Starting phenix.real_space_refine on Tue Feb 13 14:54:37 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sqf_25383/02_2024/7sqf_25383.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sqf_25383/02_2024/7sqf_25383.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sqf_25383/02_2024/7sqf_25383.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sqf_25383/02_2024/7sqf_25383.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sqf_25383/02_2024/7sqf_25383.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sqf_25383/02_2024/7sqf_25383.pdb" } resolution = 3.1 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= 0.000 sd= 0.013 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: 4 Type Number sf(0) Gaussians S 27 5.16 5 C 4296 2.51 5 N 1089 2.21 5 O 1218 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 257": "OE1" <-> "OE2" Residue "A GLU 261": "OE1" <-> "OE2" Residue "A PHE 318": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 257": "OE1" <-> "OE2" Residue "B GLU 261": "OE1" <-> "OE2" Residue "B PHE 318": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 257": "OE1" <-> "OE2" Residue "C GLU 261": "OE1" <-> "OE2" Residue "C PHE 318": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 6630 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 2154 Number of conformers: 1 Conformer: "" Number of residues, atoms: 273, 2154 Classifications: {'peptide': 273} Incomplete info: {'truncation_to_alanine': 17} Link IDs: {'PTRANS': 13, 'TRANS': 259} Unresolved non-hydrogen bonds: 69 Unresolved non-hydrogen angles: 81 Unresolved non-hydrogen dihedrals: 61 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'PHE:plan': 2, 'GLU:plan': 2, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 30 Chain: "B" Number of atoms: 2154 Number of conformers: 1 Conformer: "" Number of residues, atoms: 273, 2154 Classifications: {'peptide': 273} Incomplete info: {'truncation_to_alanine': 17} Link IDs: {'PTRANS': 13, 'TRANS': 259} Unresolved non-hydrogen bonds: 69 Unresolved non-hydrogen angles: 81 Unresolved non-hydrogen dihedrals: 61 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'PHE:plan': 2, 'GLU:plan': 2, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 30 Chain: "C" Number of atoms: 2154 Number of conformers: 1 Conformer: "" Number of residues, atoms: 273, 2154 Classifications: {'peptide': 273} Incomplete info: {'truncation_to_alanine': 17} Link IDs: {'PTRANS': 13, 'TRANS': 259} Unresolved non-hydrogen bonds: 69 Unresolved non-hydrogen angles: 81 Unresolved non-hydrogen dihedrals: 61 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'PHE:plan': 2, 'GLU:plan': 2, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 30 Chain: "A" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "B" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "C" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Time building chain proxies: 4.23, per 1000 atoms: 0.64 Number of scatterers: 6630 At special positions: 0 Unit cell: (80.2481, 82.73, 122.44, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 27 16.00 O 1218 8.00 N 1089 7.00 C 4296 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 Links applied NAG-ASN " NAG A 401 " - " ASN A 148 " " NAG A 402 " - " ASN A 162 " " NAG A 403 " - " ASN A 190 " " NAG A 404 " - " ASN A 155 " " NAG B 401 " - " ASN B 148 " " NAG B 402 " - " ASN B 162 " " NAG B 403 " - " ASN B 190 " " NAG B 404 " - " ASN B 155 " " NAG C 401 " - " ASN C 148 " " NAG C 402 " - " ASN C 162 " " NAG C 403 " - " ASN C 190 " " NAG C 404 " - " ASN C 155 " Time building additional restraints: 2.25 Conformation dependent library (CDL) restraints added in 1.4 seconds 1626 Ramachandran restraints generated. 813 Oldfield, 0 Emsley, 813 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1578 Finding SS restraints... Secondary structure from input PDB file: 18 helices and 1 sheets defined 36.0% alpha, 9.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.49 Creating SS restraints... Processing helix chain 'A' and resid 65 through 98 removed outlier: 4.047A pdb=" N LEU A 69 " --> pdb=" O VAL A 65 " (cutoff:3.500A) Processing helix chain 'A' and resid 206 through 213 Processing helix chain 'A' and resid 217 through 226 Processing helix chain 'A' and resid 272 through 276 Processing helix chain 'A' and resid 297 through 302 Processing helix chain 'A' and resid 302 through 337 Processing helix chain 'B' and resid 66 through 98 Processing helix chain 'B' and resid 206 through 213 Processing helix chain 'B' and resid 217 through 226 Processing helix chain 'B' and resid 272 through 276 Processing helix chain 'B' and resid 297 through 302 Processing helix chain 'B' and resid 302 through 337 Processing helix chain 'C' and resid 66 through 98 Processing helix chain 'C' and resid 206 through 213 Processing helix chain 'C' and resid 217 through 226 Processing helix chain 'C' and resid 272 through 276 Processing helix chain 'C' and resid 297 through 302 Processing helix chain 'C' and resid 302 through 337 Processing sheet with id=AA1, first strand: chain 'A' and resid 100 through 107 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 100 through 107 current: chain 'A' and resid 165 through 172 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 165 through 172 current: chain 'A' and resid 229 through 233 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 229 through 233 current: chain 'A' and resid 254 through 267 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 254 through 267 current: chain 'B' and resid 165 through 172 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 165 through 172 current: chain 'B' and resid 229 through 233 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 229 through 233 current: chain 'B' and resid 254 through 267 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 254 through 267 current: chain 'C' and resid 165 through 172 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 165 through 172 current: chain 'C' and resid 229 through 233 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 229 through 233 current: chain 'C' and resid 254 through 267 No H-bonds generated for sheet with id=AA1 225 hydrogen bonds defined for protein. 657 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: 1.68 Time building geometry restraints manager: 2.44 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 2058 1.34 - 1.46: 1607 1.46 - 1.58: 3088 1.58 - 1.69: 0 1.69 - 1.81: 42 Bond restraints: 6795 Sorted by residual: bond pdb=" N GLU C 133 " pdb=" CA GLU C 133 " ideal model delta sigma weight residual 1.457 1.501 -0.043 1.29e-02 6.01e+03 1.14e+01 bond pdb=" N GLU A 133 " pdb=" CA GLU A 133 " ideal model delta sigma weight residual 1.457 1.501 -0.043 1.29e-02 6.01e+03 1.13e+01 bond pdb=" N GLU B 133 " pdb=" CA GLU B 133 " ideal model delta sigma weight residual 1.457 1.500 -0.043 1.29e-02 6.01e+03 1.11e+01 bond pdb=" N LYS A 231 " pdb=" CA LYS A 231 " ideal model delta sigma weight residual 1.455 1.489 -0.034 1.25e-02 6.40e+03 7.55e+00 bond pdb=" N LYS C 231 " pdb=" CA LYS C 231 " ideal model delta sigma weight residual 1.455 1.489 -0.034 1.25e-02 6.40e+03 7.53e+00 ... (remaining 6790 not shown) Histogram of bond angle deviations from ideal: 100.23 - 106.99: 201 106.99 - 113.75: 3775 113.75 - 120.50: 2564 120.50 - 127.26: 2622 127.26 - 134.02: 66 Bond angle restraints: 9228 Sorted by residual: angle pdb=" CA ASP A 269 " pdb=" CB ASP A 269 " pdb=" CG ASP A 269 " ideal model delta sigma weight residual 112.60 116.15 -3.55 1.00e+00 1.00e+00 1.26e+01 angle pdb=" CA ASP C 269 " pdb=" CB ASP C 269 " pdb=" CG ASP C 269 " ideal model delta sigma weight residual 112.60 116.15 -3.55 1.00e+00 1.00e+00 1.26e+01 angle pdb=" CA ASP B 269 " pdb=" CB ASP B 269 " pdb=" CG ASP B 269 " ideal model delta sigma weight residual 112.60 116.11 -3.51 1.00e+00 1.00e+00 1.23e+01 angle pdb=" N GLU B 94 " pdb=" CA GLU B 94 " pdb=" CB GLU B 94 " ideal model delta sigma weight residual 110.28 115.03 -4.75 1.55e+00 4.16e-01 9.39e+00 angle pdb=" CA ASN C 215 " pdb=" C ASN C 215 " pdb=" O ASN C 215 " ideal model delta sigma weight residual 120.24 116.85 3.39 1.11e+00 8.12e-01 9.35e+00 ... (remaining 9223 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.35: 3834 17.35 - 34.70: 279 34.70 - 52.05: 57 52.05 - 69.40: 24 69.40 - 86.75: 6 Dihedral angle restraints: 4200 sinusoidal: 1776 harmonic: 2424 Sorted by residual: dihedral pdb=" CA PHE A 258 " pdb=" C PHE A 258 " pdb=" N ARG A 259 " pdb=" CA ARG A 259 " ideal model delta harmonic sigma weight residual 180.00 163.75 16.25 0 5.00e+00 4.00e-02 1.06e+01 dihedral pdb=" CA PHE C 258 " pdb=" C PHE C 258 " pdb=" N ARG C 259 " pdb=" CA ARG C 259 " ideal model delta harmonic sigma weight residual 180.00 163.76 16.24 0 5.00e+00 4.00e-02 1.05e+01 dihedral pdb=" CA PHE B 258 " pdb=" C PHE B 258 " pdb=" N ARG B 259 " pdb=" CA ARG B 259 " ideal model delta harmonic sigma weight residual 180.00 163.80 16.20 0 5.00e+00 4.00e-02 1.05e+01 ... (remaining 4197 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.068: 936 0.068 - 0.136: 114 0.136 - 0.203: 9 0.203 - 0.271: 0 0.271 - 0.339: 3 Chirality restraints: 1062 Sorted by residual: chirality pdb=" C1 NAG C 402 " pdb=" ND2 ASN C 162 " pdb=" C2 NAG C 402 " pdb=" O5 NAG C 402 " both_signs ideal model delta sigma weight residual False -2.40 -2.06 -0.34 2.00e-01 2.50e+01 2.87e+00 chirality pdb=" C1 NAG B 402 " pdb=" ND2 ASN B 162 " pdb=" C2 NAG B 402 " pdb=" O5 NAG B 402 " both_signs ideal model delta sigma weight residual False -2.40 -2.06 -0.34 2.00e-01 2.50e+01 2.86e+00 chirality pdb=" C1 NAG A 402 " pdb=" ND2 ASN A 162 " pdb=" C2 NAG A 402 " pdb=" O5 NAG A 402 " both_signs ideal model delta sigma weight residual False -2.40 -2.07 -0.33 2.00e-01 2.50e+01 2.80e+00 ... (remaining 1059 not shown) Planarity restraints: 1170 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN B 148 " -0.003 2.00e-02 2.50e+03 1.74e-02 3.77e+00 pdb=" CG ASN B 148 " 0.025 2.00e-02 2.50e+03 pdb=" OD1 ASN B 148 " -0.021 2.00e-02 2.50e+03 pdb=" ND2 ASN B 148 " 0.014 2.00e-02 2.50e+03 pdb=" C1 NAG B 401 " -0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN C 148 " 0.003 2.00e-02 2.50e+03 1.74e-02 3.77e+00 pdb=" CG ASN C 148 " -0.025 2.00e-02 2.50e+03 pdb=" OD1 ASN C 148 " 0.021 2.00e-02 2.50e+03 pdb=" ND2 ASN C 148 " -0.014 2.00e-02 2.50e+03 pdb=" C1 NAG C 401 " 0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 148 " 0.003 2.00e-02 2.50e+03 1.73e-02 3.73e+00 pdb=" CG ASN A 148 " -0.026 2.00e-02 2.50e+03 pdb=" OD1 ASN A 148 " 0.021 2.00e-02 2.50e+03 pdb=" ND2 ASN A 148 " -0.013 2.00e-02 2.50e+03 pdb=" C1 NAG A 401 " 0.015 2.00e-02 2.50e+03 ... (remaining 1167 not shown) Histogram of nonbonded interaction distances: 2.41 - 2.91: 2671 2.91 - 3.41: 6176 3.41 - 3.90: 11174 3.90 - 4.40: 12569 4.40 - 4.90: 20489 Nonbonded interactions: 53079 Sorted by model distance: nonbonded pdb=" O THR B 90 " pdb=" OE1 GLU B 94 " model vdw 2.409 3.040 nonbonded pdb=" O THR C 90 " pdb=" OE1 GLU C 94 " model vdw 2.409 3.040 nonbonded pdb=" O THR A 90 " pdb=" OE1 GLU A 94 " model vdw 2.409 3.040 nonbonded pdb=" OH TYR A 156 " pdb=" OE1 GLU A 224 " model vdw 2.475 2.440 nonbonded pdb=" OH TYR B 156 " pdb=" OE1 GLU B 224 " model vdw 2.475 2.440 ... (remaining 53074 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 'B' selection = chain 'C' } 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 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: 2.540 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: 11.720 Check model and map are aligned: 0.080 Set scattering table: 0.060 Process input model: 20.840 Find NCS groups from input model: 0.420 Set up NCS constraints: 0.050 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: 38.510 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7243 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 : 0.005 0.043 6795 Z= 0.302 Angle : 0.602 5.593 9228 Z= 0.342 Chirality : 0.048 0.339 1062 Planarity : 0.004 0.029 1158 Dihedral : 13.840 86.752 2622 Min Nonbonded Distance : 2.409 Molprobity Statistics. All-atom Clashscore : 5.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 0.00 % Allowed : 0.44 % Favored : 99.56 % 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: 1.39 (0.29), residues: 813 helix: 2.71 (0.29), residues: 279 sheet: 0.39 (0.28), residues: 315 loop : -0.58 (0.42), residues: 219 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 287 HIS 0.002 0.001 HIS C 130 PHE 0.012 0.002 PHE B 204 TYR 0.026 0.002 TYR A 111 ARG 0.001 0.000 ARG A 188 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1626 Ramachandran restraints generated. 813 Oldfield, 0 Emsley, 813 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1626 Ramachandran restraints generated. 813 Oldfield, 0 Emsley, 813 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 267 residues out of total 729 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 267 time to evaluate : 0.729 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 71 ILE cc_start: 0.8386 (mt) cc_final: 0.8125 (mm) REVERT: A 75 LEU cc_start: 0.8258 (mt) cc_final: 0.7905 (mm) REVERT: A 86 TYR cc_start: 0.7086 (t80) cc_final: 0.6754 (t80) REVERT: A 87 ARG cc_start: 0.7548 (tpp-160) cc_final: 0.6993 (tpt-90) REVERT: A 90 THR cc_start: 0.7730 (m) cc_final: 0.6830 (p) REVERT: A 93 ARG cc_start: 0.7819 (ttt180) cc_final: 0.7418 (ttt180) REVERT: A 94 GLU cc_start: 0.7320 (mp0) cc_final: 0.6693 (mp0) REVERT: A 106 LYS cc_start: 0.7918 (ttpt) cc_final: 0.7669 (ttmt) REVERT: A 292 ILE cc_start: 0.8082 (mt) cc_final: 0.7863 (mt) REVERT: A 294 LYS cc_start: 0.8845 (mttp) cc_final: 0.8615 (mmtp) REVERT: A 306 THR cc_start: 0.7355 (m) cc_final: 0.6982 (p) REVERT: A 314 PHE cc_start: 0.8333 (t80) cc_final: 0.8077 (t80) REVERT: B 71 ILE cc_start: 0.8425 (mt) cc_final: 0.8146 (mm) REVERT: B 73 ILE cc_start: 0.8006 (mm) cc_final: 0.7800 (mm) REVERT: B 75 LEU cc_start: 0.8256 (mt) cc_final: 0.7952 (mm) REVERT: B 94 GLU cc_start: 0.7548 (mp0) cc_final: 0.6719 (mp0) REVERT: B 96 LEU cc_start: 0.8735 (mt) cc_final: 0.8515 (mt) REVERT: B 106 LYS cc_start: 0.7898 (ttpt) cc_final: 0.7664 (ptmt) REVERT: B 292 ILE cc_start: 0.8056 (mt) cc_final: 0.7843 (mt) REVERT: C 80 VAL cc_start: 0.8169 (t) cc_final: 0.7969 (p) REVERT: C 92 PHE cc_start: 0.8279 (t80) cc_final: 0.8047 (t80) REVERT: C 94 GLU cc_start: 0.7428 (mp0) cc_final: 0.6689 (mp0) REVERT: C 95 LYS cc_start: 0.8535 (mttt) cc_final: 0.8332 (ttmm) REVERT: C 96 LEU cc_start: 0.8886 (mt) cc_final: 0.8526 (mp) REVERT: C 106 LYS cc_start: 0.7794 (ttpt) cc_final: 0.7314 (ttmm) REVERT: C 206 SER cc_start: 0.7842 (p) cc_final: 0.7619 (p) REVERT: C 249 GLU cc_start: 0.7499 (mm-30) cc_final: 0.7261 (mt-10) REVERT: C 314 PHE cc_start: 0.8337 (t80) cc_final: 0.7946 (t80) outliers start: 0 outliers final: 0 residues processed: 267 average time/residue: 0.3023 time to fit residues: 95.8795 Evaluate side-chains 242 residues out of total 729 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 242 time to evaluate : 0.707 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: chunk 68 optimal weight: 0.8980 chunk 61 optimal weight: 1.9990 chunk 34 optimal weight: 1.9990 chunk 20 optimal weight: 0.8980 chunk 41 optimal weight: 0.8980 chunk 32 optimal weight: 0.0770 chunk 63 optimal weight: 2.9990 chunk 24 optimal weight: 1.9990 chunk 38 optimal weight: 0.9990 chunk 47 optimal weight: 0.0370 chunk 73 optimal weight: 0.9990 overall best weight: 0.5616 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 208 GLN B 124 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7314 moved from start: 0.2122 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 6795 Z= 0.267 Angle : 0.535 9.802 9228 Z= 0.278 Chirality : 0.046 0.326 1062 Planarity : 0.004 0.030 1158 Dihedral : 6.311 50.975 1134 Min Nonbonded Distance : 2.179 Molprobity Statistics. All-atom Clashscore : 8.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % Rotamer: Outliers : 1.18 % Allowed : 11.80 % Favored : 87.02 % 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: 1.73 (0.30), residues: 813 helix: 3.00 (0.29), residues: 282 sheet: 0.61 (0.28), residues: 318 loop : -0.54 (0.42), residues: 213 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 230 HIS 0.003 0.001 HIS C 130 PHE 0.014 0.002 PHE C 232 TYR 0.012 0.001 TYR C 201 ARG 0.006 0.000 ARG B 253 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1626 Ramachandran restraints generated. 813 Oldfield, 0 Emsley, 813 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1626 Ramachandran restraints generated. 813 Oldfield, 0 Emsley, 813 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 255 residues out of total 729 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 247 time to evaluate : 0.815 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 75 LEU cc_start: 0.8312 (mt) cc_final: 0.8052 (mm) REVERT: A 93 ARG cc_start: 0.7978 (ttt180) cc_final: 0.7549 (ttt180) REVERT: A 94 GLU cc_start: 0.7551 (mp0) cc_final: 0.6616 (mp0) REVERT: A 106 LYS cc_start: 0.7828 (ttpt) cc_final: 0.7551 (ptmt) REVERT: A 294 LYS cc_start: 0.8784 (mttp) cc_final: 0.8552 (mttm) REVERT: A 314 PHE cc_start: 0.8375 (t80) cc_final: 0.8086 (t80) REVERT: A 323 PHE cc_start: 0.8508 (m-80) cc_final: 0.8265 (m-80) REVERT: B 96 LEU cc_start: 0.8756 (mt) cc_final: 0.8520 (mt) REVERT: B 97 LYS cc_start: 0.8104 (ttmt) cc_final: 0.7875 (ttmt) REVERT: B 106 LYS cc_start: 0.7812 (ttpt) cc_final: 0.7514 (ptmt) REVERT: B 306 THR cc_start: 0.7446 (m) cc_final: 0.7031 (p) REVERT: C 71 ILE cc_start: 0.8324 (mt) cc_final: 0.8038 (mp) REVERT: C 75 LEU cc_start: 0.8093 (mt) cc_final: 0.7748 (mt) REVERT: C 87 ARG cc_start: 0.7466 (tpt-90) cc_final: 0.7121 (tpt-90) REVERT: C 92 PHE cc_start: 0.8445 (t80) cc_final: 0.8214 (t80) REVERT: C 96 LEU cc_start: 0.8786 (mt) cc_final: 0.8411 (mp) REVERT: C 106 LYS cc_start: 0.7722 (ttpt) cc_final: 0.7359 (ttpp) REVERT: C 260 GLN cc_start: 0.7376 (pt0) cc_final: 0.7096 (pt0) REVERT: C 314 PHE cc_start: 0.8372 (t80) cc_final: 0.7924 (t80) outliers start: 8 outliers final: 6 residues processed: 251 average time/residue: 0.3278 time to fit residues: 97.8923 Evaluate side-chains 248 residues out of total 729 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 242 time to evaluate : 0.771 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 104 SER Chi-restraints excluded: chain A residue 154 ILE Chi-restraints excluded: chain B residue 135 ILE Chi-restraints excluded: chain B residue 299 VAL Chi-restraints excluded: chain C residue 104 SER Chi-restraints excluded: chain C residue 251 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: chunk 40 optimal weight: 1.9990 chunk 22 optimal weight: 0.9980 chunk 61 optimal weight: 0.3980 chunk 50 optimal weight: 1.9990 chunk 20 optimal weight: 0.8980 chunk 73 optimal weight: 0.7980 chunk 79 optimal weight: 0.9980 chunk 65 optimal weight: 0.9990 chunk 25 optimal weight: 0.9980 chunk 59 optimal weight: 2.9990 chunk 72 optimal weight: 0.9980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 208 GLN A 260 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7360 moved from start: 0.2969 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 6795 Z= 0.353 Angle : 0.577 8.560 9228 Z= 0.299 Chirality : 0.046 0.335 1062 Planarity : 0.004 0.031 1158 Dihedral : 5.961 39.912 1134 Min Nonbonded Distance : 2.120 Molprobity Statistics. All-atom Clashscore : 11.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.20 % Favored : 96.80 % Rotamer: Outliers : 3.10 % Allowed : 13.27 % Favored : 83.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.52 (0.30), residues: 813 helix: 2.84 (0.29), residues: 282 sheet: 0.56 (0.30), residues: 315 loop : -0.77 (0.42), residues: 216 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 230 HIS 0.004 0.002 HIS C 131 PHE 0.021 0.002 PHE B 314 TYR 0.011 0.002 TYR B 119 ARG 0.005 0.000 ARG C 153 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1626 Ramachandran restraints generated. 813 Oldfield, 0 Emsley, 813 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1626 Ramachandran restraints generated. 813 Oldfield, 0 Emsley, 813 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 266 residues out of total 729 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 245 time to evaluate : 0.771 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 75 LEU cc_start: 0.8455 (mt) cc_final: 0.8201 (mm) REVERT: A 93 ARG cc_start: 0.8059 (ttt180) cc_final: 0.7624 (ttt180) REVERT: A 101 MET cc_start: 0.8865 (mtt) cc_final: 0.8628 (mtt) REVERT: A 106 LYS cc_start: 0.7751 (ttpt) cc_final: 0.7478 (ptmt) REVERT: A 314 PHE cc_start: 0.8410 (t80) cc_final: 0.8079 (t80) REVERT: B 92 PHE cc_start: 0.8728 (t80) cc_final: 0.8379 (t80) REVERT: B 95 LYS cc_start: 0.8739 (OUTLIER) cc_final: 0.8217 (mtmm) REVERT: B 96 LEU cc_start: 0.8762 (mt) cc_final: 0.8412 (mt) REVERT: B 106 LYS cc_start: 0.7756 (ttpt) cc_final: 0.7489 (ptmt) REVERT: B 188 ARG cc_start: 0.8537 (tmm-80) cc_final: 0.8252 (ttt-90) REVERT: B 306 THR cc_start: 0.7500 (m) cc_final: 0.7152 (p) REVERT: C 80 VAL cc_start: 0.8163 (t) cc_final: 0.7916 (p) REVERT: C 87 ARG cc_start: 0.7646 (tpt-90) cc_final: 0.7443 (tpt-90) REVERT: C 95 LYS cc_start: 0.8577 (mttt) cc_final: 0.8331 (ttmm) REVERT: C 106 LYS cc_start: 0.7710 (ttpt) cc_final: 0.7365 (ttmm) REVERT: C 243 SER cc_start: 0.8544 (m) cc_final: 0.8265 (p) REVERT: C 314 PHE cc_start: 0.8382 (t80) cc_final: 0.7950 (t80) outliers start: 21 outliers final: 13 residues processed: 253 average time/residue: 0.3111 time to fit residues: 93.7399 Evaluate side-chains 261 residues out of total 729 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 247 time to evaluate : 0.714 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 94 GLU Chi-restraints excluded: chain A residue 104 SER Chi-restraints excluded: chain A residue 151 THR Chi-restraints excluded: chain A residue 154 ILE Chi-restraints excluded: chain A residue 242 MET Chi-restraints excluded: chain A residue 306 THR Chi-restraints excluded: chain B residue 94 GLU Chi-restraints excluded: chain B residue 95 LYS Chi-restraints excluded: chain B residue 135 ILE Chi-restraints excluded: chain B residue 242 MET Chi-restraints excluded: chain C residue 94 GLU Chi-restraints excluded: chain C residue 104 SER Chi-restraints excluded: chain C residue 242 MET Chi-restraints excluded: chain C residue 299 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: chunk 55 optimal weight: 0.9990 chunk 38 optimal weight: 0.7980 chunk 8 optimal weight: 0.8980 chunk 35 optimal weight: 0.7980 chunk 49 optimal weight: 0.9980 chunk 73 optimal weight: 0.8980 chunk 78 optimal weight: 1.9990 chunk 70 optimal weight: 0.6980 chunk 21 optimal weight: 0.9980 chunk 65 optimal weight: 0.9990 chunk 44 optimal weight: 0.7980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7371 moved from start: 0.3395 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.033 6795 Z= 0.341 Angle : 0.540 6.924 9228 Z= 0.286 Chirality : 0.046 0.337 1062 Planarity : 0.003 0.026 1158 Dihedral : 5.250 45.147 1134 Min Nonbonded Distance : 2.119 Molprobity Statistics. All-atom Clashscore : 10.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.32 % Favored : 96.68 % Rotamer: Outliers : 3.69 % Allowed : 17.55 % Favored : 78.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.34 (0.30), residues: 813 helix: 2.74 (0.29), residues: 282 sheet: 0.38 (0.30), residues: 315 loop : -0.80 (0.42), residues: 216 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 230 HIS 0.004 0.001 HIS B 98 PHE 0.019 0.002 PHE C 92 TYR 0.010 0.002 TYR A 111 ARG 0.004 0.000 ARG C 153 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1626 Ramachandran restraints generated. 813 Oldfield, 0 Emsley, 813 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1626 Ramachandran restraints generated. 813 Oldfield, 0 Emsley, 813 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 271 residues out of total 729 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 246 time to evaluate : 0.809 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 92 PHE cc_start: 0.8763 (t80) cc_final: 0.8459 (t80) REVERT: A 93 ARG cc_start: 0.8134 (ttt180) cc_final: 0.7687 (ttt180) REVERT: A 106 LYS cc_start: 0.7817 (ttpt) cc_final: 0.7545 (ttpt) REVERT: A 242 MET cc_start: 0.8810 (OUTLIER) cc_final: 0.8507 (ptp) REVERT: A 297 ASP cc_start: 0.6964 (p0) cc_final: 0.6739 (p0) REVERT: A 306 THR cc_start: 0.7429 (m) cc_final: 0.7041 (p) REVERT: A 314 PHE cc_start: 0.8418 (t80) cc_final: 0.8096 (t80) REVERT: B 92 PHE cc_start: 0.8747 (t80) cc_final: 0.8439 (t80) REVERT: B 94 GLU cc_start: 0.7473 (OUTLIER) cc_final: 0.6610 (mp0) REVERT: B 96 LEU cc_start: 0.8715 (mt) cc_final: 0.8350 (mt) REVERT: B 106 LYS cc_start: 0.7798 (ttpt) cc_final: 0.7460 (ptmt) REVERT: B 306 THR cc_start: 0.7516 (m) cc_final: 0.7190 (p) REVERT: B 318 PHE cc_start: 0.8468 (t80) cc_final: 0.8158 (t80) REVERT: C 75 LEU cc_start: 0.8317 (mt) cc_final: 0.8078 (mm) REVERT: C 80 VAL cc_start: 0.8233 (t) cc_final: 0.7943 (p) REVERT: C 87 ARG cc_start: 0.7662 (tpt-90) cc_final: 0.7338 (tpt-90) REVERT: C 94 GLU cc_start: 0.7439 (OUTLIER) cc_final: 0.6547 (mp0) REVERT: C 95 LYS cc_start: 0.8638 (mttt) cc_final: 0.8340 (ttmm) REVERT: C 297 ASP cc_start: 0.7289 (p0) cc_final: 0.7068 (p0) REVERT: C 314 PHE cc_start: 0.8379 (t80) cc_final: 0.7939 (t80) outliers start: 25 outliers final: 15 residues processed: 253 average time/residue: 0.2978 time to fit residues: 89.6187 Evaluate side-chains 255 residues out of total 729 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 237 time to evaluate : 0.697 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 94 GLU Chi-restraints excluded: chain A residue 104 SER Chi-restraints excluded: chain A residue 107 GLU Chi-restraints excluded: chain A residue 124 GLN Chi-restraints excluded: chain A residue 151 THR Chi-restraints excluded: chain A residue 154 ILE Chi-restraints excluded: chain A residue 242 MET Chi-restraints excluded: chain A residue 251 ASP Chi-restraints excluded: chain B residue 94 GLU Chi-restraints excluded: chain B residue 135 ILE Chi-restraints excluded: chain B residue 166 LYS Chi-restraints excluded: chain B residue 248 LYS Chi-restraints excluded: chain B residue 251 ASP Chi-restraints excluded: chain C residue 94 GLU Chi-restraints excluded: chain C residue 200 ASP Chi-restraints excluded: chain C residue 242 MET Chi-restraints excluded: chain C residue 251 ASP Chi-restraints excluded: chain C residue 299 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: chunk 1 optimal weight: 0.9990 chunk 58 optimal weight: 0.9990 chunk 32 optimal weight: 0.7980 chunk 66 optimal weight: 2.9990 chunk 54 optimal weight: 3.9990 chunk 0 optimal weight: 0.6980 chunk 39 optimal weight: 0.9990 chunk 70 optimal weight: 1.9990 chunk 19 optimal weight: 0.8980 chunk 26 optimal weight: 0.5980 chunk 15 optimal weight: 0.7980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 143 GLN C 186 GLN C 260 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7373 moved from start: 0.3646 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.032 6795 Z= 0.327 Angle : 0.532 7.219 9228 Z= 0.286 Chirality : 0.045 0.337 1062 Planarity : 0.003 0.026 1158 Dihedral : 4.998 39.206 1134 Min Nonbonded Distance : 2.159 Molprobity Statistics. All-atom Clashscore : 10.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % Rotamer: Outliers : 5.01 % Allowed : 17.99 % Favored : 76.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.13 (0.30), residues: 813 helix: 2.56 (0.28), residues: 282 sheet: 0.19 (0.30), residues: 318 loop : -0.76 (0.43), residues: 213 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 230 HIS 0.003 0.001 HIS B 98 PHE 0.017 0.002 PHE B 314 TYR 0.010 0.001 TYR A 201 ARG 0.004 0.000 ARG C 153 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1626 Ramachandran restraints generated. 813 Oldfield, 0 Emsley, 813 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1626 Ramachandran restraints generated. 813 Oldfield, 0 Emsley, 813 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 283 residues out of total 729 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 249 time to evaluate : 0.711 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 90 THR cc_start: 0.7811 (m) cc_final: 0.6813 (m) REVERT: A 93 ARG cc_start: 0.8139 (ttt180) cc_final: 0.7669 (ttt180) REVERT: A 94 GLU cc_start: 0.7496 (OUTLIER) cc_final: 0.6501 (mp0) REVERT: A 106 LYS cc_start: 0.7796 (ttpt) cc_final: 0.7557 (tptp) REVERT: A 242 MET cc_start: 0.8805 (OUTLIER) cc_final: 0.8508 (ptp) REVERT: A 314 PHE cc_start: 0.8437 (t80) cc_final: 0.8124 (t80) REVERT: B 92 PHE cc_start: 0.8734 (t80) cc_final: 0.8459 (t80) REVERT: B 94 GLU cc_start: 0.7456 (OUTLIER) cc_final: 0.6608 (mp0) REVERT: B 95 LYS cc_start: 0.8730 (OUTLIER) cc_final: 0.8309 (mtmm) REVERT: B 96 LEU cc_start: 0.8707 (mt) cc_final: 0.8343 (mt) REVERT: B 104 SER cc_start: 0.8443 (p) cc_final: 0.8095 (m) REVERT: B 106 LYS cc_start: 0.7771 (ttpt) cc_final: 0.7430 (ptmt) REVERT: B 306 THR cc_start: 0.7553 (m) cc_final: 0.7232 (p) REVERT: B 318 PHE cc_start: 0.8499 (t80) cc_final: 0.8205 (t80) REVERT: C 75 LEU cc_start: 0.8349 (mt) cc_final: 0.8127 (mm) REVERT: C 80 VAL cc_start: 0.8209 (t) cc_final: 0.7921 (p) REVERT: C 87 ARG cc_start: 0.7702 (tpt-90) cc_final: 0.7409 (tpt-90) REVERT: C 94 GLU cc_start: 0.7404 (OUTLIER) cc_final: 0.6520 (mp0) REVERT: C 95 LYS cc_start: 0.8619 (mttt) cc_final: 0.8319 (ttmm) REVERT: C 297 ASP cc_start: 0.7262 (p0) cc_final: 0.7015 (p0) REVERT: C 314 PHE cc_start: 0.8376 (t80) cc_final: 0.7922 (t80) outliers start: 34 outliers final: 20 residues processed: 255 average time/residue: 0.2905 time to fit residues: 88.1142 Evaluate side-chains 273 residues out of total 729 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 248 time to evaluate : 0.730 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 94 GLU Chi-restraints excluded: chain A residue 104 SER Chi-restraints excluded: chain A residue 124 GLN Chi-restraints excluded: chain A residue 151 THR Chi-restraints excluded: chain A residue 154 ILE Chi-restraints excluded: chain A residue 242 MET Chi-restraints excluded: chain A residue 248 LYS Chi-restraints excluded: chain A residue 251 ASP Chi-restraints excluded: chain A residue 306 THR Chi-restraints excluded: chain B residue 94 GLU Chi-restraints excluded: chain B residue 95 LYS Chi-restraints excluded: chain B residue 135 ILE Chi-restraints excluded: chain B residue 147 MET Chi-restraints excluded: chain B residue 166 LYS Chi-restraints excluded: chain B residue 242 MET Chi-restraints excluded: chain B residue 248 LYS Chi-restraints excluded: chain B residue 251 ASP Chi-restraints excluded: chain C residue 94 GLU Chi-restraints excluded: chain C residue 200 ASP Chi-restraints excluded: chain C residue 202 LEU Chi-restraints excluded: chain C residue 242 MET Chi-restraints excluded: chain C residue 251 ASP Chi-restraints excluded: chain C residue 260 GLN Chi-restraints excluded: chain C residue 279 GLN Chi-restraints excluded: chain C residue 299 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: chunk 45 optimal weight: 0.8980 chunk 19 optimal weight: 0.9990 chunk 78 optimal weight: 0.6980 chunk 65 optimal weight: 0.5980 chunk 36 optimal weight: 0.9990 chunk 6 optimal weight: 0.8980 chunk 25 optimal weight: 0.5980 chunk 41 optimal weight: 0.8980 chunk 75 optimal weight: 0.9980 chunk 8 optimal weight: 0.9980 chunk 44 optimal weight: 0.9980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 98 HIS C 208 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7375 moved from start: 0.3812 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.033 6795 Z= 0.325 Angle : 0.537 8.635 9228 Z= 0.290 Chirality : 0.045 0.336 1062 Planarity : 0.003 0.025 1158 Dihedral : 5.007 46.602 1134 Min Nonbonded Distance : 2.130 Molprobity Statistics. All-atom Clashscore : 10.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.94 % Favored : 96.06 % Rotamer: Outliers : 3.69 % Allowed : 20.35 % Favored : 75.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.99 (0.30), residues: 813 helix: 2.45 (0.28), residues: 282 sheet: 0.16 (0.30), residues: 315 loop : -0.92 (0.43), residues: 216 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 230 HIS 0.003 0.001 HIS B 98 PHE 0.016 0.002 PHE A 232 TYR 0.009 0.001 TYR A 201 ARG 0.003 0.000 ARG C 153 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1626 Ramachandran restraints generated. 813 Oldfield, 0 Emsley, 813 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1626 Ramachandran restraints generated. 813 Oldfield, 0 Emsley, 813 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 276 residues out of total 729 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 251 time to evaluate : 0.746 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 90 THR cc_start: 0.7855 (m) cc_final: 0.6821 (m) REVERT: A 93 ARG cc_start: 0.8152 (ttt180) cc_final: 0.7681 (ttt180) REVERT: A 94 GLU cc_start: 0.7464 (OUTLIER) cc_final: 0.6487 (mp0) REVERT: A 106 LYS cc_start: 0.7791 (ttpt) cc_final: 0.7569 (tptp) REVERT: A 209 GLU cc_start: 0.6723 (pt0) cc_final: 0.6448 (pt0) REVERT: A 242 MET cc_start: 0.8813 (OUTLIER) cc_final: 0.8522 (ptp) REVERT: A 314 PHE cc_start: 0.8439 (t80) cc_final: 0.8112 (t80) REVERT: B 92 PHE cc_start: 0.8744 (t80) cc_final: 0.8468 (t80) REVERT: B 94 GLU cc_start: 0.7438 (OUTLIER) cc_final: 0.6596 (mp0) REVERT: B 96 LEU cc_start: 0.8732 (mt) cc_final: 0.8389 (mt) REVERT: B 104 SER cc_start: 0.8412 (p) cc_final: 0.8098 (m) REVERT: B 306 THR cc_start: 0.7510 (m) cc_final: 0.7193 (p) REVERT: B 318 PHE cc_start: 0.8490 (t80) cc_final: 0.8220 (t80) REVERT: C 75 LEU cc_start: 0.8365 (mt) cc_final: 0.8149 (mm) REVERT: C 80 VAL cc_start: 0.8197 (t) cc_final: 0.7907 (p) REVERT: C 87 ARG cc_start: 0.7715 (tpt-90) cc_final: 0.7406 (tpt-90) REVERT: C 94 GLU cc_start: 0.7414 (OUTLIER) cc_final: 0.6531 (mp0) REVERT: C 95 LYS cc_start: 0.8629 (mttt) cc_final: 0.8336 (ttmm) REVERT: C 314 PHE cc_start: 0.8371 (t80) cc_final: 0.7913 (t80) outliers start: 25 outliers final: 18 residues processed: 255 average time/residue: 0.2957 time to fit residues: 89.7499 Evaluate side-chains 267 residues out of total 729 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 245 time to evaluate : 0.705 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 94 GLU Chi-restraints excluded: chain A residue 104 SER Chi-restraints excluded: chain A residue 107 GLU Chi-restraints excluded: chain A residue 151 THR Chi-restraints excluded: chain A residue 157 THR Chi-restraints excluded: chain A residue 242 MET Chi-restraints excluded: chain A residue 251 ASP Chi-restraints excluded: chain A residue 306 THR Chi-restraints excluded: chain B residue 94 GLU Chi-restraints excluded: chain B residue 134 VAL Chi-restraints excluded: chain B residue 135 ILE Chi-restraints excluded: chain B residue 147 MET Chi-restraints excluded: chain B residue 166 LYS Chi-restraints excluded: chain B residue 248 LYS Chi-restraints excluded: chain B residue 251 ASP Chi-restraints excluded: chain C residue 94 GLU Chi-restraints excluded: chain C residue 200 ASP Chi-restraints excluded: chain C residue 202 LEU Chi-restraints excluded: chain C residue 242 MET Chi-restraints excluded: chain C residue 251 ASP Chi-restraints excluded: chain C residue 279 GLN Chi-restraints excluded: chain C residue 299 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: chunk 57 optimal weight: 0.9990 chunk 44 optimal weight: 0.9990 chunk 65 optimal weight: 0.5980 chunk 43 optimal weight: 0.0980 chunk 78 optimal weight: 0.9990 chunk 48 optimal weight: 0.6980 chunk 47 optimal weight: 0.9980 chunk 36 optimal weight: 0.6980 chunk 31 optimal weight: 0.9980 chunk 46 optimal weight: 1.9990 chunk 23 optimal weight: 0.2980 overall best weight: 0.4780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 98 HIS C 260 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7350 moved from start: 0.3898 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 6795 Z= 0.237 Angle : 0.504 9.521 9228 Z= 0.271 Chirality : 0.044 0.331 1062 Planarity : 0.003 0.026 1158 Dihedral : 5.068 55.115 1134 Min Nonbonded Distance : 2.159 Molprobity Statistics. All-atom Clashscore : 9.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.32 % Favored : 96.68 % Rotamer: Outliers : 3.54 % Allowed : 21.39 % Favored : 75.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.07 (0.30), residues: 813 helix: 2.58 (0.29), residues: 282 sheet: 0.08 (0.29), residues: 318 loop : -0.76 (0.44), residues: 213 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 230 HIS 0.003 0.001 HIS A 131 PHE 0.017 0.002 PHE A 92 TYR 0.009 0.001 TYR A 201 ARG 0.004 0.000 ARG C 153 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1626 Ramachandran restraints generated. 813 Oldfield, 0 Emsley, 813 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1626 Ramachandran restraints generated. 813 Oldfield, 0 Emsley, 813 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 280 residues out of total 729 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 256 time to evaluate : 0.772 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 75 LEU cc_start: 0.8359 (mt) cc_final: 0.8121 (mm) REVERT: A 93 ARG cc_start: 0.8171 (ttt180) cc_final: 0.7712 (ttt180) REVERT: A 106 LYS cc_start: 0.7792 (ttpt) cc_final: 0.7550 (tptp) REVERT: A 209 GLU cc_start: 0.6574 (pt0) cc_final: 0.6290 (pt0) REVERT: A 314 PHE cc_start: 0.8416 (t80) cc_final: 0.8091 (t80) REVERT: B 92 PHE cc_start: 0.8738 (t80) cc_final: 0.8469 (t80) REVERT: B 94 GLU cc_start: 0.7446 (OUTLIER) cc_final: 0.6594 (mp0) REVERT: B 96 LEU cc_start: 0.8709 (mt) cc_final: 0.8365 (mt) REVERT: B 97 LYS cc_start: 0.8191 (ttmt) cc_final: 0.7913 (ttmt) REVERT: B 227 TYR cc_start: 0.8512 (m-80) cc_final: 0.8304 (m-80) REVERT: B 306 THR cc_start: 0.7473 (m) cc_final: 0.7161 (p) REVERT: B 318 PHE cc_start: 0.8444 (t80) cc_final: 0.8175 (t80) REVERT: C 75 LEU cc_start: 0.8364 (mt) cc_final: 0.8147 (mm) REVERT: C 80 VAL cc_start: 0.8172 (t) cc_final: 0.7883 (p) REVERT: C 87 ARG cc_start: 0.7682 (tpt-90) cc_final: 0.7433 (tpt-90) REVERT: C 94 GLU cc_start: 0.7414 (OUTLIER) cc_final: 0.6519 (mp0) REVERT: C 95 LYS cc_start: 0.8626 (mttt) cc_final: 0.8316 (ttmm) REVERT: C 101 MET cc_start: 0.8948 (mtt) cc_final: 0.8686 (mtt) REVERT: C 179 LYS cc_start: 0.7770 (mttp) cc_final: 0.7509 (mttp) REVERT: C 314 PHE cc_start: 0.8346 (t80) cc_final: 0.7892 (t80) outliers start: 24 outliers final: 21 residues processed: 262 average time/residue: 0.2813 time to fit residues: 88.1266 Evaluate side-chains 280 residues out of total 729 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 257 time to evaluate : 0.692 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 94 GLU Chi-restraints excluded: chain A residue 104 SER Chi-restraints excluded: chain A residue 157 THR Chi-restraints excluded: chain A residue 242 MET Chi-restraints excluded: chain A residue 251 ASP Chi-restraints excluded: chain A residue 306 THR Chi-restraints excluded: chain A residue 315 LEU Chi-restraints excluded: chain B residue 94 GLU Chi-restraints excluded: chain B residue 98 HIS Chi-restraints excluded: chain B residue 134 VAL Chi-restraints excluded: chain B residue 135 ILE Chi-restraints excluded: chain B residue 147 MET Chi-restraints excluded: chain B residue 166 LYS Chi-restraints excluded: chain B residue 242 MET Chi-restraints excluded: chain B residue 251 ASP Chi-restraints excluded: chain C residue 94 GLU Chi-restraints excluded: chain C residue 134 VAL Chi-restraints excluded: chain C residue 200 ASP Chi-restraints excluded: chain C residue 202 LEU Chi-restraints excluded: chain C residue 242 MET Chi-restraints excluded: chain C residue 251 ASP Chi-restraints excluded: chain C residue 260 GLN Chi-restraints excluded: chain C residue 299 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: chunk 15 optimal weight: 0.7980 chunk 49 optimal weight: 0.5980 chunk 53 optimal weight: 0.5980 chunk 38 optimal weight: 0.4980 chunk 7 optimal weight: 0.8980 chunk 61 optimal weight: 0.0470 chunk 71 optimal weight: 0.7980 chunk 74 optimal weight: 0.4980 chunk 68 optimal weight: 0.1980 chunk 72 optimal weight: 0.0770 chunk 43 optimal weight: 0.7980 overall best weight: 0.2636 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 98 HIS B 186 GLN C 208 GLN C 260 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7321 moved from start: 0.4013 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 6795 Z= 0.193 Angle : 0.527 9.383 9228 Z= 0.279 Chirality : 0.047 0.536 1062 Planarity : 0.003 0.026 1158 Dihedral : 5.808 59.524 1134 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 9.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.20 % Favored : 96.80 % Rotamer: Outliers : 2.80 % Allowed : 23.16 % Favored : 74.04 % Cbeta Deviations : 0.13 % 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: 1.19 (0.30), residues: 813 helix: 2.65 (0.29), residues: 279 sheet: 0.09 (0.30), residues: 318 loop : -0.50 (0.45), residues: 216 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 230 HIS 0.015 0.002 HIS B 98 PHE 0.012 0.001 PHE C 160 TYR 0.010 0.001 TYR A 132 ARG 0.003 0.000 ARG C 153 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1626 Ramachandran restraints generated. 813 Oldfield, 0 Emsley, 813 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1626 Ramachandran restraints generated. 813 Oldfield, 0 Emsley, 813 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 269 residues out of total 729 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 250 time to evaluate : 0.754 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 75 LEU cc_start: 0.8330 (mt) cc_final: 0.8085 (mm) REVERT: A 93 ARG cc_start: 0.8149 (ttt180) cc_final: 0.7653 (ttt180) REVERT: A 94 GLU cc_start: 0.7410 (OUTLIER) cc_final: 0.6500 (mp0) REVERT: A 106 LYS cc_start: 0.7804 (ttpt) cc_final: 0.7581 (tptp) REVERT: A 209 GLU cc_start: 0.6579 (pt0) cc_final: 0.6332 (pt0) REVERT: A 306 THR cc_start: 0.7334 (OUTLIER) cc_final: 0.6922 (p) REVERT: A 314 PHE cc_start: 0.8406 (t80) cc_final: 0.8082 (t80) REVERT: B 92 PHE cc_start: 0.8739 (t80) cc_final: 0.8487 (t80) REVERT: B 94 GLU cc_start: 0.7470 (OUTLIER) cc_final: 0.6598 (mp0) REVERT: B 96 LEU cc_start: 0.8700 (mt) cc_final: 0.8368 (mt) REVERT: B 97 LYS cc_start: 0.8290 (ttmt) cc_final: 0.8029 (ttmt) REVERT: B 306 THR cc_start: 0.7487 (m) cc_final: 0.7164 (p) REVERT: B 318 PHE cc_start: 0.8397 (t80) cc_final: 0.8141 (t80) REVERT: C 75 LEU cc_start: 0.8361 (mt) cc_final: 0.8151 (mm) REVERT: C 80 VAL cc_start: 0.8179 (t) cc_final: 0.7886 (p) REVERT: C 87 ARG cc_start: 0.7700 (tpt-90) cc_final: 0.7443 (tpt-90) REVERT: C 94 GLU cc_start: 0.7407 (OUTLIER) cc_final: 0.6504 (mp0) REVERT: C 95 LYS cc_start: 0.8642 (mttt) cc_final: 0.8337 (ttmm) REVERT: C 101 MET cc_start: 0.8908 (mtt) cc_final: 0.8676 (mtt) REVERT: C 314 PHE cc_start: 0.8334 (t80) cc_final: 0.7867 (t80) outliers start: 19 outliers final: 15 residues processed: 253 average time/residue: 0.2913 time to fit residues: 87.8623 Evaluate side-chains 264 residues out of total 729 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 245 time to evaluate : 0.706 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 ILE Chi-restraints excluded: chain A residue 94 GLU Chi-restraints excluded: chain A residue 242 MET Chi-restraints excluded: chain A residue 251 ASP Chi-restraints excluded: chain A residue 306 THR Chi-restraints excluded: chain B residue 71 ILE Chi-restraints excluded: chain B residue 94 GLU Chi-restraints excluded: chain B residue 134 VAL Chi-restraints excluded: chain B residue 147 MET Chi-restraints excluded: chain B residue 166 LYS Chi-restraints excluded: chain B residue 242 MET Chi-restraints excluded: chain B residue 251 ASP Chi-restraints excluded: chain C residue 94 GLU Chi-restraints excluded: chain C residue 134 VAL Chi-restraints excluded: chain C residue 200 ASP Chi-restraints excluded: chain C residue 242 MET Chi-restraints excluded: chain C residue 251 ASP Chi-restraints excluded: chain C residue 260 GLN Chi-restraints excluded: chain C residue 279 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: chunk 31 optimal weight: 1.9990 chunk 57 optimal weight: 0.3980 chunk 22 optimal weight: 0.9980 chunk 65 optimal weight: 1.9990 chunk 68 optimal weight: 0.2980 chunk 72 optimal weight: 0.0270 chunk 47 optimal weight: 1.9990 chunk 76 optimal weight: 0.3980 chunk 46 optimal weight: 0.7980 chunk 36 optimal weight: 0.1980 chunk 53 optimal weight: 0.5980 overall best weight: 0.2638 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 98 HIS B 186 GLN B 221 GLN C 260 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7313 moved from start: 0.4032 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 6795 Z= 0.182 Angle : 0.508 9.634 9228 Z= 0.270 Chirality : 0.045 0.341 1062 Planarity : 0.003 0.027 1158 Dihedral : 5.339 59.987 1134 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 8.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.20 % Favored : 96.80 % Rotamer: Outliers : 3.39 % Allowed : 22.27 % Favored : 74.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.20 (0.30), residues: 813 helix: 2.65 (0.29), residues: 282 sheet: 0.15 (0.29), residues: 321 loop : -0.63 (0.44), residues: 210 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP C 230 HIS 0.002 0.001 HIS A 131 PHE 0.017 0.001 PHE A 83 TYR 0.017 0.001 TYR B 227 ARG 0.003 0.000 ARG C 153 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1626 Ramachandran restraints generated. 813 Oldfield, 0 Emsley, 813 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1626 Ramachandran restraints generated. 813 Oldfield, 0 Emsley, 813 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 270 residues out of total 729 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 247 time to evaluate : 0.747 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 75 LEU cc_start: 0.8311 (mt) cc_final: 0.8060 (mm) REVERT: A 93 ARG cc_start: 0.8186 (ttt180) cc_final: 0.7669 (ttt180) REVERT: A 94 GLU cc_start: 0.7417 (OUTLIER) cc_final: 0.6453 (mp0) REVERT: A 106 LYS cc_start: 0.7784 (ttpt) cc_final: 0.7537 (tptp) REVERT: A 209 GLU cc_start: 0.6512 (pt0) cc_final: 0.6269 (pt0) REVERT: A 306 THR cc_start: 0.7358 (OUTLIER) cc_final: 0.6966 (p) REVERT: A 314 PHE cc_start: 0.8422 (t80) cc_final: 0.8090 (t80) REVERT: B 92 PHE cc_start: 0.8755 (t80) cc_final: 0.8512 (t80) REVERT: B 94 GLU cc_start: 0.7478 (OUTLIER) cc_final: 0.6603 (mp0) REVERT: B 96 LEU cc_start: 0.8652 (mt) cc_final: 0.8321 (mt) REVERT: B 97 LYS cc_start: 0.8278 (ttmt) cc_final: 0.8030 (ttmt) REVERT: B 306 THR cc_start: 0.7479 (m) cc_final: 0.7136 (p) REVERT: B 318 PHE cc_start: 0.8393 (t80) cc_final: 0.8138 (t80) REVERT: C 75 LEU cc_start: 0.8406 (mt) cc_final: 0.8192 (mm) REVERT: C 80 VAL cc_start: 0.8175 (t) cc_final: 0.7884 (p) REVERT: C 87 ARG cc_start: 0.7687 (tpt-90) cc_final: 0.7422 (tpt-90) REVERT: C 94 GLU cc_start: 0.7401 (OUTLIER) cc_final: 0.6498 (mp0) REVERT: C 95 LYS cc_start: 0.8624 (mttt) cc_final: 0.8331 (ttmm) REVERT: C 101 MET cc_start: 0.8888 (mtt) cc_final: 0.8676 (mtt) REVERT: C 209 GLU cc_start: 0.6468 (tt0) cc_final: 0.6238 (pt0) REVERT: C 314 PHE cc_start: 0.8338 (t80) cc_final: 0.7846 (t80) outliers start: 23 outliers final: 14 residues processed: 253 average time/residue: 0.3234 time to fit residues: 98.7639 Evaluate side-chains 271 residues out of total 729 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 253 time to evaluate : 0.792 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 ILE Chi-restraints excluded: chain A residue 94 GLU Chi-restraints excluded: chain A residue 104 SER Chi-restraints excluded: chain A residue 157 THR Chi-restraints excluded: chain A residue 242 MET Chi-restraints excluded: chain A residue 251 ASP Chi-restraints excluded: chain A residue 306 THR Chi-restraints excluded: chain B residue 71 ILE Chi-restraints excluded: chain B residue 94 GLU Chi-restraints excluded: chain B residue 147 MET Chi-restraints excluded: chain B residue 166 LYS Chi-restraints excluded: chain B residue 242 MET Chi-restraints excluded: chain B residue 251 ASP Chi-restraints excluded: chain C residue 94 GLU Chi-restraints excluded: chain C residue 251 ASP Chi-restraints excluded: chain C residue 260 GLN Chi-restraints excluded: chain C residue 279 GLN Chi-restraints excluded: chain C residue 299 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: chunk 80 optimal weight: 0.3980 chunk 74 optimal weight: 0.4980 chunk 64 optimal weight: 0.8980 chunk 6 optimal weight: 1.9990 chunk 49 optimal weight: 0.0970 chunk 39 optimal weight: 0.9980 chunk 51 optimal weight: 0.7980 chunk 68 optimal weight: 0.9990 chunk 19 optimal weight: 0.8980 chunk 59 optimal weight: 0.7980 chunk 9 optimal weight: 0.8980 overall best weight: 0.5178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 143 GLN B 98 HIS B 186 GLN C 260 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7347 moved from start: 0.4112 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 6795 Z= 0.255 Angle : 0.533 10.022 9228 Z= 0.286 Chirality : 0.045 0.329 1062 Planarity : 0.003 0.026 1158 Dihedral : 5.160 54.887 1134 Min Nonbonded Distance : 2.141 Molprobity Statistics. All-atom Clashscore : 8.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.32 % Favored : 96.68 % Rotamer: Outliers : 2.95 % Allowed : 22.42 % Favored : 74.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.13 (0.30), residues: 813 helix: 2.60 (0.29), residues: 282 sheet: 0.11 (0.29), residues: 321 loop : -0.68 (0.44), residues: 210 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 230 HIS 0.002 0.001 HIS C 130 PHE 0.014 0.002 PHE C 232 TYR 0.009 0.001 TYR A 201 ARG 0.004 0.000 ARG C 175 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1626 Ramachandran restraints generated. 813 Oldfield, 0 Emsley, 813 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1626 Ramachandran restraints generated. 813 Oldfield, 0 Emsley, 813 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 274 residues out of total 729 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 254 time to evaluate : 0.788 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 75 LEU cc_start: 0.8372 (mt) cc_final: 0.8140 (mm) REVERT: A 93 ARG cc_start: 0.8197 (ttt180) cc_final: 0.7688 (ttt180) REVERT: A 94 GLU cc_start: 0.7423 (OUTLIER) cc_final: 0.6471 (mp0) REVERT: A 106 LYS cc_start: 0.7780 (ttpt) cc_final: 0.7553 (tptp) REVERT: A 209 GLU cc_start: 0.6596 (pt0) cc_final: 0.6369 (pt0) REVERT: A 314 PHE cc_start: 0.8449 (t80) cc_final: 0.8122 (t80) REVERT: B 92 PHE cc_start: 0.8760 (t80) cc_final: 0.8485 (t80) REVERT: B 96 LEU cc_start: 0.8675 (mt) cc_final: 0.8325 (mt) REVERT: B 97 LYS cc_start: 0.8280 (ttmt) cc_final: 0.8032 (ttmt) REVERT: B 104 SER cc_start: 0.8411 (p) cc_final: 0.8073 (m) REVERT: B 206 SER cc_start: 0.7573 (p) cc_final: 0.7326 (p) REVERT: B 306 THR cc_start: 0.7498 (m) cc_final: 0.7161 (p) REVERT: B 318 PHE cc_start: 0.8406 (t80) cc_final: 0.8154 (t80) REVERT: C 80 VAL cc_start: 0.8200 (t) cc_final: 0.7908 (p) REVERT: C 87 ARG cc_start: 0.7711 (tpt-90) cc_final: 0.7435 (tpt-90) REVERT: C 94 GLU cc_start: 0.7401 (OUTLIER) cc_final: 0.6514 (mp0) REVERT: C 95 LYS cc_start: 0.8624 (mttt) cc_final: 0.8332 (ttmm) REVERT: C 224 GLU cc_start: 0.7609 (mt-10) cc_final: 0.7359 (mt-10) REVERT: C 293 GLN cc_start: 0.8693 (tt0) cc_final: 0.8387 (tt0) REVERT: C 314 PHE cc_start: 0.8356 (t80) cc_final: 0.7878 (t80) outliers start: 20 outliers final: 16 residues processed: 258 average time/residue: 0.2915 time to fit residues: 89.8224 Evaluate side-chains 269 residues out of total 729 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 251 time to evaluate : 0.786 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 94 GLU Chi-restraints excluded: chain A residue 104 SER Chi-restraints excluded: chain A residue 157 THR Chi-restraints excluded: chain A residue 242 MET Chi-restraints excluded: chain A residue 306 THR Chi-restraints excluded: chain A residue 315 LEU Chi-restraints excluded: chain B residue 71 ILE Chi-restraints excluded: chain B residue 94 GLU Chi-restraints excluded: chain B residue 134 VAL Chi-restraints excluded: chain B residue 147 MET Chi-restraints excluded: chain B residue 166 LYS Chi-restraints excluded: chain B residue 242 MET Chi-restraints excluded: chain B residue 248 LYS Chi-restraints excluded: chain C residue 94 GLU Chi-restraints excluded: chain C residue 242 MET Chi-restraints excluded: chain C residue 260 GLN Chi-restraints excluded: chain C residue 279 GLN Chi-restraints excluded: chain C residue 299 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: chunk 17 optimal weight: 0.9980 chunk 64 optimal weight: 0.6980 chunk 26 optimal weight: 0.5980 chunk 66 optimal weight: 0.9990 chunk 8 optimal weight: 1.9990 chunk 11 optimal weight: 0.9990 chunk 56 optimal weight: 0.7980 chunk 3 optimal weight: 0.9990 chunk 46 optimal weight: 1.9990 chunk 73 optimal weight: 0.9990 chunk 43 optimal weight: 0.8980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 98 HIS B 186 GLN C 260 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3728 r_free = 0.3728 target = 0.120320 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 22)----------------| | r_work = 0.3516 r_free = 0.3516 target = 0.106984 restraints weight = 12649.290| |-----------------------------------------------------------------------------| r_work (start): 0.3532 rms_B_bonded: 2.84 r_work: 0.3384 rms_B_bonded: 3.47 restraints_weight: 0.5000 r_work (final): 0.3384 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7952 moved from start: 0.4220 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 6795 Z= 0.347 Angle : 0.562 10.719 9228 Z= 0.303 Chirality : 0.046 0.333 1062 Planarity : 0.003 0.026 1158 Dihedral : 5.204 50.584 1134 Min Nonbonded Distance : 2.008 Molprobity Statistics. All-atom Clashscore : 9.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.69 % Favored : 96.31 % Rotamer: Outliers : 3.24 % Allowed : 22.27 % Favored : 74.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.97 (0.30), residues: 813 helix: 2.44 (0.29), residues: 282 sheet: 0.05 (0.29), residues: 321 loop : -0.79 (0.43), residues: 210 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 230 HIS 0.004 0.001 HIS C 98 PHE 0.018 0.002 PHE A 232 TYR 0.012 0.001 TYR B 227 ARG 0.004 0.000 ARG C 175 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2527.30 seconds wall clock time: 46 minutes 18.52 seconds (2778.52 seconds total)