Starting phenix.real_space_refine on Thu Mar 6 04:58:28 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7mjl_23877/03_2025/7mjl_23877.cif Found real_map, /net/cci-nas-00/data/ceres_data/7mjl_23877/03_2025/7mjl_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/7mjl_23877/03_2025/7mjl_23877.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7mjl_23877/03_2025/7mjl_23877.map" model { file = "/net/cci-nas-00/data/ceres_data/7mjl_23877/03_2025/7mjl_23877.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7mjl_23877/03_2025/7mjl_23877.cif" } resolution = 2.95 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.024 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): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/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 dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 5.14, per 1000 atoms: 1.07 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: 1.16 Conformation dependent library (CDL) restraints added in 584.0 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: 0.68 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: 1.31 Time building geometry restraints manager: 1.39 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: 2713 16.53 - 33.06: 151 33.06 - 49.59: 38 49.59 - 66.12: 11 66.12 - 82.65: 8 Dihedral angle restraints: 2921 sinusoidal: 1124 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 2918 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: 4.000 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: 0.230 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 17.280 Find NCS groups from input model: 0.060 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:12.110 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.780 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8474 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 4909 Z= 0.325 Angle : 0.818 8.326 6682 Z= 0.444 Chirality : 0.054 0.236 737 Planarity : 0.006 0.055 858 Dihedral : 12.247 82.651 1757 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.85 (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 TRP 0.010 0.001 TRP A 436 HIS 0.005 0.002 HIS H 72 PHE 0.015 0.002 PHE L 71 TYR 0.025 0.002 TYR A 495 ARG 0.006 0.001 ARG H 19 *********************** 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 : 0.589 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: 1.4306 time to fit residues: 133.2123 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 : 0.600 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 51 optimal weight: 0.8980 chunk 46 optimal weight: 5.9990 chunk 25 optimal weight: 0.6980 chunk 15 optimal weight: 1.9990 chunk 31 optimal weight: 0.0670 chunk 24 optimal weight: 0.9990 chunk 47 optimal weight: 0.5980 chunk 18 optimal weight: 0.0270 chunk 29 optimal weight: 0.2980 chunk 35 optimal weight: 3.9990 chunk 55 optimal weight: 0.9980 overall best weight: 0.3376 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 201 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3142 r_free = 0.3142 target = 0.065525 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2910 r_free = 0.2910 target = 0.054844 restraints weight = 12328.801| |-----------------------------------------------------------------------------| r_work (start): 0.2902 rms_B_bonded: 2.88 r_work: 0.2781 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work (final): 0.2781 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8547 moved from start: 0.1474 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 4909 Z= 0.158 Angle : 0.531 6.643 6682 Z= 0.277 Chirality : 0.043 0.138 737 Planarity : 0.005 0.055 858 Dihedral : 4.852 36.343 699 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 4.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 0.38 % Allowed : 9.23 % Favored : 90.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.19 (0.33), residues: 613 helix: -4.70 (0.49), residues: 20 sheet: 0.65 (0.33), residues: 244 loop : -0.36 (0.32), residues: 349 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 436 HIS 0.003 0.001 HIS H 72 PHE 0.006 0.001 PHE L 71 TYR 0.013 0.001 TYR A 495 ARG 0.010 0.001 ARG L 24 *********************** 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 78 residues out of total 531 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 76 time to evaluate : 0.569 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 420 ASP cc_start: 0.9170 (m-30) cc_final: 0.8800 (m-30) REVERT: A 516 GLU cc_start: 0.8101 (pp20) cc_final: 0.7648 (pp20) REVERT: A 528 LYS cc_start: 0.6280 (tttm) cc_final: 0.4896 (pptt) REVERT: H 3 GLN cc_start: 0.8286 (mm110) cc_final: 0.8051 (mm110) REVERT: H 88 GLU cc_start: 0.9035 (pm20) cc_final: 0.8800 (pm20) REVERT: L 17 GLU cc_start: 0.8605 (mt-10) cc_final: 0.8216 (mt-10) REVERT: L 158 ASN cc_start: 0.7819 (m110) cc_final: 0.7573 (m110) REVERT: L 167 ASP cc_start: 0.8937 (t0) cc_final: 0.8418 (t0) REVERT: L 170 ASP cc_start: 0.8699 (p0) cc_final: 0.8487 (p0) outliers start: 2 outliers final: 0 residues processed: 76 average time/residue: 1.6261 time to fit residues: 127.7074 Evaluate side-chains 63 residues out of total 531 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 63 time to evaluate : 0.530 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 40 optimal weight: 2.9990 chunk 29 optimal weight: 0.5980 chunk 32 optimal weight: 1.9990 chunk 39 optimal weight: 4.9990 chunk 0 optimal weight: 2.9990 chunk 1 optimal weight: 1.9990 chunk 28 optimal weight: 2.9990 chunk 43 optimal weight: 2.9990 chunk 58 optimal weight: 0.9980 chunk 41 optimal weight: 4.9990 chunk 56 optimal weight: 4.9990 overall best weight: 1.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 414 GLN H 109 GLN L 137 ASN L 152 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2998 r_free = 0.2998 target = 0.060134 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2750 r_free = 0.2750 target = 0.049392 restraints weight = 12813.497| |-----------------------------------------------------------------------------| r_work (start): 0.2747 rms_B_bonded: 2.86 r_work: 0.2626 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work (final): 0.2626 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8540 moved from start: 0.1828 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.033 4909 Z= 0.444 Angle : 0.621 6.984 6682 Z= 0.325 Chirality : 0.045 0.146 737 Planarity : 0.005 0.067 858 Dihedral : 5.242 34.564 699 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 4.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.59 % Favored : 96.41 % Rotamer: Outliers : 2.07 % Allowed : 10.36 % Favored : 87.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.28 (0.34), residues: 613 helix: -4.53 (0.65), residues: 26 sheet: 0.50 (0.33), residues: 244 loop : -0.27 (0.34), residues: 343 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 436 HIS 0.005 0.002 HIS H 72 PHE 0.011 0.001 PHE L 71 TYR 0.017 0.002 TYR A 495 ARG 0.011 0.001 ARG L 24 *********************** 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: 11 poor density : 59 time to evaluate : 0.583 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 420 ASP cc_start: 0.9166 (m-30) cc_final: 0.8662 (m-30) REVERT: A 462 LYS cc_start: 0.9105 (OUTLIER) cc_final: 0.8675 (mtmm) REVERT: A 516 GLU cc_start: 0.8050 (pp20) cc_final: 0.7484 (pp20) REVERT: H 3 GLN cc_start: 0.8243 (mm110) cc_final: 0.7963 (mp10) REVERT: H 88 GLU cc_start: 0.9078 (pm20) cc_final: 0.8702 (pm20) REVERT: H 205 LYS cc_start: 0.9134 (mmmm) cc_final: 0.8613 (tptp) REVERT: L 4 MET cc_start: 0.8860 (mmm) cc_final: 0.7815 (mmm) REVERT: L 158 ASN cc_start: 0.7911 (m110) cc_final: 0.7681 (m110) REVERT: L 165 GLU cc_start: 0.8219 (pp20) cc_final: 0.7975 (pp20) REVERT: L 167 ASP cc_start: 0.8919 (t0) cc_final: 0.8406 (t0) outliers start: 11 outliers final: 4 residues processed: 65 average time/residue: 1.2505 time to fit residues: 84.6284 Evaluate side-chains 63 residues out of total 531 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 58 time to evaluate : 0.545 ------------------------------------------------------------------------------- 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 13 LEU Chi-restraints excluded: chain L residue 105 GLU Chi-restraints excluded: chain L residue 161 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 25 optimal weight: 0.5980 chunk 29 optimal weight: 0.0770 chunk 40 optimal weight: 2.9990 chunk 30 optimal weight: 0.7980 chunk 5 optimal weight: 0.0870 chunk 1 optimal weight: 0.7980 chunk 35 optimal weight: 0.9980 chunk 45 optimal weight: 0.0570 chunk 9 optimal weight: 0.7980 chunk 20 optimal weight: 0.9980 chunk 47 optimal weight: 0.9980 overall best weight: 0.3234 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 414 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3115 r_free = 0.3115 target = 0.064486 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.2876 r_free = 0.2876 target = 0.053555 restraints weight = 12574.737| |-----------------------------------------------------------------------------| r_work (start): 0.2872 rms_B_bonded: 2.98 r_work: 0.2747 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work (final): 0.2747 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8604 moved from start: 0.1967 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 4909 Z= 0.152 Angle : 0.486 6.619 6682 Z= 0.254 Chirality : 0.042 0.152 737 Planarity : 0.004 0.059 858 Dihedral : 4.305 18.559 699 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 4.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 1.13 % Allowed : 12.24 % Favored : 86.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.04 (0.34), residues: 613 helix: -4.50 (0.58), residues: 26 sheet: 0.75 (0.33), residues: 244 loop : -0.17 (0.34), residues: 343 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP H 158 HIS 0.002 0.001 HIS A 519 PHE 0.006 0.001 PHE H 67 TYR 0.011 0.001 TYR L 192 ARG 0.007 0.001 ARG L 24 *********************** 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: 6 poor density : 73 time to evaluate : 0.636 Fit side-chains revert: symmetry clash REVERT: A 420 ASP cc_start: 0.9176 (m-30) cc_final: 0.8685 (m-30) REVERT: A 462 LYS cc_start: 0.9178 (OUTLIER) cc_final: 0.8677 (mtmm) REVERT: A 516 GLU cc_start: 0.8191 (pp20) cc_final: 0.7610 (pp20) REVERT: A 528 LYS cc_start: 0.6544 (tttt) cc_final: 0.4810 (pptt) REVERT: H 3 GLN cc_start: 0.8384 (mm110) cc_final: 0.8125 (mp10) REVERT: H 86 ARG cc_start: 0.8388 (mtt-85) cc_final: 0.8102 (mtt-85) REVERT: H 88 GLU cc_start: 0.9075 (pm20) cc_final: 0.8795 (pm20) REVERT: H 205 LYS cc_start: 0.9154 (mmmm) cc_final: 0.8910 (mmmt) REVERT: L 17 GLU cc_start: 0.8524 (mt-10) cc_final: 0.7999 (mt-10) REVERT: L 81 GLU cc_start: 0.9223 (pm20) cc_final: 0.9005 (pm20) REVERT: L 142 ARG cc_start: 0.9117 (tpp80) cc_final: 0.8425 (ttp80) REVERT: L 158 ASN cc_start: 0.7852 (m110) cc_final: 0.7648 (m110) REVERT: L 167 ASP cc_start: 0.9005 (t0) cc_final: 0.8505 (t0) REVERT: L 170 ASP cc_start: 0.8714 (p0) cc_final: 0.8463 (p0) outliers start: 6 outliers final: 1 residues processed: 75 average time/residue: 1.5614 time to fit residues: 121.4558 Evaluate side-chains 64 residues out of total 531 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 62 time to evaluate : 0.539 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 462 LYS Chi-restraints excluded: chain H residue 145 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 18 optimal weight: 0.6980 chunk 41 optimal weight: 0.9980 chunk 7 optimal weight: 0.6980 chunk 24 optimal weight: 1.9990 chunk 34 optimal weight: 0.0670 chunk 49 optimal weight: 2.9990 chunk 22 optimal weight: 0.7980 chunk 6 optimal weight: 0.5980 chunk 50 optimal weight: 2.9990 chunk 1 optimal weight: 0.5980 chunk 33 optimal weight: 0.8980 overall best weight: 0.5318 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3103 r_free = 0.3103 target = 0.063793 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2867 r_free = 0.2867 target = 0.053057 restraints weight = 12600.103| |-----------------------------------------------------------------------------| r_work (start): 0.2858 rms_B_bonded: 2.94 r_work: 0.2734 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work (final): 0.2734 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8607 moved from start: 0.2008 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 4909 Z= 0.180 Angle : 0.489 6.589 6682 Z= 0.255 Chirality : 0.042 0.148 737 Planarity : 0.004 0.061 858 Dihedral : 4.198 19.791 699 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 3.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 1.51 % Allowed : 13.75 % Favored : 84.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.09 (0.34), residues: 613 helix: -4.46 (0.58), residues: 26 sheet: 0.88 (0.33), residues: 244 loop : -0.11 (0.34), residues: 343 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 436 HIS 0.002 0.001 HIS H 72 PHE 0.006 0.001 PHE L 98 TYR 0.016 0.001 TYR H 79 ARG 0.008 0.001 ARG H 19 *********************** 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 78 residues out of total 531 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 70 time to evaluate : 0.637 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 420 ASP cc_start: 0.9189 (m-30) cc_final: 0.8663 (m-30) REVERT: A 462 LYS cc_start: 0.9148 (OUTLIER) cc_final: 0.8643 (mtmm) REVERT: A 516 GLU cc_start: 0.8184 (pp20) cc_final: 0.7580 (pp20) REVERT: A 518 LEU cc_start: 0.8974 (mt) cc_final: 0.8714 (mp) REVERT: A 528 LYS cc_start: 0.6443 (tttt) cc_final: 0.4920 (pptt) REVERT: H 3 GLN cc_start: 0.8384 (mm110) cc_final: 0.8112 (mp10) REVERT: H 86 ARG cc_start: 0.8396 (mtt-85) cc_final: 0.8092 (mtt-85) REVERT: H 88 GLU cc_start: 0.9081 (pm20) cc_final: 0.8795 (pm20) REVERT: H 205 LYS cc_start: 0.9135 (mmmm) cc_final: 0.8887 (mmmt) REVERT: L 17 GLU cc_start: 0.8530 (mt-10) cc_final: 0.8118 (mt-10) REVERT: L 81 GLU cc_start: 0.9167 (pm20) cc_final: 0.8922 (pm20) REVERT: L 142 ARG cc_start: 0.9108 (tpp80) cc_final: 0.8763 (ttt-90) REVERT: L 147 GLN cc_start: 0.6421 (OUTLIER) cc_final: 0.6041 (mt0) REVERT: L 158 ASN cc_start: 0.7833 (m110) cc_final: 0.7613 (m110) REVERT: L 167 ASP cc_start: 0.8976 (t0) cc_final: 0.8440 (t0) outliers start: 8 outliers final: 3 residues processed: 73 average time/residue: 1.6365 time to fit residues: 123.9633 Evaluate side-chains 70 residues out of total 531 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 65 time to evaluate : 0.601 ------------------------------------------------------------------------------- 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 147 GLN 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 54 optimal weight: 3.9990 chunk 3 optimal weight: 0.9980 chunk 0 optimal weight: 0.5980 chunk 28 optimal weight: 2.9990 chunk 5 optimal weight: 0.9990 chunk 23 optimal weight: 2.9990 chunk 13 optimal weight: 0.9980 chunk 1 optimal weight: 1.9990 chunk 6 optimal weight: 0.7980 chunk 26 optimal weight: 1.9990 chunk 20 optimal weight: 0.0770 overall best weight: 0.6938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3089 r_free = 0.3089 target = 0.063230 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2852 r_free = 0.2852 target = 0.052452 restraints weight = 12628.334| |-----------------------------------------------------------------------------| r_work (start): 0.2848 rms_B_bonded: 2.93 r_work: 0.2723 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work (final): 0.2723 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8620 moved from start: 0.2080 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 4909 Z= 0.209 Angle : 0.504 6.743 6682 Z= 0.261 Chirality : 0.042 0.143 737 Planarity : 0.004 0.061 858 Dihedral : 4.197 20.001 699 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 4.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 1.88 % Allowed : 14.50 % Favored : 83.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.15 (0.35), residues: 613 helix: -4.44 (0.60), residues: 26 sheet: 0.94 (0.33), residues: 244 loop : -0.09 (0.35), residues: 343 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 436 HIS 0.002 0.001 HIS A 519 PHE 0.006 0.001 PHE L 98 TYR 0.015 0.001 TYR H 79 ARG 0.007 0.001 ARG H 19 *********************** 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 80 residues out of total 531 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 70 time to evaluate : 0.578 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 462 LYS cc_start: 0.9149 (OUTLIER) cc_final: 0.8640 (mtmm) REVERT: A 516 GLU cc_start: 0.8177 (OUTLIER) cc_final: 0.7532 (pp20) REVERT: A 528 LYS cc_start: 0.6471 (tttt) cc_final: 0.4933 (pptt) REVERT: H 3 GLN cc_start: 0.8406 (mm110) cc_final: 0.8123 (mp10) REVERT: H 86 ARG cc_start: 0.8407 (mtt-85) cc_final: 0.8106 (mtt-85) REVERT: H 88 GLU cc_start: 0.9084 (pm20) cc_final: 0.8787 (pm20) REVERT: H 205 LYS cc_start: 0.9139 (mmmm) cc_final: 0.8877 (mmmt) REVERT: L 17 GLU cc_start: 0.8438 (mt-10) cc_final: 0.7982 (mt-10) REVERT: L 81 GLU cc_start: 0.9135 (pm20) cc_final: 0.8925 (pm20) REVERT: L 142 ARG cc_start: 0.9105 (tpp80) cc_final: 0.8745 (ttt-90) REVERT: L 167 ASP cc_start: 0.8983 (t0) cc_final: 0.8206 (t0) REVERT: L 170 ASP cc_start: 0.8693 (p0) cc_final: 0.8396 (p0) outliers start: 10 outliers final: 6 residues processed: 72 average time/residue: 1.4575 time to fit residues: 108.9224 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 : 0.568 ------------------------------------------------------------------------------- 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 106 ILE 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 3 optimal weight: 1.9990 chunk 17 optimal weight: 1.9990 chunk 36 optimal weight: 1.9990 chunk 24 optimal weight: 1.9990 chunk 34 optimal weight: 4.9990 chunk 6 optimal weight: 0.8980 chunk 30 optimal weight: 4.9990 chunk 60 optimal weight: 0.8980 chunk 11 optimal weight: 0.0470 chunk 25 optimal weight: 0.1980 chunk 57 optimal weight: 4.9990 overall best weight: 0.8080 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 155 GLN L 158 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3087 r_free = 0.3087 target = 0.063082 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2844 r_free = 0.2844 target = 0.052093 restraints weight = 12596.355| |-----------------------------------------------------------------------------| r_work (start): 0.2836 rms_B_bonded: 2.95 r_work: 0.2712 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work (final): 0.2712 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8622 moved from start: 0.2121 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 4909 Z= 0.232 Angle : 0.518 6.805 6682 Z= 0.265 Chirality : 0.043 0.138 737 Planarity : 0.004 0.062 858 Dihedral : 4.276 20.376 699 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 4.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 2.07 % Allowed : 15.25 % Favored : 82.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.21 (0.35), residues: 613 helix: -4.40 (0.63), residues: 26 sheet: 0.98 (0.33), residues: 241 loop : -0.03 (0.35), residues: 346 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP H 47 HIS 0.003 0.001 HIS A 519 PHE 0.006 0.001 PHE L 98 TYR 0.015 0.001 TYR H 79 ARG 0.008 0.001 ARG H 19 *********************** 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 73 residues out of total 531 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 62 time to evaluate : 0.740 Fit side-chains revert: symmetry clash REVERT: A 420 ASP cc_start: 0.9171 (m-30) cc_final: 0.8586 (m-30) REVERT: A 462 LYS cc_start: 0.9149 (OUTLIER) cc_final: 0.8648 (mtmm) REVERT: A 528 LYS cc_start: 0.6491 (tttt) cc_final: 0.4912 (pptt) REVERT: H 3 GLN cc_start: 0.8394 (mm110) cc_final: 0.8088 (mp10) REVERT: H 86 ARG cc_start: 0.8418 (mtt-85) cc_final: 0.8089 (mtt-85) REVERT: H 88 GLU cc_start: 0.9096 (pm20) cc_final: 0.8753 (pm20) REVERT: H 205 LYS cc_start: 0.9143 (mmmm) cc_final: 0.8882 (mmmt) REVERT: L 142 ARG cc_start: 0.9132 (tpp80) cc_final: 0.8343 (ttp80) REVERT: L 147 GLN cc_start: 0.6456 (OUTLIER) cc_final: 0.6007 (mt0) REVERT: L 167 ASP cc_start: 0.8918 (t0) cc_final: 0.8431 (t0) REVERT: L 170 ASP cc_start: 0.8657 (p0) cc_final: 0.8400 (p0) outliers start: 11 outliers final: 5 residues processed: 67 average time/residue: 2.1004 time to fit residues: 146.9583 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 : 0.561 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 367 VAL 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 147 GLN 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 30 optimal weight: 4.9990 chunk 40 optimal weight: 2.9990 chunk 3 optimal weight: 1.9990 chunk 45 optimal weight: 0.9980 chunk 49 optimal weight: 1.9990 chunk 44 optimal weight: 0.0060 chunk 50 optimal weight: 1.9990 chunk 33 optimal weight: 0.6980 chunk 60 optimal weight: 0.6980 chunk 0 optimal weight: 0.5980 chunk 39 optimal weight: 4.9990 overall best weight: 0.5996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3096 r_free = 0.3096 target = 0.063570 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2861 r_free = 0.2861 target = 0.052711 restraints weight = 12545.579| |-----------------------------------------------------------------------------| r_work (start): 0.2853 rms_B_bonded: 2.94 r_work: 0.2728 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work (final): 0.2728 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8612 moved from start: 0.2248 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 4909 Z= 0.199 Angle : 0.517 8.628 6682 Z= 0.266 Chirality : 0.043 0.135 737 Planarity : 0.004 0.061 858 Dihedral : 4.145 19.815 699 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 3.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 1.32 % Allowed : 16.38 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.26 (0.35), residues: 613 helix: -4.35 (0.61), residues: 26 sheet: 1.06 (0.33), residues: 242 loop : -0.06 (0.35), residues: 345 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 436 HIS 0.002 0.001 HIS A 519 PHE 0.005 0.001 PHE L 71 TYR 0.015 0.001 TYR H 79 ARG 0.004 0.000 ARG H 86 *********************** 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 76 residues out of total 531 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 69 time to evaluate : 0.599 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 430 THR cc_start: 0.9302 (OUTLIER) cc_final: 0.8980 (p) REVERT: A 462 LYS cc_start: 0.9146 (OUTLIER) cc_final: 0.8643 (mtmm) REVERT: A 516 GLU cc_start: 0.8121 (pp20) cc_final: 0.7626 (pp20) REVERT: A 528 LYS cc_start: 0.6477 (tttt) cc_final: 0.4933 (pptt) REVERT: H 3 GLN cc_start: 0.8395 (mm110) cc_final: 0.8085 (mp10) REVERT: H 86 ARG cc_start: 0.8387 (mtt-85) cc_final: 0.8078 (mtt-85) REVERT: H 88 GLU cc_start: 0.9087 (pm20) cc_final: 0.8752 (pm20) REVERT: H 205 LYS cc_start: 0.9137 (mmmm) cc_final: 0.8859 (mmmt) REVERT: L 17 GLU cc_start: 0.8345 (mt-10) cc_final: 0.7948 (mt-10) REVERT: L 81 GLU cc_start: 0.9128 (pm20) cc_final: 0.8916 (pm20) REVERT: L 142 ARG cc_start: 0.9118 (tpp80) cc_final: 0.8751 (ttt-90) REVERT: L 167 ASP cc_start: 0.8986 (t0) cc_final: 0.8254 (t0) REVERT: L 170 ASP cc_start: 0.8637 (p0) cc_final: 0.8396 (p0) outliers start: 7 outliers final: 5 residues processed: 72 average time/residue: 2.0292 time to fit residues: 151.2277 Evaluate side-chains 67 residues out of total 531 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 60 time to evaluate : 0.641 ------------------------------------------------------------------------------- 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 25 optimal weight: 0.5980 chunk 42 optimal weight: 0.6980 chunk 6 optimal weight: 0.5980 chunk 36 optimal weight: 1.9990 chunk 17 optimal weight: 0.8980 chunk 39 optimal weight: 3.9990 chunk 37 optimal weight: 0.9980 chunk 34 optimal weight: 0.5980 chunk 50 optimal weight: 1.9990 chunk 16 optimal weight: 1.9990 chunk 57 optimal weight: 4.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3095 r_free = 0.3095 target = 0.063374 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2859 r_free = 0.2859 target = 0.052733 restraints weight = 12609.096| |-----------------------------------------------------------------------------| r_work (start): 0.2853 rms_B_bonded: 2.93 r_work: 0.2729 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work (final): 0.2729 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8613 moved from start: 0.2231 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 4909 Z= 0.210 Angle : 0.512 6.587 6682 Z= 0.264 Chirality : 0.043 0.137 737 Planarity : 0.004 0.061 858 Dihedral : 4.158 20.205 699 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 4.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 1.51 % Allowed : 16.01 % Favored : 82.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.31 (0.35), residues: 613 helix: -4.33 (0.61), residues: 26 sheet: 1.08 (0.33), residues: 242 loop : -0.00 (0.35), residues: 345 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 436 HIS 0.002 0.001 HIS A 519 PHE 0.005 0.001 PHE L 71 TYR 0.014 0.001 TYR H 79 ARG 0.005 0.001 ARG H 19 *********************** 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: 8 poor density : 63 time to evaluate : 0.525 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 430 THR cc_start: 0.9288 (OUTLIER) cc_final: 0.8965 (p) REVERT: A 462 LYS cc_start: 0.9149 (OUTLIER) cc_final: 0.8656 (mtmm) REVERT: A 516 GLU cc_start: 0.8143 (pp20) cc_final: 0.7494 (pp20) REVERT: A 518 LEU cc_start: 0.8995 (mt) cc_final: 0.8746 (mp) REVERT: A 528 LYS cc_start: 0.6557 (tttt) cc_final: 0.4959 (pptt) REVERT: H 3 GLN cc_start: 0.8386 (mm110) cc_final: 0.8056 (mp10) REVERT: H 86 ARG cc_start: 0.8369 (mtt-85) cc_final: 0.8044 (mtt-85) REVERT: H 88 GLU cc_start: 0.9093 (pm20) cc_final: 0.8738 (pm20) REVERT: H 205 LYS cc_start: 0.9122 (mmmm) cc_final: 0.8860 (mmmt) REVERT: L 142 ARG cc_start: 0.9135 (tpp80) cc_final: 0.8362 (ttp80) REVERT: L 165 GLU cc_start: 0.8909 (mm-30) cc_final: 0.8666 (pm20) REVERT: L 167 ASP cc_start: 0.8880 (t0) cc_final: 0.8240 (t0) outliers start: 8 outliers final: 5 residues processed: 68 average time/residue: 2.5048 time to fit residues: 178.1528 Evaluate side-chains 67 residues out of total 531 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 60 time to evaluate : 0.569 ------------------------------------------------------------------------------- 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 60 optimal weight: 0.8980 chunk 12 optimal weight: 1.9990 chunk 1 optimal weight: 1.9990 chunk 46 optimal weight: 1.9990 chunk 16 optimal weight: 0.6980 chunk 10 optimal weight: 0.4980 chunk 30 optimal weight: 4.9990 chunk 19 optimal weight: 0.9990 chunk 5 optimal weight: 2.9990 chunk 41 optimal weight: 0.0000 chunk 34 optimal weight: 0.6980 overall best weight: 0.5584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3104 r_free = 0.3104 target = 0.063848 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2872 r_free = 0.2872 target = 0.053318 restraints weight = 12531.369| |-----------------------------------------------------------------------------| r_work (start): 0.2866 rms_B_bonded: 2.92 r_work: 0.2743 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work (final): 0.2743 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8595 moved from start: 0.2321 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 4909 Z= 0.198 Angle : 0.544 9.294 6682 Z= 0.277 Chirality : 0.043 0.136 737 Planarity : 0.004 0.060 858 Dihedral : 4.082 19.873 699 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 4.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 1.32 % Allowed : 16.20 % Favored : 82.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.33 (0.35), residues: 613 helix: -4.31 (0.60), residues: 26 sheet: 1.09 (0.33), residues: 242 loop : 0.01 (0.35), residues: 345 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 436 HIS 0.002 0.001 HIS H 72 PHE 0.005 0.001 PHE L 98 TYR 0.014 0.001 TYR L 192 ARG 0.003 0.000 ARG H 86 ********************** 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 68 residues out of total 531 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 61 time to evaluate : 0.596 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 430 THR cc_start: 0.9264 (OUTLIER) cc_final: 0.8945 (p) REVERT: A 462 LYS cc_start: 0.9136 (OUTLIER) cc_final: 0.8631 (mtmm) REVERT: A 516 GLU cc_start: 0.8155 (pp20) cc_final: 0.7512 (pp20) REVERT: A 518 LEU cc_start: 0.8961 (mt) cc_final: 0.8701 (mp) REVERT: A 528 LYS cc_start: 0.6540 (tttt) cc_final: 0.4967 (pptt) REVERT: H 3 GLN cc_start: 0.8370 (mm110) cc_final: 0.8039 (mp10) REVERT: H 86 ARG cc_start: 0.8351 (mtt-85) cc_final: 0.8030 (mtt-85) REVERT: H 88 GLU cc_start: 0.9091 (pm20) cc_final: 0.8756 (pm20) REVERT: H 205 LYS cc_start: 0.9136 (mmmm) cc_final: 0.8840 (mmmt) REVERT: L 142 ARG cc_start: 0.9132 (tpp80) cc_final: 0.8354 (ttp80) REVERT: L 165 GLU cc_start: 0.8909 (mm-30) cc_final: 0.8642 (pm20) REVERT: L 167 ASP cc_start: 0.8865 (t0) cc_final: 0.8245 (t0) REVERT: L 170 ASP cc_start: 0.8719 (p0) cc_final: 0.8425 (p0) outliers start: 7 outliers final: 5 residues processed: 65 average time/residue: 1.4354 time to fit residues: 97.3789 Evaluate side-chains 67 residues out of total 531 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 60 time to evaluate : 0.515 ------------------------------------------------------------------------------- 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 52 optimal weight: 0.0770 chunk 20 optimal weight: 0.1980 chunk 38 optimal weight: 4.9990 chunk 9 optimal weight: 1.9990 chunk 13 optimal weight: 0.4980 chunk 56 optimal weight: 0.2980 chunk 4 optimal weight: 1.9990 chunk 24 optimal weight: 0.7980 chunk 57 optimal weight: 0.9990 chunk 49 optimal weight: 1.9990 chunk 10 optimal weight: 1.9990 overall best weight: 0.3738 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3127 r_free = 0.3127 target = 0.064862 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2897 r_free = 0.2897 target = 0.054308 restraints weight = 12656.802| |-----------------------------------------------------------------------------| r_work (start): 0.2890 rms_B_bonded: 2.95 r_work: 0.2766 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work (final): 0.2766 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8586 moved from start: 0.2388 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 4909 Z= 0.159 Angle : 0.517 8.221 6682 Z= 0.264 Chirality : 0.042 0.135 737 Planarity : 0.004 0.060 858 Dihedral : 3.912 19.398 699 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 4.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 1.51 % Allowed : 16.20 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.31 (0.35), residues: 613 helix: -4.29 (0.50), residues: 33 sheet: 1.28 (0.34), residues: 232 loop : -0.03 (0.34), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 436 HIS 0.002 0.001 HIS A 519 PHE 0.006 0.001 PHE A 377 TYR 0.015 0.001 TYR H 79 ARG 0.003 0.000 ARG A 346 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4255.40 seconds wall clock time: 77 minutes 50.01 seconds (4670.01 seconds total)