Starting phenix.real_space_refine on Thu Mar 6 05:03:54 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ez3_28728/03_2025/8ez3_28728.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ez3_28728/03_2025/8ez3_28728.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8ez3_28728/03_2025/8ez3_28728.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ez3_28728/03_2025/8ez3_28728.map" model { file = "/net/cci-nas-00/data/ceres_data/8ez3_28728/03_2025/8ez3_28728.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ez3_28728/03_2025/8ez3_28728.cif" } resolution = 2.5 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 ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.002 sd= 0.123 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 26 5.16 5 C 3039 2.51 5 N 839 2.21 5 O 990 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 9 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib" Total number of atoms: 4894 Number of models: 1 Model: "" Number of chains: 5 Chain: "H" Number of atoms: 969 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 969 Classifications: {'peptide': 123} Link IDs: {'PTRANS': 4, 'TRANS': 118} Chain: "L" Number of atoms: 815 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 815 Classifications: {'peptide': 111} Incomplete info: {'backbone_only': 1} Link IDs: {'PTRANS': 8, 'TRANS': 102} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "A" Number of atoms: 2996 Number of conformers: 1 Conformer: "" Number of residues, atoms: 388, 2996 Classifications: {'peptide': 388} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PCIS': 2, 'PTRANS': 13, 'TRANS': 371} Chain: "B" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "A" Number of atoms: 53 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 53 Unusual residues: {'MAN': 1, 'NAG': 3} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Time building chain proxies: 4.09, per 1000 atoms: 0.84 Number of scatterers: 4894 At special positions: 0 Unit cell: (96.46, 80.56, 93.28, 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 26 16.00 O 990 8.00 N 839 7.00 C 3039 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=11, symmetry=0 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 92 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.03 Simple disulfide: pdb=" SG CYS A 92 " - pdb=" SG CYS A 417 " distance=2.03 Simple disulfide: pdb=" SG CYS A 124 " - pdb=" SG CYS A 129 " distance=2.03 Simple disulfide: pdb=" SG CYS A 175 " - pdb=" SG CYS A 193 " distance=2.03 Simple disulfide: pdb=" SG CYS A 183 " - pdb=" SG CYS A 230 " distance=2.03 Simple disulfide: pdb=" SG CYS A 232 " - pdb=" SG CYS A 237 " distance=2.03 Simple disulfide: pdb=" SG CYS A 278 " - pdb=" SG CYS A 291 " distance=2.03 Simple disulfide: pdb=" SG CYS A 280 " - pdb=" SG CYS A 289 " distance=2.03 Simple disulfide: pdb=" SG CYS A 318 " - pdb=" SG CYS A 337 " distance=2.03 Simple disulfide: pdb=" SG CYS A 421 " - pdb=" SG CYS A 447 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied ALPHA1-2 " MAN B 4 " - " MAN B 5 " ALPHA1-3 " BMA B 3 " - " MAN B 4 " BETA1-4 " NAG B 1 " - " NAG B 2 " " NAG B 2 " - " BMA B 3 " NAG-ASN " NAG A 502 " - " ASN A 146 " " NAG A 503 " - " ASN A 329 " " NAG A 504 " - " ASN A 234 " " NAG B 1 " - " ASN A 200 " Time building additional restraints: 1.20 Conformation dependent library (CDL) restraints added in 538.1 milliseconds 1232 Ramachandran restraints generated. 616 Oldfield, 0 Emsley, 616 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1122 Finding SS restraints... Secondary structure from input PDB file: 4 helices and 13 sheets defined 3.5% alpha, 43.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.59 Creating SS restraints... Processing helix chain 'L' and resid 27B through 30 Processing helix chain 'A' and resid 104 through 110 Processing helix chain 'A' and resid 142 through 146 removed outlier: 3.651A pdb=" N ASN A 146 " --> pdb=" O GLY A 143 " (cutoff:3.500A) Processing helix chain 'A' and resid 463 through 467 Processing sheet with id=AA1, first strand: chain 'H' and resid 3 through 7 Processing sheet with id=AA2, first strand: chain 'H' and resid 11 through 12 removed outlier: 6.642A pdb=" N TRP H 36 " --> pdb=" O ILE H 48 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'H' and resid 11 through 12 removed outlier: 4.054A pdb=" N HIS H 102 " --> pdb=" O ARG H 94 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'L' and resid 9 through 12 removed outlier: 6.396A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'L' and resid 9 through 12 Processing sheet with id=AA6, first strand: chain 'L' and resid 18 through 24 Processing sheet with id=AA7, first strand: chain 'A' and resid 96 through 102 removed outlier: 3.511A pdb=" N GLY A 96 " --> pdb=" O THR A 449 " (cutoff:3.500A) removed outlier: 6.512A pdb=" N VAL A 445 " --> pdb=" O PHE A 100 " (cutoff:3.500A) removed outlier: 4.697A pdb=" N LYS A 102 " --> pdb=" O ILE A 443 " (cutoff:3.500A) removed outlier: 7.329A pdb=" N ILE A 443 " --> pdb=" O LYS A 102 " (cutoff:3.500A) removed outlier: 5.618A pdb=" N ARG A 420 " --> pdb=" O GLY A 448 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 115 through 124 removed outlier: 4.820A pdb=" N TRP A 115 " --> pdb=" O THR A 138 " (cutoff:3.500A) removed outlier: 7.404A pdb=" N THR A 138 " --> pdb=" O TRP A 115 " (cutoff:3.500A) removed outlier: 7.636A pdb=" N THR A 117 " --> pdb=" O GLN A 136 " (cutoff:3.500A) removed outlier: 6.387A pdb=" N GLN A 136 " --> pdb=" O THR A 117 " (cutoff:3.500A) removed outlier: 5.696A pdb=" N GLU A 119 " --> pdb=" O LEU A 134 " (cutoff:3.500A) removed outlier: 4.197A pdb=" N LEU A 134 " --> pdb=" O GLU A 119 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N CYS A 175 " --> pdb=" O LEU A 158 " (cutoff:3.500A) removed outlier: 7.180A pdb=" N MET A 160 " --> pdb=" O GLN A 173 " (cutoff:3.500A) removed outlier: 5.738A pdb=" N GLN A 173 " --> pdb=" O MET A 160 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 179 through 184 removed outlier: 6.167A pdb=" N TYR A 207 " --> pdb=" O LEU A 211 " (cutoff:3.500A) removed outlier: 5.126A pdb=" N LEU A 211 " --> pdb=" O TYR A 207 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 223 through 224 removed outlier: 3.858A pdb=" N VAL A 231 " --> pdb=" O THR A 238 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 223 through 224 removed outlier: 6.624A pdb=" N GLU A 258 " --> pdb=" O ILE A 262 " (cutoff:3.500A) removed outlier: 5.441A pdb=" N ILE A 262 " --> pdb=" O GLU A 258 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 276 through 283 removed outlier: 5.249A pdb=" N GLU A 277 " --> pdb=" O ARG A 292 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N ARG A 292 " --> pdb=" O GLU A 277 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N SER A 311 " --> pdb=" O ASN A 306 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 352 through 356 removed outlier: 4.514A pdb=" N TRP A 352 " --> pdb=" O GLY A 363 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N GLY A 363 " --> pdb=" O TRP A 352 " (cutoff:3.500A) removed outlier: 6.982A pdb=" N SER A 372 " --> pdb=" O ASP A 399 " (cutoff:3.500A) removed outlier: 7.285A pdb=" N ASP A 399 " --> pdb=" O SER A 372 " (cutoff:3.500A) removed outlier: 6.276A pdb=" N TYR A 374 " --> pdb=" O ILE A 397 " (cutoff:3.500A) removed outlier: 4.584A pdb=" N LYS A 378 " --> pdb=" O ASN A 393 " (cutoff:3.500A) removed outlier: 5.082A pdb=" N ASN A 393 " --> pdb=" O LYS A 378 " (cutoff:3.500A) 171 hydrogen bonds defined for protein. 441 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: 1.55 Time building geometry restraints manager: 1.42 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: 1596 1.35 - 1.48: 1352 1.48 - 1.60: 2030 1.60 - 1.73: 0 1.73 - 1.85: 30 Bond restraints: 5008 Sorted by residual: bond pdb=" C1 NAG A 503 " pdb=" O5 NAG A 503 " ideal model delta sigma weight residual 1.406 1.482 -0.076 2.00e-02 2.50e+03 1.44e+01 bond pdb=" C5 MAN B 4 " pdb=" O5 MAN B 4 " ideal model delta sigma weight residual 1.418 1.449 -0.031 2.00e-02 2.50e+03 2.47e+00 bond pdb=" C2 BMA B 3 " pdb=" C3 BMA B 3 " ideal model delta sigma weight residual 1.544 1.513 0.031 2.00e-02 2.50e+03 2.41e+00 bond pdb=" C1 MAN B 4 " pdb=" O5 MAN B 4 " ideal model delta sigma weight residual 1.399 1.430 -0.031 2.00e-02 2.50e+03 2.33e+00 bond pdb=" C5 NAG A 503 " pdb=" O5 NAG A 503 " ideal model delta sigma weight residual 1.413 1.441 -0.028 2.00e-02 2.50e+03 2.01e+00 ... (remaining 5003 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.57: 6738 2.57 - 5.15: 62 5.15 - 7.72: 9 7.72 - 10.29: 0 10.29 - 12.86: 1 Bond angle restraints: 6810 Sorted by residual: angle pdb=" CA CYS A 417 " pdb=" CB CYS A 417 " pdb=" SG CYS A 417 " ideal model delta sigma weight residual 114.40 127.26 -12.86 2.30e+00 1.89e-01 3.13e+01 angle pdb=" C GLY L 50 " pdb=" N ASN L 51 " pdb=" CA ASN L 51 " ideal model delta sigma weight residual 121.54 128.05 -6.51 1.91e+00 2.74e-01 1.16e+01 angle pdb=" C HIS A 336 " pdb=" N CYS A 337 " pdb=" CA CYS A 337 " ideal model delta sigma weight residual 121.54 127.51 -5.97 1.91e+00 2.74e-01 9.77e+00 angle pdb=" C CYS A 417 " pdb=" CA CYS A 417 " pdb=" CB CYS A 417 " ideal model delta sigma weight residual 109.68 115.29 -5.61 1.98e+00 2.55e-01 8.04e+00 angle pdb=" C ARG A 430 " pdb=" N LYS A 431 " pdb=" CA LYS A 431 " ideal model delta sigma weight residual 121.70 126.41 -4.71 1.80e+00 3.09e-01 6.86e+00 ... (remaining 6805 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.03: 2777 23.03 - 46.05: 228 46.05 - 69.08: 49 69.08 - 92.11: 14 92.11 - 115.13: 7 Dihedral angle restraints: 3075 sinusoidal: 1309 harmonic: 1766 Sorted by residual: dihedral pdb=" CB CYS A 318 " pdb=" SG CYS A 318 " pdb=" SG CYS A 337 " pdb=" CB CYS A 337 " ideal model delta sinusoidal sigma weight residual 93.00 135.77 -42.77 1 1.00e+01 1.00e-02 2.55e+01 dihedral pdb=" CB CYS H 22 " pdb=" SG CYS H 22 " pdb=" SG CYS H 92 " pdb=" CB CYS H 92 " ideal model delta sinusoidal sigma weight residual 93.00 50.93 42.07 1 1.00e+01 1.00e-02 2.47e+01 dihedral pdb=" CA ASN L 51 " pdb=" C ASN L 51 " pdb=" N SER L 52 " pdb=" CA SER L 52 " ideal model delta harmonic sigma weight residual 180.00 158.50 21.50 0 5.00e+00 4.00e-02 1.85e+01 ... (remaining 3072 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.052: 604 0.052 - 0.105: 135 0.105 - 0.157: 27 0.157 - 0.210: 0 0.210 - 0.262: 1 Chirality restraints: 767 Sorted by residual: chirality pdb=" C5 BMA B 3 " pdb=" C4 BMA B 3 " pdb=" C6 BMA B 3 " pdb=" O5 BMA B 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.54 0.26 2.00e-01 2.50e+01 1.72e+00 chirality pdb=" C2 MAN B 4 " pdb=" C1 MAN B 4 " pdb=" C3 MAN B 4 " pdb=" O2 MAN B 4 " both_signs ideal model delta sigma weight residual False 2.52 2.66 -0.14 2.00e-01 2.50e+01 4.89e-01 chirality pdb=" CA VAL L 39 " pdb=" N VAL L 39 " pdb=" C VAL L 39 " pdb=" CB VAL L 39 " both_signs ideal model delta sigma weight residual False 2.44 2.58 -0.14 2.00e-01 2.50e+01 4.74e-01 ... (remaining 764 not shown) Planarity restraints: 874 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN A 329 " 0.001 2.00e-02 2.50e+03 1.61e-02 3.23e+00 pdb=" CG ASN A 329 " -0.020 2.00e-02 2.50e+03 pdb=" OD1 ASN A 329 " 0.019 2.00e-02 2.50e+03 pdb=" ND2 ASN A 329 " -0.016 2.00e-02 2.50e+03 pdb=" C1 NAG A 503 " 0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASP A 125 " -0.027 5.00e-02 4.00e+02 4.04e-02 2.61e+00 pdb=" N PRO A 126 " 0.070 5.00e-02 4.00e+02 pdb=" CA PRO A 126 " -0.021 5.00e-02 4.00e+02 pdb=" CD PRO A 126 " -0.023 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 329 " 0.005 2.00e-02 2.50e+03 9.49e-03 9.00e-01 pdb=" CG ASN A 329 " -0.016 2.00e-02 2.50e+03 pdb=" OD1 ASN A 329 " 0.006 2.00e-02 2.50e+03 pdb=" ND2 ASN A 329 " 0.006 2.00e-02 2.50e+03 ... (remaining 871 not shown) Histogram of nonbonded interaction distances: 2.08 - 2.64: 107 2.64 - 3.21: 4308 3.21 - 3.77: 8010 3.77 - 4.34: 11814 4.34 - 4.90: 19472 Nonbonded interactions: 43711 Sorted by model distance: nonbonded pdb=" NE ARG A 403 " pdb=" OE1 GLN A 432 " model vdw 2.080 3.120 nonbonded pdb=" OG SER A 331 " pdb=" O7 NAG A 503 " model vdw 2.147 3.040 nonbonded pdb=" OG SER A 219 " pdb=" OD2 ASP A 251 " model vdw 2.220 3.040 nonbonded pdb=" ND2 ASN H 56 " pdb=" O TYR A 284 " model vdw 2.252 3.120 nonbonded pdb=" O SER H 82B" pdb=" OG SER H 82B" model vdw 2.256 3.040 ... (remaining 43706 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== 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=0.39 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: 2.950 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.210 Check model and map are aligned: 0.040 Set scattering table: 0.050 Process input model: 16.120 Find NCS groups from input model: 0.050 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:12.320 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.760 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8319 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.076 5008 Z= 0.283 Angle : 0.639 12.864 6810 Z= 0.318 Chirality : 0.046 0.262 767 Planarity : 0.003 0.040 870 Dihedral : 18.429 115.131 1920 Min Nonbonded Distance : 2.080 Molprobity Statistics. All-atom Clashscore : 8.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.06 % Favored : 95.94 % Rotamer: Outliers : 4.85 % Allowed : 22.01 % Favored : 73.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.41 % Cis-general : 0.17 % 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: -0.81 (0.34), residues: 616 helix: -0.15 (2.39), residues: 6 sheet: -0.23 (0.34), residues: 223 loop : -0.71 (0.32), residues: 387 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 178 HIS 0.002 0.001 HIS A 336 PHE 0.011 0.002 PHE A 354 TYR 0.013 0.001 TYR A 121 ARG 0.004 0.000 ARG H 81 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1232 Ramachandran restraints generated. 616 Oldfield, 0 Emsley, 616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1232 Ramachandran restraints generated. 616 Oldfield, 0 Emsley, 616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 62 time to evaluate : 0.561 Fit side-chains revert: symmetry clash outliers start: 26 outliers final: 26 residues processed: 86 average time/residue: 0.8232 time to fit residues: 75.3270 Evaluate side-chains 87 residues out of total 536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 61 time to evaluate : 0.547 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 12 VAL Chi-restraints excluded: chain H residue 21 THR Chi-restraints excluded: chain H residue 25 SER Chi-restraints excluded: chain H residue 45 LEU Chi-restraints excluded: chain H residue 50 TYR Chi-restraints excluded: chain H residue 65 SER Chi-restraints excluded: chain H residue 97 SER Chi-restraints excluded: chain H residue 100 SER Chi-restraints excluded: chain H residue 107 THR Chi-restraints excluded: chain L residue 18 ARG Chi-restraints excluded: chain L residue 67 SER Chi-restraints excluded: chain L residue 69 THR Chi-restraints excluded: chain L residue 106 LEU Chi-restraints excluded: chain A residue 101 SER Chi-restraints excluded: chain A residue 140 LEU Chi-restraints excluded: chain A residue 148 THR Chi-restraints excluded: chain A residue 174 VAL Chi-restraints excluded: chain A residue 183 CYS Chi-restraints excluded: chain A residue 194 VAL Chi-restraints excluded: chain A residue 228 SER Chi-restraints excluded: chain A residue 238 THR Chi-restraints excluded: chain A residue 251 ASP Chi-restraints excluded: chain A residue 325 THR Chi-restraints excluded: chain A residue 329 ASN Chi-restraints excluded: chain A residue 407 SER Chi-restraints excluded: chain A residue 431 LYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 51 optimal weight: 0.8980 chunk 46 optimal weight: 0.7980 chunk 25 optimal weight: 0.9990 chunk 15 optimal weight: 5.9990 chunk 31 optimal weight: 1.9990 chunk 24 optimal weight: 0.8980 chunk 47 optimal weight: 0.9990 chunk 18 optimal weight: 0.1980 chunk 29 optimal weight: 4.9990 chunk 35 optimal weight: 0.9990 chunk 55 optimal weight: 4.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 76 ASN A 347 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.118718 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3039 r_free = 0.3039 target = 0.088403 restraints weight = 5685.554| |-----------------------------------------------------------------------------| r_work (start): 0.3046 rms_B_bonded: 2.23 r_work: 0.2919 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.2779 rms_B_bonded: 4.05 restraints_weight: 0.2500 r_work (final): 0.2779 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2787 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2787 r_free = 0.2787 target_work(ls_wunit_k1) = 0.071 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2787 r_free = 0.2787 target_work(ls_wunit_k1) = 0.071 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2787 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7866 moved from start: 0.0702 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 5008 Z= 0.226 Angle : 0.589 7.798 6810 Z= 0.312 Chirality : 0.047 0.191 767 Planarity : 0.004 0.043 870 Dihedral : 12.453 102.684 894 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 6.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.55 % Favored : 95.45 % Rotamer: Outliers : 5.04 % Allowed : 20.34 % Favored : 74.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.41 % Cis-general : 0.17 % 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: -0.77 (0.33), residues: 616 helix: -1.63 (1.63), residues: 7 sheet: -0.06 (0.34), residues: 222 loop : -0.75 (0.32), residues: 387 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 178 HIS 0.003 0.001 HIS A 336 PHE 0.013 0.002 PHE A 132 TYR 0.016 0.001 TYR A 121 ARG 0.004 0.000 ARG A 85 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1232 Ramachandran restraints generated. 616 Oldfield, 0 Emsley, 616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1232 Ramachandran restraints generated. 616 Oldfield, 0 Emsley, 616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 74 time to evaluate : 0.576 Fit side-chains revert: symmetry clash REVERT: A 142 ASN cc_start: 0.7785 (t0) cc_final: 0.7495 (t160) REVERT: A 304 ASP cc_start: 0.8586 (m-30) cc_final: 0.8366 (m-30) REVERT: A 430 ARG cc_start: 0.8326 (mmt90) cc_final: 0.7946 (mpt90) outliers start: 27 outliers final: 19 residues processed: 94 average time/residue: 0.8277 time to fit residues: 82.6167 Evaluate side-chains 87 residues out of total 536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 68 time to evaluate : 0.859 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 12 VAL Chi-restraints excluded: chain H residue 21 THR Chi-restraints excluded: chain H residue 45 LEU Chi-restraints excluded: chain H residue 50 TYR Chi-restraints excluded: chain H residue 87 THR Chi-restraints excluded: chain H residue 100 SER Chi-restraints excluded: chain H residue 107 THR Chi-restraints excluded: chain L residue 24 THR Chi-restraints excluded: chain L residue 67 SER Chi-restraints excluded: chain L residue 106 LEU Chi-restraints excluded: chain A residue 101 SER Chi-restraints excluded: chain A residue 140 LEU Chi-restraints excluded: chain A residue 157 THR Chi-restraints excluded: chain A residue 183 CYS Chi-restraints excluded: chain A residue 194 VAL Chi-restraints excluded: chain A residue 238 THR Chi-restraints excluded: chain A residue 325 THR Chi-restraints excluded: chain A residue 443 ILE Chi-restraints excluded: chain A residue 452 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 42 optimal weight: 5.9990 chunk 59 optimal weight: 4.9990 chunk 38 optimal weight: 0.9990 chunk 17 optimal weight: 0.6980 chunk 49 optimal weight: 4.9990 chunk 9 optimal weight: 5.9990 chunk 39 optimal weight: 0.0980 chunk 30 optimal weight: 2.9990 chunk 45 optimal weight: 1.9990 chunk 29 optimal weight: 0.9980 chunk 37 optimal weight: 2.9990 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 76 ASN L 27BASN A 131 GLN A 347 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.118494 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3037 r_free = 0.3037 target = 0.088271 restraints weight = 5739.684| |-----------------------------------------------------------------------------| r_work (start): 0.3041 rms_B_bonded: 2.22 r_work: 0.2915 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.2776 rms_B_bonded: 4.06 restraints_weight: 0.2500 r_work (final): 0.2776 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2788 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2788 r_free = 0.2788 target_work(ls_wunit_k1) = 0.071 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2788 r_free = 0.2788 target_work(ls_wunit_k1) = 0.071 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2788 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7868 moved from start: 0.0918 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 5008 Z= 0.253 Angle : 0.589 8.919 6810 Z= 0.308 Chirality : 0.047 0.202 767 Planarity : 0.004 0.043 870 Dihedral : 11.173 95.558 874 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 7.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.06 % Favored : 95.94 % Rotamer: Outliers : 4.29 % Allowed : 22.01 % Favored : 73.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.41 % Cis-general : 0.17 % 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: -0.80 (0.33), residues: 616 helix: -1.62 (1.65), residues: 7 sheet: -0.11 (0.33), residues: 222 loop : -0.74 (0.32), residues: 387 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 178 HIS 0.003 0.001 HIS A 336 PHE 0.012 0.002 PHE A 354 TYR 0.016 0.001 TYR A 121 ARG 0.004 0.000 ARG A 85 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1232 Ramachandran restraints generated. 616 Oldfield, 0 Emsley, 616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1232 Ramachandran restraints generated. 616 Oldfield, 0 Emsley, 616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 72 time to evaluate : 0.576 Fit side-chains revert: symmetry clash REVERT: A 142 ASN cc_start: 0.7947 (t0) cc_final: 0.7733 (t160) REVERT: A 304 ASP cc_start: 0.8353 (m-30) cc_final: 0.8131 (m-30) REVERT: A 430 ARG cc_start: 0.8254 (mmt90) cc_final: 0.7759 (mmm160) outliers start: 23 outliers final: 16 residues processed: 86 average time/residue: 1.0181 time to fit residues: 92.6211 Evaluate side-chains 85 residues out of total 536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 69 time to evaluate : 0.548 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 12 VAL Chi-restraints excluded: chain H residue 21 THR Chi-restraints excluded: chain H residue 50 TYR Chi-restraints excluded: chain H residue 87 THR Chi-restraints excluded: chain H residue 100 SER Chi-restraints excluded: chain L residue 24 THR Chi-restraints excluded: chain L residue 106 LEU Chi-restraints excluded: chain A residue 140 LEU Chi-restraints excluded: chain A residue 157 THR Chi-restraints excluded: chain A residue 174 VAL Chi-restraints excluded: chain A residue 183 CYS Chi-restraints excluded: chain A residue 194 VAL Chi-restraints excluded: chain A residue 307 VAL Chi-restraints excluded: chain A residue 407 SER Chi-restraints excluded: chain A residue 443 ILE Chi-restraints excluded: chain A residue 452 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 57 optimal weight: 3.9990 chunk 4 optimal weight: 4.9990 chunk 11 optimal weight: 3.9990 chunk 8 optimal weight: 6.9990 chunk 14 optimal weight: 2.9990 chunk 41 optimal weight: 6.9990 chunk 19 optimal weight: 10.0000 chunk 43 optimal weight: 0.6980 chunk 56 optimal weight: 0.7980 chunk 15 optimal weight: 0.6980 chunk 38 optimal weight: 1.9990 overall best weight: 1.4384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 76 ASN A 91 GLN A 131 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.116291 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3006 r_free = 0.3006 target = 0.086303 restraints weight = 5822.376| |-----------------------------------------------------------------------------| r_work (start): 0.3021 rms_B_bonded: 2.19 r_work: 0.2893 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.2754 rms_B_bonded: 4.01 restraints_weight: 0.2500 r_work (final): 0.2754 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2761 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2761 r_free = 0.2761 target_work(ls_wunit_k1) = 0.070 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2761 r_free = 0.2761 target_work(ls_wunit_k1) = 0.070 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2761 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7901 moved from start: 0.0987 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 5008 Z= 0.330 Angle : 0.607 9.728 6810 Z= 0.316 Chirality : 0.048 0.216 767 Planarity : 0.004 0.045 870 Dihedral : 10.350 88.212 867 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 6.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.38 % Favored : 95.62 % Rotamer: Outliers : 5.41 % Allowed : 20.15 % Favored : 74.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.41 % Cis-general : 0.17 % 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: -0.90 (0.33), residues: 616 helix: -1.63 (1.60), residues: 7 sheet: -0.23 (0.33), residues: 222 loop : -0.78 (0.31), residues: 387 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 178 HIS 0.004 0.001 HIS A 336 PHE 0.013 0.002 PHE A 354 TYR 0.016 0.002 TYR A 121 ARG 0.004 0.000 ARG A 85 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1232 Ramachandran restraints generated. 616 Oldfield, 0 Emsley, 616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1232 Ramachandran restraints generated. 616 Oldfield, 0 Emsley, 616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 65 time to evaluate : 0.510 Fit side-chains revert: symmetry clash outliers start: 29 outliers final: 21 residues processed: 85 average time/residue: 0.8928 time to fit residues: 80.1645 Evaluate side-chains 81 residues out of total 536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 60 time to evaluate : 0.492 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 12 VAL Chi-restraints excluded: chain H residue 21 THR Chi-restraints excluded: chain H residue 50 TYR Chi-restraints excluded: chain H residue 87 THR Chi-restraints excluded: chain H residue 107 THR Chi-restraints excluded: chain L residue 24 THR Chi-restraints excluded: chain L residue 27 SER Chi-restraints excluded: chain L residue 106 LEU Chi-restraints excluded: chain A residue 140 LEU Chi-restraints excluded: chain A residue 157 THR Chi-restraints excluded: chain A residue 174 VAL Chi-restraints excluded: chain A residue 183 CYS Chi-restraints excluded: chain A residue 194 VAL Chi-restraints excluded: chain A residue 261 LYS Chi-restraints excluded: chain A residue 307 VAL Chi-restraints excluded: chain A residue 325 THR Chi-restraints excluded: chain A residue 407 SER Chi-restraints excluded: chain A residue 426 LEU Chi-restraints excluded: chain A residue 431 LYS Chi-restraints excluded: chain A residue 443 ILE Chi-restraints excluded: chain A residue 452 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 59 optimal weight: 0.9990 chunk 27 optimal weight: 0.9980 chunk 29 optimal weight: 0.6980 chunk 16 optimal weight: 7.9990 chunk 53 optimal weight: 2.9990 chunk 20 optimal weight: 5.9990 chunk 38 optimal weight: 4.9990 chunk 5 optimal weight: 2.9990 chunk 10 optimal weight: 0.5980 chunk 23 optimal weight: 1.9990 chunk 11 optimal weight: 2.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 76 ASN H 101 GLN A 91 GLN A 131 GLN A 347 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.117368 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3028 r_free = 0.3028 target = 0.087668 restraints weight = 5801.788| |-----------------------------------------------------------------------------| r_work (start): 0.3039 rms_B_bonded: 2.19 r_work: 0.2912 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.2773 rms_B_bonded: 4.03 restraints_weight: 0.2500 r_work (final): 0.2773 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2780 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2780 r_free = 0.2780 target_work(ls_wunit_k1) = 0.071 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2780 r_free = 0.2780 target_work(ls_wunit_k1) = 0.071 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2780 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7878 moved from start: 0.1061 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 5008 Z= 0.259 Angle : 0.587 10.304 6810 Z= 0.304 Chirality : 0.047 0.201 767 Planarity : 0.003 0.043 870 Dihedral : 9.647 81.789 866 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 6.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.06 % Favored : 95.94 % Rotamer: Outliers : 5.41 % Allowed : 20.52 % Favored : 74.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.41 % Cis-general : 0.17 % 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: -0.86 (0.33), residues: 616 helix: -1.63 (1.55), residues: 7 sheet: -0.23 (0.33), residues: 222 loop : -0.73 (0.31), residues: 387 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 178 HIS 0.003 0.001 HIS A 336 PHE 0.012 0.002 PHE A 354 TYR 0.015 0.001 TYR A 121 ARG 0.003 0.000 ARG A 85 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1232 Ramachandran restraints generated. 616 Oldfield, 0 Emsley, 616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1232 Ramachandran restraints generated. 616 Oldfield, 0 Emsley, 616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 69 time to evaluate : 0.968 Fit side-chains revert: symmetry clash outliers start: 29 outliers final: 21 residues processed: 87 average time/residue: 1.2446 time to fit residues: 114.7562 Evaluate side-chains 85 residues out of total 536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 64 time to evaluate : 0.613 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 12 VAL Chi-restraints excluded: chain H residue 21 THR Chi-restraints excluded: chain H residue 50 TYR Chi-restraints excluded: chain H residue 87 THR Chi-restraints excluded: chain H residue 107 THR Chi-restraints excluded: chain L residue 24 THR Chi-restraints excluded: chain L residue 27 SER Chi-restraints excluded: chain L residue 106 LEU Chi-restraints excluded: chain A residue 140 LEU Chi-restraints excluded: chain A residue 157 THR Chi-restraints excluded: chain A residue 174 VAL Chi-restraints excluded: chain A residue 183 CYS Chi-restraints excluded: chain A residue 194 VAL Chi-restraints excluded: chain A residue 307 VAL Chi-restraints excluded: chain A residue 325 THR Chi-restraints excluded: chain A residue 338 LEU Chi-restraints excluded: chain A residue 407 SER Chi-restraints excluded: chain A residue 426 LEU Chi-restraints excluded: chain A residue 431 LYS Chi-restraints excluded: chain A residue 443 ILE Chi-restraints excluded: chain A residue 452 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 54 optimal weight: 2.9990 chunk 41 optimal weight: 2.9990 chunk 15 optimal weight: 6.9990 chunk 24 optimal weight: 0.0970 chunk 44 optimal weight: 0.9990 chunk 9 optimal weight: 2.9990 chunk 60 optimal weight: 0.9980 chunk 16 optimal weight: 0.9990 chunk 59 optimal weight: 1.9990 chunk 32 optimal weight: 1.9990 chunk 46 optimal weight: 2.9990 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 76 ASN H 101 GLN A 91 GLN A 131 GLN A 142 ASN A 347 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.118014 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3029 r_free = 0.3029 target = 0.087782 restraints weight = 5828.540| |-----------------------------------------------------------------------------| r_work (start): 0.3043 rms_B_bonded: 2.22 r_work: 0.2916 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.2778 rms_B_bonded: 4.05 restraints_weight: 0.2500 r_work (final): 0.2778 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2785 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2785 r_free = 0.2785 target_work(ls_wunit_k1) = 0.071 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2785 r_free = 0.2785 target_work(ls_wunit_k1) = 0.071 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2785 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7904 moved from start: 0.1120 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 5008 Z= 0.253 Angle : 0.584 10.818 6810 Z= 0.302 Chirality : 0.047 0.202 767 Planarity : 0.003 0.043 870 Dihedral : 8.995 70.517 866 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 6.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.38 % Favored : 95.62 % Rotamer: Outliers : 5.22 % Allowed : 21.46 % Favored : 73.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.41 % Cis-general : 0.17 % 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: -0.84 (0.33), residues: 616 helix: -1.45 (1.58), residues: 7 sheet: -0.21 (0.33), residues: 222 loop : -0.72 (0.31), residues: 387 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 178 HIS 0.002 0.001 HIS A 336 PHE 0.013 0.002 PHE A 354 TYR 0.015 0.001 TYR A 121 ARG 0.003 0.000 ARG A 85 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1232 Ramachandran restraints generated. 616 Oldfield, 0 Emsley, 616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1232 Ramachandran restraints generated. 616 Oldfield, 0 Emsley, 616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 65 time to evaluate : 0.558 Fit side-chains revert: symmetry clash outliers start: 28 outliers final: 20 residues processed: 84 average time/residue: 1.0964 time to fit residues: 97.0942 Evaluate side-chains 87 residues out of total 536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 67 time to evaluate : 0.691 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 50 TYR Chi-restraints excluded: chain H residue 87 THR Chi-restraints excluded: chain H residue 107 THR Chi-restraints excluded: chain L residue 24 THR Chi-restraints excluded: chain L residue 27 SER Chi-restraints excluded: chain A residue 140 LEU Chi-restraints excluded: chain A residue 157 THR Chi-restraints excluded: chain A residue 174 VAL Chi-restraints excluded: chain A residue 183 CYS Chi-restraints excluded: chain A residue 194 VAL Chi-restraints excluded: chain A residue 229 GLU Chi-restraints excluded: chain A residue 261 LYS Chi-restraints excluded: chain A residue 307 VAL Chi-restraints excluded: chain A residue 325 THR Chi-restraints excluded: chain A residue 338 LEU Chi-restraints excluded: chain A residue 407 SER Chi-restraints excluded: chain A residue 426 LEU Chi-restraints excluded: chain A residue 431 LYS Chi-restraints excluded: chain A residue 443 ILE Chi-restraints excluded: chain A residue 452 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 21 optimal weight: 4.9990 chunk 42 optimal weight: 3.9990 chunk 7 optimal weight: 7.9990 chunk 26 optimal weight: 0.0370 chunk 29 optimal weight: 0.9990 chunk 34 optimal weight: 4.9990 chunk 19 optimal weight: 9.9990 chunk 58 optimal weight: 0.9980 chunk 33 optimal weight: 1.9990 chunk 3 optimal weight: 0.9980 chunk 53 optimal weight: 2.9990 overall best weight: 1.0062 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 76 ASN H 101 GLN A 91 GLN A 131 GLN A 142 ASN A 347 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.118107 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3039 r_free = 0.3039 target = 0.088359 restraints weight = 5762.779| |-----------------------------------------------------------------------------| r_work (start): 0.3051 rms_B_bonded: 2.18 r_work: 0.2924 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.2786 rms_B_bonded: 4.02 restraints_weight: 0.2500 r_work (final): 0.2786 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2793 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2793 r_free = 0.2793 target_work(ls_wunit_k1) = 0.072 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2793 r_free = 0.2793 target_work(ls_wunit_k1) = 0.072 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2793 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7873 moved from start: 0.1190 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 5008 Z= 0.250 Angle : 0.585 10.749 6810 Z= 0.302 Chirality : 0.047 0.193 767 Planarity : 0.003 0.043 870 Dihedral : 8.331 58.618 862 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 6.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.06 % Favored : 95.94 % Rotamer: Outliers : 5.78 % Allowed : 20.52 % Favored : 73.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.41 % Cis-general : 0.17 % 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: -0.75 (0.33), residues: 616 helix: -1.48 (1.58), residues: 7 sheet: -0.24 (0.32), residues: 237 loop : -0.60 (0.32), residues: 372 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 178 HIS 0.002 0.001 HIS A 336 PHE 0.013 0.002 PHE A 354 TYR 0.015 0.001 TYR A 121 ARG 0.003 0.000 ARG H 81 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1232 Ramachandran restraints generated. 616 Oldfield, 0 Emsley, 616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1232 Ramachandran restraints generated. 616 Oldfield, 0 Emsley, 616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 66 time to evaluate : 0.574 Fit side-chains revert: symmetry clash REVERT: L 72 SER cc_start: 0.8248 (OUTLIER) cc_final: 0.8029 (t) outliers start: 31 outliers final: 22 residues processed: 88 average time/residue: 1.3818 time to fit residues: 128.1447 Evaluate side-chains 87 residues out of total 536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 64 time to evaluate : 0.521 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 21 THR Chi-restraints excluded: chain H residue 50 TYR Chi-restraints excluded: chain H residue 74 SER Chi-restraints excluded: chain H residue 87 THR Chi-restraints excluded: chain H residue 107 THR Chi-restraints excluded: chain L residue 24 THR Chi-restraints excluded: chain L residue 27 SER Chi-restraints excluded: chain L residue 72 SER Chi-restraints excluded: chain L residue 106 LEU Chi-restraints excluded: chain A residue 140 LEU Chi-restraints excluded: chain A residue 157 THR Chi-restraints excluded: chain A residue 174 VAL Chi-restraints excluded: chain A residue 183 CYS Chi-restraints excluded: chain A residue 194 VAL Chi-restraints excluded: chain A residue 261 LYS Chi-restraints excluded: chain A residue 307 VAL Chi-restraints excluded: chain A residue 325 THR Chi-restraints excluded: chain A residue 338 LEU Chi-restraints excluded: chain A residue 407 SER Chi-restraints excluded: chain A residue 426 LEU Chi-restraints excluded: chain A residue 431 LYS Chi-restraints excluded: chain A residue 443 ILE Chi-restraints excluded: chain A residue 452 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 5 optimal weight: 0.2980 chunk 21 optimal weight: 4.9990 chunk 1 optimal weight: 0.9980 chunk 48 optimal weight: 1.9990 chunk 59 optimal weight: 2.9990 chunk 12 optimal weight: 3.9990 chunk 56 optimal weight: 1.9990 chunk 36 optimal weight: 2.9990 chunk 30 optimal weight: 2.9990 chunk 28 optimal weight: 1.9990 chunk 27 optimal weight: 1.9990 overall best weight: 1.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 76 ASN A 91 GLN A 131 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.116981 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3010 r_free = 0.3010 target = 0.086630 restraints weight = 5847.035| |-----------------------------------------------------------------------------| r_work (start): 0.3022 rms_B_bonded: 2.21 r_work: 0.2898 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.2758 rms_B_bonded: 4.02 restraints_weight: 0.2500 r_work (final): 0.2758 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2762 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2762 r_free = 0.2762 target_work(ls_wunit_k1) = 0.070 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2762 r_free = 0.2762 target_work(ls_wunit_k1) = 0.070 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2762 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7928 moved from start: 0.1153 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 5008 Z= 0.331 Angle : 0.606 9.503 6810 Z= 0.316 Chirality : 0.047 0.194 767 Planarity : 0.004 0.045 870 Dihedral : 8.115 58.990 862 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 7.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.71 % Favored : 95.29 % Rotamer: Outliers : 5.04 % Allowed : 22.01 % Favored : 72.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.41 % Cis-general : 0.17 % 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 (0.32), residues: 616 helix: -1.45 (1.58), residues: 7 sheet: -0.28 (0.33), residues: 222 loop : -0.71 (0.31), residues: 387 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 178 HIS 0.003 0.001 HIS A 336 PHE 0.014 0.002 PHE A 354 TYR 0.016 0.002 TYR A 121 ARG 0.003 0.000 ARG H 81 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1232 Ramachandran restraints generated. 616 Oldfield, 0 Emsley, 616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1232 Ramachandran restraints generated. 616 Oldfield, 0 Emsley, 616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 64 time to evaluate : 0.988 Fit side-chains revert: symmetry clash REVERT: H 38 ARG cc_start: 0.8928 (OUTLIER) cc_final: 0.7542 (ptt-90) REVERT: L 72 SER cc_start: 0.8326 (OUTLIER) cc_final: 0.8107 (t) REVERT: A 85 ARG cc_start: 0.8467 (mtt180) cc_final: 0.8182 (mtt180) outliers start: 27 outliers final: 22 residues processed: 84 average time/residue: 1.2253 time to fit residues: 109.1913 Evaluate side-chains 87 residues out of total 536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 63 time to evaluate : 0.603 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 21 THR Chi-restraints excluded: chain H residue 38 ARG Chi-restraints excluded: chain H residue 50 TYR Chi-restraints excluded: chain H residue 74 SER Chi-restraints excluded: chain H residue 87 THR Chi-restraints excluded: chain H residue 107 THR Chi-restraints excluded: chain L residue 24 THR Chi-restraints excluded: chain L residue 27 SER Chi-restraints excluded: chain L residue 72 SER Chi-restraints excluded: chain L residue 106 LEU Chi-restraints excluded: chain A residue 140 LEU Chi-restraints excluded: chain A residue 157 THR Chi-restraints excluded: chain A residue 174 VAL Chi-restraints excluded: chain A residue 183 CYS Chi-restraints excluded: chain A residue 194 VAL Chi-restraints excluded: chain A residue 261 LYS Chi-restraints excluded: chain A residue 307 VAL Chi-restraints excluded: chain A residue 325 THR Chi-restraints excluded: chain A residue 338 LEU Chi-restraints excluded: chain A residue 407 SER Chi-restraints excluded: chain A residue 426 LEU Chi-restraints excluded: chain A residue 431 LYS Chi-restraints excluded: chain A residue 443 ILE Chi-restraints excluded: chain A residue 452 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 35 optimal weight: 1.9990 chunk 49 optimal weight: 2.9990 chunk 44 optimal weight: 0.9990 chunk 33 optimal weight: 0.9980 chunk 41 optimal weight: 0.9990 chunk 59 optimal weight: 2.9990 chunk 25 optimal weight: 0.6980 chunk 19 optimal weight: 9.9990 chunk 36 optimal weight: 0.6980 chunk 17 optimal weight: 5.9990 chunk 42 optimal weight: 1.9990 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 76 ASN H 101 GLN A 131 GLN A 347 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.118823 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3052 r_free = 0.3052 target = 0.089131 restraints weight = 5697.276| |-----------------------------------------------------------------------------| r_work (start): 0.3063 rms_B_bonded: 2.17 r_work: 0.2936 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.2799 rms_B_bonded: 4.02 restraints_weight: 0.2500 r_work (final): 0.2799 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2803 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2803 r_free = 0.2803 target_work(ls_wunit_k1) = 0.072 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2803 r_free = 0.2803 target_work(ls_wunit_k1) = 0.072 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2803 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7871 moved from start: 0.1207 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 5008 Z= 0.233 Angle : 0.571 7.835 6810 Z= 0.298 Chirality : 0.046 0.162 767 Planarity : 0.003 0.043 870 Dihedral : 7.577 58.079 862 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 6.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.22 % Favored : 95.78 % Rotamer: Outliers : 4.29 % Allowed : 22.76 % Favored : 72.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.41 % Cis-general : 0.17 % 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: -0.83 (0.33), residues: 616 helix: -1.45 (1.61), residues: 7 sheet: -0.26 (0.33), residues: 227 loop : -0.67 (0.32), residues: 382 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 178 HIS 0.002 0.001 HIS A 336 PHE 0.013 0.002 PHE A 354 TYR 0.014 0.001 TYR A 121 ARG 0.003 0.000 ARG A 85 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1232 Ramachandran restraints generated. 616 Oldfield, 0 Emsley, 616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1232 Ramachandran restraints generated. 616 Oldfield, 0 Emsley, 616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 72 time to evaluate : 0.464 Fit side-chains revert: symmetry clash REVERT: L 72 SER cc_start: 0.8253 (OUTLIER) cc_final: 0.8038 (t) REVERT: A 140 LEU cc_start: 0.8995 (OUTLIER) cc_final: 0.8593 (tp) REVERT: A 142 ASN cc_start: 0.7873 (t0) cc_final: 0.7672 (t160) outliers start: 23 outliers final: 18 residues processed: 87 average time/residue: 1.2890 time to fit residues: 118.3076 Evaluate side-chains 89 residues out of total 536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 69 time to evaluate : 0.549 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 21 THR Chi-restraints excluded: chain H residue 50 TYR Chi-restraints excluded: chain H residue 74 SER Chi-restraints excluded: chain H residue 87 THR Chi-restraints excluded: chain H residue 107 THR Chi-restraints excluded: chain L residue 24 THR Chi-restraints excluded: chain L residue 27 SER Chi-restraints excluded: chain L residue 72 SER Chi-restraints excluded: chain A residue 140 LEU Chi-restraints excluded: chain A residue 157 THR Chi-restraints excluded: chain A residue 174 VAL Chi-restraints excluded: chain A residue 194 VAL Chi-restraints excluded: chain A residue 261 LYS Chi-restraints excluded: chain A residue 307 VAL Chi-restraints excluded: chain A residue 338 LEU Chi-restraints excluded: chain A residue 407 SER Chi-restraints excluded: chain A residue 426 LEU Chi-restraints excluded: chain A residue 431 LYS Chi-restraints excluded: chain A residue 443 ILE Chi-restraints excluded: chain A residue 452 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 37 optimal weight: 0.8980 chunk 57 optimal weight: 3.9990 chunk 43 optimal weight: 0.3980 chunk 46 optimal weight: 0.9980 chunk 12 optimal weight: 0.9980 chunk 42 optimal weight: 0.6980 chunk 13 optimal weight: 0.6980 chunk 39 optimal weight: 0.9980 chunk 48 optimal weight: 1.9990 chunk 56 optimal weight: 0.7980 chunk 50 optimal weight: 0.6980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 76 ASN H 101 GLN A 91 GLN A 131 GLN A 347 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.120186 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3066 r_free = 0.3066 target = 0.090125 restraints weight = 5786.130| |-----------------------------------------------------------------------------| r_work (start): 0.3077 rms_B_bonded: 2.21 r_work: 0.2953 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.2815 rms_B_bonded: 4.08 restraints_weight: 0.2500 r_work (final): 0.2815 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2819 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2819 r_free = 0.2819 target_work(ls_wunit_k1) = 0.073 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2819 r_free = 0.2819 target_work(ls_wunit_k1) = 0.073 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2819 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7863 moved from start: 0.1327 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 5008 Z= 0.195 Angle : 0.550 6.644 6810 Z= 0.290 Chirality : 0.046 0.149 767 Planarity : 0.003 0.042 870 Dihedral : 7.065 58.392 861 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 7.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.06 % Favored : 95.94 % Rotamer: Outliers : 4.10 % Allowed : 23.13 % Favored : 72.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.41 % Cis-general : 0.17 % 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: -0.79 (0.33), residues: 616 helix: -1.38 (1.65), residues: 7 sheet: -0.21 (0.33), residues: 227 loop : -0.68 (0.32), residues: 382 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP H 35A HIS 0.002 0.001 HIS A 336 PHE 0.013 0.002 PHE A 354 TYR 0.013 0.001 TYR A 121 ARG 0.003 0.000 ARG H 81 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1232 Ramachandran restraints generated. 616 Oldfield, 0 Emsley, 616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1232 Ramachandran restraints generated. 616 Oldfield, 0 Emsley, 616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 69 time to evaluate : 0.579 Fit side-chains revert: symmetry clash REVERT: H 38 ARG cc_start: 0.8854 (OUTLIER) cc_final: 0.7534 (ptt-90) REVERT: L 72 SER cc_start: 0.8222 (OUTLIER) cc_final: 0.8015 (t) REVERT: A 85 ARG cc_start: 0.8391 (mtt180) cc_final: 0.8122 (mtt180) REVERT: A 140 LEU cc_start: 0.8960 (OUTLIER) cc_final: 0.8737 (tp) REVERT: A 142 ASN cc_start: 0.7774 (t0) cc_final: 0.7568 (t160) REVERT: A 259 GLU cc_start: 0.8075 (mm-30) cc_final: 0.7400 (mm-30) outliers start: 22 outliers final: 15 residues processed: 82 average time/residue: 1.0301 time to fit residues: 90.0071 Evaluate side-chains 87 residues out of total 536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 69 time to evaluate : 0.511 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 21 THR Chi-restraints excluded: chain H residue 38 ARG Chi-restraints excluded: chain H residue 50 TYR Chi-restraints excluded: chain H residue 87 THR Chi-restraints excluded: chain H residue 107 THR Chi-restraints excluded: chain L residue 24 THR Chi-restraints excluded: chain L residue 27 SER Chi-restraints excluded: chain L residue 72 SER Chi-restraints excluded: chain A residue 140 LEU Chi-restraints excluded: chain A residue 157 THR Chi-restraints excluded: chain A residue 174 VAL Chi-restraints excluded: chain A residue 194 VAL Chi-restraints excluded: chain A residue 261 LYS Chi-restraints excluded: chain A residue 407 SER Chi-restraints excluded: chain A residue 426 LEU Chi-restraints excluded: chain A residue 431 LYS Chi-restraints excluded: chain A residue 443 ILE Chi-restraints excluded: chain A residue 452 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 30 optimal weight: 2.9990 chunk 18 optimal weight: 7.9990 chunk 34 optimal weight: 4.9990 chunk 49 optimal weight: 4.9990 chunk 50 optimal weight: 0.8980 chunk 19 optimal weight: 3.9990 chunk 20 optimal weight: 0.7980 chunk 23 optimal weight: 4.9990 chunk 17 optimal weight: 0.8980 chunk 57 optimal weight: 0.7980 chunk 33 optimal weight: 1.9990 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 76 ASN A 131 GLN A 347 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.118773 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3036 r_free = 0.3036 target = 0.088404 restraints weight = 5782.969| |-----------------------------------------------------------------------------| r_work (start): 0.3050 rms_B_bonded: 2.22 r_work: 0.2926 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.2788 rms_B_bonded: 4.05 restraints_weight: 0.2500 r_work (final): 0.2788 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2794 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2794 r_free = 0.2794 target_work(ls_wunit_k1) = 0.072 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2794 r_free = 0.2794 target_work(ls_wunit_k1) = 0.072 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2794 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7870 moved from start: 0.1291 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 5008 Z= 0.267 Angle : 0.568 6.646 6810 Z= 0.300 Chirality : 0.046 0.153 767 Planarity : 0.003 0.044 870 Dihedral : 7.099 59.443 861 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 6.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.06 % Favored : 95.94 % Rotamer: Outliers : 3.54 % Allowed : 24.25 % Favored : 72.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.41 % Cis-general : 0.17 % 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: -0.82 (0.33), residues: 616 helix: -1.32 (1.65), residues: 7 sheet: -0.25 (0.33), residues: 227 loop : -0.69 (0.31), residues: 382 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 178 HIS 0.003 0.001 HIS A 336 PHE 0.014 0.002 PHE A 354 TYR 0.015 0.002 TYR A 121 ARG 0.004 0.000 ARG A 400 =============================================================================== Job complete usr+sys time: 5566.52 seconds wall clock time: 100 minutes 28.76 seconds (6028.76 seconds total)