sheets defined 33.3% alpha, 33.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.27 Creating SS restraints... Processing helix chain 'B' and resid 87 through 134 Proline residue: B 112 - end of helix Processing helix chain 'C' and resid 14 through 48 Proline residue: C 39 - end of helix Processing helix chain 'D' and resid 31 through 50 Processing helix chain 'D' and resid 52 through 57 Processing helix chain 'E' and resid 20 through 43 removed outlier: 4.265A pdb=" N ASN E 26 " --> pdb=" O THR E 22 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N VAL E 27 " --> pdb=" O LEU E 23 " (cutoff:3.500A) removed outlier: 5.428A pdb=" N ILE E 33 " --> pdb=" O HIS E 29 " (cutoff:3.500A) Proline residue: E 34 - end of helix Processing helix chain 'E' and resid 50 through 54 Processing helix chain 'J' and resid 87 through 134 Proline residue: J 112 - end of helix Processing helix chain 'K' and resid 14 through 48 Proline residue: K 39 - end of helix Processing helix chain 'L' and resid 31 through 50 Processing helix chain 'L' and resid 52 through 57 Processing helix chain 'M' and resid 20 through 30 removed outlier: 3.604A pdb=" N HIS M 29 " --> pdb=" O HIS M 25 " (cutoff:3.500A) Processing helix chain 'M' and resid 32 through 43 Processing helix chain 'M' and resid 50 through 54 Processing helix chain 'F' and resid 50 through 55 Processing helix chain 'F' and resid 68 through 71 No H-bonds generated for 'chain 'F' and resid 68 through 71' Processing helix chain 'F' and resid 365 through 372 Processing helix chain 'I' and resid 50 through 55 Processing helix chain 'I' and resid 63 through 65 No H-bonds generated for 'chain 'I' and resid 63 through 65' Processing helix chain 'I' and resid 68 through 71 No H-bonds generated for 'chain 'I' and resid 68 through 71' Processing helix chain 'I' and resid 365 through 372 removed outlier: 3.588A pdb=" N GLN I 372 " --> pdb=" O LEU I 368 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'F' and resid 83 through 87 removed outlier: 3.918A pdb=" N LYS F 323 " --> pdb=" O ASP F 319 " (cutoff:3.500A) removed outlier: 7.013A pdb=" N ALA F 269 " --> pdb=" O LYS F 262 " (cutoff:3.500A) removed outlier: 5.314A pdb=" N LYS F 262 " --> pdb=" O ALA F 269 " (cutoff:3.500A) removed outlier: 7.356A pdb=" N ILE F 271 " --> pdb=" O TRP F 260 " (cutoff:3.500A) removed outlier: 5.491A pdb=" N TRP F 260 " --> pdb=" O ILE F 271 " (cutoff:3.500A) removed outlier: 7.262A pdb=" N THR F 273 " --> pdb=" O SER F 258 " (cutoff:3.500A) removed outlier: 5.456A pdb=" N SER F 258 " --> pdb=" O THR F 273 " (cutoff:3.500A) removed outlier: 7.597A pdb=" N LEU F 275 " --> pdb=" O ILE F 256 " (cutoff:3.500A) removed outlier: 5.635A pdb=" N ILE F 256 " --> pdb=" O LEU F 275 " (cutoff:3.500A) removed outlier: 6.463A pdb=" N LEU F 211 " --> pdb=" O SER F 204 " (cutoff:3.500A) removed outlier: 4.913A pdb=" N SER F 204 " --> pdb=" O LEU F 211 " (cutoff:3.500A) removed outlier: 7.159A pdb=" N LEU F 213 " --> pdb=" O LEU F 202 " (cutoff:3.500A) removed outlier: 4.885A pdb=" N LEU F 202 " --> pdb=" O LEU F 213 " (cutoff:3.500A) removed outlier: 6.948A pdb=" N THR F 215 " --> pdb=" O SER F 200 " (cutoff:3.500A) removed outlier: 4.891A pdb=" N SER F 200 " --> pdb=" O THR F 215 " (cutoff:3.500A) removed outlier: 7.023A pdb=" N TYR F 217 " --> pdb=" O VAL F 198 " (cutoff:3.500A) removed outlier: 5.098A pdb=" N VAL F 198 " --> pdb=" O TYR F 217 " (cutoff:3.500A) removed outlier: 7.014A pdb=" N ARG F 219 " --> pdb=" O VAL F 196 " (cutoff:3.500A) removed outlier: 4.997A pdb=" N VAL F 196 " --> pdb=" O ARG F 219 " (cutoff:3.500A) removed outlier: 6.916A pdb=" N THR F 100 " --> pdb=" O ALA F 91 " (cutoff:3.500A) removed outlier: 5.261A pdb=" N ALA F 91 " --> pdb=" O THR F 100 " (cutoff:3.500A) removed outlier: 6.786A pdb=" N HIS F 102 " --> pdb=" O ASN F 89 " (cutoff:3.500A) removed outlier: 4.577A pdb=" N ASN F 89 " --> pdb=" O HIS F 102 " (cutoff:3.500A) removed outlier: 7.121A pdb=" N PHE F 104 " --> pdb=" O ASP F 87 " (cutoff:3.500A) removed outlier: 5.055A pdb=" N ASP F 87 " --> pdb=" O PHE F 104 " (cutoff:3.500A) removed outlier: 7.530A pdb=" N ILE F 106 " --> pdb=" O ARG F 85 " (cutoff:3.500A) removed outlier: 5.372A pdb=" N ARG F 85 " --> pdb=" O ILE F 106 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'I' and resid 83 through 91 removed outlier: 4.168A pdb=" N LYS I 323 " --> pdb=" O ASP I 319 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N SER I 93 " --> pdb=" O PHE I 98 " (cutoff:3.500A) removed outlier: 7.021A pdb=" N THR I 100 " --> pdb=" O ALA I 91 " (cutoff:3.500A) removed outlier: 5.284A pdb=" N ALA I 91 " --> pdb=" O THR I 100 " (cutoff:3.500A) removed outlier: 7.095A pdb=" N HIS I 102 " --> pdb=" O ASN I 89 " (cutoff:3.500A) removed outlier: 4.943A pdb=" N ASN I 89 " --> pdb=" O HIS I 102 " (cutoff:3.500A) removed outlier: 7.160A pdb=" N PHE I 104 " --> pdb=" O ASP I 87 " (cutoff:3.500A) removed outlier: 5.176A pdb=" N ASP I 87 " --> pdb=" O PHE I 104 " (cutoff:3.500A) removed outlier: 7.650A pdb=" N ILE I 106 " --> pdb=" O ARG I 85 " (cutoff:3.500A) removed outlier: 5.547A pdb=" N ARG I 85 " --> pdb=" O ILE I 106 " (cutoff:3.500A) 475 hydrogen bonds defined for protein. 1377 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: 2.27 Time building geometry restraints manager: 2.94 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 1374 1.33 - 1.45: 1926 1.45 - 1.57: 4200 1.57 - 1.69: 2 1.69 - 1.81: 36 Bond restraints: 7538 Sorted by residual: bond pdb=" CG GLU C 19 " pdb=" CD GLU C 19 " ideal model delta sigma weight residual 1.516 1.471 0.045 2.50e-02 1.60e+03 3.26e+00 bond pdb=" N ASP I 134 " pdb=" CA ASP I 134 " ideal model delta sigma weight residual 1.458 1.479 -0.021 1.77e-02 3.19e+03 1.39e+00 bond pdb=" CB PRO E 34 " pdb=" CG PRO E 34 " ideal model delta sigma weight residual 1.492 1.551 -0.059 5.00e-02 4.00e+02 1.39e+00 bond pdb=" CA ASP F 134 " pdb=" CB ASP F 134 " ideal model delta sigma weight residual 1.532 1.549 -0.017 1.43e-02 4.89e+03 1.38e+00 bond pdb=" CA VAL K 37 " pdb=" C VAL K 37 " ideal model delta sigma weight residual 1.519 1.532 -0.013 1.14e-02 7.69e+03 1.26e+00 ... (remaining 7533 not shown) Histogram of bond angle deviations from ideal: 93.12 - 101.31: 11 101.31 - 109.50: 748 109.50 - 117.69: 4875 117.69 - 125.89: 4461 125.89 - 134.08: 124 Bond angle restraints: 10219 Sorted by residual: angle pdb=" CA GLU C 19 " pdb=" CB GLU C 19 " pdb=" CG GLU C 19 " ideal model delta sigma weight residual 114.10 123.34 -9.24 2.00e+00 2.50e-01 2.13e+01 angle pdb=" C ASN I 133 " pdb=" N ASP I 134 " pdb=" CA ASP I 134 " ideal model delta sigma weight residual 125.66 133.77 -8.11 1.85e+00 2.92e-01 1.92e+01 angle pdb=" N GLU C 19 " pdb=" CA GLU C 19 " pdb=" CB GLU C 19 " ideal model delta sigma weight residual 110.28 116.32 -6.04 1.55e+00 4.16e-01 1.52e+01 angle pdb=" CA PRO E 34 " pdb=" N PRO E 34 " pdb=" CD PRO E 34 " ideal model delta sigma weight residual 112.00 106.75 5.25 1.40e+00 5.10e-01 1.40e+01 angle pdb=" C ASN F 133 " pdb=" N ASP F 134 " pdb=" CA ASP F 134 " ideal model delta sigma weight residual 124.31 130.08 -5.77 1.67e+00 3.59e-01 1.19e+01 ... (remaining 10214 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.27: 3998 22.27 - 44.53: 382 44.53 - 66.80: 62 66.80 - 89.06: 12 89.06 - 111.33: 1 Dihedral angle restraints: 4455 sinusoidal: 1737 harmonic: 2718 Sorted by residual: dihedral pdb=" CA ASN F 95 " pdb=" C ASN F 95 " pdb=" N PRO F 96 " pdb=" CA PRO F 96 " ideal model delta harmonic sigma weight residual 180.00 150.89 29.11 0 5.00e+00 4.00e-02 3.39e+01 dihedral pdb=" CA ASN F 133 " pdb=" C ASN F 133 " pdb=" N ASP F 134 " pdb=" CA ASP F 134 " ideal model delta harmonic sigma weight residual -180.00 -152.69 -27.31 0 5.00e+00 4.00e-02 2.98e+01 dihedral pdb=" CA ASN I 95 " pdb=" C ASN I 95 " pdb=" N PRO I 96 " pdb=" CA PRO I 96 " ideal model delta harmonic sigma weight residual 180.00 153.89 26.11 0 5.00e+00 4.00e-02 2.73e+01 ... (remaining 4452 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.047: 894 0.047 - 0.095: 207 0.095 - 0.142: 54 0.142 - 0.190: 1 0.190 - 0.237: 1 Chirality restraints: 1157 Sorted by residual: chirality pdb=" CA GLU C 19 " pdb=" N GLU C 19 " pdb=" C GLU C 19 " pdb=" CB GLU C 19 " both_signs ideal model delta sigma weight residual False 2.51 2.27 0.24 2.00e-01 2.50e+01 1.40e+00 chirality pdb=" CA PRO E 34 " pdb=" N PRO E 34 " pdb=" C PRO E 34 " pdb=" CB PRO E 34 " both_signs ideal model delta sigma weight residual False 2.72 2.54 0.17 2.00e-01 2.50e+01 7.52e-01 chirality pdb=" CB THR J 129 " pdb=" CA THR J 129 " pdb=" OG1 THR J 129 " pdb=" CG2 THR J 129 " both_signs ideal model delta sigma weight residual False 2.55 2.41 0.14 2.00e-01 2.50e+01 5.02e-01 ... (remaining 1154 not shown) Planarity restraints: 1298 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE E 33 " -0.056 5.00e-02 4.00e+02 8.17e-02 1.07e+01 pdb=" N PRO E 34 " 0.141 5.00e-02 4.00e+02 pdb=" CA PRO E 34 " -0.040 5.00e-02 4.00e+02 pdb=" CD PRO E 34 " -0.046 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR F 206 " 0.034 5.00e-02 4.00e+02 5.11e-02 4.18e+00 pdb=" N PRO F 207 " -0.088 5.00e-02 4.00e+02 pdb=" CA PRO F 207 " 0.026 5.00e-02 4.00e+02 pdb=" CD PRO F 207 " 0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR I 206 " -0.026 5.00e-02 4.00e+02 3.91e-02 2.44e+00 pdb=" N PRO I 207 " 0.068 5.00e-02 4.00e+02 pdb=" CA PRO I 207 " -0.020 5.00e-02 4.00e+02 pdb=" CD PRO I 207 " -0.022 5.00e-02 4.00e+02 ... (remaining 1295 not shown) Histogram of nonbonded interaction distances: 2.08 - 2.64: 85 2.64 - 3.21: 6605 3.21 - 3.77: 11025 3.77 - 4.34: 14311 4.34 - 4.90: 24993 Nonbonded interactions: 57019 Sorted by model distance: nonbonded pdb=" OG SER I 218 " pdb=" OD1 ASP I 227 " model vdw 2.076 2.440 nonbonded pdb=" OD1 ASN I 179 " pdb=" OG SER I 200 " model vdw 2.095 2.440 nonbonded pdb=" OD1 ASN I 149 " pdb=" NE2 GLN I 169 " model vdw 2.190 2.520 nonbonded pdb=" OG SER I 186 " pdb=" O THR I 194 " model vdw 2.203 2.440 nonbonded pdb=" NE2 GLN I 166 " pdb=" OE2 GLU I 168 " model vdw 2.221 2.520 ... (remaining 57014 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 'B' selection = chain 'J' } ncs_group { reference = chain 'C' selection = chain 'K' } ncs_group { reference = chain 'D' selection = chain 'L' } ncs_group { reference = chain 'E' selection = chain 'M' } ncs_group { reference = chain 'F' selection = (chain 'I' and resid 49 through 373) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators 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: 2.910 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 7.260 Check model and map are aligned: 0.100 Set scattering table: 0.060 Process input model: 22.880 Find NCS groups from input model: 0.390 Set up NCS constraints: 0.050 Set refine NCS operators: 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:2.930 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.590 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7477 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 7538 Z= 0.230 Angle : 0.717 9.239 10219 Z= 0.364 Chirality : 0.043 0.237 1157 Planarity : 0.005 0.082 1298 Dihedral : 17.116 111.328 2695 Min Nonbonded Distance : 2.076 Molprobity Statistics. All-atom Clashscore : 8.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 0.88 % Allowed : 25.82 % Favored : 73.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.90 (0.29), residues: 918 helix: 2.28 (0.29), residues: 329 sheet: -0.09 (0.26), residues: 406 loop : -0.69 (0.49), residues: 183 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP I 260 HIS 0.002 0.001 HIS I 346 PHE 0.013 0.001 PHE E 50 TYR 0.020 0.001 TYR I 217 ARG 0.004 0.000 ARG F 310 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1836 Ramachandran restraints generated. 918 Oldfield, 0 Emsley, 918 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1836 Ramachandran restraints generated. 918 Oldfield, 0 Emsley, 918 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 804 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 117 time to evaluate : 0.835 Fit side-chains revert: symmetry clash REVERT: K 23 LYS cc_start: 0.8239 (ptpp) cc_final: 0.7942 (ptpt) outliers start: 7 outliers final: 5 residues processed: 118 average time/residue: 0.2221 time to fit residues: 34.4781 Evaluate side-chains 103 residues out of total 804 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 98 time to evaluate : 1.367 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 113 LEU Chi-restraints excluded: chain L residue 56 MET Chi-restraints excluded: chain F residue 182 THR Chi-restraints excluded: chain I residue 347 PHE Chi-restraints excluded: chain I residue 368 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 75 optimal weight: 0.3980 chunk 68 optimal weight: 1.9990 chunk 37 optimal weight: 2.9990 chunk 23 optimal weight: 0.8980 chunk 46 optimal weight: 0.8980 chunk 36 optimal weight: 1.9990 chunk 70 optimal weight: 0.7980 chunk 27 optimal weight: 1.9990 chunk 42 optimal weight: 3.9990 chunk 52 optimal weight: 0.8980 chunk 81 optimal weight: 1.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 26 ASN I 266 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7511 moved from start: 0.0632 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 7538 Z= 0.236 Angle : 0.650 7.750 10219 Z= 0.322 Chirality : 0.042 0.154 1157 Planarity : 0.004 0.052 1298 Dihedral : 7.983 109.898 1033 Min Nonbonded Distance : 2.067 Molprobity Statistics. All-atom Clashscore : 8.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 5.42 % Allowed : 23.80 % Favored : 70.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.83 (0.29), residues: 918 helix: 2.35 (0.29), residues: 329 sheet: -0.16 (0.26), residues: 410 loop : -0.92 (0.49), residues: 179 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP I 260 HIS 0.008 0.001 HIS C 17 PHE 0.012 0.001 PHE I 340 TYR 0.016 0.001 TYR I 217 ARG 0.002 0.000 ARG F 330 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1836 Ramachandran restraints generated. 918 Oldfield, 0 Emsley, 918 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1836 Ramachandran restraints generated. 918 Oldfield, 0 Emsley, 918 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 804 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 100 time to evaluate : 0.785 Fit side-chains revert: symmetry clash REVERT: K 23 LYS cc_start: 0.8241 (ptpp) cc_final: 0.7948 (ptpt) outliers start: 43 outliers final: 23 residues processed: 134 average time/residue: 0.1862 time to fit residues: 33.9021 Evaluate side-chains 117 residues out of total 804 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 94 time to evaluate : 0.842 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 30 SER Chi-restraints excluded: chain J residue 113 LEU Chi-restraints excluded: chain L residue 32 LEU Chi-restraints excluded: chain L residue 37 LEU Chi-restraints excluded: chain M residue 25 HIS Chi-restraints excluded: chain F residue 51 HIS Chi-restraints excluded: chain F residue 119 LEU Chi-restraints excluded: chain F residue 153 VAL Chi-restraints excluded: chain F residue 227 ASP Chi-restraints excluded: chain F residue 302 THR Chi-restraints excluded: chain F residue 313 VAL Chi-restraints excluded: chain I residue 51 HIS Chi-restraints excluded: chain I residue 89 ASN Chi-restraints excluded: chain I residue 119 LEU Chi-restraints excluded: chain I residue 153 VAL Chi-restraints excluded: chain I residue 163 THR Chi-restraints excluded: chain I residue 182 THR Chi-restraints excluded: chain I residue 259 LEU Chi-restraints excluded: chain I residue 326 CYS Chi-restraints excluded: chain I residue 337 SER Chi-restraints excluded: chain I residue 357 LEU Chi-restraints excluded: chain I residue 367 LEU Chi-restraints excluded: chain I residue 368 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 45 optimal weight: 0.9980 chunk 25 optimal weight: 0.9990 chunk 68 optimal weight: 0.5980 chunk 55 optimal weight: 0.4980 chunk 22 optimal weight: 0.8980 chunk 81 optimal weight: 0.9980 chunk 88 optimal weight: 1.9990 chunk 72 optimal weight: 1.9990 chunk 27 optimal weight: 1.9990 chunk 65 optimal weight: 0.9980 chunk 80 optimal weight: 0.0980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** K 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 26 ASN F 365 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7509 moved from start: 0.0927 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 7538 Z= 0.206 Angle : 0.619 7.490 10219 Z= 0.304 Chirality : 0.041 0.162 1157 Planarity : 0.004 0.050 1298 Dihedral : 7.295 105.419 1027 Min Nonbonded Distance : 2.084 Molprobity Statistics. All-atom Clashscore : 7.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 6.05 % Allowed : 23.80 % Favored : 70.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.87 (0.29), residues: 918 helix: 2.35 (0.29), residues: 331 sheet: -0.15 (0.26), residues: 410 loop : -0.80 (0.50), residues: 177 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP I 260 HIS 0.008 0.001 HIS C 17 PHE 0.010 0.001 PHE I 340 TYR 0.011 0.001 TYR I 307 ARG 0.004 0.001 ARG I 85 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1836 Ramachandran restraints generated. 918 Oldfield, 0 Emsley, 918 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1836 Ramachandran restraints generated. 918 Oldfield, 0 Emsley, 918 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 804 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 91 time to evaluate : 0.797 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: K 23 LYS cc_start: 0.8219 (ptpp) cc_final: 0.7919 (ptpt) REVERT: L 61 LEU cc_start: 0.5214 (OUTLIER) cc_final: 0.4969 (pt) outliers start: 48 outliers final: 33 residues processed: 129 average time/residue: 0.1824 time to fit residues: 32.0319 Evaluate side-chains 122 residues out of total 804 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 88 time to evaluate : 0.785 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 20 GLN Chi-restraints excluded: chain D residue 30 SER Chi-restraints excluded: chain E residue 29 HIS Chi-restraints excluded: chain E residue 55 SER Chi-restraints excluded: chain J residue 113 LEU Chi-restraints excluded: chain J residue 117 ILE Chi-restraints excluded: chain K residue 21 THR Chi-restraints excluded: chain L residue 32 LEU Chi-restraints excluded: chain L residue 37 LEU Chi-restraints excluded: chain L residue 61 LEU Chi-restraints excluded: chain M residue 25 HIS Chi-restraints excluded: chain M residue 45 SER Chi-restraints excluded: chain M residue 49 ASN Chi-restraints excluded: chain M residue 54 LEU Chi-restraints excluded: chain F residue 51 HIS Chi-restraints excluded: chain F residue 94 MET Chi-restraints excluded: chain F residue 119 LEU Chi-restraints excluded: chain F residue 157 ILE Chi-restraints excluded: chain F residue 213 LEU Chi-restraints excluded: chain F residue 227 ASP Chi-restraints excluded: chain F residue 337 SER Chi-restraints excluded: chain I residue 51 HIS Chi-restraints excluded: chain I residue 119 LEU Chi-restraints excluded: chain I residue 153 VAL Chi-restraints excluded: chain I residue 163 THR Chi-restraints excluded: chain I residue 181 LYS Chi-restraints excluded: chain I residue 259 LEU Chi-restraints excluded: chain I residue 267 VAL Chi-restraints excluded: chain I residue 326 CYS Chi-restraints excluded: chain I residue 337 SER Chi-restraints excluded: chain I residue 347 PHE Chi-restraints excluded: chain I residue 357 LEU Chi-restraints excluded: chain I residue 367 LEU Chi-restraints excluded: chain I residue 368 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 61 optimal weight: 0.8980 chunk 42 optimal weight: 0.7980 chunk 9 optimal weight: 2.9990 chunk 39 optimal weight: 4.9990 chunk 54 optimal weight: 0.6980 chunk 82 optimal weight: 2.9990 chunk 86 optimal weight: 0.7980 chunk 77 optimal weight: 0.0470 chunk 23 optimal weight: 0.0670 chunk 72 optimal weight: 2.9990 chunk 49 optimal weight: 0.7980 overall best weight: 0.4816 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** K 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 26 ASN F 99 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7495 moved from start: 0.1119 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 7538 Z= 0.181 Angle : 0.597 7.560 10219 Z= 0.292 Chirality : 0.041 0.159 1157 Planarity : 0.004 0.047 1298 Dihedral : 6.997 98.892 1027 Min Nonbonded Distance : 2.092 Molprobity Statistics. All-atom Clashscore : 7.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 5.67 % Allowed : 24.94 % Favored : 69.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.07 (0.29), residues: 918 helix: 2.48 (0.29), residues: 321 sheet: -0.09 (0.26), residues: 410 loop : -0.33 (0.50), residues: 187 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP I 260 HIS 0.008 0.001 HIS C 17 PHE 0.009 0.001 PHE I 340 TYR 0.012 0.001 TYR I 217 ARG 0.003 0.000 ARG M 47 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1836 Ramachandran restraints generated. 918 Oldfield, 0 Emsley, 918 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1836 Ramachandran restraints generated. 918 Oldfield, 0 Emsley, 918 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 804 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 94 time to evaluate : 0.845 Fit side-chains revert: symmetry clash REVERT: J 113 LEU cc_start: 0.8540 (OUTLIER) cc_final: 0.8180 (tp) REVERT: J 128 LYS cc_start: 0.8761 (mptt) cc_final: 0.8499 (mmtp) REVERT: K 23 LYS cc_start: 0.8178 (ptpp) cc_final: 0.7917 (ptpt) REVERT: L 61 LEU cc_start: 0.5288 (OUTLIER) cc_final: 0.5066 (pt) outliers start: 45 outliers final: 34 residues processed: 127 average time/residue: 0.1951 time to fit residues: 33.5460 Evaluate side-chains 126 residues out of total 804 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 90 time to evaluate : 0.928 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 30 SER Chi-restraints excluded: chain E residue 29 HIS Chi-restraints excluded: chain J residue 113 LEU Chi-restraints excluded: chain J residue 117 ILE Chi-restraints excluded: chain L residue 32 LEU Chi-restraints excluded: chain L residue 37 LEU Chi-restraints excluded: chain L residue 61 LEU Chi-restraints excluded: chain M residue 25 HIS Chi-restraints excluded: chain M residue 49 ASN Chi-restraints excluded: chain M residue 54 LEU Chi-restraints excluded: chain F residue 51 HIS Chi-restraints excluded: chain F residue 94 MET Chi-restraints excluded: chain F residue 119 LEU Chi-restraints excluded: chain F residue 153 VAL Chi-restraints excluded: chain F residue 157 ILE Chi-restraints excluded: chain F residue 182 THR Chi-restraints excluded: chain F residue 213 LEU Chi-restraints excluded: chain F residue 227 ASP Chi-restraints excluded: chain F residue 313 VAL Chi-restraints excluded: chain F residue 340 PHE Chi-restraints excluded: chain I residue 51 HIS Chi-restraints excluded: chain I residue 89 ASN Chi-restraints excluded: chain I residue 100 THR Chi-restraints excluded: chain I residue 119 LEU Chi-restraints excluded: chain I residue 153 VAL Chi-restraints excluded: chain I residue 163 THR Chi-restraints excluded: chain I residue 181 LYS Chi-restraints excluded: chain I residue 182 THR Chi-restraints excluded: chain I residue 216 LEU Chi-restraints excluded: chain I residue 259 LEU Chi-restraints excluded: chain I residue 267 VAL Chi-restraints excluded: chain I residue 337 SER Chi-restraints excluded: chain I residue 347 PHE Chi-restraints excluded: chain I residue 357 LEU Chi-restraints excluded: chain I residue 367 LEU Chi-restraints excluded: chain I residue 368 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 1 optimal weight: 0.5980 chunk 64 optimal weight: 0.8980 chunk 35 optimal weight: 0.5980 chunk 74 optimal weight: 8.9990 chunk 60 optimal weight: 0.1980 chunk 0 optimal weight: 7.9990 chunk 44 optimal weight: 9.9990 chunk 78 optimal weight: 0.9980 chunk 21 optimal weight: 0.8980 chunk 29 optimal weight: 2.9990 chunk 17 optimal weight: 0.0870 overall best weight: 0.4758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** K 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 26 ASN F 99 GLN I 156 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7496 moved from start: 0.1255 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 7538 Z= 0.181 Angle : 0.593 9.344 10219 Z= 0.289 Chirality : 0.040 0.158 1157 Planarity : 0.004 0.046 1298 Dihedral : 6.785 92.468 1027 Min Nonbonded Distance : 2.093 Molprobity Statistics. All-atom Clashscore : 8.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Rotamer: Outliers : 7.43 % Allowed : 24.06 % Favored : 68.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.17 (0.30), residues: 918 helix: 2.54 (0.29), residues: 321 sheet: -0.03 (0.26), residues: 410 loop : -0.27 (0.50), residues: 187 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP I 260 HIS 0.006 0.001 HIS C 17 PHE 0.009 0.001 PHE F 120 TYR 0.008 0.001 TYR I 307 ARG 0.004 0.000 ARG M 47 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1836 Ramachandran restraints generated. 918 Oldfield, 0 Emsley, 918 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1836 Ramachandran restraints generated. 918 Oldfield, 0 Emsley, 918 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 804 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 94 time to evaluate : 0.855 Fit side-chains revert: symmetry clash REVERT: J 113 LEU cc_start: 0.8708 (OUTLIER) cc_final: 0.8503 (tp) REVERT: J 128 LYS cc_start: 0.8764 (mptt) cc_final: 0.8500 (mmtp) REVERT: K 23 LYS cc_start: 0.8176 (ptpp) cc_final: 0.7896 (ptpt) REVERT: L 61 LEU cc_start: 0.5265 (OUTLIER) cc_final: 0.5030 (pt) REVERT: M 38 TYR cc_start: 0.7058 (t80) cc_final: 0.6792 (t80) REVERT: F 275 LEU cc_start: 0.7123 (OUTLIER) cc_final: 0.6750 (pp) outliers start: 59 outliers final: 43 residues processed: 140 average time/residue: 0.1960 time to fit residues: 36.9185 Evaluate side-chains 137 residues out of total 804 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 91 time to evaluate : 0.865 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 115 LEU Chi-restraints excluded: chain B residue 123 LEU Chi-restraints excluded: chain C residue 25 LEU Chi-restraints excluded: chain D residue 30 SER Chi-restraints excluded: chain E residue 29 HIS Chi-restraints excluded: chain E residue 49 ASN Chi-restraints excluded: chain J residue 113 LEU Chi-restraints excluded: chain J residue 117 ILE Chi-restraints excluded: chain K residue 21 THR Chi-restraints excluded: chain L residue 32 LEU Chi-restraints excluded: chain L residue 37 LEU Chi-restraints excluded: chain L residue 61 LEU Chi-restraints excluded: chain M residue 25 HIS Chi-restraints excluded: chain M residue 45 SER Chi-restraints excluded: chain M residue 49 ASN Chi-restraints excluded: chain M residue 54 LEU Chi-restraints excluded: chain F residue 51 HIS Chi-restraints excluded: chain F residue 94 MET Chi-restraints excluded: chain F residue 119 LEU Chi-restraints excluded: chain F residue 153 VAL Chi-restraints excluded: chain F residue 157 ILE Chi-restraints excluded: chain F residue 182 THR Chi-restraints excluded: chain F residue 213 LEU Chi-restraints excluded: chain F residue 227 ASP Chi-restraints excluded: chain F residue 275 LEU Chi-restraints excluded: chain F residue 302 THR Chi-restraints excluded: chain F residue 313 VAL Chi-restraints excluded: chain F residue 338 VAL Chi-restraints excluded: chain F residue 340 PHE Chi-restraints excluded: chain I residue 51 HIS Chi-restraints excluded: chain I residue 89 ASN Chi-restraints excluded: chain I residue 100 THR Chi-restraints excluded: chain I residue 119 LEU Chi-restraints excluded: chain I residue 153 VAL Chi-restraints excluded: chain I residue 163 THR Chi-restraints excluded: chain I residue 181 LYS Chi-restraints excluded: chain I residue 182 THR Chi-restraints excluded: chain I residue 216 LEU Chi-restraints excluded: chain I residue 259 LEU Chi-restraints excluded: chain I residue 267 VAL Chi-restraints excluded: chain I residue 326 CYS Chi-restraints excluded: chain I residue 337 SER Chi-restraints excluded: chain I residue 347 PHE Chi-restraints excluded: chain I residue 357 LEU Chi-restraints excluded: chain I residue 367 LEU Chi-restraints excluded: chain I residue 368 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 51 optimal weight: 0.9990 chunk 21 optimal weight: 0.9990 chunk 87 optimal weight: 1.9990 chunk 72 optimal weight: 3.9990 chunk 40 optimal weight: 1.9990 chunk 7 optimal weight: 2.9990 chunk 28 optimal weight: 0.0970 chunk 45 optimal weight: 0.0770 chunk 83 optimal weight: 0.9980 chunk 9 optimal weight: 1.9990 chunk 49 optimal weight: 1.9990 overall best weight: 0.6340 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** K 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 26 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7520 moved from start: 0.1400 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 7538 Z= 0.207 Angle : 0.599 7.500 10219 Z= 0.295 Chirality : 0.041 0.158 1157 Planarity : 0.004 0.046 1298 Dihedral : 6.632 86.720 1027 Min Nonbonded Distance : 2.095 Molprobity Statistics. All-atom Clashscore : 7.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % Rotamer: Outliers : 7.30 % Allowed : 24.43 % Favored : 68.26 % 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: 1.19 (0.30), residues: 918 helix: 2.56 (0.29), residues: 321 sheet: -0.04 (0.26), residues: 410 loop : -0.19 (0.51), residues: 187 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP I 260 HIS 0.004 0.001 HIS C 17 PHE 0.009 0.001 PHE I 340 TYR 0.012 0.001 TYR I 217 ARG 0.003 0.000 ARG M 47 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1836 Ramachandran restraints generated. 918 Oldfield, 0 Emsley, 918 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1836 Ramachandran restraints generated. 918 Oldfield, 0 Emsley, 918 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 804 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 91 time to evaluate : 0.867 Fit side-chains REVERT: J 113 LEU cc_start: 0.8839 (OUTLIER) cc_final: 0.8568 (tp) REVERT: J 128 LYS cc_start: 0.8754 (mptt) cc_final: 0.8473 (mmtp) REVERT: K 23 LYS cc_start: 0.8181 (ptpp) cc_final: 0.7921 (ptpt) REVERT: L 61 LEU cc_start: 0.5323 (OUTLIER) cc_final: 0.5110 (pt) REVERT: F 275 LEU cc_start: 0.7199 (OUTLIER) cc_final: 0.6792 (pp) outliers start: 58 outliers final: 46 residues processed: 134 average time/residue: 0.1911 time to fit residues: 34.6922 Evaluate side-chains 139 residues out of total 804 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 90 time to evaluate : 0.837 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 115 LEU Chi-restraints excluded: chain B residue 123 LEU Chi-restraints excluded: chain C residue 25 LEU Chi-restraints excluded: chain D residue 30 SER Chi-restraints excluded: chain E residue 29 HIS Chi-restraints excluded: chain E residue 47 ARG Chi-restraints excluded: chain E residue 49 ASN Chi-restraints excluded: chain J residue 113 LEU Chi-restraints excluded: chain J residue 117 ILE Chi-restraints excluded: chain K residue 21 THR Chi-restraints excluded: chain K residue 25 LEU Chi-restraints excluded: chain K residue 47 LYS Chi-restraints excluded: chain L residue 32 LEU Chi-restraints excluded: chain L residue 37 LEU Chi-restraints excluded: chain L residue 61 LEU Chi-restraints excluded: chain M residue 25 HIS Chi-restraints excluded: chain M residue 45 SER Chi-restraints excluded: chain M residue 49 ASN Chi-restraints excluded: chain M residue 54 LEU Chi-restraints excluded: chain F residue 51 HIS Chi-restraints excluded: chain F residue 94 MET Chi-restraints excluded: chain F residue 119 LEU Chi-restraints excluded: chain F residue 153 VAL Chi-restraints excluded: chain F residue 157 ILE Chi-restraints excluded: chain F residue 182 THR Chi-restraints excluded: chain F residue 213 LEU Chi-restraints excluded: chain F residue 227 ASP Chi-restraints excluded: chain F residue 275 LEU Chi-restraints excluded: chain F residue 302 THR Chi-restraints excluded: chain F residue 313 VAL Chi-restraints excluded: chain F residue 338 VAL Chi-restraints excluded: chain F residue 340 PHE Chi-restraints excluded: chain I residue 51 HIS Chi-restraints excluded: chain I residue 89 ASN Chi-restraints excluded: chain I residue 100 THR Chi-restraints excluded: chain I residue 119 LEU Chi-restraints excluded: chain I residue 153 VAL Chi-restraints excluded: chain I residue 163 THR Chi-restraints excluded: chain I residue 181 LYS Chi-restraints excluded: chain I residue 182 THR Chi-restraints excluded: chain I residue 216 LEU Chi-restraints excluded: chain I residue 259 LEU Chi-restraints excluded: chain I residue 267 VAL Chi-restraints excluded: chain I residue 326 CYS Chi-restraints excluded: chain I residue 337 SER Chi-restraints excluded: chain I residue 347 PHE Chi-restraints excluded: chain I residue 357 LEU Chi-restraints excluded: chain I residue 367 LEU Chi-restraints excluded: chain I residue 368 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 63 optimal weight: 1.9990 chunk 49 optimal weight: 2.9990 chunk 73 optimal weight: 0.9980 chunk 48 optimal weight: 0.8980 chunk 86 optimal weight: 0.7980 chunk 54 optimal weight: 1.9990 chunk 52 optimal weight: 1.9990 chunk 40 optimal weight: 3.9990 chunk 53 optimal weight: 1.9990 chunk 34 optimal weight: 0.5980 chunk 51 optimal weight: 0.6980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** K 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 26 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7553 moved from start: 0.1573 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 7538 Z= 0.238 Angle : 0.622 8.462 10219 Z= 0.307 Chirality : 0.041 0.160 1157 Planarity : 0.004 0.046 1298 Dihedral : 6.580 82.940 1027 Min Nonbonded Distance : 2.087 Molprobity Statistics. All-atom Clashscore : 8.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % Rotamer: Outliers : 6.93 % Allowed : 23.93 % Favored : 69.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.15 (0.30), residues: 918 helix: 2.53 (0.29), residues: 321 sheet: -0.07 (0.26), residues: 410 loop : -0.21 (0.51), residues: 187 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP I 260 HIS 0.005 0.001 HIS C 17 PHE 0.010 0.001 PHE I 340 TYR 0.007 0.001 TYR I 307 ARG 0.004 0.000 ARG M 47 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1836 Ramachandran restraints generated. 918 Oldfield, 0 Emsley, 918 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1836 Ramachandran restraints generated. 918 Oldfield, 0 Emsley, 918 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 804 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 90 time to evaluate : 0.823 Fit side-chains REVERT: J 113 LEU cc_start: 0.8925 (OUTLIER) cc_final: 0.8706 (tp) REVERT: J 128 LYS cc_start: 0.8740 (mptt) cc_final: 0.8453 (mmtp) REVERT: K 23 LYS cc_start: 0.8208 (ptpp) cc_final: 0.7949 (ptpt) REVERT: K 36 TRP cc_start: 0.6956 (t60) cc_final: 0.6743 (t60) REVERT: K 49 TRP cc_start: 0.6896 (m100) cc_final: 0.6539 (m100) REVERT: L 61 LEU cc_start: 0.5445 (OUTLIER) cc_final: 0.5220 (pt) outliers start: 55 outliers final: 44 residues processed: 132 average time/residue: 0.1808 time to fit residues: 32.9302 Evaluate side-chains 135 residues out of total 804 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 89 time to evaluate : 0.798 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 115 LEU Chi-restraints excluded: chain B residue 123 LEU Chi-restraints excluded: chain C residue 25 LEU Chi-restraints excluded: chain D residue 30 SER Chi-restraints excluded: chain D residue 55 ASP Chi-restraints excluded: chain E residue 49 ASN Chi-restraints excluded: chain J residue 113 LEU Chi-restraints excluded: chain J residue 117 ILE Chi-restraints excluded: chain K residue 21 THR Chi-restraints excluded: chain K residue 25 LEU Chi-restraints excluded: chain K residue 47 LYS Chi-restraints excluded: chain L residue 32 LEU Chi-restraints excluded: chain L residue 37 LEU Chi-restraints excluded: chain L residue 61 LEU Chi-restraints excluded: chain M residue 25 HIS Chi-restraints excluded: chain M residue 49 ASN Chi-restraints excluded: chain F residue 51 HIS Chi-restraints excluded: chain F residue 94 MET Chi-restraints excluded: chain F residue 119 LEU Chi-restraints excluded: chain F residue 153 VAL Chi-restraints excluded: chain F residue 157 ILE Chi-restraints excluded: chain F residue 182 THR Chi-restraints excluded: chain F residue 213 LEU Chi-restraints excluded: chain F residue 227 ASP Chi-restraints excluded: chain F residue 302 THR Chi-restraints excluded: chain F residue 313 VAL Chi-restraints excluded: chain F residue 338 VAL Chi-restraints excluded: chain F residue 340 PHE Chi-restraints excluded: chain I residue 51 HIS Chi-restraints excluded: chain I residue 58 VAL Chi-restraints excluded: chain I residue 89 ASN Chi-restraints excluded: chain I residue 100 THR Chi-restraints excluded: chain I residue 119 LEU Chi-restraints excluded: chain I residue 153 VAL Chi-restraints excluded: chain I residue 163 THR Chi-restraints excluded: chain I residue 181 LYS Chi-restraints excluded: chain I residue 182 THR Chi-restraints excluded: chain I residue 216 LEU Chi-restraints excluded: chain I residue 259 LEU Chi-restraints excluded: chain I residue 267 VAL Chi-restraints excluded: chain I residue 326 CYS Chi-restraints excluded: chain I residue 337 SER Chi-restraints excluded: chain I residue 347 PHE Chi-restraints excluded: chain I residue 357 LEU Chi-restraints excluded: chain I residue 367 LEU Chi-restraints excluded: chain I residue 368 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 26 optimal weight: 3.9990 chunk 17 optimal weight: 0.8980 chunk 16 optimal weight: 1.9990 chunk 55 optimal weight: 0.6980 chunk 59 optimal weight: 0.6980 chunk 42 optimal weight: 1.9990 chunk 8 optimal weight: 1.9990 chunk 68 optimal weight: 0.8980 chunk 78 optimal weight: 0.9980 chunk 83 optimal weight: 0.7980 chunk 75 optimal weight: 0.7980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** K 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7556 moved from start: 0.1692 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 7538 Z= 0.233 Angle : 0.629 8.666 10219 Z= 0.307 Chirality : 0.041 0.159 1157 Planarity : 0.004 0.046 1298 Dihedral : 6.494 80.892 1027 Min Nonbonded Distance : 2.093 Molprobity Statistics. All-atom Clashscore : 8.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer: Outliers : 7.30 % Allowed : 23.55 % Favored : 69.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.02 (0.30), residues: 918 helix: 2.43 (0.29), residues: 333 sheet: -0.09 (0.26), residues: 410 loop : -0.63 (0.52), residues: 175 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP I 260 HIS 0.006 0.001 HIS C 17 PHE 0.010 0.001 PHE I 340 TYR 0.014 0.001 TYR I 217 ARG 0.004 0.000 ARG M 47 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1836 Ramachandran restraints generated. 918 Oldfield, 0 Emsley, 918 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1836 Ramachandran restraints generated. 918 Oldfield, 0 Emsley, 918 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 804 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 87 time to evaluate : 0.810 Fit side-chains revert: symmetry clash REVERT: J 113 LEU cc_start: 0.8931 (OUTLIER) cc_final: 0.8656 (tp) REVERT: J 128 LYS cc_start: 0.8728 (mptt) cc_final: 0.8448 (mmtp) REVERT: K 23 LYS cc_start: 0.8222 (ptpp) cc_final: 0.7984 (ptpt) REVERT: K 36 TRP cc_start: 0.6938 (t60) cc_final: 0.6712 (t60) REVERT: K 49 TRP cc_start: 0.6864 (m100) cc_final: 0.6515 (m100) REVERT: L 28 LYS cc_start: 0.6527 (ptpp) cc_final: 0.5489 (mmtm) REVERT: L 54 MET cc_start: 0.8524 (tmm) cc_final: 0.8136 (tpp) REVERT: L 61 LEU cc_start: 0.5459 (OUTLIER) cc_final: 0.5240 (pt) outliers start: 58 outliers final: 49 residues processed: 132 average time/residue: 0.1830 time to fit residues: 33.0196 Evaluate side-chains 137 residues out of total 804 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 86 time to evaluate : 0.936 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 123 LEU Chi-restraints excluded: chain C residue 20 GLN Chi-restraints excluded: chain C residue 25 LEU Chi-restraints excluded: chain D residue 30 SER Chi-restraints excluded: chain D residue 55 ASP Chi-restraints excluded: chain E residue 29 HIS Chi-restraints excluded: chain E residue 47 ARG Chi-restraints excluded: chain E residue 49 ASN Chi-restraints excluded: chain J residue 113 LEU Chi-restraints excluded: chain J residue 117 ILE Chi-restraints excluded: chain K residue 21 THR Chi-restraints excluded: chain L residue 32 LEU Chi-restraints excluded: chain L residue 37 LEU Chi-restraints excluded: chain L residue 61 LEU Chi-restraints excluded: chain M residue 25 HIS Chi-restraints excluded: chain M residue 45 SER Chi-restraints excluded: chain M residue 49 ASN Chi-restraints excluded: chain M residue 54 LEU Chi-restraints excluded: chain F residue 51 HIS Chi-restraints excluded: chain F residue 94 MET Chi-restraints excluded: chain F residue 119 LEU Chi-restraints excluded: chain F residue 153 VAL Chi-restraints excluded: chain F residue 157 ILE Chi-restraints excluded: chain F residue 182 THR Chi-restraints excluded: chain F residue 213 LEU Chi-restraints excluded: chain F residue 227 ASP Chi-restraints excluded: chain F residue 255 LEU Chi-restraints excluded: chain F residue 302 THR Chi-restraints excluded: chain F residue 313 VAL Chi-restraints excluded: chain F residue 338 VAL Chi-restraints excluded: chain F residue 340 PHE Chi-restraints excluded: chain I residue 51 HIS Chi-restraints excluded: chain I residue 58 VAL Chi-restraints excluded: chain I residue 89 ASN Chi-restraints excluded: chain I residue 100 THR Chi-restraints excluded: chain I residue 119 LEU Chi-restraints excluded: chain I residue 153 VAL Chi-restraints excluded: chain I residue 163 THR Chi-restraints excluded: chain I residue 181 LYS Chi-restraints excluded: chain I residue 182 THR Chi-restraints excluded: chain I residue 216 LEU Chi-restraints excluded: chain I residue 255 LEU Chi-restraints excluded: chain I residue 259 LEU Chi-restraints excluded: chain I residue 267 VAL Chi-restraints excluded: chain I residue 326 CYS Chi-restraints excluded: chain I residue 337 SER Chi-restraints excluded: chain I residue 339 LEU Chi-restraints excluded: chain I residue 347 PHE Chi-restraints excluded: chain I residue 357 LEU Chi-restraints excluded: chain I residue 367 LEU Chi-restraints excluded: chain I residue 368 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 80 optimal weight: 1.9990 chunk 83 optimal weight: 1.9990 chunk 48 optimal weight: 1.9990 chunk 35 optimal weight: 0.9980 chunk 63 optimal weight: 0.8980 chunk 24 optimal weight: 0.8980 chunk 73 optimal weight: 0.8980 chunk 76 optimal weight: 2.9990 chunk 53 optimal weight: 1.9990 chunk 85 optimal weight: 0.9990 chunk 52 optimal weight: 0.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** K 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 321 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7582 moved from start: 0.1843 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 7538 Z= 0.266 Angle : 0.654 9.382 10219 Z= 0.320 Chirality : 0.042 0.159 1157 Planarity : 0.004 0.047 1298 Dihedral : 6.591 82.017 1027 Min Nonbonded Distance : 2.095 Molprobity Statistics. All-atom Clashscore : 8.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 6.80 % Allowed : 23.80 % Favored : 69.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.91 (0.29), residues: 918 helix: 2.39 (0.29), residues: 333 sheet: -0.18 (0.26), residues: 410 loop : -0.69 (0.51), residues: 175 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP I 260 HIS 0.006 0.001 HIS C 17 PHE 0.011 0.001 PHE I 340 TYR 0.008 0.001 TYR I 307 ARG 0.004 0.000 ARG M 47 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1836 Ramachandran restraints generated. 918 Oldfield, 0 Emsley, 918 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1836 Ramachandran restraints generated. 918 Oldfield, 0 Emsley, 918 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 804 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 90 time to evaluate : 0.852 Fit side-chains REVERT: J 128 LYS cc_start: 0.8730 (mptt) cc_final: 0.8463 (mmtp) REVERT: K 23 LYS cc_start: 0.8270 (ptpp) cc_final: 0.8030 (ptpt) REVERT: K 36 TRP cc_start: 0.6995 (t60) cc_final: 0.6748 (t60) REVERT: K 49 TRP cc_start: 0.6868 (m100) cc_final: 0.6523 (m100) REVERT: L 54 MET cc_start: 0.8523 (tmm) cc_final: 0.8063 (tpp) REVERT: L 61 LEU cc_start: 0.5554 (OUTLIER) cc_final: 0.5353 (pt) REVERT: M 38 TYR cc_start: 0.6990 (t80) cc_final: 0.6755 (t80) outliers start: 54 outliers final: 48 residues processed: 134 average time/residue: 0.1866 time to fit residues: 34.0634 Evaluate side-chains 137 residues out of total 804 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 88 time to evaluate : 0.799 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 115 LEU Chi-restraints excluded: chain B residue 123 LEU Chi-restraints excluded: chain C residue 25 LEU Chi-restraints excluded: chain D residue 30 SER Chi-restraints excluded: chain D residue 55 ASP Chi-restraints excluded: chain E residue 29 HIS Chi-restraints excluded: chain E residue 49 ASN Chi-restraints excluded: chain E residue 55 SER Chi-restraints excluded: chain J residue 117 ILE Chi-restraints excluded: chain K residue 21 THR Chi-restraints excluded: chain L residue 32 LEU Chi-restraints excluded: chain L residue 37 LEU Chi-restraints excluded: chain L residue 61 LEU Chi-restraints excluded: chain M residue 25 HIS Chi-restraints excluded: chain M residue 45 SER Chi-restraints excluded: chain M residue 49 ASN Chi-restraints excluded: chain F residue 51 HIS Chi-restraints excluded: chain F residue 94 MET Chi-restraints excluded: chain F residue 119 LEU Chi-restraints excluded: chain F residue 153 VAL Chi-restraints excluded: chain F residue 157 ILE Chi-restraints excluded: chain F residue 182 THR Chi-restraints excluded: chain F residue 213 LEU Chi-restraints excluded: chain F residue 227 ASP Chi-restraints excluded: chain F residue 255 LEU Chi-restraints excluded: chain F residue 302 THR Chi-restraints excluded: chain F residue 313 VAL Chi-restraints excluded: chain F residue 338 VAL Chi-restraints excluded: chain F residue 340 PHE Chi-restraints excluded: chain I residue 51 HIS Chi-restraints excluded: chain I residue 58 VAL Chi-restraints excluded: chain I residue 89 ASN Chi-restraints excluded: chain I residue 100 THR Chi-restraints excluded: chain I residue 119 LEU Chi-restraints excluded: chain I residue 153 VAL Chi-restraints excluded: chain I residue 163 THR Chi-restraints excluded: chain I residue 181 LYS Chi-restraints excluded: chain I residue 182 THR Chi-restraints excluded: chain I residue 216 LEU Chi-restraints excluded: chain I residue 255 LEU Chi-restraints excluded: chain I residue 259 LEU Chi-restraints excluded: chain I residue 267 VAL Chi-restraints excluded: chain I residue 326 CYS Chi-restraints excluded: chain I residue 337 SER Chi-restraints excluded: chain I residue 339 LEU Chi-restraints excluded: chain I residue 347 PHE Chi-restraints excluded: chain I residue 357 LEU Chi-restraints excluded: chain I residue 367 LEU Chi-restraints excluded: chain I residue 368 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 40 optimal weight: 3.9990 chunk 59 optimal weight: 0.9990 chunk 89 optimal weight: 3.9990 chunk 82 optimal weight: 2.9990 chunk 71 optimal weight: 7.9990 chunk 7 optimal weight: 2.9990 chunk 55 optimal weight: 0.6980 chunk 43 optimal weight: 0.6980 chunk 56 optimal weight: 0.9980 chunk 76 optimal weight: 2.9990 chunk 21 optimal weight: 0.8980 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** K 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 321 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7580 moved from start: 0.1946 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 7538 Z= 0.250 Angle : 0.643 9.440 10219 Z= 0.313 Chirality : 0.041 0.159 1157 Planarity : 0.004 0.046 1298 Dihedral : 6.560 81.128 1025 Min Nonbonded Distance : 2.098 Molprobity Statistics. All-atom Clashscore : 8.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer: Outliers : 6.17 % Allowed : 24.43 % Favored : 69.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.90 (0.30), residues: 918 helix: 2.41 (0.29), residues: 333 sheet: -0.21 (0.26), residues: 410 loop : -0.68 (0.51), residues: 175 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP I 260 HIS 0.007 0.001 HIS C 17 PHE 0.012 0.001 PHE L 41 TYR 0.015 0.001 TYR I 217 ARG 0.004 0.000 ARG M 47 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1836 Ramachandran restraints generated. 918 Oldfield, 0 Emsley, 918 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1836 Ramachandran restraints generated. 918 Oldfield, 0 Emsley, 918 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 804 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 90 time to evaluate : 0.804 Fit side-chains revert: symmetry clash REVERT: D 55 ASP cc_start: 0.6529 (OUTLIER) cc_final: 0.6043 (m-30) REVERT: J 128 LYS cc_start: 0.8722 (mptt) cc_final: 0.8449 (mmtp) REVERT: K 36 TRP cc_start: 0.6991 (t60) cc_final: 0.6733 (t60) REVERT: K 49 TRP cc_start: 0.6863 (m100) cc_final: 0.6506 (m100) REVERT: L 28 LYS cc_start: 0.6520 (ptpp) cc_final: 0.5472 (mmtm) REVERT: L 54 MET cc_start: 0.8579 (tmm) cc_final: 0.8223 (tpp) REVERT: L 61 LEU cc_start: 0.5667 (OUTLIER) cc_final: 0.5447 (pt) REVERT: F 175 ASP cc_start: 0.8186 (t0) cc_final: 0.7857 (t0) outliers start: 49 outliers final: 45 residues processed: 127 average time/residue: 0.1743 time to fit residues: 30.8415 Evaluate side-chains 136 residues out of total 804 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 89 time to evaluate : 0.823 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 115 LEU Chi-restraints excluded: chain B residue 123 LEU Chi-restraints excluded: chain C residue 25 LEU Chi-restraints excluded: chain D residue 30 SER Chi-restraints excluded: chain D residue 55 ASP Chi-restraints excluded: chain E residue 29 HIS Chi-restraints excluded: chain E residue 49 ASN Chi-restraints excluded: chain J residue 117 ILE Chi-restraints excluded: chain K residue 21 THR Chi-restraints excluded: chain L residue 32 LEU Chi-restraints excluded: chain L residue 37 LEU Chi-restraints excluded: chain L residue 61 LEU Chi-restraints excluded: chain M residue 25 HIS Chi-restraints excluded: chain M residue 45 SER Chi-restraints excluded: chain M residue 49 ASN Chi-restraints excluded: chain F residue 94 MET Chi-restraints excluded: chain F residue 119 LEU Chi-restraints excluded: chain F residue 153 VAL Chi-restraints excluded: chain F residue 157 ILE Chi-restraints excluded: chain F residue 182 THR Chi-restraints excluded: chain F residue 213 LEU Chi-restraints excluded: chain F residue 227 ASP Chi-restraints excluded: chain F residue 255 LEU Chi-restraints excluded: chain F residue 302 THR Chi-restraints excluded: chain F residue 313 VAL Chi-restraints excluded: chain F residue 338 VAL Chi-restraints excluded: chain F residue 340 PHE Chi-restraints excluded: chain I residue 51 HIS Chi-restraints excluded: chain I residue 58 VAL Chi-restraints excluded: chain I residue 89 ASN Chi-restraints excluded: chain I residue 100 THR Chi-restraints excluded: chain I residue 119 LEU Chi-restraints excluded: chain I residue 153 VAL Chi-restraints excluded: chain I residue 163 THR Chi-restraints excluded: chain I residue 181 LYS Chi-restraints excluded: chain I residue 182 THR Chi-restraints excluded: chain I residue 216 LEU Chi-restraints excluded: chain I residue 255 LEU Chi-restraints excluded: chain I residue 259 LEU Chi-restraints excluded: chain I residue 267 VAL Chi-restraints excluded: chain I residue 326 CYS Chi-restraints excluded: chain I residue 337 SER Chi-restraints excluded: chain I residue 339 LEU Chi-restraints excluded: chain I residue 347 PHE Chi-restraints excluded: chain I residue 357 LEU Chi-restraints excluded: chain I residue 367 LEU Chi-restraints excluded: chain I residue 368 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 65 optimal weight: 2.9990 chunk 10 optimal weight: 0.7980 chunk 19 optimal weight: 3.9990 chunk 71 optimal weight: 3.9990 chunk 29 optimal weight: 2.9990 chunk 73 optimal weight: 0.8980 chunk 9 optimal weight: 1.9990 chunk 13 optimal weight: 0.9990 chunk 62 optimal weight: 0.6980 chunk 4 optimal weight: 3.9990 chunk 51 optimal weight: 0.6980 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** K 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 321 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4151 r_free = 0.4151 target = 0.181236 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3989 r_free = 0.3989 target = 0.164586 restraints weight = 7958.547| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3968 r_free = 0.3968 target = 0.162866 restraints weight = 16615.853| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3958 r_free = 0.3958 target = 0.162062 restraints weight = 16172.547| |-----------------------------------------------------------------------------| r_work (final): 0.3964 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7235 moved from start: 0.1994 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 7538 Z= 0.244 Angle : 0.653 9.729 10219 Z= 0.321 Chirality : 0.042 0.179 1157 Planarity : 0.004 0.046 1298 Dihedral : 6.546 80.611 1025 Min Nonbonded Distance : 2.105 Molprobity Statistics. All-atom Clashscore : 8.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 6.42 % Allowed : 24.81 % Favored : 68.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.86 (0.29), residues: 918 helix: 2.36 (0.29), residues: 333 sheet: -0.24 (0.26), residues: 410 loop : -0.66 (0.51), residues: 175 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP I 260 HIS 0.007 0.001 HIS C 17 PHE 0.010 0.001 PHE L 41 TYR 0.008 0.001 TYR I 307 ARG 0.004 0.000 ARG F 310 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1706.29 seconds wall clock time: 31 minutes 59.64 seconds (1919.64 seconds total)