Starting phenix.real_space_refine (version: dev) on Sat Feb 18 10:09:20 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7oqz_13035/02_2023/7oqz_13035_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7oqz_13035/02_2023/7oqz_13035.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.27 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7oqz_13035/02_2023/7oqz_13035.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7oqz_13035/02_2023/7oqz_13035.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7oqz_13035/02_2023/7oqz_13035_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7oqz_13035/02_2023/7oqz_13035_updated.pdb" } resolution = 3.27 write_initial_geo_file = False refinement { macro_cycles = 10 } 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 ------------------------------------------------------------------------------- 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= 0.037 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 Process input model Symmetric amino acids flipped Residue "A PHE 15": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 96": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 15": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 96": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 15": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 96": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 15": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 96": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/modules/chem_data/mon_lib" Total number of atoms: 7996 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 1885 Number of conformers: 1 Conformer: "" Number of residues, atoms: 237, 1885 Classifications: {'peptide': 237} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 6, 'TRANS': 230} Chain breaks: 1 Unresolved non-hydrogen bonds: 50 Unresolved non-hydrogen angles: 62 Unresolved non-hydrogen dihedrals: 44 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'TYR:plan': 2, 'ARG:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 25 Chain: "B" Number of atoms: 1885 Number of conformers: 1 Conformer: "" Number of residues, atoms: 237, 1885 Classifications: {'peptide': 237} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 6, 'TRANS': 230} Chain breaks: 1 Unresolved non-hydrogen bonds: 50 Unresolved non-hydrogen angles: 62 Unresolved non-hydrogen dihedrals: 44 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'TYR:plan': 2, 'ARG:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 25 Chain: "C" Number of atoms: 1885 Number of conformers: 1 Conformer: "" Number of residues, atoms: 237, 1885 Classifications: {'peptide': 237} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 6, 'TRANS': 230} Chain breaks: 1 Unresolved non-hydrogen bonds: 50 Unresolved non-hydrogen angles: 62 Unresolved non-hydrogen dihedrals: 44 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'TYR:plan': 2, 'ARG:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 25 Chain: "D" Number of atoms: 1885 Number of conformers: 1 Conformer: "" Number of residues, atoms: 237, 1885 Classifications: {'peptide': 237} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 6, 'TRANS': 230} Chain breaks: 1 Unresolved non-hydrogen bonds: 50 Unresolved non-hydrogen angles: 62 Unresolved non-hydrogen dihedrals: 44 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'TYR:plan': 2, 'ARG:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 25 Chain: "A" Number of atoms: 114 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 114 Unusual residues: {'PC1': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 102 Unresolved non-hydrogen angles: 123 Unresolved non-hydrogen dihedrals: 76 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'PC1:plan-2': 2, 'PC1:plan-1': 2} Unresolved non-hydrogen planarities: 12 Chain: "B" Number of atoms: 114 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 114 Unusual residues: {'PC1': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 102 Unresolved non-hydrogen angles: 123 Unresolved non-hydrogen dihedrals: 76 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'PC1:plan-2': 2, 'PC1:plan-1': 2} Unresolved non-hydrogen planarities: 12 Chain: "C" Number of atoms: 114 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 114 Unusual residues: {'PC1': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 102 Unresolved non-hydrogen angles: 123 Unresolved non-hydrogen dihedrals: 76 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'PC1:plan-2': 2, 'PC1:plan-1': 2} Unresolved non-hydrogen planarities: 12 Chain: "D" Number of atoms: 114 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 114 Unusual residues: {'PC1': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 102 Unresolved non-hydrogen angles: 123 Unresolved non-hydrogen dihedrals: 76 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'PC1:plan-2': 2, 'PC1:plan-1': 2} Unresolved non-hydrogen planarities: 12 Time building chain proxies: 4.96, per 1000 atoms: 0.62 Number of scatterers: 7996 At special positions: 0 Unit cell: (92.65, 92.65, 76.3, 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 52 16.00 P 8 15.00 O 1272 8.00 N 1196 7.00 C 5468 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: 3.33 Conformation dependent library (CDL) restraints added in 1.1 seconds 1864 Ramachandran restraints generated. 932 Oldfield, 0 Emsley, 932 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1744 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 28 helices and 0 sheets defined 79.3% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.61 Creating SS restraints... Processing helix chain 'A' and resid 4 through 33 Proline residue: A 10 - end of helix Processing helix chain 'A' and resid 43 through 68 Processing helix chain 'A' and resid 90 through 114 Processing helix chain 'A' and resid 121 through 140 removed outlier: 3.574A pdb=" N ASN A 140 " --> pdb=" O PHE A 136 " (cutoff:3.500A) Processing helix chain 'A' and resid 147 through 172 Processing helix chain 'A' and resid 177 through 201 Processing helix chain 'A' and resid 215 through 250 Processing helix chain 'B' and resid 4 through 33 Proline residue: B 10 - end of helix Processing helix chain 'B' and resid 43 through 68 Processing helix chain 'B' and resid 90 through 114 Processing helix chain 'B' and resid 121 through 140 removed outlier: 3.574A pdb=" N ASN B 140 " --> pdb=" O PHE B 136 " (cutoff:3.500A) Processing helix chain 'B' and resid 147 through 172 Processing helix chain 'B' and resid 177 through 201 Processing helix chain 'B' and resid 215 through 250 Processing helix chain 'C' and resid 4 through 33 Proline residue: C 10 - end of helix Processing helix chain 'C' and resid 43 through 68 Processing helix chain 'C' and resid 90 through 114 Processing helix chain 'C' and resid 121 through 140 removed outlier: 3.573A pdb=" N ASN C 140 " --> pdb=" O PHE C 136 " (cutoff:3.500A) Processing helix chain 'C' and resid 147 through 172 Processing helix chain 'C' and resid 177 through 201 Processing helix chain 'C' and resid 215 through 250 Processing helix chain 'D' and resid 4 through 33 Proline residue: D 10 - end of helix Processing helix chain 'D' and resid 43 through 68 Processing helix chain 'D' and resid 90 through 114 Processing helix chain 'D' and resid 121 through 140 removed outlier: 3.574A pdb=" N ASN D 140 " --> pdb=" O PHE D 136 " (cutoff:3.500A) Processing helix chain 'D' and resid 147 through 172 Processing helix chain 'D' and resid 177 through 201 Processing helix chain 'D' and resid 215 through 250 628 hydrogen bonds defined for protein. 1620 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: 2.21 Time building geometry restraints manager: 3.59 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.31: 1104 1.31 - 1.43: 2440 1.43 - 1.56: 4461 1.56 - 1.68: 130 1.68 - 1.81: 81 Bond restraints: 8216 Sorted by residual: bond pdb=" C31 PC1 C 302 " pdb=" O31 PC1 C 302 " ideal model delta sigma weight residual 1.330 1.439 -0.109 2.00e-02 2.50e+03 2.99e+01 bond pdb=" C31 PC1 A 301 " pdb=" O31 PC1 A 301 " ideal model delta sigma weight residual 1.330 1.439 -0.109 2.00e-02 2.50e+03 2.97e+01 bond pdb=" C31 PC1 B 302 " pdb=" O31 PC1 B 302 " ideal model delta sigma weight residual 1.330 1.439 -0.109 2.00e-02 2.50e+03 2.96e+01 bond pdb=" C31 PC1 C 303 " pdb=" O31 PC1 C 303 " ideal model delta sigma weight residual 1.330 1.439 -0.109 2.00e-02 2.50e+03 2.95e+01 bond pdb=" C31 PC1 D 303 " pdb=" O31 PC1 D 303 " ideal model delta sigma weight residual 1.330 1.439 -0.109 2.00e-02 2.50e+03 2.94e+01 ... (remaining 8211 not shown) Histogram of bond angle deviations from ideal: 100.73 - 107.38: 261 107.38 - 114.03: 4882 114.03 - 120.68: 3435 120.68 - 127.33: 2374 127.33 - 133.98: 116 Bond angle restraints: 11068 Sorted by residual: angle pdb=" O12 PC1 D 303 " pdb=" P PC1 D 303 " pdb=" O14 PC1 D 303 " ideal model delta sigma weight residual 123.67 109.34 14.33 3.00e+00 1.11e-01 2.28e+01 angle pdb=" O12 PC1 C 302 " pdb=" P PC1 C 302 " pdb=" O14 PC1 C 302 " ideal model delta sigma weight residual 123.67 109.35 14.32 3.00e+00 1.11e-01 2.28e+01 angle pdb=" O12 PC1 A 302 " pdb=" P PC1 A 302 " pdb=" O14 PC1 A 302 " ideal model delta sigma weight residual 123.67 109.35 14.32 3.00e+00 1.11e-01 2.28e+01 angle pdb=" O12 PC1 B 302 " pdb=" P PC1 B 302 " pdb=" O14 PC1 B 302 " ideal model delta sigma weight residual 123.67 109.36 14.31 3.00e+00 1.11e-01 2.28e+01 angle pdb=" O12 PC1 A 301 " pdb=" P PC1 A 301 " pdb=" O14 PC1 A 301 " ideal model delta sigma weight residual 123.67 109.36 14.31 3.00e+00 1.11e-01 2.28e+01 ... (remaining 11063 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.33: 4157 14.33 - 28.65: 315 28.65 - 42.98: 80 42.98 - 57.31: 64 57.31 - 71.63: 16 Dihedral angle restraints: 4632 sinusoidal: 1924 harmonic: 2708 Sorted by residual: dihedral pdb=" N PHE A 194 " pdb=" CA PHE A 194 " pdb=" CB PHE A 194 " pdb=" CG PHE A 194 " ideal model delta sinusoidal sigma weight residual -60.00 -118.53 58.53 3 1.50e+01 4.44e-03 9.47e+00 dihedral pdb=" N PHE B 194 " pdb=" CA PHE B 194 " pdb=" CB PHE B 194 " pdb=" CG PHE B 194 " ideal model delta sinusoidal sigma weight residual -60.00 -118.52 58.52 3 1.50e+01 4.44e-03 9.47e+00 dihedral pdb=" N PHE D 194 " pdb=" CA PHE D 194 " pdb=" CB PHE D 194 " pdb=" CG PHE D 194 " ideal model delta sinusoidal sigma weight residual -60.00 -118.51 58.51 3 1.50e+01 4.44e-03 9.47e+00 ... (remaining 4629 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.024: 811 0.024 - 0.049: 253 0.049 - 0.073: 128 0.073 - 0.098: 20 0.098 - 0.122: 8 Chirality restraints: 1220 Sorted by residual: chirality pdb=" CA ILE A 71 " pdb=" N ILE A 71 " pdb=" C ILE A 71 " pdb=" CB ILE A 71 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.12 2.00e-01 2.50e+01 3.72e-01 chirality pdb=" CA ILE B 71 " pdb=" N ILE B 71 " pdb=" C ILE B 71 " pdb=" CB ILE B 71 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.12 2.00e-01 2.50e+01 3.71e-01 chirality pdb=" CA ILE D 71 " pdb=" N ILE D 71 " pdb=" C ILE D 71 " pdb=" CB ILE D 71 " both_signs ideal model delta sigma weight residual False 2.43 2.55 -0.12 2.00e-01 2.50e+01 3.67e-01 ... (remaining 1217 not shown) Planarity restraints: 1288 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ALA A 130 " -0.006 2.00e-02 2.50e+03 1.20e-02 1.44e+00 pdb=" C ALA A 130 " 0.021 2.00e-02 2.50e+03 pdb=" O ALA A 130 " -0.008 2.00e-02 2.50e+03 pdb=" N LEU A 131 " -0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA B 130 " -0.006 2.00e-02 2.50e+03 1.20e-02 1.44e+00 pdb=" C ALA B 130 " 0.021 2.00e-02 2.50e+03 pdb=" O ALA B 130 " -0.008 2.00e-02 2.50e+03 pdb=" N LEU B 131 " -0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA D 130 " 0.006 2.00e-02 2.50e+03 1.20e-02 1.43e+00 pdb=" C ALA D 130 " -0.021 2.00e-02 2.50e+03 pdb=" O ALA D 130 " 0.008 2.00e-02 2.50e+03 pdb=" N LEU D 131 " 0.007 2.00e-02 2.50e+03 ... (remaining 1285 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.79: 1712 2.79 - 3.31: 8129 3.31 - 3.84: 12951 3.84 - 4.37: 13568 4.37 - 4.90: 25055 Nonbonded interactions: 61415 Sorted by model distance: nonbonded pdb=" O LEU D 125 " pdb=" OG SER D 128 " model vdw 2.257 2.440 nonbonded pdb=" O LEU B 125 " pdb=" OG SER B 128 " model vdw 2.257 2.440 nonbonded pdb=" O LEU C 125 " pdb=" OG SER C 128 " model vdw 2.257 2.440 nonbonded pdb=" O LEU A 125 " pdb=" OG SER A 128 " model vdw 2.257 2.440 nonbonded pdb=" NE1 TRP B 21 " pdb=" OE2 GLU B 53 " model vdw 2.342 2.520 ... (remaining 61410 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' and (resid 3 through 251 or (resid 301 and (name C21 or name C22 or n \ ame C23 or name C24 or name C25 or name C26 or name C27 or name C28 or name C29 \ or name C2A or name C2B or name C2C or name C2D or name C2E or name C2F or name \ C2G)) or (resid 302 through 304 and (name C21 or name C22 or name C23 or name C2 \ 4 or name C25 or name C26 or name C27 or name C28)))) selection = (chain 'B' and (resid 3 through 251 or (resid 301 and (name C21 or name C22 or n \ ame C23 or name C24 or name C25 or name C26 or name C27 or name C28 or name C29 \ or name C2A or name C2B or name C2C or name C2D or name C2E or name C2F or name \ C2G)) or (resid 302 through 304 and (name C21 or name C22 or name C23 or name C2 \ 4 or name C25 or name C26 or name C27 or name C28)))) selection = (chain 'C' and (resid 3 through 251 or (resid 301 and (name C21 or name C22 or n \ ame C23 or name C24 or name C25 or name C26 or name C27 or name C28 or name C29 \ or name C2A or name C2B or name C2C or name C2D or name C2E or name C2F or name \ C2G)) or (resid 302 through 304 and (name C21 or name C22 or name C23 or name C2 \ 4 or name C25 or name C26 or name C27 or name C28)))) selection = (chain 'D' and (resid 3 through 251 or (resid 301 and (name C21 or name C22 or n \ ame C23 or name C24 or name C25 or name C26 or name C27 or name C28 or name C29 \ or name C2A or name C2B or name C2C or name C2D or name C2E or name C2F or name \ C2G)) or (resid 302 through 304 and (name C21 or name C22 or name C23 or name C2 \ 4 or name C25 or name C26 or name C27 or name C28)))) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 8 5.49 5 S 52 5.16 5 C 5468 2.51 5 N 1196 2.21 5 O 1272 1.98 5 sf(0) = scattering factor at diffraction angle 0. 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 individual isotropic 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: 0.520 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 3.160 Check model and map are aligned: 0.120 Process input model: 24.060 Find NCS groups from input model: 0.550 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Set scattering table: 0.080 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:2.840 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.380 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7823 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 : 0.009 0.109 8216 Z= 0.577 Angle : 0.981 14.327 11068 Z= 0.384 Chirality : 0.030 0.122 1220 Planarity : 0.003 0.019 1288 Dihedral : 13.713 71.632 2888 Min Nonbonded Distance : 2.257 Molprobity Statistics. All-atom Clashscore : 3.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.29 % Favored : 98.71 % Rotamer Outliers : 0.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 4.83 (0.27), residues: 932 helix: 3.85 (0.17), residues: 780 sheet: None (None), residues: 0 loop : -0.84 (0.52), residues: 152 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1864 Ramachandran restraints generated. 932 Oldfield, 0 Emsley, 932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1864 Ramachandran restraints generated. 932 Oldfield, 0 Emsley, 932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 381 residues out of total 832 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 377 time to evaluate : 0.816 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 4 outliers final: 4 residues processed: 381 average time/residue: 0.2074 time to fit residues: 105.7612 Evaluate side-chains 215 residues out of total 832 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 211 time to evaluate : 0.945 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.0939 time to fit residues: 1.8473 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 77 optimal weight: 0.8980 chunk 69 optimal weight: 10.0000 chunk 38 optimal weight: 0.8980 chunk 23 optimal weight: 10.0000 chunk 47 optimal weight: 5.9990 chunk 37 optimal weight: 0.8980 chunk 72 optimal weight: 0.0060 chunk 27 optimal weight: 4.9990 chunk 43 optimal weight: 0.0870 chunk 53 optimal weight: 6.9990 chunk 83 optimal weight: 0.9980 overall best weight: 0.5574 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 215 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 215 HIS B 217 ASN C 34 GLN C 217 ASN D 34 GLN ** D 143 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 217 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7894 moved from start: 0.2690 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.026 8216 Z= 0.170 Angle : 0.534 11.756 11068 Z= 0.281 Chirality : 0.035 0.120 1220 Planarity : 0.005 0.024 1288 Dihedral : 14.133 75.776 1308 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 9.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer Outliers : 3.06 % 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: 4.38 (0.26), residues: 932 helix: 3.57 (0.16), residues: 776 sheet: None (None), residues: 0 loop : -1.08 (0.50), residues: 156 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1864 Ramachandran restraints generated. 932 Oldfield, 0 Emsley, 932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1864 Ramachandran restraints generated. 932 Oldfield, 0 Emsley, 932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 255 residues out of total 832 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 231 time to evaluate : 0.910 Fit side-chains revert: symmetry clash outliers start: 24 outliers final: 13 residues processed: 244 average time/residue: 0.2116 time to fit residues: 68.1702 Evaluate side-chains 218 residues out of total 832 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 205 time to evaluate : 0.941 Switching outliers to nearest non-outliers outliers start: 13 outliers final: 0 residues processed: 13 average time/residue: 0.0783 time to fit residues: 3.1211 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 46 optimal weight: 10.0000 chunk 25 optimal weight: 3.9990 chunk 69 optimal weight: 10.0000 chunk 56 optimal weight: 0.5980 chunk 23 optimal weight: 10.0000 chunk 83 optimal weight: 4.9990 chunk 90 optimal weight: 0.6980 chunk 74 optimal weight: 3.9990 chunk 82 optimal weight: 3.9990 chunk 28 optimal weight: 3.9990 chunk 67 optimal weight: 0.8980 overall best weight: 2.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 215 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 3 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8072 moved from start: 0.3625 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.033 8216 Z= 0.256 Angle : 0.557 7.215 11068 Z= 0.299 Chirality : 0.037 0.139 1220 Planarity : 0.004 0.030 1288 Dihedral : 13.454 78.258 1308 Min Nonbonded Distance : 2.189 Molprobity Statistics. All-atom Clashscore : 10.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % Rotamer Outliers : 2.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.78 (0.27), residues: 932 helix: 3.23 (0.17), residues: 764 sheet: None (None), residues: 0 loop : -1.32 (0.45), residues: 168 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1864 Ramachandran restraints generated. 932 Oldfield, 0 Emsley, 932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1864 Ramachandran restraints generated. 932 Oldfield, 0 Emsley, 932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 236 residues out of total 832 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 218 time to evaluate : 0.970 Fit side-chains revert: symmetry clash outliers start: 18 outliers final: 13 residues processed: 227 average time/residue: 0.2205 time to fit residues: 66.0755 Evaluate side-chains 214 residues out of total 832 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 201 time to evaluate : 0.847 Switching outliers to nearest non-outliers outliers start: 13 outliers final: 0 residues processed: 13 average time/residue: 0.0717 time to fit residues: 2.8412 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 82 optimal weight: 1.9990 chunk 62 optimal weight: 2.9990 chunk 43 optimal weight: 3.9990 chunk 9 optimal weight: 0.9990 chunk 39 optimal weight: 4.9990 chunk 56 optimal weight: 2.9990 chunk 83 optimal weight: 0.9990 chunk 88 optimal weight: 9.9990 chunk 79 optimal weight: 4.9990 chunk 23 optimal weight: 10.0000 chunk 74 optimal weight: 0.9990 overall best weight: 1.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 34 GLN D 34 GLN D 129 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8057 moved from start: 0.3971 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.040 8216 Z= 0.223 Angle : 0.549 6.588 11068 Z= 0.289 Chirality : 0.036 0.134 1220 Planarity : 0.004 0.030 1288 Dihedral : 13.013 79.172 1308 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 10.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer Outliers : 2.81 % 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: 3.53 (0.27), residues: 932 helix: 3.09 (0.18), residues: 760 sheet: None (None), residues: 0 loop : -1.48 (0.44), residues: 172 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1864 Ramachandran restraints generated. 932 Oldfield, 0 Emsley, 932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1864 Ramachandran restraints generated. 932 Oldfield, 0 Emsley, 932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 229 residues out of total 832 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 207 time to evaluate : 0.937 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 22 outliers final: 14 residues processed: 219 average time/residue: 0.2223 time to fit residues: 64.7117 Evaluate side-chains 207 residues out of total 832 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 193 time to evaluate : 1.000 Switching outliers to nearest non-outliers outliers start: 14 outliers final: 0 residues processed: 14 average time/residue: 0.0873 time to fit residues: 3.2608 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 50 optimal weight: 5.9990 chunk 1 optimal weight: 0.9980 chunk 66 optimal weight: 4.9990 chunk 36 optimal weight: 5.9990 chunk 75 optimal weight: 4.9990 chunk 61 optimal weight: 2.9990 chunk 0 optimal weight: 8.9990 chunk 45 optimal weight: 1.9990 chunk 79 optimal weight: 3.9990 chunk 22 optimal weight: 0.9990 chunk 29 optimal weight: 3.9990 overall best weight: 2.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 215 HIS ** C 94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8104 moved from start: 0.4338 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.042 8216 Z= 0.272 Angle : 0.568 6.860 11068 Z= 0.303 Chirality : 0.037 0.132 1220 Planarity : 0.004 0.024 1288 Dihedral : 12.921 81.785 1308 Min Nonbonded Distance : 2.159 Molprobity Statistics. All-atom Clashscore : 10.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % Rotamer Outliers : 1.66 % 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: 3.36 (0.27), residues: 932 helix: 2.94 (0.18), residues: 756 sheet: None (None), residues: 0 loop : -1.26 (0.45), residues: 176 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1864 Ramachandran restraints generated. 932 Oldfield, 0 Emsley, 932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1864 Ramachandran restraints generated. 932 Oldfield, 0 Emsley, 932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 214 residues out of total 832 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 201 time to evaluate : 1.005 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 13 outliers final: 5 residues processed: 206 average time/residue: 0.2098 time to fit residues: 57.8865 Evaluate side-chains 199 residues out of total 832 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 194 time to evaluate : 0.890 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.0856 time to fit residues: 1.9760 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 80 optimal weight: 3.9990 chunk 17 optimal weight: 0.8980 chunk 52 optimal weight: 2.9990 chunk 21 optimal weight: 0.9980 chunk 89 optimal weight: 0.9980 chunk 73 optimal weight: 7.9990 chunk 41 optimal weight: 0.0980 chunk 7 optimal weight: 0.8980 chunk 29 optimal weight: 4.9990 chunk 46 optimal weight: 10.0000 chunk 85 optimal weight: 3.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 215 HIS C 3 ASN ** C 94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 3 ASN D 143 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8018 moved from start: 0.4448 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.035 8216 Z= 0.181 Angle : 0.545 9.034 11068 Z= 0.282 Chirality : 0.035 0.125 1220 Planarity : 0.004 0.032 1288 Dihedral : 12.238 79.943 1308 Min Nonbonded Distance : 2.160 Molprobity Statistics. All-atom Clashscore : 9.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer Outliers : 1.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.54 (0.27), residues: 932 helix: 3.09 (0.18), residues: 756 sheet: None (None), residues: 0 loop : -1.30 (0.45), residues: 176 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1864 Ramachandran restraints generated. 932 Oldfield, 0 Emsley, 932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1864 Ramachandran restraints generated. 932 Oldfield, 0 Emsley, 932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 224 residues out of total 832 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 210 time to evaluate : 1.043 Fit side-chains revert: symmetry clash outliers start: 14 outliers final: 4 residues processed: 217 average time/residue: 0.2225 time to fit residues: 64.0903 Evaluate side-chains 198 residues out of total 832 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 194 time to evaluate : 0.910 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.1834 time to fit residues: 2.2132 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 10 optimal weight: 4.9990 chunk 50 optimal weight: 6.9990 chunk 65 optimal weight: 10.0000 chunk 74 optimal weight: 0.6980 chunk 49 optimal weight: 7.9990 chunk 88 optimal weight: 0.2980 chunk 55 optimal weight: 0.9980 chunk 54 optimal weight: 0.9980 chunk 40 optimal weight: 0.8980 chunk 35 optimal weight: 4.9990 chunk 52 optimal weight: 10.0000 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 143 HIS A 215 HIS B 129 ASN ** C 94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 129 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7998 moved from start: 0.4608 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.040 8216 Z= 0.189 Angle : 0.563 9.339 11068 Z= 0.291 Chirality : 0.036 0.155 1220 Planarity : 0.004 0.031 1288 Dihedral : 11.927 77.295 1308 Min Nonbonded Distance : 2.156 Molprobity Statistics. All-atom Clashscore : 9.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer Outliers : 1.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.53 (0.28), residues: 932 helix: 3.08 (0.18), residues: 756 sheet: None (None), residues: 0 loop : -1.31 (0.45), residues: 176 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1864 Ramachandran restraints generated. 932 Oldfield, 0 Emsley, 932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1864 Ramachandran restraints generated. 932 Oldfield, 0 Emsley, 932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 215 residues out of total 832 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 201 time to evaluate : 0.966 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 14 outliers final: 3 residues processed: 205 average time/residue: 0.2234 time to fit residues: 61.5571 Evaluate side-chains 195 residues out of total 832 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 192 time to evaluate : 0.887 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.0778 time to fit residues: 1.5556 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 26 optimal weight: 0.0970 chunk 17 optimal weight: 1.9990 chunk 56 optimal weight: 3.9990 chunk 60 optimal weight: 4.9990 chunk 43 optimal weight: 4.9990 chunk 8 optimal weight: 0.7980 chunk 69 optimal weight: 10.0000 chunk 80 optimal weight: 2.9990 chunk 84 optimal weight: 0.6980 chunk 77 optimal weight: 3.9990 chunk 82 optimal weight: 2.9990 overall best weight: 1.3182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 215 HIS B 143 HIS B 215 HIS ** C 94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 3 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8024 moved from start: 0.4781 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.036 8216 Z= 0.219 Angle : 0.595 8.392 11068 Z= 0.305 Chirality : 0.037 0.152 1220 Planarity : 0.004 0.038 1288 Dihedral : 11.950 76.094 1308 Min Nonbonded Distance : 2.136 Molprobity Statistics. All-atom Clashscore : 9.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % Rotamer Outliers : 1.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.35 (0.27), residues: 932 helix: 2.94 (0.18), residues: 756 sheet: None (None), residues: 0 loop : -1.31 (0.45), residues: 176 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1864 Ramachandran restraints generated. 932 Oldfield, 0 Emsley, 932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1864 Ramachandran restraints generated. 932 Oldfield, 0 Emsley, 932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 832 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 190 time to evaluate : 0.932 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 12 outliers final: 4 residues processed: 193 average time/residue: 0.2221 time to fit residues: 56.7653 Evaluate side-chains 190 residues out of total 832 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 186 time to evaluate : 0.913 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.0792 time to fit residues: 1.7222 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 84 optimal weight: 0.9980 chunk 49 optimal weight: 4.9990 chunk 35 optimal weight: 0.0770 chunk 64 optimal weight: 0.7980 chunk 25 optimal weight: 0.9990 chunk 74 optimal weight: 1.9990 chunk 78 optimal weight: 1.9990 chunk 82 optimal weight: 3.9990 chunk 54 optimal weight: 0.7980 chunk 87 optimal weight: 4.9990 chunk 53 optimal weight: 6.9990 overall best weight: 0.7340 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 215 HIS B 129 ASN ** C 94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 215 HIS D 3 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7972 moved from start: 0.4872 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.038 8216 Z= 0.186 Angle : 0.625 10.624 11068 Z= 0.311 Chirality : 0.037 0.152 1220 Planarity : 0.004 0.032 1288 Dihedral : 11.481 73.185 1308 Min Nonbonded Distance : 2.148 Molprobity Statistics. All-atom Clashscore : 8.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer Outliers : 1.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.42 (0.28), residues: 932 helix: 3.00 (0.18), residues: 756 sheet: None (None), residues: 0 loop : -1.31 (0.45), residues: 176 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1864 Ramachandran restraints generated. 932 Oldfield, 0 Emsley, 932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1864 Ramachandran restraints generated. 932 Oldfield, 0 Emsley, 932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 213 residues out of total 832 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 201 time to evaluate : 0.938 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 12 outliers final: 6 residues processed: 205 average time/residue: 0.2193 time to fit residues: 59.7109 Evaluate side-chains 194 residues out of total 832 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 188 time to evaluate : 0.937 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.0984 time to fit residues: 2.2454 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 41 optimal weight: 5.9990 chunk 60 optimal weight: 4.9990 chunk 91 optimal weight: 0.6980 chunk 84 optimal weight: 2.9990 chunk 72 optimal weight: 10.0000 chunk 7 optimal weight: 1.9990 chunk 56 optimal weight: 4.9990 chunk 44 optimal weight: 0.8980 chunk 57 optimal weight: 0.8980 chunk 77 optimal weight: 0.8980 chunk 22 optimal weight: 1.9990 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 129 ASN B 129 ASN ** C 94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 129 ASN D 129 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7994 moved from start: 0.4999 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.036 8216 Z= 0.208 Angle : 0.644 9.737 11068 Z= 0.320 Chirality : 0.037 0.160 1220 Planarity : 0.004 0.055 1288 Dihedral : 11.410 71.898 1308 Min Nonbonded Distance : 2.192 Molprobity Statistics. All-atom Clashscore : 9.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer Outliers : 1.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.27 (0.28), residues: 932 helix: 2.91 (0.18), residues: 760 sheet: None (None), residues: 0 loop : -1.52 (0.45), residues: 172 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1864 Ramachandran restraints generated. 932 Oldfield, 0 Emsley, 932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1864 Ramachandran restraints generated. 932 Oldfield, 0 Emsley, 932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 832 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 194 time to evaluate : 0.975 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 11 outliers final: 3 residues processed: 197 average time/residue: 0.2296 time to fit residues: 60.4026 Evaluate side-chains 193 residues out of total 832 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 190 time to evaluate : 0.964 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.0785 time to fit residues: 1.5535 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 67 optimal weight: 4.9990 chunk 10 optimal weight: 9.9990 chunk 20 optimal weight: 6.9990 chunk 73 optimal weight: 5.9990 chunk 30 optimal weight: 3.9990 chunk 75 optimal weight: 5.9990 chunk 9 optimal weight: 3.9990 chunk 13 optimal weight: 3.9990 chunk 64 optimal weight: 0.9990 chunk 4 optimal weight: 0.9980 chunk 52 optimal weight: 0.9980 overall best weight: 2.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 3 ASN ** C 94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 3 ASN ** D 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 143 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3682 r_free = 0.3682 target = 0.115189 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3198 r_free = 0.3198 target = 0.083756 restraints weight = 17034.396| |-----------------------------------------------------------------------------| r_work (start): 0.3173 rms_B_bonded: 3.61 r_work (final): 0.3173 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8144 moved from start: 0.5133 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.039 8216 Z= 0.284 Angle : 0.717 10.421 11068 Z= 0.357 Chirality : 0.038 0.157 1220 Planarity : 0.005 0.067 1288 Dihedral : 11.960 73.524 1308 Min Nonbonded Distance : 2.109 Molprobity Statistics. All-atom Clashscore : 11.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer Outliers : 1.02 % 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: 3.11 (0.27), residues: 932 helix: 2.75 (0.18), residues: 760 sheet: None (None), residues: 0 loop : -1.39 (0.46), residues: 172 =============================================================================== Job complete usr+sys time: 1835.82 seconds wall clock time: 34 minutes 19.95 seconds (2059.95 seconds total)