Starting phenix.real_space_refine on Thu Dec 7 17:29:55 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pqg_13593/12_2023/7pqg_13593.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pqg_13593/12_2023/7pqg_13593.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pqg_13593/12_2023/7pqg_13593.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pqg_13593/12_2023/7pqg_13593.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pqg_13593/12_2023/7pqg_13593.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pqg_13593/12_2023/7pqg_13593.pdb" } resolution = 3.7 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.008 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 31 5.16 5 C 2134 2.51 5 N 522 2.21 5 O 564 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B ARG 38": "NH1" <-> "NH2" Residue "B TYR 95": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 106": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 115": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 21": "NH1" <-> "NH2" Residue "A PHE 128": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 139": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 143": "NH1" <-> "NH2" Residue "A TYR 146": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 186": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 249": "NH1" <-> "NH2" Residue "A ARG 251": "NH1" <-> "NH2" Residue "A PHE 274": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/chem_data/mon_lib" Total number of atoms: 3251 Number of models: 1 Model: "" Number of chains: 2 Chain: "B" Number of atoms: 955 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 955 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 3, 'TRANS': 120} Chain: "A" Number of atoms: 2296 Number of conformers: 1 Conformer: "" Number of residues, atoms: 299, 2296 Classifications: {'peptide': 299} Link IDs: {'PTRANS': 16, 'TRANS': 282} Time building chain proxies: 2.28, per 1000 atoms: 0.70 Number of scatterers: 3251 At special positions: 0 Unit cell: (61.488, 75.6, 99.792, 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 31 16.00 O 564 8.00 N 522 7.00 C 2134 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS B 22 " - pdb=" SG CYS B 96 " distance=2.03 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: 1.35 Conformation dependent library (CDL) restraints added in 591.2 milliseconds 838 Ramachandran restraints generated. 419 Oldfield, 0 Emsley, 419 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 770 Finding SS restraints... Secondary structure from input PDB file: 20 helices and 3 sheets defined 67.8% alpha, 6.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.36 Creating SS restraints... Processing helix chain 'B' and resid 62 through 65 Processing helix chain 'B' and resid 87 through 91 removed outlier: 3.715A pdb=" N ASP B 90 " --> pdb=" O LYS B 87 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N THR B 91 " --> pdb=" O PRO B 88 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 87 through 91' Processing helix chain 'B' and resid 109 through 113 removed outlier: 3.610A pdb=" N TYR B 113 " --> pdb=" O PRO B 110 " (cutoff:3.500A) Processing helix chain 'A' and resid 20 through 44 removed outlier: 4.031A pdb=" N ASP A 24 " --> pdb=" O LYS A 20 " (cutoff:3.500A) Processing helix chain 'A' and resid 47 through 55 removed outlier: 3.588A pdb=" N ALA A 53 " --> pdb=" O SER A 49 " (cutoff:3.500A) Processing helix chain 'A' and resid 58 through 83 removed outlier: 3.686A pdb=" N MET A 72 " --> pdb=" O GLN A 68 " (cutoff:3.500A) Proline residue: A 73 - end of helix Processing helix chain 'A' and resid 86 through 98 Processing helix chain 'A' and resid 102 through 113 Processing helix chain 'A' and resid 115 through 143 removed outlier: 3.970A pdb=" N SER A 119 " --> pdb=" O ASP A 115 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N LEU A 131 " --> pdb=" O THR A 127 " (cutoff:3.500A) removed outlier: 5.328A pdb=" N GLY A 132 " --> pdb=" O PHE A 128 " (cutoff:3.500A) Proline residue: A 135 - end of helix removed outlier: 3.785A pdb=" N ARG A 143 " --> pdb=" O TYR A 139 " (cutoff:3.500A) Processing helix chain 'A' and resid 148 through 153 removed outlier: 4.475A pdb=" N ASP A 152 " --> pdb=" O ASP A 149 " (cutoff:3.500A) Processing helix chain 'A' and resid 155 through 179 Proline residue: A 169 - end of helix Processing helix chain 'A' and resid 180 through 182 No H-bonds generated for 'chain 'A' and resid 180 through 182' Processing helix chain 'A' and resid 183 through 210 removed outlier: 3.590A pdb=" N VAL A 187 " --> pdb=" O TYR A 183 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N ILE A 188 " --> pdb=" O MET A 184 " (cutoff:3.500A) removed outlier: 5.388A pdb=" N LYS A 189 " --> pdb=" O ARG A 185 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N GLY A 190 " --> pdb=" O TYR A 186 " (cutoff:3.500A) removed outlier: 4.293A pdb=" N VAL A 210 " --> pdb=" O SER A 206 " (cutoff:3.500A) Processing helix chain 'A' and resid 211 through 218 removed outlier: 4.281A pdb=" N MET A 215 " --> pdb=" O GLY A 211 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N PHE A 216 " --> pdb=" O LYS A 212 " (cutoff:3.500A) Processing helix chain 'A' and resid 219 through 244 Proline residue: A 230 - end of helix Processing helix chain 'A' and resid 247 through 260 removed outlier: 3.568A pdb=" N CYS A 260 " --> pdb=" O MET A 256 " (cutoff:3.500A) Processing helix chain 'A' and resid 262 through 274 Processing helix chain 'A' and resid 275 through 280 Processing helix chain 'A' and resid 281 through 283 No H-bonds generated for 'chain 'A' and resid 281 through 283' Processing helix chain 'A' and resid 284 through 310 removed outlier: 3.535A pdb=" N LEU A 288 " --> pdb=" O PHE A 284 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N LYS A 309 " --> pdb=" O TRP A 305 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N PHE A 310 " --> pdb=" O CYS A 306 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 3 through 4 removed outlier: 3.800A pdb=" N MET B 83 " --> pdb=" O LEU B 18 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N LEU B 20 " --> pdb=" O LEU B 81 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 58 through 60 removed outlier: 3.933A pdb=" N ALA B 49 " --> pdb=" O TRP B 36 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N ALA B 98 " --> pdb=" O TYR B 115 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N TYR B 115 " --> pdb=" O ALA B 98 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 92 through 93 removed outlier: 3.707A pdb=" N VAL B 122 " --> pdb=" O ALA B 92 " (cutoff:3.500A) 199 hydrogen bonds defined for protein. 567 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: 0.86 Time building geometry restraints manager: 1.46 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 863 1.33 - 1.45: 598 1.45 - 1.57: 1814 1.57 - 1.69: 0 1.69 - 1.81: 49 Bond restraints: 3324 Sorted by residual: bond pdb=" CG GLN A 293 " pdb=" CD GLN A 293 " ideal model delta sigma weight residual 1.516 1.466 0.050 2.50e-02 1.60e+03 4.06e+00 bond pdb=" N LYS A 189 " pdb=" CA LYS A 189 " ideal model delta sigma weight residual 1.457 1.474 -0.016 1.29e-02 6.01e+03 1.58e+00 bond pdb=" C VAL A 187 " pdb=" N ILE A 188 " ideal model delta sigma weight residual 1.335 1.321 0.014 1.26e-02 6.30e+03 1.21e+00 bond pdb=" CB CYS A 125 " pdb=" SG CYS A 125 " ideal model delta sigma weight residual 1.808 1.773 0.035 3.30e-02 9.18e+02 1.11e+00 bond pdb=" N THR A 13 " pdb=" CA THR A 13 " ideal model delta sigma weight residual 1.457 1.470 -0.013 1.29e-02 6.01e+03 9.94e-01 ... (remaining 3319 not shown) Histogram of bond angle deviations from ideal: 96.64 - 104.11: 60 104.11 - 111.58: 1467 111.58 - 119.06: 1210 119.06 - 126.53: 1726 126.53 - 134.00: 43 Bond angle restraints: 4506 Sorted by residual: angle pdb=" N VAL A 187 " pdb=" CA VAL A 187 " pdb=" C VAL A 187 " ideal model delta sigma weight residual 110.62 114.37 -3.75 1.02e+00 9.61e-01 1.35e+01 angle pdb=" N GLN A 293 " pdb=" CA GLN A 293 " pdb=" CB GLN A 293 " ideal model delta sigma weight residual 110.28 115.50 -5.22 1.55e+00 4.16e-01 1.14e+01 angle pdb=" N ILE A 188 " pdb=" CA ILE A 188 " pdb=" C ILE A 188 " ideal model delta sigma weight residual 110.62 114.01 -3.39 1.02e+00 9.61e-01 1.10e+01 angle pdb=" N GLN A 261 " pdb=" CA GLN A 261 " pdb=" C GLN A 261 " ideal model delta sigma weight residual 109.96 114.98 -5.02 1.58e+00 4.01e-01 1.01e+01 angle pdb=" N TYR A 186 " pdb=" CA TYR A 186 " pdb=" C TYR A 186 " ideal model delta sigma weight residual 113.50 109.63 3.87 1.23e+00 6.61e-01 9.89e+00 ... (remaining 4501 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.01: 1809 17.01 - 34.02: 131 34.02 - 51.03: 22 51.03 - 68.04: 3 68.04 - 85.05: 3 Dihedral angle restraints: 1968 sinusoidal: 758 harmonic: 1210 Sorted by residual: dihedral pdb=" CB CYS B 22 " pdb=" SG CYS B 22 " pdb=" SG CYS B 96 " pdb=" CB CYS B 96 " ideal model delta sinusoidal sigma weight residual 93.00 164.83 -71.83 1 1.00e+01 1.00e-02 6.61e+01 dihedral pdb=" CA LYS A 309 " pdb=" C LYS A 309 " pdb=" N PHE A 310 " pdb=" CA PHE A 310 " ideal model delta harmonic sigma weight residual -180.00 -158.01 -21.99 0 5.00e+00 4.00e-02 1.93e+01 dihedral pdb=" CA GLU B 89 " pdb=" C GLU B 89 " pdb=" N ASP B 90 " pdb=" CA ASP B 90 " ideal model delta harmonic sigma weight residual -180.00 -158.48 -21.52 0 5.00e+00 4.00e-02 1.85e+01 ... (remaining 1965 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.037: 335 0.037 - 0.074: 120 0.074 - 0.112: 50 0.112 - 0.149: 19 0.149 - 0.186: 3 Chirality restraints: 527 Sorted by residual: chirality pdb=" CB ILE A 88 " pdb=" CA ILE A 88 " pdb=" CG1 ILE A 88 " pdb=" CG2 ILE A 88 " both_signs ideal model delta sigma weight residual False 2.64 2.46 0.19 2.00e-01 2.50e+01 8.65e-01 chirality pdb=" CA MET A 229 " pdb=" N MET A 229 " pdb=" C MET A 229 " pdb=" CB MET A 229 " both_signs ideal model delta sigma weight residual False 2.51 2.33 0.18 2.00e-01 2.50e+01 7.85e-01 chirality pdb=" CG LEU A 79 " pdb=" CB LEU A 79 " pdb=" CD1 LEU A 79 " pdb=" CD2 LEU A 79 " both_signs ideal model delta sigma weight residual False -2.59 -2.43 -0.16 2.00e-01 2.50e+01 6.18e-01 ... (remaining 524 not shown) Planarity restraints: 551 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C SER B 109 " 0.033 5.00e-02 4.00e+02 4.93e-02 3.89e+00 pdb=" N PRO B 110 " -0.085 5.00e-02 4.00e+02 pdb=" CA PRO B 110 " 0.025 5.00e-02 4.00e+02 pdb=" CD PRO B 110 " 0.027 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA TYR A 289 " 0.009 2.00e-02 2.50e+03 1.90e-02 3.62e+00 pdb=" C TYR A 289 " -0.033 2.00e-02 2.50e+03 pdb=" O TYR A 289 " 0.012 2.00e-02 2.50e+03 pdb=" N MET A 290 " 0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 36 " -0.011 2.00e-02 2.50e+03 1.33e-02 3.08e+00 pdb=" CG PHE A 36 " 0.031 2.00e-02 2.50e+03 pdb=" CD1 PHE A 36 " -0.009 2.00e-02 2.50e+03 pdb=" CD2 PHE A 36 " -0.009 2.00e-02 2.50e+03 pdb=" CE1 PHE A 36 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 PHE A 36 " -0.001 2.00e-02 2.50e+03 pdb=" CZ PHE A 36 " -0.001 2.00e-02 2.50e+03 ... (remaining 548 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 389 2.74 - 3.28: 3900 3.28 - 3.82: 5577 3.82 - 4.36: 6655 4.36 - 4.90: 10332 Nonbonded interactions: 26853 Sorted by model distance: nonbonded pdb=" O THR A 124 " pdb=" OG1 THR A 127 " model vdw 2.204 2.440 nonbonded pdb=" O TRP B 53 " pdb=" NH2 ARG B 72 " model vdw 2.223 2.520 nonbonded pdb=" O LYS A 113 " pdb=" NH2 ARG A 249 " model vdw 2.225 2.520 nonbonded pdb=" OG SER B 7 " pdb=" OG SER B 21 " model vdw 2.247 2.440 nonbonded pdb=" O ILE A 168 " pdb=" OG1 THR A 171 " model vdw 2.252 2.440 ... (remaining 26848 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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: 1.550 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: 6.100 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 13.860 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.840 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.550 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7847 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 : 0.004 0.050 3324 Z= 0.271 Angle : 0.880 7.914 4506 Z= 0.481 Chirality : 0.049 0.186 527 Planarity : 0.006 0.049 551 Dihedral : 12.564 85.048 1195 Min Nonbonded Distance : 2.204 Molprobity Statistics. All-atom Clashscore : 28.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.40 % Favored : 92.60 % Rotamer: Outliers : 0.28 % Allowed : 0.28 % Favored : 99.44 % 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: -0.87 (0.41), residues: 419 helix: 0.44 (0.32), residues: 241 sheet: -3.49 (0.73), residues: 34 loop : -1.44 (0.53), residues: 144 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 116 HIS 0.003 0.001 HIS A 54 PHE 0.031 0.003 PHE A 36 TYR 0.018 0.002 TYR A 69 ARG 0.013 0.002 ARG B 38 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 838 Ramachandran restraints generated. 419 Oldfield, 0 Emsley, 419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 838 Ramachandran restraints generated. 419 Oldfield, 0 Emsley, 419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 357 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 142 time to evaluate : 0.449 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 143 average time/residue: 0.1594 time to fit residues: 27.1346 Evaluate side-chains 115 residues out of total 357 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 115 time to evaluate : 0.367 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.4945 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 34 optimal weight: 3.9990 chunk 31 optimal weight: 0.8980 chunk 17 optimal weight: 4.9990 chunk 10 optimal weight: 4.9990 chunk 20 optimal weight: 0.7980 chunk 16 optimal weight: 0.0020 chunk 32 optimal weight: 0.7980 chunk 12 optimal weight: 3.9990 chunk 19 optimal weight: 0.9990 chunk 23 optimal weight: 3.9990 chunk 37 optimal weight: 0.9990 overall best weight: 0.6990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 1 GLN B 39 GLN ** B 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 261 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 264 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 271 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7880 moved from start: 0.2179 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 3324 Z= 0.272 Angle : 0.885 8.190 4506 Z= 0.464 Chirality : 0.052 0.179 527 Planarity : 0.005 0.031 551 Dihedral : 5.697 20.162 454 Min Nonbonded Distance : 2.158 Molprobity Statistics. All-atom Clashscore : 32.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.49 % Favored : 94.51 % Rotamer: Outliers : 2.24 % Allowed : 14.29 % Favored : 83.47 % 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: -1.10 (0.40), residues: 419 helix: 0.22 (0.31), residues: 253 sheet: -2.74 (0.74), residues: 44 loop : -1.75 (0.58), residues: 122 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 36 HIS 0.003 0.002 HIS A 54 PHE 0.055 0.004 PHE A 36 TYR 0.020 0.002 TYR B 59 ARG 0.006 0.001 ARG B 45 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 838 Ramachandran restraints generated. 419 Oldfield, 0 Emsley, 419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 838 Ramachandran restraints generated. 419 Oldfield, 0 Emsley, 419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 357 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 133 time to evaluate : 0.386 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 8 outliers final: 4 residues processed: 135 average time/residue: 0.1566 time to fit residues: 25.4639 Evaluate side-chains 113 residues out of total 357 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 109 time to evaluate : 0.384 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.0401 time to fit residues: 0.7413 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 20 optimal weight: 2.9990 chunk 11 optimal weight: 3.9990 chunk 30 optimal weight: 0.9980 chunk 25 optimal weight: 2.9990 chunk 10 optimal weight: 0.9990 chunk 37 optimal weight: 0.9980 chunk 40 optimal weight: 1.9990 chunk 33 optimal weight: 2.9990 chunk 36 optimal weight: 5.9990 chunk 12 optimal weight: 3.9990 chunk 29 optimal weight: 0.0980 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 39 GLN ** A 261 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 264 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7907 moved from start: 0.2674 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 3324 Z= 0.287 Angle : 0.915 9.124 4506 Z= 0.484 Chirality : 0.054 0.332 527 Planarity : 0.005 0.030 551 Dihedral : 5.660 20.921 454 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 33.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.97 % Favored : 94.03 % Rotamer: Outliers : 2.52 % Allowed : 21.57 % Favored : 75.91 % 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: -1.37 (0.40), residues: 419 helix: -0.04 (0.31), residues: 255 sheet: -2.52 (0.78), residues: 44 loop : -1.93 (0.58), residues: 120 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 105 HIS 0.003 0.002 HIS A 221 PHE 0.047 0.003 PHE A 36 TYR 0.026 0.002 TYR B 32 ARG 0.006 0.001 ARG B 27 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 838 Ramachandran restraints generated. 419 Oldfield, 0 Emsley, 419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 838 Ramachandran restraints generated. 419 Oldfield, 0 Emsley, 419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 357 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 125 time to evaluate : 0.383 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 9 outliers final: 5 residues processed: 131 average time/residue: 0.1440 time to fit residues: 22.9881 Evaluate side-chains 118 residues out of total 357 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 113 time to evaluate : 0.343 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 5 outliers final: 1 residues processed: 5 average time/residue: 0.1260 time to fit residues: 1.2833 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 36 optimal weight: 7.9990 chunk 28 optimal weight: 1.9990 chunk 19 optimal weight: 2.9990 chunk 4 optimal weight: 0.8980 chunk 17 optimal weight: 0.8980 chunk 25 optimal weight: 5.9990 chunk 37 optimal weight: 0.7980 chunk 39 optimal weight: 0.9980 chunk 35 optimal weight: 0.8980 chunk 10 optimal weight: 0.7980 chunk 33 optimal weight: 0.9980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7889 moved from start: 0.3234 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 3324 Z= 0.270 Angle : 0.939 9.987 4506 Z= 0.482 Chirality : 0.053 0.266 527 Planarity : 0.005 0.040 551 Dihedral : 5.594 20.174 454 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 31.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.68 % Favored : 93.32 % Rotamer: Outliers : 2.52 % Allowed : 21.85 % Favored : 75.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.31 (0.40), residues: 419 helix: 0.02 (0.31), residues: 254 sheet: -2.50 (0.79), residues: 44 loop : -1.93 (0.59), residues: 121 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 56 HIS 0.003 0.001 HIS A 221 PHE 0.042 0.003 PHE A 36 TYR 0.026 0.002 TYR B 32 ARG 0.004 0.001 ARG B 38 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 838 Ramachandran restraints generated. 419 Oldfield, 0 Emsley, 419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 838 Ramachandran restraints generated. 419 Oldfield, 0 Emsley, 419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 357 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 122 time to evaluate : 0.375 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 9 outliers final: 2 residues processed: 124 average time/residue: 0.1560 time to fit residues: 22.9916 Evaluate side-chains 113 residues out of total 357 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 111 time to evaluate : 0.319 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.2194 time to fit residues: 0.9062 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 22 optimal weight: 3.9990 chunk 0 optimal weight: 7.9990 chunk 29 optimal weight: 2.9990 chunk 16 optimal weight: 0.4980 chunk 33 optimal weight: 2.9990 chunk 27 optimal weight: 0.7980 chunk 20 optimal weight: 2.9990 chunk 35 optimal weight: 0.8980 chunk 10 optimal weight: 5.9990 chunk 13 optimal weight: 3.9990 chunk 7 optimal weight: 2.9990 overall best weight: 1.6384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7940 moved from start: 0.3521 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 3324 Z= 0.326 Angle : 0.966 10.249 4506 Z= 0.501 Chirality : 0.054 0.358 527 Planarity : 0.006 0.037 551 Dihedral : 5.711 27.544 454 Min Nonbonded Distance : 2.143 Molprobity Statistics. All-atom Clashscore : 37.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.88 % Favored : 92.12 % Rotamer: Outliers : 3.64 % Allowed : 26.05 % Favored : 70.31 % 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: -1.45 (0.40), residues: 419 helix: -0.10 (0.30), residues: 254 sheet: -2.58 (0.79), residues: 43 loop : -1.94 (0.59), residues: 122 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP B 36 HIS 0.002 0.001 HIS A 54 PHE 0.048 0.004 PHE A 108 TYR 0.037 0.003 TYR A 289 ARG 0.010 0.002 ARG B 19 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 838 Ramachandran restraints generated. 419 Oldfield, 0 Emsley, 419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 838 Ramachandran restraints generated. 419 Oldfield, 0 Emsley, 419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 357 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 115 time to evaluate : 0.382 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 13 outliers final: 8 residues processed: 121 average time/residue: 0.1333 time to fit residues: 19.9083 Evaluate side-chains 117 residues out of total 357 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 109 time to evaluate : 0.382 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.0419 time to fit residues: 1.0481 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 23 optimal weight: 0.9990 chunk 9 optimal weight: 2.9990 chunk 39 optimal weight: 0.3980 chunk 32 optimal weight: 0.0970 chunk 18 optimal weight: 0.9980 chunk 3 optimal weight: 1.9990 chunk 13 optimal weight: 2.9990 chunk 20 optimal weight: 0.9980 chunk 38 optimal weight: 0.9980 chunk 4 optimal weight: 0.8980 chunk 22 optimal weight: 0.8980 overall best weight: 0.6578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7877 moved from start: 0.3768 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 3324 Z= 0.258 Angle : 0.992 11.927 4506 Z= 0.504 Chirality : 0.054 0.332 527 Planarity : 0.005 0.039 551 Dihedral : 5.652 25.489 454 Min Nonbonded Distance : 2.160 Molprobity Statistics. All-atom Clashscore : 34.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.40 % Favored : 92.60 % Rotamer: Outliers : 1.96 % Allowed : 29.13 % Favored : 68.91 % 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: -1.23 (0.41), residues: 419 helix: 0.08 (0.30), residues: 254 sheet: -2.09 (0.69), residues: 59 loop : -1.93 (0.65), residues: 106 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP B 116 HIS 0.003 0.001 HIS A 221 PHE 0.046 0.004 PHE A 36 TYR 0.030 0.002 TYR B 32 ARG 0.008 0.001 ARG B 19 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 838 Ramachandran restraints generated. 419 Oldfield, 0 Emsley, 419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 838 Ramachandran restraints generated. 419 Oldfield, 0 Emsley, 419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 357 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 116 time to evaluate : 0.392 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 7 outliers final: 5 residues processed: 117 average time/residue: 0.1515 time to fit residues: 21.4338 Evaluate side-chains 113 residues out of total 357 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 108 time to evaluate : 0.381 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.0460 time to fit residues: 0.8997 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 28 optimal weight: 2.9990 chunk 22 optimal weight: 0.2980 chunk 33 optimal weight: 0.9980 chunk 39 optimal weight: 0.2980 chunk 24 optimal weight: 0.9990 chunk 18 optimal weight: 1.9990 chunk 15 optimal weight: 0.9990 chunk 23 optimal weight: 0.2980 chunk 11 optimal weight: 0.9990 chunk 7 optimal weight: 0.0980 chunk 25 optimal weight: 0.6980 overall best weight: 0.3380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7836 moved from start: 0.4102 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 3324 Z= 0.261 Angle : 1.014 13.014 4506 Z= 0.509 Chirality : 0.056 0.382 527 Planarity : 0.005 0.038 551 Dihedral : 5.596 23.452 454 Min Nonbonded Distance : 2.158 Molprobity Statistics. All-atom Clashscore : 31.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.40 % Favored : 92.60 % Rotamer: Outliers : 0.56 % Allowed : 32.21 % Favored : 67.23 % 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 (0.40), residues: 419 helix: 0.11 (0.31), residues: 252 sheet: -2.35 (0.77), residues: 44 loop : -1.82 (0.57), residues: 123 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 116 HIS 0.004 0.001 HIS A 221 PHE 0.051 0.003 PHE A 108 TYR 0.025 0.002 TYR B 32 ARG 0.016 0.001 ARG B 45 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 838 Ramachandran restraints generated. 419 Oldfield, 0 Emsley, 419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 838 Ramachandran restraints generated. 419 Oldfield, 0 Emsley, 419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 357 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 124 time to evaluate : 0.397 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 2 outliers final: 0 residues processed: 124 average time/residue: 0.1457 time to fit residues: 21.8119 Evaluate side-chains 106 residues out of total 357 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 106 time to evaluate : 0.449 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.5195 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 26 optimal weight: 0.4980 chunk 19 optimal weight: 0.5980 chunk 3 optimal weight: 5.9990 chunk 31 optimal weight: 0.7980 chunk 35 optimal weight: 1.9990 chunk 37 optimal weight: 0.9980 chunk 34 optimal weight: 0.7980 chunk 36 optimal weight: 2.9990 chunk 22 optimal weight: 0.5980 chunk 16 optimal weight: 3.9990 chunk 28 optimal weight: 0.5980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7841 moved from start: 0.4400 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 3324 Z= 0.285 Angle : 1.080 12.993 4506 Z= 0.547 Chirality : 0.060 0.397 527 Planarity : 0.005 0.037 551 Dihedral : 5.709 25.839 454 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 35.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.40 % Favored : 92.60 % Rotamer: Outliers : 0.56 % Allowed : 35.29 % Favored : 64.15 % 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: -1.25 (0.40), residues: 419 helix: 0.04 (0.31), residues: 250 sheet: -2.14 (0.72), residues: 52 loop : -1.85 (0.58), residues: 117 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 36 HIS 0.001 0.000 HIS A 54 PHE 0.056 0.004 PHE A 108 TYR 0.028 0.002 TYR B 32 ARG 0.005 0.001 ARG B 45 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 838 Ramachandran restraints generated. 419 Oldfield, 0 Emsley, 419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 838 Ramachandran restraints generated. 419 Oldfield, 0 Emsley, 419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 357 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 115 time to evaluate : 0.378 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 2 outliers final: 0 residues processed: 115 average time/residue: 0.1511 time to fit residues: 21.1634 Evaluate side-chains 108 residues out of total 357 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 108 time to evaluate : 0.367 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.5016 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 11 optimal weight: 2.9990 chunk 33 optimal weight: 0.3980 chunk 34 optimal weight: 0.9980 chunk 36 optimal weight: 1.9990 chunk 24 optimal weight: 0.3980 chunk 38 optimal weight: 0.8980 chunk 23 optimal weight: 1.9990 chunk 18 optimal weight: 0.9990 chunk 27 optimal weight: 0.8980 chunk 40 optimal weight: 0.9990 chunk 37 optimal weight: 0.7980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7849 moved from start: 0.4485 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 3324 Z= 0.276 Angle : 1.093 14.728 4506 Z= 0.547 Chirality : 0.059 0.381 527 Planarity : 0.005 0.035 551 Dihedral : 5.688 26.860 454 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 34.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.40 % Favored : 92.60 % Rotamer: Outliers : 1.12 % Allowed : 33.61 % Favored : 65.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.34 (0.40), residues: 419 helix: -0.03 (0.31), residues: 253 sheet: -2.03 (0.72), residues: 52 loop : -2.00 (0.56), residues: 114 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 36 HIS 0.001 0.001 HIS A 54 PHE 0.056 0.003 PHE A 108 TYR 0.027 0.002 TYR B 32 ARG 0.004 0.001 ARG B 27 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 838 Ramachandran restraints generated. 419 Oldfield, 0 Emsley, 419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 838 Ramachandran restraints generated. 419 Oldfield, 0 Emsley, 419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 357 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 109 time to evaluate : 0.332 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 4 outliers final: 2 residues processed: 111 average time/residue: 0.1515 time to fit residues: 20.2669 Evaluate side-chains 109 residues out of total 357 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 107 time to evaluate : 0.397 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0514 time to fit residues: 0.7073 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 32 optimal weight: 0.6980 chunk 3 optimal weight: 3.9990 chunk 25 optimal weight: 3.9990 chunk 19 optimal weight: 0.8980 chunk 34 optimal weight: 0.8980 chunk 9 optimal weight: 1.9990 chunk 29 optimal weight: 0.8980 chunk 4 optimal weight: 0.7980 chunk 13 optimal weight: 2.9990 chunk 33 optimal weight: 0.8980 chunk 6 optimal weight: 1.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 271 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7871 moved from start: 0.4629 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 3324 Z= 0.289 Angle : 1.123 13.448 4506 Z= 0.564 Chirality : 0.060 0.407 527 Planarity : 0.005 0.031 551 Dihedral : 5.735 26.518 454 Min Nonbonded Distance : 2.090 Molprobity Statistics. All-atom Clashscore : 35.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.16 % Favored : 92.84 % Rotamer: Outliers : 0.56 % Allowed : 32.77 % 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: -1.34 (0.40), residues: 419 helix: -0.08 (0.31), residues: 254 sheet: -2.03 (0.72), residues: 52 loop : -1.87 (0.58), residues: 113 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 36 HIS 0.001 0.001 HIS A 54 PHE 0.055 0.003 PHE A 108 TYR 0.031 0.002 TYR B 95 ARG 0.004 0.001 ARG B 38 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 838 Ramachandran restraints generated. 419 Oldfield, 0 Emsley, 419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 838 Ramachandran restraints generated. 419 Oldfield, 0 Emsley, 419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 357 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 105 time to evaluate : 0.382 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 2 outliers final: 1 residues processed: 106 average time/residue: 0.1573 time to fit residues: 20.0760 Evaluate side-chains 106 residues out of total 357 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 105 time to evaluate : 0.376 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0353 time to fit residues: 0.5683 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 28 optimal weight: 0.4980 chunk 1 optimal weight: 0.9980 chunk 23 optimal weight: 2.9990 chunk 37 optimal weight: 1.9990 chunk 21 optimal weight: 0.8980 chunk 27 optimal weight: 0.4980 chunk 26 optimal weight: 0.6980 chunk 24 optimal weight: 0.9980 chunk 16 optimal weight: 3.9990 chunk 15 optimal weight: 0.9980 chunk 40 optimal weight: 0.6980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 271 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3761 r_free = 0.3761 target = 0.078735 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.066026 restraints weight = 14296.844| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3576 r_free = 0.3576 target = 0.067983 restraints weight = 10117.756| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3600 r_free = 0.3600 target = 0.069417 restraints weight = 7634.884| |-----------------------------------------------------------------------------| r_work (final): 0.3598 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7906 moved from start: 0.4701 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 3324 Z= 0.276 Angle : 1.130 15.612 4506 Z= 0.574 Chirality : 0.060 0.376 527 Planarity : 0.005 0.033 551 Dihedral : 5.651 25.980 454 Min Nonbonded Distance : 2.146 Molprobity Statistics. All-atom Clashscore : 34.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.88 % Favored : 92.12 % Rotamer: Outliers : 0.56 % Allowed : 33.05 % Favored : 66.39 % 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 (0.41), residues: 419 helix: -0.09 (0.31), residues: 254 sheet: -1.83 (0.77), residues: 52 loop : -1.83 (0.58), residues: 113 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 36 HIS 0.001 0.000 HIS A 221 PHE 0.054 0.003 PHE A 108 TYR 0.031 0.002 TYR B 32 ARG 0.004 0.001 ARG B 27 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1207.14 seconds wall clock time: 22 minutes 44.09 seconds (1364.09 seconds total)