Starting phenix.real_space_refine on Wed Sep 17 06:30:39 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9jim_61510/09_2025/9jim_61510.cif Found real_map, /net/cci-nas-00/data/ceres_data/9jim_61510/09_2025/9jim_61510.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.86 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9jim_61510/09_2025/9jim_61510.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9jim_61510/09_2025/9jim_61510.map" model { file = "/net/cci-nas-00/data/ceres_data/9jim_61510/09_2025/9jim_61510.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9jim_61510/09_2025/9jim_61510.cif" } resolution = 2.86 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= 0.017 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 24 5.16 5 C 3762 2.51 5 N 1006 2.21 5 O 1176 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 5 residue(s): 0.00s 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: 5968 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1175 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 151, 1169 Classifications: {'peptide': 151} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 143} Conformer: "B" Number of residues, atoms: 151, 1169 Classifications: {'peptide': 151} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 143} bond proxies already assigned to first conformer: 1199 Chain: "L" Number of atoms: 790 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 790 Classifications: {'peptide': 108} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 8, 'TRANS': 99} Chain: "H" Number of atoms: 1019 Number of conformers: 1 Conformer: "" Number of residues, atoms: 130, 1019 Classifications: {'peptide': 130} Link IDs: {'PTRANS': 3, 'TRANS': 126} Chain: "B" Number of atoms: 1175 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 151, 1169 Classifications: {'peptide': 151} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 143} Conformer: "B" Number of residues, atoms: 151, 1169 Classifications: {'peptide': 151} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 143} bond proxies already assigned to first conformer: 1199 Chain: "D" Number of atoms: 790 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 790 Classifications: {'peptide': 108} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 8, 'TRANS': 99} Chain: "C" Number of atoms: 1019 Number of conformers: 1 Conformer: "" Number of residues, atoms: 130, 1019 Classifications: {'peptide': 130} Link IDs: {'PTRANS': 3, 'TRANS': 126} Residues with excluded nonbonded symmetry interactions: 2 residue: pdb=" N ASER A 474 " occ=0.51 ... (10 atoms not shown) pdb=" OG BSER A 474 " occ=0.49 residue: pdb=" N ASER B 474 " occ=0.51 ... (10 atoms not shown) pdb=" OG BSER B 474 " occ=0.49 Time building chain proxies: 2.43, per 1000 atoms: 0.41 Number of scatterers: 5968 At special positions: 0 Unit cell: (113.75, 67.6, 84.5, 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 24 16.00 O 1176 8.00 N 1006 7.00 C 3762 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS L 22 " - pdb=" SG CYS L 89 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.03 Simple disulfide: pdb=" SG CYS D 22 " - pdb=" SG CYS D 89 " distance=2.03 Simple disulfide: pdb=" SG CYS C 22 " - pdb=" SG CYS C 96 " 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 Time building additional restraints: 0.51 Conformation dependent library (CDL) restraints added in 413.4 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 1544 Ramachandran restraints generated. 772 Oldfield, 0 Emsley, 772 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1396 Finding SS restraints... Secondary structure from input PDB file: 9 helices and 20 sheets defined 5.1% alpha, 51.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.32 Creating SS restraints... Processing helix chain 'A' and resid 473 through 477 removed outlier: 3.630A pdb=" N GLY A 477 " --> pdb=" O ASER A 474 " (cutoff:3.500A) Processing helix chain 'A' and resid 501 through 503 No H-bonds generated for 'chain 'A' and resid 501 through 503' Processing helix chain 'L' and resid 80 through 84 removed outlier: 3.545A pdb=" N GLU L 84 " --> pdb=" O THR L 81 " (cutoff:3.500A) Processing helix chain 'H' and resid 28 through 32 removed outlier: 4.018A pdb=" N TYR H 32 " --> pdb=" O PHE H 29 " (cutoff:3.500A) Processing helix chain 'H' and resid 87 through 90 removed outlier: 3.718A pdb=" N ASP H 90 " --> pdb=" O ARG H 87 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 87 through 90' Processing helix chain 'B' and resid 473 through 477 removed outlier: 3.583A pdb=" N GLY B 477 " --> pdb=" O ASER B 474 " (cutoff:3.500A) Processing helix chain 'B' and resid 501 through 503 No H-bonds generated for 'chain 'B' and resid 501 through 503' Processing helix chain 'D' and resid 80 through 84 removed outlier: 3.660A pdb=" N GLU D 84 " --> pdb=" O THR D 81 " (cutoff:3.500A) Processing helix chain 'C' and resid 28 through 32 removed outlier: 4.030A pdb=" N TYR C 32 " --> pdb=" O PHE C 29 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 453 through 454 Processing sheet with id=AA2, first strand: chain 'A' and resid 496 through 499 removed outlier: 3.573A pdb=" N GLN A 496 " --> pdb=" O ASN A 491 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N LEU A 570 " --> pdb=" O SER A 484 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N TRP A 559 " --> pdb=" O TYR A 571 " (cutoff:3.500A) removed outlier: 5.217A pdb=" N SER A 573 " --> pdb=" O SER A 557 " (cutoff:3.500A) removed outlier: 8.237A pdb=" N SER A 557 " --> pdb=" O SER A 573 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N HIS A 516 " --> pdb=" O GLN A 527 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 496 through 499 removed outlier: 3.573A pdb=" N GLN A 496 " --> pdb=" O ASN A 491 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N SER A 466 " --> pdb=" O VAL A 584 " (cutoff:3.500A) removed outlier: 4.769A pdb=" N VAL A 584 " --> pdb=" O SER A 466 " (cutoff:3.500A) removed outlier: 5.714A pdb=" N ALA A 591 " --> pdb=" O LYS A 533 " (cutoff:3.500A) removed outlier: 7.222A pdb=" N LYS A 533 " --> pdb=" O ALA A 591 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N HIS A 516 " --> pdb=" O GLN A 527 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'L' and resid 9 through 12 removed outlier: 3.700A pdb=" N ALA L 12 " --> pdb=" O THR L 108 " (cutoff:3.500A) removed outlier: 6.359A pdb=" N TRP L 36 " --> pdb=" O LEU L 48 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'L' and resid 9 through 12 removed outlier: 3.700A pdb=" N ALA L 12 " --> pdb=" O THR L 108 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'L' and resid 19 through 21 Processing sheet with id=AA7, first strand: chain 'H' and resid 3 through 6 Processing sheet with id=AA8, first strand: chain 'H' and resid 3 through 6 Processing sheet with id=AA9, first strand: chain 'H' and resid 10 through 12 removed outlier: 6.286A pdb=" N GLU H 10 " --> pdb=" O THR H 128 " (cutoff:3.500A) removed outlier: 6.443A pdb=" N ILE H 34 " --> pdb=" O TRP H 50 " (cutoff:3.500A) removed outlier: 4.458A pdb=" N TRP H 50 " --> pdb=" O ILE H 34 " (cutoff:3.500A) removed outlier: 6.509A pdb=" N TRP H 36 " --> pdb=" O MET H 48 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'H' and resid 10 through 12 removed outlier: 6.286A pdb=" N GLU H 10 " --> pdb=" O THR H 128 " (cutoff:3.500A) removed outlier: 6.575A pdb=" N CYS H 96 " --> pdb=" O TRP H 121 " (cutoff:3.500A) removed outlier: 4.592A pdb=" N TRP H 121 " --> pdb=" O CYS H 96 " (cutoff:3.500A) removed outlier: 6.416A pdb=" N ARG H 98 " --> pdb=" O ASP H 119 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 453 through 454 Processing sheet with id=AB3, first strand: chain 'B' and resid 497 through 499 removed outlier: 3.696A pdb=" N TRP B 559 " --> pdb=" O TYR B 571 " (cutoff:3.500A) removed outlier: 5.168A pdb=" N SER B 573 " --> pdb=" O SER B 557 " (cutoff:3.500A) removed outlier: 8.051A pdb=" N SER B 557 " --> pdb=" O SER B 573 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N HIS B 516 " --> pdb=" O GLN B 527 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 497 through 499 removed outlier: 3.715A pdb=" N SER B 466 " --> pdb=" O VAL B 584 " (cutoff:3.500A) removed outlier: 4.796A pdb=" N VAL B 584 " --> pdb=" O SER B 466 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 9 through 12 removed outlier: 3.665A pdb=" N ALA D 12 " --> pdb=" O THR D 108 " (cutoff:3.500A) removed outlier: 6.386A 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: 3.665A pdb=" N ALA D 12 " --> pdb=" O THR D 108 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 19 through 21 Processing sheet with id=AB8, first strand: chain 'C' and resid 3 through 6 Processing sheet with id=AB9, first strand: chain 'C' and resid 3 through 6 Processing sheet with id=AC1, first strand: chain 'C' and resid 10 through 12 removed outlier: 6.347A pdb=" N ILE C 34 " --> pdb=" O TRP C 50 " (cutoff:3.500A) removed outlier: 4.446A pdb=" N TRP C 50 " --> pdb=" O ILE C 34 " (cutoff:3.500A) removed outlier: 6.591A pdb=" N TRP C 36 " --> pdb=" O MET C 48 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 10 through 12 removed outlier: 6.604A pdb=" N CYS C 96 " --> pdb=" O TRP C 121 " (cutoff:3.500A) removed outlier: 4.648A pdb=" N TRP C 121 " --> pdb=" O CYS C 96 " (cutoff:3.500A) removed outlier: 6.543A pdb=" N ARG C 98 " --> pdb=" O ASP C 119 " (cutoff:3.500A) 244 hydrogen bonds defined for protein. 585 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: 1.16 Time building geometry restraints manager: 0.71 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: 1903 1.34 - 1.46: 1416 1.46 - 1.57: 2767 1.57 - 1.69: 0 1.69 - 1.81: 40 Bond restraints: 6126 Sorted by residual: bond pdb=" C ILE D 59 " pdb=" N PRO D 60 " ideal model delta sigma weight residual 1.330 1.361 -0.031 1.22e-02 6.72e+03 6.54e+00 bond pdb=" C GLY D 58 " pdb=" N ILE D 59 " ideal model delta sigma weight residual 1.329 1.349 -0.020 1.13e-02 7.83e+03 3.15e+00 bond pdb=" C LYS H 63 " pdb=" N PHE H 64 " ideal model delta sigma weight residual 1.332 1.354 -0.021 1.29e-02 6.01e+03 2.74e+00 bond pdb=" C TRP H 47 " pdb=" N MET H 48 " ideal model delta sigma weight residual 1.332 1.313 0.019 1.36e-02 5.41e+03 2.01e+00 bond pdb=" C ILE B 490 " pdb=" N ASN B 491 " ideal model delta sigma weight residual 1.331 1.349 -0.019 1.43e-02 4.89e+03 1.69e+00 ... (remaining 6121 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.28: 8069 1.28 - 2.57: 244 2.57 - 3.85: 42 3.85 - 5.13: 6 5.13 - 6.42: 3 Bond angle restraints: 8364 Sorted by residual: angle pdb=" C ASP L 51 " pdb=" CA ASP L 51 " pdb=" CB ASP L 51 " ideal model delta sigma weight residual 116.54 111.80 4.74 1.15e+00 7.56e-01 1.70e+01 angle pdb=" C ASP D 51 " pdb=" CA ASP D 51 " pdb=" CB ASP D 51 " ideal model delta sigma weight residual 116.54 111.86 4.68 1.15e+00 7.56e-01 1.65e+01 angle pdb=" CA PRO C 111 " pdb=" C PRO C 111 " pdb=" O PRO C 111 " ideal model delta sigma weight residual 121.38 119.16 2.22 7.70e-01 1.69e+00 8.30e+00 angle pdb=" C LEU D 74 " pdb=" N GLY D 75 " pdb=" CA GLY D 75 " ideal model delta sigma weight residual 122.18 120.48 1.70 6.90e-01 2.10e+00 6.06e+00 angle pdb=" N GLY A 580 " pdb=" CA GLY A 580 " pdb=" C GLY A 580 " ideal model delta sigma weight residual 111.85 114.38 -2.53 1.06e+00 8.90e-01 5.71e+00 ... (remaining 8359 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.95: 3311 17.95 - 35.89: 173 35.89 - 53.84: 38 53.84 - 71.79: 13 71.79 - 89.73: 5 Dihedral angle restraints: 3540 sinusoidal: 1322 harmonic: 2218 Sorted by residual: dihedral pdb=" CB CYS D 22 " pdb=" SG CYS D 22 " pdb=" SG CYS D 89 " pdb=" CB CYS D 89 " ideal model delta sinusoidal sigma weight residual 93.00 124.36 -31.36 1 1.00e+01 1.00e-02 1.40e+01 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 93.00 122.79 -29.79 1 1.00e+01 1.00e-02 1.27e+01 dihedral pdb=" CA VAL B 560 " pdb=" C VAL B 560 " pdb=" N TRP B 561 " pdb=" CA TRP B 561 " ideal model delta harmonic sigma weight residual 180.00 162.66 17.34 0 5.00e+00 4.00e-02 1.20e+01 ... (remaining 3537 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.028: 506 0.028 - 0.056: 259 0.056 - 0.085: 82 0.085 - 0.113: 55 0.113 - 0.141: 10 Chirality restraints: 912 Sorted by residual: chirality pdb=" CA ILE D 49 " pdb=" N ILE D 49 " pdb=" C ILE D 49 " pdb=" CB ILE D 49 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.96e-01 chirality pdb=" CA ASN L 31 " pdb=" N ASN L 31 " pdb=" C ASN L 31 " pdb=" CB ASN L 31 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.14 2.00e-01 2.50e+01 4.96e-01 chirality pdb=" CA ASN D 31 " pdb=" N ASN D 31 " pdb=" C ASN D 31 " pdb=" CB ASN D 31 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.14 2.00e-01 2.50e+01 4.84e-01 ... (remaining 909 not shown) Planarity restraints: 1066 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ALA D 13 " 0.025 5.00e-02 4.00e+02 3.82e-02 2.33e+00 pdb=" N PRO D 14 " -0.066 5.00e-02 4.00e+02 pdb=" CA PRO D 14 " 0.020 5.00e-02 4.00e+02 pdb=" CD PRO D 14 " 0.021 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CD ARG C 98 " -0.134 9.50e-02 1.11e+02 6.01e-02 2.22e+00 pdb=" NE ARG C 98 " 0.008 2.00e-02 2.50e+03 pdb=" CZ ARG C 98 " 0.002 2.00e-02 2.50e+03 pdb=" NH1 ARG C 98 " 0.001 2.00e-02 2.50e+03 pdb=" NH2 ARG C 98 " -0.005 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP H 50 " -0.012 2.00e-02 2.50e+03 8.70e-03 1.89e+00 pdb=" CG TRP H 50 " 0.024 2.00e-02 2.50e+03 pdb=" CD1 TRP H 50 " -0.007 2.00e-02 2.50e+03 pdb=" CD2 TRP H 50 " -0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP H 50 " -0.002 2.00e-02 2.50e+03 pdb=" CE2 TRP H 50 " -0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP H 50 " -0.000 2.00e-02 2.50e+03 pdb=" CZ2 TRP H 50 " -0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP H 50 " -0.000 2.00e-02 2.50e+03 pdb=" CH2 TRP H 50 " -0.001 2.00e-02 2.50e+03 ... (remaining 1063 not shown) Histogram of nonbonded interaction distances: 2.28 - 2.80: 1659 2.80 - 3.33: 4882 3.33 - 3.85: 10146 3.85 - 4.38: 12123 4.38 - 4.90: 20933 Nonbonded interactions: 49743 Sorted by model distance: nonbonded pdb=" O CYS D 22 " pdb=" OG SER D 71 " model vdw 2.280 3.040 nonbonded pdb=" NZ LYS A 533 " pdb=" O ASN A 549 " model vdw 2.320 3.120 nonbonded pdb=" O CYS L 22 " pdb=" OG SER L 71 " model vdw 2.328 3.040 nonbonded pdb=" O PHE C 110 " pdb=" ND2 ASN C 114 " model vdw 2.389 3.120 nonbonded pdb=" O ASN H 109 " pdb=" OD1 ASN H 109 " model vdw 2.401 3.040 ... (remaining 49738 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' and (resid 447 through 473 or resid 475 through 597)) selection = (chain 'B' and (resid 447 through 473 or resid 475 through 597)) } 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=0.49 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: 8.690 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: 0.160 Check model and map are aligned: 0.010 Set scattering table: 0.020 Process input model: 9.130 Find NCS groups from input model: 0.090 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:8.720 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.840 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7763 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 6130 Z= 0.186 Angle : 0.550 6.415 8372 Z= 0.316 Chirality : 0.042 0.141 912 Planarity : 0.004 0.060 1066 Dihedral : 12.482 89.734 2132 Min Nonbonded Distance : 2.280 Molprobity Statistics. All-atom Clashscore : 4.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.57 % Favored : 95.43 % Rotamer: Outliers : 0.00 % Allowed : 9.32 % Favored : 90.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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: -1.61 (0.30), residues: 772 helix: -4.10 (0.43), residues: 12 sheet: -0.22 (0.26), residues: 374 loop : -1.86 (0.31), residues: 386 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 38 TYR 0.014 0.002 TYR B 482 PHE 0.015 0.002 PHE H 64 TRP 0.024 0.002 TRP H 50 HIS 0.005 0.001 HIS B 479 Details of bonding type rmsd covalent geometry : bond 0.00376 ( 6126) covalent geometry : angle 0.54985 ( 8364) SS BOND : bond 0.00226 ( 4) SS BOND : angle 0.47640 ( 8) hydrogen bonds : bond 0.22443 ( 189) hydrogen bonds : angle 8.73138 ( 585) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1544 Ramachandran restraints generated. 772 Oldfield, 0 Emsley, 772 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1544 Ramachandran restraints generated. 772 Oldfield, 0 Emsley, 772 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 138 time to evaluate : 0.242 Fit side-chains REVERT: A 472 SER cc_start: 0.8384 (m) cc_final: 0.8056 (p) REVERT: A 482 TYR cc_start: 0.8326 (m-80) cc_final: 0.8120 (m-80) REVERT: A 483 TRP cc_start: 0.8544 (p-90) cc_final: 0.8269 (p-90) REVERT: L 39 GLN cc_start: 0.8370 (tt0) cc_final: 0.8156 (tt0) REVERT: L 89 CYS cc_start: 0.7015 (m) cc_final: 0.6685 (m) REVERT: L 96 LEU cc_start: 0.7941 (tt) cc_final: 0.7711 (tt) REVERT: H 31 SER cc_start: 0.7844 (t) cc_final: 0.7638 (m) REVERT: H 54 THR cc_start: 0.7728 (t) cc_final: 0.7508 (p) REVERT: H 78 THR cc_start: 0.7862 (m) cc_final: 0.7662 (t) REVERT: H 81 MET cc_start: 0.7837 (ttp) cc_final: 0.7632 (ttt) REVERT: D 10 VAL cc_start: 0.8671 (t) cc_final: 0.8461 (t) REVERT: D 50 TYR cc_start: 0.8567 (p90) cc_final: 0.8358 (p90) REVERT: C 28 THR cc_start: 0.8198 (m) cc_final: 0.7813 (m) REVERT: C 31 SER cc_start: 0.7845 (m) cc_final: 0.7569 (m) REVERT: C 125 THR cc_start: 0.8261 (m) cc_final: 0.8051 (m) outliers start: 0 outliers final: 0 residues processed: 138 average time/residue: 0.3164 time to fit residues: 47.4657 Evaluate side-chains 127 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 127 time to evaluate : 0.227 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 49 optimal weight: 1.9990 chunk 53 optimal weight: 0.6980 chunk 5 optimal weight: 0.6980 chunk 33 optimal weight: 0.4980 chunk 65 optimal weight: 1.9990 chunk 62 optimal weight: 0.7980 chunk 51 optimal weight: 0.9990 chunk 38 optimal weight: 1.9990 chunk 61 optimal weight: 0.5980 chunk 45 optimal weight: 1.9990 chunk 74 optimal weight: 0.8980 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 453 ASN A 527 GLN A 585 ASN L 16 GLN L 28 ASN L 39 GLN B 585 ASN D 39 GLN D 52 ASN C 33 ASN C 39 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.113798 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3167 r_free = 0.3167 target = 0.096043 restraints weight = 24677.029| |-----------------------------------------------------------------------------| r_work (start): 0.3166 rms_B_bonded: 3.43 r_work: 0.2991 rms_B_bonded: 3.75 restraints_weight: 0.5000 r_work (final): 0.2991 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2993 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2993 r_free = 0.2993 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2993 r_free = 0.2993 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2993 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7787 moved from start: 0.1762 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.033 6130 Z= 0.223 Angle : 0.587 5.208 8372 Z= 0.319 Chirality : 0.045 0.163 912 Planarity : 0.005 0.044 1066 Dihedral : 5.082 27.478 850 Min Nonbonded Distance : 2.572 Molprobity Statistics. All-atom Clashscore : 7.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.01 % Favored : 93.99 % Rotamer: Outliers : 3.42 % Allowed : 13.51 % Favored : 83.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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: -1.17 (0.30), residues: 772 helix: -4.19 (0.39), residues: 12 sheet: 0.28 (0.27), residues: 356 loop : -1.71 (0.29), residues: 404 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG H 100 TYR 0.019 0.002 TYR C 94 PHE 0.020 0.002 PHE C 64 TRP 0.033 0.003 TRP H 50 HIS 0.010 0.002 HIS A 479 Details of bonding type rmsd covalent geometry : bond 0.00507 ( 6126) covalent geometry : angle 0.58676 ( 8364) SS BOND : bond 0.00267 ( 4) SS BOND : angle 0.83985 ( 8) hydrogen bonds : bond 0.03749 ( 189) hydrogen bonds : angle 5.93407 ( 585) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1544 Ramachandran restraints generated. 772 Oldfield, 0 Emsley, 772 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1544 Ramachandran restraints generated. 772 Oldfield, 0 Emsley, 772 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 128 time to evaluate : 0.218 Fit side-chains REVERT: L 39 GLN cc_start: 0.8397 (tt0) cc_final: 0.8146 (tt0) REVERT: L 62 ARG cc_start: 0.8123 (OUTLIER) cc_final: 0.7454 (ptt90) REVERT: L 83 ASP cc_start: 0.8015 (m-30) cc_final: 0.7707 (m-30) REVERT: H 81 MET cc_start: 0.8096 (OUTLIER) cc_final: 0.7886 (ttt) REVERT: B 483 TRP cc_start: 0.8582 (p-90) cc_final: 0.8319 (p-90) REVERT: C 31 SER cc_start: 0.7563 (m) cc_final: 0.7217 (m) REVERT: C 81 MET cc_start: 0.8318 (tmm) cc_final: 0.8077 (ttp) outliers start: 22 outliers final: 11 residues processed: 134 average time/residue: 0.3148 time to fit residues: 45.8036 Evaluate side-chains 137 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 124 time to evaluate : 0.224 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 62 ARG Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 81 MET Chi-restraints excluded: chain H residue 128 THR Chi-restraints excluded: chain B residue 574 THR Chi-restraints excluded: chain D residue 10 VAL Chi-restraints excluded: chain D residue 73 THR Chi-restraints excluded: chain D residue 99 VAL Chi-restraints excluded: chain C residue 5 VAL Chi-restraints excluded: chain C residue 7 SER Chi-restraints excluded: chain C residue 102 THR Chi-restraints excluded: chain C residue 128 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 65 optimal weight: 1.9990 chunk 28 optimal weight: 1.9990 chunk 39 optimal weight: 0.7980 chunk 72 optimal weight: 0.9980 chunk 3 optimal weight: 0.9980 chunk 62 optimal weight: 0.6980 chunk 17 optimal weight: 2.9990 chunk 34 optimal weight: 0.5980 chunk 26 optimal weight: 0.6980 chunk 47 optimal weight: 0.9980 chunk 1 optimal weight: 0.3980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 453 ASN A 471 GLN A 551 ASN L 32 ASN H 33 ASN D 39 GLN D 52 ASN C 33 ASN C 39 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.114492 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3165 r_free = 0.3165 target = 0.095999 restraints weight = 29248.009| |-----------------------------------------------------------------------------| r_work (start): 0.3165 rms_B_bonded: 3.80 r_work: 0.2978 rms_B_bonded: 4.04 restraints_weight: 0.5000 r_work (final): 0.2978 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2971 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2971 r_free = 0.2971 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2971 r_free = 0.2971 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2971 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7804 moved from start: 0.2188 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.032 6130 Z= 0.215 Angle : 0.563 5.089 8372 Z= 0.308 Chirality : 0.044 0.147 912 Planarity : 0.004 0.046 1066 Dihedral : 4.988 24.257 850 Min Nonbonded Distance : 2.587 Molprobity Statistics. All-atom Clashscore : 6.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.61 % Favored : 94.39 % Rotamer: Outliers : 3.42 % Allowed : 15.84 % Favored : 80.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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: -1.00 (0.30), residues: 772 helix: -4.22 (0.37), residues: 12 sheet: 0.53 (0.27), residues: 354 loop : -1.73 (0.29), residues: 406 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 449 TYR 0.016 0.002 TYR D 50 PHE 0.023 0.002 PHE C 64 TRP 0.020 0.002 TRP C 50 HIS 0.008 0.002 HIS A 479 Details of bonding type rmsd covalent geometry : bond 0.00488 ( 6126) covalent geometry : angle 0.56262 ( 8364) SS BOND : bond 0.00284 ( 4) SS BOND : angle 0.96307 ( 8) hydrogen bonds : bond 0.03446 ( 189) hydrogen bonds : angle 5.60786 ( 585) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1544 Ramachandran restraints generated. 772 Oldfield, 0 Emsley, 772 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1544 Ramachandran restraints generated. 772 Oldfield, 0 Emsley, 772 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 113 time to evaluate : 0.260 Fit side-chains REVERT: L 39 GLN cc_start: 0.8422 (tt0) cc_final: 0.8157 (tt0) REVERT: L 62 ARG cc_start: 0.8084 (OUTLIER) cc_final: 0.7435 (ptt90) REVERT: H 81 MET cc_start: 0.8096 (OUTLIER) cc_final: 0.7853 (ttt) REVERT: H 128 THR cc_start: 0.8459 (OUTLIER) cc_final: 0.8216 (p) REVERT: B 483 TRP cc_start: 0.8585 (p-90) cc_final: 0.8328 (p-90) REVERT: C 28 THR cc_start: 0.8217 (m) cc_final: 0.7549 (t) REVERT: C 31 SER cc_start: 0.7516 (m) cc_final: 0.6897 (m) outliers start: 22 outliers final: 15 residues processed: 121 average time/residue: 0.3037 time to fit residues: 40.1094 Evaluate side-chains 127 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 109 time to evaluate : 0.246 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 23 SER Chi-restraints excluded: chain L residue 62 ARG Chi-restraints excluded: chain L residue 94 SER Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 81 MET Chi-restraints excluded: chain H residue 128 THR Chi-restraints excluded: chain B residue 453 ASN Chi-restraints excluded: chain B residue 574 THR Chi-restraints excluded: chain D residue 10 VAL Chi-restraints excluded: chain D residue 18 VAL Chi-restraints excluded: chain D residue 73 THR Chi-restraints excluded: chain D residue 99 VAL Chi-restraints excluded: chain C residue 5 VAL Chi-restraints excluded: chain C residue 7 SER Chi-restraints excluded: chain C residue 54 THR Chi-restraints excluded: chain C residue 102 THR Chi-restraints excluded: chain C residue 128 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 75 optimal weight: 0.9980 chunk 12 optimal weight: 0.9990 chunk 60 optimal weight: 3.9990 chunk 8 optimal weight: 0.1980 chunk 16 optimal weight: 1.9990 chunk 42 optimal weight: 0.0470 chunk 46 optimal weight: 0.9980 chunk 52 optimal weight: 0.9990 chunk 35 optimal weight: 1.9990 chunk 51 optimal weight: 0.9980 chunk 23 optimal weight: 0.0970 overall best weight: 0.4676 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 453 ASN D 39 GLN D 52 ASN C 33 ASN C 39 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.114965 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3198 r_free = 0.3198 target = 0.097896 restraints weight = 20841.073| |-----------------------------------------------------------------------------| r_work (start): 0.3195 rms_B_bonded: 3.16 r_work: 0.3031 rms_B_bonded: 3.51 restraints_weight: 0.5000 r_work (final): 0.3031 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3030 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3030 r_free = 0.3030 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3030 r_free = 0.3030 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 12 | |-----------------------------------------------------------------------------| r_final: 0.3030 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7752 moved from start: 0.2340 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.025 6130 Z= 0.165 Angle : 0.521 4.901 8372 Z= 0.284 Chirality : 0.043 0.140 912 Planarity : 0.004 0.044 1066 Dihedral : 4.773 19.655 850 Min Nonbonded Distance : 2.617 Molprobity Statistics. All-atom Clashscore : 6.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.48 % Favored : 94.52 % Rotamer: Outliers : 4.04 % Allowed : 15.68 % Favored : 80.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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: -0.82 (0.30), residues: 772 helix: -4.21 (0.37), residues: 12 sheet: 0.72 (0.28), residues: 354 loop : -1.68 (0.29), residues: 406 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 449 TYR 0.018 0.002 TYR D 50 PHE 0.016 0.002 PHE H 64 TRP 0.016 0.002 TRP C 50 HIS 0.007 0.002 HIS A 479 Details of bonding type rmsd covalent geometry : bond 0.00372 ( 6126) covalent geometry : angle 0.52045 ( 8364) SS BOND : bond 0.00219 ( 4) SS BOND : angle 0.81495 ( 8) hydrogen bonds : bond 0.02993 ( 189) hydrogen bonds : angle 5.29364 ( 585) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1544 Ramachandran restraints generated. 772 Oldfield, 0 Emsley, 772 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1544 Ramachandran restraints generated. 772 Oldfield, 0 Emsley, 772 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 112 time to evaluate : 0.229 Fit side-chains REVERT: L 62 ARG cc_start: 0.8060 (OUTLIER) cc_final: 0.7326 (ptt90) REVERT: B 483 TRP cc_start: 0.8557 (p-90) cc_final: 0.8292 (p-90) REVERT: C 28 THR cc_start: 0.8197 (m) cc_final: 0.7474 (p) REVERT: C 31 SER cc_start: 0.7446 (m) cc_final: 0.7011 (m) outliers start: 26 outliers final: 16 residues processed: 124 average time/residue: 0.3087 time to fit residues: 41.5584 Evaluate side-chains 126 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 109 time to evaluate : 0.225 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 10 VAL Chi-restraints excluded: chain L residue 23 SER Chi-restraints excluded: chain L residue 34 VAL Chi-restraints excluded: chain L residue 62 ARG Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 128 THR Chi-restraints excluded: chain B residue 453 ASN Chi-restraints excluded: chain B residue 574 THR Chi-restraints excluded: chain D residue 10 VAL Chi-restraints excluded: chain D residue 18 VAL Chi-restraints excluded: chain D residue 99 VAL Chi-restraints excluded: chain C residue 5 VAL Chi-restraints excluded: chain C residue 7 SER Chi-restraints excluded: chain C residue 102 THR Chi-restraints excluded: chain C residue 106 SER Chi-restraints excluded: chain C residue 128 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 29 optimal weight: 0.4980 chunk 53 optimal weight: 0.8980 chunk 2 optimal weight: 0.9990 chunk 64 optimal weight: 0.8980 chunk 28 optimal weight: 0.9990 chunk 31 optimal weight: 0.9980 chunk 42 optimal weight: 0.8980 chunk 62 optimal weight: 0.9990 chunk 15 optimal weight: 0.9990 chunk 70 optimal weight: 0.9990 chunk 65 optimal weight: 0.9980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 453 ASN A 471 GLN L 6 GLN ** L 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 6 GLN B 527 GLN D 39 GLN D 52 ASN C 33 ASN C 39 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.113721 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3149 r_free = 0.3149 target = 0.094828 restraints weight = 35091.455| |-----------------------------------------------------------------------------| r_work (start): 0.3150 rms_B_bonded: 4.13 r_work: 0.2943 rms_B_bonded: 4.37 restraints_weight: 0.5000 r_work (final): 0.2943 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2940 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2940 r_free = 0.2940 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 12 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2940 r_free = 0.2940 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.03 number of occupancies < 0.1: 12 | |-----------------------------------------------------------------------------| r_final: 0.2940 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7837 moved from start: 0.2592 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.040 6130 Z= 0.273 Angle : 0.623 9.083 8372 Z= 0.338 Chirality : 0.046 0.149 912 Planarity : 0.005 0.049 1066 Dihedral : 5.154 18.508 850 Min Nonbonded Distance : 2.587 Molprobity Statistics. All-atom Clashscore : 7.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.18 % Favored : 92.82 % Rotamer: Outliers : 3.57 % Allowed : 17.08 % Favored : 79.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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: -0.90 (0.30), residues: 772 helix: -4.24 (0.36), residues: 12 sheet: 0.59 (0.28), residues: 358 loop : -1.68 (0.29), residues: 402 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 449 TYR 0.022 0.002 TYR D 50 PHE 0.023 0.002 PHE H 64 TRP 0.018 0.003 TRP B 483 HIS 0.007 0.002 HIS A 479 Details of bonding type rmsd covalent geometry : bond 0.00627 ( 6126) covalent geometry : angle 0.62000 ( 8364) SS BOND : bond 0.00374 ( 4) SS BOND : angle 2.14043 ( 8) hydrogen bonds : bond 0.03569 ( 189) hydrogen bonds : angle 5.47281 ( 585) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1544 Ramachandran restraints generated. 772 Oldfield, 0 Emsley, 772 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1544 Ramachandran restraints generated. 772 Oldfield, 0 Emsley, 772 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 112 time to evaluate : 0.231 Fit side-chains REVERT: L 62 ARG cc_start: 0.8066 (OUTLIER) cc_final: 0.7458 (ptt90) REVERT: H 28 THR cc_start: 0.8370 (m) cc_final: 0.7968 (p) REVERT: B 476 MET cc_start: 0.7927 (OUTLIER) cc_final: 0.7367 (mmm) REVERT: C 28 THR cc_start: 0.8239 (m) cc_final: 0.7563 (t) REVERT: C 31 SER cc_start: 0.7558 (m) cc_final: 0.6946 (m) outliers start: 23 outliers final: 14 residues processed: 121 average time/residue: 0.3040 time to fit residues: 40.1337 Evaluate side-chains 126 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 110 time to evaluate : 0.209 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 10 VAL Chi-restraints excluded: chain L residue 62 ARG Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 128 THR Chi-restraints excluded: chain B residue 453 ASN Chi-restraints excluded: chain B residue 476 MET Chi-restraints excluded: chain B residue 574 THR Chi-restraints excluded: chain D residue 10 VAL Chi-restraints excluded: chain D residue 18 VAL Chi-restraints excluded: chain D residue 48 LEU Chi-restraints excluded: chain D residue 99 VAL Chi-restraints excluded: chain C residue 5 VAL Chi-restraints excluded: chain C residue 7 SER Chi-restraints excluded: chain C residue 102 THR Chi-restraints excluded: chain C residue 106 SER Chi-restraints excluded: chain C residue 128 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 6 optimal weight: 0.9980 chunk 18 optimal weight: 0.9990 chunk 15 optimal weight: 0.0770 chunk 20 optimal weight: 0.5980 chunk 72 optimal weight: 0.6980 chunk 11 optimal weight: 0.8980 chunk 16 optimal weight: 1.9990 chunk 14 optimal weight: 0.6980 chunk 37 optimal weight: 0.6980 chunk 73 optimal weight: 0.0470 chunk 40 optimal weight: 0.6980 overall best weight: 0.4236 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 39 GLN ** L 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 6 GLN B 527 GLN D 39 GLN D 52 ASN C 39 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.115098 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3185 r_free = 0.3185 target = 0.096976 restraints weight = 28596.328| |-----------------------------------------------------------------------------| r_work (start): 0.3181 rms_B_bonded: 3.76 r_work: 0.2993 rms_B_bonded: 4.06 restraints_weight: 0.5000 r_work (final): 0.2993 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2987 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2987 r_free = 0.2987 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.03 number of occupancies < 0.1: 12 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2987 r_free = 0.2987 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.03 number of occupancies < 0.1: 12 | |-----------------------------------------------------------------------------| r_final: 0.2987 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7786 moved from start: 0.2613 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.024 6130 Z= 0.157 Angle : 0.531 6.910 8372 Z= 0.289 Chirality : 0.042 0.134 912 Planarity : 0.004 0.049 1066 Dihedral : 4.790 16.494 850 Min Nonbonded Distance : 2.579 Molprobity Statistics. All-atom Clashscore : 6.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.74 % Favored : 94.26 % Rotamer: Outliers : 2.95 % Allowed : 17.39 % Favored : 79.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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: -0.77 (0.30), residues: 772 helix: -4.21 (0.37), residues: 12 sheet: 0.67 (0.28), residues: 358 loop : -1.58 (0.30), residues: 402 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 449 TYR 0.019 0.002 TYR D 50 PHE 0.015 0.002 PHE H 64 TRP 0.016 0.002 TRP B 483 HIS 0.006 0.001 HIS A 479 Details of bonding type rmsd covalent geometry : bond 0.00354 ( 6126) covalent geometry : angle 0.52808 ( 8364) SS BOND : bond 0.00199 ( 4) SS BOND : angle 1.92122 ( 8) hydrogen bonds : bond 0.02990 ( 189) hydrogen bonds : angle 5.16624 ( 585) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1544 Ramachandran restraints generated. 772 Oldfield, 0 Emsley, 772 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1544 Ramachandran restraints generated. 772 Oldfield, 0 Emsley, 772 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 104 time to evaluate : 0.235 Fit side-chains REVERT: H 117 TYR cc_start: 0.8531 (p90) cc_final: 0.8272 (p90) REVERT: D 50 TYR cc_start: 0.8666 (p90) cc_final: 0.8443 (p90) REVERT: C 28 THR cc_start: 0.8234 (m) cc_final: 0.7508 (p) REVERT: C 31 SER cc_start: 0.7419 (m) cc_final: 0.6981 (m) outliers start: 19 outliers final: 11 residues processed: 109 average time/residue: 0.3355 time to fit residues: 39.6288 Evaluate side-chains 115 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 104 time to evaluate : 0.246 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 87 ARG Chi-restraints excluded: chain B residue 574 THR Chi-restraints excluded: chain D residue 10 VAL Chi-restraints excluded: chain D residue 18 VAL Chi-restraints excluded: chain D residue 99 VAL Chi-restraints excluded: chain C residue 5 VAL Chi-restraints excluded: chain C residue 7 SER Chi-restraints excluded: chain C residue 102 THR Chi-restraints excluded: chain C residue 106 SER Chi-restraints excluded: chain C residue 128 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 7 optimal weight: 2.9990 chunk 50 optimal weight: 0.9980 chunk 64 optimal weight: 0.7980 chunk 57 optimal weight: 0.0060 chunk 37 optimal weight: 1.9990 chunk 9 optimal weight: 0.8980 chunk 24 optimal weight: 0.8980 chunk 22 optimal weight: 3.9990 chunk 59 optimal weight: 1.9990 chunk 18 optimal weight: 0.5980 chunk 16 optimal weight: 0.6980 overall best weight: 0.5996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 471 GLN ** L 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 39 GLN D 52 ASN C 39 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.114469 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3174 r_free = 0.3174 target = 0.096404 restraints weight = 28385.330| |-----------------------------------------------------------------------------| r_work (start): 0.3174 rms_B_bonded: 3.74 r_work: 0.2986 rms_B_bonded: 4.02 restraints_weight: 0.5000 r_work (final): 0.2986 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2981 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2981 r_free = 0.2981 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.03 number of occupancies < 0.1: 12 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2981 r_free = 0.2981 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.03 number of occupancies < 0.1: 12 | |-----------------------------------------------------------------------------| r_final: 0.2981 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7796 moved from start: 0.2676 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.030 6130 Z= 0.204 Angle : 0.564 6.952 8372 Z= 0.306 Chirality : 0.043 0.140 912 Planarity : 0.004 0.047 1066 Dihedral : 4.920 18.383 850 Min Nonbonded Distance : 2.616 Molprobity Statistics. All-atom Clashscore : 7.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.92 % Favored : 93.08 % Rotamer: Outliers : 2.48 % Allowed : 17.70 % Favored : 79.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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: -0.82 (0.30), residues: 772 helix: -4.21 (0.36), residues: 12 sheet: 0.64 (0.28), residues: 358 loop : -1.61 (0.29), residues: 402 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 449 TYR 0.019 0.002 TYR D 50 PHE 0.017 0.002 PHE H 64 TRP 0.020 0.002 TRP A 483 HIS 0.006 0.001 HIS A 479 Details of bonding type rmsd covalent geometry : bond 0.00466 ( 6126) covalent geometry : angle 0.56152 ( 8364) SS BOND : bond 0.00190 ( 4) SS BOND : angle 1.71226 ( 8) hydrogen bonds : bond 0.03217 ( 189) hydrogen bonds : angle 5.19476 ( 585) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1544 Ramachandran restraints generated. 772 Oldfield, 0 Emsley, 772 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1544 Ramachandran restraints generated. 772 Oldfield, 0 Emsley, 772 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 106 time to evaluate : 0.223 Fit side-chains REVERT: L 39 GLN cc_start: 0.8411 (tt0) cc_final: 0.8117 (tt0) REVERT: H 117 TYR cc_start: 0.8564 (p90) cc_final: 0.8355 (p90) REVERT: B 476 MET cc_start: 0.7914 (OUTLIER) cc_final: 0.7244 (mmm) REVERT: C 28 THR cc_start: 0.8218 (m) cc_final: 0.7523 (p) REVERT: C 31 SER cc_start: 0.7469 (m) cc_final: 0.7043 (m) outliers start: 16 outliers final: 12 residues processed: 111 average time/residue: 0.3179 time to fit residues: 38.2647 Evaluate side-chains 118 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 105 time to evaluate : 0.222 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 87 ARG Chi-restraints excluded: chain B residue 476 MET Chi-restraints excluded: chain B residue 574 THR Chi-restraints excluded: chain D residue 10 VAL Chi-restraints excluded: chain D residue 18 VAL Chi-restraints excluded: chain D residue 48 LEU Chi-restraints excluded: chain D residue 99 VAL Chi-restraints excluded: chain C residue 5 VAL Chi-restraints excluded: chain C residue 7 SER Chi-restraints excluded: chain C residue 102 THR Chi-restraints excluded: chain C residue 106 SER Chi-restraints excluded: chain C residue 128 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 50 optimal weight: 0.8980 chunk 21 optimal weight: 1.9990 chunk 17 optimal weight: 0.9990 chunk 4 optimal weight: 0.9990 chunk 54 optimal weight: 0.9980 chunk 18 optimal weight: 0.9990 chunk 7 optimal weight: 2.9990 chunk 33 optimal weight: 1.9990 chunk 72 optimal weight: 1.9990 chunk 15 optimal weight: 0.8980 chunk 43 optimal weight: 0.8980 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 453 ASN ** L 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 527 GLN D 39 GLN D 52 ASN C 33 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.113641 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3150 r_free = 0.3150 target = 0.095036 restraints weight = 33024.427| |-----------------------------------------------------------------------------| r_work (start): 0.3148 rms_B_bonded: 4.02 r_work: 0.2947 rms_B_bonded: 4.28 restraints_weight: 0.5000 r_work (final): 0.2947 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2946 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2946 r_free = 0.2946 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.03 number of occupancies < 0.1: 12 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2946 r_free = 0.2946 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.03 number of occupancies < 0.1: 12 | |-----------------------------------------------------------------------------| r_final: 0.2946 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7833 moved from start: 0.2845 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.044 6130 Z= 0.300 Angle : 0.634 7.508 8372 Z= 0.344 Chirality : 0.046 0.147 912 Planarity : 0.005 0.050 1066 Dihedral : 5.280 19.015 850 Min Nonbonded Distance : 2.599 Molprobity Statistics. All-atom Clashscore : 7.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.57 % Favored : 92.43 % Rotamer: Outliers : 2.80 % Allowed : 17.24 % Favored : 79.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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: -0.92 (0.30), residues: 772 helix: -4.24 (0.35), residues: 12 sheet: 0.57 (0.28), residues: 354 loop : -1.65 (0.29), residues: 406 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 449 TYR 0.025 0.002 TYR D 50 PHE 0.022 0.002 PHE H 64 TRP 0.022 0.003 TRP A 483 HIS 0.005 0.002 HIS A 479 Details of bonding type rmsd covalent geometry : bond 0.00692 ( 6126) covalent geometry : angle 0.63250 ( 8364) SS BOND : bond 0.00191 ( 4) SS BOND : angle 1.57173 ( 8) hydrogen bonds : bond 0.03614 ( 189) hydrogen bonds : angle 5.43556 ( 585) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1544 Ramachandran restraints generated. 772 Oldfield, 0 Emsley, 772 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1544 Ramachandran restraints generated. 772 Oldfield, 0 Emsley, 772 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 109 time to evaluate : 0.214 Fit side-chains REVERT: L 39 GLN cc_start: 0.8432 (tt0) cc_final: 0.8124 (tt0) REVERT: H 28 THR cc_start: 0.8352 (m) cc_final: 0.7967 (p) REVERT: B 476 MET cc_start: 0.7926 (OUTLIER) cc_final: 0.7286 (mmm) REVERT: C 28 THR cc_start: 0.8241 (m) cc_final: 0.7596 (t) REVERT: C 31 SER cc_start: 0.7579 (m) cc_final: 0.7003 (m) outliers start: 18 outliers final: 12 residues processed: 115 average time/residue: 0.2550 time to fit residues: 31.8708 Evaluate side-chains 121 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 108 time to evaluate : 0.174 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 10 VAL Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 87 ARG Chi-restraints excluded: chain B residue 476 MET Chi-restraints excluded: chain B residue 574 THR Chi-restraints excluded: chain D residue 10 VAL Chi-restraints excluded: chain D residue 18 VAL Chi-restraints excluded: chain D residue 48 LEU Chi-restraints excluded: chain D residue 99 VAL Chi-restraints excluded: chain C residue 5 VAL Chi-restraints excluded: chain C residue 7 SER Chi-restraints excluded: chain C residue 102 THR Chi-restraints excluded: chain C residue 128 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 51 optimal weight: 0.0870 chunk 32 optimal weight: 1.9990 chunk 18 optimal weight: 0.7980 chunk 17 optimal weight: 0.9980 chunk 31 optimal weight: 0.9980 chunk 70 optimal weight: 2.9990 chunk 43 optimal weight: 0.8980 chunk 11 optimal weight: 0.9980 chunk 30 optimal weight: 0.9980 chunk 40 optimal weight: 0.5980 chunk 7 optimal weight: 1.9990 overall best weight: 0.6758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 39 GLN D 52 ASN C 33 ASN C 39 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.114212 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.3170 r_free = 0.3170 target = 0.096155 restraints weight = 29340.900| |-----------------------------------------------------------------------------| r_work (start): 0.3165 rms_B_bonded: 3.79 r_work: 0.2973 rms_B_bonded: 4.08 restraints_weight: 0.5000 r_work (final): 0.2973 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2971 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2971 r_free = 0.2971 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.03 number of occupancies < 0.1: 12 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2971 r_free = 0.2971 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.05 number of occupancies < 0.1: 12 | |-----------------------------------------------------------------------------| r_final: 0.2971 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7805 moved from start: 0.2834 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.033 6130 Z= 0.225 Angle : 0.581 6.942 8372 Z= 0.315 Chirality : 0.044 0.137 912 Planarity : 0.005 0.052 1066 Dihedral : 5.097 18.632 850 Min Nonbonded Distance : 2.598 Molprobity Statistics. All-atom Clashscore : 7.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.40 % Favored : 93.60 % Rotamer: Outliers : 2.48 % Allowed : 17.39 % Favored : 80.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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: -0.89 (0.30), residues: 772 helix: -4.23 (0.36), residues: 12 sheet: 0.57 (0.28), residues: 354 loop : -1.60 (0.29), residues: 406 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 449 TYR 0.027 0.002 TYR D 50 PHE 0.018 0.002 PHE H 64 TRP 0.020 0.002 TRP A 483 HIS 0.005 0.001 HIS A 479 Details of bonding type rmsd covalent geometry : bond 0.00514 ( 6126) covalent geometry : angle 0.57935 ( 8364) SS BOND : bond 0.00209 ( 4) SS BOND : angle 1.49784 ( 8) hydrogen bonds : bond 0.03313 ( 189) hydrogen bonds : angle 5.28536 ( 585) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1544 Ramachandran restraints generated. 772 Oldfield, 0 Emsley, 772 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1544 Ramachandran restraints generated. 772 Oldfield, 0 Emsley, 772 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 108 time to evaluate : 0.201 Fit side-chains REVERT: H 28 THR cc_start: 0.8338 (m) cc_final: 0.7940 (p) REVERT: H 117 TYR cc_start: 0.8550 (p90) cc_final: 0.8321 (p90) REVERT: B 476 MET cc_start: 0.7895 (OUTLIER) cc_final: 0.7232 (mmm) REVERT: D 39 GLN cc_start: 0.8407 (OUTLIER) cc_final: 0.8142 (tt0) REVERT: C 28 THR cc_start: 0.8236 (m) cc_final: 0.7560 (p) REVERT: C 31 SER cc_start: 0.7486 (m) cc_final: 0.7074 (m) outliers start: 16 outliers final: 12 residues processed: 114 average time/residue: 0.3022 time to fit residues: 37.5380 Evaluate side-chains 122 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 108 time to evaluate : 0.236 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 94 SER Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 87 ARG Chi-restraints excluded: chain B residue 476 MET Chi-restraints excluded: chain B residue 574 THR Chi-restraints excluded: chain D residue 10 VAL Chi-restraints excluded: chain D residue 18 VAL Chi-restraints excluded: chain D residue 39 GLN Chi-restraints excluded: chain D residue 48 LEU Chi-restraints excluded: chain D residue 99 VAL Chi-restraints excluded: chain C residue 5 VAL Chi-restraints excluded: chain C residue 7 SER Chi-restraints excluded: chain C residue 102 THR Chi-restraints excluded: chain C residue 128 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 32 optimal weight: 2.9990 chunk 28 optimal weight: 0.6980 chunk 52 optimal weight: 0.7980 chunk 17 optimal weight: 0.9990 chunk 49 optimal weight: 0.9980 chunk 0 optimal weight: 0.9990 chunk 54 optimal weight: 0.0060 chunk 30 optimal weight: 1.9990 chunk 26 optimal weight: 2.9990 chunk 48 optimal weight: 0.0670 chunk 62 optimal weight: 0.4980 overall best weight: 0.4134 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 551 ASN L 6 GLN ** L 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 39 GLN D 52 ASN C 39 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.115157 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3195 r_free = 0.3195 target = 0.097651 restraints weight = 25358.831| |-----------------------------------------------------------------------------| r_work (start): 0.3190 rms_B_bonded: 3.53 r_work: 0.3012 rms_B_bonded: 3.84 restraints_weight: 0.5000 r_work (final): 0.3012 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3010 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3010 r_free = 0.3010 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.05 number of occupancies < 0.1: 12 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3010 r_free = 0.3010 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.05 number of occupancies < 0.1: 12 | |-----------------------------------------------------------------------------| r_final: 0.3010 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7767 moved from start: 0.2829 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 6130 Z= 0.152 Angle : 0.531 6.038 8372 Z= 0.289 Chirality : 0.043 0.136 912 Planarity : 0.004 0.050 1066 Dihedral : 4.880 18.687 850 Min Nonbonded Distance : 2.618 Molprobity Statistics. All-atom Clashscore : 6.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.87 % Favored : 94.13 % Rotamer: Outliers : 2.33 % Allowed : 17.55 % Favored : 80.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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: -0.76 (0.30), residues: 772 helix: -4.21 (0.37), residues: 12 sheet: 0.64 (0.28), residues: 354 loop : -1.50 (0.30), residues: 406 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 449 TYR 0.027 0.002 TYR D 50 PHE 0.013 0.001 PHE H 64 TRP 0.018 0.002 TRP A 483 HIS 0.005 0.001 HIS A 479 Details of bonding type rmsd covalent geometry : bond 0.00343 ( 6126) covalent geometry : angle 0.52862 ( 8364) SS BOND : bond 0.00190 ( 4) SS BOND : angle 1.58354 ( 8) hydrogen bonds : bond 0.03009 ( 189) hydrogen bonds : angle 5.09822 ( 585) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1544 Ramachandran restraints generated. 772 Oldfield, 0 Emsley, 772 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1544 Ramachandran restraints generated. 772 Oldfield, 0 Emsley, 772 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 106 time to evaluate : 0.203 Fit side-chains REVERT: H 28 THR cc_start: 0.8331 (m) cc_final: 0.7921 (p) REVERT: H 117 TYR cc_start: 0.8510 (p90) cc_final: 0.8248 (p90) REVERT: B 476 MET cc_start: 0.7873 (OUTLIER) cc_final: 0.7205 (mmm) REVERT: C 28 THR cc_start: 0.8229 (m) cc_final: 0.7528 (p) REVERT: C 31 SER cc_start: 0.7418 (m) cc_final: 0.6985 (m) outliers start: 15 outliers final: 11 residues processed: 111 average time/residue: 0.3309 time to fit residues: 39.7625 Evaluate side-chains 117 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 105 time to evaluate : 0.237 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 94 SER Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 87 ARG Chi-restraints excluded: chain B residue 476 MET Chi-restraints excluded: chain B residue 574 THR Chi-restraints excluded: chain D residue 10 VAL Chi-restraints excluded: chain D residue 18 VAL Chi-restraints excluded: chain D residue 99 VAL Chi-restraints excluded: chain C residue 5 VAL Chi-restraints excluded: chain C residue 98 ARG Chi-restraints excluded: chain C residue 102 THR Chi-restraints excluded: chain C residue 128 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 23 optimal weight: 0.9980 chunk 65 optimal weight: 0.8980 chunk 69 optimal weight: 0.9990 chunk 58 optimal weight: 0.0970 chunk 63 optimal weight: 0.6980 chunk 37 optimal weight: 1.9990 chunk 52 optimal weight: 0.7980 chunk 4 optimal weight: 0.6980 chunk 48 optimal weight: 0.9980 chunk 61 optimal weight: 0.9980 chunk 45 optimal weight: 1.9990 overall best weight: 0.6378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 6 GLN L 39 GLN D 52 ASN C 6 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.114447 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3181 r_free = 0.3181 target = 0.096791 restraints weight = 26374.949| |-----------------------------------------------------------------------------| r_work (start): 0.3176 rms_B_bonded: 3.58 r_work: 0.2993 rms_B_bonded: 3.90 restraints_weight: 0.5000 r_work (final): 0.2993 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2992 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2992 r_free = 0.2992 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.05 number of occupancies < 0.1: 12 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2992 r_free = 0.2992 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.05 number of occupancies < 0.1: 12 | |-----------------------------------------------------------------------------| r_final: 0.2992 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7787 moved from start: 0.2879 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.035 6130 Z= 0.215 Angle : 0.572 6.677 8372 Z= 0.310 Chirality : 0.044 0.138 912 Planarity : 0.004 0.049 1066 Dihedral : 5.015 19.106 850 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 7.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.05 % Favored : 92.95 % Rotamer: Outliers : 2.33 % Allowed : 17.86 % Favored : 79.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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: -0.81 (0.30), residues: 772 helix: -4.20 (0.37), residues: 12 sheet: 0.62 (0.28), residues: 354 loop : -1.55 (0.30), residues: 406 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 449 TYR 0.026 0.002 TYR C 117 PHE 0.017 0.002 PHE H 64 TRP 0.025 0.002 TRP A 483 HIS 0.005 0.001 HIS A 479 Details of bonding type rmsd covalent geometry : bond 0.00491 ( 6126) covalent geometry : angle 0.57026 ( 8364) SS BOND : bond 0.00214 ( 4) SS BOND : angle 1.57849 ( 8) hydrogen bonds : bond 0.03242 ( 189) hydrogen bonds : angle 5.20354 ( 585) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2173.33 seconds wall clock time: 37 minutes 54.53 seconds (2274.53 seconds total)