Starting phenix.real_space_refine on Sat Aug 3 06:58:07 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8w5k_37295/08_2024/8w5k_37295.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8w5k_37295/08_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_37295/08_2024/8w5k_37295.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8w5k_37295/08_2024/8w5k_37295.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8w5k_37295/08_2024/8w5k_37295.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8w5k_37295/08_2024/8w5k_37295.cif" } 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-5409/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: 4.95, per 1000 atoms: 0.67 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: 2.73 Conformation dependent library (CDL) restraints added in 1.4 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... Secondary structure from input PDB file: 21 helices and 2 sheets defined 37.2% alpha, 36.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.94 Creating SS restraints... Processing helix chain 'B' and resid 86 through 135 Proline residue: B 112 - end of helix Processing helix chain 'C' and resid 14 through 49 Proline residue: C 39 - end of helix Processing helix chain 'D' and resid 30 through 51 Processing helix chain 'D' and resid 51 through 58 removed outlier: 4.142A pdb=" N ASP D 55 " --> pdb=" O SER D 51 " (cutoff:3.500A) Processing helix chain 'E' and resid 20 through 44 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 49 through 55 Processing helix chain 'J' and resid 87 through 135 Proline residue: J 112 - end of helix Processing helix chain 'K' and resid 14 through 49 Proline residue: K 39 - end of helix Processing helix chain 'L' and resid 30 through 51 Processing helix chain 'L' and resid 51 through 58 removed outlier: 3.818A pdb=" N ASP L 55 " --> pdb=" O SER L 51 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ALA L 58 " --> pdb=" O MET L 54 " (cutoff:3.500A) Processing helix chain 'M' and resid 20 through 31 removed outlier: 3.604A pdb=" N HIS M 29 " --> pdb=" O HIS M 25 " (cutoff:3.500A) Processing helix chain 'M' and resid 31 through 44 Processing helix chain 'M' and resid 49 through 55 Processing helix chain 'F' and resid 50 through 55 Processing helix chain 'F' and resid 62 through 66 Processing helix chain 'F' and resid 67 through 72 Processing helix chain 'F' and resid 364 through 373 Processing helix chain 'I' and resid 50 through 55 Processing helix chain 'I' and resid 62 through 66 Processing helix chain 'I' and resid 67 through 72 Processing helix chain 'I' and resid 364 through 373 removed outlier: 3.588A pdb=" N GLN I 372 " --> pdb=" O LEU I 368 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'F' and resid 361 through 362 removed outlier: 7.437A pdb=" N THR F 361 " --> pdb=" O ASP F 87 " (cutoff:3.500A) removed outlier: 6.711A pdb=" N ASN F 89 " --> pdb=" O THR F 361 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N ASN F 89 " --> pdb=" O PHE F 359 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N LYS F 323 " --> pdb=" O ASP F 319 " (cutoff:3.500A) removed outlier: 6.540A pdb=" N VAL F 267 " --> pdb=" O VAL F 263 " (cutoff:3.500A) removed outlier: 6.662A pdb=" N LEU F 209 " --> pdb=" O VAL F 205 " (cutoff:3.500A) removed outlier: 4.687A pdb=" N VAL F 196 " --> pdb=" O ASN F 184 " (cutoff:3.500A) removed outlier: 5.424A pdb=" N ASN F 184 " --> pdb=" O VAL F 196 " (cutoff:3.500A) removed outlier: 7.417A pdb=" N VAL F 198 " --> pdb=" O THR F 182 " (cutoff:3.500A) removed outlier: 5.402A pdb=" N THR F 182 " --> pdb=" O VAL F 198 " (cutoff:3.500A) removed outlier: 7.305A pdb=" N SER F 200 " --> pdb=" O VAL F 180 " (cutoff:3.500A) removed outlier: 5.466A pdb=" N VAL F 180 " --> pdb=" O SER F 200 " (cutoff:3.500A) removed outlier: 7.254A pdb=" N LEU F 202 " --> pdb=" O VAL F 178 " (cutoff:3.500A) removed outlier: 5.391A pdb=" N VAL F 178 " --> pdb=" O LEU F 202 " (cutoff:3.500A) removed outlier: 7.428A pdb=" N SER F 204 " --> pdb=" O PHE F 176 " (cutoff:3.500A) removed outlier: 7.039A pdb=" N PHE F 176 " --> pdb=" O SER F 204 " (cutoff:3.500A) removed outlier: 7.668A pdb=" N CYS F 165 " --> pdb=" O ASN F 184 " (cutoff:3.500A) removed outlier: 6.503A pdb=" N PHE F 98 " --> pdb=" O PHE F 92 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'I' and resid 83 through 93 removed outlier: 6.755A pdb=" N PHE I 98 " --> pdb=" O PHE I 92 " (cutoff:3.500A) removed outlier: 7.492A pdb=" N CYS I 165 " --> pdb=" O ASN I 184 " (cutoff:3.500A) removed outlier: 6.978A pdb=" N THR I 194 " --> pdb=" O PRO I 185 " (cutoff:3.500A) removed outlier: 6.728A pdb=" N LEU I 209 " --> pdb=" O VAL I 205 " (cutoff:3.500A) removed outlier: 4.168A pdb=" N LYS I 323 " --> pdb=" O ASP I 319 " (cutoff:3.500A) removed outlier: 5.977A pdb=" N GLY I 83 " --> pdb=" O CYS I 355 " (cutoff:3.500A) removed outlier: 8.057A pdb=" N LEU I 357 " --> pdb=" O GLY I 83 " (cutoff:3.500A) removed outlier: 6.477A pdb=" N ARG I 85 " --> pdb=" O LEU I 357 " (cutoff:3.500A) removed outlier: 7.912A pdb=" N PHE I 359 " --> pdb=" O ARG I 85 " (cutoff:3.500A) removed outlier: 6.701A pdb=" N ASP I 87 " --> pdb=" O PHE I 359 " (cutoff:3.500A) removed outlier: 7.938A pdb=" N THR I 361 " --> pdb=" O ASP I 87 " (cutoff:3.500A) removed outlier: 6.694A pdb=" N ASN I 89 " --> pdb=" O THR I 361 " (cutoff:3.500A) 524 hydrogen bonds defined for protein. 1518 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: 2.96 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: 83 2.64 - 3.21: 6562 3.21 - 3.77: 10971 3.77 - 4.34: 14222 4.34 - 4.90: 24985 Nonbonded interactions: 56823 Sorted by model distance: nonbonded pdb=" OG SER I 218 " pdb=" OD1 ASP I 227 " model vdw 2.076 3.040 nonbonded pdb=" OD1 ASN I 179 " pdb=" OG SER I 200 " model vdw 2.095 3.040 nonbonded pdb=" OD1 ASN I 149 " pdb=" NE2 GLN I 169 " model vdw 2.190 3.120 nonbonded pdb=" OG SER I 186 " pdb=" O THR I 194 " model vdw 2.203 3.040 nonbonded pdb=" NE2 GLN I 166 " pdb=" OE2 GLU I 168 " model vdw 2.221 3.120 ... (remaining 56818 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 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: 2.470 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: 0.320 Check model and map are aligned: 0.050 Set scattering table: 0.060 Process input model: 23.490 Find NCS groups from input model: 0.260 Set up NCS constraints: 0.040 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:2.680 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.380 ------------------------------------------------------------------------------- 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= 0.232 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 : 0.788 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: 0.2216 time to fit residues: 34.3019 Evaluate side-chains 103 residues out of total 804 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 98 time to evaluate : 0.807 ------------------------------------------------------------------------------- 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: 2.9990 chunk 37 optimal weight: 2.9990 chunk 23 optimal weight: 1.9990 chunk 46 optimal weight: 0.6980 chunk 36 optimal weight: 0.7980 chunk 70 optimal weight: 3.9990 chunk 27 optimal weight: 1.9990 chunk 42 optimal weight: 0.2980 chunk 52 optimal weight: 0.8980 chunk 81 optimal weight: 1.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- 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** M 26 ASN I 266 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7491 moved from start: 0.0745 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= 0.215 Angle : 0.658 7.161 10219 Z= 0.329 Chirality : 0.043 0.154 1157 Planarity : 0.004 0.054 1298 Dihedral : 7.965 109.186 1033 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 7.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 4.28 % Allowed : 23.93 % Favored : 71.79 % 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: 0.95 (0.29), residues: 918 helix: 2.43 (0.29), residues: 329 sheet: -0.10 (0.26), residues: 410 loop : -0.79 (0.49), residues: 179 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 0.011 0.001 PHE E 50 TYR 0.015 0.001 TYR I 217 ARG 0.002 0.000 ARG F 261 *********************** 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 141 residues out of total 804 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 107 time to evaluate : 0.799 Fit side-chains revert: symmetry clash REVERT: K 23 LYS cc_start: 0.8257 (ptpp) cc_final: 0.7962 (ptpt) REVERT: I 369 MET cc_start: 0.7147 (mmm) cc_final: 0.6923 (mmm) outliers start: 34 outliers final: 20 residues processed: 132 average time/residue: 0.1942 time to fit residues: 34.3860 Evaluate side-chains 118 residues out of total 804 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 98 time to evaluate : 0.807 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 30 SER Chi-restraints excluded: chain E residue 55 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 M residue 45 SER 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 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 Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 45 optimal weight: 0.7980 chunk 25 optimal weight: 1.9990 chunk 68 optimal weight: 0.7980 chunk 55 optimal weight: 0.6980 chunk 22 optimal weight: 0.9990 chunk 81 optimal weight: 0.9980 chunk 88 optimal weight: 3.9990 chunk 72 optimal weight: 5.9990 chunk 27 optimal weight: 0.0970 chunk 65 optimal weight: 1.9990 chunk 80 optimal weight: 0.3980 overall best weight: 0.5578 ------------------------------------------------------------------------------- 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** F 99 GLN F 365 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7494 moved from start: 0.1093 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= 0.201 Angle : 0.633 7.279 10219 Z= 0.314 Chirality : 0.042 0.162 1157 Planarity : 0.004 0.052 1298 Dihedral : 7.238 105.263 1025 Min Nonbonded Distance : 2.385 Molprobity Statistics. All-atom Clashscore : 7.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 5.29 % Allowed : 24.18 % Favored : 70.53 % 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: 0.97 (0.29), residues: 918 helix: 2.37 (0.29), residues: 331 sheet: -0.08 (0.26), residues: 410 loop : -0.66 (0.50), residues: 177 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP I 260 HIS 0.007 0.001 HIS C 17 PHE 0.011 0.001 PHE E 50 TYR 0.011 0.001 TYR I 307 ARG 0.003 0.000 ARG M 47 *********************** 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 143 residues out of total 804 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 101 time to evaluate : 0.845 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 23 LYS cc_start: 0.8239 (ptpp) cc_final: 0.7964 (ptpt) REVERT: L 28 LYS cc_start: 0.6887 (ptpp) cc_final: 0.6067 (mmtm) REVERT: L 54 MET cc_start: 0.8416 (tmm) cc_final: 0.7983 (tpp) REVERT: L 61 LEU cc_start: 0.5179 (OUTLIER) cc_final: 0.4945 (pt) REVERT: M 26 ASN cc_start: 0.7746 (t0) cc_final: 0.7056 (p0) REVERT: F 242 ASP cc_start: 0.8386 (OUTLIER) cc_final: 0.8093 (t0) outliers start: 42 outliers final: 28 residues processed: 134 average time/residue: 0.1948 time to fit residues: 34.9535 Evaluate side-chains 125 residues out of total 804 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 95 time to evaluate : 0.870 ------------------------------------------------------------------------------- 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 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 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 242 ASP Chi-restraints excluded: chain F residue 313 VAL Chi-restraints excluded: chain F residue 337 SER 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 200 SER Chi-restraints excluded: chain I residue 259 LEU Chi-restraints excluded: chain I residue 267 VAL Chi-restraints excluded: chain I residue 347 PHE Chi-restraints excluded: chain I residue 357 LEU Chi-restraints excluded: chain I residue 367 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 61 optimal weight: 0.7980 chunk 42 optimal weight: 0.5980 chunk 9 optimal weight: 0.9990 chunk 39 optimal weight: 3.9990 chunk 54 optimal weight: 0.7980 chunk 82 optimal weight: 2.9990 chunk 86 optimal weight: 0.4980 chunk 77 optimal weight: 10.0000 chunk 23 optimal weight: 0.8980 chunk 72 optimal weight: 0.4980 chunk 49 optimal weight: 1.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- 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: 0.7507 moved from start: 0.1323 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 7538 Z= 0.213 Angle : 0.625 7.284 10219 Z= 0.311 Chirality : 0.042 0.161 1157 Planarity : 0.004 0.050 1298 Dihedral : 7.040 101.402 1025 Min Nonbonded Distance : 2.390 Molprobity Statistics. All-atom Clashscore : 7.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Rotamer: Outliers : 5.54 % Allowed : 24.81 % Favored : 69.65 % 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: 0.99 (0.29), residues: 918 helix: 2.36 (0.29), residues: 333 sheet: -0.08 (0.26), residues: 410 loop : -0.61 (0.51), residues: 175 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP I 260 HIS 0.009 0.001 HIS C 17 PHE 0.022 0.001 PHE L 42 TYR 0.015 0.001 TYR I 217 ARG 0.004 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 140 residues out of total 804 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 96 time to evaluate : 0.818 Fit side-chains revert: symmetry clash REVERT: J 128 LYS cc_start: 0.8774 (mptt) cc_final: 0.8529 (mmtp) REVERT: K 23 LYS cc_start: 0.8236 (ptpp) cc_final: 0.7963 (ptpt) REVERT: L 28 LYS cc_start: 0.6887 (ptpp) cc_final: 0.6049 (mmtm) REVERT: L 61 LEU cc_start: 0.5180 (OUTLIER) cc_final: 0.4969 (pt) REVERT: M 26 ASN cc_start: 0.7744 (t0) cc_final: 0.7051 (p0) REVERT: F 242 ASP cc_start: 0.8408 (OUTLIER) cc_final: 0.8094 (t0) outliers start: 44 outliers final: 33 residues processed: 130 average time/residue: 0.1873 time to fit residues: 32.9055 Evaluate side-chains 128 residues out of total 804 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 93 time to evaluate : 0.804 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 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 242 ASP Chi-restraints excluded: chain F residue 302 THR Chi-restraints excluded: chain F residue 313 VAL Chi-restraints excluded: chain F residue 340 PHE 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 180 VAL Chi-restraints excluded: chain I residue 181 LYS Chi-restraints excluded: chain I residue 182 THR Chi-restraints excluded: chain I residue 200 SER 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 1 optimal weight: 0.7980 chunk 64 optimal weight: 3.9990 chunk 35 optimal weight: 2.9990 chunk 74 optimal weight: 9.9990 chunk 60 optimal weight: 0.9980 chunk 0 optimal weight: 10.0000 chunk 44 optimal weight: 9.9990 chunk 78 optimal weight: 1.9990 chunk 21 optimal weight: 0.8980 chunk 29 optimal weight: 0.4980 chunk 17 optimal weight: 0.0020 overall best weight: 0.6388 ------------------------------------------------------------------------------- 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: 0.7514 moved from start: 0.1473 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= 0.214 Angle : 0.621 8.001 10219 Z= 0.310 Chirality : 0.042 0.163 1157 Planarity : 0.004 0.050 1298 Dihedral : 6.909 96.537 1025 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 7.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 6.55 % Allowed : 24.81 % Favored : 68.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.10 (0.29), residues: 918 helix: 2.43 (0.29), residues: 321 sheet: -0.07 (0.26), residues: 410 loop : -0.17 (0.51), residues: 187 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP I 260 HIS 0.007 0.001 HIS C 17 PHE 0.010 0.001 PHE I 340 TYR 0.009 0.001 TYR I 307 ARG 0.003 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 149 residues out of total 804 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 97 time to evaluate : 0.855 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: J 113 LEU cc_start: 0.8522 (OUTLIER) cc_final: 0.8149 (tp) REVERT: J 128 LYS cc_start: 0.8774 (mptt) cc_final: 0.8519 (mmtp) REVERT: L 28 LYS cc_start: 0.6787 (ptpp) cc_final: 0.5992 (mmtm) REVERT: L 61 LEU cc_start: 0.5289 (OUTLIER) cc_final: 0.5030 (pt) REVERT: F 242 ASP cc_start: 0.8391 (OUTLIER) cc_final: 0.8088 (t0) outliers start: 52 outliers final: 38 residues processed: 137 average time/residue: 0.1958 time to fit residues: 36.6860 Evaluate side-chains 133 residues out of total 804 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 92 time to evaluate : 0.805 ------------------------------------------------------------------------------- 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 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 25 LEU 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 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 200 SER Chi-restraints excluded: chain F residue 242 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 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 164 MET Chi-restraints excluded: chain I residue 180 VAL 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 357 LEU Chi-restraints excluded: chain I residue 367 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 51 optimal weight: 1.9990 chunk 21 optimal weight: 5.9990 chunk 87 optimal weight: 1.9990 chunk 72 optimal weight: 0.7980 chunk 40 optimal weight: 6.9990 chunk 7 optimal weight: 0.4980 chunk 28 optimal weight: 1.9990 chunk 45 optimal weight: 0.0010 chunk 83 optimal weight: 0.7980 chunk 9 optimal weight: 0.7980 chunk 49 optimal weight: 1.9990 overall best weight: 0.5786 ------------------------------------------------------------------------------- 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: 0.7514 moved from start: 0.1650 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 7538 Z= 0.206 Angle : 0.613 7.989 10219 Z= 0.307 Chirality : 0.041 0.163 1157 Planarity : 0.004 0.049 1298 Dihedral : 6.643 89.321 1025 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 7.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Rotamer: Outliers : 6.80 % Allowed : 24.56 % Favored : 68.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.16 (0.29), residues: 918 helix: 2.48 (0.29), residues: 321 sheet: -0.05 (0.26), residues: 410 loop : -0.12 (0.51), residues: 187 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP I 260 HIS 0.007 0.001 HIS C 17 PHE 0.013 0.001 PHE L 42 TYR 0.008 0.001 TYR I 307 ARG 0.003 0.000 ARG F 310 *********************** 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 152 residues out of total 804 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 98 time to evaluate : 0.820 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 40 MET cc_start: 0.5606 (mmt) cc_final: 0.5323 (mpp) REVERT: J 113 LEU cc_start: 0.8728 (OUTLIER) cc_final: 0.8409 (tp) REVERT: J 128 LYS cc_start: 0.8779 (mptt) cc_final: 0.8520 (mmtp) REVERT: L 28 LYS cc_start: 0.6806 (ptpp) cc_final: 0.6001 (mmtm) REVERT: L 61 LEU cc_start: 0.5298 (OUTLIER) cc_final: 0.5059 (pt) REVERT: M 38 TYR cc_start: 0.7090 (t80) cc_final: 0.6848 (t80) REVERT: F 242 ASP cc_start: 0.8393 (OUTLIER) cc_final: 0.8108 (t0) REVERT: F 275 LEU cc_start: 0.7487 (OUTLIER) cc_final: 0.7195 (pp) outliers start: 54 outliers final: 39 residues processed: 140 average time/residue: 0.1812 time to fit residues: 34.2901 Evaluate side-chains 136 residues out of total 804 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 93 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 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 K residue 25 LEU 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 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 200 SER Chi-restraints excluded: chain F residue 242 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 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 200 SER 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 Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 63 optimal weight: 0.0770 chunk 49 optimal weight: 2.9990 chunk 73 optimal weight: 0.9980 chunk 48 optimal weight: 0.8980 chunk 86 optimal weight: 0.5980 chunk 54 optimal weight: 0.5980 chunk 52 optimal weight: 0.9980 chunk 40 optimal weight: 5.9990 chunk 53 optimal weight: 2.9990 chunk 34 optimal weight: 0.0970 chunk 51 optimal weight: 0.8980 overall best weight: 0.4536 ------------------------------------------------------------------------------- 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: 0.7503 moved from start: 0.1759 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 7538 Z= 0.190 Angle : 0.631 10.470 10219 Z= 0.308 Chirality : 0.041 0.164 1157 Planarity : 0.004 0.048 1298 Dihedral : 6.341 81.677 1025 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 7.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 6.42 % Allowed : 25.19 % Favored : 68.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.22 (0.30), residues: 918 helix: 2.50 (0.29), residues: 321 sheet: -0.01 (0.26), residues: 410 loop : -0.02 (0.52), 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 0.012 0.001 PHE L 42 TYR 0.008 0.001 TYR I 307 ARG 0.003 0.000 ARG I 85 *********************** 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 147 residues out of total 804 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 96 time to evaluate : 0.813 Fit side-chains revert: symmetry clash REVERT: J 113 LEU cc_start: 0.8811 (OUTLIER) cc_final: 0.8585 (tp) REVERT: J 128 LYS cc_start: 0.8773 (mptt) cc_final: 0.8507 (mmtp) REVERT: K 36 TRP cc_start: 0.6949 (t60) cc_final: 0.6717 (t60) REVERT: L 28 LYS cc_start: 0.6778 (ptpp) cc_final: 0.5929 (mmtm) REVERT: L 54 MET cc_start: 0.8458 (tmm) cc_final: 0.7995 (tpp) REVERT: L 61 LEU cc_start: 0.5313 (OUTLIER) cc_final: 0.5053 (pt) REVERT: F 242 ASP cc_start: 0.8399 (OUTLIER) cc_final: 0.8121 (t0) REVERT: F 275 LEU cc_start: 0.7369 (OUTLIER) cc_final: 0.7088 (pp) REVERT: I 94 MET cc_start: 0.7842 (tpp) cc_final: 0.7555 (tpt) outliers start: 51 outliers final: 37 residues processed: 137 average time/residue: 0.1839 time to fit residues: 33.9976 Evaluate side-chains 135 residues out of total 804 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 94 time to evaluate : 0.865 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 123 LEU Chi-restraints excluded: chain D residue 33 TYR 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 K residue 25 LEU 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 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 200 SER Chi-restraints excluded: chain F residue 216 LEU Chi-restraints excluded: chain F residue 242 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 200 SER 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 357 LEU Chi-restraints excluded: chain I residue 367 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 26 optimal weight: 4.9990 chunk 17 optimal weight: 0.7980 chunk 16 optimal weight: 0.7980 chunk 55 optimal weight: 0.9980 chunk 59 optimal weight: 1.9990 chunk 42 optimal weight: 4.9990 chunk 8 optimal weight: 0.6980 chunk 68 optimal weight: 1.9990 chunk 78 optimal weight: 0.8980 chunk 83 optimal weight: 0.8980 chunk 75 optimal weight: 0.6980 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** I 156 GLN I 321 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7547 moved from start: 0.1878 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 : 0.655 11.158 10219 Z= 0.323 Chirality : 0.042 0.161 1157 Planarity : 0.004 0.050 1298 Dihedral : 6.369 81.058 1025 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 7.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 6.55 % Allowed : 25.19 % 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: 1.05 (0.29), residues: 918 helix: 2.37 (0.29), residues: 333 sheet: -0.07 (0.26), residues: 410 loop : -0.43 (0.52), residues: 175 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP F 260 HIS 0.009 0.001 HIS C 17 PHE 0.012 0.001 PHE L 42 TYR 0.015 0.001 TYR I 217 ARG 0.004 0.001 ARG I 85 *********************** 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 147 residues out of total 804 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 95 time to evaluate : 0.828 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: J 128 LYS cc_start: 0.8768 (mptt) cc_final: 0.8500 (mmtp) REVERT: K 36 TRP cc_start: 0.6954 (t60) cc_final: 0.6680 (t60) REVERT: L 28 LYS cc_start: 0.6824 (ptpp) cc_final: 0.6045 (mmtm) REVERT: L 54 MET cc_start: 0.8499 (tmm) cc_final: 0.8038 (tpp) REVERT: L 61 LEU cc_start: 0.5374 (OUTLIER) cc_final: 0.5150 (pt) REVERT: F 242 ASP cc_start: 0.8434 (OUTLIER) cc_final: 0.8121 (t0) REVERT: F 275 LEU cc_start: 0.7446 (OUTLIER) cc_final: 0.7057 (pp) REVERT: I 94 MET cc_start: 0.7929 (tpp) cc_final: 0.7689 (tpt) outliers start: 52 outliers final: 43 residues processed: 135 average time/residue: 0.1862 time to fit residues: 34.4186 Evaluate side-chains 137 residues out of total 804 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 91 time to evaluate : 0.831 ------------------------------------------------------------------------------- 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 20 GLN Chi-restraints excluded: chain E residue 29 HIS Chi-restraints excluded: chain E residue 54 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 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 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 200 SER Chi-restraints excluded: chain F residue 242 ASP Chi-restraints excluded: chain F residue 273 THR 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 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 200 SER 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 80 optimal weight: 0.9990 chunk 83 optimal weight: 2.9990 chunk 48 optimal weight: 1.9990 chunk 35 optimal weight: 2.9990 chunk 63 optimal weight: 0.0970 chunk 24 optimal weight: 0.7980 chunk 73 optimal weight: 1.9990 chunk 76 optimal weight: 2.9990 chunk 53 optimal weight: 2.9990 chunk 85 optimal weight: 0.7980 chunk 52 optimal weight: 1.9990 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: 0.7578 moved from start: 0.2059 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= 0.275 Angle : 0.683 11.266 10219 Z= 0.337 Chirality : 0.043 0.163 1157 Planarity : 0.004 0.049 1298 Dihedral : 6.434 82.617 1023 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 7.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Rotamer: Outliers : 6.42 % Allowed : 25.94 % Favored : 67.63 % 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: 2.26 (0.28), residues: 333 sheet: -0.15 (0.26), residues: 410 loop : -0.51 (0.52), residues: 175 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP I 260 HIS 0.010 0.001 HIS C 17 PHE 0.012 0.001 PHE L 42 TYR 0.008 0.001 TYR I 307 ARG 0.004 0.001 ARG I 310 *********************** 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 143 residues out of total 804 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 92 time to evaluate : 0.787 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: K 23 LYS cc_start: 0.8177 (ptpp) cc_final: 0.7937 (ptpt) REVERT: K 36 TRP cc_start: 0.6962 (t60) cc_final: 0.6635 (t60) REVERT: L 28 LYS cc_start: 0.6893 (ptpp) cc_final: 0.6068 (mmtm) REVERT: L 54 MET cc_start: 0.8532 (tmm) cc_final: 0.8059 (tpp) REVERT: F 242 ASP cc_start: 0.8422 (OUTLIER) cc_final: 0.8215 (t70) REVERT: F 275 LEU cc_start: 0.7408 (OUTLIER) cc_final: 0.7009 (pp) REVERT: I 94 MET cc_start: 0.7880 (tpp) cc_final: 0.7646 (tpt) outliers start: 51 outliers final: 43 residues processed: 131 average time/residue: 0.1715 time to fit residues: 30.9123 Evaluate side-chains 136 residues out of total 804 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 91 time to evaluate : 0.731 ------------------------------------------------------------------------------- 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 20 GLN Chi-restraints excluded: chain E residue 29 HIS Chi-restraints excluded: chain E residue 54 LEU Chi-restraints excluded: chain E residue 55 SER Chi-restraints excluded: chain K residue 25 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 M residue 45 SER 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 200 SER Chi-restraints excluded: chain F residue 242 ASP Chi-restraints excluded: chain F residue 273 THR 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 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 200 SER 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 303 ILE 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 40 optimal weight: 0.9990 chunk 59 optimal weight: 0.3980 chunk 89 optimal weight: 0.9980 chunk 82 optimal weight: 0.9980 chunk 71 optimal weight: 3.9990 chunk 7 optimal weight: 3.9990 chunk 55 optimal weight: 0.9980 chunk 43 optimal weight: 0.0070 chunk 56 optimal weight: 0.7980 chunk 76 optimal weight: 0.9990 chunk 21 optimal weight: 0.9990 overall best weight: 0.6398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 121 GLN ** K 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 321 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7551 moved from start: 0.2113 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 7538 Z= 0.226 Angle : 0.670 11.619 10219 Z= 0.328 Chirality : 0.042 0.163 1157 Planarity : 0.004 0.049 1298 Dihedral : 6.356 79.878 1023 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 7.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Rotamer: Outliers : 5.92 % Allowed : 26.45 % Favored : 67.63 % 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: 0.98 (0.29), residues: 918 helix: 2.29 (0.28), residues: 333 sheet: -0.10 (0.26), residues: 410 loop : -0.43 (0.52), residues: 175 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP I 260 HIS 0.010 0.001 HIS C 17 PHE 0.009 0.001 PHE D 42 TYR 0.020 0.001 TYR I 217 ARG 0.004 0.001 ARG I 310 ********************** 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 141 residues out of total 804 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 94 time to evaluate : 0.831 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: J 128 LYS cc_start: 0.8738 (mptt) cc_final: 0.8476 (mmtp) REVERT: K 23 LYS cc_start: 0.8137 (ptpp) cc_final: 0.7918 (ptpt) REVERT: K 36 TRP cc_start: 0.7044 (t60) cc_final: 0.6702 (t60) REVERT: L 28 LYS cc_start: 0.6728 (ptpp) cc_final: 0.5998 (mmtm) REVERT: L 54 MET cc_start: 0.8529 (tmm) cc_final: 0.8036 (tpp) REVERT: F 242 ASP cc_start: 0.8435 (OUTLIER) cc_final: 0.8232 (t70) REVERT: F 275 LEU cc_start: 0.7361 (OUTLIER) cc_final: 0.6980 (pp) REVERT: I 94 MET cc_start: 0.7878 (tpp) cc_final: 0.7644 (tpt) outliers start: 47 outliers final: 43 residues processed: 131 average time/residue: 0.1795 time to fit residues: 32.3424 Evaluate side-chains 135 residues out of total 804 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 90 time to evaluate : 0.802 ------------------------------------------------------------------------------- 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 20 GLN Chi-restraints excluded: chain E residue 29 HIS Chi-restraints excluded: chain E residue 54 LEU Chi-restraints excluded: chain K residue 25 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 M residue 45 SER Chi-restraints excluded: chain M residue 54 LEU 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 200 SER Chi-restraints excluded: chain F residue 242 ASP Chi-restraints excluded: chain F residue 273 THR 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 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 200 SER 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 303 ILE 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: 0.6980 chunk 10 optimal weight: 0.6980 chunk 19 optimal weight: 6.9990 chunk 71 optimal weight: 4.9990 chunk 29 optimal weight: 0.6980 chunk 73 optimal weight: 0.9980 chunk 9 optimal weight: 1.9990 chunk 13 optimal weight: 0.1980 chunk 62 optimal weight: 0.9990 chunk 4 optimal weight: 10.0000 chunk 51 optimal weight: 0.9980 overall best weight: 0.6580 ------------------------------------------------------------------------------- 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 = 0.4176 r_free = 0.4176 target = 0.183563 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4015 r_free = 0.4015 target = 0.167186 restraints weight = 7887.678| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.4007 r_free = 0.4007 target = 0.166477 restraints weight = 18090.567| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.4005 r_free = 0.4005 target = 0.166556 restraints weight = 15519.970| |-----------------------------------------------------------------------------| r_work (final): 0.4013 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7165 moved from start: 0.2180 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 7538 Z= 0.228 Angle : 0.670 11.059 10219 Z= 0.329 Chirality : 0.042 0.163 1157 Planarity : 0.004 0.049 1298 Dihedral : 6.329 78.665 1023 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 7.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 6.05 % Allowed : 26.20 % Favored : 67.76 % 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: 0.95 (0.29), residues: 918 helix: 2.27 (0.28), residues: 333 sheet: -0.11 (0.26), residues: 410 loop : -0.45 (0.52), residues: 175 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP I 260 HIS 0.010 0.001 HIS C 17 PHE 0.010 0.001 PHE D 42 TYR 0.008 0.001 TYR I 307 ARG 0.005 0.001 ARG I 310 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1723.05 seconds wall clock time: 31 minutes 49.25 seconds (1909.25 seconds total)