Starting phenix.real_space_refine on Fri Jul 19 09:33:03 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8w5k_37295/07_2024/8w5k_37295.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8w5k_37295/07_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_37295/07_2024/8w5k_37295.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8w5k_37295/07_2024/8w5k_37295.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8w5k_37295/07_2024/8w5k_37295.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8w5k_37295/07_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: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/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: 5.21, per 1000 atoms: 0.71 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: 2.94 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: 1.07 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: 2.39 Time building geometry restraints manager: 3.20 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 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 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 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: 3.320 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.240 Check model and map are aligned: 0.050 Set scattering table: 0.080 Process input model: 25.000 Find NCS groups from input model: 0.300 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:2.740 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.770 ------------------------------------------------------------------------------- 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 : 0.839 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: 0.2238 time to fit residues: 34.6441 Evaluate side-chains 103 residues out of total 804 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 98 time to evaluate : 0.864 ------------------------------------------------------------------------------- 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: 0.8980 chunk 68 optimal weight: 1.9990 chunk 37 optimal weight: 2.9990 chunk 23 optimal weight: 0.6980 chunk 46 optimal weight: 2.9990 chunk 36 optimal weight: 1.9990 chunk 70 optimal weight: 0.9980 chunk 27 optimal weight: 1.9990 chunk 42 optimal weight: 0.3980 chunk 52 optimal weight: 1.9990 chunk 81 optimal weight: 1.9990 overall best weight: 0.9982 ------------------------------------------------------------------------------- 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: 0.7533 moved from start: 0.0729 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 7538 Z= 0.282 Angle : 0.678 8.464 10219 Z= 0.338 Chirality : 0.043 0.161 1157 Planarity : 0.004 0.051 1298 Dihedral : 8.103 111.374 1033 Min Nonbonded Distance : 2.067 Molprobity Statistics. All-atom Clashscore : 8.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 5.92 % Allowed : 23.05 % Favored : 71.03 % 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: 0.88 (0.29), residues: 918 helix: 2.40 (0.29), residues: 329 sheet: -0.15 (0.26), residues: 410 loop : -0.88 (0.49), residues: 179 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 0.013 0.002 PHE I 340 TYR 0.016 0.001 TYR I 307 ARG 0.003 0.000 ARG I 315 *********************** 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 149 residues out of total 804 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 102 time to evaluate : 0.844 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 23 LYS cc_start: 0.8270 (ptpp) cc_final: 0.7967 (ptpt) outliers start: 47 outliers final: 29 residues processed: 137 average time/residue: 0.1822 time to fit residues: 33.7900 Evaluate side-chains 123 residues out of total 804 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 94 time to evaluate : 0.817 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 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 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 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 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: 0.0050 chunk 25 optimal weight: 0.4980 chunk 68 optimal weight: 0.7980 chunk 55 optimal weight: 0.3980 chunk 22 optimal weight: 0.8980 chunk 81 optimal weight: 0.8980 chunk 88 optimal weight: 1.9990 chunk 72 optimal weight: 5.9990 chunk 27 optimal weight: 1.9990 chunk 65 optimal weight: 0.7980 chunk 80 optimal weight: 0.0050 overall best weight: 0.3408 ------------------------------------------------------------------------------- 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: 0.7478 moved from start: 0.0972 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= 0.168 Angle : 0.608 7.353 10219 Z= 0.299 Chirality : 0.041 0.161 1157 Planarity : 0.004 0.048 1298 Dihedral : 7.271 105.135 1027 Min Nonbonded Distance : 2.083 Molprobity Statistics. All-atom Clashscore : 8.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 5.54 % Allowed : 24.56 % Favored : 69.90 % 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: 1.01 (0.29), residues: 918 helix: 2.44 (0.29), residues: 331 sheet: -0.07 (0.26), residues: 410 loop : -0.70 (0.50), residues: 177 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP F 260 HIS 0.008 0.001 HIS C 17 PHE 0.010 0.001 PHE E 50 TYR 0.011 0.001 TYR I 307 ARG 0.003 0.000 ARG F 310 *********************** 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 146 residues out of total 804 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 102 time to evaluate : 0.793 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 23 LYS cc_start: 0.8204 (ptpp) cc_final: 0.7914 (ptpt) REVERT: L 28 LYS cc_start: 0.6857 (ptpp) cc_final: 0.6043 (mmtm) REVERT: L 61 LEU cc_start: 0.5195 (OUTLIER) cc_final: 0.4962 (pt) REVERT: I 89 ASN cc_start: 0.7042 (OUTLIER) cc_final: 0.6741 (p0) outliers start: 44 outliers final: 30 residues processed: 135 average time/residue: 0.1971 time to fit residues: 35.6413 Evaluate side-chains 127 residues out of total 804 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 95 time to evaluate : 0.764 ------------------------------------------------------------------------------- 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 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 182 THR 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 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 181 LYS Chi-restraints excluded: chain I residue 259 LEU 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: 3.9990 chunk 54 optimal weight: 0.7980 chunk 82 optimal weight: 0.9980 chunk 86 optimal weight: 0.8980 chunk 77 optimal weight: 0.0770 chunk 23 optimal weight: 0.6980 chunk 72 optimal weight: 0.9990 chunk 49 optimal weight: 1.9990 overall best weight: 0.6538 ------------------------------------------------------------------------------- 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 I 321 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7512 moved from start: 0.1218 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= 0.212 Angle : 0.612 7.937 10219 Z= 0.302 Chirality : 0.041 0.158 1157 Planarity : 0.004 0.045 1298 Dihedral : 7.168 100.482 1027 Min Nonbonded Distance : 2.099 Molprobity Statistics. All-atom Clashscore : 8.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 6.05 % Allowed : 24.69 % Favored : 69.27 % 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: 1.13 (0.30), residues: 918 helix: 2.54 (0.29), residues: 321 sheet: -0.06 (0.26), residues: 410 loop : -0.28 (0.50), residues: 187 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP I 260 HIS 0.009 0.001 HIS C 17 PHE 0.015 0.001 PHE F 120 TYR 0.013 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 137 residues out of total 804 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 89 time to evaluate : 0.827 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: J 113 LEU cc_start: 0.8548 (OUTLIER) cc_final: 0.8176 (tp) REVERT: J 128 LYS cc_start: 0.8780 (mptt) cc_final: 0.8499 (mmtp) REVERT: K 23 LYS cc_start: 0.8208 (ptpp) cc_final: 0.7939 (ptpt) REVERT: L 28 LYS cc_start: 0.6698 (ptpp) cc_final: 0.5919 (mmtm) REVERT: L 61 LEU cc_start: 0.5289 (OUTLIER) cc_final: 0.5070 (pt) outliers start: 48 outliers final: 39 residues processed: 126 average time/residue: 0.1935 time to fit residues: 32.9766 Evaluate side-chains 130 residues out of total 804 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 89 time to evaluate : 0.865 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 115 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 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 153 VAL Chi-restraints excluded: chain F residue 157 ILE Chi-restraints excluded: chain F residue 182 THR Chi-restraints excluded: chain F residue 337 SER 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 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 1 optimal weight: 0.0570 chunk 64 optimal weight: 2.9990 chunk 35 optimal weight: 2.9990 chunk 74 optimal weight: 10.0000 chunk 60 optimal weight: 2.9990 chunk 0 optimal weight: 9.9990 chunk 44 optimal weight: 3.9990 chunk 78 optimal weight: 0.9990 chunk 21 optimal weight: 0.8980 chunk 29 optimal weight: 2.9990 chunk 17 optimal weight: 0.8980 overall best weight: 1.1702 ------------------------------------------------------------------------------- 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: 0.7590 moved from start: 0.1543 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 7538 Z= 0.315 Angle : 0.680 10.949 10219 Z= 0.336 Chirality : 0.043 0.159 1157 Planarity : 0.004 0.046 1298 Dihedral : 7.416 102.223 1027 Min Nonbonded Distance : 2.083 Molprobity Statistics. All-atom Clashscore : 9.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer: Outliers : 7.56 % Allowed : 24.18 % 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: 0.98 (0.29), residues: 918 helix: 2.43 (0.29), residues: 321 sheet: -0.17 (0.26), residues: 410 loop : -0.34 (0.50), residues: 187 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP I 260 HIS 0.006 0.001 HIS C 17 PHE 0.025 0.002 PHE L 42 TYR 0.009 0.001 TYR F 232 ARG 0.004 0.001 ARG I 315 *********************** 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 151 residues out of total 804 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 91 time to evaluate : 0.731 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: J 113 LEU cc_start: 0.8856 (OUTLIER) cc_final: 0.8540 (tp) REVERT: K 23 LYS cc_start: 0.8281 (ptpp) cc_final: 0.8026 (ptpt) REVERT: L 61 LEU cc_start: 0.5469 (OUTLIER) cc_final: 0.5251 (pt) REVERT: F 275 LEU cc_start: 0.7576 (OUTLIER) cc_final: 0.7142 (pp) outliers start: 60 outliers final: 42 residues processed: 141 average time/residue: 0.1877 time to fit residues: 35.3451 Evaluate side-chains 130 residues out of total 804 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 85 time to evaluate : 0.708 ------------------------------------------------------------------------------- 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 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 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 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 275 LEU Chi-restraints excluded: chain F residue 302 THR Chi-restraints excluded: chain F residue 313 VAL Chi-restraints excluded: chain F residue 337 SER 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 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: 1.9990 chunk 21 optimal weight: 0.8980 chunk 87 optimal weight: 1.9990 chunk 72 optimal weight: 1.9990 chunk 40 optimal weight: 0.7980 chunk 7 optimal weight: 0.3980 chunk 28 optimal weight: 3.9990 chunk 45 optimal weight: 0.5980 chunk 83 optimal weight: 1.9990 chunk 9 optimal weight: 1.9990 chunk 49 optimal weight: 0.5980 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** M 26 ASN I 156 GLN I 321 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7552 moved from start: 0.1629 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 7538 Z= 0.216 Angle : 0.625 7.969 10219 Z= 0.307 Chirality : 0.041 0.161 1157 Planarity : 0.004 0.046 1298 Dihedral : 7.111 96.997 1027 Min Nonbonded Distance : 2.095 Molprobity Statistics. All-atom Clashscore : 8.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 6.05 % Allowed : 25.69 % 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: 1.12 (0.30), residues: 918 helix: 2.52 (0.30), residues: 321 sheet: -0.10 (0.26), residues: 410 loop : -0.18 (0.50), residues: 187 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 0.011 0.001 PHE I 340 TYR 0.009 0.001 TYR I 307 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 136 residues out of total 804 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 88 time to evaluate : 0.801 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 40 MET cc_start: 0.5862 (mmt) cc_final: 0.5557 (mpp) REVERT: D 55 ASP cc_start: 0.6379 (OUTLIER) cc_final: 0.5927 (m-30) REVERT: J 113 LEU cc_start: 0.8897 (OUTLIER) cc_final: 0.8686 (tp) REVERT: J 128 LYS cc_start: 0.8753 (mptt) cc_final: 0.8484 (mmtp) REVERT: K 23 LYS cc_start: 0.8260 (ptpp) cc_final: 0.8003 (ptpt) REVERT: K 36 TRP cc_start: 0.6976 (t60) cc_final: 0.6755 (t60) REVERT: L 61 LEU cc_start: 0.5475 (OUTLIER) cc_final: 0.5259 (pt) REVERT: F 275 LEU cc_start: 0.7412 (OUTLIER) cc_final: 0.7037 (pp) REVERT: I 94 MET cc_start: 0.7840 (tpp) cc_final: 0.7574 (tpt) outliers start: 48 outliers final: 37 residues processed: 127 average time/residue: 0.1893 time to fit residues: 32.8464 Evaluate side-chains 127 residues out of total 804 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 86 time to evaluate : 0.876 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 123 LEU Chi-restraints excluded: chain D residue 55 ASP 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 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 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 275 LEU Chi-restraints excluded: chain F residue 302 THR Chi-restraints excluded: chain F residue 313 VAL Chi-restraints excluded: chain F residue 337 SER 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 216 LEU Chi-restraints excluded: chain I residue 255 LEU 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 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: 0.0060 chunk 49 optimal weight: 0.9990 chunk 73 optimal weight: 0.9990 chunk 48 optimal weight: 0.6980 chunk 86 optimal weight: 1.9990 chunk 54 optimal weight: 1.9990 chunk 52 optimal weight: 0.9980 chunk 40 optimal weight: 5.9990 chunk 53 optimal weight: 2.9990 chunk 34 optimal weight: 0.3980 chunk 51 optimal weight: 0.8980 overall best weight: 0.5996 ------------------------------------------------------------------------------- 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: 0.7545 moved from start: 0.1766 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= 0.207 Angle : 0.617 7.538 10219 Z= 0.303 Chirality : 0.040 0.160 1157 Planarity : 0.004 0.046 1298 Dihedral : 6.757 87.987 1027 Min Nonbonded Distance : 2.090 Molprobity Statistics. All-atom Clashscore : 8.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Rotamer: Outliers : 6.68 % Allowed : 25.19 % Favored : 68.14 % 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: 1.07 (0.30), residues: 918 helix: 2.44 (0.29), residues: 333 sheet: -0.05 (0.26), residues: 410 loop : -0.56 (0.51), residues: 175 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 0.010 0.001 PHE D 42 TYR 0.013 0.001 TYR I 217 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 143 residues out of total 804 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 90 time to evaluate : 0.815 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 55 ASP cc_start: 0.6297 (OUTLIER) cc_final: 0.5862 (m-30) REVERT: J 128 LYS cc_start: 0.8735 (mptt) cc_final: 0.8471 (mmtp) REVERT: K 23 LYS cc_start: 0.8256 (ptpp) cc_final: 0.7996 (ptpt) REVERT: K 36 TRP cc_start: 0.6973 (t60) cc_final: 0.6744 (t60) REVERT: L 28 LYS cc_start: 0.6790 (ptpp) cc_final: 0.6028 (mmtm) REVERT: L 54 MET cc_start: 0.8531 (tmm) cc_final: 0.8104 (tpp) REVERT: L 61 LEU cc_start: 0.5446 (OUTLIER) cc_final: 0.5230 (pt) REVERT: F 275 LEU cc_start: 0.7375 (OUTLIER) cc_final: 0.6989 (pp) REVERT: I 94 MET cc_start: 0.7835 (tpp) cc_final: 0.7596 (tpt) outliers start: 53 outliers final: 40 residues processed: 133 average time/residue: 0.1762 time to fit residues: 31.8282 Evaluate side-chains 131 residues out of total 804 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 88 time to evaluate : 0.789 ------------------------------------------------------------------------------- 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 55 ASP 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 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 200 SER 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 337 SER 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 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 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: 0.9980 chunk 17 optimal weight: 0.9980 chunk 16 optimal weight: 0.5980 chunk 55 optimal weight: 0.5980 chunk 59 optimal weight: 1.9990 chunk 42 optimal weight: 5.9990 chunk 8 optimal weight: 0.7980 chunk 68 optimal weight: 0.9990 chunk 78 optimal weight: 1.9990 chunk 83 optimal weight: 1.9990 chunk 75 optimal weight: 0.0000 overall best weight: 0.5984 ------------------------------------------------------------------------------- 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: 0.7545 moved from start: 0.1866 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 7538 Z= 0.206 Angle : 0.614 9.126 10219 Z= 0.301 Chirality : 0.041 0.161 1157 Planarity : 0.004 0.046 1298 Dihedral : 6.454 80.985 1025 Min Nonbonded Distance : 2.088 Molprobity Statistics. All-atom Clashscore : 8.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 6.93 % Allowed : 24.69 % 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: 1.10 (0.30), residues: 918 helix: 2.46 (0.29), residues: 333 sheet: -0.05 (0.26), residues: 410 loop : -0.50 (0.51), residues: 175 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP I 260 HIS 0.009 0.001 HIS C 17 PHE 0.010 0.001 PHE D 42 TYR 0.008 0.001 TYR I 307 ARG 0.005 0.000 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 146 residues out of total 804 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 91 time to evaluate : 0.735 Fit side-chains revert: symmetry clash REVERT: D 55 ASP cc_start: 0.6335 (OUTLIER) cc_final: 0.5875 (m-30) REVERT: J 128 LYS cc_start: 0.8726 (mptt) cc_final: 0.8454 (mmtp) REVERT: K 23 LYS cc_start: 0.8222 (ptpp) cc_final: 0.7985 (ptpt) REVERT: K 36 TRP cc_start: 0.6972 (t60) cc_final: 0.6729 (t60) REVERT: L 28 LYS cc_start: 0.6831 (ptpp) cc_final: 0.6041 (mmtm) REVERT: L 54 MET cc_start: 0.8555 (tmm) cc_final: 0.8075 (tpp) REVERT: L 61 LEU cc_start: 0.5463 (OUTLIER) cc_final: 0.5235 (pt) REVERT: F 275 LEU cc_start: 0.7385 (OUTLIER) cc_final: 0.7088 (pp) REVERT: I 94 MET cc_start: 0.7844 (tpp) cc_final: 0.7623 (tpt) outliers start: 55 outliers final: 46 residues processed: 136 average time/residue: 0.1807 time to fit residues: 33.3485 Evaluate side-chains 136 residues out of total 804 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 87 time to evaluate : 0.803 ------------------------------------------------------------------------------- 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 33 TYR 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 54 LEU 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 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 200 SER 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 337 SER 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: 0.8980 chunk 83 optimal weight: 1.9990 chunk 48 optimal weight: 1.9990 chunk 35 optimal weight: 0.9990 chunk 63 optimal weight: 0.7980 chunk 24 optimal weight: 0.6980 chunk 73 optimal weight: 3.9990 chunk 76 optimal weight: 0.7980 chunk 53 optimal weight: 1.9990 chunk 85 optimal weight: 0.9990 chunk 52 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 321 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7565 moved from start: 0.1977 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= 0.238 Angle : 0.641 9.290 10219 Z= 0.313 Chirality : 0.041 0.158 1157 Planarity : 0.004 0.046 1298 Dihedral : 6.478 81.096 1025 Min Nonbonded Distance : 2.093 Molprobity Statistics. All-atom Clashscore : 8.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 6.42 % Allowed : 25.57 % Favored : 68.01 % 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: 1.06 (0.30), residues: 918 helix: 2.46 (0.29), residues: 333 sheet: -0.08 (0.26), residues: 410 loop : -0.55 (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 42 TYR 0.015 0.001 TYR I 217 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 138 residues out of total 804 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 87 time to evaluate : 0.840 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 55 ASP cc_start: 0.6288 (OUTLIER) cc_final: 0.6055 (m-30) REVERT: K 23 LYS cc_start: 0.8261 (ptpp) cc_final: 0.8028 (ptpt) REVERT: K 36 TRP cc_start: 0.6978 (t60) cc_final: 0.6717 (t60) REVERT: L 28 LYS cc_start: 0.6725 (ptpp) cc_final: 0.5984 (mmtm) REVERT: L 54 MET cc_start: 0.8537 (tmm) cc_final: 0.8074 (tpp) REVERT: L 61 LEU cc_start: 0.5660 (OUTLIER) cc_final: 0.5398 (pt) REVERT: M 38 TYR cc_start: 0.7056 (t80) cc_final: 0.6820 (t80) REVERT: F 275 LEU cc_start: 0.7448 (OUTLIER) cc_final: 0.7083 (pp) REVERT: I 94 MET cc_start: 0.7924 (tpp) cc_final: 0.7688 (tpt) outliers start: 51 outliers final: 47 residues processed: 128 average time/residue: 0.1870 time to fit residues: 32.6209 Evaluate side-chains 137 residues out of total 804 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 87 time to evaluate : 0.807 ------------------------------------------------------------------------------- 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 C residue 25 LEU Chi-restraints excluded: chain D residue 33 TYR Chi-restraints excluded: chain D residue 55 ASP Chi-restraints excluded: chain E residue 29 HIS Chi-restraints excluded: chain E residue 54 LEU 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 22 THR 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 200 SER 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 337 SER 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 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 40 optimal weight: 2.9990 chunk 59 optimal weight: 1.9990 chunk 89 optimal weight: 2.9990 chunk 82 optimal weight: 1.9990 chunk 71 optimal weight: 3.9990 chunk 7 optimal weight: 1.9990 chunk 55 optimal weight: 0.6980 chunk 43 optimal weight: 0.0470 chunk 56 optimal weight: 0.3980 chunk 76 optimal weight: 2.9990 chunk 21 optimal weight: 0.9990 overall best weight: 0.8282 ------------------------------------------------------------------------------- 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: 0.7575 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 0.043 7538 Z= 0.249 Angle : 0.650 9.540 10219 Z= 0.318 Chirality : 0.042 0.159 1157 Planarity : 0.004 0.047 1298 Dihedral : 6.534 81.940 1025 Min Nonbonded Distance : 2.097 Molprobity Statistics. All-atom Clashscore : 8.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 6.17 % Allowed : 26.07 % 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: 1.09 (0.30), residues: 918 helix: 2.49 (0.29), residues: 333 sheet: -0.06 (0.26), residues: 410 loop : -0.57 (0.51), residues: 175 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP I 260 HIS 0.008 0.001 HIS C 17 PHE 0.010 0.001 PHE D 42 TYR 0.008 0.001 TYR I 307 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 : 0.867 Fit side-chains revert: symmetry clash REVERT: D 55 ASP cc_start: 0.6438 (OUTLIER) cc_final: 0.6207 (m-30) REVERT: K 23 LYS cc_start: 0.8269 (ptpp) cc_final: 0.8030 (ptpt) REVERT: K 36 TRP cc_start: 0.6972 (t60) cc_final: 0.6699 (t60) REVERT: L 28 LYS cc_start: 0.6761 (ptpp) cc_final: 0.5994 (mmtm) REVERT: L 54 MET cc_start: 0.8519 (tmm) cc_final: 0.8048 (tpp) REVERT: L 61 LEU cc_start: 0.5677 (OUTLIER) cc_final: 0.5457 (pt) REVERT: F 175 ASP cc_start: 0.8212 (t0) cc_final: 0.7891 (t0) REVERT: F 275 LEU cc_start: 0.7412 (OUTLIER) cc_final: 0.7014 (pp) REVERT: I 94 MET cc_start: 0.7845 (tpp) cc_final: 0.7621 (tpt) outliers start: 49 outliers final: 45 residues processed: 129 average time/residue: 0.1791 time to fit residues: 31.6453 Evaluate side-chains 133 residues out of total 804 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 85 time to evaluate : 0.808 ------------------------------------------------------------------------------- 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 55 ASP Chi-restraints excluded: chain E residue 29 HIS Chi-restraints excluded: chain E residue 54 LEU 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 22 THR 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 200 SER 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 337 SER 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 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: 0.8980 chunk 10 optimal weight: 0.7980 chunk 19 optimal weight: 4.9990 chunk 71 optimal weight: 4.9990 chunk 29 optimal weight: 0.0770 chunk 73 optimal weight: 1.9990 chunk 9 optimal weight: 1.9990 chunk 13 optimal weight: 0.0770 chunk 62 optimal weight: 0.9990 chunk 4 optimal weight: 8.9990 chunk 51 optimal weight: 0.4980 overall best weight: 0.4696 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 17 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 89 ASN ** 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 = 0.4179 r_free = 0.4179 target = 0.183873 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.4020 r_free = 0.4020 target = 0.167411 restraints weight = 7891.307| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3988 r_free = 0.3988 target = 0.164568 restraints weight = 17086.769| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3983 r_free = 0.3983 target = 0.164472 restraints weight = 17365.644| |-----------------------------------------------------------------------------| r_work (final): 0.3991 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7195 moved from start: 0.2131 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 7538 Z= 0.191 Angle : 0.621 9.670 10219 Z= 0.303 Chirality : 0.041 0.159 1157 Planarity : 0.004 0.046 1298 Dihedral : 6.325 76.958 1025 Min Nonbonded Distance : 2.093 Molprobity Statistics. All-atom Clashscore : 9.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 5.54 % Allowed : 26.95 % Favored : 67.51 % 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: 1.20 (0.30), residues: 918 helix: 2.53 (0.29), residues: 333 sheet: 0.02 (0.26), residues: 410 loop : -0.47 (0.51), residues: 175 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP I 260 HIS 0.012 0.001 HIS C 17 PHE 0.011 0.001 PHE D 42 TYR 0.013 0.001 TYR I 217 ARG 0.004 0.000 ARG M 47 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1763.70 seconds wall clock time: 32 minutes 29.28 seconds (1949.28 seconds total)