Starting phenix.real_space_refine on Fri Jul 19 09:47:24 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8w5j_37294/07_2024/8w5j_37294.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8w5j_37294/07_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_37294/07_2024/8w5j_37294.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8w5j_37294/07_2024/8w5j_37294.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8w5j_37294/07_2024/8w5j_37294.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8w5j_37294/07_2024/8w5j_37294.cif" } 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-5388/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: 4.96, per 1000 atoms: 0.67 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: 3.02 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, 35.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.95 Creating SS restraints... Processing helix chain 'A' and resid 49 through 55 removed outlier: 3.671A pdb=" N GLN A 53 " --> pdb=" O HIS A 49 " (cutoff:3.500A) Processing helix chain 'A' and resid 62 through 66 Processing helix chain 'A' and resid 67 through 72 Processing helix chain 'A' and resid 364 through 373 Processing helix chain 'B' and resid 87 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 52 through 58 Processing helix chain 'E' and resid 20 through 44 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 49 through 55 Processing helix chain 'I' and resid 50 through 56 removed outlier: 3.953A pdb=" N GLU I 56 " --> pdb=" O ARG I 52 " (cutoff:3.500A) 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: 3.575A pdb=" N GLN I 372 " --> pdb=" O LEU I 368 " (cutoff:3.500A) 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: 4.019A pdb=" N ASP L 55 " --> pdb=" O SER L 51 " (cutoff:3.500A) Processing helix chain 'M' and resid 20 through 31 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) Processing helix chain 'M' and resid 31 through 44 Processing helix chain 'M' and resid 49 through 55 Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 93 removed outlier: 6.930A pdb=" N PHE A 98 " --> pdb=" O PHE A 92 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N LEU A 209 " --> pdb=" O VAL A 205 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N ALA A 269 " --> pdb=" O ARG A 261 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N VAL A 263 " --> pdb=" O VAL A 267 " (cutoff:3.500A) removed outlier: 6.634A pdb=" N VAL A 267 " --> pdb=" O VAL A 263 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N THR A 302 " --> pdb=" O GLU A 272 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N VAL A 313 " --> pdb=" O GLU A 329 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N THR A 317 " --> pdb=" O ALA A 325 " (cutoff:3.500A) removed outlier: 4.142A pdb=" N LYS A 323 " --> pdb=" O ASP A 319 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N LEU A 357 " --> pdb=" O ARG A 85 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'I' and resid 84 through 93 removed outlier: 7.274A pdb=" N PHE I 98 " --> pdb=" O PHE I 92 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N MET I 164 " --> pdb=" O GLN I 156 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N VAL I 196 " --> pdb=" O LEU I 183 " (cutoff:3.500A) removed outlier: 6.910A pdb=" N LEU I 209 " --> pdb=" O VAL I 205 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N LEU I 255 " --> pdb=" O LEU I 275 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N GLU I 268 " --> pdb=" O LYS I 306 " (cutoff:3.500A) removed outlier: 4.214A pdb=" N LYS I 323 " --> pdb=" O ASP I 319 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N SER I 337 " --> pdb=" O GLN I 358 " (cutoff:3.500A) removed outlier: 6.765A pdb=" N ARG I 85 " --> pdb=" O LEU I 357 " (cutoff:3.500A) removed outlier: 8.268A pdb=" N PHE I 359 " --> pdb=" O ARG I 85 " (cutoff:3.500A) removed outlier: 6.640A pdb=" N ASP I 87 " --> pdb=" O PHE I 359 " (cutoff:3.500A) removed outlier: 8.187A pdb=" N THR I 361 " --> pdb=" O ASP I 87 " (cutoff:3.500A) removed outlier: 7.240A pdb=" N ASN I 89 " --> pdb=" O THR I 361 " (cutoff:3.500A) 518 hydrogen bonds defined for protein. 1500 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: 2.20 Time building geometry restraints manager: 3.31 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: 302 2.72 - 3.26: 7779 3.26 - 3.81: 12230 3.81 - 4.35: 13958 4.35 - 4.90: 24143 Nonbonded interactions: 58412 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 58407 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: 1.940 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.300 Check model and map are aligned: 0.060 Set scattering table: 0.080 Process input model: 24.560 Find NCS groups from input model: 0.340 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:2.790 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.120 ------------------------------------------------------------------------------- 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= 0.154 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 : 0.865 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: 0.1268 time to fit residues: 14.4690 Evaluate side-chains 56 residues out of total 804 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 56 time to evaluate : 0.918 ------------------------------------------------------------------------------- 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: 6.9990 chunk 36 optimal weight: 2.9990 chunk 70 optimal weight: 3.9990 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: 2.0344 ------------------------------------------------------------------------------- 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 203 GLN ** 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: 0.7998 moved from start: 0.1026 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= 0.216 Angle : 0.625 7.406 10196 Z= 0.325 Chirality : 0.042 0.201 1157 Planarity : 0.005 0.069 1298 Dihedral : 6.879 80.339 1000 Min Nonbonded Distance : 2.012 Molprobity Statistics. All-atom Clashscore : 14.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 0.00 % Allowed : 4.53 % Favored : 95.47 % 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: 1.18 (0.29), residues: 918 helix: 2.27 (0.28), residues: 328 sheet: 0.01 (0.25), residues: 404 loop : 0.14 (0.57), residues: 186 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 260 HIS 0.005 0.001 HIS A 346 PHE 0.011 0.001 PHE I 116 TYR 0.014 0.002 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 71 residues out of total 804 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 71 time to evaluate : 0.901 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 71 average time/residue: 0.1290 time to fit residues: 14.6620 Evaluate side-chains 52 residues out of total 804 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 52 time to evaluate : 0.924 ------------------------------------------------------------------------------- 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: 10.0000 chunk 25 optimal weight: 0.2980 chunk 68 optimal weight: 9.9990 chunk 55 optimal weight: 10.0000 chunk 22 optimal weight: 9.9990 chunk 81 optimal weight: 3.9990 chunk 88 optimal weight: 5.9990 chunk 72 optimal weight: 3.9990 chunk 27 optimal weight: 3.9990 chunk 65 optimal weight: 0.9980 chunk 80 optimal weight: 3.9990 overall best weight: 2.6586 ------------------------------------------------------------------------------- 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: 0.8041 moved from start: 0.1654 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= 0.251 Angle : 0.624 10.809 10196 Z= 0.320 Chirality : 0.040 0.169 1157 Planarity : 0.005 0.059 1298 Dihedral : 6.873 77.977 1000 Min Nonbonded Distance : 2.020 Molprobity Statistics. All-atom Clashscore : 17.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 0.25 % Allowed : 6.30 % Favored : 93.45 % 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: 1.01 (0.29), residues: 918 helix: 2.15 (0.27), residues: 328 sheet: -0.12 (0.25), residues: 404 loop : 0.16 (0.56), residues: 186 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 260 HIS 0.005 0.001 HIS A 346 PHE 0.014 0.001 PHE A 359 TYR 0.016 0.002 TYR I 114 ARG 0.003 0.000 ARG I 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 70 residues out of total 804 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 68 time to evaluate : 0.924 Fit side-chains revert: symmetry clash REVERT: A 79 TYR cc_start: 0.8667 (m-80) cc_final: 0.8240 (m-10) outliers start: 2 outliers final: 1 residues processed: 70 average time/residue: 0.1410 time to fit residues: 16.0504 Evaluate side-chains 51 residues out of total 804 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 50 time to evaluate : 0.891 ------------------------------------------------------------------------------- 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: 5.9990 chunk 42 optimal weight: 3.9990 chunk 9 optimal weight: 6.9990 chunk 39 optimal weight: 8.9990 chunk 54 optimal weight: 5.9990 chunk 82 optimal weight: 0.4980 chunk 86 optimal weight: 8.9990 chunk 77 optimal weight: 0.8980 chunk 23 optimal weight: 7.9990 chunk 72 optimal weight: 4.9990 chunk 49 optimal weight: 10.0000 overall best weight: 3.2786 ------------------------------------------------------------------------------- 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 ** M 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8074 moved from start: 0.2154 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 7515 Z= 0.295 Angle : 0.649 12.022 10196 Z= 0.335 Chirality : 0.041 0.168 1157 Planarity : 0.004 0.053 1298 Dihedral : 7.126 76.462 1000 Min Nonbonded Distance : 2.013 Molprobity Statistics. All-atom Clashscore : 19.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 0.00 % Allowed : 6.55 % Favored : 93.45 % 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: 0.83 (0.29), residues: 918 helix: 2.01 (0.27), residues: 328 sheet: -0.21 (0.25), residues: 406 loop : 0.04 (0.56), residues: 184 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 260 HIS 0.006 0.001 HIS A 346 PHE 0.018 0.002 PHE A 359 TYR 0.017 0.002 TYR I 114 ARG 0.006 0.001 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 66 residues out of total 804 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 66 time to evaluate : 0.813 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 79 TYR cc_start: 0.8694 (m-80) cc_final: 0.8378 (m-10) REVERT: A 307 TYR cc_start: 0.9015 (m-80) cc_final: 0.8552 (m-80) outliers start: 0 outliers final: 0 residues processed: 66 average time/residue: 0.1290 time to fit residues: 13.5185 Evaluate side-chains 51 residues out of total 804 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 51 time to evaluate : 0.876 ------------------------------------------------------------------------------- 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: 5.9990 chunk 64 optimal weight: 0.8980 chunk 35 optimal weight: 0.9990 chunk 74 optimal weight: 9.9990 chunk 60 optimal weight: 6.9990 chunk 0 optimal weight: 6.9990 chunk 44 optimal weight: 0.0970 chunk 78 optimal weight: 8.9990 chunk 21 optimal weight: 0.9980 chunk 29 optimal weight: 5.9990 chunk 17 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: ** 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 ** M 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8023 moved from start: 0.2324 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 7515 Z= 0.158 Angle : 0.621 9.024 10196 Z= 0.305 Chirality : 0.042 0.176 1157 Planarity : 0.004 0.059 1298 Dihedral : 6.859 75.839 1000 Min Nonbonded Distance : 2.038 Molprobity Statistics. All-atom Clashscore : 14.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % 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: 1.02 (0.29), residues: 918 helix: 2.26 (0.27), residues: 328 sheet: -0.24 (0.25), residues: 406 loop : 0.26 (0.58), residues: 184 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP K 42 HIS 0.003 0.001 HIS A 346 PHE 0.025 0.001 PHE D 42 TYR 0.014 0.001 TYR D 33 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 75 residues out of total 804 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 75 time to evaluate : 0.908 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 79 TYR cc_start: 0.8524 (m-80) cc_final: 0.7907 (m-80) REVERT: A 303 ILE cc_start: 0.9372 (pt) cc_final: 0.9049 (pt) REVERT: A 317 THR cc_start: 0.8525 (p) cc_final: 0.8322 (t) REVERT: B 126 MET cc_start: 0.9590 (ppp) cc_final: 0.9333 (ppp) outliers start: 0 outliers final: 0 residues processed: 75 average time/residue: 0.1286 time to fit residues: 15.1826 Evaluate side-chains 55 residues out of total 804 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 55 time to evaluate : 0.889 ------------------------------------------------------------------------------- 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: 0.9990 chunk 21 optimal weight: 3.9990 chunk 87 optimal weight: 4.9990 chunk 72 optimal weight: 7.9990 chunk 40 optimal weight: 4.9990 chunk 7 optimal weight: 9.9990 chunk 28 optimal weight: 5.9990 chunk 45 optimal weight: 9.9990 chunk 83 optimal weight: 5.9990 chunk 9 optimal weight: 9.9990 chunk 49 optimal weight: 0.9980 overall best weight: 3.1988 ------------------------------------------------------------------------------- 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 ** M 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8088 moved from start: 0.2653 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= 0.285 Angle : 0.646 12.587 10196 Z= 0.330 Chirality : 0.041 0.183 1157 Planarity : 0.005 0.079 1298 Dihedral : 7.019 75.329 1000 Min Nonbonded Distance : 2.025 Molprobity Statistics. All-atom Clashscore : 18.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % 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: 0.83 (0.29), residues: 918 helix: 2.09 (0.27), residues: 328 sheet: -0.29 (0.25), residues: 406 loop : 0.06 (0.56), residues: 184 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP I 243 HIS 0.005 0.001 HIS A 346 PHE 0.031 0.002 PHE D 42 TYR 0.017 0.002 TYR I 114 ARG 0.003 0.000 ARG I 315 *********************** 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 67 residues out of total 804 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 67 time to evaluate : 0.923 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 79 TYR cc_start: 0.8697 (m-80) cc_final: 0.8009 (m-80) outliers start: 0 outliers final: 0 residues processed: 67 average time/residue: 0.1336 time to fit residues: 14.1770 Evaluate side-chains 50 residues out of total 804 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 50 time to evaluate : 0.925 ------------------------------------------------------------------------------- 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: 5.9990 chunk 49 optimal weight: 1.9990 chunk 73 optimal weight: 6.9990 chunk 48 optimal weight: 0.9990 chunk 86 optimal weight: 20.0000 chunk 54 optimal weight: 4.9990 chunk 52 optimal weight: 0.9980 chunk 40 optimal weight: 5.9990 chunk 53 optimal weight: 8.9990 chunk 34 optimal weight: 0.9990 chunk 51 optimal weight: 0.8980 overall best weight: 1.1786 ------------------------------------------------------------------------------- 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 ** M 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8045 moved from start: 0.2757 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 7515 Z= 0.156 Angle : 0.619 9.482 10196 Z= 0.303 Chirality : 0.041 0.171 1157 Planarity : 0.004 0.063 1298 Dihedral : 6.778 74.701 1000 Min Nonbonded Distance : 2.043 Molprobity Statistics. All-atom Clashscore : 15.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 0.13 % Allowed : 2.64 % Favored : 97.23 % 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: 1.03 (0.29), residues: 918 helix: 2.24 (0.27), residues: 328 sheet: -0.17 (0.25), residues: 404 loop : 0.13 (0.57), residues: 186 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 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 0.002 0.000 ARG I 52 *********************** 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: 1 poor density : 71 time to evaluate : 0.838 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 79 TYR cc_start: 0.8508 (m-80) cc_final: 0.7878 (m-80) REVERT: A 303 ILE cc_start: 0.9383 (pt) cc_final: 0.9054 (pt) REVERT: B 126 MET cc_start: 0.9591 (ppp) cc_final: 0.9339 (ppp) REVERT: I 259 LEU cc_start: 0.9299 (tp) cc_final: 0.9097 (tp) outliers start: 1 outliers final: 0 residues processed: 72 average time/residue: 0.1355 time to fit residues: 15.0464 Evaluate side-chains 51 residues out of total 804 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 51 time to evaluate : 0.888 ------------------------------------------------------------------------------- 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: 0.7980 chunk 17 optimal weight: 8.9990 chunk 16 optimal weight: 10.0000 chunk 55 optimal weight: 5.9990 chunk 59 optimal weight: 7.9990 chunk 42 optimal weight: 0.4980 chunk 8 optimal weight: 7.9990 chunk 68 optimal weight: 5.9990 chunk 78 optimal weight: 0.9990 chunk 83 optimal weight: 8.9990 chunk 75 optimal weight: 6.9990 overall best weight: 2.8586 ------------------------------------------------------------------------------- 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 I 248 GLN ** M 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8085 moved from start: 0.2947 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= 0.253 Angle : 0.637 11.826 10196 Z= 0.322 Chirality : 0.040 0.159 1157 Planarity : 0.004 0.056 1298 Dihedral : 6.928 74.142 1000 Min Nonbonded Distance : 2.035 Molprobity Statistics. All-atom Clashscore : 18.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % 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 : 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: 0.85 (0.29), residues: 918 helix: 2.11 (0.27), residues: 330 sheet: -0.28 (0.25), residues: 406 loop : 0.02 (0.58), residues: 182 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP I 243 HIS 0.005 0.001 HIS A 346 PHE 0.018 0.001 PHE A 359 TYR 0.015 0.002 TYR I 114 ARG 0.002 0.000 ARG I 315 *********************** 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 64 residues out of total 804 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 64 time to evaluate : 0.920 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 79 TYR cc_start: 0.8602 (m-80) cc_final: 0.7910 (m-80) REVERT: C 40 MET cc_start: 0.9611 (mpp) cc_final: 0.9397 (mpp) REVERT: L 55 ASP cc_start: 0.9148 (t70) cc_final: 0.8822 (m-30) outliers start: 0 outliers final: 0 residues processed: 64 average time/residue: 0.1334 time to fit residues: 13.5990 Evaluate side-chains 50 residues out of total 804 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 50 time to evaluate : 0.896 ------------------------------------------------------------------------------- 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: 8.9990 chunk 83 optimal weight: 0.7980 chunk 48 optimal weight: 0.9990 chunk 35 optimal weight: 8.9990 chunk 63 optimal weight: 7.9990 chunk 24 optimal weight: 0.8980 chunk 73 optimal weight: 6.9990 chunk 76 optimal weight: 7.9990 chunk 53 optimal weight: 7.9990 chunk 85 optimal weight: 0.3980 chunk 52 optimal weight: 7.9990 overall best weight: 2.0184 ------------------------------------------------------------------------------- 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 ** M 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8074 moved from start: 0.3090 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= 0.201 Angle : 0.620 10.236 10196 Z= 0.308 Chirality : 0.041 0.165 1157 Planarity : 0.004 0.055 1298 Dihedral : 6.822 73.641 1000 Min Nonbonded Distance : 2.036 Molprobity Statistics. All-atom Clashscore : 17.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 0.13 % Allowed : 0.76 % Favored : 99.12 % 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: 0.93 (0.29), residues: 918 helix: 2.22 (0.27), residues: 329 sheet: -0.23 (0.25), residues: 404 loop : -0.02 (0.57), residues: 185 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 0.014 0.001 PHE D 42 TYR 0.012 0.001 TYR I 114 ARG 0.002 0.000 ARG I 52 *********************** 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 66 residues out of total 804 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 65 time to evaluate : 0.899 Fit side-chains revert: symmetry clash REVERT: A 79 TYR cc_start: 0.8584 (m-80) cc_final: 0.7977 (m-80) REVERT: A 307 TYR cc_start: 0.8976 (m-80) cc_final: 0.8310 (m-80) REVERT: B 126 MET cc_start: 0.9594 (ppp) cc_final: 0.9340 (ppp) REVERT: I 259 LEU cc_start: 0.9301 (tp) cc_final: 0.9089 (tp) REVERT: L 55 ASP cc_start: 0.9115 (t70) cc_final: 0.8790 (m-30) REVERT: L 61 LEU cc_start: 0.8603 (pt) cc_final: 0.8270 (mm) outliers start: 1 outliers final: 0 residues processed: 66 average time/residue: 0.1316 time to fit residues: 13.8674 Evaluate side-chains 52 residues out of total 804 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 52 time to evaluate : 0.940 ------------------------------------------------------------------------------- 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: 1.9990 chunk 59 optimal weight: 1.9990 chunk 89 optimal weight: 9.9990 chunk 82 optimal weight: 1.9990 chunk 71 optimal weight: 10.0000 chunk 7 optimal weight: 3.9990 chunk 55 optimal weight: 7.9990 chunk 43 optimal weight: 0.9990 chunk 56 optimal weight: 9.9990 chunk 76 optimal weight: 10.0000 chunk 21 optimal weight: 4.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- 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 311 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 K 43 HIS ** M 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8083 moved from start: 0.3308 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 7515 Z= 0.216 Angle : 0.627 10.535 10196 Z= 0.313 Chirality : 0.041 0.161 1157 Planarity : 0.004 0.055 1298 Dihedral : 6.843 72.738 1000 Min Nonbonded Distance : 2.040 Molprobity Statistics. All-atom Clashscore : 17.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 0.13 % Allowed : 0.38 % Favored : 99.50 % 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: 0.88 (0.29), residues: 918 helix: 2.21 (0.27), residues: 329 sheet: -0.30 (0.26), residues: 406 loop : 0.01 (0.57), residues: 183 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 260 HIS 0.004 0.001 HIS A 346 PHE 0.017 0.001 PHE A 359 TYR 0.013 0.002 TYR I 114 ARG 0.004 0.000 ARG I 315 ********************** 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 67 residues out of total 804 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 66 time to evaluate : 1.008 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 79 TYR cc_start: 0.8632 (m-80) cc_final: 0.8032 (m-80) REVERT: A 307 TYR cc_start: 0.9062 (m-80) cc_final: 0.8382 (m-80) REVERT: I 259 LEU cc_start: 0.9325 (tp) cc_final: 0.9116 (tp) REVERT: L 55 ASP cc_start: 0.9059 (t70) cc_final: 0.8788 (m-30) REVERT: L 61 LEU cc_start: 0.8727 (pt) cc_final: 0.8419 (mm) outliers start: 1 outliers final: 0 residues processed: 67 average time/residue: 0.1293 time to fit residues: 13.7481 Evaluate side-chains 54 residues out of total 804 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 54 time to evaluate : 0.804 ------------------------------------------------------------------------------- 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: 3.9990 chunk 10 optimal weight: 7.9990 chunk 19 optimal weight: 4.9990 chunk 71 optimal weight: 1.9990 chunk 29 optimal weight: 0.8980 chunk 73 optimal weight: 0.8980 chunk 9 optimal weight: 2.9990 chunk 13 optimal weight: 0.2980 chunk 62 optimal weight: 9.9990 chunk 4 optimal weight: 0.9980 chunk 51 optimal weight: 4.9990 overall best weight: 1.0182 ------------------------------------------------------------------------------- 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 ** M 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3220 r_free = 0.3220 target = 0.043743 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2921 r_free = 0.2921 target = 0.035995 restraints weight = 76669.965| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2959 r_free = 0.2959 target = 0.037005 restraints weight = 45779.493| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.2984 r_free = 0.2984 target = 0.037692 restraints weight = 31764.631| |-----------------------------------------------------------------------------| r_work (final): 0.2970 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8124 moved from start: 0.3392 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 7515 Z= 0.156 Angle : 0.617 7.895 10196 Z= 0.302 Chirality : 0.041 0.168 1157 Planarity : 0.004 0.057 1298 Dihedral : 6.646 72.298 1000 Min Nonbonded Distance : 2.051 Molprobity Statistics. All-atom Clashscore : 13.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Rotamer: Outliers : 0.13 % Allowed : 0.63 % Favored : 99.24 % 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: 2.36 (0.28), residues: 329 sheet: -0.21 (0.25), residues: 404 loop : 0.11 (0.58), residues: 185 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP K 42 HIS 0.003 0.001 HIS A 346 PHE 0.017 0.001 PHE I 340 TYR 0.010 0.001 TYR I 314 ARG 0.001 0.000 ARG A 330 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1440.30 seconds wall clock time: 26 minutes 58.24 seconds (1618.24 seconds total)