Starting phenix.real_space_refine on Thu Jul 18 22:32:33 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7f3u_31441/07_2024/7f3u_31441.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7f3u_31441/07_2024/7f3u_31441.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7f3u_31441/07_2024/7f3u_31441.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7f3u_31441/07_2024/7f3u_31441.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7f3u_31441/07_2024/7f3u_31441.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7f3u_31441/07_2024/7f3u_31441.cif" } resolution = 4.0 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= 1.000 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 18 5.16 5 C 2716 2.51 5 N 740 2.21 5 O 800 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 134": "OE1" <-> "OE2" Residue "A ARG 152": "NH1" <-> "NH2" Residue "A ARG 178": "NH1" <-> "NH2" Residue "B GLU 134": "OE1" <-> "OE2" Residue "B ARG 152": "NH1" <-> "NH2" Residue "B ARG 178": "NH1" <-> "NH2" Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/chem_data/mon_lib" Total number of atoms: 4274 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 2137 Number of conformers: 1 Conformer: "" Number of residues, atoms: 328, 2137 Classifications: {'peptide': 328} Incomplete info: {'truncation_to_alanine': 153} Link IDs: {'PTRANS': 8, 'TRANS': 319} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 653 Unresolved non-hydrogen angles: 828 Unresolved non-hydrogen dihedrals: 568 Unresolved non-hydrogen chiralities: 45 Planarities with less than four sites: {'GLN:plan1': 16, 'HIS:plan': 6, 'TYR:plan': 2, 'ASN:plan1': 6, 'TRP:plan': 5, 'ASP:plan': 5, 'PHE:plan': 18, 'GLU:plan': 12, 'ARG:plan': 11} Unresolved non-hydrogen planarities: 397 Chain: "B" Number of atoms: 2137 Number of conformers: 1 Conformer: "" Number of residues, atoms: 328, 2137 Classifications: {'peptide': 328} Incomplete info: {'truncation_to_alanine': 153} Link IDs: {'PTRANS': 8, 'TRANS': 319} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 653 Unresolved non-hydrogen angles: 828 Unresolved non-hydrogen dihedrals: 568 Unresolved non-hydrogen chiralities: 45 Planarities with less than four sites: {'GLN:plan1': 16, 'HIS:plan': 6, 'TYR:plan': 2, 'ASN:plan1': 6, 'TRP:plan': 5, 'ASP:plan': 5, 'PHE:plan': 18, 'GLU:plan': 12, 'ARG:plan': 11} Unresolved non-hydrogen planarities: 397 Time building chain proxies: 3.34, per 1000 atoms: 0.78 Number of scatterers: 4274 At special positions: 0 Unit cell: (71.34, 113.98, 88.56, 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 18 16.00 O 800 8.00 N 740 7.00 C 2716 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.81 Conformation dependent library (CDL) restraints added in 1.0 seconds 1304 Ramachandran restraints generated. 652 Oldfield, 0 Emsley, 652 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1244 Finding SS restraints... Secondary structure from input PDB file: 18 helices and 0 sheets defined 85.2% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.44 Creating SS restraints... Processing helix chain 'A' and resid 7 through 72 Proline residue: A 70 - end of helix Processing helix chain 'A' and resid 73 through 99 removed outlier: 4.186A pdb=" N ALA A 79 " --> pdb=" O GLU A 75 " (cutoff:3.500A) Processing helix chain 'A' and resid 108 through 113 Processing helix chain 'A' and resid 122 through 154 Processing helix chain 'A' and resid 157 through 186 removed outlier: 3.623A pdb=" N ASP A 161 " --> pdb=" O SER A 157 " (cutoff:3.500A) Processing helix chain 'A' and resid 193 through 209 Processing helix chain 'A' and resid 213 through 252 removed outlier: 4.526A pdb=" N ASN A 221 " --> pdb=" O GLN A 217 " (cutoff:3.500A) removed outlier: 5.145A pdb=" N GLN A 222 " --> pdb=" O LYS A 218 " (cutoff:3.500A) Processing helix chain 'A' and resid 266 through 297 Proline residue: A 277 - end of helix Processing helix chain 'A' and resid 306 through 334 Proline residue: A 313 - end of helix Processing helix chain 'B' and resid 8 through 72 Proline residue: B 70 - end of helix Processing helix chain 'B' and resid 73 through 99 removed outlier: 4.185A pdb=" N ALA B 79 " --> pdb=" O GLU B 75 " (cutoff:3.500A) Processing helix chain 'B' and resid 108 through 113 Processing helix chain 'B' and resid 122 through 154 Processing helix chain 'B' and resid 157 through 186 removed outlier: 3.623A pdb=" N ASP B 161 " --> pdb=" O SER B 157 " (cutoff:3.500A) Processing helix chain 'B' and resid 193 through 209 Processing helix chain 'B' and resid 213 through 252 removed outlier: 4.527A pdb=" N ASN B 221 " --> pdb=" O GLN B 217 " (cutoff:3.500A) removed outlier: 5.145A pdb=" N GLN B 222 " --> pdb=" O LYS B 218 " (cutoff:3.500A) Processing helix chain 'B' and resid 266 through 297 Proline residue: B 277 - end of helix Processing helix chain 'B' and resid 306 through 334 Proline residue: B 313 - end of helix 461 hydrogen bonds defined for protein. 1383 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: 1.22 Time building geometry restraints manager: 1.97 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 1428 1.34 - 1.45: 646 1.45 - 1.57: 2258 1.57 - 1.69: 0 1.69 - 1.81: 24 Bond restraints: 4356 Sorted by residual: bond pdb=" CG ARG A 178 " pdb=" CD ARG A 178 " ideal model delta sigma weight residual 1.520 1.470 0.050 3.00e-02 1.11e+03 2.80e+00 bond pdb=" CG ARG B 178 " pdb=" CD ARG B 178 " ideal model delta sigma weight residual 1.520 1.470 0.050 3.00e-02 1.11e+03 2.79e+00 bond pdb=" CA VAL A 233 " pdb=" CB VAL A 233 " ideal model delta sigma weight residual 1.540 1.525 0.015 1.25e-02 6.40e+03 1.51e+00 bond pdb=" CB TRP A 170 " pdb=" CG TRP A 170 " ideal model delta sigma weight residual 1.498 1.460 0.038 3.10e-02 1.04e+03 1.49e+00 bond pdb=" CA ILE B 145 " pdb=" CB ILE B 145 " ideal model delta sigma weight residual 1.540 1.525 0.014 1.17e-02 7.31e+03 1.49e+00 ... (remaining 4351 not shown) Histogram of bond angle deviations from ideal: 97.23 - 104.59: 40 104.59 - 111.94: 2201 111.94 - 119.30: 1312 119.30 - 126.65: 2399 126.65 - 134.01: 42 Bond angle restraints: 5994 Sorted by residual: angle pdb=" N PRO B 8 " pdb=" CA PRO B 8 " pdb=" CB PRO B 8 " ideal model delta sigma weight residual 103.39 110.08 -6.69 1.08e+00 8.57e-01 3.84e+01 angle pdb=" N PRO A 8 " pdb=" CA PRO A 8 " pdb=" CB PRO A 8 " ideal model delta sigma weight residual 103.39 110.07 -6.68 1.08e+00 8.57e-01 3.83e+01 angle pdb=" NE ARG B 178 " pdb=" CZ ARG B 178 " pdb=" NH1 ARG B 178 " ideal model delta sigma weight residual 121.50 117.42 4.08 1.00e+00 1.00e+00 1.66e+01 angle pdb=" NE ARG A 178 " pdb=" CZ ARG A 178 " pdb=" NH1 ARG A 178 " ideal model delta sigma weight residual 121.50 117.52 3.98 1.00e+00 1.00e+00 1.58e+01 angle pdb=" CB MET A 87 " pdb=" CG MET A 87 " pdb=" SD MET A 87 " ideal model delta sigma weight residual 112.70 123.98 -11.28 3.00e+00 1.11e-01 1.41e+01 ... (remaining 5989 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 12.29: 2272 12.29 - 24.58: 152 24.58 - 36.86: 74 36.86 - 49.15: 6 49.15 - 61.44: 6 Dihedral angle restraints: 2510 sinusoidal: 586 harmonic: 1924 Sorted by residual: dihedral pdb=" CA LEU B 154 " pdb=" C LEU B 154 " pdb=" N LEU B 155 " pdb=" CA LEU B 155 " ideal model delta harmonic sigma weight residual -180.00 -153.52 -26.48 0 5.00e+00 4.00e-02 2.80e+01 dihedral pdb=" CA LEU A 154 " pdb=" C LEU A 154 " pdb=" N LEU A 155 " pdb=" CA LEU A 155 " ideal model delta harmonic sigma weight residual -180.00 -153.53 -26.47 0 5.00e+00 4.00e-02 2.80e+01 dihedral pdb=" CA GLY A 106 " pdb=" C GLY A 106 " pdb=" N LEU A 107 " pdb=" CA LEU A 107 " ideal model delta harmonic sigma weight residual 180.00 154.77 25.23 0 5.00e+00 4.00e-02 2.55e+01 ... (remaining 2507 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.046: 524 0.046 - 0.093: 174 0.093 - 0.139: 17 0.139 - 0.185: 7 0.185 - 0.231: 2 Chirality restraints: 724 Sorted by residual: chirality pdb=" CA PRO A 8 " pdb=" N PRO A 8 " pdb=" C PRO A 8 " pdb=" CB PRO A 8 " both_signs ideal model delta sigma weight residual False 2.72 2.49 0.23 2.00e-01 2.50e+01 1.34e+00 chirality pdb=" CA PRO B 8 " pdb=" N PRO B 8 " pdb=" C PRO B 8 " pdb=" CB PRO B 8 " both_signs ideal model delta sigma weight residual False 2.72 2.49 0.23 2.00e-01 2.50e+01 1.30e+00 chirality pdb=" CG LEU B 140 " pdb=" CB LEU B 140 " pdb=" CD1 LEU B 140 " pdb=" CD2 LEU B 140 " both_signs ideal model delta sigma weight residual False -2.59 -2.75 0.16 2.00e-01 2.50e+01 6.10e-01 ... (remaining 721 not shown) Planarity restraints: 790 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR B 139 " 0.016 2.00e-02 2.50e+03 1.39e-02 3.84e+00 pdb=" CG TYR B 139 " -0.034 2.00e-02 2.50e+03 pdb=" CD1 TYR B 139 " 0.007 2.00e-02 2.50e+03 pdb=" CD2 TYR B 139 " 0.004 2.00e-02 2.50e+03 pdb=" CE1 TYR B 139 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 TYR B 139 " 0.004 2.00e-02 2.50e+03 pdb=" CZ TYR B 139 " 0.001 2.00e-02 2.50e+03 pdb=" OH TYR B 139 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 139 " -0.016 2.00e-02 2.50e+03 1.38e-02 3.79e+00 pdb=" CG TYR A 139 " 0.034 2.00e-02 2.50e+03 pdb=" CD1 TYR A 139 " -0.008 2.00e-02 2.50e+03 pdb=" CD2 TYR A 139 " -0.004 2.00e-02 2.50e+03 pdb=" CE1 TYR A 139 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 TYR A 139 " -0.004 2.00e-02 2.50e+03 pdb=" CZ TYR A 139 " -0.001 2.00e-02 2.50e+03 pdb=" OH TYR A 139 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 238 " 0.016 2.00e-02 2.50e+03 9.75e-03 1.90e+00 pdb=" CG TYR A 238 " -0.020 2.00e-02 2.50e+03 pdb=" CD1 TYR A 238 " -0.003 2.00e-02 2.50e+03 pdb=" CD2 TYR A 238 " -0.003 2.00e-02 2.50e+03 pdb=" CE1 TYR A 238 " 0.002 2.00e-02 2.50e+03 pdb=" CE2 TYR A 238 " 0.002 2.00e-02 2.50e+03 pdb=" CZ TYR A 238 " 0.007 2.00e-02 2.50e+03 pdb=" OH TYR A 238 " 0.000 2.00e-02 2.50e+03 ... (remaining 787 not shown) Histogram of nonbonded interaction distances: 2.29 - 2.82: 1454 2.82 - 3.34: 5127 3.34 - 3.86: 7295 3.86 - 4.38: 7293 4.38 - 4.90: 11642 Nonbonded interactions: 32811 Sorted by model distance: nonbonded pdb=" ND2 ASN A 105 " pdb=" O ASN A 115 " model vdw 2.295 2.520 nonbonded pdb=" ND2 ASN B 105 " pdb=" O ASN B 115 " model vdw 2.295 2.520 nonbonded pdb=" ND2 ASN B 165 " pdb=" OG SER B 204 " model vdw 2.320 2.520 nonbonded pdb=" ND2 ASN A 165 " pdb=" OG SER A 204 " model vdw 2.321 2.520 nonbonded pdb=" O MET A 228 " pdb=" OG SER A 231 " model vdw 2.324 2.440 ... (remaining 32806 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' } 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=0.00 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: 0.950 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.190 Check model and map are aligned: 0.030 Set scattering table: 0.050 Process input model: 17.300 Find NCS groups from input model: 0.140 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.770 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.460 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8013 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 : 0.006 0.050 4356 Z= 0.390 Angle : 0.885 11.280 5994 Z= 0.512 Chirality : 0.045 0.231 724 Planarity : 0.004 0.029 790 Dihedral : 11.591 61.439 1266 Min Nonbonded Distance : 2.295 Molprobity Statistics. All-atom Clashscore : 21.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.59 % Favored : 91.41 % Rotamer: Outliers : 0.00 % Allowed : 0.69 % Favored : 99.31 % 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: 2.22 (0.33), residues: 652 helix: 2.47 (0.21), residues: 524 sheet: None (None), residues: 0 loop : -3.11 (0.53), residues: 128 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 210 HIS 0.009 0.003 HIS A 197 PHE 0.021 0.002 PHE A 153 TYR 0.034 0.003 TYR B 139 ARG 0.009 0.001 ARG B 152 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1304 Ramachandran restraints generated. 652 Oldfield, 0 Emsley, 652 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1304 Ramachandran restraints generated. 652 Oldfield, 0 Emsley, 652 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 594 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 168 time to evaluate : 0.493 Fit side-chains revert: symmetry clash REVERT: A 135 LYS cc_start: 0.8931 (mmmm) cc_final: 0.7947 (mmmm) REVERT: A 139 TYR cc_start: 0.7886 (m-80) cc_final: 0.7335 (m-80) REVERT: B 135 LYS cc_start: 0.8908 (mmmm) cc_final: 0.7930 (mmmm) REVERT: B 136 PHE cc_start: 0.8159 (t80) cc_final: 0.7954 (t80) REVERT: B 139 TYR cc_start: 0.7900 (m-80) cc_final: 0.7287 (m-80) outliers start: 0 outliers final: 0 residues processed: 168 average time/residue: 0.1407 time to fit residues: 29.6839 Evaluate side-chains 120 residues out of total 594 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 120 time to evaluate : 0.487 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 54 optimal weight: 0.8980 chunk 48 optimal weight: 0.7980 chunk 26 optimal weight: 20.0000 chunk 16 optimal weight: 0.9980 chunk 32 optimal weight: 9.9990 chunk 25 optimal weight: 30.0000 chunk 50 optimal weight: 10.0000 chunk 19 optimal weight: 1.9990 chunk 30 optimal weight: 3.9990 chunk 37 optimal weight: 0.7980 chunk 58 optimal weight: 6.9990 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 165 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 185 ASN ** A 306 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 165 ASN B 185 ASN ** B 306 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7917 moved from start: 0.2160 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 4356 Z= 0.182 Angle : 0.710 10.519 5994 Z= 0.362 Chirality : 0.040 0.146 724 Planarity : 0.003 0.024 790 Dihedral : 4.723 23.287 690 Min Nonbonded Distance : 2.230 Molprobity Statistics. All-atom Clashscore : 14.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.06 % Favored : 92.94 % Rotamer: Outliers : 5.90 % Allowed : 20.49 % Favored : 73.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.50 (0.34), residues: 652 helix: 3.41 (0.21), residues: 524 sheet: None (None), residues: 0 loop : -2.90 (0.54), residues: 128 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 210 HIS 0.003 0.001 HIS A 197 PHE 0.019 0.001 PHE A 153 TYR 0.023 0.002 TYR B 139 ARG 0.004 0.001 ARG B 90 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1304 Ramachandran restraints generated. 652 Oldfield, 0 Emsley, 652 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1304 Ramachandran restraints generated. 652 Oldfield, 0 Emsley, 652 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 594 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 158 time to evaluate : 0.476 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 139 TYR cc_start: 0.7872 (m-80) cc_final: 0.7466 (m-80) REVERT: A 153 PHE cc_start: 0.8334 (m-80) cc_final: 0.8020 (m-80) REVERT: A 314 PHE cc_start: 0.9066 (m-80) cc_final: 0.8753 (m-80) REVERT: B 129 TYR cc_start: 0.8172 (t80) cc_final: 0.7897 (t80) REVERT: B 135 LYS cc_start: 0.8924 (mmmm) cc_final: 0.8133 (mmmm) REVERT: B 139 TYR cc_start: 0.7840 (m-80) cc_final: 0.7254 (m-80) REVERT: B 153 PHE cc_start: 0.8328 (m-80) cc_final: 0.8032 (m-80) outliers start: 17 outliers final: 12 residues processed: 164 average time/residue: 0.1398 time to fit residues: 28.9143 Evaluate side-chains 152 residues out of total 594 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 140 time to evaluate : 0.477 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 LEU Chi-restraints excluded: chain A residue 167 LEU Chi-restraints excluded: chain A residue 185 ASN Chi-restraints excluded: chain A residue 203 LEU Chi-restraints excluded: chain A residue 206 VAL Chi-restraints excluded: chain A residue 232 PHE Chi-restraints excluded: chain B residue 167 LEU Chi-restraints excluded: chain B residue 177 ILE Chi-restraints excluded: chain B residue 185 ASN Chi-restraints excluded: chain B residue 203 LEU Chi-restraints excluded: chain B residue 206 VAL Chi-restraints excluded: chain B residue 232 PHE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 32 optimal weight: 4.9990 chunk 18 optimal weight: 0.6980 chunk 48 optimal weight: 0.8980 chunk 39 optimal weight: 6.9990 chunk 16 optimal weight: 5.9990 chunk 58 optimal weight: 7.9990 chunk 62 optimal weight: 0.8980 chunk 51 optimal weight: 3.9990 chunk 57 optimal weight: 50.0000 chunk 19 optimal weight: 2.9990 chunk 46 optimal weight: 20.0000 overall best weight: 1.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 165 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 185 ASN A 196 HIS ** A 306 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 185 ASN ** B 306 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7952 moved from start: 0.2473 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 4356 Z= 0.203 Angle : 0.725 8.541 5994 Z= 0.377 Chirality : 0.040 0.153 724 Planarity : 0.003 0.022 790 Dihedral : 4.591 21.666 690 Min Nonbonded Distance : 2.118 Molprobity Statistics. All-atom Clashscore : 16.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.36 % Favored : 92.64 % Rotamer: Outliers : 6.60 % Allowed : 26.74 % Favored : 66.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.70 (0.34), residues: 652 helix: 3.56 (0.21), residues: 524 sheet: None (None), residues: 0 loop : -2.86 (0.54), residues: 128 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 210 HIS 0.005 0.002 HIS A 196 PHE 0.012 0.001 PHE A 153 TYR 0.017 0.002 TYR B 171 ARG 0.004 0.001 ARG A 178 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1304 Ramachandran restraints generated. 652 Oldfield, 0 Emsley, 652 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1304 Ramachandran restraints generated. 652 Oldfield, 0 Emsley, 652 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 594 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 144 time to evaluate : 0.482 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 139 TYR cc_start: 0.7874 (m-80) cc_final: 0.7609 (m-80) REVERT: A 153 PHE cc_start: 0.8420 (m-10) cc_final: 0.8010 (m-80) REVERT: A 314 PHE cc_start: 0.9118 (m-80) cc_final: 0.8759 (m-80) REVERT: B 139 TYR cc_start: 0.7828 (m-80) cc_final: 0.7575 (m-80) REVERT: B 153 PHE cc_start: 0.8445 (m-10) cc_final: 0.8046 (m-80) REVERT: B 314 PHE cc_start: 0.9158 (m-80) cc_final: 0.8807 (m-80) outliers start: 19 outliers final: 15 residues processed: 152 average time/residue: 0.1426 time to fit residues: 27.4769 Evaluate side-chains 149 residues out of total 594 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 134 time to evaluate : 0.491 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 LEU Chi-restraints excluded: chain A residue 167 LEU Chi-restraints excluded: chain A residue 184 ASN Chi-restraints excluded: chain A residue 185 ASN Chi-restraints excluded: chain A residue 203 LEU Chi-restraints excluded: chain A residue 206 VAL Chi-restraints excluded: chain A residue 232 PHE Chi-restraints excluded: chain B residue 167 LEU Chi-restraints excluded: chain B residue 184 ASN Chi-restraints excluded: chain B residue 185 ASN Chi-restraints excluded: chain B residue 203 LEU Chi-restraints excluded: chain B residue 206 VAL Chi-restraints excluded: chain B residue 224 LEU Chi-restraints excluded: chain B residue 232 PHE Chi-restraints excluded: chain B residue 235 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 57 optimal weight: 0.0040 chunk 43 optimal weight: 0.3980 chunk 30 optimal weight: 0.9990 chunk 6 optimal weight: 0.9990 chunk 27 optimal weight: 9.9990 chunk 39 optimal weight: 6.9990 chunk 58 optimal weight: 20.0000 chunk 61 optimal weight: 0.9980 chunk 55 optimal weight: 0.9990 chunk 16 optimal weight: 1.9990 chunk 51 optimal weight: 0.9990 overall best weight: 0.6796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 165 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 185 ASN A 237 GLN ** A 306 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 185 ASN B 237 GLN ** B 306 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7877 moved from start: 0.3042 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 4356 Z= 0.178 Angle : 0.701 8.449 5994 Z= 0.348 Chirality : 0.039 0.139 724 Planarity : 0.003 0.019 790 Dihedral : 4.403 20.400 690 Min Nonbonded Distance : 2.197 Molprobity Statistics. All-atom Clashscore : 12.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.60 % Favored : 93.40 % Rotamer: Outliers : 6.25 % Allowed : 29.51 % Favored : 64.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.65 (0.34), residues: 652 helix: 3.54 (0.21), residues: 518 sheet: None (None), residues: 0 loop : -2.69 (0.52), residues: 134 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 210 HIS 0.003 0.001 HIS A 197 PHE 0.019 0.001 PHE B 219 TYR 0.014 0.001 TYR B 238 ARG 0.004 0.001 ARG A 178 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1304 Ramachandran restraints generated. 652 Oldfield, 0 Emsley, 652 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1304 Ramachandran restraints generated. 652 Oldfield, 0 Emsley, 652 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 594 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 151 time to evaluate : 0.461 Fit side-chains REVERT: A 223 PHE cc_start: 0.8737 (t80) cc_final: 0.8326 (t80) outliers start: 18 outliers final: 15 residues processed: 160 average time/residue: 0.1361 time to fit residues: 27.7143 Evaluate side-chains 150 residues out of total 594 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 135 time to evaluate : 0.488 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 LEU Chi-restraints excluded: chain A residue 138 LEU Chi-restraints excluded: chain A residue 167 LEU Chi-restraints excluded: chain A residue 184 ASN Chi-restraints excluded: chain A residue 185 ASN Chi-restraints excluded: chain A residue 206 VAL Chi-restraints excluded: chain A residue 232 PHE Chi-restraints excluded: chain B residue 138 LEU Chi-restraints excluded: chain B residue 167 LEU Chi-restraints excluded: chain B residue 184 ASN Chi-restraints excluded: chain B residue 185 ASN Chi-restraints excluded: chain B residue 206 VAL Chi-restraints excluded: chain B residue 224 LEU Chi-restraints excluded: chain B residue 232 PHE Chi-restraints excluded: chain B residue 235 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 35 optimal weight: 8.9990 chunk 0 optimal weight: 30.0000 chunk 46 optimal weight: 10.0000 chunk 25 optimal weight: 4.9990 chunk 52 optimal weight: 5.9990 chunk 42 optimal weight: 2.9990 chunk 31 optimal weight: 3.9990 chunk 55 optimal weight: 1.9990 chunk 15 optimal weight: 0.9990 chunk 20 optimal weight: 0.4980 chunk 12 optimal weight: 9.9990 overall best weight: 2.0988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 185 ASN ** A 306 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 185 ASN ** B 306 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7933 moved from start: 0.3048 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 4356 Z= 0.201 Angle : 0.732 8.401 5994 Z= 0.374 Chirality : 0.040 0.202 724 Planarity : 0.003 0.021 790 Dihedral : 4.426 23.419 690 Min Nonbonded Distance : 2.119 Molprobity Statistics. All-atom Clashscore : 13.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.44 % Favored : 93.56 % Rotamer: Outliers : 6.60 % Allowed : 34.03 % Favored : 59.38 % 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: 3.84 (0.34), residues: 652 helix: 3.56 (0.21), residues: 526 sheet: None (None), residues: 0 loop : -2.45 (0.57), residues: 126 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 210 HIS 0.002 0.001 HIS B 197 PHE 0.032 0.001 PHE A 153 TYR 0.022 0.002 TYR B 171 ARG 0.005 0.001 ARG A 178 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1304 Ramachandran restraints generated. 652 Oldfield, 0 Emsley, 652 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1304 Ramachandran restraints generated. 652 Oldfield, 0 Emsley, 652 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 594 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 136 time to evaluate : 0.484 Fit side-chains outliers start: 19 outliers final: 18 residues processed: 146 average time/residue: 0.1449 time to fit residues: 26.6571 Evaluate side-chains 153 residues out of total 594 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 135 time to evaluate : 0.491 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 LEU Chi-restraints excluded: chain A residue 138 LEU Chi-restraints excluded: chain A residue 167 LEU Chi-restraints excluded: chain A residue 184 ASN Chi-restraints excluded: chain A residue 185 ASN Chi-restraints excluded: chain A residue 203 LEU Chi-restraints excluded: chain A residue 206 VAL Chi-restraints excluded: chain A residue 232 PHE Chi-restraints excluded: chain A residue 235 PHE Chi-restraints excluded: chain B residue 138 LEU Chi-restraints excluded: chain B residue 167 LEU Chi-restraints excluded: chain B residue 184 ASN Chi-restraints excluded: chain B residue 185 ASN Chi-restraints excluded: chain B residue 203 LEU Chi-restraints excluded: chain B residue 206 VAL Chi-restraints excluded: chain B residue 224 LEU Chi-restraints excluded: chain B residue 232 PHE Chi-restraints excluded: chain B residue 235 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 36 optimal weight: 9.9990 chunk 15 optimal weight: 1.9990 chunk 61 optimal weight: 5.9990 chunk 51 optimal weight: 3.9990 chunk 28 optimal weight: 5.9990 chunk 5 optimal weight: 20.0000 chunk 20 optimal weight: 0.0570 chunk 32 optimal weight: 10.0000 chunk 59 optimal weight: 20.0000 chunk 6 optimal weight: 0.9990 chunk 35 optimal weight: 6.9990 overall best weight: 2.6106 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 185 ASN ** A 306 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 185 ASN ** B 306 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7958 moved from start: 0.3000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 4356 Z= 0.221 Angle : 0.732 8.641 5994 Z= 0.380 Chirality : 0.040 0.178 724 Planarity : 0.003 0.020 790 Dihedral : 4.549 24.030 690 Min Nonbonded Distance : 2.107 Molprobity Statistics. All-atom Clashscore : 14.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.29 % Favored : 93.71 % Rotamer: Outliers : 7.64 % Allowed : 32.99 % Favored : 59.38 % 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: 3.77 (0.34), residues: 652 helix: 3.51 (0.21), residues: 526 sheet: None (None), residues: 0 loop : -2.45 (0.57), residues: 126 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 210 HIS 0.002 0.001 HIS B 197 PHE 0.026 0.002 PHE A 153 TYR 0.016 0.002 TYR A 33 ARG 0.004 0.001 ARG B 178 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1304 Ramachandran restraints generated. 652 Oldfield, 0 Emsley, 652 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1304 Ramachandran restraints generated. 652 Oldfield, 0 Emsley, 652 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 594 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 135 time to evaluate : 0.452 Fit side-chains outliers start: 22 outliers final: 18 residues processed: 147 average time/residue: 0.1404 time to fit residues: 26.2567 Evaluate side-chains 149 residues out of total 594 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 131 time to evaluate : 0.480 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 LEU Chi-restraints excluded: chain A residue 138 LEU Chi-restraints excluded: chain A residue 167 LEU Chi-restraints excluded: chain A residue 184 ASN Chi-restraints excluded: chain A residue 185 ASN Chi-restraints excluded: chain A residue 203 LEU Chi-restraints excluded: chain A residue 206 VAL Chi-restraints excluded: chain A residue 232 PHE Chi-restraints excluded: chain A residue 235 PHE Chi-restraints excluded: chain B residue 138 LEU Chi-restraints excluded: chain B residue 167 LEU Chi-restraints excluded: chain B residue 182 LEU Chi-restraints excluded: chain B residue 184 ASN Chi-restraints excluded: chain B residue 185 ASN Chi-restraints excluded: chain B residue 203 LEU Chi-restraints excluded: chain B residue 224 LEU Chi-restraints excluded: chain B residue 232 PHE Chi-restraints excluded: chain B residue 235 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 45 optimal weight: 2.9990 chunk 35 optimal weight: 8.9990 chunk 52 optimal weight: 6.9990 chunk 34 optimal weight: 9.9990 chunk 61 optimal weight: 6.9990 chunk 38 optimal weight: 0.0060 chunk 37 optimal weight: 9.9990 chunk 28 optimal weight: 0.9990 chunk 24 optimal weight: 20.0000 chunk 36 optimal weight: 2.9990 chunk 18 optimal weight: 4.9990 overall best weight: 2.4004 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 185 ASN ** A 306 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 185 ASN ** B 306 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7956 moved from start: 0.3048 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 4356 Z= 0.216 Angle : 0.741 8.663 5994 Z= 0.388 Chirality : 0.041 0.175 724 Planarity : 0.003 0.019 790 Dihedral : 4.560 23.566 690 Min Nonbonded Distance : 2.113 Molprobity Statistics. All-atom Clashscore : 15.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.44 % Favored : 93.56 % Rotamer: Outliers : 6.60 % Allowed : 32.29 % Favored : 61.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.70 (0.34), residues: 652 helix: 3.45 (0.21), residues: 526 sheet: None (None), residues: 0 loop : -2.44 (0.57), residues: 126 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 210 HIS 0.001 0.001 HIS A 197 PHE 0.025 0.002 PHE B 153 TYR 0.023 0.002 TYR B 33 ARG 0.004 0.001 ARG B 178 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1304 Ramachandran restraints generated. 652 Oldfield, 0 Emsley, 652 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1304 Ramachandran restraints generated. 652 Oldfield, 0 Emsley, 652 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 594 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 133 time to evaluate : 0.510 Fit side-chains REVERT: B 87 MET cc_start: 0.8057 (mmt) cc_final: 0.7751 (mmt) outliers start: 19 outliers final: 18 residues processed: 143 average time/residue: 0.1434 time to fit residues: 26.1400 Evaluate side-chains 150 residues out of total 594 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 132 time to evaluate : 0.496 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 LEU Chi-restraints excluded: chain A residue 138 LEU Chi-restraints excluded: chain A residue 167 LEU Chi-restraints excluded: chain A residue 184 ASN Chi-restraints excluded: chain A residue 185 ASN Chi-restraints excluded: chain A residue 203 LEU Chi-restraints excluded: chain A residue 206 VAL Chi-restraints excluded: chain A residue 232 PHE Chi-restraints excluded: chain A residue 235 PHE Chi-restraints excluded: chain B residue 138 LEU Chi-restraints excluded: chain B residue 167 LEU Chi-restraints excluded: chain B residue 182 LEU Chi-restraints excluded: chain B residue 184 ASN Chi-restraints excluded: chain B residue 185 ASN Chi-restraints excluded: chain B residue 203 LEU Chi-restraints excluded: chain B residue 224 LEU Chi-restraints excluded: chain B residue 232 PHE Chi-restraints excluded: chain B residue 235 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 12 optimal weight: 10.0000 chunk 11 optimal weight: 9.9990 chunk 39 optimal weight: 5.9990 chunk 42 optimal weight: 0.9980 chunk 30 optimal weight: 0.7980 chunk 5 optimal weight: 20.0000 chunk 48 optimal weight: 0.8980 chunk 56 optimal weight: 4.9990 chunk 59 optimal weight: 0.0270 chunk 53 optimal weight: 3.9990 chunk 57 optimal weight: 0.4980 overall best weight: 0.6438 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 185 ASN A 306 GLN B 185 ASN ** B 306 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7873 moved from start: 0.3495 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 4356 Z= 0.187 Angle : 0.755 9.014 5994 Z= 0.381 Chirality : 0.040 0.177 724 Planarity : 0.003 0.017 790 Dihedral : 4.412 22.552 690 Min Nonbonded Distance : 2.119 Molprobity Statistics. All-atom Clashscore : 12.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.90 % Favored : 93.10 % Rotamer: Outliers : 5.56 % Allowed : 35.42 % Favored : 59.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.53 (0.34), residues: 652 helix: 3.38 (0.22), residues: 516 sheet: None (None), residues: 0 loop : -2.24 (0.53), residues: 136 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.001 TRP B 210 HIS 0.001 0.001 HIS B 196 PHE 0.028 0.001 PHE B 153 TYR 0.022 0.002 TYR A 33 ARG 0.004 0.001 ARG B 178 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1304 Ramachandran restraints generated. 652 Oldfield, 0 Emsley, 652 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1304 Ramachandran restraints generated. 652 Oldfield, 0 Emsley, 652 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 594 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 140 time to evaluate : 0.439 Fit side-chains outliers start: 16 outliers final: 16 residues processed: 148 average time/residue: 0.1599 time to fit residues: 29.2728 Evaluate side-chains 149 residues out of total 594 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 133 time to evaluate : 0.481 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 138 LEU Chi-restraints excluded: chain A residue 160 THR Chi-restraints excluded: chain A residue 167 LEU Chi-restraints excluded: chain A residue 184 ASN Chi-restraints excluded: chain A residue 185 ASN Chi-restraints excluded: chain A residue 206 VAL Chi-restraints excluded: chain A residue 232 PHE Chi-restraints excluded: chain A residue 235 PHE Chi-restraints excluded: chain B residue 138 LEU Chi-restraints excluded: chain B residue 167 LEU Chi-restraints excluded: chain B residue 184 ASN Chi-restraints excluded: chain B residue 185 ASN Chi-restraints excluded: chain B residue 210 TRP Chi-restraints excluded: chain B residue 224 LEU Chi-restraints excluded: chain B residue 232 PHE Chi-restraints excluded: chain B residue 235 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 59 optimal weight: 8.9990 chunk 34 optimal weight: 0.9980 chunk 25 optimal weight: 50.0000 chunk 45 optimal weight: 1.9990 chunk 17 optimal weight: 4.9990 chunk 51 optimal weight: 0.9990 chunk 54 optimal weight: 0.9990 chunk 57 optimal weight: 50.0000 chunk 37 optimal weight: 20.0000 chunk 60 optimal weight: 9.9990 chunk 28 optimal weight: 6.9990 overall best weight: 1.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 185 ASN B 185 ASN ** B 306 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7930 moved from start: 0.3520 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 4356 Z= 0.231 Angle : 0.806 12.701 5994 Z= 0.416 Chirality : 0.041 0.209 724 Planarity : 0.004 0.047 790 Dihedral : 4.474 22.912 690 Min Nonbonded Distance : 2.130 Molprobity Statistics. All-atom Clashscore : 15.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.83 % Favored : 94.17 % Rotamer: Outliers : 6.25 % Allowed : 35.42 % Favored : 58.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.65 (0.34), residues: 652 helix: 3.40 (0.21), residues: 526 sheet: None (None), residues: 0 loop : -2.38 (0.57), residues: 126 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP B 210 HIS 0.001 0.001 HIS A 196 PHE 0.027 0.002 PHE A 136 TYR 0.023 0.002 TYR A 33 ARG 0.015 0.001 ARG B 90 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1304 Ramachandran restraints generated. 652 Oldfield, 0 Emsley, 652 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1304 Ramachandran restraints generated. 652 Oldfield, 0 Emsley, 652 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 594 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 138 time to evaluate : 0.490 Fit side-chains outliers start: 18 outliers final: 16 residues processed: 149 average time/residue: 0.1531 time to fit residues: 28.3270 Evaluate side-chains 149 residues out of total 594 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 133 time to evaluate : 0.489 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 138 LEU Chi-restraints excluded: chain A residue 160 THR Chi-restraints excluded: chain A residue 167 LEU Chi-restraints excluded: chain A residue 184 ASN Chi-restraints excluded: chain A residue 185 ASN Chi-restraints excluded: chain A residue 206 VAL Chi-restraints excluded: chain A residue 232 PHE Chi-restraints excluded: chain A residue 235 PHE Chi-restraints excluded: chain B residue 138 LEU Chi-restraints excluded: chain B residue 167 LEU Chi-restraints excluded: chain B residue 184 ASN Chi-restraints excluded: chain B residue 185 ASN Chi-restraints excluded: chain B residue 210 TRP Chi-restraints excluded: chain B residue 224 LEU Chi-restraints excluded: chain B residue 232 PHE Chi-restraints excluded: chain B residue 235 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 42 optimal weight: 0.9980 chunk 63 optimal weight: 8.9990 chunk 58 optimal weight: 5.9990 chunk 50 optimal weight: 20.0000 chunk 5 optimal weight: 20.0000 chunk 39 optimal weight: 5.9990 chunk 31 optimal weight: 6.9990 chunk 40 optimal weight: 4.9990 chunk 54 optimal weight: 0.7980 chunk 15 optimal weight: 0.9980 chunk 46 optimal weight: 0.1980 overall best weight: 1.5982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 185 ASN B 185 ASN ** B 306 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7907 moved from start: 0.3648 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 4356 Z= 0.219 Angle : 0.832 12.896 5994 Z= 0.421 Chirality : 0.042 0.235 724 Planarity : 0.004 0.037 790 Dihedral : 4.447 22.904 690 Min Nonbonded Distance : 2.117 Molprobity Statistics. All-atom Clashscore : 15.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.44 % Favored : 93.56 % Rotamer: Outliers : 5.90 % Allowed : 36.46 % Favored : 57.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.56 (0.34), residues: 652 helix: 3.26 (0.22), residues: 538 sheet: None (None), residues: 0 loop : -2.64 (0.58), residues: 114 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.001 TRP B 210 HIS 0.001 0.001 HIS B 196 PHE 0.024 0.001 PHE A 153 TYR 0.022 0.002 TYR A 33 ARG 0.012 0.002 ARG A 90 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1304 Ramachandran restraints generated. 652 Oldfield, 0 Emsley, 652 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1304 Ramachandran restraints generated. 652 Oldfield, 0 Emsley, 652 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 594 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 134 time to evaluate : 0.495 Fit side-chains outliers start: 17 outliers final: 17 residues processed: 144 average time/residue: 0.1412 time to fit residues: 25.6860 Evaluate side-chains 154 residues out of total 594 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 137 time to evaluate : 0.488 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 LEU Chi-restraints excluded: chain A residue 138 LEU Chi-restraints excluded: chain A residue 160 THR Chi-restraints excluded: chain A residue 167 LEU Chi-restraints excluded: chain A residue 184 ASN Chi-restraints excluded: chain A residue 185 ASN Chi-restraints excluded: chain A residue 206 VAL Chi-restraints excluded: chain A residue 232 PHE Chi-restraints excluded: chain A residue 235 PHE Chi-restraints excluded: chain B residue 138 LEU Chi-restraints excluded: chain B residue 167 LEU Chi-restraints excluded: chain B residue 184 ASN Chi-restraints excluded: chain B residue 185 ASN Chi-restraints excluded: chain B residue 210 TRP Chi-restraints excluded: chain B residue 224 LEU Chi-restraints excluded: chain B residue 232 PHE Chi-restraints excluded: chain B residue 235 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 7 optimal weight: 7.9990 chunk 14 optimal weight: 0.5980 chunk 50 optimal weight: 20.0000 chunk 21 optimal weight: 2.9990 chunk 52 optimal weight: 8.9990 chunk 6 optimal weight: 0.0470 chunk 9 optimal weight: 5.9990 chunk 44 optimal weight: 1.9990 chunk 2 optimal weight: 6.9990 chunk 36 optimal weight: 10.0000 chunk 58 optimal weight: 8.9990 overall best weight: 2.3284 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 185 ASN B 185 ASN ** B 306 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3773 r_free = 0.3773 target = 0.099880 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.081173 restraints weight = 15225.677| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3497 r_free = 0.3497 target = 0.083237 restraints weight = 9420.446| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.084718 restraints weight = 6711.161| |-----------------------------------------------------------------------------| r_work (final): 0.3522 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7939 moved from start: 0.3593 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 4356 Z= 0.234 Angle : 0.817 12.850 5994 Z= 0.421 Chirality : 0.042 0.220 724 Planarity : 0.004 0.032 790 Dihedral : 4.498 22.631 690 Min Nonbonded Distance : 2.136 Molprobity Statistics. All-atom Clashscore : 16.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.13 % Favored : 93.87 % Rotamer: Outliers : 5.90 % Allowed : 36.46 % Favored : 57.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.58 (0.34), residues: 652 helix: 3.27 (0.22), residues: 538 sheet: None (None), residues: 0 loop : -2.56 (0.59), residues: 114 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP B 210 HIS 0.001 0.001 HIS A 197 PHE 0.027 0.002 PHE A 136 TYR 0.026 0.002 TYR B 33 ARG 0.011 0.001 ARG A 90 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1233.92 seconds wall clock time: 23 minutes 41.73 seconds (1421.73 seconds total)