Starting phenix.real_space_refine on Thu Jul 2 00:54:55 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7mjl_23877/07_2026/7mjl_23877.cif Found real_map, /net/cci-nas-00/data/ceres_data/7mjl_23877/07_2026/7mjl_23877.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 { model { file = "/net/cci-nas-00/data/ceres_data/7mjl_23877/07_2026/7mjl_23877.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7mjl_23877/07_2026/7mjl_23877.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/7mjl_23877/07_2026/7mjl_23877.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7mjl_23877/07_2026/7mjl_23877.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7mjl_23877/07_2026/7mjl_23877.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7mjl_23877/07_2026/7mjl_23877.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= 0.000 sd= 0.024 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 19 5.16 5 C 3037 2.51 5 N 793 2.21 5 O 939 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 19 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: 4788 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 1564 Number of conformers: 1 Conformer: "" Number of residues, atoms: 197, 1564 Classifications: {'peptide': 197} Link IDs: {'PTRANS': 11, 'TRANS': 185} Chain: "H" Number of atoms: 1585 Number of conformers: 1 Conformer: "" Number of residues, atoms: 211, 1585 Classifications: {'peptide': 211} Link IDs: {'PCIS': 2, 'PTRANS': 9, 'TRANS': 199} Chain breaks: 1 Chain: "L" Number of atoms: 1625 Number of conformers: 1 Conformer: "" Number of residues, atoms: 213, 1625 Classifications: {'peptide': 213} Link IDs: {'PCIS': 2, 'PTRANS': 10, 'TRANS': 200} Chain: "A" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 1.12, per 1000 atoms: 0.23 Number of scatterers: 4788 At special positions: 0 Unit cell: (75, 62, 129, 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 19 16.00 O 939 8.00 N 793 7.00 C 3037 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=2.03 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.03 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 95 " distance=2.03 Simple disulfide: pdb=" SG CYS H 144 " - pdb=" SG CYS H 200 " distance=2.04 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.03 Simple disulfide: pdb=" SG CYS L 134 " - pdb=" SG CYS L 194 " 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 343 " Time building additional restraints: 0.37 Conformation dependent library (CDL) restraints added in 238.3 milliseconds 1226 Ramachandran restraints generated. 613 Oldfield, 0 Emsley, 613 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1140 Finding SS restraints... Secondary structure from input PDB file: 11 helices and 14 sheets defined 9.5% alpha, 42.2% 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 338 through 343 Processing helix chain 'A' and resid 349 through 353 removed outlier: 3.873A 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 384 through 389 removed outlier: 4.098A pdb=" N ASN A 388 " --> pdb=" O THR A 385 " (cutoff:3.500A) Processing helix chain 'A' and resid 406 through 410 Processing helix chain 'A' and resid 416 through 422 Processing helix chain 'H' and resid 28 through 32 removed outlier: 3.697A pdb=" N ASN H 32 " --> pdb=" O VAL H 29 " (cutoff:3.500A) 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 removed outlier: 3.734A pdb=" N THR H 90 " --> pdb=" O ALA H 87 " (cutoff:3.500A) Processing helix chain 'L' and resid 79 through 83 removed outlier: 3.652A pdb=" N ASP L 82 " --> pdb=" O GLN L 79 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N VAL L 83 " --> pdb=" O ALA L 80 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 79 through 83' Processing helix chain 'L' and resid 121 through 126 removed outlier: 3.641A pdb=" N LYS L 126 " --> pdb=" O ASP L 122 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 354 through 358 removed outlier: 3.613A pdb=" N ASN A 394 " --> pdb=" O GLU A 516 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AA3, first strand: chain 'A' and resid 473 through 474 Processing sheet with id=AA4, first strand: chain 'H' and resid 3 through 7 removed outlier: 3.594A pdb=" N THR H 77 " --> pdb=" O HIS H 72 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'H' and resid 11 through 12 removed outlier: 4.318A pdb=" N TYR H 33 " --> pdb=" O GLY H 98 " (cutoff:3.500A) removed outlier: 6.735A pdb=" N MET H 34 " --> pdb=" O VAL H 50 " (cutoff:3.500A) removed outlier: 4.422A pdb=" N VAL H 50 " --> pdb=" O MET H 34 " (cutoff:3.500A) removed outlier: 6.606A pdb=" N TRP H 36 " --> pdb=" O VAL H 48 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'H' and resid 11 through 12 removed outlier: 3.921A pdb=" N TYR H 106 " --> pdb=" O ARG H 97 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'H' and resid 124 through 128 removed outlier: 4.135A pdb=" N GLY H 143 " --> pdb=" O LEU H 128 " (cutoff:3.500A) removed outlier: 6.017A pdb=" N TYR H 180 " --> pdb=" O ASP H 148 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'H' and resid 124 through 128 removed outlier: 4.135A pdb=" N GLY H 143 " --> pdb=" O LEU H 128 " (cutoff:3.500A) removed outlier: 6.017A pdb=" N TYR H 180 " --> pdb=" O ASP H 148 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'H' and resid 155 through 158 removed outlier: 4.055A pdb=" N TYR H 198 " --> pdb=" O VAL H 215 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N LYS H 213 " --> pdb=" O CYS H 200 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'L' and resid 4 through 7 removed outlier: 3.632A pdb=" N ASP L 70 " --> pdb=" O SER L 67 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'L' and resid 10 through 13 removed outlier: 6.390A pdb=" N LEU L 11 " --> pdb=" O GLU L 105 " (cutoff:3.500A) removed outlier: 6.712A pdb=" N LEU L 33 " --> pdb=" O TYR L 49 " (cutoff:3.500A) removed outlier: 4.669A pdb=" N TYR L 49 " --> pdb=" O LEU L 33 " (cutoff:3.500A) removed outlier: 6.670A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'L' and resid 10 through 13 removed outlier: 6.390A pdb=" N LEU L 11 " --> pdb=" O GLU L 105 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N THR L 97 " --> pdb=" O GLN L 90 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'L' and resid 114 through 118 removed outlier: 5.437A pdb=" N SER L 131 " --> pdb=" O LEU L 181 " (cutoff:3.500A) removed outlier: 7.403A pdb=" N LEU L 181 " --> pdb=" O SER L 131 " (cutoff:3.500A) removed outlier: 5.606A pdb=" N VAL L 133 " --> pdb=" O LEU L 179 " (cutoff:3.500A) removed outlier: 7.298A pdb=" N LEU L 179 " --> pdb=" O VAL L 133 " (cutoff:3.500A) removed outlier: 5.490A pdb=" N LEU L 135 " --> pdb=" O SER L 177 " (cutoff:3.500A) removed outlier: 7.289A pdb=" N SER L 177 " --> pdb=" O LEU L 135 " (cutoff:3.500A) removed outlier: 5.235A pdb=" N ASN L 137 " --> pdb=" O LEU L 175 " (cutoff:3.500A) removed outlier: 7.248A pdb=" N LEU L 175 " --> pdb=" O ASN L 137 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'L' and resid 145 through 150 181 hydrogen bonds defined for protein. 453 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: 0.78 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: 1.22 - 1.34: 1500 1.34 - 1.46: 1168 1.46 - 1.58: 2219 1.58 - 1.69: 0 1.69 - 1.81: 22 Bond restraints: 4909 Sorted by residual: bond pdb=" N ASP H 101 " pdb=" CA ASP H 101 " ideal model delta sigma weight residual 1.457 1.489 -0.032 1.29e-02 6.01e+03 5.98e+00 bond pdb=" C1 NAG A1301 " pdb=" O5 NAG A1301 " ideal model delta sigma weight residual 1.406 1.438 -0.032 2.00e-02 2.50e+03 2.60e+00 bond pdb=" C LYS H 205 " pdb=" N PRO H 206 " ideal model delta sigma weight residual 1.336 1.355 -0.019 1.20e-02 6.94e+03 2.59e+00 bond pdb=" CB ASN H 73 " pdb=" CG ASN H 73 " ideal model delta sigma weight residual 1.516 1.552 -0.036 2.50e-02 1.60e+03 2.05e+00 bond pdb=" C SER L 94 " pdb=" N PRO L 95 " ideal model delta sigma weight residual 1.334 1.366 -0.032 2.34e-02 1.83e+03 1.87e+00 ... (remaining 4904 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.67: 6337 1.67 - 3.33: 284 3.33 - 5.00: 44 5.00 - 6.66: 11 6.66 - 8.33: 6 Bond angle restraints: 6682 Sorted by residual: angle pdb=" C GLY H 100 " pdb=" N ASP H 101 " pdb=" CA ASP H 101 " ideal model delta sigma weight residual 121.54 129.87 -8.33 1.91e+00 2.74e-01 1.90e+01 angle pdb=" C TRP L 50 " pdb=" N ALA L 51 " pdb=" CA ALA L 51 " ideal model delta sigma weight residual 121.54 128.33 -6.79 1.91e+00 2.74e-01 1.26e+01 angle pdb=" C PHE A 515 " pdb=" N GLU A 516 " pdb=" CA GLU A 516 " ideal model delta sigma weight residual 122.94 117.62 5.32 1.50e+00 4.44e-01 1.26e+01 angle pdb=" CA ASP H 101 " pdb=" CB ASP H 101 " pdb=" CG ASP H 101 " ideal model delta sigma weight residual 112.60 115.97 -3.37 1.00e+00 1.00e+00 1.14e+01 angle pdb=" CA LYS H 210 " pdb=" CB LYS H 210 " pdb=" CG LYS H 210 " ideal model delta sigma weight residual 114.10 120.52 -6.42 2.00e+00 2.50e-01 1.03e+01 ... (remaining 6677 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.53: 2696 16.53 - 33.06: 149 33.06 - 49.59: 38 49.59 - 66.12: 9 66.12 - 82.65: 8 Dihedral angle restraints: 2900 sinusoidal: 1103 harmonic: 1797 Sorted by residual: dihedral pdb=" CB CYS A 480 " pdb=" SG CYS A 480 " pdb=" SG CYS A 488 " pdb=" CB CYS A 488 " ideal model delta sinusoidal sigma weight residual 93.00 167.49 -74.49 1 1.00e+01 1.00e-02 7.03e+01 dihedral pdb=" CB CYS H 144 " pdb=" SG CYS H 144 " pdb=" SG CYS H 200 " pdb=" CB CYS H 200 " ideal model delta sinusoidal sigma weight residual 93.00 144.05 -51.05 1 1.00e+01 1.00e-02 3.56e+01 dihedral pdb=" CA HIS H 72 " pdb=" C HIS H 72 " pdb=" N ASN H 73 " pdb=" CA ASN H 73 " ideal model delta harmonic sigma weight residual 180.00 -157.47 -22.53 0 5.00e+00 4.00e-02 2.03e+01 ... (remaining 2897 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.047: 506 0.047 - 0.094: 159 0.094 - 0.142: 61 0.142 - 0.189: 9 0.189 - 0.236: 2 Chirality restraints: 737 Sorted by residual: chirality pdb=" CA ASP H 101 " pdb=" N ASP H 101 " pdb=" C ASP H 101 " pdb=" CB ASP H 101 " both_signs ideal model delta sigma weight residual False 2.51 2.27 0.24 2.00e-01 2.50e+01 1.39e+00 chirality pdb=" CB ILE A 332 " pdb=" CA ILE A 332 " pdb=" CG1 ILE A 332 " pdb=" CG2 ILE A 332 " both_signs ideal model delta sigma weight residual False 2.64 2.44 0.20 2.00e-01 2.50e+01 1.03e+00 chirality pdb=" CB ILE L 117 " pdb=" CA ILE L 117 " pdb=" CG1 ILE L 117 " pdb=" CG2 ILE L 117 " both_signs ideal model delta sigma weight residual False 2.64 2.46 0.18 2.00e-01 2.50e+01 8.17e-01 ... (remaining 734 not shown) Planarity restraints: 859 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR A 478 " 0.036 5.00e-02 4.00e+02 5.48e-02 4.80e+00 pdb=" N PRO A 479 " -0.095 5.00e-02 4.00e+02 pdb=" CA PRO A 479 " 0.028 5.00e-02 4.00e+02 pdb=" CD PRO A 479 " 0.031 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLU H 152 " -0.034 5.00e-02 4.00e+02 5.15e-02 4.24e+00 pdb=" N PRO H 153 " 0.089 5.00e-02 4.00e+02 pdb=" CA PRO H 153 " -0.030 5.00e-02 4.00e+02 pdb=" CD PRO H 153 " -0.025 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB ASP L 60 " 0.009 2.00e-02 2.50e+03 1.86e-02 3.47e+00 pdb=" CG ASP L 60 " -0.032 2.00e-02 2.50e+03 pdb=" OD1 ASP L 60 " 0.012 2.00e-02 2.50e+03 pdb=" OD2 ASP L 60 " 0.011 2.00e-02 2.50e+03 ... (remaining 856 not shown) Histogram of nonbonded interaction distances: 2.35 - 2.86: 1635 2.86 - 3.37: 3870 3.37 - 3.88: 8010 3.88 - 4.39: 9038 4.39 - 4.90: 15985 Nonbonded interactions: 38538 Sorted by model distance: nonbonded pdb=" O TRP A 353 " pdb=" NH1 ARG A 466 " model vdw 2.351 3.120 nonbonded pdb=" OG SER A 366 " pdb=" OD1 ASN A 388 " model vdw 2.354 3.040 nonbonded pdb=" OD2 ASP A 420 " pdb=" OG SER H 56 " model vdw 2.359 3.040 nonbonded pdb=" OH TYR A 453 " pdb=" OH TYR H 102 " model vdw 2.371 3.040 nonbonded pdb=" OG SER H 207 " pdb=" OG1 THR H 209 " model vdw 2.404 3.040 ... (remaining 38533 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: 4.370 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: 0.100 Check model and map are aligned: 0.010 Set scattering table: 0.020 Process input model: 6.350 Find NCS groups from input model: 0.030 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:6.390 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.280 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8655 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 4918 Z= 0.230 Angle : 0.819 8.326 6701 Z= 0.444 Chirality : 0.054 0.236 737 Planarity : 0.006 0.055 858 Dihedral : 12.166 82.651 1736 Min Nonbonded Distance : 2.351 Molprobity Statistics. All-atom Clashscore : 2.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.92 % Favored : 96.08 % Rotamer: Outliers : 0.00 % Allowed : 0.38 % Favored : 99.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.76 % 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: -0.85 (0.32), residues: 613 helix: -4.72 (0.22), residues: 37 sheet: 0.46 (0.32), residues: 243 loop : -0.82 (0.32), residues: 333 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG H 19 TYR 0.025 0.002 TYR A 495 PHE 0.015 0.002 PHE L 71 TRP 0.010 0.001 TRP A 436 HIS 0.005 0.002 HIS H 72 Details of bonding type rmsd/Z covalent geometry : bond 0.00500 / 0.23 ( 4909) covalent geometry : angle 0.81755 / 0.44 ( 6682) SS BOND : bond 0.00228 / 0.11 ( 8) SS BOND : angle 1.11351 / 0.60 ( 16) hydrogen bonds : bond 0.14625 / 10.36 ( 160) hydrogen bonds : angle 7.89792 / 5.60 ( 453) link_NAG-ASN : bond 0.00349 / 0.18 ( 1) link_NAG-ASN : angle 1.41317 / 0.82 ( 3) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1226 Ramachandran restraints generated. 613 Oldfield, 0 Emsley, 613 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1226 Ramachandran restraints generated. 613 Oldfield, 0 Emsley, 613 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 531 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 90 time to evaluate : 0.134 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 516 GLU cc_start: 0.8034 (pp20) cc_final: 0.7555 (pp20) REVERT: A 528 LYS cc_start: 0.5794 (tttm) cc_final: 0.4720 (pptt) REVERT: L 158 ASN cc_start: 0.7795 (m110) cc_final: 0.7591 (m110) REVERT: L 167 ASP cc_start: 0.8609 (t0) cc_final: 0.8273 (t0) outliers start: 0 outliers final: 0 residues processed: 90 average time/residue: 0.6291 time to fit residues: 58.5150 Evaluate side-chains 61 residues out of total 531 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 61 time to evaluate : 0.188 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 54 optimal weight: 2.9990 chunk 24 optimal weight: 1.9990 chunk 48 optimal weight: 0.6980 chunk 56 optimal weight: 3.9990 chunk 26 optimal weight: 2.9990 chunk 2 optimal weight: 2.9990 chunk 16 optimal weight: 2.9990 chunk 32 optimal weight: 2.9990 chunk 31 optimal weight: 0.5980 chunk 25 optimal weight: 0.6980 chunk 58 optimal weight: 0.6980 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... H 201 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3089 r_free = 0.3089 target = 0.063179 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2845 r_free = 0.2845 target = 0.052210 restraints weight = 12642.767| |-----------------------------------------------------------------------------| r_work (start): 0.2839 rms_B_bonded: 2.93 r_work: 0.2716 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work (final): 0.2716 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8774 moved from start: 0.1437 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 4918 Z= 0.191 Angle : 0.569 6.763 6701 Z= 0.297 Chirality : 0.043 0.134 737 Planarity : 0.005 0.060 858 Dihedral : 4.686 17.322 678 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 4.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 0.75 % Allowed : 9.60 % Favored : 89.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.76 % 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: -0.24 (0.33), residues: 613 helix: -4.73 (0.50), residues: 20 sheet: 0.58 (0.33), residues: 244 loop : -0.36 (0.33), residues: 349 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG L 24 TYR 0.016 0.001 TYR A 495 PHE 0.008 0.001 PHE L 71 TRP 0.008 0.001 TRP A 436 HIS 0.004 0.001 HIS H 72 Details of bonding type rmsd/Z covalent geometry : bond 0.00415 / 0.19 ( 4909) covalent geometry : angle 0.56855 / 0.30 ( 6682) SS BOND : bond 0.00187 / 0.09 ( 8) SS BOND : angle 0.54829 / 0.28 ( 16) hydrogen bonds : bond 0.03308 / 2.20 ( 160) hydrogen bonds : angle 6.16531 / 4.42 ( 453) link_NAG-ASN : bond 0.00156 / 0.08 ( 1) link_NAG-ASN : angle 1.11390 / 0.65 ( 3) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1226 Ramachandran restraints generated. 613 Oldfield, 0 Emsley, 613 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1226 Ramachandran restraints generated. 613 Oldfield, 0 Emsley, 613 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 69 residues out of total 531 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 65 time to evaluate : 0.183 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 420 ASP cc_start: 0.9146 (m-30) cc_final: 0.8778 (m-30) REVERT: A 516 GLU cc_start: 0.8132 (pp20) cc_final: 0.7631 (pp20) REVERT: A 528 LYS cc_start: 0.6010 (tttm) cc_final: 0.5017 (pptt) REVERT: H 3 GLN cc_start: 0.8314 (mm110) cc_final: 0.8103 (mm110) REVERT: H 88 GLU cc_start: 0.9054 (pm20) cc_final: 0.8830 (pm20) REVERT: L 158 ASN cc_start: 0.7836 (m110) cc_final: 0.7625 (m110) REVERT: L 167 ASP cc_start: 0.8989 (t0) cc_final: 0.8491 (t0) REVERT: L 170 ASP cc_start: 0.8699 (p0) cc_final: 0.8491 (p0) outliers start: 4 outliers final: 1 residues processed: 67 average time/residue: 0.5326 time to fit residues: 36.9765 Evaluate side-chains 59 residues out of total 531 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 58 time to evaluate : 0.110 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 161 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 48 optimal weight: 0.9990 chunk 14 optimal weight: 0.9980 chunk 46 optimal weight: 3.9990 chunk 11 optimal weight: 0.9980 chunk 57 optimal weight: 4.9990 chunk 50 optimal weight: 3.9990 chunk 23 optimal weight: 2.9990 chunk 24 optimal weight: 0.4980 chunk 41 optimal weight: 7.9990 chunk 60 optimal weight: 3.9990 chunk 33 optimal weight: 0.9980 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 414 GLN L 137 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3083 r_free = 0.3083 target = 0.062886 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2839 r_free = 0.2839 target = 0.052158 restraints weight = 12466.690| |-----------------------------------------------------------------------------| r_work (start): 0.2831 rms_B_bonded: 2.90 r_work: 0.2707 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work (final): 0.2707 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8738 moved from start: 0.1693 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.026 4918 Z= 0.181 Angle : 0.536 6.773 6701 Z= 0.280 Chirality : 0.043 0.154 737 Planarity : 0.005 0.062 858 Dihedral : 4.470 15.594 678 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 4.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Rotamer: Outliers : 1.13 % Allowed : 10.55 % Favored : 88.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.76 % 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: -0.11 (0.34), residues: 613 helix: -4.56 (0.59), residues: 26 sheet: 0.69 (0.33), residues: 244 loop : -0.21 (0.34), residues: 343 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG L 24 TYR 0.014 0.001 TYR A 495 PHE 0.008 0.001 PHE L 71 TRP 0.007 0.001 TRP A 436 HIS 0.003 0.001 HIS A 519 Details of bonding type rmsd/Z covalent geometry : bond 0.00395 / 0.18 ( 4909) covalent geometry : angle 0.53594 / 0.28 ( 6682) SS BOND : bond 0.00160 / 0.07 ( 8) SS BOND : angle 0.51584 / 0.27 ( 16) hydrogen bonds : bond 0.03011 / 1.98 ( 160) hydrogen bonds : angle 5.82036 / 4.19 ( 453) link_NAG-ASN : bond 0.00219 / 0.12 ( 1) link_NAG-ASN : angle 1.15249 / 0.67 ( 3) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1226 Ramachandran restraints generated. 613 Oldfield, 0 Emsley, 613 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1226 Ramachandran restraints generated. 613 Oldfield, 0 Emsley, 613 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 70 residues out of total 531 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 64 time to evaluate : 0.144 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 420 ASP cc_start: 0.9172 (m-30) cc_final: 0.8705 (m-30) REVERT: A 516 GLU cc_start: 0.8113 (pp20) cc_final: 0.7567 (pp20) REVERT: A 528 LYS cc_start: 0.5982 (tttm) cc_final: 0.5014 (pptt) REVERT: H 3 GLN cc_start: 0.8324 (mm110) cc_final: 0.8066 (mp10) REVERT: H 88 GLU cc_start: 0.9063 (pm20) cc_final: 0.8787 (pm20) REVERT: H 205 LYS cc_start: 0.9112 (mmmm) cc_final: 0.8909 (mmmt) REVERT: L 158 ASN cc_start: 0.7830 (m110) cc_final: 0.7627 (m110) REVERT: L 167 ASP cc_start: 0.8953 (t0) cc_final: 0.8406 (t0) outliers start: 6 outliers final: 2 residues processed: 66 average time/residue: 0.4273 time to fit residues: 29.4036 Evaluate side-chains 60 residues out of total 531 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 58 time to evaluate : 0.186 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 72 HIS Chi-restraints excluded: chain L residue 105 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 47 optimal weight: 0.8980 chunk 37 optimal weight: 8.9990 chunk 30 optimal weight: 3.9990 chunk 56 optimal weight: 2.9990 chunk 19 optimal weight: 2.9990 chunk 58 optimal weight: 1.9990 chunk 24 optimal weight: 0.6980 chunk 15 optimal weight: 2.9990 chunk 54 optimal weight: 0.3980 chunk 60 optimal weight: 0.9990 chunk 1 optimal weight: 1.9990 overall best weight: 0.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 414 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3070 r_free = 0.3070 target = 0.062274 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2823 r_free = 0.2823 target = 0.051530 restraints weight = 12479.748| |-----------------------------------------------------------------------------| r_work (start): 0.2817 rms_B_bonded: 2.93 r_work: 0.2691 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work (final): 0.2691 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8769 moved from start: 0.1878 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.025 4918 Z= 0.196 Angle : 0.528 6.779 6701 Z= 0.275 Chirality : 0.043 0.151 737 Planarity : 0.004 0.063 858 Dihedral : 4.414 16.027 678 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 4.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Rotamer: Outliers : 1.88 % Allowed : 12.24 % Favored : 85.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.76 % 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: -0.01 (0.34), residues: 613 helix: -4.45 (0.65), residues: 26 sheet: 0.76 (0.33), residues: 244 loop : -0.15 (0.35), residues: 343 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG L 24 TYR 0.016 0.001 TYR H 79 PHE 0.007 0.001 PHE L 71 TRP 0.007 0.001 TRP A 436 HIS 0.003 0.001 HIS A 519 Details of bonding type rmsd/Z covalent geometry : bond 0.00428 / 0.20 ( 4909) covalent geometry : angle 0.52732 / 0.28 ( 6682) SS BOND : bond 0.00158 / 0.07 ( 8) SS BOND : angle 0.62089 / 0.33 ( 16) hydrogen bonds : bond 0.02961 / 1.95 ( 160) hydrogen bonds : angle 5.70361 / 4.11 ( 453) link_NAG-ASN : bond 0.00247 / 0.13 ( 1) link_NAG-ASN : angle 1.20761 / 0.71 ( 3) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1226 Ramachandran restraints generated. 613 Oldfield, 0 Emsley, 613 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1226 Ramachandran restraints generated. 613 Oldfield, 0 Emsley, 613 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 531 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 69 time to evaluate : 0.119 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 420 ASP cc_start: 0.9171 (m-30) cc_final: 0.8639 (m-30) REVERT: A 462 LYS cc_start: 0.9185 (OUTLIER) cc_final: 0.8753 (mtmm) REVERT: A 516 GLU cc_start: 0.8152 (pp20) cc_final: 0.7554 (pp20) REVERT: A 528 LYS cc_start: 0.6043 (tttm) cc_final: 0.5032 (pptt) REVERT: H 3 GLN cc_start: 0.8374 (mm110) cc_final: 0.8092 (mp10) REVERT: H 86 ARG cc_start: 0.8477 (mtt-85) cc_final: 0.8192 (mtt-85) REVERT: H 88 GLU cc_start: 0.9101 (pm20) cc_final: 0.8771 (pm20) REVERT: H 205 LYS cc_start: 0.9154 (mmmm) cc_final: 0.8921 (mmmt) REVERT: L 17 GLU cc_start: 0.8531 (mt-10) cc_final: 0.8145 (mt-10) REVERT: L 55 GLU cc_start: 0.8863 (mm-30) cc_final: 0.8580 (tm-30) REVERT: L 81 GLU cc_start: 0.9165 (pm20) cc_final: 0.8950 (pm20) REVERT: L 167 ASP cc_start: 0.9023 (t0) cc_final: 0.8520 (t0) REVERT: L 170 ASP cc_start: 0.8665 (p0) cc_final: 0.8423 (p0) outliers start: 10 outliers final: 4 residues processed: 73 average time/residue: 0.5142 time to fit residues: 38.9549 Evaluate side-chains 66 residues out of total 531 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 61 time to evaluate : 0.203 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 462 LYS Chi-restraints excluded: chain H residue 72 HIS Chi-restraints excluded: chain L residue 10 THR Chi-restraints excluded: chain L residue 105 GLU Chi-restraints excluded: chain L residue 161 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 1 optimal weight: 1.9990 chunk 8 optimal weight: 0.5980 chunk 26 optimal weight: 0.8980 chunk 11 optimal weight: 2.9990 chunk 52 optimal weight: 3.9990 chunk 57 optimal weight: 3.9990 chunk 7 optimal weight: 0.8980 chunk 0 optimal weight: 1.9990 chunk 15 optimal weight: 0.4980 chunk 25 optimal weight: 0.1980 chunk 48 optimal weight: 0.9980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 414 GLN L 155 GLN L 158 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3095 r_free = 0.3095 target = 0.063452 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2850 r_free = 0.2850 target = 0.052604 restraints weight = 12648.614| |-----------------------------------------------------------------------------| r_work (start): 0.2838 rms_B_bonded: 2.98 r_work: 0.2713 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work (final): 0.2713 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8751 moved from start: 0.1985 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 4918 Z= 0.135 Angle : 0.494 6.643 6701 Z= 0.258 Chirality : 0.042 0.149 737 Planarity : 0.004 0.061 858 Dihedral : 4.184 15.528 678 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 4.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Rotamer: Outliers : 1.88 % Allowed : 13.75 % Favored : 84.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.76 % 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: 0.11 (0.35), residues: 613 helix: -4.43 (0.62), residues: 26 sheet: 0.86 (0.33), residues: 244 loop : -0.07 (0.35), residues: 343 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG L 24 TYR 0.012 0.001 TYR H 79 PHE 0.006 0.001 PHE L 98 TRP 0.007 0.001 TRP A 436 HIS 0.002 0.001 HIS A 519 Details of bonding type rmsd/Z covalent geometry : bond 0.00297 / 0.14 ( 4909) covalent geometry : angle 0.49389 / 0.26 ( 6682) SS BOND : bond 0.00169 / 0.07 ( 8) SS BOND : angle 0.46624 / 0.24 ( 16) hydrogen bonds : bond 0.02721 / 1.79 ( 160) hydrogen bonds : angle 5.42937 / 3.91 ( 453) link_NAG-ASN : bond 0.00090 / 0.05 ( 1) link_NAG-ASN : angle 1.08476 / 0.63 ( 3) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1226 Ramachandran restraints generated. 613 Oldfield, 0 Emsley, 613 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1226 Ramachandran restraints generated. 613 Oldfield, 0 Emsley, 613 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 531 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 71 time to evaluate : 0.122 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 462 LYS cc_start: 0.9185 (OUTLIER) cc_final: 0.8748 (mtmm) REVERT: A 516 GLU cc_start: 0.8169 (OUTLIER) cc_final: 0.7528 (pp20) REVERT: A 518 LEU cc_start: 0.8991 (mt) cc_final: 0.8710 (mp) REVERT: A 528 LYS cc_start: 0.6055 (tttm) cc_final: 0.5066 (pptt) REVERT: H 3 GLN cc_start: 0.8380 (mm110) cc_final: 0.8095 (mp10) REVERT: H 86 ARG cc_start: 0.8436 (mtt-85) cc_final: 0.8141 (mtt-85) REVERT: H 88 GLU cc_start: 0.9104 (pm20) cc_final: 0.8788 (pm20) REVERT: H 205 LYS cc_start: 0.9154 (mmmm) cc_final: 0.8895 (mmmt) REVERT: L 17 GLU cc_start: 0.8515 (mt-10) cc_final: 0.8101 (mt-10) REVERT: L 55 GLU cc_start: 0.8841 (mm-30) cc_final: 0.8576 (tm-30) REVERT: L 81 GLU cc_start: 0.9127 (pm20) cc_final: 0.8910 (pm20) REVERT: L 167 ASP cc_start: 0.8983 (t0) cc_final: 0.8275 (t0) outliers start: 10 outliers final: 5 residues processed: 74 average time/residue: 0.5936 time to fit residues: 45.3994 Evaluate side-chains 68 residues out of total 531 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 61 time to evaluate : 0.121 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 367 VAL Chi-restraints excluded: chain A residue 462 LYS Chi-restraints excluded: chain A residue 516 GLU Chi-restraints excluded: chain H residue 72 HIS Chi-restraints excluded: chain L residue 10 THR Chi-restraints excluded: chain L residue 105 GLU Chi-restraints excluded: chain L residue 161 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 6 optimal weight: 1.9990 chunk 3 optimal weight: 0.8980 chunk 48 optimal weight: 1.9990 chunk 51 optimal weight: 0.0370 chunk 60 optimal weight: 0.9980 chunk 16 optimal weight: 0.8980 chunk 5 optimal weight: 3.9990 chunk 53 optimal weight: 1.9990 chunk 56 optimal weight: 5.9990 chunk 18 optimal weight: 0.8980 chunk 33 optimal weight: 0.9990 overall best weight: 0.7458 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3078 r_free = 0.3078 target = 0.062691 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2836 r_free = 0.2836 target = 0.051930 restraints weight = 12801.968| |-----------------------------------------------------------------------------| r_work (start): 0.2832 rms_B_bonded: 2.95 r_work: 0.2706 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work (final): 0.2706 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8758 moved from start: 0.2084 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 4918 Z= 0.155 Angle : 0.508 6.657 6701 Z= 0.264 Chirality : 0.043 0.142 737 Planarity : 0.004 0.062 858 Dihedral : 4.154 15.074 678 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 4.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Rotamer: Outliers : 1.69 % Allowed : 15.44 % Favored : 82.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.76 % 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 (0.35), residues: 613 helix: -4.39 (0.64), residues: 26 sheet: 1.01 (0.33), residues: 242 loop : -0.04 (0.35), residues: 345 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG H 19 TYR 0.012 0.001 TYR L 192 PHE 0.006 0.001 PHE L 98 TRP 0.006 0.001 TRP A 436 HIS 0.002 0.001 HIS A 519 Details of bonding type rmsd/Z covalent geometry : bond 0.00341 / 0.16 ( 4909) covalent geometry : angle 0.50780 / 0.26 ( 6682) SS BOND : bond 0.00158 / 0.06 ( 8) SS BOND : angle 0.49098 / 0.26 ( 16) hydrogen bonds : bond 0.02759 / 1.81 ( 160) hydrogen bonds : angle 5.36154 / 3.86 ( 453) link_NAG-ASN : bond 0.00128 / 0.07 ( 1) link_NAG-ASN : angle 1.14146 / 0.66 ( 3) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1226 Ramachandran restraints generated. 613 Oldfield, 0 Emsley, 613 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1226 Ramachandran restraints generated. 613 Oldfield, 0 Emsley, 613 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 531 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 64 time to evaluate : 0.122 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 462 LYS cc_start: 0.9187 (OUTLIER) cc_final: 0.8754 (mtmm) REVERT: A 516 GLU cc_start: 0.8141 (OUTLIER) cc_final: 0.7506 (pp20) REVERT: A 528 LYS cc_start: 0.6083 (tttm) cc_final: 0.5060 (pptt) REVERT: H 3 GLN cc_start: 0.8377 (mm110) cc_final: 0.8083 (mp10) REVERT: H 88 GLU cc_start: 0.9094 (pm20) cc_final: 0.8760 (pm20) REVERT: H 205 LYS cc_start: 0.9157 (mmmm) cc_final: 0.8881 (mmmt) REVERT: L 167 ASP cc_start: 0.8994 (t0) cc_final: 0.8499 (t0) REVERT: L 170 ASP cc_start: 0.8665 (p0) cc_final: 0.8396 (p0) outliers start: 9 outliers final: 5 residues processed: 69 average time/residue: 0.5096 time to fit residues: 36.5287 Evaluate side-chains 69 residues out of total 531 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 62 time to evaluate : 0.137 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 367 VAL Chi-restraints excluded: chain A residue 462 LYS Chi-restraints excluded: chain A residue 516 GLU Chi-restraints excluded: chain H residue 72 HIS Chi-restraints excluded: chain L residue 10 THR Chi-restraints excluded: chain L residue 105 GLU Chi-restraints excluded: chain L residue 161 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 39 optimal weight: 4.9990 chunk 57 optimal weight: 4.9990 chunk 43 optimal weight: 0.7980 chunk 51 optimal weight: 0.5980 chunk 36 optimal weight: 0.7980 chunk 55 optimal weight: 0.3980 chunk 56 optimal weight: 4.9990 chunk 21 optimal weight: 0.0270 chunk 42 optimal weight: 1.9990 chunk 14 optimal weight: 0.8980 chunk 35 optimal weight: 2.9990 overall best weight: 0.5238 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3098 r_free = 0.3098 target = 0.063671 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2863 r_free = 0.2863 target = 0.053048 restraints weight = 12694.921| |-----------------------------------------------------------------------------| r_work (start): 0.2855 rms_B_bonded: 2.93 r_work: 0.2730 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work (final): 0.2730 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8746 moved from start: 0.2156 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 4918 Z= 0.122 Angle : 0.502 6.661 6701 Z= 0.257 Chirality : 0.042 0.139 737 Planarity : 0.004 0.061 858 Dihedral : 4.028 16.851 678 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 4.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer: Outliers : 2.07 % Allowed : 16.20 % Favored : 81.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.76 % 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: 0.30 (0.35), residues: 613 helix: -4.35 (0.61), residues: 26 sheet: 1.11 (0.34), residues: 242 loop : -0.04 (0.35), residues: 345 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG H 19 TYR 0.017 0.001 TYR H 79 PHE 0.006 0.001 PHE L 98 TRP 0.007 0.001 TRP A 436 HIS 0.002 0.001 HIS A 519 Details of bonding type rmsd/Z covalent geometry : bond 0.00270 / 0.12 ( 4909) covalent geometry : angle 0.50164 / 0.26 ( 6682) SS BOND : bond 0.00145 / 0.06 ( 8) SS BOND : angle 0.38620 / 0.20 ( 16) hydrogen bonds : bond 0.02603 / 1.70 ( 160) hydrogen bonds : angle 5.18095 / 3.72 ( 453) link_NAG-ASN : bond 0.00007 / 0.00 ( 1) link_NAG-ASN : angle 1.04143 / 0.61 ( 3) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1226 Ramachandran restraints generated. 613 Oldfield, 0 Emsley, 613 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1226 Ramachandran restraints generated. 613 Oldfield, 0 Emsley, 613 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 531 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 67 time to evaluate : 0.123 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 430 THR cc_start: 0.9279 (OUTLIER) cc_final: 0.8957 (p) REVERT: A 462 LYS cc_start: 0.9176 (OUTLIER) cc_final: 0.8719 (mtmm) REVERT: A 528 LYS cc_start: 0.6072 (tttm) cc_final: 0.5086 (pptt) REVERT: H 3 GLN cc_start: 0.8380 (mm110) cc_final: 0.8075 (mp10) REVERT: H 88 GLU cc_start: 0.9107 (pm20) cc_final: 0.8855 (pm20) REVERT: H 205 LYS cc_start: 0.9156 (mmmm) cc_final: 0.8869 (mmmt) REVERT: L 17 GLU cc_start: 0.8369 (mt-10) cc_final: 0.7940 (mt-10) REVERT: L 81 GLU cc_start: 0.9112 (pm20) cc_final: 0.8889 (pm20) REVERT: L 142 ARG cc_start: 0.9129 (tpp80) cc_final: 0.8746 (ttt-90) REVERT: L 167 ASP cc_start: 0.8974 (t0) cc_final: 0.8241 (t0) REVERT: L 170 ASP cc_start: 0.8605 (p0) cc_final: 0.8343 (p0) outliers start: 11 outliers final: 5 residues processed: 70 average time/residue: 0.4945 time to fit residues: 35.8883 Evaluate side-chains 68 residues out of total 531 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 61 time to evaluate : 0.139 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 367 VAL Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 462 LYS Chi-restraints excluded: chain H residue 72 HIS Chi-restraints excluded: chain L residue 10 THR Chi-restraints excluded: chain L residue 106 ILE Chi-restraints excluded: chain L residue 161 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 37 optimal weight: 0.8980 chunk 0 optimal weight: 2.9990 chunk 42 optimal weight: 0.6980 chunk 38 optimal weight: 4.9990 chunk 3 optimal weight: 0.9990 chunk 52 optimal weight: 3.9990 chunk 40 optimal weight: 0.9990 chunk 29 optimal weight: 0.5980 chunk 18 optimal weight: 0.0170 chunk 24 optimal weight: 1.9990 chunk 45 optimal weight: 0.6980 overall best weight: 0.5818 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3103 r_free = 0.3103 target = 0.063776 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2859 r_free = 0.2859 target = 0.052905 restraints weight = 12890.244| |-----------------------------------------------------------------------------| r_work (start): 0.2849 rms_B_bonded: 3.00 r_work: 0.2722 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work (final): 0.2722 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8756 moved from start: 0.2241 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 4918 Z= 0.130 Angle : 0.493 6.559 6701 Z= 0.256 Chirality : 0.042 0.136 737 Planarity : 0.004 0.061 858 Dihedral : 4.002 15.566 678 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 4.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 1.69 % Allowed : 16.01 % Favored : 82.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.76 % 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: 0.34 (0.35), residues: 613 helix: -4.30 (0.62), residues: 26 sheet: 1.12 (0.34), residues: 242 loop : -0.01 (0.35), residues: 345 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG H 19 TYR 0.018 0.001 TYR H 79 PHE 0.006 0.001 PHE L 98 TRP 0.007 0.001 TRP A 436 HIS 0.002 0.001 HIS A 519 Details of bonding type rmsd/Z covalent geometry : bond 0.00286 / 0.13 ( 4909) covalent geometry : angle 0.49322 / 0.26 ( 6682) SS BOND : bond 0.00147 / 0.06 ( 8) SS BOND : angle 0.38819 / 0.20 ( 16) hydrogen bonds : bond 0.02650 / 1.74 ( 160) hydrogen bonds : angle 5.13285 / 3.69 ( 453) link_NAG-ASN : bond 0.00057 / 0.03 ( 1) link_NAG-ASN : angle 1.10398 / 0.64 ( 3) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1226 Ramachandran restraints generated. 613 Oldfield, 0 Emsley, 613 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1226 Ramachandran restraints generated. 613 Oldfield, 0 Emsley, 613 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 531 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 63 time to evaluate : 0.143 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 430 THR cc_start: 0.9272 (OUTLIER) cc_final: 0.8956 (p) REVERT: A 462 LYS cc_start: 0.9146 (OUTLIER) cc_final: 0.8678 (mttm) REVERT: A 516 GLU cc_start: 0.8110 (pp20) cc_final: 0.7591 (pp20) REVERT: A 528 LYS cc_start: 0.6076 (tttm) cc_final: 0.5112 (pptt) REVERT: H 3 GLN cc_start: 0.8375 (mm110) cc_final: 0.8048 (mp10) REVERT: H 88 GLU cc_start: 0.9095 (pm20) cc_final: 0.8757 (pm20) REVERT: H 205 LYS cc_start: 0.9163 (mmmm) cc_final: 0.8860 (mmmt) REVERT: L 142 ARG cc_start: 0.9146 (tpp80) cc_final: 0.8763 (ttt-90) REVERT: L 165 GLU cc_start: 0.8954 (mm-30) cc_final: 0.8677 (pm20) REVERT: L 167 ASP cc_start: 0.8880 (t0) cc_final: 0.8246 (t0) REVERT: L 170 ASP cc_start: 0.8549 (p0) cc_final: 0.8348 (p0) outliers start: 9 outliers final: 6 residues processed: 69 average time/residue: 0.4960 time to fit residues: 35.5486 Evaluate side-chains 70 residues out of total 531 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 62 time to evaluate : 0.185 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 367 VAL Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 462 LYS Chi-restraints excluded: chain H residue 72 HIS Chi-restraints excluded: chain L residue 10 THR Chi-restraints excluded: chain L residue 13 LEU Chi-restraints excluded: chain L residue 106 ILE Chi-restraints excluded: chain L residue 161 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 29 optimal weight: 0.9980 chunk 55 optimal weight: 2.9990 chunk 50 optimal weight: 0.6980 chunk 2 optimal weight: 0.5980 chunk 18 optimal weight: 1.9990 chunk 38 optimal weight: 3.9990 chunk 53 optimal weight: 3.9990 chunk 56 optimal weight: 2.9990 chunk 25 optimal weight: 0.5980 chunk 42 optimal weight: 0.9990 chunk 13 optimal weight: 2.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3084 r_free = 0.3084 target = 0.062917 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2840 r_free = 0.2840 target = 0.052107 restraints weight = 12721.100| |-----------------------------------------------------------------------------| r_work (start): 0.2835 rms_B_bonded: 2.96 r_work: 0.2709 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work (final): 0.2709 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8769 moved from start: 0.2212 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 4918 Z= 0.160 Angle : 0.511 6.610 6701 Z= 0.265 Chirality : 0.043 0.136 737 Planarity : 0.004 0.062 858 Dihedral : 4.098 15.801 678 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 4.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 1.69 % Allowed : 16.01 % Favored : 82.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.76 % 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: 0.31 (0.35), residues: 613 helix: -4.34 (0.62), residues: 26 sheet: 1.06 (0.33), residues: 241 loop : 0.03 (0.35), residues: 346 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 346 TYR 0.014 0.001 TYR H 79 PHE 0.006 0.001 PHE L 98 TRP 0.006 0.001 TRP A 436 HIS 0.003 0.001 HIS A 519 Details of bonding type rmsd/Z covalent geometry : bond 0.00352 / 0.16 ( 4909) covalent geometry : angle 0.51038 / 0.26 ( 6682) SS BOND : bond 0.00148 / 0.06 ( 8) SS BOND : angle 0.41498 / 0.21 ( 16) hydrogen bonds : bond 0.02725 / 1.79 ( 160) hydrogen bonds : angle 5.19615 / 3.74 ( 453) link_NAG-ASN : bond 0.00150 / 0.08 ( 1) link_NAG-ASN : angle 1.19333 / 0.69 ( 3) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1226 Ramachandran restraints generated. 613 Oldfield, 0 Emsley, 613 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1226 Ramachandran restraints generated. 613 Oldfield, 0 Emsley, 613 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 531 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 62 time to evaluate : 0.173 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 430 THR cc_start: 0.9274 (OUTLIER) cc_final: 0.8959 (p) REVERT: A 462 LYS cc_start: 0.9152 (OUTLIER) cc_final: 0.8691 (mtmm) REVERT: A 516 GLU cc_start: 0.8130 (pp20) cc_final: 0.7561 (pp20) REVERT: A 528 LYS cc_start: 0.6067 (tttm) cc_final: 0.5043 (pptt) REVERT: H 3 GLN cc_start: 0.8382 (mm110) cc_final: 0.8034 (mp10) REVERT: H 19 ARG cc_start: 0.8955 (tmm-80) cc_final: 0.8752 (tpt-90) REVERT: H 88 GLU cc_start: 0.9103 (pm20) cc_final: 0.8748 (pm20) REVERT: H 205 LYS cc_start: 0.9173 (mmmm) cc_final: 0.8873 (mmmt) REVERT: L 142 ARG cc_start: 0.9128 (tpp80) cc_final: 0.8328 (ttp80) REVERT: L 165 GLU cc_start: 0.8935 (mm-30) cc_final: 0.8644 (pm20) REVERT: L 167 ASP cc_start: 0.8892 (t0) cc_final: 0.8252 (t0) REVERT: L 170 ASP cc_start: 0.8517 (p0) cc_final: 0.8311 (p0) outliers start: 9 outliers final: 6 residues processed: 68 average time/residue: 0.5135 time to fit residues: 36.3970 Evaluate side-chains 69 residues out of total 531 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 61 time to evaluate : 0.189 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 367 VAL Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 462 LYS Chi-restraints excluded: chain H residue 72 HIS Chi-restraints excluded: chain L residue 10 THR Chi-restraints excluded: chain L residue 13 LEU Chi-restraints excluded: chain L residue 106 ILE Chi-restraints excluded: chain L residue 161 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 50 optimal weight: 0.9980 chunk 1 optimal weight: 1.9990 chunk 41 optimal weight: 0.0670 chunk 58 optimal weight: 0.0050 chunk 59 optimal weight: 2.9990 chunk 6 optimal weight: 0.6980 chunk 56 optimal weight: 1.9990 chunk 52 optimal weight: 1.9990 chunk 3 optimal weight: 0.6980 chunk 13 optimal weight: 0.0570 chunk 42 optimal weight: 0.8980 overall best weight: 0.3050 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3124 r_free = 0.3124 target = 0.064677 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.2891 r_free = 0.2891 target = 0.054127 restraints weight = 12655.698| |-----------------------------------------------------------------------------| r_work (start): 0.2881 rms_B_bonded: 2.94 r_work: 0.2757 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work (final): 0.2757 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8730 moved from start: 0.2382 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 4918 Z= 0.098 Angle : 0.489 6.515 6701 Z= 0.252 Chirality : 0.042 0.136 737 Planarity : 0.004 0.060 858 Dihedral : 3.837 15.557 678 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 4.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 1.13 % Allowed : 16.57 % Favored : 82.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.76 % 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: 0.43 (0.35), residues: 613 helix: -4.19 (0.62), residues: 26 sheet: 1.29 (0.34), residues: 232 loop : 0.00 (0.34), residues: 355 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 346 TYR 0.014 0.001 TYR L 192 PHE 0.005 0.001 PHE A 377 TRP 0.007 0.001 TRP A 436 HIS 0.002 0.001 HIS H 72 Details of bonding type rmsd/Z covalent geometry : bond 0.00220 / 0.10 ( 4909) covalent geometry : angle 0.48921 / 0.25 ( 6682) SS BOND : bond 0.00183 / 0.09 ( 8) SS BOND : angle 0.41468 / 0.21 ( 16) hydrogen bonds : bond 0.02429 / 1.59 ( 160) hydrogen bonds : angle 4.86152 / 3.50 ( 453) link_NAG-ASN : bond 0.00082 / 0.04 ( 1) link_NAG-ASN : angle 0.93238 / 0.54 ( 3) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1226 Ramachandran restraints generated. 613 Oldfield, 0 Emsley, 613 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1226 Ramachandran restraints generated. 613 Oldfield, 0 Emsley, 613 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 531 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 65 time to evaluate : 0.187 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 516 GLU cc_start: 0.8150 (pp20) cc_final: 0.7557 (pp20) REVERT: A 528 LYS cc_start: 0.6064 (tttm) cc_final: 0.5180 (pptt) REVERT: H 3 GLN cc_start: 0.8372 (mm110) cc_final: 0.8042 (mp10) REVERT: H 88 GLU cc_start: 0.9075 (pm20) cc_final: 0.8781 (pm20) REVERT: H 205 LYS cc_start: 0.9146 (mmmm) cc_final: 0.8844 (mmmt) REVERT: L 142 ARG cc_start: 0.9148 (tpp80) cc_final: 0.8780 (ttt-90) REVERT: L 165 GLU cc_start: 0.8915 (mm-30) cc_final: 0.8657 (pm20) REVERT: L 167 ASP cc_start: 0.8862 (t0) cc_final: 0.8225 (t0) outliers start: 6 outliers final: 5 residues processed: 69 average time/residue: 0.5578 time to fit residues: 40.0058 Evaluate side-chains 65 residues out of total 531 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 60 time to evaluate : 0.176 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 367 VAL Chi-restraints excluded: chain H residue 72 HIS Chi-restraints excluded: chain L residue 10 THR Chi-restraints excluded: chain L residue 106 ILE Chi-restraints excluded: chain L residue 161 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 47 optimal weight: 2.9990 chunk 14 optimal weight: 0.3980 chunk 27 optimal weight: 1.9990 chunk 49 optimal weight: 2.9990 chunk 5 optimal weight: 0.0770 chunk 55 optimal weight: 2.9990 chunk 6 optimal weight: 0.5980 chunk 32 optimal weight: 4.9990 chunk 54 optimal weight: 0.8980 chunk 58 optimal weight: 3.9990 chunk 15 optimal weight: 0.0670 overall best weight: 0.4076 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 409 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3119 r_free = 0.3119 target = 0.064391 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.2883 r_free = 0.2883 target = 0.053802 restraints weight = 12554.490| |-----------------------------------------------------------------------------| r_work (start): 0.2881 rms_B_bonded: 2.93 r_work: 0.2758 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work (final): 0.2758 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8741 moved from start: 0.2347 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 4918 Z= 0.110 Angle : 0.510 8.240 6701 Z= 0.259 Chirality : 0.043 0.135 737 Planarity : 0.004 0.061 858 Dihedral : 3.841 15.088 678 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 4.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 1.69 % Allowed : 16.20 % Favored : 82.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.76 % 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: 0.49 (0.35), residues: 613 helix: -3.93 (0.65), residues: 27 sheet: 1.33 (0.34), residues: 232 loop : 0.04 (0.35), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG H 86 TYR 0.016 0.001 TYR H 79 PHE 0.005 0.001 PHE A 377 TRP 0.006 0.001 TRP A 436 HIS 0.002 0.001 HIS A 519 Details of bonding type rmsd/Z covalent geometry : bond 0.00246 / 0.11 ( 4909) covalent geometry : angle 0.51026 / 0.26 ( 6682) SS BOND : bond 0.00134 / 0.06 ( 8) SS BOND : angle 0.44871 / 0.22 ( 16) hydrogen bonds : bond 0.02535 / 1.68 ( 160) hydrogen bonds : angle 4.81505 / 3.46 ( 453) link_NAG-ASN : bond 0.00016 / 0.01 ( 1) link_NAG-ASN : angle 1.03816 / 0.60 ( 3) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1432.58 seconds wall clock time: 25 minutes 14.11 seconds (1514.11 seconds total)