Starting phenix.real_space_refine on Thu Jul 2 01:01:53 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7m7b_23709/07_2026/7m7b_23709.cif Found real_map, /net/cci-nas-00/data/ceres_data/7m7b_23709/07_2026/7m7b_23709.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.95 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/7m7b_23709/07_2026/7m7b_23709.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7m7b_23709/07_2026/7m7b_23709.cif" model { file = "/net/cci-nas-00/data/ceres_data/7m7b_23709/07_2026/7m7b_23709.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7m7b_23709/07_2026/7m7b_23709.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7m7b_23709/07_2026/7m7b_23709.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7m7b_23709/07_2026/7m7b_23709.map" } resolution = 2.95 write_initial_geo_file = False refinement { macro_cycles = 10 } 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= 0.001 sd= 0.056 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 17 5.16 5 C 3103 2.51 5 N 820 2.21 5 O 958 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 12 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 4898 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 1657 Number of conformers: 1 Conformer: "" Number of residues, atoms: 209, 1657 Classifications: {'peptide': 209} Link IDs: {'PTRANS': 12, 'TRANS': 196} Chain: "H" Number of atoms: 1622 Number of conformers: 1 Conformer: "" Number of residues, atoms: 214, 1622 Classifications: {'peptide': 214} Link IDs: {'PCIS': 2, 'PTRANS': 11, 'TRANS': 200} Chain: "L" Number of atoms: 1591 Number of conformers: 1 Conformer: "" Number of residues, atoms: 212, 1591 Classifications: {'peptide': 212} Link IDs: {'PCIS': 1, 'PTRANS': 15, 'TRANS': 195} Chain: "A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Time building chain proxies: 1.26, per 1000 atoms: 0.26 Number of scatterers: 4898 At special positions: 0 Unit cell: (105.692, 91.4418, 104.505, 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 17 16.00 O 958 8.00 N 820 7.00 C 3103 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=8, symmetry=0 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.04 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.04 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.01 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 95 " distance=2.03 Simple disulfide: pdb=" SG CYS H 140 " - pdb=" SG CYS H 196 " distance=2.05 Simple disulfide: pdb=" SG CYS L 22 " - pdb=" SG CYS L 91 " distance=2.02 Simple disulfide: pdb=" SG CYS L 138 " - pdb=" SG CYS L 197 " 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 NAG-ASN " NAG A1301 " - " ASN A 331 " " NAG A1302 " - " ASN A 343 " Time building additional restraints: 0.37 Conformation dependent library (CDL) restraints added in 184.8 milliseconds 1258 Ramachandran restraints generated. 629 Oldfield, 0 Emsley, 629 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1172 Finding SS restraints... Secondary structure from input PDB file: 15 helices and 15 sheets defined 12.4% alpha, 41.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.17 Creating SS restraints... Processing helix chain 'A' and resid 337 through 343 removed outlier: 3.570A pdb=" N VAL A 341 " --> pdb=" O PRO A 337 " (cutoff:3.500A) Processing helix chain 'A' and resid 349 through 353 removed outlier: 3.804A pdb=" N TRP A 353 " --> pdb=" O VAL A 350 " (cutoff:3.500A) Processing helix chain 'A' and resid 365 through 370 Processing helix chain 'A' and resid 383 through 387 Processing helix chain 'A' and resid 406 through 410 Processing helix chain 'A' and resid 416 through 422 Processing helix chain 'A' and resid 438 through 443 removed outlier: 3.758A pdb=" N SER A 443 " --> pdb=" O ASN A 439 " (cutoff:3.500A) Processing helix chain 'A' and resid 502 through 505 Processing helix chain 'H' and resid 73 through 75 No H-bonds generated for 'chain 'H' and resid 73 through 75' Processing helix chain 'H' and resid 86 through 90 Processing helix chain 'H' and resid 156 through 158 No H-bonds generated for 'chain 'H' and resid 156 through 158' Processing helix chain 'L' and resid 28 through 32 removed outlier: 3.833A pdb=" N ASN L 32 " --> pdb=" O ILE L 29 " (cutoff:3.500A) Processing helix chain 'L' and resid 82 through 86 removed outlier: 3.674A pdb=" N GLU L 86 " --> pdb=" O THR L 83 " (cutoff:3.500A) Processing helix chain 'L' and resid 125 through 130 Processing helix chain 'L' and resid 185 through 191 Processing sheet with id=AA1, first strand: chain 'A' and resid 354 through 358 Processing sheet with id=AA2, first strand: chain 'A' and resid 361 through 362 removed outlier: 6.764A pdb=" N CYS A 361 " --> pdb=" O CYS A 525 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AA4, first strand: chain 'A' and resid 473 through 474 Processing sheet with id=AA5, first strand: chain 'H' and resid 3 through 8 Processing sheet with id=AA6, first strand: chain 'H' and resid 11 through 12 removed outlier: 6.594A pdb=" N TRP H 34 " --> pdb=" O GLU H 50 " (cutoff:3.500A) removed outlier: 4.398A pdb=" N GLU H 50 " --> pdb=" O TRP H 34 " (cutoff:3.500A) removed outlier: 6.779A pdb=" N TRP H 36 " --> pdb=" O ILE H 48 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'H' and resid 11 through 12 removed outlier: 3.753A pdb=" N ILE H 107 " --> pdb=" O ARG H 97 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'H' and resid 126 through 132 removed outlier: 6.800A pdb=" N ALA H 137 " --> pdb=" O PRO H 131 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ALA H 136 " --> pdb=" O VAL H 184 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N ASP H 144 " --> pdb=" O TYR H 176 " (cutoff:3.500A) removed outlier: 6.490A pdb=" N TYR H 176 " --> pdb=" O ASP H 144 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'H' and resid 126 through 132 removed outlier: 6.800A pdb=" N ALA H 137 " --> pdb=" O PRO H 131 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ALA H 136 " --> pdb=" O VAL H 184 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N ASP H 144 " --> pdb=" O TYR H 176 " (cutoff:3.500A) removed outlier: 6.490A pdb=" N TYR H 176 " --> pdb=" O ASP H 144 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'H' and resid 151 through 154 Processing sheet with id=AB2, first strand: chain 'L' and resid 3 through 5 Processing sheet with id=AB3, first strand: chain 'L' and resid 9 through 12 removed outlier: 3.532A pdb=" N ALA L 12 " --> pdb=" O THR L 108 " (cutoff:3.500A) removed outlier: 6.553A pdb=" N TRP L 36 " --> pdb=" O VAL L 48 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'L' and resid 9 through 12 removed outlier: 3.532A pdb=" N ALA L 12 " --> pdb=" O THR L 108 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'L' and resid 118 through 122 removed outlier: 5.541A pdb=" N TYR L 176 " --> pdb=" O ASP L 142 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'L' and resid 149 through 152 203 hydrogen bonds defined for protein. 486 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: 0.82 Time building geometry restraints manager: 0.51 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 1318 1.33 - 1.46: 990 1.46 - 1.58: 2703 1.58 - 1.70: 0 1.70 - 1.82: 18 Bond restraints: 5029 Sorted by residual: bond pdb=" CZ ARG A 457 " pdb=" NH2 ARG A 457 " ideal model delta sigma weight residual 1.330 1.286 0.044 1.30e-02 5.92e+03 1.13e+01 bond pdb=" CZ ARG H 98 " pdb=" NH2 ARG H 98 " ideal model delta sigma weight residual 1.330 1.288 0.042 1.30e-02 5.92e+03 1.06e+01 bond pdb=" C5 NAG A1302 " pdb=" O5 NAG A1302 " ideal model delta sigma weight residual 1.413 1.478 -0.065 2.00e-02 2.50e+03 1.04e+01 bond pdb=" C5 NAG A1301 " pdb=" O5 NAG A1301 " ideal model delta sigma weight residual 1.413 1.477 -0.064 2.00e-02 2.50e+03 1.04e+01 bond pdb=" CZ ARG A 509 " pdb=" NH2 ARG A 509 " ideal model delta sigma weight residual 1.330 1.289 0.041 1.30e-02 5.92e+03 1.02e+01 ... (remaining 5024 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.87: 4771 1.87 - 3.74: 1779 3.74 - 5.61: 278 5.61 - 7.49: 34 7.49 - 9.36: 1 Bond angle restraints: 6863 Sorted by residual: angle pdb=" CA ASP H 106 " pdb=" CB ASP H 106 " pdb=" CG ASP H 106 " ideal model delta sigma weight residual 112.60 118.17 -5.57 1.00e+00 1.00e+00 3.10e+01 angle pdb=" CA VAL L 163 " pdb=" CB VAL L 163 " pdb=" CG1 VAL L 163 " ideal model delta sigma weight residual 110.40 119.76 -9.36 1.70e+00 3.46e-01 3.03e+01 angle pdb=" N LYS H 143 " pdb=" CA LYS H 143 " pdb=" C LYS H 143 " ideal model delta sigma weight residual 111.69 118.38 -6.69 1.23e+00 6.61e-01 2.96e+01 angle pdb=" CA PHE H 78 " pdb=" CB PHE H 78 " pdb=" CG PHE H 78 " ideal model delta sigma weight residual 113.80 118.81 -5.01 1.00e+00 1.00e+00 2.51e+01 angle pdb=" CB HIS H 53 " pdb=" CG HIS H 53 " pdb=" CD2 HIS H 53 " ideal model delta sigma weight residual 131.20 124.76 6.44 1.30e+00 5.92e-01 2.45e+01 ... (remaining 6858 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.30: 2724 17.30 - 34.60: 200 34.60 - 51.90: 28 51.90 - 69.21: 11 69.21 - 86.51: 4 Dihedral angle restraints: 2967 sinusoidal: 1129 harmonic: 1838 Sorted by residual: dihedral pdb=" CA VAL H 142 " pdb=" C VAL H 142 " pdb=" N LYS H 143 " pdb=" CA LYS H 143 " ideal model delta harmonic sigma weight residual -180.00 -150.46 -29.54 0 5.00e+00 4.00e-02 3.49e+01 dihedral pdb=" CA PRO H 185 " pdb=" C PRO H 185 " pdb=" N SER H 186 " pdb=" CA SER H 186 " ideal model delta harmonic sigma weight residual -180.00 -150.77 -29.23 0 5.00e+00 4.00e-02 3.42e+01 dihedral pdb=" CA VAL L 109 " pdb=" C VAL L 109 " pdb=" N LEU L 110 " pdb=" CA LEU L 110 " ideal model delta harmonic sigma weight residual -180.00 -151.09 -28.91 0 5.00e+00 4.00e-02 3.34e+01 ... (remaining 2964 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.104: 534 0.104 - 0.207: 191 0.207 - 0.311: 29 0.311 - 0.414: 8 0.414 - 0.518: 2 Chirality restraints: 764 Sorted by residual: chirality pdb=" CA ASN L 173 " pdb=" N ASN L 173 " pdb=" C ASN L 173 " pdb=" CB ASN L 173 " both_signs ideal model delta sigma weight residual False 2.51 1.99 0.52 2.00e-01 2.50e+01 6.71e+00 chirality pdb=" CA ASN A 370 " pdb=" N ASN A 370 " pdb=" C ASN A 370 " pdb=" CB ASN A 370 " both_signs ideal model delta sigma weight residual False 2.51 2.02 0.49 2.00e-01 2.50e+01 6.11e+00 chirality pdb=" CA SER H 15 " pdb=" N SER H 15 " pdb=" C SER H 15 " pdb=" CB SER H 15 " both_signs ideal model delta sigma weight residual False 2.51 2.11 0.40 2.00e-01 2.50e+01 4.02e+00 ... (remaining 761 not shown) Planarity restraints: 883 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP L 152 " 0.143 2.00e-02 2.50e+03 7.99e-02 1.60e+02 pdb=" CG TRP L 152 " -0.010 2.00e-02 2.50e+03 pdb=" CD1 TRP L 152 " -0.014 2.00e-02 2.50e+03 pdb=" CD2 TRP L 152 " -0.089 2.00e-02 2.50e+03 pdb=" NE1 TRP L 152 " -0.055 2.00e-02 2.50e+03 pdb=" CE2 TRP L 152 " -0.027 2.00e-02 2.50e+03 pdb=" CE3 TRP L 152 " -0.115 2.00e-02 2.50e+03 pdb=" CZ2 TRP L 152 " 0.084 2.00e-02 2.50e+03 pdb=" CZ3 TRP L 152 " -0.021 2.00e-02 2.50e+03 pdb=" CH2 TRP L 152 " 0.103 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 495 " 0.131 2.00e-02 2.50e+03 7.23e-02 1.05e+02 pdb=" CG TYR A 495 " -0.041 2.00e-02 2.50e+03 pdb=" CD1 TYR A 495 " -0.053 2.00e-02 2.50e+03 pdb=" CD2 TYR A 495 " -0.059 2.00e-02 2.50e+03 pdb=" CE1 TYR A 495 " -0.045 2.00e-02 2.50e+03 pdb=" CE2 TYR A 495 " -0.040 2.00e-02 2.50e+03 pdb=" CZ TYR A 495 " -0.007 2.00e-02 2.50e+03 pdb=" OH TYR A 495 " 0.114 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR L 33 " -0.114 2.00e-02 2.50e+03 6.29e-02 7.91e+01 pdb=" CG TYR L 33 " 0.031 2.00e-02 2.50e+03 pdb=" CD1 TYR L 33 " 0.053 2.00e-02 2.50e+03 pdb=" CD2 TYR L 33 " 0.052 2.00e-02 2.50e+03 pdb=" CE1 TYR L 33 " 0.038 2.00e-02 2.50e+03 pdb=" CE2 TYR L 33 " 0.039 2.00e-02 2.50e+03 pdb=" CZ TYR L 33 " -0.003 2.00e-02 2.50e+03 pdb=" OH TYR L 33 " -0.096 2.00e-02 2.50e+03 ... (remaining 880 not shown) Histogram of nonbonded interaction distances: 2.51 - 2.99: 2340 2.99 - 3.47: 4488 3.47 - 3.94: 8045 3.94 - 4.42: 8899 4.42 - 4.90: 15303 Nonbonded interactions: 39075 Sorted by model distance: nonbonded pdb=" N GLU L 51 " pdb=" O GLU L 51 " model vdw 2.512 2.496 nonbonded pdb=" OD2 ASP L 68 " pdb=" OG SER L 71 " model vdw 2.559 3.040 nonbonded pdb=" OD1 ASP L 68 " pdb=" OG SER L 70 " model vdw 2.562 3.040 nonbonded pdb=" OH TYR H 145 " pdb=" OE2 GLU H 148 " model vdw 2.568 3.040 nonbonded pdb=" OE2 GLU L 128 " pdb=" OG1 THR L 135 " model vdw 2.568 3.040 ... (remaining 39070 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=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: 3.010 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: 0.090 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 6.410 Find NCS groups from input model: 0.020 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.310 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.900 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8565 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 : 0.012 0.065 5039 Z= 0.741 Angle : 1.877 9.357 6885 Z= 1.251 Chirality : 0.108 0.518 764 Planarity : 0.015 0.172 881 Dihedral : 13.123 86.508 1771 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 0.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.50 % Favored : 96.50 % Rotamer: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Cbeta Deviations : 0.85 % Peptide Plane: Cis-proline : 7.32 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.73 (0.32), residues: 629 helix: -3.61 (0.50), residues: 41 sheet: 0.44 (0.37), residues: 200 loop : -0.61 (0.29), residues: 388 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG L 55 TYR 0.131 0.021 TYR A 495 PHE 0.074 0.014 PHE H 29 TRP 0.143 0.019 TRP L 152 HIS 0.011 0.004 HIS H 164 Details of bonding type rmsd/Z covalent geometry : bond 0.01241 / 0.74 ( 5029) covalent geometry : angle 1.87442 / 1.25 ( 6863) SS BOND : bond 0.01119 / 0.53 ( 8) SS BOND : angle 1.53725 / 1.00 ( 16) hydrogen bonds : bond 0.14397 / 9.02 ( 181) hydrogen bonds : angle 8.85591 / 6.13 ( 486) link_NAG-ASN : bond 0.01155 / 0.58 ( 2) link_NAG-ASN : angle 4.42540 / 2.75 ( 6) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1258 Ramachandran restraints generated. 629 Oldfield, 0 Emsley, 629 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1258 Ramachandran restraints generated. 629 Oldfield, 0 Emsley, 629 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 38 residues out of total 545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 38 time to evaluate : 0.166 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 428 ASP cc_start: 0.7689 (p0) cc_final: 0.7397 (p0) outliers start: 0 outliers final: 0 residues processed: 38 average time/residue: 0.5642 time to fit residues: 22.2965 Evaluate side-chains 21 residues out of total 545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 21 time to evaluate : 0.167 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 54 optimal weight: 5.9990 chunk 24 optimal weight: 0.7980 chunk 48 optimal weight: 2.9990 chunk 56 optimal weight: 5.9990 chunk 26 optimal weight: 0.6980 chunk 2 optimal weight: 0.8980 chunk 16 optimal weight: 0.8980 chunk 61 optimal weight: 6.9990 chunk 32 optimal weight: 4.9990 chunk 31 optimal weight: 2.9990 chunk 25 optimal weight: 0.9980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 354 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 394 ASN A 437 ASN ** L 201 HIS ** 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 = 0.3333 r_free = 0.3333 target = 0.054468 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2897 r_free = 0.2897 target = 0.039336 restraints weight = 21841.267| |-----------------------------------------------------------------------------| r_work (start): 0.2858 rms_B_bonded: 3.41 r_work: 0.2751 rms_B_bonded: 3.51 restraints_weight: 0.5000 r_work (final): 0.2751 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8775 moved from start: 0.2270 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 5039 Z= 0.138 Angle : 0.618 5.150 6885 Z= 0.340 Chirality : 0.047 0.186 764 Planarity : 0.005 0.041 881 Dihedral : 6.097 23.765 685 Min Nonbonded Distance : 2.587 Molprobity Statistics. All-atom Clashscore : 3.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.91 % Favored : 98.09 % Rotamer: Outliers : 0.37 % Allowed : 5.87 % Favored : 93.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.32 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.23 (0.32), residues: 629 helix: -2.68 (0.70), residues: 41 sheet: 0.55 (0.35), residues: 218 loop : -0.22 (0.31), residues: 370 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 357 TYR 0.026 0.001 TYR A 369 PHE 0.017 0.001 PHE H 78 TRP 0.011 0.001 TRP L 152 HIS 0.002 0.001 HIS H 53 Details of bonding type rmsd/Z covalent geometry : bond 0.00302 / 0.14 ( 5029) covalent geometry : angle 0.61682 / 0.34 ( 6863) SS BOND : bond 0.00298 / 0.15 ( 8) SS BOND : angle 0.55333 / 0.30 ( 16) hydrogen bonds : bond 0.03674 / 2.30 ( 181) hydrogen bonds : angle 6.30310 / 4.23 ( 486) link_NAG-ASN : bond 0.00168 / 0.08 ( 2) link_NAG-ASN : angle 1.62178 / 0.98 ( 6) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1258 Ramachandran restraints generated. 629 Oldfield, 0 Emsley, 629 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1258 Ramachandran restraints generated. 629 Oldfield, 0 Emsley, 629 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 29 residues out of total 545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 27 time to evaluate : 0.119 Fit side-chains revert: symmetry clash REVERT: A 340 GLU cc_start: 0.9121 (mt-10) cc_final: 0.8841 (tp30) REVERT: A 428 ASP cc_start: 0.9391 (p0) cc_final: 0.9127 (p0) REVERT: L 84 GLU cc_start: 0.9076 (pm20) cc_final: 0.8622 (pm20) REVERT: L 85 ASP cc_start: 0.8078 (m-30) cc_final: 0.7790 (m-30) REVERT: L 164 GLU cc_start: 0.7484 (pt0) cc_final: 0.7279 (pm20) outliers start: 2 outliers final: 0 residues processed: 28 average time/residue: 0.6679 time to fit residues: 19.3697 Evaluate side-chains 21 residues out of total 545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 21 time to evaluate : 0.219 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 14 optimal weight: 6.9990 chunk 48 optimal weight: 3.9990 chunk 38 optimal weight: 2.9990 chunk 36 optimal weight: 0.9980 chunk 28 optimal weight: 0.6980 chunk 18 optimal weight: 4.9990 chunk 6 optimal weight: 0.9980 chunk 8 optimal weight: 5.9990 chunk 26 optimal weight: 3.9990 chunk 53 optimal weight: 9.9990 chunk 47 optimal weight: 5.9990 overall best weight: 1.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 354 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.053366 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2868 r_free = 0.2868 target = 0.038344 restraints weight = 21742.423| |-----------------------------------------------------------------------------| r_work (start): 0.2828 rms_B_bonded: 3.43 r_work: 0.2720 rms_B_bonded: 3.51 restraints_weight: 0.5000 r_work (final): 0.2720 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8817 moved from start: 0.2556 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.032 5039 Z= 0.212 Angle : 0.608 5.670 6885 Z= 0.332 Chirality : 0.047 0.187 764 Planarity : 0.005 0.043 881 Dihedral : 5.761 19.184 685 Min Nonbonded Distance : 2.569 Molprobity Statistics. All-atom Clashscore : 3.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 0.37 % Allowed : 7.71 % Favored : 91.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.32 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.17 (0.33), residues: 629 helix: -2.50 (0.75), residues: 35 sheet: 0.63 (0.35), residues: 224 loop : -0.29 (0.31), residues: 370 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 346 TYR 0.023 0.002 TYR A 369 PHE 0.014 0.001 PHE H 78 TRP 0.010 0.001 TRP H 47 HIS 0.003 0.001 HIS L 192 Details of bonding type rmsd/Z covalent geometry : bond 0.00496 / 0.21 ( 5029) covalent geometry : angle 0.60620 / 0.33 ( 6863) SS BOND : bond 0.00248 / 0.15 ( 8) SS BOND : angle 0.66758 / 0.35 ( 16) hydrogen bonds : bond 0.03791 / 2.36 ( 181) hydrogen bonds : angle 6.13316 / 4.16 ( 486) link_NAG-ASN : bond 0.00174 / 0.09 ( 2) link_NAG-ASN : angle 1.50622 / 0.97 ( 6) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1258 Ramachandran restraints generated. 629 Oldfield, 0 Emsley, 629 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1258 Ramachandran restraints generated. 629 Oldfield, 0 Emsley, 629 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 26 residues out of total 545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 24 time to evaluate : 0.135 Fit side-chains revert: symmetry clash REVERT: A 340 GLU cc_start: 0.9165 (mt-10) cc_final: 0.8836 (tp30) REVERT: A 428 ASP cc_start: 0.9388 (p0) cc_final: 0.9133 (p0) REVERT: L 84 GLU cc_start: 0.9020 (pm20) cc_final: 0.8769 (pm20) REVERT: L 85 ASP cc_start: 0.8105 (m-30) cc_final: 0.7663 (m-30) REVERT: L 164 GLU cc_start: 0.7553 (pt0) cc_final: 0.7323 (pm20) outliers start: 2 outliers final: 2 residues processed: 26 average time/residue: 0.5531 time to fit residues: 15.0202 Evaluate side-chains 22 residues out of total 545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 20 time to evaluate : 0.119 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 461 LEU Chi-restraints excluded: chain L residue 47 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 38 optimal weight: 0.9980 chunk 21 optimal weight: 0.9980 chunk 52 optimal weight: 5.9990 chunk 8 optimal weight: 4.9990 chunk 9 optimal weight: 0.7980 chunk 7 optimal weight: 0.8980 chunk 46 optimal weight: 0.9990 chunk 22 optimal weight: 3.9990 chunk 5 optimal weight: 0.8980 chunk 17 optimal weight: 4.9990 chunk 58 optimal weight: 2.9990 overall best weight: 0.9180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... H 164 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.053698 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2887 r_free = 0.2887 target = 0.039012 restraints weight = 21668.949| |-----------------------------------------------------------------------------| r_work (start): 0.2851 rms_B_bonded: 3.27 r_work: 0.2749 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.2749 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8839 moved from start: 0.2866 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 5039 Z= 0.124 Angle : 0.547 8.180 6885 Z= 0.294 Chirality : 0.045 0.174 764 Planarity : 0.005 0.043 881 Dihedral : 5.185 17.491 685 Min Nonbonded Distance : 2.600 Molprobity Statistics. All-atom Clashscore : 3.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 1.10 % Allowed : 8.26 % Favored : 90.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.32 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.07 (0.33), residues: 629 helix: -2.32 (0.76), residues: 34 sheet: 0.62 (0.34), residues: 228 loop : -0.19 (0.32), residues: 367 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG H 210 TYR 0.022 0.001 TYR A 369 PHE 0.012 0.001 PHE H 78 TRP 0.009 0.001 TRP H 100 HIS 0.002 0.001 HIS L 201 Details of bonding type rmsd/Z covalent geometry : bond 0.00283 / 0.12 ( 5029) covalent geometry : angle 0.54532 / 0.29 ( 6863) SS BOND : bond 0.00249 / 0.14 ( 8) SS BOND : angle 0.53703 / 0.32 ( 16) hydrogen bonds : bond 0.03346 / 2.07 ( 181) hydrogen bonds : angle 5.80916 / 3.93 ( 486) link_NAG-ASN : bond 0.00019 / 0.01 ( 2) link_NAG-ASN : angle 1.34818 / 0.88 ( 6) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1258 Ramachandran restraints generated. 629 Oldfield, 0 Emsley, 629 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1258 Ramachandran restraints generated. 629 Oldfield, 0 Emsley, 629 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 27 residues out of total 545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 21 time to evaluate : 0.141 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 428 ASP cc_start: 0.9338 (p0) cc_final: 0.9043 (p0) REVERT: L 85 ASP cc_start: 0.8120 (m-30) cc_final: 0.7608 (m-30) outliers start: 6 outliers final: 1 residues processed: 27 average time/residue: 0.5575 time to fit residues: 15.7160 Evaluate side-chains 19 residues out of total 545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 18 time to evaluate : 0.127 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 47 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 1 optimal weight: 0.7980 chunk 31 optimal weight: 8.9990 chunk 14 optimal weight: 4.9990 chunk 8 optimal weight: 3.9990 chunk 41 optimal weight: 0.9980 chunk 56 optimal weight: 9.9990 chunk 5 optimal weight: 3.9990 chunk 55 optimal weight: 3.9990 chunk 49 optimal weight: 5.9990 chunk 4 optimal weight: 0.0170 chunk 47 optimal weight: 2.9990 overall best weight: 1.7622 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... L 201 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.052930 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2855 r_free = 0.2855 target = 0.038124 restraints weight = 21975.712| |-----------------------------------------------------------------------------| r_work (start): 0.2819 rms_B_bonded: 3.26 r_work: 0.2718 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.2718 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8885 moved from start: 0.2992 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.034 5039 Z= 0.201 Angle : 0.601 8.182 6885 Z= 0.322 Chirality : 0.046 0.179 764 Planarity : 0.005 0.041 881 Dihedral : 5.283 16.644 685 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 3.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 0.37 % Allowed : 10.28 % Favored : 89.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.32 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.17 (0.33), residues: 629 helix: -2.66 (0.64), residues: 40 sheet: 0.63 (0.35), residues: 226 loop : -0.23 (0.32), residues: 363 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG A 346 TYR 0.021 0.001 TYR A 369 PHE 0.013 0.001 PHE H 78 TRP 0.009 0.001 TRP H 154 HIS 0.003 0.001 HIS L 192 Details of bonding type rmsd/Z covalent geometry : bond 0.00467 / 0.20 ( 5029) covalent geometry : angle 0.60009 / 0.32 ( 6863) SS BOND : bond 0.00255 / 0.15 ( 8) SS BOND : angle 0.65088 / 0.36 ( 16) hydrogen bonds : bond 0.03680 / 2.31 ( 181) hydrogen bonds : angle 5.95160 / 4.06 ( 486) link_NAG-ASN : bond 0.00181 / 0.09 ( 2) link_NAG-ASN : angle 1.39673 / 1.01 ( 6) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1258 Ramachandran restraints generated. 629 Oldfield, 0 Emsley, 629 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1258 Ramachandran restraints generated. 629 Oldfield, 0 Emsley, 629 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 21 residues out of total 545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 19 time to evaluate : 0.176 Fit side-chains revert: symmetry clash REVERT: A 428 ASP cc_start: 0.9319 (p0) cc_final: 0.9013 (p0) REVERT: H 3 GLN cc_start: 0.8928 (tm-30) cc_final: 0.8351 (tm-30) REVERT: L 85 ASP cc_start: 0.8246 (m-30) cc_final: 0.7853 (m-30) outliers start: 2 outliers final: 2 residues processed: 21 average time/residue: 0.5188 time to fit residues: 11.4226 Evaluate side-chains 21 residues out of total 545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 19 time to evaluate : 0.142 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 138 LEU Chi-restraints excluded: chain L residue 47 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 22 optimal weight: 1.9990 chunk 37 optimal weight: 2.9990 chunk 56 optimal weight: 6.9990 chunk 30 optimal weight: 1.9990 chunk 27 optimal weight: 4.9990 chunk 48 optimal weight: 3.9990 chunk 43 optimal weight: 3.9990 chunk 36 optimal weight: 3.9990 chunk 35 optimal weight: 4.9990 chunk 6 optimal weight: 3.9990 chunk 26 optimal weight: 1.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... H 3 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3260 r_free = 0.3260 target = 0.051883 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2825 r_free = 0.2825 target = 0.037216 restraints weight = 22532.146| |-----------------------------------------------------------------------------| r_work (start): 0.2786 rms_B_bonded: 3.29 r_work: 0.2685 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.2685 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8891 moved from start: 0.3019 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.036 5039 Z= 0.278 Angle : 0.631 10.112 6885 Z= 0.337 Chirality : 0.047 0.180 764 Planarity : 0.005 0.041 881 Dihedral : 5.488 17.579 685 Min Nonbonded Distance : 2.563 Molprobity Statistics. All-atom Clashscore : 4.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 1.10 % Allowed : 10.83 % Favored : 88.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.32 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.33 (0.33), residues: 629 helix: -2.59 (0.65), residues: 41 sheet: 0.61 (0.35), residues: 226 loop : -0.43 (0.32), residues: 362 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 509 TYR 0.021 0.002 TYR A 369 PHE 0.012 0.001 PHE H 78 TRP 0.009 0.001 TRP H 154 HIS 0.003 0.001 HIS L 192 Details of bonding type rmsd/Z covalent geometry : bond 0.00643 / 0.28 ( 5029) covalent geometry : angle 0.62916 / 0.34 ( 6863) SS BOND : bond 0.00306 / 0.17 ( 8) SS BOND : angle 0.86114 / 0.46 ( 16) hydrogen bonds : bond 0.03941 / 2.48 ( 181) hydrogen bonds : angle 6.18271 / 4.21 ( 486) link_NAG-ASN : bond 0.00247 / 0.12 ( 2) link_NAG-ASN : angle 1.46970 / 1.05 ( 6) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1258 Ramachandran restraints generated. 629 Oldfield, 0 Emsley, 629 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1258 Ramachandran restraints generated. 629 Oldfield, 0 Emsley, 629 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 27 residues out of total 545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 21 time to evaluate : 0.184 Fit side-chains revert: symmetry clash REVERT: A 340 GLU cc_start: 0.9139 (OUTLIER) cc_final: 0.8639 (mp0) REVERT: A 428 ASP cc_start: 0.9354 (p0) cc_final: 0.9061 (p0) REVERT: H 3 GLN cc_start: 0.9002 (OUTLIER) cc_final: 0.8407 (tm-30) REVERT: L 85 ASP cc_start: 0.8325 (m-30) cc_final: 0.7845 (m-30) outliers start: 6 outliers final: 2 residues processed: 24 average time/residue: 0.5485 time to fit residues: 13.8857 Evaluate side-chains 25 residues out of total 545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 21 time to evaluate : 0.175 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 340 GLU Chi-restraints excluded: chain H residue 3 GLN Chi-restraints excluded: chain H residue 138 LEU Chi-restraints excluded: chain L residue 47 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 37 optimal weight: 0.0870 chunk 13 optimal weight: 0.0470 chunk 49 optimal weight: 3.9990 chunk 23 optimal weight: 1.9990 chunk 35 optimal weight: 2.9990 chunk 36 optimal weight: 0.8980 chunk 18 optimal weight: 0.9990 chunk 42 optimal weight: 0.6980 chunk 27 optimal weight: 2.9990 chunk 12 optimal weight: 0.7980 chunk 19 optimal weight: 5.9990 overall best weight: 0.5056 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... H 3 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.053868 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2896 r_free = 0.2896 target = 0.039061 restraints weight = 21595.227| |-----------------------------------------------------------------------------| r_work (start): 0.2858 rms_B_bonded: 3.27 r_work: 0.2756 rms_B_bonded: 3.38 restraints_weight: 0.5000 r_work (final): 0.2756 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8854 moved from start: 0.3323 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 5039 Z= 0.108 Angle : 0.556 10.153 6885 Z= 0.294 Chirality : 0.045 0.167 764 Planarity : 0.005 0.041 881 Dihedral : 4.784 16.147 685 Min Nonbonded Distance : 2.606 Molprobity Statistics. All-atom Clashscore : 3.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.91 % Favored : 98.09 % Rotamer: Outliers : 0.73 % Allowed : 12.48 % Favored : 86.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.32 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.10 (0.33), residues: 629 helix: -2.53 (0.71), residues: 34 sheet: 0.71 (0.35), residues: 224 loop : -0.25 (0.32), residues: 371 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 457 TYR 0.021 0.001 TYR A 369 PHE 0.010 0.001 PHE L 2 TRP 0.012 0.001 TRP H 100 HIS 0.001 0.000 HIS L 201 Details of bonding type rmsd/Z covalent geometry : bond 0.00245 / 0.11 ( 5029) covalent geometry : angle 0.55459 / 0.29 ( 6863) SS BOND : bond 0.00232 / 0.14 ( 8) SS BOND : angle 0.46629 / 0.28 ( 16) hydrogen bonds : bond 0.03281 / 2.07 ( 181) hydrogen bonds : angle 5.63958 / 3.84 ( 486) link_NAG-ASN : bond 0.00120 / 0.06 ( 2) link_NAG-ASN : angle 1.30793 / 0.85 ( 6) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1258 Ramachandran restraints generated. 629 Oldfield, 0 Emsley, 629 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1258 Ramachandran restraints generated. 629 Oldfield, 0 Emsley, 629 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 27 residues out of total 545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 23 time to evaluate : 0.193 Fit side-chains REVERT: A 340 GLU cc_start: 0.9135 (mt-10) cc_final: 0.8653 (mp0) REVERT: A 428 ASP cc_start: 0.9328 (p0) cc_final: 0.9013 (p0) REVERT: H 3 GLN cc_start: 0.8832 (OUTLIER) cc_final: 0.8535 (tm-30) REVERT: L 85 ASP cc_start: 0.8199 (m-30) cc_final: 0.7662 (m-30) REVERT: L 164 GLU cc_start: 0.7159 (pm20) cc_final: 0.6740 (pt0) outliers start: 4 outliers final: 1 residues processed: 27 average time/residue: 0.6064 time to fit residues: 17.1097 Evaluate side-chains 20 residues out of total 545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 18 time to evaluate : 0.143 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 3 GLN Chi-restraints excluded: chain L residue 47 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 5 optimal weight: 0.8980 chunk 21 optimal weight: 1.9990 chunk 38 optimal weight: 0.8980 chunk 45 optimal weight: 5.9990 chunk 24 optimal weight: 3.9990 chunk 14 optimal weight: 5.9990 chunk 48 optimal weight: 0.7980 chunk 60 optimal weight: 8.9990 chunk 49 optimal weight: 1.9990 chunk 42 optimal weight: 0.6980 chunk 9 optimal weight: 4.9990 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... H 3 GLN L 1 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.053271 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2876 r_free = 0.2876 target = 0.038470 restraints weight = 21994.759| |-----------------------------------------------------------------------------| r_work (start): 0.2837 rms_B_bonded: 3.28 r_work: 0.2736 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.2736 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8872 moved from start: 0.3379 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 5039 Z= 0.136 Angle : 0.528 5.320 6885 Z= 0.284 Chirality : 0.045 0.169 764 Planarity : 0.005 0.039 881 Dihedral : 4.736 15.982 685 Min Nonbonded Distance : 2.603 Molprobity Statistics. All-atom Clashscore : 4.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 1.10 % Allowed : 12.48 % Favored : 86.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.32 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.00 (0.34), residues: 629 helix: -2.13 (0.71), residues: 40 sheet: 0.72 (0.35), residues: 224 loop : -0.14 (0.33), residues: 365 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG H 210 TYR 0.021 0.001 TYR A 369 PHE 0.012 0.001 PHE H 78 TRP 0.023 0.001 TRP L 189 HIS 0.001 0.000 HIS L 192 Details of bonding type rmsd/Z covalent geometry : bond 0.00314 / 0.14 ( 5029) covalent geometry : angle 0.52737 / 0.28 ( 6863) SS BOND : bond 0.00217 / 0.13 ( 8) SS BOND : angle 0.51756 / 0.29 ( 16) hydrogen bonds : bond 0.03279 / 2.06 ( 181) hydrogen bonds : angle 5.65894 / 3.84 ( 486) link_NAG-ASN : bond 0.00024 / 0.01 ( 2) link_NAG-ASN : angle 1.24592 / 0.86 ( 6) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1258 Ramachandran restraints generated. 629 Oldfield, 0 Emsley, 629 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1258 Ramachandran restraints generated. 629 Oldfield, 0 Emsley, 629 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 29 residues out of total 545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 23 time to evaluate : 0.196 Fit side-chains revert: symmetry clash REVERT: A 340 GLU cc_start: 0.9133 (mt-10) cc_final: 0.8636 (mp0) REVERT: A 428 ASP cc_start: 0.9334 (p0) cc_final: 0.8989 (p0) REVERT: H 3 GLN cc_start: 0.8864 (OUTLIER) cc_final: 0.8475 (tm-30) REVERT: L 164 GLU cc_start: 0.7331 (pm20) cc_final: 0.6806 (pt0) outliers start: 6 outliers final: 1 residues processed: 28 average time/residue: 0.4954 time to fit residues: 14.5927 Evaluate side-chains 23 residues out of total 545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 21 time to evaluate : 0.190 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 3 GLN Chi-restraints excluded: chain H residue 138 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 28 optimal weight: 1.9990 chunk 8 optimal weight: 4.9990 chunk 26 optimal weight: 2.9990 chunk 61 optimal weight: 7.9990 chunk 56 optimal weight: 5.9990 chunk 21 optimal weight: 0.6980 chunk 51 optimal weight: 4.9990 chunk 9 optimal weight: 3.9990 chunk 6 optimal weight: 4.9990 chunk 30 optimal weight: 0.9980 chunk 3 optimal weight: 0.4980 overall best weight: 1.4384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... H 3 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.053010 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2869 r_free = 0.2869 target = 0.038300 restraints weight = 21541.251| |-----------------------------------------------------------------------------| r_work (start): 0.2831 rms_B_bonded: 3.27 r_work: 0.2730 rms_B_bonded: 3.39 restraints_weight: 0.5000 r_work (final): 0.2730 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8884 moved from start: 0.3408 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 5039 Z= 0.171 Angle : 0.577 9.634 6885 Z= 0.306 Chirality : 0.045 0.168 764 Planarity : 0.005 0.039 881 Dihedral : 4.828 16.028 685 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 4.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 1.10 % Allowed : 13.21 % Favored : 85.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.32 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.04 (0.34), residues: 629 helix: -2.02 (0.73), residues: 40 sheet: 0.76 (0.36), residues: 222 loop : -0.13 (0.33), residues: 367 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG H 210 TYR 0.021 0.001 TYR A 369 PHE 0.012 0.001 PHE H 78 TRP 0.020 0.001 TRP L 189 HIS 0.003 0.001 HIS L 201 Details of bonding type rmsd/Z covalent geometry : bond 0.00397 / 0.17 ( 5029) covalent geometry : angle 0.57652 / 0.31 ( 6863) SS BOND : bond 0.00226 / 0.14 ( 8) SS BOND : angle 0.57490 / 0.31 ( 16) hydrogen bonds : bond 0.03388 / 2.13 ( 181) hydrogen bonds : angle 5.72231 / 3.89 ( 486) link_NAG-ASN : bond 0.00067 / 0.03 ( 2) link_NAG-ASN : angle 1.27274 / 0.90 ( 6) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1258 Ramachandran restraints generated. 629 Oldfield, 0 Emsley, 629 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1258 Ramachandran restraints generated. 629 Oldfield, 0 Emsley, 629 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 26 residues out of total 545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 20 time to evaluate : 0.192 Fit side-chains REVERT: A 340 GLU cc_start: 0.9113 (mt-10) cc_final: 0.8621 (mp0) REVERT: A 428 ASP cc_start: 0.9342 (p0) cc_final: 0.9000 (p0) REVERT: H 3 GLN cc_start: 0.8828 (OUTLIER) cc_final: 0.8474 (tm130) REVERT: L 164 GLU cc_start: 0.7286 (pm20) cc_final: 0.6698 (pt0) outliers start: 6 outliers final: 4 residues processed: 25 average time/residue: 0.5856 time to fit residues: 15.3779 Evaluate side-chains 24 residues out of total 545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 19 time to evaluate : 0.133 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 3 GLN Chi-restraints excluded: chain H residue 138 LEU Chi-restraints excluded: chain L residue 47 THR Chi-restraints excluded: chain L residue 66 SER Chi-restraints excluded: chain L residue 200 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 35 optimal weight: 3.9990 chunk 42 optimal weight: 0.4980 chunk 44 optimal weight: 1.9990 chunk 58 optimal weight: 2.9990 chunk 23 optimal weight: 2.9990 chunk 12 optimal weight: 2.9990 chunk 43 optimal weight: 0.8980 chunk 45 optimal weight: 1.9990 chunk 31 optimal weight: 5.9990 chunk 51 optimal weight: 1.9990 chunk 24 optimal weight: 0.4980 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... H 3 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.053215 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2872 r_free = 0.2872 target = 0.038399 restraints weight = 21667.305| |-----------------------------------------------------------------------------| r_work (start): 0.2834 rms_B_bonded: 3.28 r_work: 0.2732 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.2732 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8874 moved from start: 0.3453 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 5039 Z= 0.150 Angle : 0.577 12.622 6885 Z= 0.304 Chirality : 0.045 0.168 764 Planarity : 0.005 0.039 881 Dihedral : 4.793 16.072 685 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 4.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 0.92 % Allowed : 13.94 % Favored : 85.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.32 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.03 (0.34), residues: 629 helix: -2.02 (0.72), residues: 40 sheet: 0.76 (0.36), residues: 222 loop : -0.14 (0.33), residues: 367 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG H 210 TYR 0.021 0.001 TYR A 369 PHE 0.011 0.001 PHE H 78 TRP 0.018 0.001 TRP L 189 HIS 0.002 0.001 HIS L 201 Details of bonding type rmsd/Z covalent geometry : bond 0.00348 / 0.15 ( 5029) covalent geometry : angle 0.57598 / 0.30 ( 6863) SS BOND : bond 0.00216 / 0.13 ( 8) SS BOND : angle 0.53202 / 0.29 ( 16) hydrogen bonds : bond 0.03386 / 2.11 ( 181) hydrogen bonds : angle 5.67049 / 3.85 ( 486) link_NAG-ASN : bond 0.00026 / 0.01 ( 2) link_NAG-ASN : angle 1.25710 / 0.87 ( 6) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1258 Ramachandran restraints generated. 629 Oldfield, 0 Emsley, 629 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1258 Ramachandran restraints generated. 629 Oldfield, 0 Emsley, 629 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 25 residues out of total 545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 20 time to evaluate : 0.209 Fit side-chains REVERT: A 340 GLU cc_start: 0.9126 (mt-10) cc_final: 0.8628 (mp0) REVERT: A 428 ASP cc_start: 0.9325 (p0) cc_final: 0.8971 (p0) REVERT: H 3 GLN cc_start: 0.8672 (OUTLIER) cc_final: 0.8445 (tm130) REVERT: H 5 GLN cc_start: 0.9066 (mm-40) cc_final: 0.8789 (mm-40) REVERT: L 164 GLU cc_start: 0.7211 (pm20) cc_final: 0.6535 (pt0) outliers start: 5 outliers final: 4 residues processed: 24 average time/residue: 0.5544 time to fit residues: 14.0236 Evaluate side-chains 25 residues out of total 545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 20 time to evaluate : 0.110 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 3 GLN Chi-restraints excluded: chain H residue 138 LEU Chi-restraints excluded: chain L residue 47 THR Chi-restraints excluded: chain L residue 66 SER Chi-restraints excluded: chain L residue 200 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 46 optimal weight: 0.5980 chunk 51 optimal weight: 2.9990 chunk 30 optimal weight: 0.0570 chunk 0 optimal weight: 4.9990 chunk 17 optimal weight: 0.3980 chunk 12 optimal weight: 2.9990 chunk 4 optimal weight: 0.9990 chunk 11 optimal weight: 0.2980 chunk 42 optimal weight: 0.7980 chunk 54 optimal weight: 8.9990 chunk 58 optimal weight: 0.8980 overall best weight: 0.4298 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... H 3 GLN L 1 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.054080 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2904 r_free = 0.2904 target = 0.039267 restraints weight = 21672.451| |-----------------------------------------------------------------------------| r_work (start): 0.2866 rms_B_bonded: 3.29 r_work: 0.2764 rms_B_bonded: 3.43 restraints_weight: 0.5000 r_work (final): 0.2764 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8835 moved from start: 0.3627 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 5039 Z= 0.104 Angle : 0.559 10.803 6885 Z= 0.293 Chirality : 0.044 0.161 764 Planarity : 0.005 0.040 881 Dihedral : 4.511 15.833 685 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 4.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 1.28 % Allowed : 13.76 % Favored : 84.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.32 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.10 (0.34), residues: 629 helix: -2.09 (0.81), residues: 34 sheet: 0.79 (0.36), residues: 224 loop : -0.12 (0.33), residues: 371 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 457 TYR 0.021 0.001 TYR A 369 PHE 0.009 0.001 PHE H 78 TRP 0.015 0.001 TRP L 189 HIS 0.003 0.000 HIS L 201 Details of bonding type rmsd/Z covalent geometry : bond 0.00241 / 0.10 ( 5029) covalent geometry : angle 0.55839 / 0.29 ( 6863) SS BOND : bond 0.00220 / 0.14 ( 8) SS BOND : angle 0.43392 / 0.25 ( 16) hydrogen bonds : bond 0.03040 / 1.93 ( 181) hydrogen bonds : angle 5.43541 / 3.68 ( 486) link_NAG-ASN : bond 0.00112 / 0.05 ( 2) link_NAG-ASN : angle 1.25349 / 0.82 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1479.25 seconds wall clock time: 26 minutes 1.86 seconds (1561.86 seconds total)