Starting phenix.real_space_refine on Mon Sep 23 20:56:23 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qbc_13886/09_2024/7qbc_13886.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qbc_13886/09_2024/7qbc_13886.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.53 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qbc_13886/09_2024/7qbc_13886.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qbc_13886/09_2024/7qbc_13886.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qbc_13886/09_2024/7qbc_13886.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qbc_13886/09_2024/7qbc_13886.cif" } resolution = 3.53 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.088 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 22 5.16 5 C 3400 2.51 5 N 728 2.21 5 O 904 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 6 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 5054 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 2169 Number of conformers: 1 Conformer: "" Number of residues, atoms: 298, 2169 Classifications: {'peptide': 298} Incomplete info: {'truncation_to_alanine': 38} Link IDs: {'PTRANS': 8, 'TRANS': 289} Unresolved non-hydrogen bonds: 140 Unresolved non-hydrogen angles: 175 Unresolved non-hydrogen dihedrals: 113 Unresolved non-hydrogen chiralities: 15 Planarities with less than four sites: {'GLN:plan1': 2, 'ASP:plan': 3, 'ASN:plan1': 3, 'HIS:plan': 1, 'PHE:plan': 3, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 69 Chain: "I" Number of atoms: 120 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 120 Classifications: {'peptide': 13} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 10} Chain: "K" Number of atoms: 120 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 120 Classifications: {'peptide': 13} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 10} Chain: "B" Number of atoms: 2169 Number of conformers: 1 Conformer: "" Number of residues, atoms: 298, 2169 Classifications: {'peptide': 298} Incomplete info: {'truncation_to_alanine': 38} Link IDs: {'PTRANS': 8, 'TRANS': 289} Unresolved non-hydrogen bonds: 140 Unresolved non-hydrogen angles: 175 Unresolved non-hydrogen dihedrals: 113 Unresolved non-hydrogen chiralities: 15 Planarities with less than four sites: {'GLN:plan1': 2, 'ASP:plan': 3, 'ASN:plan1': 3, 'HIS:plan': 1, 'PHE:plan': 3, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 69 Chain: "A" Number of atoms: 238 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 238 Unusual residues: {'NAG': 2, 'Y01': 6} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "B" Number of atoms: 238 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 238 Unusual residues: {'NAG': 2, 'Y01': 6} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Time building chain proxies: 3.95, per 1000 atoms: 0.78 Number of scatterers: 5054 At special positions: 0 Unit cell: (75.9, 78.1, 96.8, 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 22 16.00 O 904 8.00 N 728 7.00 C 3400 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 - 3.00 Amino acid : True - 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 501 " - " ASN A 25 " " NAG A 502 " - " ASN A 32 " " NAG B 501 " - " ASN B 25 " " NAG B 502 " - " ASN B 32 " Time building additional restraints: 1.34 Conformation dependent library (CDL) restraints added in 616.0 milliseconds 1228 Ramachandran restraints generated. 614 Oldfield, 0 Emsley, 614 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1180 Finding SS restraints... Secondary structure from input PDB file: 22 helices and 2 sheets defined 73.0% alpha, 1.6% 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 9 through 13 Processing helix chain 'A' and resid 37 through 73 removed outlier: 3.520A pdb=" N THR A 48 " --> pdb=" O LEU A 44 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N ILE A 53 " --> pdb=" O VAL A 49 " (cutoff:3.500A) removed outlier: 4.128A pdb=" N MET A 54 " --> pdb=" O THR A 50 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N PHE A 55 " --> pdb=" O GLN A 51 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N VAL A 68 " --> pdb=" O LEU A 64 " (cutoff:3.500A) Processing helix chain 'A' and resid 78 through 103 removed outlier: 3.583A pdb=" N ILE A 82 " --> pdb=" O THR A 78 " (cutoff:3.500A) Processing helix chain 'A' and resid 108 through 114 Processing helix chain 'A' and resid 116 through 120 Processing helix chain 'A' and resid 123 through 154 removed outlier: 3.865A pdb=" N VAL A 136 " --> pdb=" O ASN A 132 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N SER A 141 " --> pdb=" O LEU A 137 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N PHE A 148 " --> pdb=" O THR A 144 " (cutoff:3.500A) removed outlier: 4.238A pdb=" N VAL A 152 " --> pdb=" O PHE A 148 " (cutoff:3.500A) Processing helix chain 'A' and resid 159 through 195 removed outlier: 3.514A pdb=" N GLY A 163 " --> pdb=" O PHE A 159 " (cutoff:3.500A) Processing helix chain 'A' and resid 201 through 237 Processing helix chain 'A' and resid 244 through 249 removed outlier: 4.471A pdb=" N LEU A 248 " --> pdb=" O PHE A 244 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N ILE A 249 " --> pdb=" O HIS A 245 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 244 through 249' Processing helix chain 'A' and resid 255 through 266 removed outlier: 3.731A pdb=" N ILE A 263 " --> pdb=" O SER A 259 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N TYR A 266 " --> pdb=" O PHE A 262 " (cutoff:3.500A) Processing helix chain 'A' and resid 275 through 297 removed outlier: 3.642A pdb=" N THR A 279 " --> pdb=" O ASP A 275 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N THR A 282 " --> pdb=" O THR A 278 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N LEU A 283 " --> pdb=" O THR A 279 " (cutoff:3.500A) Proline residue: A 290 - end of helix Processing helix chain 'B' and resid 9 through 13 Processing helix chain 'B' and resid 37 through 73 removed outlier: 3.519A pdb=" N THR B 48 " --> pdb=" O LEU B 44 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N ILE B 53 " --> pdb=" O VAL B 49 " (cutoff:3.500A) removed outlier: 4.129A pdb=" N MET B 54 " --> pdb=" O THR B 50 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N PHE B 55 " --> pdb=" O GLN B 51 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N VAL B 68 " --> pdb=" O LEU B 64 " (cutoff:3.500A) Processing helix chain 'B' and resid 78 through 103 removed outlier: 3.583A pdb=" N ILE B 82 " --> pdb=" O THR B 78 " (cutoff:3.500A) Processing helix chain 'B' and resid 108 through 114 Processing helix chain 'B' and resid 116 through 120 Processing helix chain 'B' and resid 123 through 154 removed outlier: 3.864A pdb=" N VAL B 136 " --> pdb=" O ASN B 132 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N SER B 141 " --> pdb=" O LEU B 137 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N PHE B 148 " --> pdb=" O THR B 144 " (cutoff:3.500A) removed outlier: 4.238A pdb=" N VAL B 152 " --> pdb=" O PHE B 148 " (cutoff:3.500A) Processing helix chain 'B' and resid 159 through 195 removed outlier: 3.513A pdb=" N GLY B 163 " --> pdb=" O PHE B 159 " (cutoff:3.500A) Processing helix chain 'B' and resid 201 through 237 Processing helix chain 'B' and resid 244 through 249 removed outlier: 4.471A pdb=" N LEU B 248 " --> pdb=" O PHE B 244 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N ILE B 249 " --> pdb=" O HIS B 245 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 244 through 249' Processing helix chain 'B' and resid 255 through 266 removed outlier: 3.732A pdb=" N ILE B 263 " --> pdb=" O SER B 259 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N TYR B 266 " --> pdb=" O PHE B 262 " (cutoff:3.500A) Processing helix chain 'B' and resid 275 through 297 removed outlier: 3.641A pdb=" N THR B 279 " --> pdb=" O ASP B 275 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N THR B 282 " --> pdb=" O THR B 278 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N LEU B 283 " --> pdb=" O THR B 279 " (cutoff:3.500A) Proline residue: B 290 - end of helix Processing sheet with id=AA1, first strand: chain 'A' and resid 26 through 28 removed outlier: 6.823A pdb=" N TYR A 26 " --> pdb=" O GLY A 33 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N GLY A 33 " --> pdb=" O TYR A 26 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 26 through 28 removed outlier: 6.823A pdb=" N TYR B 26 " --> pdb=" O GLY B 33 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N GLY B 33 " --> pdb=" O TYR B 26 " (cutoff:3.500A) 332 hydrogen bonds defined for protein. 966 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: 1.32 Time building geometry restraints manager: 1.54 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 738 1.31 - 1.44: 1336 1.44 - 1.56: 3062 1.56 - 1.69: 14 1.69 - 1.81: 40 Bond restraints: 5190 Sorted by residual: bond pdb=" C7 NAG B 501 " pdb=" N2 NAG B 501 " ideal model delta sigma weight residual 1.346 1.454 -0.108 2.00e-02 2.50e+03 2.92e+01 bond pdb=" C7 NAG A 501 " pdb=" N2 NAG A 501 " ideal model delta sigma weight residual 1.346 1.454 -0.108 2.00e-02 2.50e+03 2.89e+01 bond pdb=" C7 NAG A 502 " pdb=" N2 NAG A 502 " ideal model delta sigma weight residual 1.346 1.452 -0.106 2.00e-02 2.50e+03 2.83e+01 bond pdb=" C7 NAG B 502 " pdb=" N2 NAG B 502 " ideal model delta sigma weight residual 1.346 1.451 -0.105 2.00e-02 2.50e+03 2.77e+01 bond pdb=" C1 NAG A 502 " pdb=" O5 NAG A 502 " ideal model delta sigma weight residual 1.406 1.504 -0.098 2.00e-02 2.50e+03 2.39e+01 ... (remaining 5185 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.64: 6615 1.64 - 3.27: 418 3.27 - 4.91: 98 4.91 - 6.54: 30 6.54 - 8.18: 5 Bond angle restraints: 7166 Sorted by residual: angle pdb=" N TYR A 181 " pdb=" CA TYR A 181 " pdb=" C TYR A 181 " ideal model delta sigma weight residual 111.28 105.83 5.45 1.09e+00 8.42e-01 2.50e+01 angle pdb=" N TYR B 181 " pdb=" CA TYR B 181 " pdb=" C TYR B 181 " ideal model delta sigma weight residual 111.28 105.94 5.34 1.09e+00 8.42e-01 2.40e+01 angle pdb=" N MET B 294 " pdb=" CA MET B 294 " pdb=" C MET B 294 " ideal model delta sigma weight residual 113.28 107.62 5.66 1.22e+00 6.72e-01 2.15e+01 angle pdb=" N MET A 294 " pdb=" CA MET A 294 " pdb=" C MET A 294 " ideal model delta sigma weight residual 113.28 107.67 5.61 1.22e+00 6.72e-01 2.12e+01 angle pdb=" N MET B 69 " pdb=" CA MET B 69 " pdb=" C MET B 69 " ideal model delta sigma weight residual 111.28 106.32 4.96 1.09e+00 8.42e-01 2.07e+01 ... (remaining 7161 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.42: 3284 15.42 - 30.84: 245 30.84 - 46.25: 83 46.25 - 61.67: 34 61.67 - 77.09: 8 Dihedral angle restraints: 3654 sinusoidal: 1828 harmonic: 1826 Sorted by residual: dihedral pdb=" CA PHE B 55 " pdb=" C PHE B 55 " pdb=" N GLY B 56 " pdb=" CA GLY B 56 " ideal model delta harmonic sigma weight residual 180.00 161.45 18.55 0 5.00e+00 4.00e-02 1.38e+01 dihedral pdb=" CA PHE A 55 " pdb=" C PHE A 55 " pdb=" N GLY A 56 " pdb=" CA GLY A 56 " ideal model delta harmonic sigma weight residual 180.00 161.50 18.50 0 5.00e+00 4.00e-02 1.37e+01 dihedral pdb=" CA THR B 144 " pdb=" C THR B 144 " pdb=" N SER B 145 " pdb=" CA SER B 145 " ideal model delta harmonic sigma weight residual 180.00 162.88 17.12 0 5.00e+00 4.00e-02 1.17e+01 ... (remaining 3651 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.046: 650 0.046 - 0.092: 202 0.092 - 0.138: 50 0.138 - 0.184: 12 0.184 - 0.230: 2 Chirality restraints: 916 Sorted by residual: chirality pdb=" CB VAL B 191 " pdb=" CA VAL B 191 " pdb=" CG1 VAL B 191 " pdb=" CG2 VAL B 191 " both_signs ideal model delta sigma weight residual False -2.63 -2.40 -0.23 2.00e-01 2.50e+01 1.32e+00 chirality pdb=" CB VAL A 191 " pdb=" CA VAL A 191 " pdb=" CG1 VAL A 191 " pdb=" CG2 VAL A 191 " both_signs ideal model delta sigma weight residual False -2.63 -2.40 -0.22 2.00e-01 2.50e+01 1.26e+00 chirality pdb=" CA VAL A 191 " pdb=" N VAL A 191 " pdb=" C VAL A 191 " pdb=" CB VAL A 191 " both_signs ideal model delta sigma weight residual False 2.44 2.27 0.18 2.00e-01 2.50e+01 7.75e-01 ... (remaining 913 not shown) Planarity restraints: 816 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA SER A 293 " 0.021 2.00e-02 2.50e+03 4.36e-02 1.90e+01 pdb=" C SER A 293 " -0.075 2.00e-02 2.50e+03 pdb=" O SER A 293 " 0.029 2.00e-02 2.50e+03 pdb=" N MET A 294 " 0.025 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER B 293 " -0.021 2.00e-02 2.50e+03 4.26e-02 1.81e+01 pdb=" C SER B 293 " 0.074 2.00e-02 2.50e+03 pdb=" O SER B 293 " -0.028 2.00e-02 2.50e+03 pdb=" N MET B 294 " -0.025 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR A 179 " -0.020 2.00e-02 2.50e+03 4.11e-02 1.69e+01 pdb=" C THR A 179 " 0.071 2.00e-02 2.50e+03 pdb=" O THR A 179 " -0.027 2.00e-02 2.50e+03 pdb=" N MET A 180 " -0.024 2.00e-02 2.50e+03 ... (remaining 813 not shown) Histogram of nonbonded interaction distances: 2.06 - 2.62: 40 2.62 - 3.19: 4851 3.19 - 3.76: 7546 3.76 - 4.33: 10065 4.33 - 4.90: 16455 Nonbonded interactions: 38957 Sorted by model distance: nonbonded pdb=" O LYS B 100 " pdb=" OG SER B 104 " model vdw 2.055 3.040 nonbonded pdb=" O LYS A 100 " pdb=" OG SER A 104 " model vdw 2.056 3.040 nonbonded pdb=" O LEU B 102 " pdb=" OG SER B 107 " model vdw 2.194 3.040 nonbonded pdb=" O LEU A 102 " pdb=" OG SER A 107 " model vdw 2.195 3.040 nonbonded pdb=" O ILE A 142 " pdb=" OG SER A 145 " model vdw 2.210 3.040 ... (remaining 38952 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } ncs_group { reference = chain 'I' selection = chain 'K' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.020 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.180 Check model and map are aligned: 0.050 Set scattering table: 0.060 Process input model: 16.400 Find NCS groups from input model: 0.150 Set up NCS constraints: 0.030 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:3.150 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.050 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7177 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 : 0.008 0.108 5190 Z= 0.502 Angle : 0.975 8.181 7166 Z= 0.532 Chirality : 0.049 0.230 916 Planarity : 0.007 0.047 812 Dihedral : 13.182 77.087 2474 Min Nonbonded Distance : 2.055 Molprobity Statistics. All-atom Clashscore : 3.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.89 % Favored : 95.11 % Rotamer: Outliers : 0.43 % Allowed : 0.43 % Favored : 99.15 % 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: -2.40 (0.31), residues: 614 helix: -1.04 (0.24), residues: 414 sheet: -3.35 (1.02), residues: 24 loop : -2.33 (0.40), residues: 176 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.004 TRP A 70 HIS 0.002 0.001 HIS B 126 PHE 0.034 0.002 PHE A 262 TYR 0.025 0.002 TYR B 193 ARG 0.002 0.000 ARG A 58 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1228 Ramachandran restraints generated. 614 Oldfield, 0 Emsley, 614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1228 Ramachandran restraints generated. 614 Oldfield, 0 Emsley, 614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 546 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 106 time to evaluate : 0.502 Fit side-chains outliers start: 2 outliers final: 0 residues processed: 108 average time/residue: 0.1437 time to fit residues: 20.9970 Evaluate side-chains 87 residues out of total 546 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 87 time to evaluate : 0.462 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 50 optimal weight: 0.7980 chunk 45 optimal weight: 0.9980 chunk 25 optimal weight: 0.9980 chunk 15 optimal weight: 20.0000 chunk 30 optimal weight: 0.8980 chunk 24 optimal weight: 0.5980 chunk 47 optimal weight: 0.6980 chunk 18 optimal weight: 0.7980 chunk 28 optimal weight: 0.8980 chunk 35 optimal weight: 0.5980 chunk 54 optimal weight: 8.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 205 ASN B 205 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7309 moved from start: 0.1800 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 5190 Z= 0.242 Angle : 0.653 7.019 7166 Z= 0.321 Chirality : 0.042 0.128 916 Planarity : 0.005 0.061 812 Dihedral : 9.377 59.483 1592 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 7.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.40 % Favored : 95.60 % Rotamer: Outliers : 1.28 % Allowed : 8.94 % Favored : 89.79 % 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: -0.31 (0.34), residues: 614 helix: 0.72 (0.26), residues: 408 sheet: -3.05 (1.19), residues: 20 loop : -1.88 (0.40), residues: 186 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 295 HIS 0.001 0.001 HIS A 126 PHE 0.029 0.002 PHE B 244 TYR 0.014 0.002 TYR B 17 ARG 0.001 0.000 ARG A 76 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1228 Ramachandran restraints generated. 614 Oldfield, 0 Emsley, 614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1228 Ramachandran restraints generated. 614 Oldfield, 0 Emsley, 614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 546 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 110 time to evaluate : 0.535 Fit side-chains REVERT: A 64 LEU cc_start: 0.8232 (mt) cc_final: 0.8027 (tt) REVERT: A 111 TYR cc_start: 0.8713 (t80) cc_final: 0.8268 (t80) REVERT: B 205 ASN cc_start: 0.7603 (OUTLIER) cc_final: 0.7324 (t0) outliers start: 6 outliers final: 3 residues processed: 110 average time/residue: 0.1508 time to fit residues: 21.9133 Evaluate side-chains 107 residues out of total 546 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 103 time to evaluate : 0.520 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 150 ILE Chi-restraints excluded: chain B residue 149 GLN Chi-restraints excluded: chain B residue 150 ILE Chi-restraints excluded: chain B residue 205 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 30 optimal weight: 4.9990 chunk 16 optimal weight: 0.5980 chunk 45 optimal weight: 2.9990 chunk 37 optimal weight: 0.7980 chunk 15 optimal weight: 9.9990 chunk 54 optimal weight: 0.9990 chunk 58 optimal weight: 0.8980 chunk 48 optimal weight: 2.9990 chunk 18 optimal weight: 0.8980 chunk 43 optimal weight: 0.6980 chunk 53 optimal weight: 2.9990 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 149 GLN A 205 ASN I 2 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7377 moved from start: 0.2365 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 5190 Z= 0.236 Angle : 0.618 6.190 7166 Z= 0.307 Chirality : 0.041 0.124 916 Planarity : 0.005 0.073 812 Dihedral : 9.279 58.956 1592 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 8.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.75 % Favored : 96.25 % Rotamer: Outliers : 1.70 % Allowed : 12.13 % Favored : 86.17 % 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: 0.36 (0.34), residues: 614 helix: 1.27 (0.26), residues: 410 sheet: -2.81 (1.22), residues: 20 loop : -1.75 (0.42), residues: 184 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 295 HIS 0.001 0.000 HIS K 2 PHE 0.017 0.001 PHE B 55 TYR 0.011 0.001 TYR B 98 ARG 0.002 0.000 ARG A 76 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1228 Ramachandran restraints generated. 614 Oldfield, 0 Emsley, 614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1228 Ramachandran restraints generated. 614 Oldfield, 0 Emsley, 614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 546 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 110 time to evaluate : 0.803 Fit side-chains REVERT: A 69 MET cc_start: 0.7955 (mmm) cc_final: 0.7542 (mmm) REVERT: B 69 MET cc_start: 0.7973 (mmm) cc_final: 0.7555 (mmm) outliers start: 8 outliers final: 4 residues processed: 114 average time/residue: 0.1634 time to fit residues: 24.4287 Evaluate side-chains 105 residues out of total 546 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 101 time to evaluate : 0.553 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 149 GLN Chi-restraints excluded: chain B residue 64 LEU Chi-restraints excluded: chain B residue 149 GLN Chi-restraints excluded: chain B residue 150 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 41 optimal weight: 0.8980 chunk 28 optimal weight: 1.9990 chunk 6 optimal weight: 0.6980 chunk 26 optimal weight: 0.4980 chunk 36 optimal weight: 0.8980 chunk 54 optimal weight: 7.9990 chunk 57 optimal weight: 3.9990 chunk 51 optimal weight: 0.9980 chunk 15 optimal weight: 20.0000 chunk 48 optimal weight: 1.9990 chunk 32 optimal weight: 0.4980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 149 GLN A 205 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7405 moved from start: 0.2739 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 5190 Z= 0.226 Angle : 0.613 7.110 7166 Z= 0.303 Chirality : 0.040 0.124 916 Planarity : 0.005 0.075 812 Dihedral : 9.342 58.907 1592 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 7.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.23 % Favored : 95.77 % Rotamer: Outliers : 2.55 % Allowed : 15.32 % Favored : 82.13 % 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: 0.71 (0.35), residues: 614 helix: 1.56 (0.26), residues: 412 sheet: -2.87 (1.14), residues: 20 loop : -1.69 (0.44), residues: 182 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP B 295 HIS 0.001 0.000 HIS I 2 PHE 0.017 0.001 PHE B 244 TYR 0.012 0.001 TYR B 98 ARG 0.002 0.000 ARG B 76 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1228 Ramachandran restraints generated. 614 Oldfield, 0 Emsley, 614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1228 Ramachandran restraints generated. 614 Oldfield, 0 Emsley, 614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 546 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 105 time to evaluate : 0.603 Fit side-chains REVERT: A 205 ASN cc_start: 0.7695 (OUTLIER) cc_final: 0.7376 (m-40) REVERT: A 295 TRP cc_start: 0.7815 (t-100) cc_final: 0.7459 (t-100) outliers start: 12 outliers final: 5 residues processed: 113 average time/residue: 0.1471 time to fit residues: 21.9376 Evaluate side-chains 107 residues out of total 546 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 101 time to evaluate : 0.525 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 149 GLN Chi-restraints excluded: chain A residue 205 ASN Chi-restraints excluded: chain B residue 64 LEU Chi-restraints excluded: chain B residue 149 GLN Chi-restraints excluded: chain B residue 150 ILE Chi-restraints excluded: chain B residue 173 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 0 optimal weight: 7.9990 chunk 43 optimal weight: 0.5980 chunk 23 optimal weight: 7.9990 chunk 49 optimal weight: 0.8980 chunk 40 optimal weight: 0.8980 chunk 29 optimal weight: 4.9990 chunk 52 optimal weight: 0.9990 chunk 14 optimal weight: 0.0870 chunk 19 optimal weight: 0.9980 chunk 11 optimal weight: 0.0010 chunk 34 optimal weight: 1.9990 overall best weight: 0.4964 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 149 GLN A 205 ASN A 253 GLN B 205 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7398 moved from start: 0.2989 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 5190 Z= 0.196 Angle : 0.599 6.950 7166 Z= 0.296 Chirality : 0.040 0.123 916 Planarity : 0.005 0.074 812 Dihedral : 9.388 62.265 1592 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 8.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.07 % Favored : 95.93 % Rotamer: Outliers : 2.13 % Allowed : 18.09 % Favored : 79.79 % 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: 0.89 (0.35), residues: 614 helix: 1.69 (0.26), residues: 414 sheet: -2.82 (1.16), residues: 20 loop : -1.64 (0.45), residues: 180 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP K 3 HIS 0.002 0.001 HIS I 2 PHE 0.016 0.001 PHE B 262 TYR 0.012 0.001 TYR B 98 ARG 0.002 0.000 ARG B 76 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1228 Ramachandran restraints generated. 614 Oldfield, 0 Emsley, 614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1228 Ramachandran restraints generated. 614 Oldfield, 0 Emsley, 614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 546 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 107 time to evaluate : 0.506 Fit side-chains REVERT: A 76 ARG cc_start: 0.6698 (mtm-85) cc_final: 0.6434 (mtm-85) REVERT: A 295 TRP cc_start: 0.7761 (t-100) cc_final: 0.7487 (t-100) REVERT: B 76 ARG cc_start: 0.6727 (mtm-85) cc_final: 0.6456 (mtm-85) REVERT: B 295 TRP cc_start: 0.7832 (t-100) cc_final: 0.7375 (t-100) outliers start: 10 outliers final: 5 residues processed: 112 average time/residue: 0.1491 time to fit residues: 22.0791 Evaluate side-chains 104 residues out of total 546 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 99 time to evaluate : 0.499 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 173 LEU Chi-restraints excluded: chain A residue 253 GLN Chi-restraints excluded: chain B residue 64 LEU Chi-restraints excluded: chain B residue 149 GLN Chi-restraints excluded: chain B residue 173 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 14 optimal weight: 0.7980 chunk 58 optimal weight: 0.9980 chunk 48 optimal weight: 0.6980 chunk 26 optimal weight: 0.9980 chunk 4 optimal weight: 0.0970 chunk 19 optimal weight: 2.9990 chunk 30 optimal weight: 0.6980 chunk 55 optimal weight: 0.8980 chunk 6 optimal weight: 0.9990 chunk 33 optimal weight: 0.6980 chunk 42 optimal weight: 1.9990 overall best weight: 0.5978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 205 ASN B 205 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7414 moved from start: 0.3167 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 5190 Z= 0.215 Angle : 0.602 9.043 7166 Z= 0.295 Chirality : 0.040 0.142 916 Planarity : 0.005 0.074 812 Dihedral : 9.563 69.283 1592 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 8.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.23 % Favored : 95.77 % Rotamer: Outliers : 1.70 % Allowed : 19.36 % Favored : 78.94 % 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 (0.35), residues: 614 helix: 1.79 (0.26), residues: 414 sheet: -2.81 (1.14), residues: 20 loop : -1.46 (0.46), residues: 180 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 70 HIS 0.001 0.000 HIS I 2 PHE 0.015 0.001 PHE A 262 TYR 0.013 0.001 TYR B 98 ARG 0.002 0.000 ARG B 76 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1228 Ramachandran restraints generated. 614 Oldfield, 0 Emsley, 614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1228 Ramachandran restraints generated. 614 Oldfield, 0 Emsley, 614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 546 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 107 time to evaluate : 0.494 Fit side-chains REVERT: A 76 ARG cc_start: 0.6821 (mtm-85) cc_final: 0.6534 (mtm-85) REVERT: A 85 GLN cc_start: 0.7927 (mm-40) cc_final: 0.7285 (tt0) REVERT: A 295 TRP cc_start: 0.7802 (t-100) cc_final: 0.7528 (t-100) REVERT: B 85 GLN cc_start: 0.7943 (mm-40) cc_final: 0.7309 (tt0) REVERT: B 295 TRP cc_start: 0.7799 (t-100) cc_final: 0.7408 (t-100) outliers start: 8 outliers final: 4 residues processed: 112 average time/residue: 0.1458 time to fit residues: 21.4088 Evaluate side-chains 104 residues out of total 546 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 100 time to evaluate : 0.505 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 173 LEU Chi-restraints excluded: chain B residue 64 LEU Chi-restraints excluded: chain B residue 149 GLN Chi-restraints excluded: chain B residue 173 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 32 optimal weight: 3.9990 chunk 48 optimal weight: 0.5980 chunk 57 optimal weight: 2.9990 chunk 36 optimal weight: 0.9990 chunk 35 optimal weight: 0.9990 chunk 26 optimal weight: 0.6980 chunk 23 optimal weight: 8.9990 chunk 34 optimal weight: 0.7980 chunk 17 optimal weight: 0.8980 chunk 11 optimal weight: 0.8980 chunk 39 optimal weight: 0.9990 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 205 ASN ** A 253 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 205 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7455 moved from start: 0.3469 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 5190 Z= 0.246 Angle : 0.609 7.013 7166 Z= 0.301 Chirality : 0.041 0.147 916 Planarity : 0.005 0.073 812 Dihedral : 9.678 81.067 1592 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 9.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.40 % Favored : 95.60 % Rotamer: Outliers : 2.34 % Allowed : 20.64 % Favored : 77.02 % 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: 1.18 (0.35), residues: 614 helix: 1.81 (0.26), residues: 414 sheet: -2.64 (1.12), residues: 20 loop : -1.27 (0.47), residues: 180 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 70 HIS 0.002 0.000 HIS I 2 PHE 0.014 0.002 PHE B 55 TYR 0.015 0.001 TYR B 98 ARG 0.002 0.000 ARG A 76 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1228 Ramachandran restraints generated. 614 Oldfield, 0 Emsley, 614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1228 Ramachandran restraints generated. 614 Oldfield, 0 Emsley, 614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 546 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 107 time to evaluate : 0.554 Fit side-chains REVERT: A 85 GLN cc_start: 0.7955 (mm-40) cc_final: 0.7118 (mm-40) REVERT: A 295 TRP cc_start: 0.7762 (t-100) cc_final: 0.7547 (t-100) REVERT: B 295 TRP cc_start: 0.7790 (t-100) cc_final: 0.7554 (t-100) outliers start: 11 outliers final: 6 residues processed: 114 average time/residue: 0.1497 time to fit residues: 22.6218 Evaluate side-chains 107 residues out of total 546 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 101 time to evaluate : 0.500 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 173 LEU Chi-restraints excluded: chain A residue 205 ASN Chi-restraints excluded: chain B residue 64 LEU Chi-restraints excluded: chain B residue 149 GLN Chi-restraints excluded: chain B residue 173 LEU Chi-restraints excluded: chain B residue 279 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 28 optimal weight: 0.7980 chunk 5 optimal weight: 0.6980 chunk 45 optimal weight: 1.9990 chunk 52 optimal weight: 0.8980 chunk 55 optimal weight: 5.9990 chunk 50 optimal weight: 7.9990 chunk 53 optimal weight: 2.9990 chunk 32 optimal weight: 3.9990 chunk 23 optimal weight: 9.9990 chunk 42 optimal weight: 2.9990 chunk 16 optimal weight: 0.6980 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 205 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 253 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7486 moved from start: 0.3670 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 5190 Z= 0.291 Angle : 0.633 7.656 7166 Z= 0.314 Chirality : 0.042 0.140 916 Planarity : 0.005 0.073 812 Dihedral : 9.638 82.691 1592 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 9.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.07 % Favored : 95.93 % Rotamer: Outliers : 2.13 % Allowed : 21.06 % Favored : 76.81 % 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: 1.17 (0.35), residues: 614 helix: 1.78 (0.25), residues: 414 sheet: -2.64 (1.08), residues: 20 loop : -1.20 (0.47), residues: 180 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP I 3 HIS 0.002 0.001 HIS I 2 PHE 0.016 0.002 PHE B 262 TYR 0.013 0.001 TYR B 98 ARG 0.001 0.000 ARG B 74 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1228 Ramachandran restraints generated. 614 Oldfield, 0 Emsley, 614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1228 Ramachandran restraints generated. 614 Oldfield, 0 Emsley, 614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 546 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 110 time to evaluate : 0.499 Fit side-chains REVERT: B 111 TYR cc_start: 0.9020 (t80) cc_final: 0.8787 (t80) REVERT: B 295 TRP cc_start: 0.7827 (t-100) cc_final: 0.7620 (t-100) outliers start: 10 outliers final: 8 residues processed: 115 average time/residue: 0.1514 time to fit residues: 22.9786 Evaluate side-chains 111 residues out of total 546 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 103 time to evaluate : 0.524 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 97 LEU Chi-restraints excluded: chain A residue 173 LEU Chi-restraints excluded: chain A residue 253 GLN Chi-restraints excluded: chain B residue 64 LEU Chi-restraints excluded: chain B residue 106 TYR Chi-restraints excluded: chain B residue 149 GLN Chi-restraints excluded: chain B residue 173 LEU Chi-restraints excluded: chain B residue 279 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 48 optimal weight: 2.9990 chunk 50 optimal weight: 0.9990 chunk 53 optimal weight: 1.9990 chunk 35 optimal weight: 0.9990 chunk 56 optimal weight: 0.6980 chunk 34 optimal weight: 0.7980 chunk 27 optimal weight: 1.9990 chunk 39 optimal weight: 0.5980 chunk 59 optimal weight: 0.6980 chunk 55 optimal weight: 5.9990 chunk 47 optimal weight: 0.6980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 205 ASN A 253 GLN B 51 GLN B 205 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7468 moved from start: 0.3762 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 5190 Z= 0.235 Angle : 0.613 7.199 7166 Z= 0.307 Chirality : 0.041 0.138 916 Planarity : 0.005 0.073 812 Dihedral : 9.500 82.655 1592 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 8.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.40 % Favored : 95.60 % Rotamer: Outliers : 3.19 % Allowed : 20.43 % Favored : 76.38 % 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: 1.21 (0.35), residues: 614 helix: 1.81 (0.25), residues: 416 sheet: -2.77 (1.01), residues: 20 loop : -1.21 (0.48), residues: 178 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP A 295 HIS 0.001 0.000 HIS I 2 PHE 0.017 0.001 PHE B 55 TYR 0.014 0.001 TYR B 98 ARG 0.001 0.000 ARG B 76 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1228 Ramachandran restraints generated. 614 Oldfield, 0 Emsley, 614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1228 Ramachandran restraints generated. 614 Oldfield, 0 Emsley, 614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 546 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 110 time to evaluate : 0.533 Fit side-chains REVERT: A 205 ASN cc_start: 0.7774 (OUTLIER) cc_final: 0.7533 (t0) REVERT: B 85 GLN cc_start: 0.8121 (mm-40) cc_final: 0.7425 (tt0) REVERT: B 111 TYR cc_start: 0.8988 (t80) cc_final: 0.8765 (t80) REVERT: B 165 MET cc_start: 0.7337 (ttt) cc_final: 0.7031 (ttp) outliers start: 15 outliers final: 9 residues processed: 120 average time/residue: 0.1444 time to fit residues: 23.0221 Evaluate side-chains 112 residues out of total 546 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 102 time to evaluate : 0.553 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 97 LEU Chi-restraints excluded: chain A residue 173 LEU Chi-restraints excluded: chain A residue 205 ASN Chi-restraints excluded: chain A residue 253 GLN Chi-restraints excluded: chain A residue 279 THR Chi-restraints excluded: chain B residue 64 LEU Chi-restraints excluded: chain B residue 106 TYR Chi-restraints excluded: chain B residue 149 GLN Chi-restraints excluded: chain B residue 173 LEU Chi-restraints excluded: chain B residue 279 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 4 optimal weight: 0.4980 chunk 36 optimal weight: 0.5980 chunk 29 optimal weight: 0.2980 chunk 37 optimal weight: 0.9990 chunk 50 optimal weight: 0.8980 chunk 14 optimal weight: 2.9990 chunk 43 optimal weight: 1.9990 chunk 7 optimal weight: 0.7980 chunk 13 optimal weight: 0.9980 chunk 47 optimal weight: 0.9990 chunk 19 optimal weight: 0.1980 overall best weight: 0.4780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 205 ASN B 205 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7449 moved from start: 0.3782 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 5190 Z= 0.217 Angle : 0.613 7.328 7166 Z= 0.310 Chirality : 0.041 0.138 916 Planarity : 0.005 0.073 812 Dihedral : 9.393 82.289 1592 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 9.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.07 % Favored : 95.93 % Rotamer: Outliers : 2.13 % Allowed : 21.91 % 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: 1.27 (0.35), residues: 614 helix: 1.85 (0.26), residues: 416 sheet: -2.74 (1.02), residues: 20 loop : -1.16 (0.49), residues: 178 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP B 295 HIS 0.001 0.000 HIS I 2 PHE 0.018 0.001 PHE B 55 TYR 0.021 0.001 TYR B 17 ARG 0.002 0.000 ARG B 74 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1228 Ramachandran restraints generated. 614 Oldfield, 0 Emsley, 614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1228 Ramachandran restraints generated. 614 Oldfield, 0 Emsley, 614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 546 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 109 time to evaluate : 0.517 Fit side-chains revert: symmetry clash REVERT: A 85 GLN cc_start: 0.8117 (mm-40) cc_final: 0.7239 (mm-40) REVERT: A 205 ASN cc_start: 0.7572 (OUTLIER) cc_final: 0.7235 (m-40) REVERT: B 85 GLN cc_start: 0.8139 (mm-40) cc_final: 0.7404 (tt0) REVERT: B 111 TYR cc_start: 0.8989 (t80) cc_final: 0.8760 (t80) REVERT: B 165 MET cc_start: 0.7330 (ttt) cc_final: 0.7029 (ttp) outliers start: 10 outliers final: 7 residues processed: 115 average time/residue: 0.1485 time to fit residues: 22.5545 Evaluate side-chains 112 residues out of total 546 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 104 time to evaluate : 0.673 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 173 LEU Chi-restraints excluded: chain A residue 205 ASN Chi-restraints excluded: chain A residue 279 THR Chi-restraints excluded: chain B residue 64 LEU Chi-restraints excluded: chain B residue 106 TYR Chi-restraints excluded: chain B residue 149 GLN Chi-restraints excluded: chain B residue 173 LEU Chi-restraints excluded: chain B residue 279 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 48 optimal weight: 2.9990 chunk 6 optimal weight: 0.7980 chunk 8 optimal weight: 0.6980 chunk 41 optimal weight: 0.8980 chunk 2 optimal weight: 0.0870 chunk 34 optimal weight: 0.5980 chunk 54 optimal weight: 0.9990 chunk 32 optimal weight: 0.7980 chunk 40 optimal weight: 0.8980 chunk 1 optimal weight: 0.9980 chunk 38 optimal weight: 0.7980 overall best weight: 0.5958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 205 ASN B 51 GLN B 205 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4078 r_free = 0.4078 target = 0.179502 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3749 r_free = 0.3749 target = 0.148364 restraints weight = 6603.166| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3790 r_free = 0.3790 target = 0.152092 restraints weight = 3862.090| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3819 r_free = 0.3819 target = 0.154512 restraints weight = 2833.057| |-----------------------------------------------------------------------------| r_work (final): 0.3818 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7679 moved from start: 0.3848 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 5190 Z= 0.232 Angle : 0.619 7.095 7166 Z= 0.313 Chirality : 0.041 0.142 916 Planarity : 0.005 0.073 812 Dihedral : 9.331 82.400 1592 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 9.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.72 % Favored : 95.28 % Rotamer: Outliers : 1.91 % Allowed : 22.34 % Favored : 75.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.29 (0.35), residues: 614 helix: 1.86 (0.26), residues: 416 sheet: -2.71 (1.04), residues: 20 loop : -1.13 (0.49), residues: 178 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP B 295 HIS 0.002 0.000 HIS I 2 PHE 0.017 0.001 PHE B 55 TYR 0.018 0.001 TYR B 26 ARG 0.002 0.000 ARG B 74 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1291.05 seconds wall clock time: 24 minutes 2.20 seconds (1442.20 seconds total)