Starting phenix.real_space_refine on Thu Dec 7 19:26:54 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sdz_40355/12_2023/8sdz_40355_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sdz_40355/12_2023/8sdz_40355.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sdz_40355/12_2023/8sdz_40355_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.86 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sdz_40355/12_2023/8sdz_40355_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sdz_40355/12_2023/8sdz_40355_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sdz_40355/12_2023/8sdz_40355.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sdz_40355/12_2023/8sdz_40355.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sdz_40355/12_2023/8sdz_40355_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sdz_40355/12_2023/8sdz_40355_updated.pdb" } resolution = 2.86 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= 0.002 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 2533 2.51 5 N 654 2.21 5 O 695 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 154": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 188": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 444": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 449": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 506": "OE1" <-> "OE2" Residue "A ASP 514": "OD1" <-> "OD2" 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: 3913 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 3872 Number of conformers: 1 Conformer: "" Number of residues, atoms: 500, 3872 Classifications: {'peptide': 500} Link IDs: {'PTRANS': 26, 'TRANS': 473} Chain breaks: 3 Chain: "A" Number of atoms: 41 Number of conformers: 1 Conformer: "" Number of residues, atoms: 23, 41 Unusual residues: {'RTO': 1} Classifications: {'undetermined': 1, 'water': 22} Link IDs: {None: 22} Time building chain proxies: 2.55, per 1000 atoms: 0.65 Number of scatterers: 3913 At special positions: 0 Unit cell: (78.85, 71.38, 98.77, 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 695 8.00 N 654 7.00 C 2533 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS A 49 " - pdb=" SG CYS A 105 " distance=2.03 Simple disulfide: pdb=" SG CYS A 78 " - pdb=" SG CYS A 128 " distance=2.02 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: 1.80 Conformation dependent library (CDL) restraints added in 741.8 milliseconds 984 Ramachandran restraints generated. 492 Oldfield, 0 Emsley, 492 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 928 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 21 helices and 1 sheets defined 72.0% alpha, 0.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.81 Creating SS restraints... Processing helix chain 'A' and resid 3 through 9 Processing helix chain 'A' and resid 15 through 35 Proline residue: A 27 - end of helix removed outlier: 4.427A pdb=" N LEU A 30 " --> pdb=" O ALA A 26 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N ALA A 32 " --> pdb=" O LEU A 28 " (cutoff:3.500A) removed outlier: 4.293A pdb=" N SER A 33 " --> pdb=" O LEU A 29 " (cutoff:3.500A) Processing helix chain 'A' and resid 37 through 41 removed outlier: 4.039A pdb=" N THR A 41 " --> pdb=" O GLN A 38 " (cutoff:3.500A) Processing helix chain 'A' and resid 120 through 124 Processing helix chain 'A' and resid 128 through 159 removed outlier: 5.212A pdb=" N ALA A 132 " --> pdb=" O SER A 129 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ALA A 137 " --> pdb=" O ARG A 134 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N VAL A 151 " --> pdb=" O GLY A 148 " (cutoff:3.500A) removed outlier: 4.568A pdb=" N PHE A 152 " --> pdb=" O ALA A 149 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N GLY A 153 " --> pdb=" O MET A 150 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N ALA A 156 " --> pdb=" O GLY A 153 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N LEU A 159 " --> pdb=" O ALA A 156 " (cutoff:3.500A) Processing helix chain 'A' and resid 161 through 180 Processing helix chain 'A' and resid 185 through 213 removed outlier: 3.569A pdb=" N SER A 198 " --> pdb=" O LEU A 194 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N SER A 201 " --> pdb=" O MET A 197 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N TRP A 213 " --> pdb=" O LEU A 209 " (cutoff:3.500A) Processing helix chain 'A' and resid 216 through 243 removed outlier: 5.263A pdb=" N ALA A 220 " --> pdb=" O HIS A 217 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N TYR A 221 " --> pdb=" O THR A 218 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ILE A 226 " --> pdb=" O GLY A 223 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N TYR A 230 " --> pdb=" O GLY A 227 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N LEU A 232 " --> pdb=" O VAL A 229 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N LEU A 237 " --> pdb=" O GLN A 234 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N ALA A 241 " --> pdb=" O ALA A 238 " (cutoff:3.500A) Processing helix chain 'A' and resid 247 through 267 removed outlier: 3.581A pdb=" N SER A 255 " --> pdb=" O GLN A 251 " (cutoff:3.500A) Proline residue: A 257 - end of helix removed outlier: 3.711A pdb=" N ILE A 260 " --> pdb=" O VAL A 256 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N TRP A 266 " --> pdb=" O PHE A 262 " (cutoff:3.500A) removed outlier: 5.085A pdb=" N PHE A 267 " --> pdb=" O ILE A 263 " (cutoff:3.500A) Processing helix chain 'A' and resid 272 through 277 Processing helix chain 'A' and resid 281 through 295 Processing helix chain 'A' and resid 298 through 303 Processing helix chain 'A' and resid 306 through 313 Processing helix chain 'A' and resid 326 through 331 removed outlier: 3.564A pdb=" N LEU A 329 " --> pdb=" O ALA A 326 " (cutoff:3.500A) Processing helix chain 'A' and resid 333 through 354 removed outlier: 3.580A pdb=" N HIS A 337 " --> pdb=" O PRO A 333 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N LEU A 338 " --> pdb=" O THR A 334 " (cutoff:3.500A) Processing helix chain 'A' and resid 367 through 391 removed outlier: 3.753A pdb=" N ASP A 378 " --> pdb=" O PHE A 374 " (cutoff:3.500A) removed outlier: 4.321A pdb=" N LEU A 379 " --> pdb=" O GLY A 375 " (cutoff:3.500A) Proline residue: A 380 - end of helix Processing helix chain 'A' and resid 394 through 414 Processing helix chain 'A' and resid 420 through 448 Processing helix chain 'A' and resid 454 through 480 Proline residue: A 473 - end of helix removed outlier: 4.020A pdb=" N THR A 478 " --> pdb=" O LEU A 474 " (cutoff:3.500A) removed outlier: 4.476A pdb=" N ALA A 479 " --> pdb=" O VAL A 475 " (cutoff:3.500A) removed outlier: 5.118A pdb=" N GLU A 480 " --> pdb=" O SER A 476 " (cutoff:3.500A) Processing helix chain 'A' and resid 485 through 503 Proline residue: A 494 - end of helix removed outlier: 3.880A pdb=" N ALA A 502 " --> pdb=" O SER A 498 " (cutoff:3.500A) removed outlier: 4.371A pdb=" N LEU A 503 " --> pdb=" O ALA A 499 " (cutoff:3.500A) Processing helix chain 'A' and resid 516 through 523 Processing sheet with id= A, first strand: chain 'A' and resid 47 through 49 232 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: 1.03 Time building geometry restraints manager: 1.89 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 1217 1.35 - 1.46: 974 1.46 - 1.58: 1743 1.58 - 1.70: 0 1.70 - 1.82: 49 Bond restraints: 3983 Sorted by residual: bond pdb=" CB PRO A 505 " pdb=" CG PRO A 505 " ideal model delta sigma weight residual 1.492 1.568 -0.076 5.00e-02 4.00e+02 2.32e+00 bond pdb=" CB MET A 23 " pdb=" CG MET A 23 " ideal model delta sigma weight residual 1.520 1.544 -0.024 3.00e-02 1.11e+03 6.28e-01 bond pdb=" C VAL A 256 " pdb=" N PRO A 257 " ideal model delta sigma weight residual 1.335 1.344 -0.010 1.28e-02 6.10e+03 5.56e-01 bond pdb=" CG LEU A 199 " pdb=" CD1 LEU A 199 " ideal model delta sigma weight residual 1.521 1.497 0.024 3.30e-02 9.18e+02 5.25e-01 bond pdb=" CA ALA A 26 " pdb=" C ALA A 26 " ideal model delta sigma weight residual 1.522 1.530 -0.008 1.26e-02 6.30e+03 3.92e-01 ... (remaining 3978 not shown) Histogram of bond angle deviations from ideal: 100.72 - 107.38: 158 107.38 - 114.04: 2270 114.04 - 120.69: 1799 120.69 - 127.35: 1142 127.35 - 134.01: 50 Bond angle restraints: 5419 Sorted by residual: angle pdb=" CB MET A 23 " pdb=" CG MET A 23 " pdb=" SD MET A 23 " ideal model delta sigma weight residual 112.70 122.34 -9.64 3.00e+00 1.11e-01 1.03e+01 angle pdb=" CA MET A 23 " pdb=" CB MET A 23 " pdb=" CG MET A 23 " ideal model delta sigma weight residual 114.10 119.50 -5.40 2.00e+00 2.50e-01 7.29e+00 angle pdb=" CA TYR A 264 " pdb=" CB TYR A 264 " pdb=" CG TYR A 264 " ideal model delta sigma weight residual 113.90 118.00 -4.10 1.80e+00 3.09e-01 5.20e+00 angle pdb=" N VAL A 256 " pdb=" CA VAL A 256 " pdb=" C VAL A 256 " ideal model delta sigma weight residual 108.88 113.75 -4.87 2.16e+00 2.14e-01 5.09e+00 angle pdb=" CA VAL A 256 " pdb=" C VAL A 256 " pdb=" N PRO A 257 " ideal model delta sigma weight residual 118.88 121.86 -2.98 1.54e+00 4.22e-01 3.75e+00 ... (remaining 5414 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.88: 2033 16.88 - 33.76: 233 33.76 - 50.64: 65 50.64 - 67.52: 17 67.52 - 84.40: 6 Dihedral angle restraints: 2354 sinusoidal: 911 harmonic: 1443 Sorted by residual: dihedral pdb=" CA CYS A 49 " pdb=" CB CYS A 49 " pdb=" SG CYS A 49 " pdb=" SG CYS A 105 " ideal model delta sinusoidal sigma weight residual -73.00 2.02 -75.02 1 2.00e+01 2.50e-03 1.78e+01 dihedral pdb=" CB CYS A 49 " pdb=" SG CYS A 49 " pdb=" SG CYS A 105 " pdb=" CB CYS A 105 " ideal model delta sinusoidal sigma weight residual -86.00 -113.39 27.39 1 1.00e+01 1.00e-02 1.08e+01 dihedral pdb=" SG CYS A 49 " pdb=" CB CYS A 105 " pdb=" SG CYS A 105 " pdb=" CA CYS A 105 " ideal model delta sinusoidal sigma weight residual 79.00 24.03 54.97 1 2.00e+01 2.50e-03 1.02e+01 ... (remaining 2351 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.039: 487 0.039 - 0.077: 116 0.077 - 0.116: 22 0.116 - 0.154: 4 0.154 - 0.193: 2 Chirality restraints: 631 Sorted by residual: chirality pdb=" CG LEU A 6 " pdb=" CB LEU A 6 " pdb=" CD1 LEU A 6 " pdb=" CD2 LEU A 6 " both_signs ideal model delta sigma weight residual False -2.59 -2.40 -0.19 2.00e-01 2.50e+01 9.28e-01 chirality pdb=" CG LEU A 232 " pdb=" CB LEU A 232 " pdb=" CD1 LEU A 232 " pdb=" CD2 LEU A 232 " both_signs ideal model delta sigma weight residual False -2.59 -2.43 -0.16 2.00e-01 2.50e+01 6.46e-01 chirality pdb=" CA ILE A 44 " pdb=" N ILE A 44 " pdb=" C ILE A 44 " pdb=" CB ILE A 44 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.12 2.00e-01 2.50e+01 3.72e-01 ... (remaining 628 not shown) Planarity restraints: 673 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP A 213 " 0.014 2.00e-02 2.50e+03 1.38e-02 4.79e+00 pdb=" CG TRP A 213 " -0.035 2.00e-02 2.50e+03 pdb=" CD1 TRP A 213 " 0.020 2.00e-02 2.50e+03 pdb=" CD2 TRP A 213 " 0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP A 213 " -0.006 2.00e-02 2.50e+03 pdb=" CE2 TRP A 213 " 0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP A 213 " 0.001 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 213 " 0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 213 " 0.001 2.00e-02 2.50e+03 pdb=" CH2 TRP A 213 " 0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ALA A 26 " -0.019 5.00e-02 4.00e+02 2.85e-02 1.30e+00 pdb=" N PRO A 27 " 0.049 5.00e-02 4.00e+02 pdb=" CA PRO A 27 " -0.014 5.00e-02 4.00e+02 pdb=" CD PRO A 27 " -0.016 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL A 256 " -0.017 5.00e-02 4.00e+02 2.52e-02 1.02e+00 pdb=" N PRO A 257 " 0.044 5.00e-02 4.00e+02 pdb=" CA PRO A 257 " -0.012 5.00e-02 4.00e+02 pdb=" CD PRO A 257 " -0.014 5.00e-02 4.00e+02 ... (remaining 670 not shown) Histogram of nonbonded interaction distances: 2.14 - 2.69: 67 2.69 - 3.24: 3941 3.24 - 3.79: 6357 3.79 - 4.35: 8786 4.35 - 4.90: 14154 Nonbonded interactions: 33305 Sorted by model distance: nonbonded pdb=" O VAL A 475 " pdb=" OG1 THR A 478 " model vdw 2.135 2.440 nonbonded pdb=" OG SER A 33 " pdb=" O HOH A 701 " model vdw 2.191 2.440 nonbonded pdb=" OD1 ASN A 168 " pdb=" OG SER A 201 " model vdw 2.211 2.440 nonbonded pdb=" O LEU A 29 " pdb=" O HOH A 701 " model vdw 2.216 2.440 nonbonded pdb=" O GLY A 233 " pdb=" O HOH A 701 " model vdw 2.234 2.440 ... (remaining 33300 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.300 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: 1.040 Check model and map are aligned: 0.060 Set scattering table: 0.040 Process input model: 15.490 Find NCS groups from input model: 0.100 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:12.800 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.850 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7842 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 : 0.003 0.076 3983 Z= 0.163 Angle : 0.506 9.642 5419 Z= 0.241 Chirality : 0.036 0.193 631 Planarity : 0.003 0.028 673 Dihedral : 16.148 84.396 1420 Min Nonbonded Distance : 2.135 Molprobity Statistics. All-atom Clashscore : 4.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.81 % Favored : 99.19 % Rotamer: Outliers : 1.43 % Allowed : 20.24 % Favored : 78.33 % 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: 0.91 (0.37), residues: 492 helix: 0.73 (0.26), residues: 374 sheet: 0.04 (1.43), residues: 10 loop : 0.67 (0.63), residues: 108 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.002 TRP A 213 HIS 0.001 0.000 HIS A 48 PHE 0.007 0.001 PHE A 191 TYR 0.013 0.001 TYR A 264 ARG 0.002 0.000 ARG A 336 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 984 Ramachandran restraints generated. 492 Oldfield, 0 Emsley, 492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 984 Ramachandran restraints generated. 492 Oldfield, 0 Emsley, 492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 65 residues out of total 420 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 59 time to evaluate : 0.382 Fit side-chains outliers start: 6 outliers final: 5 residues processed: 65 average time/residue: 1.1220 time to fit residues: 75.6069 Evaluate side-chains 59 residues out of total 420 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 54 time to evaluate : 0.403 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 5 residues processed: 0 time to fit residues: 0.5613 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 42 optimal weight: 3.9990 chunk 37 optimal weight: 1.9990 chunk 21 optimal weight: 3.9990 chunk 12 optimal weight: 0.9980 chunk 25 optimal weight: 5.9990 chunk 20 optimal weight: 7.9990 chunk 39 optimal weight: 3.9990 chunk 15 optimal weight: 2.9990 chunk 23 optimal weight: 0.8980 chunk 29 optimal weight: 7.9990 chunk 45 optimal weight: 2.9990 overall best weight: 1.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 4 ASN A 38 GLN A 234 GLN A 246 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7850 moved from start: 0.1299 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 3983 Z= 0.261 Angle : 0.550 6.068 5419 Z= 0.277 Chirality : 0.039 0.142 631 Planarity : 0.005 0.031 673 Dihedral : 5.210 69.430 549 Min Nonbonded Distance : 2.120 Molprobity Statistics. All-atom Clashscore : 5.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.02 % Favored : 98.98 % Rotamer: Outliers : 4.52 % Allowed : 18.57 % Favored : 76.90 % 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: 1.16 (0.37), residues: 492 helix: 0.94 (0.26), residues: 372 sheet: 0.55 (1.38), residues: 10 loop : 0.61 (0.63), residues: 110 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 213 HIS 0.003 0.001 HIS A 48 PHE 0.015 0.001 PHE A 191 TYR 0.026 0.002 TYR A 264 ARG 0.002 0.000 ARG A 395 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 984 Ramachandran restraints generated. 492 Oldfield, 0 Emsley, 492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 984 Ramachandran restraints generated. 492 Oldfield, 0 Emsley, 492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 420 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 60 time to evaluate : 0.419 Fit side-chains outliers start: 19 outliers final: 11 residues processed: 75 average time/residue: 1.0550 time to fit residues: 82.3690 Evaluate side-chains 68 residues out of total 420 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 57 time to evaluate : 0.471 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 8 residues processed: 3 average time/residue: 0.0560 time to fit residues: 0.8830 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 25 optimal weight: 5.9990 chunk 14 optimal weight: 3.9990 chunk 37 optimal weight: 1.9990 chunk 30 optimal weight: 6.9990 chunk 12 optimal weight: 1.9990 chunk 45 optimal weight: 5.9990 chunk 49 optimal weight: 9.9990 chunk 40 optimal weight: 0.9980 chunk 15 optimal weight: 0.6980 chunk 36 optimal weight: 1.9990 chunk 44 optimal weight: 0.7980 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 38 GLN A 439 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7837 moved from start: 0.1690 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 3983 Z= 0.196 Angle : 0.483 6.219 5419 Z= 0.240 Chirality : 0.037 0.134 631 Planarity : 0.004 0.031 673 Dihedral : 5.040 66.830 549 Min Nonbonded Distance : 2.117 Molprobity Statistics. All-atom Clashscore : 5.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.42 % Favored : 98.58 % Rotamer: Outliers : 6.19 % Allowed : 17.38 % Favored : 76.43 % 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 (0.38), residues: 492 helix: 1.00 (0.26), residues: 373 sheet: 0.63 (1.35), residues: 10 loop : 0.67 (0.63), residues: 109 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A 213 HIS 0.002 0.001 HIS A 48 PHE 0.013 0.001 PHE A 351 TYR 0.019 0.001 TYR A 264 ARG 0.002 0.000 ARG A 293 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 984 Ramachandran restraints generated. 492 Oldfield, 0 Emsley, 492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 984 Ramachandran restraints generated. 492 Oldfield, 0 Emsley, 492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 420 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 62 time to evaluate : 0.381 Fit side-chains revert: symmetry clash outliers start: 26 outliers final: 14 residues processed: 82 average time/residue: 0.9367 time to fit residues: 80.0160 Evaluate side-chains 71 residues out of total 420 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 57 time to evaluate : 0.394 Switching outliers to nearest non-outliers outliers start: 14 outliers final: 12 residues processed: 2 average time/residue: 0.0397 time to fit residues: 0.6926 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 34 optimal weight: 5.9990 chunk 23 optimal weight: 2.9990 chunk 5 optimal weight: 4.9990 chunk 21 optimal weight: 3.9990 chunk 30 optimal weight: 2.9990 chunk 45 optimal weight: 3.9990 chunk 48 optimal weight: 8.9990 chunk 43 optimal weight: 0.9990 chunk 13 optimal weight: 0.9980 chunk 40 optimal weight: 2.9990 chunk 27 optimal weight: 0.2980 overall best weight: 1.6586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 38 GLN A 234 GLN A 439 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7853 moved from start: 0.1865 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 3983 Z= 0.230 Angle : 0.508 7.667 5419 Z= 0.250 Chirality : 0.038 0.138 631 Planarity : 0.004 0.032 673 Dihedral : 5.150 67.955 549 Min Nonbonded Distance : 2.110 Molprobity Statistics. All-atom Clashscore : 5.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.02 % Favored : 98.98 % Rotamer: Outliers : 5.48 % Allowed : 17.14 % Favored : 77.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.20 (0.38), residues: 492 helix: 0.96 (0.26), residues: 373 sheet: 0.23 (1.37), residues: 10 loop : 0.67 (0.63), residues: 109 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 213 HIS 0.003 0.001 HIS A 48 PHE 0.012 0.001 PHE A 191 TYR 0.017 0.001 TYR A 264 ARG 0.001 0.000 ARG A 131 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 984 Ramachandran restraints generated. 492 Oldfield, 0 Emsley, 492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 984 Ramachandran restraints generated. 492 Oldfield, 0 Emsley, 492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 420 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 61 time to evaluate : 0.421 Fit side-chains revert: symmetry clash outliers start: 23 outliers final: 16 residues processed: 81 average time/residue: 0.8955 time to fit residues: 75.6983 Evaluate side-chains 75 residues out of total 420 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 59 time to evaluate : 0.395 Switching outliers to nearest non-outliers outliers start: 16 outliers final: 14 residues processed: 2 average time/residue: 0.0402 time to fit residues: 0.7145 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 0 optimal weight: 10.0000 chunk 35 optimal weight: 2.9990 chunk 19 optimal weight: 9.9990 chunk 41 optimal weight: 0.9980 chunk 33 optimal weight: 0.9990 chunk 24 optimal weight: 0.7980 chunk 43 optimal weight: 9.9990 chunk 12 optimal weight: 2.9990 chunk 16 optimal weight: 4.9990 chunk 9 optimal weight: 2.9990 chunk 28 optimal weight: 5.9990 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 38 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7860 moved from start: 0.2036 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 3983 Z= 0.238 Angle : 0.503 5.556 5419 Z= 0.250 Chirality : 0.038 0.138 631 Planarity : 0.004 0.032 673 Dihedral : 5.243 68.750 549 Min Nonbonded Distance : 2.134 Molprobity Statistics. All-atom Clashscore : 5.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.61 % Favored : 99.39 % Rotamer: Outliers : 5.71 % Allowed : 17.38 % Favored : 76.90 % 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: 1.11 (0.37), residues: 492 helix: 0.92 (0.26), residues: 373 sheet: 0.08 (1.45), residues: 10 loop : 0.60 (0.63), residues: 109 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP A 213 HIS 0.003 0.001 HIS A 48 PHE 0.012 0.001 PHE A 191 TYR 0.017 0.001 TYR A 264 ARG 0.001 0.000 ARG A 336 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 984 Ramachandran restraints generated. 492 Oldfield, 0 Emsley, 492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 984 Ramachandran restraints generated. 492 Oldfield, 0 Emsley, 492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 420 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 58 time to evaluate : 0.441 Fit side-chains revert: symmetry clash outliers start: 24 outliers final: 18 residues processed: 77 average time/residue: 0.8525 time to fit residues: 68.8318 Evaluate side-chains 75 residues out of total 420 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 57 time to evaluate : 0.429 Switching outliers to nearest non-outliers outliers start: 18 outliers final: 14 residues processed: 4 average time/residue: 0.0793 time to fit residues: 1.0368 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 11 optimal weight: 0.5980 chunk 48 optimal weight: 0.5980 chunk 40 optimal weight: 0.9980 chunk 22 optimal weight: 0.6980 chunk 4 optimal weight: 0.0870 chunk 16 optimal weight: 0.8980 chunk 25 optimal weight: 2.9990 chunk 46 optimal weight: 0.9980 chunk 5 optimal weight: 9.9990 chunk 27 optimal weight: 0.9990 chunk 35 optimal weight: 2.9990 overall best weight: 0.5758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 38 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7812 moved from start: 0.2164 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 3983 Z= 0.148 Angle : 0.468 8.015 5419 Z= 0.229 Chirality : 0.036 0.124 631 Planarity : 0.003 0.031 673 Dihedral : 4.799 62.617 549 Min Nonbonded Distance : 2.128 Molprobity Statistics. All-atom Clashscore : 5.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.81 % Favored : 99.19 % Rotamer: Outliers : 4.52 % Allowed : 18.33 % Favored : 77.14 % 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: 1.41 (0.38), residues: 492 helix: 1.12 (0.27), residues: 373 sheet: 0.03 (1.45), residues: 10 loop : 0.78 (0.64), residues: 109 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP A 213 HIS 0.002 0.000 HIS A 217 PHE 0.014 0.001 PHE A 351 TYR 0.024 0.001 TYR A 264 ARG 0.001 0.000 ARG A 394 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 984 Ramachandran restraints generated. 492 Oldfield, 0 Emsley, 492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 984 Ramachandran restraints generated. 492 Oldfield, 0 Emsley, 492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 420 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 60 time to evaluate : 0.439 Fit side-chains revert: symmetry clash outliers start: 19 outliers final: 16 residues processed: 78 average time/residue: 0.9164 time to fit residues: 74.6453 Evaluate side-chains 74 residues out of total 420 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 58 time to evaluate : 0.382 Switching outliers to nearest non-outliers outliers start: 16 outliers final: 15 residues processed: 1 average time/residue: 0.0373 time to fit residues: 0.6614 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 27 optimal weight: 0.8980 chunk 40 optimal weight: 5.9990 chunk 48 optimal weight: 0.3980 chunk 30 optimal weight: 8.9990 chunk 29 optimal weight: 5.9990 chunk 22 optimal weight: 2.9990 chunk 19 optimal weight: 0.9990 chunk 28 optimal weight: 0.6980 chunk 14 optimal weight: 3.9990 chunk 9 optimal weight: 0.9980 chunk 32 optimal weight: 4.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 38 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7817 moved from start: 0.2284 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 3983 Z= 0.160 Angle : 0.477 6.535 5419 Z= 0.234 Chirality : 0.036 0.138 631 Planarity : 0.003 0.030 673 Dihedral : 4.708 61.460 549 Min Nonbonded Distance : 2.146 Molprobity Statistics. All-atom Clashscore : 5.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.81 % Favored : 99.19 % Rotamer: Outliers : 5.24 % Allowed : 17.86 % Favored : 76.90 % 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: 1.48 (0.38), residues: 492 helix: 1.16 (0.27), residues: 373 sheet: -0.02 (1.58), residues: 10 loop : 0.85 (0.64), residues: 109 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP A 213 HIS 0.002 0.000 HIS A 217 PHE 0.012 0.001 PHE A 351 TYR 0.021 0.001 TYR A 264 ARG 0.001 0.000 ARG A 394 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 984 Ramachandran restraints generated. 492 Oldfield, 0 Emsley, 492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 984 Ramachandran restraints generated. 492 Oldfield, 0 Emsley, 492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 420 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 58 time to evaluate : 0.606 Fit side-chains revert: symmetry clash outliers start: 22 outliers final: 16 residues processed: 78 average time/residue: 0.9643 time to fit residues: 78.4789 Evaluate side-chains 74 residues out of total 420 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 58 time to evaluate : 0.421 Switching outliers to nearest non-outliers outliers start: 16 outliers final: 15 residues processed: 1 average time/residue: 0.0388 time to fit residues: 0.6541 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 23 optimal weight: 3.9990 chunk 4 optimal weight: 0.9980 chunk 37 optimal weight: 0.9980 chunk 43 optimal weight: 8.9990 chunk 46 optimal weight: 2.9990 chunk 42 optimal weight: 0.6980 chunk 44 optimal weight: 0.5980 chunk 27 optimal weight: 8.9990 chunk 19 optimal weight: 3.9990 chunk 35 optimal weight: 2.9990 chunk 13 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 4 ASN A 38 GLN ** A 295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7821 moved from start: 0.2440 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 3983 Z= 0.162 Angle : 0.465 5.871 5419 Z= 0.231 Chirality : 0.036 0.124 631 Planarity : 0.004 0.031 673 Dihedral : 4.657 60.591 549 Min Nonbonded Distance : 2.158 Molprobity Statistics. All-atom Clashscore : 5.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.81 % Favored : 99.19 % Rotamer: Outliers : 4.52 % Allowed : 19.29 % Favored : 76.19 % 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: 1.53 (0.38), residues: 492 helix: 1.20 (0.27), residues: 373 sheet: -0.01 (1.67), residues: 10 loop : 0.84 (0.64), residues: 109 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP A 213 HIS 0.002 0.001 HIS A 217 PHE 0.011 0.001 PHE A 351 TYR 0.021 0.001 TYR A 264 ARG 0.001 0.000 ARG A 394 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 984 Ramachandran restraints generated. 492 Oldfield, 0 Emsley, 492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 984 Ramachandran restraints generated. 492 Oldfield, 0 Emsley, 492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 420 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 60 time to evaluate : 0.403 Fit side-chains revert: symmetry clash outliers start: 19 outliers final: 17 residues processed: 77 average time/residue: 0.9701 time to fit residues: 77.9265 Evaluate side-chains 75 residues out of total 420 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 58 time to evaluate : 0.429 Switching outliers to nearest non-outliers outliers start: 17 outliers final: 15 residues processed: 2 average time/residue: 0.0439 time to fit residues: 0.7419 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 40 optimal weight: 5.9990 chunk 42 optimal weight: 0.5980 chunk 44 optimal weight: 0.9980 chunk 29 optimal weight: 7.9990 chunk 47 optimal weight: 1.9990 chunk 28 optimal weight: 10.0000 chunk 22 optimal weight: 0.8980 chunk 33 optimal weight: 0.9990 chunk 49 optimal weight: 1.9990 chunk 45 optimal weight: 0.7980 chunk 39 optimal weight: 3.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 4 ASN A 38 GLN ** A 295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7818 moved from start: 0.2509 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 3983 Z= 0.162 Angle : 0.463 5.523 5419 Z= 0.230 Chirality : 0.036 0.123 631 Planarity : 0.004 0.030 673 Dihedral : 4.624 60.196 549 Min Nonbonded Distance : 2.153 Molprobity Statistics. All-atom Clashscore : 5.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.02 % Favored : 98.98 % Rotamer: Outliers : 4.29 % Allowed : 19.29 % Favored : 76.43 % 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: 1.43 (0.38), residues: 492 helix: 1.16 (0.27), residues: 374 sheet: 0.03 (1.72), residues: 10 loop : 0.68 (0.63), residues: 108 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.002 TRP A 213 HIS 0.002 0.001 HIS A 217 PHE 0.011 0.001 PHE A 351 TYR 0.021 0.001 TYR A 264 ARG 0.001 0.000 ARG A 290 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 984 Ramachandran restraints generated. 492 Oldfield, 0 Emsley, 492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 984 Ramachandran restraints generated. 492 Oldfield, 0 Emsley, 492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 420 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 57 time to evaluate : 0.399 Fit side-chains revert: symmetry clash outliers start: 18 outliers final: 16 residues processed: 74 average time/residue: 0.9515 time to fit residues: 73.3782 Evaluate side-chains 71 residues out of total 420 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 55 time to evaluate : 0.409 Switching outliers to nearest non-outliers outliers start: 16 outliers final: 15 residues processed: 1 average time/residue: 0.0357 time to fit residues: 0.6015 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 4 optimal weight: 0.8980 chunk 30 optimal weight: 5.9990 chunk 24 optimal weight: 2.9990 chunk 31 optimal weight: 1.9990 chunk 42 optimal weight: 0.9990 chunk 12 optimal weight: 1.9990 chunk 36 optimal weight: 3.9990 chunk 5 optimal weight: 2.9990 chunk 11 optimal weight: 3.9990 chunk 39 optimal weight: 6.9990 chunk 16 optimal weight: 1.9990 overall best weight: 1.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 4 ASN A 38 GLN ** A 295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7853 moved from start: 0.2505 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 3983 Z= 0.224 Angle : 0.508 9.375 5419 Z= 0.250 Chirality : 0.038 0.130 631 Planarity : 0.004 0.031 673 Dihedral : 5.024 65.897 549 Min Nonbonded Distance : 2.130 Molprobity Statistics. All-atom Clashscore : 5.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.81 % Favored : 99.19 % Rotamer: Outliers : 4.29 % Allowed : 19.52 % Favored : 76.19 % 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: 1.30 (0.38), residues: 492 helix: 1.06 (0.27), residues: 375 sheet: 0.08 (1.75), residues: 10 loop : 0.62 (0.63), residues: 107 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.045 0.003 TRP A 213 HIS 0.003 0.001 HIS A 48 PHE 0.012 0.001 PHE A 191 TYR 0.020 0.002 TYR A 482 ARG 0.003 0.000 ARG A 290 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 984 Ramachandran restraints generated. 492 Oldfield, 0 Emsley, 492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 984 Ramachandran restraints generated. 492 Oldfield, 0 Emsley, 492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 74 residues out of total 420 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 56 time to evaluate : 0.433 Fit side-chains outliers start: 18 outliers final: 15 residues processed: 74 average time/residue: 0.9238 time to fit residues: 71.2846 Evaluate side-chains 72 residues out of total 420 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 57 time to evaluate : 0.414 Switching outliers to nearest non-outliers outliers start: 15 outliers final: 15 residues processed: 0 time to fit residues: 0.5703 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 40 optimal weight: 4.9990 chunk 5 optimal weight: 0.8980 chunk 7 optimal weight: 0.4980 chunk 34 optimal weight: 1.9990 chunk 2 optimal weight: 2.9990 chunk 28 optimal weight: 1.9990 chunk 45 optimal weight: 6.9990 chunk 26 optimal weight: 9.9990 chunk 1 optimal weight: 1.9990 chunk 31 optimal weight: 0.9990 chunk 30 optimal weight: 8.9990 overall best weight: 1.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 4 ASN A 38 GLN ** A 295 ASN ** 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 = 0.3932 r_free = 0.3932 target = 0.165777 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3509 r_free = 0.3509 target = 0.126227 restraints weight = 4356.880| |-----------------------------------------------------------------------------| r_work (start): 0.3438 rms_B_bonded: 1.99 r_work: 0.3312 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.3183 rms_B_bonded: 4.50 restraints_weight: 0.2500 r_work (final): 0.3183 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8130 moved from start: 0.2593 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 3983 Z= 0.202 Angle : 0.500 8.803 5419 Z= 0.249 Chirality : 0.037 0.129 631 Planarity : 0.004 0.031 673 Dihedral : 4.984 65.385 549 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 5.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.02 % Favored : 98.98 % Rotamer: Outliers : 4.52 % Allowed : 19.52 % Favored : 75.95 % 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 (0.38), residues: 492 helix: 1.06 (0.27), residues: 374 sheet: -0.10 (1.66), residues: 10 loop : 0.76 (0.64), residues: 108 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.048 0.003 TRP A 213 HIS 0.002 0.001 HIS A 48 PHE 0.011 0.001 PHE A 351 TYR 0.019 0.001 TYR A 482 ARG 0.001 0.000 ARG A 131 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1801.31 seconds wall clock time: 32 minutes 46.13 seconds (1966.13 seconds total)