Starting phenix.real_space_refine on Sat Apr 6 06:21:15 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8w5j_37294/04_2024/8w5j_37294_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8w5j_37294/04_2024/8w5j_37294.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8w5j_37294/04_2024/8w5j_37294.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8w5j_37294/04_2024/8w5j_37294.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8w5j_37294/04_2024/8w5j_37294_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8w5j_37294/04_2024/8w5j_37294_updated.pdb" } resolution = 4.4 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= 0.002 sd= 0.023 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 4718 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 "A PHE 120": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 201": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 307": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 232": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 309": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 340": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M PHE 50": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 7356 Number of models: 1 Model: "" Number of chains: 11 Chain: "A" 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: "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: "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: "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: "I" Number of atoms: 20 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 20 Unusual residues: {'46E': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 23 Unresolved non-hydrogen angles: 23 Unresolved non-hydrogen dihedrals: 23 Time building chain proxies: 4.08, per 1000 atoms: 0.55 Number of scatterers: 7356 At special positions: 0 Unit cell: (94.16, 104.86, 138.03, 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 4718 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: 2.95 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... running ksdssp... Secondary structure from input PDB file: 18 helices and 2 sheets defined 33.0% alpha, 34.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.35 Creating SS restraints... Processing helix chain 'A' and resid 50 through 54 Processing helix chain 'A' and resid 68 through 71 No H-bonds generated for 'chain 'A' and resid 68 through 71' Processing helix chain 'A' and resid 365 through 372 Processing helix chain 'B' and resid 87 through 134 Proline residue: B 112 - end of helix Processing helix chain 'C' and resid 14 through 48 Proline residue: C 39 - end of helix Processing helix chain 'D' and resid 31 through 50 Processing helix chain 'D' and resid 52 through 57 Processing helix chain 'E' and resid 20 through 43 removed outlier: 3.809A pdb=" N ASN E 26 " --> pdb=" O THR E 22 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N VAL E 27 " --> pdb=" O LEU E 23 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N HIS E 29 " --> pdb=" O HIS E 25 " (cutoff:3.500A) removed outlier: 5.498A pdb=" N ILE E 33 " --> pdb=" O HIS E 29 " (cutoff:3.500A) Proline residue: E 34 - end of helix Processing helix chain 'E' and resid 50 through 54 Processing helix chain 'I' and resid 50 through 55 Processing helix chain 'I' and resid 68 through 71 No H-bonds generated for 'chain 'I' and resid 68 through 71' Processing helix chain 'I' and resid 365 through 372 removed outlier: 3.575A pdb=" N GLN I 372 " --> pdb=" O LEU I 368 " (cutoff:3.500A) Processing helix chain 'J' and resid 87 through 134 Proline residue: J 112 - end of helix Processing helix chain 'K' and resid 14 through 48 Proline residue: K 39 - end of helix Processing helix chain 'L' and resid 31 through 50 Processing helix chain 'L' and resid 52 through 57 Processing helix chain 'M' and resid 20 through 43 removed outlier: 3.558A pdb=" N ALA M 28 " --> pdb=" O THR M 24 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N HIS M 29 " --> pdb=" O HIS M 25 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N TRP M 32 " --> pdb=" O ALA M 28 " (cutoff:3.500A) removed outlier: 4.942A pdb=" N ILE M 33 " --> pdb=" O HIS M 29 " (cutoff:3.500A) Proline residue: M 34 - end of helix Processing helix chain 'M' and resid 50 through 54 Processing sheet with id= A, first strand: chain 'A' and resid 83 through 91 removed outlier: 3.576A pdb=" N LEU A 357 " --> pdb=" O ARG A 85 " (cutoff:3.500A) removed outlier: 4.142A pdb=" N LYS A 323 " --> pdb=" O ASP A 319 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N THR A 317 " --> pdb=" O ALA A 325 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N VAL A 313 " --> pdb=" O GLU A 329 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N THR A 302 " --> pdb=" O GLU A 272 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N ALA A 269 " --> pdb=" O ARG A 261 " (cutoff:3.500A) removed outlier: 6.855A pdb=" N LEU A 211 " --> pdb=" O SER A 204 " (cutoff:3.500A) removed outlier: 5.385A pdb=" N SER A 204 " --> pdb=" O LEU A 211 " (cutoff:3.500A) removed outlier: 7.169A pdb=" N LEU A 213 " --> pdb=" O LEU A 202 " (cutoff:3.500A) removed outlier: 4.893A pdb=" N LEU A 202 " --> pdb=" O LEU A 213 " (cutoff:3.500A) removed outlier: 6.617A pdb=" N THR A 215 " --> pdb=" O SER A 200 " (cutoff:3.500A) removed outlier: 4.979A pdb=" N SER A 200 " --> pdb=" O THR A 215 " (cutoff:3.500A) removed outlier: 7.264A pdb=" N TYR A 217 " --> pdb=" O VAL A 198 " (cutoff:3.500A) removed outlier: 5.232A pdb=" N VAL A 198 " --> pdb=" O TYR A 217 " (cutoff:3.500A) removed outlier: 7.021A pdb=" N ARG A 219 " --> pdb=" O VAL A 196 " (cutoff:3.500A) removed outlier: 4.925A pdb=" N VAL A 196 " --> pdb=" O ARG A 219 " (cutoff:3.500A) removed outlier: 6.834A pdb=" N THR A 100 " --> pdb=" O ALA A 91 " (cutoff:3.500A) removed outlier: 5.055A pdb=" N ALA A 91 " --> pdb=" O THR A 100 " (cutoff:3.500A) removed outlier: 6.509A pdb=" N HIS A 102 " --> pdb=" O ASN A 89 " (cutoff:3.500A) removed outlier: 4.447A pdb=" N ASN A 89 " --> pdb=" O HIS A 102 " (cutoff:3.500A) removed outlier: 7.011A pdb=" N PHE A 104 " --> pdb=" O ASP A 87 " (cutoff:3.500A) removed outlier: 5.135A pdb=" N ASP A 87 " --> pdb=" O PHE A 104 " (cutoff:3.500A) removed outlier: 7.147A pdb=" N ILE A 106 " --> pdb=" O ARG A 85 " (cutoff:3.500A) removed outlier: 5.135A pdb=" N ARG A 85 " --> pdb=" O ILE A 106 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'I' and resid 85 through 91 removed outlier: 3.646A pdb=" N THR I 361 " --> pdb=" O ASN I 89 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N SER I 337 " --> pdb=" O GLN I 358 " (cutoff:3.500A) removed outlier: 4.214A pdb=" N LYS I 323 " --> pdb=" O ASP I 319 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N GLU I 268 " --> pdb=" O LYS I 306 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N LEU I 255 " --> pdb=" O LEU I 275 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N VAL I 196 " --> pdb=" O LEU I 183 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N MET I 164 " --> pdb=" O GLN I 156 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N PHE I 98 " --> pdb=" O SER I 93 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N SER I 93 " --> pdb=" O PHE I 98 " (cutoff:3.500A) removed outlier: 7.055A pdb=" N THR I 100 " --> pdb=" O ALA I 91 " (cutoff:3.500A) removed outlier: 5.264A pdb=" N ALA I 91 " --> pdb=" O THR I 100 " (cutoff:3.500A) removed outlier: 6.698A pdb=" N HIS I 102 " --> pdb=" O ASN I 89 " (cutoff:3.500A) removed outlier: 4.545A pdb=" N ASN I 89 " --> pdb=" O HIS I 102 " (cutoff:3.500A) removed outlier: 6.753A pdb=" N PHE I 104 " --> pdb=" O ASP I 87 " (cutoff:3.500A) removed outlier: 4.753A pdb=" N ASP I 87 " --> pdb=" O PHE I 104 " (cutoff:3.500A) removed outlier: 7.266A pdb=" N ILE I 106 " --> pdb=" O ARG I 85 " (cutoff:3.500A) removed outlier: 5.251A pdb=" N ARG I 85 " --> pdb=" O ILE I 106 " (cutoff:3.500A) 467 hydrogen bonds defined for protein. 1362 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: 2.48 Time building geometry restraints manager: 3.17 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: 1306 1.33 - 1.45: 1978 1.45 - 1.57: 4192 1.57 - 1.69: 3 1.69 - 1.81: 36 Bond restraints: 7515 Sorted by residual: bond pdb=" CA ASP A 134 " pdb=" CB ASP A 134 " ideal model delta sigma weight residual 1.532 1.548 -0.016 1.33e-02 5.65e+03 1.40e+00 bond pdb=" CB ASP I 134 " pdb=" CG ASP I 134 " ideal model delta sigma weight residual 1.516 1.544 -0.028 2.50e-02 1.60e+03 1.22e+00 bond pdb=" CA VAL E 60 " pdb=" CB VAL E 60 " ideal model delta sigma weight residual 1.540 1.569 -0.029 2.70e-02 1.37e+03 1.17e+00 bond pdb=" CA VAL M 60 " pdb=" CB VAL M 60 " ideal model delta sigma weight residual 1.540 1.568 -0.028 2.70e-02 1.37e+03 1.08e+00 bond pdb=" CB ASP A 134 " pdb=" CG ASP A 134 " ideal model delta sigma weight residual 1.516 1.541 -0.025 2.50e-02 1.60e+03 1.01e+00 ... (remaining 7510 not shown) Histogram of bond angle deviations from ideal: 93.07 - 101.26: 14 101.26 - 109.45: 666 109.45 - 117.64: 4949 117.64 - 125.84: 4443 125.84 - 134.03: 124 Bond angle restraints: 10196 Sorted by residual: angle pdb=" CA PRO I 185 " pdb=" N PRO I 185 " pdb=" CD PRO I 185 " ideal model delta sigma weight residual 112.00 107.38 4.62 1.40e+00 5.10e-01 1.09e+01 angle pdb=" C ASN A 133 " pdb=" N ASP A 134 " pdb=" CA ASP A 134 " ideal model delta sigma weight residual 124.82 130.42 -5.60 1.78e+00 3.16e-01 9.90e+00 angle pdb=" C ASN I 133 " pdb=" N ASP I 134 " pdb=" CA ASP I 134 " ideal model delta sigma weight residual 125.66 130.23 -4.57 1.85e+00 2.92e-01 6.11e+00 angle pdb=" CA LEU D 57 " pdb=" CB LEU D 57 " pdb=" CG LEU D 57 " ideal model delta sigma weight residual 116.30 124.27 -7.97 3.50e+00 8.16e-02 5.19e+00 angle pdb=" C SER E 59 " pdb=" N VAL E 60 " pdb=" CA VAL E 60 " ideal model delta sigma weight residual 121.70 125.78 -4.08 1.80e+00 3.09e-01 5.13e+00 ... (remaining 10191 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.28: 4069 17.28 - 34.56: 307 34.56 - 51.84: 43 51.84 - 69.12: 11 69.12 - 86.40: 2 Dihedral angle restraints: 4432 sinusoidal: 1714 harmonic: 2718 Sorted by residual: dihedral pdb=" CA ASN A 95 " pdb=" C ASN A 95 " pdb=" N PRO A 96 " pdb=" CA PRO A 96 " ideal model delta harmonic sigma weight residual 180.00 151.93 28.07 0 5.00e+00 4.00e-02 3.15e+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 180.00 155.14 24.86 0 5.00e+00 4.00e-02 2.47e+01 dihedral pdb=" CA ASN A 133 " pdb=" C ASN A 133 " pdb=" N ASP A 134 " pdb=" CA ASP A 134 " ideal model delta harmonic sigma weight residual -180.00 -159.25 -20.75 0 5.00e+00 4.00e-02 1.72e+01 ... (remaining 4429 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.029: 701 0.029 - 0.058: 314 0.058 - 0.087: 85 0.087 - 0.116: 50 0.116 - 0.145: 7 Chirality restraints: 1157 Sorted by residual: chirality pdb=" CA ILE I 353 " pdb=" N ILE I 353 " pdb=" C ILE I 353 " pdb=" CB ILE I 353 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.27e-01 chirality pdb=" CA ILE I 344 " pdb=" N ILE I 344 " pdb=" C ILE I 344 " pdb=" CB ILE I 344 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.82e-01 chirality pdb=" CA ILE A 303 " pdb=" N ILE A 303 " pdb=" C ILE A 303 " pdb=" CB ILE A 303 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.64e-01 ... (remaining 1154 not shown) Planarity restraints: 1298 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASN I 184 " -0.073 5.00e-02 4.00e+02 1.09e-01 1.91e+01 pdb=" N PRO I 185 " 0.189 5.00e-02 4.00e+02 pdb=" CA PRO I 185 " -0.057 5.00e-02 4.00e+02 pdb=" CD PRO I 185 " -0.059 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR A 206 " -0.031 5.00e-02 4.00e+02 4.75e-02 3.61e+00 pdb=" N PRO A 207 " 0.082 5.00e-02 4.00e+02 pdb=" CA PRO A 207 " -0.024 5.00e-02 4.00e+02 pdb=" CD PRO A 207 " -0.026 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE E 33 " 0.028 5.00e-02 4.00e+02 4.16e-02 2.77e+00 pdb=" N PRO E 34 " -0.072 5.00e-02 4.00e+02 pdb=" CA PRO E 34 " 0.021 5.00e-02 4.00e+02 pdb=" CD PRO E 34 " 0.023 5.00e-02 4.00e+02 ... (remaining 1295 not shown) Histogram of nonbonded interaction distances: 2.17 - 2.72: 316 2.72 - 3.26: 7822 3.26 - 3.81: 12320 3.81 - 4.35: 14016 4.35 - 4.90: 24142 Nonbonded interactions: 58616 Sorted by model distance: nonbonded pdb=" OG SER I 218 " pdb=" OD1 ASP I 227 " model vdw 2.174 2.440 nonbonded pdb=" OD1 ASN A 179 " pdb=" OG SER A 200 " model vdw 2.191 2.440 nonbonded pdb=" OG SER I 151 " pdb=" OE1 GLN I 169 " model vdw 2.226 2.440 nonbonded pdb=" OD1 ASN I 179 " pdb=" OG SER I 200 " model vdw 2.227 2.440 nonbonded pdb=" OG1 THR A 62 " pdb=" OD1 ASN A 65 " model vdw 2.231 2.440 ... (remaining 58611 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 'A' selection = (chain 'I' and resid 49 through 373) } 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' } 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: 2.690 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: 10.350 Check model and map are aligned: 0.100 Set scattering table: 0.080 Process input model: 24.870 Find NCS groups from input model: 0.520 Set up NCS constraints: 0.160 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: 0.010 Load rotamer database and sin/cos tables:2.880 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 41.670 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7970 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 : 0.002 0.036 7515 Z= 0.156 Angle : 0.631 7.970 10196 Z= 0.310 Chirality : 0.039 0.145 1157 Planarity : 0.005 0.109 1298 Dihedral : 12.495 86.405 2672 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 13.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 0.00 % Allowed : 0.50 % Favored : 99.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.07 (0.29), residues: 918 helix: 2.12 (0.28), residues: 324 sheet: 0.18 (0.27), residues: 378 loop : -0.30 (0.49), residues: 216 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP K 42 HIS 0.004 0.001 HIS A 346 PHE 0.016 0.001 PHE I 340 TYR 0.018 0.001 TYR I 314 ARG 0.004 0.000 ARG A 315 *********************** 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 74 residues out of total 804 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 74 time to evaluate : 0.877 Fit side-chains revert: symmetry clash REVERT: D 54 MET cc_start: 0.8156 (ptt) cc_final: 0.7902 (ptt) REVERT: I 352 LYS cc_start: 0.9468 (mttp) cc_final: 0.9231 (mmtm) outliers start: 0 outliers final: 0 residues processed: 74 average time/residue: 0.1403 time to fit residues: 16.0319 Evaluate side-chains 56 residues out of total 804 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 56 time to evaluate : 0.798 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 75 optimal weight: 5.9990 chunk 68 optimal weight: 9.9990 chunk 37 optimal weight: 7.9990 chunk 23 optimal weight: 8.9990 chunk 46 optimal weight: 7.9990 chunk 36 optimal weight: 2.9990 chunk 70 optimal weight: 0.0030 chunk 27 optimal weight: 2.9990 chunk 42 optimal weight: 0.0980 chunk 52 optimal weight: 3.9990 chunk 81 optimal weight: 0.0770 overall best weight: 1.2352 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 99 GLN ** A 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 248 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 99 GLN ** I 133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 248 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7971 moved from start: 0.0839 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 7515 Z= 0.176 Angle : 0.612 7.171 10196 Z= 0.313 Chirality : 0.041 0.194 1157 Planarity : 0.005 0.071 1298 Dihedral : 6.808 80.601 1000 Min Nonbonded Distance : 2.008 Molprobity Statistics. All-atom Clashscore : 13.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 0.00 % Allowed : 3.78 % Favored : 96.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.94 % 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: 1.24 (0.29), residues: 918 helix: 2.25 (0.28), residues: 328 sheet: 0.12 (0.26), residues: 402 loop : 0.10 (0.57), residues: 188 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 260 HIS 0.004 0.001 HIS A 346 PHE 0.010 0.001 PHE A 359 TYR 0.013 0.001 TYR I 314 ARG 0.003 0.000 ARG A 330 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1836 Ramachandran restraints generated. 918 Oldfield, 0 Emsley, 918 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1836 Ramachandran restraints generated. 918 Oldfield, 0 Emsley, 918 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 804 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 75 time to evaluate : 0.929 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: I 352 LYS cc_start: 0.9457 (mttp) cc_final: 0.9231 (mmtm) outliers start: 0 outliers final: 0 residues processed: 75 average time/residue: 0.1395 time to fit residues: 16.3507 Evaluate side-chains 55 residues out of total 804 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 55 time to evaluate : 0.882 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 45 optimal weight: 9.9990 chunk 25 optimal weight: 8.9990 chunk 68 optimal weight: 6.9990 chunk 55 optimal weight: 9.9990 chunk 22 optimal weight: 10.0000 chunk 81 optimal weight: 5.9990 chunk 88 optimal weight: 3.9990 chunk 72 optimal weight: 4.9990 chunk 27 optimal weight: 1.9990 chunk 65 optimal weight: 0.7980 chunk 80 optimal weight: 0.5980 overall best weight: 2.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 99 GLN ** A 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 208 GLN ** A 248 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 371 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 99 GLN I 133 ASN ** I 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 248 GLN M 25 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8025 moved from start: 0.1448 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 7515 Z= 0.235 Angle : 0.606 9.372 10196 Z= 0.311 Chirality : 0.040 0.172 1157 Planarity : 0.004 0.057 1298 Dihedral : 6.797 78.754 1000 Min Nonbonded Distance : 2.022 Molprobity Statistics. All-atom Clashscore : 16.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 0.25 % Allowed : 5.92 % Favored : 93.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.94 % 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 (0.29), residues: 918 helix: 2.23 (0.27), residues: 324 sheet: -0.06 (0.25), residues: 404 loop : 0.03 (0.57), residues: 190 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 260 HIS 0.005 0.001 HIS A 346 PHE 0.015 0.001 PHE A 359 TYR 0.015 0.002 TYR I 114 ARG 0.003 0.000 ARG A 315 *********************** 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 71 residues out of total 804 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 69 time to evaluate : 0.953 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 79 TYR cc_start: 0.8677 (m-80) cc_final: 0.8127 (m-10) REVERT: D 54 MET cc_start: 0.8031 (ptt) cc_final: 0.7826 (ptt) outliers start: 2 outliers final: 1 residues processed: 71 average time/residue: 0.1343 time to fit residues: 15.0689 Evaluate side-chains 55 residues out of total 804 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 54 time to evaluate : 0.877 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 61 optimal weight: 4.9990 chunk 42 optimal weight: 0.5980 chunk 9 optimal weight: 0.5980 chunk 39 optimal weight: 7.9990 chunk 54 optimal weight: 7.9990 chunk 82 optimal weight: 10.0000 chunk 86 optimal weight: 20.0000 chunk 77 optimal weight: 2.9990 chunk 23 optimal weight: 6.9990 chunk 72 optimal weight: 3.9990 chunk 49 optimal weight: 9.9990 overall best weight: 2.6386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 99 GLN ** A 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 248 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 311 GLN ** A 371 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 99 GLN ** I 133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 248 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8049 moved from start: 0.1887 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 7515 Z= 0.244 Angle : 0.616 10.510 10196 Z= 0.316 Chirality : 0.040 0.168 1157 Planarity : 0.004 0.052 1298 Dihedral : 6.921 76.812 1000 Min Nonbonded Distance : 2.017 Molprobity Statistics. All-atom Clashscore : 16.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 0.00 % Allowed : 5.42 % Favored : 94.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.94 % 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: 0.94 (0.29), residues: 918 helix: 2.15 (0.27), residues: 324 sheet: -0.11 (0.25), residues: 404 loop : -0.13 (0.56), residues: 190 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 260 HIS 0.005 0.001 HIS A 346 PHE 0.017 0.001 PHE A 359 TYR 0.015 0.002 TYR I 114 ARG 0.005 0.000 ARG A 330 *********************** 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 72 residues out of total 804 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 72 time to evaluate : 0.922 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 79 TYR cc_start: 0.8659 (m-80) cc_final: 0.8347 (m-10) REVERT: D 54 MET cc_start: 0.8082 (ptt) cc_final: 0.7798 (ptt) outliers start: 0 outliers final: 0 residues processed: 72 average time/residue: 0.1221 time to fit residues: 13.9802 Evaluate side-chains 56 residues out of total 804 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 56 time to evaluate : 0.841 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 1 optimal weight: 0.5980 chunk 64 optimal weight: 3.9990 chunk 35 optimal weight: 1.9990 chunk 74 optimal weight: 2.9990 chunk 60 optimal weight: 5.9990 chunk 0 optimal weight: 5.9990 chunk 44 optimal weight: 2.9990 chunk 78 optimal weight: 9.9990 chunk 21 optimal weight: 4.9990 chunk 29 optimal weight: 3.9990 chunk 17 optimal weight: 0.6980 overall best weight: 1.8586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 248 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 371 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 99 GLN ** I 133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 248 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8037 moved from start: 0.2132 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 7515 Z= 0.196 Angle : 0.596 9.940 10196 Z= 0.299 Chirality : 0.040 0.174 1157 Planarity : 0.004 0.057 1298 Dihedral : 6.824 76.308 1000 Min Nonbonded Distance : 2.029 Molprobity Statistics. All-atom Clashscore : 15.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 0.00 % Allowed : 3.53 % Favored : 96.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.94 % 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: 2.24 (0.27), residues: 326 sheet: -0.11 (0.25), residues: 402 loop : -0.15 (0.57), residues: 190 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP K 42 HIS 0.004 0.001 HIS A 346 PHE 0.015 0.001 PHE A 359 TYR 0.012 0.002 TYR I 114 ARG 0.002 0.000 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 70 residues out of total 804 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 70 time to evaluate : 0.922 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 79 TYR cc_start: 0.8579 (m-80) cc_final: 0.8272 (m-10) REVERT: B 126 MET cc_start: 0.9589 (ppp) cc_final: 0.9334 (ppp) REVERT: D 54 MET cc_start: 0.8099 (ptt) cc_final: 0.7839 (ptt) outliers start: 0 outliers final: 0 residues processed: 70 average time/residue: 0.1268 time to fit residues: 14.1208 Evaluate side-chains 55 residues out of total 804 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 55 time to evaluate : 0.861 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 51 optimal weight: 8.9990 chunk 21 optimal weight: 0.6980 chunk 87 optimal weight: 6.9990 chunk 72 optimal weight: 2.9990 chunk 40 optimal weight: 0.9980 chunk 7 optimal weight: 10.0000 chunk 28 optimal weight: 2.9990 chunk 45 optimal weight: 10.0000 chunk 83 optimal weight: 3.9990 chunk 9 optimal weight: 9.9990 chunk 49 optimal weight: 10.0000 overall best weight: 2.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 248 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 371 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 99 GLN ** I 133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 248 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8058 moved from start: 0.2420 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 7515 Z= 0.226 Angle : 0.616 11.121 10196 Z= 0.312 Chirality : 0.041 0.165 1157 Planarity : 0.004 0.054 1298 Dihedral : 6.844 75.474 1000 Min Nonbonded Distance : 2.029 Molprobity Statistics. All-atom Clashscore : 17.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.94 % 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: 2.20 (0.27), residues: 326 sheet: -0.14 (0.25), residues: 408 loop : -0.26 (0.58), residues: 184 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP K 42 HIS 0.004 0.001 HIS A 346 PHE 0.023 0.001 PHE D 42 TYR 0.014 0.002 TYR I 114 ARG 0.004 0.000 ARG A 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 72 residues out of total 804 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 72 time to evaluate : 0.778 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 79 TYR cc_start: 0.8639 (m-80) cc_final: 0.7981 (m-80) REVERT: A 213 LEU cc_start: 0.9317 (tp) cc_final: 0.9053 (tp) outliers start: 0 outliers final: 0 residues processed: 72 average time/residue: 0.1295 time to fit residues: 14.7788 Evaluate side-chains 55 residues out of total 804 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 55 time to evaluate : 0.859 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 63 optimal weight: 9.9990 chunk 49 optimal weight: 6.9990 chunk 73 optimal weight: 4.9990 chunk 48 optimal weight: 2.9990 chunk 86 optimal weight: 20.0000 chunk 54 optimal weight: 0.8980 chunk 52 optimal weight: 5.9990 chunk 40 optimal weight: 0.8980 chunk 53 optimal weight: 0.9990 chunk 34 optimal weight: 6.9990 chunk 51 optimal weight: 1.9990 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 248 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 371 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 99 GLN ** I 133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 248 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8045 moved from start: 0.2596 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 7515 Z= 0.173 Angle : 0.601 9.744 10196 Z= 0.298 Chirality : 0.041 0.178 1157 Planarity : 0.005 0.078 1298 Dihedral : 6.693 75.074 1000 Min Nonbonded Distance : 2.041 Molprobity Statistics. All-atom Clashscore : 15.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 0.00 % Allowed : 2.02 % Favored : 97.98 % 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: 2.24 (0.27), residues: 326 sheet: -0.07 (0.25), residues: 406 loop : -0.25 (0.58), residues: 186 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP K 42 HIS 0.004 0.001 HIS A 346 PHE 0.029 0.001 PHE D 42 TYR 0.012 0.001 TYR I 307 ARG 0.002 0.000 ARG I 315 *********************** 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 72 residues out of total 804 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 72 time to evaluate : 0.874 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 79 TYR cc_start: 0.8597 (m-80) cc_final: 0.8025 (m-80) REVERT: A 213 LEU cc_start: 0.9315 (tp) cc_final: 0.9044 (tp) REVERT: A 307 TYR cc_start: 0.8942 (m-80) cc_final: 0.8312 (m-80) REVERT: B 126 MET cc_start: 0.9604 (ppp) cc_final: 0.9323 (ppp) REVERT: D 54 MET cc_start: 0.8199 (ptt) cc_final: 0.7630 (ptt) outliers start: 0 outliers final: 0 residues processed: 72 average time/residue: 0.1278 time to fit residues: 14.6018 Evaluate side-chains 55 residues out of total 804 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 55 time to evaluate : 0.893 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 26 optimal weight: 0.0670 chunk 17 optimal weight: 0.2980 chunk 16 optimal weight: 9.9990 chunk 55 optimal weight: 10.0000 chunk 59 optimal weight: 0.7980 chunk 42 optimal weight: 8.9990 chunk 8 optimal weight: 7.9990 chunk 68 optimal weight: 10.0000 chunk 78 optimal weight: 8.9990 chunk 83 optimal weight: 3.9990 chunk 75 optimal weight: 9.9990 overall best weight: 2.6322 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 248 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 371 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 99 GLN ** I 133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 248 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8078 moved from start: 0.2831 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 7515 Z= 0.238 Angle : 0.632 11.708 10196 Z= 0.318 Chirality : 0.041 0.163 1157 Planarity : 0.005 0.066 1298 Dihedral : 6.786 74.330 1000 Min Nonbonded Distance : 2.036 Molprobity Statistics. All-atom Clashscore : 18.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer: Outliers : 0.00 % Allowed : 1.64 % Favored : 98.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.94 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.87 (0.29), residues: 918 helix: 2.16 (0.27), residues: 323 sheet: -0.13 (0.25), residues: 408 loop : -0.32 (0.57), residues: 187 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP K 42 HIS 0.004 0.001 HIS A 346 PHE 0.025 0.001 PHE D 42 TYR 0.014 0.002 TYR I 114 ARG 0.002 0.000 ARG I 140 *********************** 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 69 residues out of total 804 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 69 time to evaluate : 0.877 Fit side-chains revert: symmetry clash REVERT: A 79 TYR cc_start: 0.8650 (m-80) cc_final: 0.7965 (m-80) REVERT: A 213 LEU cc_start: 0.9363 (tp) cc_final: 0.9079 (tp) REVERT: A 307 TYR cc_start: 0.8973 (m-80) cc_final: 0.8326 (m-80) REVERT: I 259 LEU cc_start: 0.9319 (tp) cc_final: 0.9109 (tp) outliers start: 0 outliers final: 0 residues processed: 69 average time/residue: 0.1312 time to fit residues: 14.4418 Evaluate side-chains 52 residues out of total 804 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 52 time to evaluate : 0.987 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 80 optimal weight: 9.9990 chunk 83 optimal weight: 0.0570 chunk 48 optimal weight: 6.9990 chunk 35 optimal weight: 4.9990 chunk 63 optimal weight: 6.9990 chunk 24 optimal weight: 4.9990 chunk 73 optimal weight: 4.9990 chunk 76 optimal weight: 5.9990 chunk 53 optimal weight: 0.8980 chunk 85 optimal weight: 6.9990 chunk 52 optimal weight: 4.9990 overall best weight: 3.1904 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 99 GLN ** A 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 248 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 371 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 99 GLN ** I 133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 248 GLN K 43 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8109 moved from start: 0.3282 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 7515 Z= 0.277 Angle : 0.663 12.268 10196 Z= 0.336 Chirality : 0.041 0.163 1157 Planarity : 0.005 0.062 1298 Dihedral : 7.005 73.475 1000 Min Nonbonded Distance : 2.026 Molprobity Statistics. All-atom Clashscore : 19.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 0.00 % Allowed : 1.26 % Favored : 98.74 % 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: 0.59 (0.29), residues: 918 helix: 1.93 (0.27), residues: 321 sheet: -0.25 (0.25), residues: 408 loop : -0.49 (0.54), residues: 189 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 243 HIS 0.005 0.001 HIS A 346 PHE 0.026 0.002 PHE D 42 TYR 0.016 0.002 TYR I 114 ARG 0.002 0.001 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 68 residues out of total 804 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 68 time to evaluate : 0.844 Fit side-chains revert: symmetry clash REVERT: A 79 TYR cc_start: 0.8628 (m-80) cc_final: 0.7927 (m-80) REVERT: A 213 LEU cc_start: 0.9360 (tp) cc_final: 0.9057 (tp) REVERT: A 307 TYR cc_start: 0.9046 (m-80) cc_final: 0.8371 (m-80) REVERT: B 126 MET cc_start: 0.9607 (ppp) cc_final: 0.9340 (ppp) REVERT: C 40 MET cc_start: 0.9640 (mpp) cc_final: 0.9398 (mpp) REVERT: I 259 LEU cc_start: 0.9335 (tp) cc_final: 0.9120 (tp) outliers start: 0 outliers final: 0 residues processed: 68 average time/residue: 0.1318 time to fit residues: 14.0063 Evaluate side-chains 52 residues out of total 804 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 52 time to evaluate : 0.857 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 40 optimal weight: 0.5980 chunk 59 optimal weight: 7.9990 chunk 89 optimal weight: 0.0060 chunk 82 optimal weight: 1.9990 chunk 71 optimal weight: 4.9990 chunk 7 optimal weight: 3.9990 chunk 55 optimal weight: 5.9990 chunk 43 optimal weight: 1.9990 chunk 56 optimal weight: 8.9990 chunk 76 optimal weight: 9.9990 chunk 21 optimal weight: 1.9990 overall best weight: 1.3202 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 248 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 371 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 99 GLN I 133 ASN I 248 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8070 moved from start: 0.3309 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 7515 Z= 0.169 Angle : 0.628 9.256 10196 Z= 0.309 Chirality : 0.041 0.168 1157 Planarity : 0.004 0.058 1298 Dihedral : 6.717 72.703 1000 Min Nonbonded Distance : 2.046 Molprobity Statistics. All-atom Clashscore : 15.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 0.13 % Allowed : 0.50 % Favored : 99.37 % 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: 0.89 (0.29), residues: 918 helix: 2.22 (0.27), residues: 323 sheet: -0.17 (0.25), residues: 402 loop : -0.26 (0.55), residues: 193 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP K 42 HIS 0.003 0.001 HIS A 346 PHE 0.019 0.001 PHE D 42 TYR 0.011 0.001 TYR I 314 ARG 0.001 0.000 ARG A 330 ********************** 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 72 residues out of total 804 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 71 time to evaluate : 1.144 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 79 TYR cc_start: 0.8612 (m-80) cc_final: 0.8009 (m-80) REVERT: A 213 LEU cc_start: 0.9239 (tp) cc_final: 0.8994 (tp) REVERT: A 307 TYR cc_start: 0.9016 (m-80) cc_final: 0.8333 (m-80) REVERT: D 56 MET cc_start: 0.6459 (ptt) cc_final: 0.6250 (ptt) REVERT: I 259 LEU cc_start: 0.9294 (tp) cc_final: 0.9068 (tp) REVERT: L 55 ASP cc_start: 0.9153 (t0) cc_final: 0.8867 (m-30) outliers start: 1 outliers final: 0 residues processed: 72 average time/residue: 0.1506 time to fit residues: 17.3859 Evaluate side-chains 58 residues out of total 804 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 58 time to evaluate : 0.871 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 65 optimal weight: 7.9990 chunk 10 optimal weight: 0.9990 chunk 19 optimal weight: 5.9990 chunk 71 optimal weight: 6.9990 chunk 29 optimal weight: 1.9990 chunk 73 optimal weight: 2.9990 chunk 9 optimal weight: 4.9990 chunk 13 optimal weight: 0.9990 chunk 62 optimal weight: 0.0270 chunk 4 optimal weight: 2.9990 chunk 51 optimal weight: 7.9990 overall best weight: 1.4046 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 248 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 371 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 99 GLN I 248 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3210 r_free = 0.3210 target = 0.043478 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2905 r_free = 0.2905 target = 0.035552 restraints weight = 74843.886| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2944 r_free = 0.2944 target = 0.036567 restraints weight = 44455.822| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.2970 r_free = 0.2970 target = 0.037275 restraints weight = 30783.642| |-----------------------------------------------------------------------------| r_work (final): 0.2959 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8126 moved from start: 0.3382 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 7515 Z= 0.169 Angle : 0.630 8.881 10196 Z= 0.311 Chirality : 0.041 0.165 1157 Planarity : 0.004 0.058 1298 Dihedral : 6.752 71.389 1000 Min Nonbonded Distance : 2.047 Molprobity Statistics. All-atom Clashscore : 15.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 0.00 % Allowed : 0.50 % Favored : 99.50 % 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: 0.96 (0.29), residues: 918 helix: 2.31 (0.27), residues: 323 sheet: -0.14 (0.25), residues: 402 loop : -0.28 (0.55), residues: 193 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP K 42 HIS 0.003 0.001 HIS A 346 PHE 0.018 0.001 PHE D 42 TYR 0.012 0.001 TYR I 314 ARG 0.004 0.000 ARG A 330 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1480.92 seconds wall clock time: 28 minutes 51.20 seconds (1731.20 seconds total)