Starting phenix.real_space_refine on Fri Dec 27 08:13:03 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8hj3_34831/12_2024/8hj3_34831_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8hj3_34831/12_2024/8hj3_34831.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.29 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8hj3_34831/12_2024/8hj3_34831.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8hj3_34831/12_2024/8hj3_34831.map" model { file = "/net/cci-nas-00/data/ceres_data/8hj3_34831/12_2024/8hj3_34831_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8hj3_34831/12_2024/8hj3_34831_neut.cif" } resolution = 3.29 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= 0.001 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: 5 Type Number sf(0) Gaussians P 3 5.49 5 S 14 5.16 5 C 2083 2.51 5 N 553 2.21 5 O 621 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 10 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/chem_data/mon_lib" Total number of atoms: 3274 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 3226 Number of conformers: 1 Conformer: "" Number of residues, atoms: 416, 3226 Classifications: {'peptide': 416} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 20, 'TRANS': 395} Unresolved non-hydrogen bonds: 39 Unresolved non-hydrogen angles: 44 Unresolved non-hydrogen dihedrals: 34 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1, 'ARG:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 21 Chain: "A" Number of atoms: 48 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 48 Unusual residues: {'NAP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 3.04, per 1000 atoms: 0.93 Number of scatterers: 3274 At special positions: 0 Unit cell: (67.048, 72.964, 71.978, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 14 16.00 P 3 15.00 O 621 8.00 N 553 7.00 C 2083 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.88 Conformation dependent library (CDL) restraints added in 412.7 milliseconds 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 758 Finding SS restraints... Secondary structure from input PDB file: 16 helices and 2 sheets defined 54.6% alpha, 12.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.37 Creating SS restraints... Processing helix chain 'A' and resid 4 through 19 removed outlier: 3.527A pdb=" N GLU A 8 " --> pdb=" O ILE A 4 " (cutoff:3.500A) Processing helix chain 'A' and resid 24 through 33 Processing helix chain 'A' and resid 79 through 97 removed outlier: 3.774A pdb=" N TRP A 92 " --> pdb=" O THR A 88 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N VAL A 97 " --> pdb=" O LYS A 93 " (cutoff:3.500A) Processing helix chain 'A' and resid 116 through 132 Processing helix chain 'A' and resid 133 through 135 No H-bonds generated for 'chain 'A' and resid 133 through 135' Processing helix chain 'A' and resid 149 through 165 Processing helix chain 'A' and resid 169 through 174 removed outlier: 3.807A pdb=" N ILE A 174 " --> pdb=" O PHE A 171 " (cutoff:3.500A) Processing helix chain 'A' and resid 189 through 207 Processing helix chain 'A' and resid 221 through 236 removed outlier: 3.720A pdb=" N GLY A 236 " --> pdb=" O LYS A 232 " (cutoff:3.500A) Processing helix chain 'A' and resid 256 through 268 Processing helix chain 'A' and resid 280 through 286 removed outlier: 3.833A pdb=" N GLU A 286 " --> pdb=" O GLU A 282 " (cutoff:3.500A) Processing helix chain 'A' and resid 323 through 333 Processing helix chain 'A' and resid 339 through 344 Processing helix chain 'A' and resid 344 through 361 removed outlier: 4.471A pdb=" N VAL A 348 " --> pdb=" O ASN A 344 " (cutoff:3.500A) Processing helix chain 'A' and resid 365 through 391 Processing helix chain 'A' and resid 394 through 415 Processing sheet with id=AA1, first strand: chain 'A' and resid 36 through 45 removed outlier: 6.572A pdb=" N GLY A 103 " --> pdb=" O HIS A 61 " (cutoff:3.500A) removed outlier: 5.936A pdb=" N LYS A 69 " --> pdb=" O GLY A 104 " (cutoff:3.500A) removed outlier: 8.056A pdb=" N GLY A 106 " --> pdb=" O LYS A 69 " (cutoff:3.500A) removed outlier: 6.133A pdb=" N GLY A 71 " --> pdb=" O GLY A 106 " (cutoff:3.500A) removed outlier: 8.240A pdb=" N ILE A 108 " --> pdb=" O GLY A 71 " (cutoff:3.500A) removed outlier: 6.780A pdb=" N ARG A 73 " --> pdb=" O ILE A 108 " (cutoff:3.500A) removed outlier: 6.863A pdb=" N THR A 68 " --> pdb=" O ILE A 141 " (cutoff:3.500A) removed outlier: 7.933A pdb=" N ALA A 143 " --> pdb=" O THR A 68 " (cutoff:3.500A) removed outlier: 6.702A pdb=" N GLY A 70 " --> pdb=" O ALA A 143 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 277 through 279 removed outlier: 4.397A pdb=" N ALA A 241 " --> pdb=" O ILE A 215 " (cutoff:3.500A) removed outlier: 6.355A pdb=" N LEU A 292 " --> pdb=" O ALA A 315 " (cutoff:3.500A) 186 hydrogen bonds defined for protein. 543 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: 0.99 Time building geometry restraints manager: 1.04 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 1062 1.34 - 1.46: 724 1.46 - 1.58: 1533 1.58 - 1.69: 5 1.69 - 1.81: 27 Bond restraints: 3351 Sorted by residual: bond pdb=" O2B NAP A 501 " pdb=" P2B NAP A 501 " ideal model delta sigma weight residual 1.736 1.614 0.122 2.00e-02 2.50e+03 3.74e+01 bond pdb=" C1D NAP A 501 " pdb=" O4D NAP A 501 " ideal model delta sigma weight residual 1.375 1.427 -0.052 2.00e-02 2.50e+03 6.76e+00 bond pdb=" N LYS A 389 " pdb=" CA LYS A 389 " ideal model delta sigma weight residual 1.458 1.488 -0.030 1.28e-02 6.10e+03 5.61e+00 bond pdb=" C5D NAP A 501 " pdb=" O5D NAP A 501 " ideal model delta sigma weight residual 1.403 1.450 -0.047 2.00e-02 2.50e+03 5.51e+00 bond pdb=" N HIS A 388 " pdb=" CA HIS A 388 " ideal model delta sigma weight residual 1.458 1.488 -0.031 1.33e-02 5.65e+03 5.37e+00 ... (remaining 3346 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.51: 4298 1.51 - 3.03: 209 3.03 - 4.54: 41 4.54 - 6.06: 8 6.06 - 7.57: 5 Bond angle restraints: 4561 Sorted by residual: angle pdb=" C TRP A 89 " pdb=" N MET A 90 " pdb=" CA MET A 90 " ideal model delta sigma weight residual 121.58 114.33 7.25 1.95e+00 2.63e-01 1.38e+01 angle pdb=" CA MET A 153 " pdb=" CB MET A 153 " pdb=" CG MET A 153 " ideal model delta sigma weight residual 114.10 106.80 7.30 2.00e+00 2.50e-01 1.33e+01 angle pdb=" N MET A 90 " pdb=" CA MET A 90 " pdb=" CB MET A 90 " ideal model delta sigma weight residual 110.41 116.33 -5.92 1.68e+00 3.54e-01 1.24e+01 angle pdb=" N GLY A 70 " pdb=" CA GLY A 70 " pdb=" C GLY A 70 " ideal model delta sigma weight residual 110.87 115.58 -4.71 1.54e+00 4.22e-01 9.37e+00 angle pdb=" CA MET A 90 " pdb=" CB MET A 90 " pdb=" CG MET A 90 " ideal model delta sigma weight residual 114.10 120.10 -6.00 2.00e+00 2.50e-01 9.01e+00 ... (remaining 4556 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.65: 1829 17.65 - 35.29: 154 35.29 - 52.94: 38 52.94 - 70.59: 7 70.59 - 88.23: 4 Dihedral angle restraints: 2032 sinusoidal: 843 harmonic: 1189 Sorted by residual: dihedral pdb=" CA MET A 90 " pdb=" C MET A 90 " pdb=" N THR A 91 " pdb=" CA THR A 91 " ideal model delta harmonic sigma weight residual 180.00 159.61 20.39 0 5.00e+00 4.00e-02 1.66e+01 dihedral pdb=" CA TYR A 101 " pdb=" C TYR A 101 " pdb=" N GLY A 102 " pdb=" CA GLY A 102 " ideal model delta harmonic sigma weight residual 180.00 161.15 18.85 0 5.00e+00 4.00e-02 1.42e+01 dihedral pdb=" CB GLU A 288 " pdb=" CG GLU A 288 " pdb=" CD GLU A 288 " pdb=" OE1 GLU A 288 " ideal model delta sinusoidal sigma weight residual 0.00 -88.23 88.23 1 3.00e+01 1.11e-03 1.03e+01 ... (remaining 2029 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.040: 346 0.040 - 0.081: 99 0.081 - 0.121: 55 0.121 - 0.161: 0 0.161 - 0.202: 1 Chirality restraints: 501 Sorted by residual: chirality pdb=" CA MET A 90 " pdb=" N MET A 90 " pdb=" C MET A 90 " pdb=" CB MET A 90 " both_signs ideal model delta sigma weight residual False 2.51 2.31 0.20 2.00e-01 2.50e+01 1.02e+00 chirality pdb=" CA ILE A 108 " pdb=" N ILE A 108 " pdb=" C ILE A 108 " pdb=" CB ILE A 108 " both_signs ideal model delta sigma weight residual False 2.43 2.55 -0.12 2.00e-01 2.50e+01 3.64e-01 chirality pdb=" CA ILE A 37 " pdb=" N ILE A 37 " pdb=" C ILE A 37 " pdb=" CB ILE A 37 " both_signs ideal model delta sigma weight residual False 2.43 2.55 -0.12 2.00e-01 2.50e+01 3.52e-01 ... (remaining 498 not shown) Planarity restraints: 579 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1D NAP A 501 " 0.053 2.00e-02 2.50e+03 7.24e-02 1.05e+02 pdb=" C2N NAP A 501 " -0.128 2.00e-02 2.50e+03 pdb=" C3N NAP A 501 " -0.032 2.00e-02 2.50e+03 pdb=" C4N NAP A 501 " -0.073 2.00e-02 2.50e+03 pdb=" C5N NAP A 501 " 0.046 2.00e-02 2.50e+03 pdb=" C6N NAP A 501 " 0.036 2.00e-02 2.50e+03 pdb=" C7N NAP A 501 " 0.113 2.00e-02 2.50e+03 pdb=" N1N NAP A 501 " -0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ILE A 141 " 0.034 5.00e-02 4.00e+02 5.18e-02 4.29e+00 pdb=" N PRO A 142 " -0.090 5.00e-02 4.00e+02 pdb=" CA PRO A 142 " 0.027 5.00e-02 4.00e+02 pdb=" CD PRO A 142 " 0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 197 " -0.013 2.00e-02 2.50e+03 1.55e-02 4.19e+00 pdb=" CG PHE A 197 " 0.035 2.00e-02 2.50e+03 pdb=" CD1 PHE A 197 " -0.015 2.00e-02 2.50e+03 pdb=" CD2 PHE A 197 " -0.005 2.00e-02 2.50e+03 pdb=" CE1 PHE A 197 " 0.004 2.00e-02 2.50e+03 pdb=" CE2 PHE A 197 " -0.006 2.00e-02 2.50e+03 pdb=" CZ PHE A 197 " -0.000 2.00e-02 2.50e+03 ... (remaining 576 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 358 2.74 - 3.28: 3489 3.28 - 3.82: 5963 3.82 - 4.36: 6952 4.36 - 4.90: 11711 Nonbonded interactions: 28473 Sorted by model distance: nonbonded pdb=" OD1 ASP A 327 " pdb=" NE2 GLN A 337 " model vdw 2.200 3.120 nonbonded pdb=" NH1 ARG A 73 " pdb=" OE2 GLU A 78 " model vdw 2.253 3.120 nonbonded pdb=" O TYR A 20 " pdb=" NZ LYS A 391 " model vdw 2.264 3.120 nonbonded pdb=" O ILE A 309 " pdb=" NZ LYS A 333 " model vdw 2.286 3.120 nonbonded pdb=" N GLU A 325 " pdb=" OE1 GLU A 325 " model vdw 2.298 3.120 ... (remaining 28468 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: 1.120 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.140 Check model and map are aligned: 0.030 Set scattering table: 0.050 Process input model: 13.870 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.000 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.270 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7558 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.122 3351 Z= 0.334 Angle : 0.802 7.569 4561 Z= 0.454 Chirality : 0.046 0.202 501 Planarity : 0.005 0.072 579 Dihedral : 14.797 88.231 1274 Min Nonbonded Distance : 2.200 Molprobity Statistics. All-atom Clashscore : 16.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.62 % Favored : 96.38 % Rotamer: Outliers : 0.30 % Allowed : 0.61 % Favored : 99.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.21 (0.42), residues: 414 helix: 1.79 (0.35), residues: 206 sheet: 0.24 (0.68), residues: 64 loop : -0.31 (0.53), residues: 144 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP A 92 HIS 0.002 0.001 HIS A 61 PHE 0.035 0.003 PHE A 197 TYR 0.013 0.001 TYR A 132 ARG 0.004 0.000 ARG A 73 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 65 residues out of total 339 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 64 time to evaluate : 0.360 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 388 HIS cc_start: 0.7164 (OUTLIER) cc_final: 0.6792 (t70) outliers start: 1 outliers final: 0 residues processed: 65 average time/residue: 0.1367 time to fit residues: 11.3328 Evaluate side-chains 57 residues out of total 339 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 56 time to evaluate : 0.365 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 388 HIS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 34 optimal weight: 1.9990 chunk 31 optimal weight: 8.9990 chunk 17 optimal weight: 0.9990 chunk 10 optimal weight: 0.7980 chunk 20 optimal weight: 4.9990 chunk 16 optimal weight: 0.8980 chunk 32 optimal weight: 1.9990 chunk 12 optimal weight: 0.7980 chunk 19 optimal weight: 0.6980 chunk 23 optimal weight: 7.9990 chunk 37 optimal weight: 0.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 278 ASN ** A 337 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7545 moved from start: 0.1195 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 3351 Z= 0.199 Angle : 0.579 8.529 4561 Z= 0.306 Chirality : 0.044 0.192 501 Planarity : 0.004 0.049 579 Dihedral : 8.820 64.492 519 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 12.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 0.91 % Allowed : 9.39 % Favored : 89.70 % 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 (0.41), residues: 414 helix: 2.00 (0.35), residues: 206 sheet: 0.02 (0.66), residues: 66 loop : -0.48 (0.52), residues: 142 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 92 HIS 0.002 0.001 HIS A 267 PHE 0.049 0.003 PHE A 197 TYR 0.008 0.001 TYR A 160 ARG 0.006 0.000 ARG A 73 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 64 residues out of total 339 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 61 time to evaluate : 0.383 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 197 PHE cc_start: 0.8456 (m-80) cc_final: 0.8233 (m-80) REVERT: A 388 HIS cc_start: 0.7089 (OUTLIER) cc_final: 0.6542 (t70) outliers start: 3 outliers final: 1 residues processed: 63 average time/residue: 0.1303 time to fit residues: 10.5386 Evaluate side-chains 55 residues out of total 339 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 53 time to evaluate : 0.383 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 261 LEU Chi-restraints excluded: chain A residue 388 HIS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 20 optimal weight: 3.9990 chunk 11 optimal weight: 0.8980 chunk 30 optimal weight: 8.9990 chunk 25 optimal weight: 8.9990 chunk 10 optimal weight: 7.9990 chunk 37 optimal weight: 3.9990 chunk 40 optimal weight: 0.4980 chunk 33 optimal weight: 7.9990 chunk 36 optimal weight: 0.8980 chunk 12 optimal weight: 2.9990 chunk 29 optimal weight: 2.9990 overall best weight: 1.6584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 267 HIS ** A 337 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7596 moved from start: 0.1547 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 3351 Z= 0.253 Angle : 0.580 8.608 4561 Z= 0.309 Chirality : 0.045 0.202 501 Planarity : 0.005 0.047 579 Dihedral : 8.516 58.725 519 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 12.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 2.42 % Allowed : 12.12 % Favored : 85.45 % 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: 1.14 (0.41), residues: 414 helix: 1.95 (0.34), residues: 207 sheet: 0.10 (0.66), residues: 66 loop : -0.70 (0.51), residues: 141 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 92 HIS 0.004 0.001 HIS A 388 PHE 0.036 0.003 PHE A 197 TYR 0.009 0.001 TYR A 132 ARG 0.004 0.000 ARG A 73 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 63 residues out of total 339 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 55 time to evaluate : 0.377 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 20 TYR cc_start: 0.6939 (m-10) cc_final: 0.6715 (m-10) REVERT: A 388 HIS cc_start: 0.7257 (OUTLIER) cc_final: 0.6511 (t70) outliers start: 8 outliers final: 5 residues processed: 59 average time/residue: 0.1409 time to fit residues: 10.6025 Evaluate side-chains 57 residues out of total 339 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 51 time to evaluate : 0.405 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 SER Chi-restraints excluded: chain A residue 53 VAL Chi-restraints excluded: chain A residue 261 LEU Chi-restraints excluded: chain A residue 290 ASP Chi-restraints excluded: chain A residue 371 GLU Chi-restraints excluded: chain A residue 388 HIS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 36 optimal weight: 0.8980 chunk 28 optimal weight: 8.9990 chunk 19 optimal weight: 0.7980 chunk 4 optimal weight: 1.9990 chunk 17 optimal weight: 0.0270 chunk 25 optimal weight: 0.6980 chunk 37 optimal weight: 0.8980 chunk 39 optimal weight: 0.7980 chunk 35 optimal weight: 0.9990 chunk 10 optimal weight: 2.9990 chunk 33 optimal weight: 3.9990 overall best weight: 0.6438 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 267 HIS ** A 337 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7525 moved from start: 0.1908 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 3351 Z= 0.169 Angle : 0.547 8.610 4561 Z= 0.289 Chirality : 0.044 0.205 501 Planarity : 0.004 0.048 579 Dihedral : 8.040 55.559 519 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 11.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.11 % Favored : 95.89 % Rotamer: Outliers : 1.82 % Allowed : 12.42 % Favored : 85.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.20 (0.41), residues: 414 helix: 2.02 (0.34), residues: 212 sheet: 0.05 (0.67), residues: 66 loop : -0.76 (0.51), residues: 136 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 63 HIS 0.002 0.001 HIS A 388 PHE 0.019 0.002 PHE A 197 TYR 0.006 0.001 TYR A 400 ARG 0.004 0.000 ARG A 73 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 63 residues out of total 339 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 57 time to evaluate : 0.380 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 21 MET cc_start: 0.7654 (ptp) cc_final: 0.7165 (ptp) REVERT: A 25 GLU cc_start: 0.8033 (tp30) cc_final: 0.7719 (tp30) REVERT: A 388 HIS cc_start: 0.6643 (OUTLIER) cc_final: 0.6158 (t70) outliers start: 6 outliers final: 4 residues processed: 61 average time/residue: 0.1195 time to fit residues: 9.4187 Evaluate side-chains 58 residues out of total 339 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 53 time to evaluate : 0.457 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 SER Chi-restraints excluded: chain A residue 57 PHE Chi-restraints excluded: chain A residue 261 LEU Chi-restraints excluded: chain A residue 371 GLU Chi-restraints excluded: chain A residue 388 HIS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 22 optimal weight: 7.9990 chunk 0 optimal weight: 10.0000 chunk 29 optimal weight: 10.0000 chunk 16 optimal weight: 4.9990 chunk 33 optimal weight: 4.9990 chunk 27 optimal weight: 9.9990 chunk 20 optimal weight: 0.6980 chunk 35 optimal weight: 0.9990 chunk 10 optimal weight: 3.9990 chunk 13 optimal weight: 1.9990 chunk 7 optimal weight: 3.9990 overall best weight: 2.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 337 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7633 moved from start: 0.1872 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 3351 Z= 0.310 Angle : 0.611 9.259 4561 Z= 0.323 Chirality : 0.045 0.199 501 Planarity : 0.005 0.047 579 Dihedral : 7.926 53.956 519 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 13.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 3.33 % Allowed : 13.33 % Favored : 83.33 % 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: 0.97 (0.40), residues: 414 helix: 1.81 (0.34), residues: 211 sheet: -0.20 (0.65), residues: 66 loop : -0.72 (0.51), residues: 137 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 89 HIS 0.006 0.002 HIS A 388 PHE 0.018 0.003 PHE A 197 TYR 0.010 0.001 TYR A 132 ARG 0.002 0.000 ARG A 165 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 339 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 55 time to evaluate : 0.394 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 11 outliers final: 10 residues processed: 62 average time/residue: 0.1507 time to fit residues: 11.8237 Evaluate side-chains 63 residues out of total 339 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 53 time to evaluate : 0.350 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 SER Chi-restraints excluded: chain A residue 53 VAL Chi-restraints excluded: chain A residue 57 PHE Chi-restraints excluded: chain A residue 75 HIS Chi-restraints excluded: chain A residue 226 TYR Chi-restraints excluded: chain A residue 239 VAL Chi-restraints excluded: chain A residue 261 LEU Chi-restraints excluded: chain A residue 277 THR Chi-restraints excluded: chain A residue 290 ASP Chi-restraints excluded: chain A residue 371 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 23 optimal weight: 1.9990 chunk 9 optimal weight: 0.0570 chunk 39 optimal weight: 4.9990 chunk 32 optimal weight: 0.8980 chunk 18 optimal weight: 0.2980 chunk 3 optimal weight: 0.0000 chunk 13 optimal weight: 0.6980 chunk 20 optimal weight: 2.9990 chunk 38 optimal weight: 1.9990 chunk 4 optimal weight: 4.9990 chunk 22 optimal weight: 1.9990 overall best weight: 0.3902 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 337 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7528 moved from start: 0.2168 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 3351 Z= 0.168 Angle : 0.561 9.616 4561 Z= 0.298 Chirality : 0.044 0.210 501 Planarity : 0.004 0.048 579 Dihedral : 7.140 59.781 517 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 12.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.86 % Favored : 96.14 % Rotamer: Outliers : 2.42 % Allowed : 13.33 % Favored : 84.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.17 (0.41), residues: 414 helix: 2.06 (0.34), residues: 211 sheet: -0.18 (0.66), residues: 64 loop : -0.74 (0.50), residues: 139 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 263 HIS 0.002 0.001 HIS A 394 PHE 0.019 0.002 PHE A 341 TYR 0.015 0.001 TYR A 160 ARG 0.001 0.000 ARG A 129 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 65 residues out of total 339 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 57 time to evaluate : 0.428 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 21 MET cc_start: 0.7587 (ptp) cc_final: 0.6976 (ptp) REVERT: A 93 LYS cc_start: 0.8512 (mttt) cc_final: 0.8215 (mtmt) outliers start: 8 outliers final: 6 residues processed: 60 average time/residue: 0.1481 time to fit residues: 11.3584 Evaluate side-chains 57 residues out of total 339 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 51 time to evaluate : 0.392 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 SER Chi-restraints excluded: chain A residue 53 VAL Chi-restraints excluded: chain A residue 57 PHE Chi-restraints excluded: chain A residue 226 TYR Chi-restraints excluded: chain A residue 261 LEU Chi-restraints excluded: chain A residue 371 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 28 optimal weight: 4.9990 chunk 22 optimal weight: 6.9990 chunk 33 optimal weight: 1.9990 chunk 39 optimal weight: 6.9990 chunk 24 optimal weight: 8.9990 chunk 18 optimal weight: 6.9990 chunk 15 optimal weight: 1.9990 chunk 23 optimal weight: 8.9990 chunk 11 optimal weight: 1.9990 chunk 7 optimal weight: 1.9990 chunk 25 optimal weight: 0.9990 overall best weight: 1.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 337 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7607 moved from start: 0.2178 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 3351 Z= 0.264 Angle : 0.611 9.749 4561 Z= 0.321 Chirality : 0.045 0.219 501 Planarity : 0.004 0.047 579 Dihedral : 6.933 55.867 517 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 13.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 2.73 % Allowed : 13.94 % Favored : 83.33 % 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: 1.04 (0.40), residues: 414 helix: 1.89 (0.34), residues: 211 sheet: -0.23 (0.66), residues: 64 loop : -0.70 (0.51), residues: 139 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 63 HIS 0.006 0.002 HIS A 388 PHE 0.019 0.003 PHE A 197 TYR 0.010 0.001 TYR A 132 ARG 0.002 0.000 ARG A 200 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 64 residues out of total 339 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 55 time to evaluate : 0.413 Fit side-chains revert: symmetry clash REVERT: A 20 TYR cc_start: 0.6838 (m-10) cc_final: 0.6457 (m-10) REVERT: A 21 MET cc_start: 0.7664 (ptp) cc_final: 0.7104 (ptp) REVERT: A 93 LYS cc_start: 0.8577 (mttt) cc_final: 0.8302 (mtmt) outliers start: 9 outliers final: 7 residues processed: 61 average time/residue: 0.1427 time to fit residues: 11.1741 Evaluate side-chains 59 residues out of total 339 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 52 time to evaluate : 0.337 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 SER Chi-restraints excluded: chain A residue 53 VAL Chi-restraints excluded: chain A residue 57 PHE Chi-restraints excluded: chain A residue 226 TYR Chi-restraints excluded: chain A residue 239 VAL Chi-restraints excluded: chain A residue 261 LEU Chi-restraints excluded: chain A residue 290 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 26 optimal weight: 20.0000 chunk 19 optimal weight: 0.9980 chunk 3 optimal weight: 0.4980 chunk 31 optimal weight: 3.9990 chunk 35 optimal weight: 1.9990 chunk 37 optimal weight: 0.8980 chunk 34 optimal weight: 5.9990 chunk 36 optimal weight: 1.9990 chunk 22 optimal weight: 0.9980 chunk 16 optimal weight: 0.7980 chunk 28 optimal weight: 2.9990 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 337 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7559 moved from start: 0.2294 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 3351 Z= 0.200 Angle : 0.624 10.528 4561 Z= 0.330 Chirality : 0.045 0.223 501 Planarity : 0.004 0.047 579 Dihedral : 6.618 51.815 517 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 12.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.62 % Favored : 96.38 % Rotamer: Outliers : 2.12 % Allowed : 14.55 % Favored : 83.33 % 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: 0.93 (0.40), residues: 414 helix: 1.78 (0.34), residues: 211 sheet: -0.20 (0.66), residues: 64 loop : -0.75 (0.51), residues: 139 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 30 HIS 0.003 0.001 HIS A 388 PHE 0.039 0.003 PHE A 197 TYR 0.015 0.001 TYR A 160 ARG 0.001 0.000 ARG A 370 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 64 residues out of total 339 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 57 time to evaluate : 0.367 Fit side-chains revert: symmetry clash REVERT: A 20 TYR cc_start: 0.6785 (m-10) cc_final: 0.6387 (m-10) REVERT: A 21 MET cc_start: 0.7581 (ptp) cc_final: 0.7041 (ptp) REVERT: A 93 LYS cc_start: 0.8518 (mttt) cc_final: 0.8245 (mtmt) outliers start: 7 outliers final: 7 residues processed: 60 average time/residue: 0.1401 time to fit residues: 10.6420 Evaluate side-chains 63 residues out of total 339 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 56 time to evaluate : 0.369 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 SER Chi-restraints excluded: chain A residue 53 VAL Chi-restraints excluded: chain A residue 57 PHE Chi-restraints excluded: chain A residue 128 ILE Chi-restraints excluded: chain A residue 226 TYR Chi-restraints excluded: chain A residue 261 LEU Chi-restraints excluded: chain A residue 290 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 11 optimal weight: 1.9990 chunk 33 optimal weight: 0.9980 chunk 34 optimal weight: 5.9990 chunk 36 optimal weight: 1.9990 chunk 24 optimal weight: 6.9990 chunk 38 optimal weight: 2.9990 chunk 23 optimal weight: 6.9990 chunk 18 optimal weight: 0.0040 chunk 27 optimal weight: 5.9990 chunk 40 optimal weight: 4.9990 chunk 37 optimal weight: 0.9980 overall best weight: 1.1996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 337 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7572 moved from start: 0.2351 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 3351 Z= 0.226 Angle : 0.632 10.988 4561 Z= 0.338 Chirality : 0.045 0.221 501 Planarity : 0.004 0.047 579 Dihedral : 6.483 48.906 517 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 13.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 2.42 % Allowed : 15.15 % Favored : 82.42 % 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: 0.93 (0.41), residues: 414 helix: 1.72 (0.34), residues: 211 sheet: -0.38 (0.62), residues: 74 loop : -0.51 (0.54), residues: 129 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 89 HIS 0.004 0.001 HIS A 388 PHE 0.061 0.004 PHE A 197 TYR 0.014 0.001 TYR A 160 ARG 0.001 0.000 ARG A 165 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 64 residues out of total 339 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 56 time to evaluate : 0.345 Fit side-chains revert: symmetry clash REVERT: A 20 TYR cc_start: 0.6889 (m-10) cc_final: 0.6475 (m-10) REVERT: A 21 MET cc_start: 0.7596 (ptp) cc_final: 0.7035 (ptp) REVERT: A 90 MET cc_start: 0.7304 (pmm) cc_final: 0.6917 (pmm) REVERT: A 93 LYS cc_start: 0.8537 (mttt) cc_final: 0.8260 (mttp) outliers start: 8 outliers final: 8 residues processed: 60 average time/residue: 0.1423 time to fit residues: 10.8121 Evaluate side-chains 61 residues out of total 339 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 53 time to evaluate : 0.387 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 SER Chi-restraints excluded: chain A residue 53 VAL Chi-restraints excluded: chain A residue 57 PHE Chi-restraints excluded: chain A residue 128 ILE Chi-restraints excluded: chain A residue 226 TYR Chi-restraints excluded: chain A residue 239 VAL Chi-restraints excluded: chain A residue 261 LEU Chi-restraints excluded: chain A residue 290 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 32 optimal weight: 2.9990 chunk 3 optimal weight: 0.0270 chunk 25 optimal weight: 2.9990 chunk 19 optimal weight: 0.6980 chunk 34 optimal weight: 2.9990 chunk 9 optimal weight: 0.5980 chunk 29 optimal weight: 10.0000 chunk 4 optimal weight: 9.9990 chunk 13 optimal weight: 0.9990 chunk 33 optimal weight: 6.9990 chunk 6 optimal weight: 0.9990 overall best weight: 0.6642 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 337 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7527 moved from start: 0.2471 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 3351 Z= 0.188 Angle : 0.621 10.443 4561 Z= 0.330 Chirality : 0.045 0.216 501 Planarity : 0.004 0.047 579 Dihedral : 6.211 45.220 517 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 12.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.62 % Favored : 96.38 % Rotamer: Outliers : 2.12 % Allowed : 14.55 % Favored : 83.33 % 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: 0.88 (0.41), residues: 414 helix: 1.84 (0.34), residues: 211 sheet: -0.81 (0.68), residues: 66 loop : -0.62 (0.52), residues: 137 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 89 HIS 0.004 0.001 HIS A 388 PHE 0.062 0.003 PHE A 197 TYR 0.008 0.001 TYR A 132 ARG 0.001 0.000 ARG A 36 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 65 residues out of total 339 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 58 time to evaluate : 0.323 Fit side-chains revert: symmetry clash REVERT: A 20 TYR cc_start: 0.6815 (m-10) cc_final: 0.6437 (m-10) REVERT: A 21 MET cc_start: 0.7497 (ptp) cc_final: 0.6942 (ptp) REVERT: A 93 LYS cc_start: 0.8471 (mttt) cc_final: 0.8264 (mttp) outliers start: 7 outliers final: 6 residues processed: 61 average time/residue: 0.1393 time to fit residues: 10.8800 Evaluate side-chains 62 residues out of total 339 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 56 time to evaluate : 0.404 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 SER Chi-restraints excluded: chain A residue 53 VAL Chi-restraints excluded: chain A residue 57 PHE Chi-restraints excluded: chain A residue 128 ILE Chi-restraints excluded: chain A residue 226 TYR Chi-restraints excluded: chain A residue 261 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 28 optimal weight: 9.9990 chunk 1 optimal weight: 8.9990 chunk 23 optimal weight: 8.9990 chunk 37 optimal weight: 0.8980 chunk 21 optimal weight: 9.9990 chunk 27 optimal weight: 0.8980 chunk 26 optimal weight: 10.0000 chunk 24 optimal weight: 8.9990 chunk 16 optimal weight: 3.9990 chunk 15 optimal weight: 0.8980 chunk 40 optimal weight: 2.9990 overall best weight: 1.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 193 GLN A 234 GLN ** A 337 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4053 r_free = 0.4053 target = 0.142037 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3733 r_free = 0.3733 target = 0.122513 restraints weight = 8158.385| |-----------------------------------------------------------------------------| r_work (start): 0.3718 rms_B_bonded: 2.78 r_work: 0.3609 rms_B_bonded: 3.61 restraints_weight: 0.5000 r_work (final): 0.3609 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7819 moved from start: 0.2431 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 3351 Z= 0.290 Angle : 0.704 11.286 4561 Z= 0.367 Chirality : 0.046 0.214 501 Planarity : 0.005 0.048 579 Dihedral : 6.349 44.361 517 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 14.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 2.12 % Allowed : 15.45 % Favored : 82.42 % 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: 414 helix: 1.66 (0.34), residues: 211 sheet: -0.25 (0.63), residues: 72 loop : -0.65 (0.54), residues: 131 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 89 HIS 0.006 0.002 HIS A 388 PHE 0.062 0.004 PHE A 197 TYR 0.011 0.001 TYR A 132 ARG 0.002 0.000 ARG A 165 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1142.38 seconds wall clock time: 21 minutes 32.36 seconds (1292.36 seconds total)