Starting phenix.real_space_refine on Wed Sep 17 06:10:40 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9jif_61504/09_2025/9jif_61504.cif Found real_map, /net/cci-nas-00/data/ceres_data/9jif_61504/09_2025/9jif_61504.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.79 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9jif_61504/09_2025/9jif_61504.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9jif_61504/09_2025/9jif_61504.map" model { file = "/net/cci-nas-00/data/ceres_data/9jif_61504/09_2025/9jif_61504.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9jif_61504/09_2025/9jif_61504.cif" } resolution = 2.79 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.020 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 10 5.16 5 C 3622 2.51 5 N 978 2.21 5 O 1132 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 5742 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1107 Number of conformers: 1 Conformer: "" Number of residues, atoms: 147, 1107 Classifications: {'peptide': 147} Link IDs: {'PTRANS': 7, 'TRANS': 139} Chain: "H" Number of atoms: 961 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 961 Classifications: {'peptide': 124} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 120} Chain: "L" Number of atoms: 803 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 803 Classifications: {'peptide': 110} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 102} Chain: "B" Number of atoms: 1107 Number of conformers: 1 Conformer: "" Number of residues, atoms: 147, 1107 Classifications: {'peptide': 147} Link IDs: {'PTRANS': 7, 'TRANS': 139} Chain: "C" Number of atoms: 961 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 961 Classifications: {'peptide': 124} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 120} Chain: "D" Number of atoms: 803 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 803 Classifications: {'peptide': 110} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 102} Time building chain proxies: 1.54, per 1000 atoms: 0.27 Number of scatterers: 5742 At special positions: 0 Unit cell: (107.25, 98.15, 85.8, 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 10 16.00 O 1132 8.00 N 978 7.00 C 3622 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.25 Simple disulfide: pdb=" SG CYS L 22 " - pdb=" SG CYS L 89 " distance=1.97 Simple disulfide: pdb=" SG CYS C 22 " - pdb=" SG CYS C 96 " distance=2.31 Simple disulfide: pdb=" SG CYS D 22 " - pdb=" SG CYS D 89 " distance=1.86 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.28 Conformation dependent library (CDL) restraints added in 158.2 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 1500 Ramachandran restraints generated. 750 Oldfield, 0 Emsley, 750 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1376 Finding SS restraints... Secondary structure from input PDB file: 6 helices and 16 sheets defined 3.9% alpha, 37.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.26 Creating SS restraints... Processing helix chain 'H' and resid 28 through 32 removed outlier: 3.529A pdb=" N SER H 31 " --> pdb=" O THR H 28 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N TYR H 32 " --> pdb=" O PHE H 29 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 28 through 32' Processing helix chain 'H' and resid 87 through 91 removed outlier: 4.018A pdb=" N THR H 91 " --> pdb=" O ALA H 88 " (cutoff:3.500A) Processing helix chain 'L' and resid 80 through 84 removed outlier: 3.703A pdb=" N ASP L 83 " --> pdb=" O GLN L 80 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N GLU L 84 " --> pdb=" O THR L 81 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 80 through 84' Processing helix chain 'C' and resid 28 through 32 removed outlier: 3.529A pdb=" N SER C 31 " --> pdb=" O THR C 28 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N TYR C 32 " --> pdb=" O PHE C 29 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 28 through 32' Processing helix chain 'C' and resid 87 through 91 removed outlier: 3.918A pdb=" N THR C 91 " --> pdb=" O ALA C 88 " (cutoff:3.500A) Processing helix chain 'D' and resid 80 through 84 removed outlier: 3.578A pdb=" N ASP D 83 " --> pdb=" O GLN D 80 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N GLU D 84 " --> pdb=" O THR D 81 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 80 through 84' Processing sheet with id=AA1, first strand: chain 'A' and resid 464 through 465 Processing sheet with id=AA2, first strand: chain 'A' and resid 508 through 510 removed outlier: 4.370A pdb=" N SER A 497 " --> pdb=" O THR A 476 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 479 through 481 removed outlier: 3.643A pdb=" N LEU A 570 " --> pdb=" O ALA A 580 " (cutoff:3.500A) removed outlier: 5.173A pdb=" N SER A 582 " --> pdb=" O GLN A 568 " (cutoff:3.500A) removed outlier: 8.003A pdb=" N GLN A 568 " --> pdb=" O SER A 582 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'H' and resid 3 through 7 Processing sheet with id=AA5, first strand: chain 'H' and resid 10 through 12 removed outlier: 6.789A pdb=" N ILE H 34 " --> pdb=" O LEU H 50 " (cutoff:3.500A) removed outlier: 4.424A pdb=" N LEU H 50 " --> pdb=" O ILE H 34 " (cutoff:3.500A) removed outlier: 6.516A pdb=" N TRP H 36 " --> pdb=" O VAL H 48 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'L' and resid 9 through 12 removed outlier: 3.765A pdb=" N ALA L 12 " --> pdb=" O THR L 108 " (cutoff:3.500A) removed outlier: 6.369A pdb=" N TRP L 36 " --> pdb=" O LEU L 48 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'L' and resid 9 through 12 removed outlier: 3.765A pdb=" N ALA L 12 " --> pdb=" O THR L 108 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'L' and resid 17 through 23 Processing sheet with id=AA9, first strand: chain 'B' and resid 464 through 465 Processing sheet with id=AB1, first strand: chain 'B' and resid 508 through 510 removed outlier: 4.293A pdb=" N SER B 497 " --> pdb=" O THR B 476 " (cutoff:3.500A) removed outlier: 4.855A pdb=" N PHE B 547 " --> pdb=" O GLY B 556 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 479 through 481 removed outlier: 3.703A pdb=" N LEU B 570 " --> pdb=" O ALA B 580 " (cutoff:3.500A) removed outlier: 5.209A pdb=" N SER B 582 " --> pdb=" O GLN B 568 " (cutoff:3.500A) removed outlier: 8.040A pdb=" N GLN B 568 " --> pdb=" O SER B 582 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 3 through 7 Processing sheet with id=AB4, first strand: chain 'C' and resid 10 through 12 removed outlier: 6.864A pdb=" N ILE C 34 " --> pdb=" O LEU C 50 " (cutoff:3.500A) removed outlier: 4.445A pdb=" N LEU C 50 " --> pdb=" O ILE C 34 " (cutoff:3.500A) removed outlier: 6.502A pdb=" N TRP C 36 " --> pdb=" O VAL C 48 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 9 through 12 removed outlier: 3.764A pdb=" N ALA D 12 " --> pdb=" O THR D 108 " (cutoff:3.500A) removed outlier: 6.372A pdb=" N TRP D 36 " --> pdb=" O LEU D 48 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 9 through 12 removed outlier: 3.764A pdb=" N ALA D 12 " --> pdb=" O THR D 108 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 17 through 23 211 hydrogen bonds defined for protein. 513 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: 0.87 Time building geometry restraints manager: 0.38 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: 1845 1.34 - 1.45: 1057 1.45 - 1.57: 2958 1.57 - 1.69: 0 1.69 - 1.80: 12 Bond restraints: 5872 Sorted by residual: bond pdb=" C VAL C 79 " pdb=" N TYR C 80 " ideal model delta sigma weight residual 1.329 1.273 0.056 1.38e-02 5.25e+03 1.67e+01 bond pdb=" C TYR D 33 " pdb=" N VAL D 34 " ideal model delta sigma weight residual 1.330 1.279 0.051 1.26e-02 6.30e+03 1.64e+01 bond pdb=" C CYS L 22 " pdb=" N SER L 23 " ideal model delta sigma weight residual 1.331 1.291 0.040 1.55e-02 4.16e+03 6.66e+00 bond pdb=" N PRO H 106 " pdb=" CD PRO H 106 " ideal model delta sigma weight residual 1.473 1.509 -0.036 1.40e-02 5.10e+03 6.63e+00 bond pdb=" C TRP D 92 " pdb=" N ASP D 93 " ideal model delta sigma weight residual 1.330 1.365 -0.035 1.46e-02 4.69e+03 5.86e+00 ... (remaining 5867 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.23: 7723 1.23 - 2.46: 228 2.46 - 3.69: 50 3.69 - 4.92: 16 4.92 - 6.15: 3 Bond angle restraints: 8020 Sorted by residual: angle pdb=" N VAL C 64 " pdb=" CA VAL C 64 " pdb=" C VAL C 64 " ideal model delta sigma weight residual 113.20 108.86 4.34 9.60e-01 1.09e+00 2.04e+01 angle pdb=" N VAL H 64 " pdb=" CA VAL H 64 " pdb=" C VAL H 64 " ideal model delta sigma weight residual 113.20 108.99 4.21 9.60e-01 1.09e+00 1.93e+01 angle pdb=" C ASP D 51 " pdb=" N ASN D 52 " pdb=" CA ASN D 52 " ideal model delta sigma weight residual 121.54 127.69 -6.15 1.91e+00 2.74e-01 1.04e+01 angle pdb=" C ASP L 51 " pdb=" N ASN L 52 " pdb=" CA ASN L 52 " ideal model delta sigma weight residual 121.54 127.29 -5.75 1.91e+00 2.74e-01 9.05e+00 angle pdb=" C ASP L 61 " pdb=" N ARG L 62 " pdb=" CA ARG L 62 " ideal model delta sigma weight residual 120.28 124.46 -4.18 1.44e+00 4.82e-01 8.42e+00 ... (remaining 8015 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.44: 3036 16.44 - 32.88: 282 32.88 - 49.32: 89 49.32 - 65.75: 11 65.75 - 82.19: 8 Dihedral angle restraints: 3426 sinusoidal: 1250 harmonic: 2176 Sorted by residual: dihedral pdb=" CB CYS L 22 " pdb=" SG CYS L 22 " pdb=" SG CYS L 89 " pdb=" CB CYS L 89 " ideal model delta sinusoidal sigma weight residual 93.00 132.44 -39.44 1 1.00e+01 1.00e-02 2.19e+01 dihedral pdb=" CA ALA A 574 " pdb=" C ALA A 574 " pdb=" N ALA A 575 " pdb=" CA ALA A 575 " ideal model delta harmonic sigma weight residual 180.00 159.20 20.80 0 5.00e+00 4.00e-02 1.73e+01 dihedral pdb=" CA ALA B 574 " pdb=" C ALA B 574 " pdb=" N ALA B 575 " pdb=" CA ALA B 575 " ideal model delta harmonic sigma weight residual 180.00 159.89 20.11 0 5.00e+00 4.00e-02 1.62e+01 ... (remaining 3423 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.028: 517 0.028 - 0.056: 254 0.056 - 0.084: 80 0.084 - 0.112: 51 0.112 - 0.139: 16 Chirality restraints: 918 Sorted by residual: chirality pdb=" CA ILE D 76 " pdb=" N ILE D 76 " pdb=" C ILE D 76 " pdb=" CB ILE D 76 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.86e-01 chirality pdb=" CA ILE L 76 " pdb=" N ILE L 76 " pdb=" C ILE L 76 " pdb=" CB ILE L 76 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.82e-01 chirality pdb=" CA VAL C 104 " pdb=" N VAL C 104 " pdb=" C VAL C 104 " pdb=" CB VAL C 104 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 4.00e-01 ... (remaining 915 not shown) Planarity restraints: 1024 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLU H 105 " 0.068 5.00e-02 4.00e+02 1.03e-01 1.69e+01 pdb=" N PRO H 106 " -0.178 5.00e-02 4.00e+02 pdb=" CA PRO H 106 " 0.055 5.00e-02 4.00e+02 pdb=" CD PRO H 106 " 0.055 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLU C 105 " -0.067 5.00e-02 4.00e+02 1.01e-01 1.64e+01 pdb=" N PRO C 106 " 0.175 5.00e-02 4.00e+02 pdb=" CA PRO C 106 " -0.054 5.00e-02 4.00e+02 pdb=" CD PRO C 106 " -0.054 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY B 490 " 0.035 5.00e-02 4.00e+02 5.28e-02 4.46e+00 pdb=" N PRO B 491 " -0.091 5.00e-02 4.00e+02 pdb=" CA PRO B 491 " 0.027 5.00e-02 4.00e+02 pdb=" CD PRO B 491 " 0.029 5.00e-02 4.00e+02 ... (remaining 1021 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 547 2.75 - 3.29: 5222 3.29 - 3.82: 9643 3.82 - 4.36: 11943 4.36 - 4.90: 20839 Nonbonded interactions: 48194 Sorted by model distance: nonbonded pdb=" OG SER A 566 " pdb=" O THR B 553 " model vdw 2.209 3.040 nonbonded pdb=" OG SER C 52 " pdb=" OD1 ASP C 54 " model vdw 2.267 3.040 nonbonded pdb=" O THR A 553 " pdb=" OG SER B 566 " model vdw 2.278 3.040 nonbonded pdb=" O SER C 52 " pdb=" NH1 ARG C 72 " model vdw 2.337 3.120 nonbonded pdb=" OG SER H 52 " pdb=" OD1 ASP H 54 " model vdw 2.345 3.040 ... (remaining 48189 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: 0.01 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } ncs_group { reference = chain 'C' selection = chain 'H' } ncs_group { reference = chain 'D' selection = chain 'L' } 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: 4.730 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: 0.170 Check model and map are aligned: 0.020 Set scattering table: 0.010 Process input model: 6.590 Find NCS groups from input model: 0.120 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:7.900 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.550 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7938 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 : 0.006 0.277 5876 Z= 0.321 Angle : 0.754 26.453 8028 Z= 0.398 Chirality : 0.042 0.139 918 Planarity : 0.006 0.103 1024 Dihedral : 14.568 82.192 2038 Min Nonbonded Distance : 2.209 Molprobity Statistics. All-atom Clashscore : 4.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.40 % Favored : 95.60 % Rotamer: Outliers : 0.32 % Allowed : 17.36 % Favored : 82.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 aren not related in a simple way. whole: 0.11 (0.32), residues: 750 helix: None (None), residues: 0 sheet: 0.66 (0.29), residues: 356 loop : -0.44 (0.33), residues: 394 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG C 16 TYR 0.019 0.001 TYR H 113 PHE 0.012 0.002 PHE B 547 TRP 0.009 0.001 TRP H 114 HIS 0.002 0.001 HIS C 35 Details of bonding type rmsd covalent geometry : bond 0.00343 ( 5872) covalent geometry : angle 0.55740 ( 8020) SS BOND : bond 0.20024 ( 4) SS BOND : angle 16.11055 ( 8) hydrogen bonds : bond 0.23028 ( 203) hydrogen bonds : angle 9.46669 ( 513) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1500 Ramachandran restraints generated. 750 Oldfield, 0 Emsley, 750 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1500 Ramachandran restraints generated. 750 Oldfield, 0 Emsley, 750 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 114 time to evaluate : 0.254 Fit side-chains REVERT: H 2 VAL cc_start: 0.8380 (p) cc_final: 0.8049 (t) REVERT: H 79 VAL cc_start: 0.8400 (p) cc_final: 0.8144 (t) REVERT: H 102 SER cc_start: 0.8061 (t) cc_final: 0.7860 (t) REVERT: L 68 SER cc_start: 0.7854 (m) cc_final: 0.7479 (p) REVERT: B 515 ASP cc_start: 0.8060 (t70) cc_final: 0.7850 (t0) REVERT: B 517 THR cc_start: 0.8209 (p) cc_final: 0.7956 (t) REVERT: B 538 VAL cc_start: 0.8563 (p) cc_final: 0.8322 (m) REVERT: C 2 VAL cc_start: 0.8301 (p) cc_final: 0.8052 (t) REVERT: C 79 VAL cc_start: 0.8399 (p) cc_final: 0.8057 (t) outliers start: 2 outliers final: 0 residues processed: 115 average time/residue: 0.2694 time to fit residues: 33.6187 Evaluate side-chains 99 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 99 time to evaluate : 0.230 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 49 optimal weight: 0.4980 chunk 53 optimal weight: 0.9990 chunk 5 optimal weight: 1.9990 chunk 33 optimal weight: 2.9990 chunk 65 optimal weight: 0.5980 chunk 62 optimal weight: 0.0030 chunk 51 optimal weight: 0.6980 chunk 38 optimal weight: 0.7980 chunk 61 optimal weight: 0.7980 chunk 45 optimal weight: 0.9980 chunk 27 optimal weight: 0.9990 overall best weight: 0.5190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 482 GLN A 577 HIS H 84 ASN B 482 GLN C 84 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3235 r_free = 0.3235 target = 0.096852 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3109 r_free = 0.3109 target = 0.089155 restraints weight = 8742.784| |-----------------------------------------------------------------------------| r_work (start): 0.3115 rms_B_bonded: 1.61 r_work: 0.3029 rms_B_bonded: 1.87 restraints_weight: 0.5000 r_work: 0.2912 rms_B_bonded: 3.35 restraints_weight: 0.2500 r_work (final): 0.2912 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7959 moved from start: 0.1642 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 5876 Z= 0.171 Angle : 0.583 5.330 8028 Z= 0.317 Chirality : 0.045 0.143 918 Planarity : 0.005 0.066 1024 Dihedral : 4.776 21.601 838 Min Nonbonded Distance : 2.575 Molprobity Statistics. All-atom Clashscore : 5.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.00 % Favored : 96.00 % Rotamer: Outliers : 2.89 % Allowed : 18.65 % Favored : 78.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 aren not related in a simple way. whole: 0.27 (0.32), residues: 750 helix: None (None), residues: 0 sheet: 0.84 (0.28), residues: 358 loop : -0.42 (0.33), residues: 392 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG L 62 TYR 0.013 0.002 TYR D 87 PHE 0.020 0.003 PHE B 547 TRP 0.013 0.002 TRP C 114 HIS 0.006 0.003 HIS D 39 Details of bonding type rmsd covalent geometry : bond 0.00396 ( 5872) covalent geometry : angle 0.58078 ( 8020) SS BOND : bond 0.00311 ( 4) SS BOND : angle 1.85860 ( 8) hydrogen bonds : bond 0.04475 ( 203) hydrogen bonds : angle 5.97962 ( 513) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1500 Ramachandran restraints generated. 750 Oldfield, 0 Emsley, 750 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1500 Ramachandran restraints generated. 750 Oldfield, 0 Emsley, 750 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 107 time to evaluate : 0.214 Fit side-chains REVERT: H 2 VAL cc_start: 0.8297 (p) cc_final: 0.8095 (t) REVERT: B 538 VAL cc_start: 0.8543 (p) cc_final: 0.8284 (m) REVERT: B 545 LEU cc_start: 0.8449 (OUTLIER) cc_final: 0.8203 (tp) REVERT: C 68 PHE cc_start: 0.8723 (m-10) cc_final: 0.8315 (m-80) REVERT: C 83 VAL cc_start: 0.8275 (m) cc_final: 0.8046 (m) REVERT: D 32 ASN cc_start: 0.8392 (m-40) cc_final: 0.8000 (m-40) outliers start: 18 outliers final: 9 residues processed: 116 average time/residue: 0.2867 time to fit residues: 36.2073 Evaluate side-chains 111 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 101 time to evaluate : 0.266 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 501 VAL Chi-restraints excluded: chain A residue 538 VAL Chi-restraints excluded: chain H residue 7 SER Chi-restraints excluded: chain H residue 25 SER Chi-restraints excluded: chain L residue 100 VAL Chi-restraints excluded: chain B residue 464 VAL Chi-restraints excluded: chain B residue 545 LEU Chi-restraints excluded: chain C residue 17 SER Chi-restraints excluded: chain C residue 25 SER Chi-restraints excluded: chain D residue 38 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 3 optimal weight: 1.9990 chunk 1 optimal weight: 1.9990 chunk 58 optimal weight: 0.9980 chunk 32 optimal weight: 0.3980 chunk 27 optimal weight: 2.9990 chunk 22 optimal weight: 1.9990 chunk 59 optimal weight: 0.7980 chunk 13 optimal weight: 1.9990 chunk 51 optimal weight: 1.9990 chunk 71 optimal weight: 0.6980 chunk 7 optimal weight: 0.3980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 482 GLN B 482 GLN C 82 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3230 r_free = 0.3230 target = 0.096444 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3106 r_free = 0.3106 target = 0.088864 restraints weight = 8562.061| |-----------------------------------------------------------------------------| r_work (start): 0.3107 rms_B_bonded: 1.58 r_work: 0.3020 rms_B_bonded: 1.83 restraints_weight: 0.5000 r_work: 0.2902 rms_B_bonded: 3.28 restraints_weight: 0.2500 r_work (final): 0.2902 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7969 moved from start: 0.2096 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 5876 Z= 0.200 Angle : 0.587 5.611 8028 Z= 0.318 Chirality : 0.044 0.146 918 Planarity : 0.005 0.052 1024 Dihedral : 5.066 22.836 838 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 5.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.27 % Favored : 95.73 % Rotamer: Outliers : 3.54 % Allowed : 17.52 % Favored : 78.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 aren not related in a simple way. whole: 0.30 (0.32), residues: 750 helix: None (None), residues: 0 sheet: 0.88 (0.28), residues: 342 loop : -0.37 (0.32), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 578 TYR 0.015 0.002 TYR H 95 PHE 0.018 0.003 PHE B 547 TRP 0.014 0.002 TRP H 114 HIS 0.008 0.003 HIS L 39 Details of bonding type rmsd covalent geometry : bond 0.00471 ( 5872) covalent geometry : angle 0.58593 ( 8020) SS BOND : bond 0.00502 ( 4) SS BOND : angle 1.44481 ( 8) hydrogen bonds : bond 0.04043 ( 203) hydrogen bonds : angle 5.68240 ( 513) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1500 Ramachandran restraints generated. 750 Oldfield, 0 Emsley, 750 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1500 Ramachandran restraints generated. 750 Oldfield, 0 Emsley, 750 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 94 time to evaluate : 0.215 Fit side-chains REVERT: B 569 LEU cc_start: 0.8225 (OUTLIER) cc_final: 0.7958 (mp) outliers start: 22 outliers final: 12 residues processed: 105 average time/residue: 0.2966 time to fit residues: 33.9388 Evaluate side-chains 103 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 90 time to evaluate : 0.205 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 501 VAL Chi-restraints excluded: chain A residue 538 VAL Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 7 SER Chi-restraints excluded: chain H residue 25 SER Chi-restraints excluded: chain L residue 38 GLN Chi-restraints excluded: chain L residue 100 VAL Chi-restraints excluded: chain B residue 517 THR Chi-restraints excluded: chain B residue 538 VAL Chi-restraints excluded: chain B residue 569 LEU Chi-restraints excluded: chain C residue 63 SER Chi-restraints excluded: chain D residue 38 GLN Chi-restraints excluded: chain D residue 89 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 54 optimal weight: 0.9980 chunk 30 optimal weight: 1.9990 chunk 57 optimal weight: 0.9980 chunk 68 optimal weight: 0.9990 chunk 7 optimal weight: 0.9990 chunk 47 optimal weight: 1.9990 chunk 13 optimal weight: 1.9990 chunk 35 optimal weight: 1.9990 chunk 72 optimal weight: 1.9990 chunk 8 optimal weight: 0.9990 chunk 63 optimal weight: 0.7980 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 482 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3219 r_free = 0.3219 target = 0.095644 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3093 r_free = 0.3093 target = 0.087999 restraints weight = 8592.552| |-----------------------------------------------------------------------------| r_work (start): 0.3093 rms_B_bonded: 1.58 r_work: 0.3007 rms_B_bonded: 1.80 restraints_weight: 0.5000 r_work: 0.2889 rms_B_bonded: 3.25 restraints_weight: 0.2500 r_work (final): 0.2889 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7989 moved from start: 0.2497 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.052 5876 Z= 0.272 Angle : 0.639 6.317 8028 Z= 0.344 Chirality : 0.046 0.162 918 Planarity : 0.006 0.053 1024 Dihedral : 5.543 28.218 838 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 5.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.27 % Favored : 95.73 % Rotamer: Outliers : 4.50 % Allowed : 16.56 % Favored : 78.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 aren not related in a simple way. whole: 0.21 (0.32), residues: 750 helix: None (None), residues: 0 sheet: 0.80 (0.27), residues: 360 loop : -0.47 (0.33), residues: 390 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 578 TYR 0.020 0.002 TYR C 95 PHE 0.020 0.003 PHE B 547 TRP 0.016 0.002 TRP H 114 HIS 0.009 0.004 HIS L 39 Details of bonding type rmsd covalent geometry : bond 0.00648 ( 5872) covalent geometry : angle 0.63737 ( 8020) SS BOND : bond 0.00567 ( 4) SS BOND : angle 1.59976 ( 8) hydrogen bonds : bond 0.04167 ( 203) hydrogen bonds : angle 5.78918 ( 513) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1500 Ramachandran restraints generated. 750 Oldfield, 0 Emsley, 750 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1500 Ramachandran restraints generated. 750 Oldfield, 0 Emsley, 750 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 83 time to evaluate : 0.277 Fit side-chains REVERT: B 569 LEU cc_start: 0.8236 (OUTLIER) cc_final: 0.7973 (mp) REVERT: C 68 PHE cc_start: 0.8752 (m-80) cc_final: 0.8245 (m-80) REVERT: C 98 ARG cc_start: 0.8377 (OUTLIER) cc_final: 0.8160 (mtp180) outliers start: 28 outliers final: 17 residues processed: 104 average time/residue: 0.3070 time to fit residues: 34.9053 Evaluate side-chains 96 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 77 time to evaluate : 0.222 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 501 VAL Chi-restraints excluded: chain A residue 510 VAL Chi-restraints excluded: chain A residue 538 VAL Chi-restraints excluded: chain A residue 545 LEU Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 7 SER Chi-restraints excluded: chain H residue 25 SER Chi-restraints excluded: chain L residue 38 GLN Chi-restraints excluded: chain L residue 100 VAL Chi-restraints excluded: chain B residue 488 SER Chi-restraints excluded: chain B residue 517 THR Chi-restraints excluded: chain B residue 538 VAL Chi-restraints excluded: chain B residue 569 LEU Chi-restraints excluded: chain C residue 17 SER Chi-restraints excluded: chain C residue 63 SER Chi-restraints excluded: chain C residue 98 ARG Chi-restraints excluded: chain D residue 17 MET Chi-restraints excluded: chain D residue 38 GLN Chi-restraints excluded: chain D residue 89 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 64 optimal weight: 0.0270 chunk 37 optimal weight: 0.9990 chunk 69 optimal weight: 0.1980 chunk 6 optimal weight: 0.7980 chunk 35 optimal weight: 0.0980 chunk 62 optimal weight: 0.9990 chunk 56 optimal weight: 0.9980 chunk 21 optimal weight: 0.6980 chunk 31 optimal weight: 1.9990 chunk 1 optimal weight: 0.9990 chunk 63 optimal weight: 0.9990 overall best weight: 0.3638 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 482 GLN B 482 GLN C 82 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3252 r_free = 0.3252 target = 0.097993 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3130 r_free = 0.3130 target = 0.090349 restraints weight = 8708.058| |-----------------------------------------------------------------------------| r_work (start): 0.3140 rms_B_bonded: 1.58 r_work: 0.3054 rms_B_bonded: 1.82 restraints_weight: 0.5000 r_work: 0.2936 rms_B_bonded: 3.28 restraints_weight: 0.2500 r_work (final): 0.2936 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7948 moved from start: 0.2467 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 5876 Z= 0.128 Angle : 0.519 5.714 8028 Z= 0.283 Chirality : 0.042 0.146 918 Planarity : 0.005 0.046 1024 Dihedral : 4.955 22.359 838 Min Nonbonded Distance : 2.591 Molprobity Statistics. All-atom Clashscore : 5.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.73 % Favored : 96.27 % Rotamer: Outliers : 3.22 % Allowed : 18.01 % Favored : 78.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 aren not related in a simple way. whole: 0.30 (0.32), residues: 750 helix: None (None), residues: 0 sheet: 0.81 (0.28), residues: 352 loop : -0.32 (0.33), residues: 398 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 578 TYR 0.015 0.001 TYR C 95 PHE 0.017 0.002 PHE B 547 TRP 0.009 0.001 TRP H 114 HIS 0.004 0.002 HIS L 39 Details of bonding type rmsd covalent geometry : bond 0.00294 ( 5872) covalent geometry : angle 0.51895 ( 8020) SS BOND : bond 0.00264 ( 4) SS BOND : angle 0.82473 ( 8) hydrogen bonds : bond 0.03320 ( 203) hydrogen bonds : angle 5.23659 ( 513) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1500 Ramachandran restraints generated. 750 Oldfield, 0 Emsley, 750 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1500 Ramachandran restraints generated. 750 Oldfield, 0 Emsley, 750 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 102 time to evaluate : 0.243 Fit side-chains REVERT: A 569 LEU cc_start: 0.8183 (OUTLIER) cc_final: 0.7919 (mp) REVERT: B 569 LEU cc_start: 0.8206 (OUTLIER) cc_final: 0.7981 (mp) REVERT: C 122 VAL cc_start: 0.8029 (t) cc_final: 0.7779 (m) REVERT: D 21 SER cc_start: 0.8417 (p) cc_final: 0.8191 (t) outliers start: 20 outliers final: 14 residues processed: 116 average time/residue: 0.3107 time to fit residues: 39.0290 Evaluate side-chains 109 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 93 time to evaluate : 0.233 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 501 VAL Chi-restraints excluded: chain A residue 538 VAL Chi-restraints excluded: chain A residue 545 LEU Chi-restraints excluded: chain A residue 569 LEU Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 7 SER Chi-restraints excluded: chain H residue 25 SER Chi-restraints excluded: chain H residue 103 ILE Chi-restraints excluded: chain L residue 38 GLN Chi-restraints excluded: chain L residue 100 VAL Chi-restraints excluded: chain B residue 517 THR Chi-restraints excluded: chain B residue 538 VAL Chi-restraints excluded: chain B residue 569 LEU Chi-restraints excluded: chain C residue 17 SER Chi-restraints excluded: chain C residue 63 SER Chi-restraints excluded: chain D residue 22 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 65 optimal weight: 1.9990 chunk 2 optimal weight: 0.8980 chunk 0 optimal weight: 0.9990 chunk 27 optimal weight: 2.9990 chunk 24 optimal weight: 1.9990 chunk 70 optimal weight: 1.9990 chunk 42 optimal weight: 1.9990 chunk 4 optimal weight: 1.9990 chunk 40 optimal weight: 1.9990 chunk 60 optimal weight: 1.9990 chunk 26 optimal weight: 0.0000 overall best weight: 1.1790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 482 GLN B 482 GLN B 577 HIS C 82 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3211 r_free = 0.3211 target = 0.095202 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3080 r_free = 0.3080 target = 0.087254 restraints weight = 8464.576| |-----------------------------------------------------------------------------| r_work (start): 0.3079 rms_B_bonded: 1.62 r_work: 0.2989 rms_B_bonded: 1.87 restraints_weight: 0.5000 r_work: 0.2867 rms_B_bonded: 3.34 restraints_weight: 0.2500 r_work (final): 0.2867 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8000 moved from start: 0.2721 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.063 5876 Z= 0.325 Angle : 0.666 6.291 8028 Z= 0.356 Chirality : 0.048 0.159 918 Planarity : 0.006 0.054 1024 Dihedral : 5.707 29.410 838 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 5.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.67 % Favored : 95.33 % Rotamer: Outliers : 4.18 % Allowed : 18.33 % Favored : 77.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 aren not related in a simple way. whole: 0.10 (0.31), residues: 750 helix: None (None), residues: 0 sheet: 0.70 (0.27), residues: 360 loop : -0.52 (0.33), residues: 390 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 578 TYR 0.022 0.003 TYR C 95 PHE 0.022 0.003 PHE A 536 TRP 0.019 0.002 TRP H 114 HIS 0.009 0.004 HIS D 39 Details of bonding type rmsd covalent geometry : bond 0.00775 ( 5872) covalent geometry : angle 0.66418 ( 8020) SS BOND : bond 0.00692 ( 4) SS BOND : angle 1.52953 ( 8) hydrogen bonds : bond 0.04160 ( 203) hydrogen bonds : angle 5.75984 ( 513) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1500 Ramachandran restraints generated. 750 Oldfield, 0 Emsley, 750 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1500 Ramachandran restraints generated. 750 Oldfield, 0 Emsley, 750 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 82 time to evaluate : 0.238 Fit side-chains REVERT: B 569 LEU cc_start: 0.8245 (OUTLIER) cc_final: 0.7978 (mp) REVERT: C 68 PHE cc_start: 0.8752 (m-80) cc_final: 0.8274 (m-80) outliers start: 26 outliers final: 18 residues processed: 101 average time/residue: 0.2917 time to fit residues: 32.1706 Evaluate side-chains 101 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 82 time to evaluate : 0.217 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 501 VAL Chi-restraints excluded: chain A residue 510 VAL Chi-restraints excluded: chain A residue 538 VAL Chi-restraints excluded: chain H residue 7 SER Chi-restraints excluded: chain H residue 18 LEU Chi-restraints excluded: chain H residue 25 SER Chi-restraints excluded: chain H residue 124 SER Chi-restraints excluded: chain L residue 38 GLN Chi-restraints excluded: chain L residue 100 VAL Chi-restraints excluded: chain B residue 500 LEU Chi-restraints excluded: chain B residue 517 THR Chi-restraints excluded: chain B residue 538 VAL Chi-restraints excluded: chain B residue 569 LEU Chi-restraints excluded: chain C residue 17 SER Chi-restraints excluded: chain C residue 25 SER Chi-restraints excluded: chain C residue 63 SER Chi-restraints excluded: chain D residue 27 SER Chi-restraints excluded: chain D residue 38 GLN Chi-restraints excluded: chain D residue 97 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 49 optimal weight: 1.9990 chunk 71 optimal weight: 1.9990 chunk 65 optimal weight: 0.8980 chunk 17 optimal weight: 0.9980 chunk 73 optimal weight: 0.9990 chunk 42 optimal weight: 0.5980 chunk 69 optimal weight: 0.0010 chunk 70 optimal weight: 0.9980 chunk 30 optimal weight: 0.9980 chunk 38 optimal weight: 0.9980 chunk 12 optimal weight: 0.0470 overall best weight: 0.5084 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 482 GLN C 82 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3243 r_free = 0.3243 target = 0.097377 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3120 r_free = 0.3120 target = 0.089748 restraints weight = 8533.947| |-----------------------------------------------------------------------------| r_work (start): 0.3111 rms_B_bonded: 1.56 r_work: 0.3024 rms_B_bonded: 1.81 restraints_weight: 0.5000 r_work: 0.2905 rms_B_bonded: 3.27 restraints_weight: 0.2500 r_work (final): 0.2905 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7964 moved from start: 0.2713 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 5876 Z= 0.160 Angle : 0.545 5.893 8028 Z= 0.296 Chirality : 0.043 0.146 918 Planarity : 0.005 0.049 1024 Dihedral : 5.192 24.562 838 Min Nonbonded Distance : 2.566 Molprobity Statistics. All-atom Clashscore : 5.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.00 % Favored : 96.00 % Rotamer: Outliers : 4.66 % Allowed : 17.68 % Favored : 77.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 aren not related in a simple way. whole: 0.17 (0.32), residues: 750 helix: None (None), residues: 0 sheet: 0.64 (0.27), residues: 362 loop : -0.35 (0.34), residues: 388 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 578 TYR 0.016 0.002 TYR C 95 PHE 0.015 0.002 PHE B 547 TRP 0.011 0.001 TRP H 114 HIS 0.005 0.002 HIS D 39 Details of bonding type rmsd covalent geometry : bond 0.00373 ( 5872) covalent geometry : angle 0.54414 ( 8020) SS BOND : bond 0.00533 ( 4) SS BOND : angle 0.97784 ( 8) hydrogen bonds : bond 0.03442 ( 203) hydrogen bonds : angle 5.27952 ( 513) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1500 Ramachandran restraints generated. 750 Oldfield, 0 Emsley, 750 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1500 Ramachandran restraints generated. 750 Oldfield, 0 Emsley, 750 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 88 time to evaluate : 0.176 Fit side-chains REVERT: A 569 LEU cc_start: 0.8179 (OUTLIER) cc_final: 0.7922 (mp) REVERT: H 89 GLU cc_start: 0.7452 (OUTLIER) cc_final: 0.7194 (tm-30) REVERT: H 98 ARG cc_start: 0.8620 (OUTLIER) cc_final: 0.8217 (mtp180) REVERT: L 88 TYR cc_start: 0.8746 (m-80) cc_final: 0.8535 (m-80) REVERT: B 569 LEU cc_start: 0.8223 (OUTLIER) cc_final: 0.7980 (mp) outliers start: 29 outliers final: 18 residues processed: 110 average time/residue: 0.3034 time to fit residues: 36.3013 Evaluate side-chains 106 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 84 time to evaluate : 0.212 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 501 VAL Chi-restraints excluded: chain A residue 510 VAL Chi-restraints excluded: chain A residue 538 VAL Chi-restraints excluded: chain A residue 545 LEU Chi-restraints excluded: chain A residue 569 LEU Chi-restraints excluded: chain A residue 600 VAL Chi-restraints excluded: chain H residue 7 SER Chi-restraints excluded: chain H residue 18 LEU Chi-restraints excluded: chain H residue 25 SER Chi-restraints excluded: chain H residue 89 GLU Chi-restraints excluded: chain H residue 98 ARG Chi-restraints excluded: chain H residue 124 SER Chi-restraints excluded: chain L residue 100 VAL Chi-restraints excluded: chain B residue 500 LEU Chi-restraints excluded: chain B residue 517 THR Chi-restraints excluded: chain B residue 538 VAL Chi-restraints excluded: chain B residue 569 LEU Chi-restraints excluded: chain C residue 17 SER Chi-restraints excluded: chain C residue 63 SER Chi-restraints excluded: chain D residue 27 SER Chi-restraints excluded: chain D residue 38 GLN Chi-restraints excluded: chain D residue 97 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 15 optimal weight: 0.8980 chunk 6 optimal weight: 1.9990 chunk 12 optimal weight: 0.5980 chunk 73 optimal weight: 0.5980 chunk 7 optimal weight: 0.8980 chunk 48 optimal weight: 1.9990 chunk 52 optimal weight: 0.9990 chunk 66 optimal weight: 0.5980 chunk 1 optimal weight: 1.9990 chunk 25 optimal weight: 0.7980 chunk 38 optimal weight: 0.9980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 482 GLN B 482 GLN C 82 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3233 r_free = 0.3233 target = 0.096668 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3110 r_free = 0.3110 target = 0.089096 restraints weight = 8487.087| |-----------------------------------------------------------------------------| r_work (start): 0.3110 rms_B_bonded: 1.54 r_work: 0.3024 rms_B_bonded: 1.79 restraints_weight: 0.5000 r_work: 0.2905 rms_B_bonded: 3.22 restraints_weight: 0.2500 r_work (final): 0.2905 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7972 moved from start: 0.2765 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 5876 Z= 0.205 Angle : 0.577 6.053 8028 Z= 0.311 Chirality : 0.044 0.149 918 Planarity : 0.005 0.050 1024 Dihedral : 5.299 24.843 838 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 5.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.00 % Favored : 96.00 % Rotamer: Outliers : 4.18 % Allowed : 18.33 % Favored : 77.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 aren not related in a simple way. whole: 0.14 (0.32), residues: 750 helix: None (None), residues: 0 sheet: 0.62 (0.27), residues: 362 loop : -0.37 (0.33), residues: 388 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 578 TYR 0.019 0.002 TYR C 95 PHE 0.017 0.002 PHE A 536 TRP 0.013 0.002 TRP H 114 HIS 0.006 0.003 HIS D 39 Details of bonding type rmsd covalent geometry : bond 0.00485 ( 5872) covalent geometry : angle 0.57524 ( 8020) SS BOND : bond 0.00532 ( 4) SS BOND : angle 1.69586 ( 8) hydrogen bonds : bond 0.03630 ( 203) hydrogen bonds : angle 5.37800 ( 513) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1500 Ramachandran restraints generated. 750 Oldfield, 0 Emsley, 750 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1500 Ramachandran restraints generated. 750 Oldfield, 0 Emsley, 750 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 82 time to evaluate : 0.231 Fit side-chains REVERT: A 569 LEU cc_start: 0.8179 (OUTLIER) cc_final: 0.7922 (mp) REVERT: H 89 GLU cc_start: 0.7459 (OUTLIER) cc_final: 0.7199 (tm-30) REVERT: H 98 ARG cc_start: 0.8625 (OUTLIER) cc_final: 0.8191 (mtp180) REVERT: B 569 LEU cc_start: 0.8231 (OUTLIER) cc_final: 0.7973 (mp) REVERT: C 68 PHE cc_start: 0.8749 (m-80) cc_final: 0.8199 (m-80) outliers start: 26 outliers final: 21 residues processed: 102 average time/residue: 0.2847 time to fit residues: 31.7116 Evaluate side-chains 106 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 81 time to evaluate : 0.225 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 501 VAL Chi-restraints excluded: chain A residue 510 VAL Chi-restraints excluded: chain A residue 538 VAL Chi-restraints excluded: chain A residue 545 LEU Chi-restraints excluded: chain A residue 569 LEU Chi-restraints excluded: chain A residue 600 VAL Chi-restraints excluded: chain H residue 7 SER Chi-restraints excluded: chain H residue 18 LEU Chi-restraints excluded: chain H residue 25 SER Chi-restraints excluded: chain H residue 89 GLU Chi-restraints excluded: chain H residue 98 ARG Chi-restraints excluded: chain H residue 124 SER Chi-restraints excluded: chain L residue 100 VAL Chi-restraints excluded: chain B residue 488 SER Chi-restraints excluded: chain B residue 500 LEU Chi-restraints excluded: chain B residue 517 THR Chi-restraints excluded: chain B residue 538 VAL Chi-restraints excluded: chain B residue 569 LEU Chi-restraints excluded: chain C residue 17 SER Chi-restraints excluded: chain C residue 25 SER Chi-restraints excluded: chain C residue 63 SER Chi-restraints excluded: chain D residue 27 SER Chi-restraints excluded: chain D residue 38 GLN Chi-restraints excluded: chain D residue 94 SER Chi-restraints excluded: chain D residue 97 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 41 optimal weight: 2.9990 chunk 62 optimal weight: 1.9990 chunk 63 optimal weight: 0.0470 chunk 39 optimal weight: 0.6980 chunk 60 optimal weight: 0.5980 chunk 73 optimal weight: 0.8980 chunk 2 optimal weight: 0.7980 chunk 50 optimal weight: 0.5980 chunk 72 optimal weight: 1.9990 chunk 54 optimal weight: 0.5980 chunk 48 optimal weight: 1.9990 overall best weight: 0.5078 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 482 GLN C 82 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3246 r_free = 0.3246 target = 0.097525 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3122 r_free = 0.3122 target = 0.089839 restraints weight = 8557.557| |-----------------------------------------------------------------------------| r_work (start): 0.3126 rms_B_bonded: 1.58 r_work: 0.3039 rms_B_bonded: 1.83 restraints_weight: 0.5000 r_work: 0.2920 rms_B_bonded: 3.30 restraints_weight: 0.2500 r_work (final): 0.2920 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7960 moved from start: 0.2740 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 5876 Z= 0.159 Angle : 0.540 5.891 8028 Z= 0.292 Chirality : 0.043 0.144 918 Planarity : 0.005 0.051 1024 Dihedral : 5.100 23.063 838 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 5.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.00 % Favored : 96.00 % Rotamer: Outliers : 4.34 % Allowed : 18.17 % Favored : 77.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 aren not related in a simple way. whole: 0.19 (0.32), residues: 750 helix: None (None), residues: 0 sheet: 0.62 (0.27), residues: 362 loop : -0.29 (0.34), residues: 388 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 578 TYR 0.017 0.002 TYR C 95 PHE 0.014 0.002 PHE A 536 TRP 0.011 0.001 TRP H 114 HIS 0.005 0.002 HIS L 39 Details of bonding type rmsd covalent geometry : bond 0.00371 ( 5872) covalent geometry : angle 0.53839 ( 8020) SS BOND : bond 0.00381 ( 4) SS BOND : angle 1.43314 ( 8) hydrogen bonds : bond 0.03365 ( 203) hydrogen bonds : angle 5.18380 ( 513) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1500 Ramachandran restraints generated. 750 Oldfield, 0 Emsley, 750 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1500 Ramachandran restraints generated. 750 Oldfield, 0 Emsley, 750 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 84 time to evaluate : 0.227 Fit side-chains REVERT: A 569 LEU cc_start: 0.8165 (OUTLIER) cc_final: 0.7904 (mp) REVERT: H 12 VAL cc_start: 0.8543 (OUTLIER) cc_final: 0.8311 (m) REVERT: H 89 GLU cc_start: 0.7465 (OUTLIER) cc_final: 0.7233 (tm-30) REVERT: H 98 ARG cc_start: 0.8619 (OUTLIER) cc_final: 0.8210 (mtp180) REVERT: B 569 LEU cc_start: 0.8215 (OUTLIER) cc_final: 0.7980 (mp) outliers start: 27 outliers final: 22 residues processed: 104 average time/residue: 0.2971 time to fit residues: 33.7022 Evaluate side-chains 110 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 83 time to evaluate : 0.214 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 501 VAL Chi-restraints excluded: chain A residue 510 VAL Chi-restraints excluded: chain A residue 538 VAL Chi-restraints excluded: chain A residue 545 LEU Chi-restraints excluded: chain A residue 569 LEU Chi-restraints excluded: chain A residue 600 VAL Chi-restraints excluded: chain H residue 7 SER Chi-restraints excluded: chain H residue 12 VAL Chi-restraints excluded: chain H residue 18 LEU Chi-restraints excluded: chain H residue 25 SER Chi-restraints excluded: chain H residue 89 GLU Chi-restraints excluded: chain H residue 98 ARG Chi-restraints excluded: chain H residue 124 SER Chi-restraints excluded: chain L residue 38 GLN Chi-restraints excluded: chain L residue 100 VAL Chi-restraints excluded: chain B residue 460 ARG Chi-restraints excluded: chain B residue 500 LEU Chi-restraints excluded: chain B residue 517 THR Chi-restraints excluded: chain B residue 538 VAL Chi-restraints excluded: chain B residue 569 LEU Chi-restraints excluded: chain C residue 17 SER Chi-restraints excluded: chain C residue 25 SER Chi-restraints excluded: chain C residue 63 SER Chi-restraints excluded: chain D residue 27 SER Chi-restraints excluded: chain D residue 38 GLN Chi-restraints excluded: chain D residue 94 SER Chi-restraints excluded: chain D residue 97 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 16 optimal weight: 1.9990 chunk 17 optimal weight: 1.9990 chunk 56 optimal weight: 0.9980 chunk 39 optimal weight: 0.5980 chunk 60 optimal weight: 1.9990 chunk 9 optimal weight: 0.5980 chunk 63 optimal weight: 0.0670 chunk 6 optimal weight: 1.9990 chunk 36 optimal weight: 2.9990 chunk 0 optimal weight: 0.9980 chunk 66 optimal weight: 0.9990 overall best weight: 0.6518 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 482 GLN B 482 GLN C 82 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3240 r_free = 0.3240 target = 0.097060 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3114 r_free = 0.3114 target = 0.089353 restraints weight = 8657.646| |-----------------------------------------------------------------------------| r_work (start): 0.3108 rms_B_bonded: 1.58 r_work: 0.3019 rms_B_bonded: 1.84 restraints_weight: 0.5000 r_work: 0.2899 rms_B_bonded: 3.31 restraints_weight: 0.2500 r_work (final): 0.2899 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7973 moved from start: 0.2802 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 5876 Z= 0.194 Angle : 0.567 5.969 8028 Z= 0.307 Chirality : 0.044 0.146 918 Planarity : 0.005 0.052 1024 Dihedral : 5.237 23.964 838 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 5.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.87 % Favored : 96.13 % Rotamer: Outliers : 4.34 % Allowed : 18.49 % Favored : 77.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 aren not related in a simple way. whole: 0.20 (0.32), residues: 750 helix: None (None), residues: 0 sheet: 0.59 (0.27), residues: 362 loop : -0.24 (0.34), residues: 388 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 578 TYR 0.018 0.002 TYR C 95 PHE 0.016 0.002 PHE A 536 TRP 0.012 0.001 TRP H 114 HIS 0.006 0.003 HIS D 39 Details of bonding type rmsd covalent geometry : bond 0.00458 ( 5872) covalent geometry : angle 0.56536 ( 8020) SS BOND : bond 0.00425 ( 4) SS BOND : angle 1.55711 ( 8) hydrogen bonds : bond 0.03528 ( 203) hydrogen bonds : angle 5.28198 ( 513) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1500 Ramachandran restraints generated. 750 Oldfield, 0 Emsley, 750 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1500 Ramachandran restraints generated. 750 Oldfield, 0 Emsley, 750 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 83 time to evaluate : 0.217 Fit side-chains REVERT: A 569 LEU cc_start: 0.8179 (OUTLIER) cc_final: 0.7919 (mp) REVERT: H 12 VAL cc_start: 0.8570 (t) cc_final: 0.8327 (m) REVERT: H 89 GLU cc_start: 0.7472 (OUTLIER) cc_final: 0.7242 (tm-30) REVERT: H 98 ARG cc_start: 0.8602 (OUTLIER) cc_final: 0.7993 (mtp180) REVERT: B 569 LEU cc_start: 0.8232 (OUTLIER) cc_final: 0.7983 (mp) REVERT: C 68 PHE cc_start: 0.8750 (m-80) cc_final: 0.8204 (m-80) outliers start: 27 outliers final: 22 residues processed: 104 average time/residue: 0.2923 time to fit residues: 33.1469 Evaluate side-chains 106 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 80 time to evaluate : 0.236 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 501 VAL Chi-restraints excluded: chain A residue 510 VAL Chi-restraints excluded: chain A residue 538 VAL Chi-restraints excluded: chain A residue 545 LEU Chi-restraints excluded: chain A residue 569 LEU Chi-restraints excluded: chain A residue 600 VAL Chi-restraints excluded: chain H residue 7 SER Chi-restraints excluded: chain H residue 18 LEU Chi-restraints excluded: chain H residue 25 SER Chi-restraints excluded: chain H residue 89 GLU Chi-restraints excluded: chain H residue 98 ARG Chi-restraints excluded: chain H residue 124 SER Chi-restraints excluded: chain L residue 38 GLN Chi-restraints excluded: chain L residue 100 VAL Chi-restraints excluded: chain B residue 460 ARG Chi-restraints excluded: chain B residue 500 LEU Chi-restraints excluded: chain B residue 517 THR Chi-restraints excluded: chain B residue 538 VAL Chi-restraints excluded: chain B residue 569 LEU Chi-restraints excluded: chain C residue 17 SER Chi-restraints excluded: chain C residue 25 SER Chi-restraints excluded: chain C residue 63 SER Chi-restraints excluded: chain D residue 27 SER Chi-restraints excluded: chain D residue 38 GLN Chi-restraints excluded: chain D residue 94 SER Chi-restraints excluded: chain D residue 97 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 28 optimal weight: 0.4980 chunk 73 optimal weight: 0.7980 chunk 65 optimal weight: 0.8980 chunk 27 optimal weight: 0.2980 chunk 53 optimal weight: 1.9990 chunk 29 optimal weight: 0.6980 chunk 26 optimal weight: 0.0370 chunk 42 optimal weight: 1.9990 chunk 41 optimal weight: 2.9990 chunk 57 optimal weight: 0.9990 chunk 19 optimal weight: 0.4980 overall best weight: 0.4058 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 482 GLN C 82 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3257 r_free = 0.3257 target = 0.098140 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3132 r_free = 0.3132 target = 0.090419 restraints weight = 8555.333| |-----------------------------------------------------------------------------| r_work (start): 0.3136 rms_B_bonded: 1.58 r_work: 0.3049 rms_B_bonded: 1.84 restraints_weight: 0.5000 r_work: 0.2930 rms_B_bonded: 3.31 restraints_weight: 0.2500 r_work (final): 0.2930 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7949 moved from start: 0.2803 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 5876 Z= 0.135 Angle : 0.521 5.725 8028 Z= 0.283 Chirality : 0.042 0.143 918 Planarity : 0.005 0.050 1024 Dihedral : 4.970 21.762 838 Min Nonbonded Distance : 2.570 Molprobity Statistics. All-atom Clashscore : 5.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.00 % Favored : 96.00 % Rotamer: Outliers : 4.02 % Allowed : 18.97 % Favored : 77.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 aren not related in a simple way. whole: 0.24 (0.32), residues: 750 helix: None (None), residues: 0 sheet: 0.63 (0.28), residues: 356 loop : -0.22 (0.33), residues: 394 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 578 TYR 0.016 0.001 TYR C 95 PHE 0.013 0.002 PHE B 547 TRP 0.009 0.001 TRP H 114 HIS 0.004 0.002 HIS L 39 Details of bonding type rmsd covalent geometry : bond 0.00314 ( 5872) covalent geometry : angle 0.51973 ( 8020) SS BOND : bond 0.00303 ( 4) SS BOND : angle 1.19128 ( 8) hydrogen bonds : bond 0.03218 ( 203) hydrogen bonds : angle 5.02642 ( 513) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2144.18 seconds wall clock time: 37 minutes 23.36 seconds (2243.36 seconds total)