Starting phenix.real_space_refine on Wed Sep 17 06:23:50 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9jin_61511/09_2025/9jin_61511.cif Found real_map, /net/cci-nas-00/data/ceres_data/9jin_61511/09_2025/9jin_61511.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.56 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9jin_61511/09_2025/9jin_61511.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9jin_61511/09_2025/9jin_61511.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9jin_61511/09_2025/9jin_61511.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9jin_61511/09_2025/9jin_61511.map" } resolution = 2.56 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= 0.023 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 28 5.16 5 C 3756 2.51 5 N 988 2.21 5 O 1142 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 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: 5914 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: "B" Number of atoms: 1187 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: 1185 Chain: "C" Number of atoms: 999 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 999 Classifications: {'peptide': 128} Link IDs: {'PTRANS': 6, 'TRANS': 121} Chain: "D" Number of atoms: 777 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 777 Classifications: {'peptide': 103} Link IDs: {'PTRANS': 7, 'TRANS': 95} Chain: "H" Number of atoms: 999 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 999 Classifications: {'peptide': 128} Link IDs: {'PTRANS': 6, 'TRANS': 121} Chain: "L" Number of atoms: 777 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 777 Classifications: {'peptide': 103} Link IDs: {'PTRANS': 7, 'TRANS': 95} Residues with excluded nonbonded symmetry interactions: 6 residue: pdb=" N ASER A 502 " occ=0.60 ... (10 atoms not shown) pdb=" OG BSER A 502 " occ=0.40 residue: pdb=" N ASER B 466 " occ=0.03 ... (10 atoms not shown) pdb=" OG BSER B 466 " occ=0.97 residue: pdb=" N ASER B 474 " occ=0.06 ... (10 atoms not shown) pdb=" OG BSER B 474 " occ=0.94 residue: pdb=" N ASER B 502 " occ=0.53 ... (10 atoms not shown) pdb=" OG BSER B 502 " occ=0.47 residue: pdb=" N ASP D 50 " occ=0.75 ... (6 atoms not shown) pdb=" OD2 ASP D 50 " occ=0.75 residue: pdb=" N ASP L 50 " occ=0.75 ... (6 atoms not shown) pdb=" OD2 ASP L 50 " occ=0.75 Time building chain proxies: 1.78, per 1000 atoms: 0.30 Number of scatterers: 5914 At special positions: 0 Unit cell: (95.55, 72.15, 79.3, 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 28 16.00 O 1142 8.00 N 988 7.00 C 3756 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS C 22 " - pdb=" SG CYS C 96 " distance=2.03 Simple disulfide: pdb=" SG CYS C 106 " - pdb=" SG CYS C 110 " distance=2.02 Simple disulfide: pdb=" SG CYS D 23 " - pdb=" SG CYS D 88 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.03 Simple disulfide: pdb=" SG CYS H 106 " - pdb=" SG CYS H 110 " distance=2.02 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " 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: 0.42 Conformation dependent library (CDL) restraints added in 363.3 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 1528 Ramachandran restraints generated. 764 Oldfield, 0 Emsley, 764 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1380 Finding SS restraints... Secondary structure from input PDB file: 10 helices and 17 sheets defined 6.0% alpha, 45.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.20 Creating SS restraints... Processing helix chain 'A' and resid 501 through 503 No H-bonds generated for 'chain 'A' and resid 501 through 503' Processing helix chain 'A' and resid 504 through 507 Processing helix chain 'B' and resid 501 through 503 No H-bonds generated for 'chain 'B' and resid 501 through 503' Processing helix chain 'B' and resid 504 through 507 Processing helix chain 'C' and resid 28 through 32 removed outlier: 3.647A pdb=" N TYR C 32 " --> pdb=" O PHE C 29 " (cutoff:3.500A) Processing helix chain 'C' and resid 106 through 111 removed outlier: 3.978A pdb=" N GLU C 109 " --> pdb=" O CYS C 106 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N CYS C 110 " --> pdb=" O GLY C 107 " (cutoff:3.500A) Processing helix chain 'D' and resid 79 through 83 Processing helix chain 'H' and resid 28 through 32 removed outlier: 3.645A pdb=" N TYR H 32 " --> pdb=" O PHE H 29 " (cutoff:3.500A) Processing helix chain 'H' and resid 106 through 111 removed outlier: 3.947A pdb=" N GLU H 109 " --> pdb=" O CYS H 106 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N CYS H 110 " --> pdb=" O GLY H 107 " (cutoff:3.500A) Processing helix chain 'L' and resid 79 through 83 removed outlier: 3.506A pdb=" N ILE L 83 " --> pdb=" O PRO L 80 " (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 497 through 499 removed outlier: 4.672A pdb=" N SER A 472 " --> pdb=" O HIS A 479 " (cutoff:3.500A) removed outlier: 5.729A pdb=" N HIS A 479 " --> pdb=" O SER A 472 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N SER A 484 " --> pdb=" O LEU A 570 " (cutoff:3.500A) removed outlier: 5.412A pdb=" N SER A 573 " --> pdb=" O SER A 557 " (cutoff:3.500A) removed outlier: 8.278A pdb=" N SER A 557 " --> pdb=" O SER A 573 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N TRP A 562 " --> pdb=" O VAL A 524 " (cutoff:3.500A) removed outlier: 4.961A pdb=" N VAL A 524 " --> pdb=" O TRP A 562 " (cutoff:3.500A) removed outlier: 4.306A pdb=" N HIS A 516 " --> pdb=" O GLN A 527 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 497 through 499 removed outlier: 3.936A pdb=" N SER A 466 " --> pdb=" O VAL A 584 " (cutoff:3.500A) removed outlier: 4.915A pdb=" N VAL A 584 " --> pdb=" O SER A 466 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 453 through 454 Processing sheet with id=AA5, first strand: chain 'B' and resid 497 through 499 removed outlier: 4.694A pdb=" N SER B 472 " --> pdb=" O HIS B 479 " (cutoff:3.500A) removed outlier: 5.699A pdb=" N HIS B 479 " --> pdb=" O SER B 472 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N SER B 484 " --> pdb=" O LEU B 570 " (cutoff:3.500A) removed outlier: 5.307A pdb=" N SER B 573 " --> pdb=" O SER B 557 " (cutoff:3.500A) removed outlier: 8.143A pdb=" N SER B 557 " --> pdb=" O SER B 573 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N TRP B 562 " --> pdb=" O VAL B 524 " (cutoff:3.500A) removed outlier: 5.022A pdb=" N VAL B 524 " --> pdb=" O TRP B 562 " (cutoff:3.500A) removed outlier: 4.231A pdb=" N HIS B 516 " --> pdb=" O GLN B 527 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 497 through 499 removed outlier: 3.712A pdb=" N ASER B 466 " --> pdb=" O VAL B 584 " (cutoff:3.500A) removed outlier: 4.704A pdb=" N VAL B 584 " --> pdb=" O ASER B 466 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 3 through 6 Processing sheet with id=AA8, first strand: chain 'C' and resid 10 through 11 removed outlier: 6.734A pdb=" N LEU C 34 " --> pdb=" O ILE C 50 " (cutoff:3.500A) removed outlier: 4.515A pdb=" N ILE C 50 " --> pdb=" O LEU C 34 " (cutoff:3.500A) removed outlier: 6.596A pdb=" N TRP C 36 " --> pdb=" O MET C 48 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 10 through 11 removed outlier: 6.505A pdb=" N CYS C 96 " --> pdb=" O TRP C 120 " (cutoff:3.500A) removed outlier: 4.585A pdb=" N TRP C 120 " --> pdb=" O CYS C 96 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 10 through 12 removed outlier: 6.762A pdb=" N LEU D 11 " --> pdb=" O GLU D 105 " (cutoff:3.500A) removed outlier: 6.921A pdb=" N TRP D 35 " --> pdb=" O LEU D 47 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 19 through 24 removed outlier: 3.842A pdb=" N TYR D 70 " --> pdb=" O SER D 67 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'H' and resid 3 through 6 Processing sheet with id=AB4, first strand: chain 'H' and resid 10 through 11 removed outlier: 6.802A pdb=" N LEU H 34 " --> pdb=" O ILE H 50 " (cutoff:3.500A) removed outlier: 4.608A pdb=" N ILE H 50 " --> pdb=" O LEU H 34 " (cutoff:3.500A) removed outlier: 6.681A pdb=" N TRP H 36 " --> pdb=" O MET H 48 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'H' and resid 10 through 11 removed outlier: 6.447A pdb=" N CYS H 96 " --> pdb=" O TRP H 120 " (cutoff:3.500A) removed outlier: 4.580A pdb=" N TRP H 120 " --> pdb=" O CYS H 96 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'L' and resid 10 through 12 removed outlier: 6.604A pdb=" N LEU L 11 " --> pdb=" O GLU L 105 " (cutoff:3.500A) removed outlier: 6.885A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'L' and resid 10 through 12 removed outlier: 6.604A pdb=" N LEU L 11 " --> pdb=" O GLU L 105 " (cutoff:3.500A) removed outlier: 4.170A pdb=" N THR L 97 " --> pdb=" O GLN L 90 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'L' and resid 19 through 24 removed outlier: 3.816A pdb=" N TYR L 70 " --> pdb=" O SER L 67 " (cutoff:3.500A) 228 hydrogen bonds defined for protein. 546 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: 0.71 Time building geometry restraints manager: 0.59 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 953 1.31 - 1.43: 1796 1.43 - 1.56: 3286 1.56 - 1.69: 1 1.69 - 1.82: 44 Bond restraints: 6080 Sorted by residual: bond pdb=" C SER A 474 " pdb=" O SER A 474 " ideal model delta sigma weight residual 1.237 1.181 0.056 1.19e-02 7.06e+03 2.21e+01 bond pdb=" CA SER A 474 " pdb=" CB SER A 474 " ideal model delta sigma weight residual 1.528 1.457 0.072 1.59e-02 3.96e+03 2.03e+01 bond pdb=" C GLN A 473 " pdb=" N SER A 474 " ideal model delta sigma weight residual 1.335 1.274 0.061 1.36e-02 5.41e+03 1.98e+01 bond pdb=" N PRO L 59 " pdb=" CD PRO L 59 " ideal model delta sigma weight residual 1.473 1.527 -0.054 1.40e-02 5.10e+03 1.47e+01 bond pdb=" CA SER A 466 " pdb=" CB SER A 466 " ideal model delta sigma weight residual 1.530 1.470 0.060 1.69e-02 3.50e+03 1.28e+01 ... (remaining 6075 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.39: 8012 1.39 - 2.78: 218 2.78 - 4.18: 59 4.18 - 5.57: 15 5.57 - 6.96: 4 Bond angle restraints: 8308 Sorted by residual: angle pdb=" CA PRO A 465 " pdb=" C PRO A 465 " pdb=" N SER A 466 " ideal model delta sigma weight residual 114.82 121.23 -6.41 1.35e+00 5.49e-01 2.25e+01 angle pdb=" N PRO A 465 " pdb=" CA PRO A 465 " pdb=" CB PRO A 465 " ideal model delta sigma weight residual 103.38 98.60 4.78 1.05e+00 9.07e-01 2.07e+01 angle pdb=" N PRO A 465 " pdb=" CD PRO A 465 " pdb=" CG PRO A 465 " ideal model delta sigma weight residual 103.20 96.49 6.71 1.50e+00 4.44e-01 2.00e+01 angle pdb=" CA PRO A 465 " pdb=" C PRO A 465 " pdb=" O PRO A 465 " ideal model delta sigma weight residual 122.08 116.98 5.10 1.28e+00 6.10e-01 1.59e+01 angle pdb=" C PRO A 465 " pdb=" N SER A 466 " pdb=" CA SER A 466 " ideal model delta sigma weight residual 121.54 128.50 -6.96 1.91e+00 2.74e-01 1.33e+01 ... (remaining 8303 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.93: 3150 17.93 - 35.87: 267 35.87 - 53.80: 84 53.80 - 71.74: 13 71.74 - 89.67: 10 Dihedral angle restraints: 3524 sinusoidal: 1330 harmonic: 2194 Sorted by residual: dihedral pdb=" CA PHE C 111 " pdb=" C PHE C 111 " pdb=" N PRO C 112 " pdb=" CA PRO C 112 " ideal model delta harmonic sigma weight residual 180.00 132.58 47.42 0 5.00e+00 4.00e-02 8.99e+01 dihedral pdb=" CA PHE H 111 " pdb=" C PHE H 111 " pdb=" N PRO H 112 " pdb=" CA PRO H 112 " ideal model delta harmonic sigma weight residual 180.00 132.59 47.41 0 5.00e+00 4.00e-02 8.99e+01 dihedral pdb=" CA ASP C 118 " pdb=" C ASP C 118 " pdb=" N PRO C 119 " pdb=" CA PRO C 119 " ideal model delta harmonic sigma weight residual -180.00 -139.21 -40.79 0 5.00e+00 4.00e-02 6.66e+01 ... (remaining 3521 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.037: 570 0.037 - 0.073: 235 0.073 - 0.110: 75 0.110 - 0.146: 21 0.146 - 0.183: 3 Chirality restraints: 904 Sorted by residual: chirality pdb=" CA SER A 466 " pdb=" N SER A 466 " pdb=" C SER A 466 " pdb=" CB SER A 466 " both_signs ideal model delta sigma weight residual False 2.51 2.33 0.18 2.00e-01 2.50e+01 8.37e-01 chirality pdb=" CA ILE B 490 " pdb=" N ILE B 490 " pdb=" C ILE B 490 " pdb=" CB ILE B 490 " both_signs ideal model delta sigma weight residual False 2.43 2.60 -0.17 2.00e-01 2.50e+01 6.94e-01 chirality pdb=" CG LEU A 464 " pdb=" CB LEU A 464 " pdb=" CD1 LEU A 464 " pdb=" CD2 LEU A 464 " both_signs ideal model delta sigma weight residual False -2.59 -2.74 0.15 2.00e-01 2.50e+01 5.85e-01 ... (remaining 901 not shown) Planarity restraints: 1058 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA SER A 474 " -0.018 2.00e-02 2.50e+03 3.63e-02 1.32e+01 pdb=" C SER A 474 " 0.063 2.00e-02 2.50e+03 pdb=" O SER A 474 " -0.023 2.00e-02 2.50e+03 pdb=" N ALA A 475 " -0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASP H 118 " 0.048 5.00e-02 4.00e+02 7.28e-02 8.47e+00 pdb=" N PRO H 119 " -0.126 5.00e-02 4.00e+02 pdb=" CA PRO H 119 " 0.037 5.00e-02 4.00e+02 pdb=" CD PRO H 119 " 0.040 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP C 118 " -0.048 5.00e-02 4.00e+02 7.26e-02 8.44e+00 pdb=" N PRO C 119 " 0.126 5.00e-02 4.00e+02 pdb=" CA PRO C 119 " -0.037 5.00e-02 4.00e+02 pdb=" CD PRO C 119 " -0.040 5.00e-02 4.00e+02 ... (remaining 1055 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 428 2.74 - 3.28: 5489 3.28 - 3.82: 10155 3.82 - 4.36: 12394 4.36 - 4.90: 21321 Nonbonded interactions: 49787 Sorted by model distance: nonbonded pdb=" OD1 ASN H 52 " pdb=" OG SER H 54 " model vdw 2.197 3.040 nonbonded pdb=" OD1 ASP C 73 " pdb=" OG SER C 75 " model vdw 2.213 3.040 nonbonded pdb=" OG SER D 63 " pdb=" OG1 THR D 74 " model vdw 2.233 3.040 nonbonded pdb=" NZ LYS H 23 " pdb=" O THR H 76 " model vdw 2.239 3.120 nonbonded pdb=" OG1 THR A 587 " pdb=" OE2 GLU C 109 " model vdw 2.295 3.040 ... (remaining 49782 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 447 through 465 or resid 467 through 473 or resid 475 thro \ ugh 501 or resid 503 through 597)) selection = (chain 'B' and (resid 447 through 465 or resid 467 through 473 or resid 475 thro \ ugh 501 or resid 503 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=0.03 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: 6.070 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: 0.180 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 7.110 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:9.460 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.930 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7437 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.147 6086 Z= 0.253 Angle : 0.627 6.962 8320 Z= 0.353 Chirality : 0.046 0.183 904 Planarity : 0.008 0.116 1058 Dihedral : 15.590 89.673 2126 Min Nonbonded Distance : 2.197 Molprobity Statistics. All-atom Clashscore : 7.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.31 % Favored : 92.69 % Rotamer: Outliers : 0.31 % Allowed : 21.38 % Favored : 78.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 15.00 % 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: -0.80 (0.31), residues: 764 helix: None (None), residues: 0 sheet: 0.28 (0.28), residues: 341 loop : -1.25 (0.32), residues: 423 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 449 TYR 0.025 0.002 TYR B 469 PHE 0.010 0.001 PHE C 111 TRP 0.014 0.002 TRP B 461 HIS 0.003 0.001 HIS B 479 Details of bonding type rmsd covalent geometry : bond 0.00533 ( 6080) covalent geometry : angle 0.62720 ( 8308) SS BOND : bond 0.00393 ( 6) SS BOND : angle 0.68946 ( 12) hydrogen bonds : bond 0.24990 ( 202) hydrogen bonds : angle 9.55993 ( 546) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1528 Ramachandran restraints generated. 764 Oldfield, 0 Emsley, 764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1528 Ramachandran restraints generated. 764 Oldfield, 0 Emsley, 764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 628 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 126 time to evaluate : 0.222 Fit side-chains REVERT: D 4 MET cc_start: 0.8472 (mtm) cc_final: 0.8255 (mtp) outliers start: 2 outliers final: 0 residues processed: 127 average time/residue: 0.3002 time to fit residues: 41.5448 Evaluate side-chains 114 residues out of total 628 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 114 time to evaluate : 0.241 ------------------------------------------------------------------------------- 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: 1.9990 chunk 53 optimal weight: 0.0030 chunk 5 optimal weight: 0.9980 chunk 33 optimal weight: 0.7980 chunk 65 optimal weight: 0.6980 chunk 62 optimal weight: 0.9990 chunk 51 optimal weight: 1.9990 chunk 38 optimal weight: 0.0970 chunk 61 optimal weight: 0.6980 chunk 45 optimal weight: 0.8980 chunk 27 optimal weight: 0.5980 overall best weight: 0.4188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 471 GLN B 535 ASN B 585 ASN D 31 ASN D 38 GLN L 38 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4214 r_free = 0.4214 target = 0.166341 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3972 r_free = 0.3972 target = 0.147042 restraints weight = 27375.347| |-----------------------------------------------------------------------------| r_work (start): 0.3970 rms_B_bonded: 4.19 r_work: 0.3778 rms_B_bonded: 4.64 restraints_weight: 0.5000 r_work (final): 0.3778 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3778 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3778 r_free = 0.3778 target_work(ls_wunit_k1) = 0.133 | | occupancies: max = 1.00 min = 0.03 number of occupancies < 0.1: 12 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3778 r_free = 0.3778 target_work(ls_wunit_k1) = 0.133 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 12 | |-----------------------------------------------------------------------------| r_final: 0.3778 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7492 moved from start: 0.1248 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 6086 Z= 0.142 Angle : 0.591 5.365 8320 Z= 0.317 Chirality : 0.045 0.171 904 Planarity : 0.007 0.074 1058 Dihedral : 5.792 46.279 838 Min Nonbonded Distance : 2.575 Molprobity Statistics. All-atom Clashscore : 6.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.18 % Favored : 92.82 % Rotamer: Outliers : 3.93 % Allowed : 19.03 % Favored : 77.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 15.00 % 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: -0.58 (0.31), residues: 764 helix: None (None), residues: 0 sheet: 0.55 (0.28), residues: 347 loop : -1.24 (0.32), residues: 417 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 449 TYR 0.011 0.001 TYR H 94 PHE 0.007 0.001 PHE A 536 TRP 0.014 0.002 TRP C 47 HIS 0.005 0.002 HIS C 31 Details of bonding type rmsd covalent geometry : bond 0.00336 ( 6080) covalent geometry : angle 0.58962 ( 8308) SS BOND : bond 0.00523 ( 6) SS BOND : angle 1.06053 ( 12) hydrogen bonds : bond 0.04099 ( 202) hydrogen bonds : angle 6.73591 ( 546) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1528 Ramachandran restraints generated. 764 Oldfield, 0 Emsley, 764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1528 Ramachandran restraints generated. 764 Oldfield, 0 Emsley, 764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 628 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 121 time to evaluate : 0.154 Fit side-chains REVERT: D 4 MET cc_start: 0.8547 (mtm) cc_final: 0.8296 (mtp) REVERT: H 19 LYS cc_start: 0.7547 (OUTLIER) cc_final: 0.6047 (tppp) outliers start: 25 outliers final: 6 residues processed: 137 average time/residue: 0.3125 time to fit residues: 46.3899 Evaluate side-chains 123 residues out of total 628 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 116 time to evaluate : 0.193 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 557 SER Chi-restraints excluded: chain C residue 71 THR Chi-restraints excluded: chain D residue 19 VAL Chi-restraints excluded: chain H residue 19 LYS Chi-restraints excluded: chain H residue 71 THR Chi-restraints excluded: chain L residue 74 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 54 optimal weight: 1.9990 chunk 31 optimal weight: 0.4980 chunk 0 optimal weight: 1.9990 chunk 46 optimal weight: 0.9990 chunk 17 optimal weight: 0.8980 chunk 3 optimal weight: 2.9990 chunk 56 optimal weight: 0.0270 chunk 52 optimal weight: 0.6980 chunk 72 optimal weight: 1.9990 chunk 12 optimal weight: 0.8980 chunk 6 optimal weight: 0.9980 overall best weight: 0.6038 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 549 ASN ** B 479 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 31 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4204 r_free = 0.4204 target = 0.165797 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3963 r_free = 0.3963 target = 0.146157 restraints weight = 29390.490| |-----------------------------------------------------------------------------| r_work (start): 0.3957 rms_B_bonded: 4.26 r_work: 0.3753 rms_B_bonded: 4.77 restraints_weight: 0.5000 r_work (final): 0.3753 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3746 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3746 r_free = 0.3746 target_work(ls_wunit_k1) = 0.130 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 12 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3746 r_free = 0.3746 target_work(ls_wunit_k1) = 0.130 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 12 | |-----------------------------------------------------------------------------| r_final: 0.3746 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7528 moved from start: 0.1583 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 6086 Z= 0.166 Angle : 0.598 5.193 8320 Z= 0.319 Chirality : 0.045 0.165 904 Planarity : 0.007 0.073 1058 Dihedral : 5.907 45.870 838 Min Nonbonded Distance : 2.592 Molprobity Statistics. All-atom Clashscore : 6.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.65 % Favored : 93.35 % Rotamer: Outliers : 4.56 % Allowed : 17.45 % Favored : 77.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 15.00 % 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: -0.61 (0.31), residues: 764 helix: None (None), residues: 0 sheet: 0.60 (0.28), residues: 353 loop : -1.37 (0.32), residues: 411 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 449 TYR 0.013 0.002 TYR H 94 PHE 0.009 0.002 PHE A 536 TRP 0.014 0.002 TRP C 120 HIS 0.006 0.001 HIS H 35 Details of bonding type rmsd covalent geometry : bond 0.00396 ( 6080) covalent geometry : angle 0.59696 ( 8308) SS BOND : bond 0.00534 ( 6) SS BOND : angle 1.15476 ( 12) hydrogen bonds : bond 0.04118 ( 202) hydrogen bonds : angle 6.38185 ( 546) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1528 Ramachandran restraints generated. 764 Oldfield, 0 Emsley, 764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1528 Ramachandran restraints generated. 764 Oldfield, 0 Emsley, 764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 628 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 116 time to evaluate : 0.236 Fit side-chains REVERT: D 4 MET cc_start: 0.8463 (mtm) cc_final: 0.8152 (mtp) REVERT: H 19 LYS cc_start: 0.7589 (OUTLIER) cc_final: 0.6088 (tppp) REVERT: H 72 ARG cc_start: 0.8491 (OUTLIER) cc_final: 0.8138 (ttp-110) REVERT: L 31 ASN cc_start: 0.8598 (m-40) cc_final: 0.8388 (m-40) outliers start: 29 outliers final: 14 residues processed: 133 average time/residue: 0.3169 time to fit residues: 45.7423 Evaluate side-chains 131 residues out of total 628 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 115 time to evaluate : 0.315 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 557 SER Chi-restraints excluded: chain C residue 5 VAL Chi-restraints excluded: chain C residue 72 ARG Chi-restraints excluded: chain C residue 83 LEU Chi-restraints excluded: chain D residue 19 VAL Chi-restraints excluded: chain D residue 22 THR Chi-restraints excluded: chain D residue 60 SER Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 7 SER Chi-restraints excluded: chain H residue 19 LYS Chi-restraints excluded: chain H residue 71 THR Chi-restraints excluded: chain H residue 72 ARG Chi-restraints excluded: chain H residue 83 LEU Chi-restraints excluded: chain L residue 19 VAL Chi-restraints excluded: chain L residue 74 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 18 optimal weight: 0.7980 chunk 28 optimal weight: 0.0970 chunk 64 optimal weight: 0.8980 chunk 52 optimal weight: 1.9990 chunk 6 optimal weight: 0.9980 chunk 36 optimal weight: 1.9990 chunk 0 optimal weight: 0.9980 chunk 9 optimal weight: 0.0970 chunk 54 optimal weight: 0.9990 chunk 8 optimal weight: 1.9990 chunk 48 optimal weight: 2.9990 overall best weight: 0.5776 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 585 ASN D 31 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4205 r_free = 0.4205 target = 0.165706 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3965 r_free = 0.3965 target = 0.146250 restraints weight = 28652.547| |-----------------------------------------------------------------------------| r_work (start): 0.3959 rms_B_bonded: 4.23 r_work: 0.3755 rms_B_bonded: 4.74 restraints_weight: 0.5000 r_work (final): 0.3755 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3755 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3755 r_free = 0.3755 target_work(ls_wunit_k1) = 0.131 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 12 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3755 r_free = 0.3755 target_work(ls_wunit_k1) = 0.131 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 12 | |-----------------------------------------------------------------------------| r_final: 0.3755 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7523 moved from start: 0.1786 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 6086 Z= 0.160 Angle : 0.582 4.854 8320 Z= 0.311 Chirality : 0.045 0.163 904 Planarity : 0.007 0.074 1058 Dihedral : 5.843 45.281 838 Min Nonbonded Distance : 2.600 Molprobity Statistics. All-atom Clashscore : 7.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.71 % Favored : 92.29 % Rotamer: Outliers : 4.72 % Allowed : 18.40 % Favored : 76.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 15.00 % 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: -0.71 (0.31), residues: 764 helix: None (None), residues: 0 sheet: 0.55 (0.27), residues: 353 loop : -1.45 (0.31), residues: 411 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 449 TYR 0.013 0.001 TYR L 91 PHE 0.009 0.001 PHE A 536 TRP 0.015 0.002 TRP C 47 HIS 0.005 0.001 HIS H 35 Details of bonding type rmsd covalent geometry : bond 0.00386 ( 6080) covalent geometry : angle 0.58124 ( 8308) SS BOND : bond 0.00539 ( 6) SS BOND : angle 1.11541 ( 12) hydrogen bonds : bond 0.03700 ( 202) hydrogen bonds : angle 6.17940 ( 546) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1528 Ramachandran restraints generated. 764 Oldfield, 0 Emsley, 764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1528 Ramachandran restraints generated. 764 Oldfield, 0 Emsley, 764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 628 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 109 time to evaluate : 0.257 Fit side-chains REVERT: D 4 MET cc_start: 0.8413 (mtm) cc_final: 0.8122 (mtp) REVERT: H 19 LYS cc_start: 0.7573 (OUTLIER) cc_final: 0.6041 (tppp) REVERT: H 72 ARG cc_start: 0.8501 (OUTLIER) cc_final: 0.8274 (ttp80) REVERT: L 31 ASN cc_start: 0.8601 (m-40) cc_final: 0.8400 (m-40) outliers start: 30 outliers final: 18 residues processed: 128 average time/residue: 0.3529 time to fit residues: 48.6408 Evaluate side-chains 129 residues out of total 628 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 109 time to evaluate : 0.241 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 501 SER Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 557 SER Chi-restraints excluded: chain C residue 5 VAL Chi-restraints excluded: chain C residue 31 HIS Chi-restraints excluded: chain C residue 69 THR Chi-restraints excluded: chain C residue 71 THR Chi-restraints excluded: chain C residue 72 ARG Chi-restraints excluded: chain C residue 83 LEU Chi-restraints excluded: chain D residue 19 VAL Chi-restraints excluded: chain D residue 22 THR Chi-restraints excluded: chain D residue 60 SER Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 7 SER Chi-restraints excluded: chain H residue 19 LYS Chi-restraints excluded: chain H residue 72 ARG Chi-restraints excluded: chain H residue 83 LEU Chi-restraints excluded: chain L residue 19 VAL Chi-restraints excluded: chain L residue 72 THR Chi-restraints excluded: chain L residue 74 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 31 optimal weight: 0.9990 chunk 30 optimal weight: 0.6980 chunk 62 optimal weight: 0.3980 chunk 61 optimal weight: 0.5980 chunk 42 optimal weight: 0.0010 chunk 66 optimal weight: 0.7980 chunk 23 optimal weight: 0.5980 chunk 41 optimal weight: 0.1980 chunk 7 optimal weight: 0.9990 chunk 72 optimal weight: 0.8980 chunk 6 optimal weight: 1.9990 overall best weight: 0.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 31 ASN D 55 GLN L 55 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4223 r_free = 0.4223 target = 0.167104 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3979 r_free = 0.3979 target = 0.147296 restraints weight = 32449.689| |-----------------------------------------------------------------------------| r_work (start): 0.3974 rms_B_bonded: 4.84 r_work (final): 0.3974 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3976 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3976 r_free = 0.3976 target_work(ls_wunit_k1) = 0.146 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 12 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3976 r_free = 0.3976 target_work(ls_wunit_k1) = 0.146 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 12 | |-----------------------------------------------------------------------------| r_final: 0.3976 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7270 moved from start: 0.1961 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 6086 Z= 0.123 Angle : 0.542 4.845 8320 Z= 0.288 Chirality : 0.044 0.160 904 Planarity : 0.006 0.071 1058 Dihedral : 5.624 44.447 838 Min Nonbonded Distance : 2.600 Molprobity Statistics. All-atom Clashscore : 6.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.05 % Favored : 92.95 % Rotamer: Outliers : 4.56 % Allowed : 19.81 % Favored : 75.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 15.00 % 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: -0.71 (0.31), residues: 764 helix: None (None), residues: 0 sheet: 0.51 (0.27), residues: 357 loop : -1.43 (0.32), residues: 407 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 38 TYR 0.009 0.001 TYR H 94 PHE 0.008 0.001 PHE A 536 TRP 0.014 0.001 TRP C 47 HIS 0.005 0.001 HIS H 35 Details of bonding type rmsd covalent geometry : bond 0.00293 ( 6080) covalent geometry : angle 0.54094 ( 8308) SS BOND : bond 0.00451 ( 6) SS BOND : angle 0.91827 ( 12) hydrogen bonds : bond 0.03270 ( 202) hydrogen bonds : angle 5.87747 ( 546) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1528 Ramachandran restraints generated. 764 Oldfield, 0 Emsley, 764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1528 Ramachandran restraints generated. 764 Oldfield, 0 Emsley, 764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 628 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 111 time to evaluate : 0.140 Fit side-chains REVERT: B 534 ILE cc_start: 0.7901 (OUTLIER) cc_final: 0.7604 (tp) REVERT: C 38 ARG cc_start: 0.8061 (OUTLIER) cc_final: 0.7013 (ttm170) REVERT: D 28 ASP cc_start: 0.6627 (OUTLIER) cc_final: 0.6427 (t0) REVERT: H 19 LYS cc_start: 0.6844 (OUTLIER) cc_final: 0.5384 (tppp) outliers start: 29 outliers final: 16 residues processed: 131 average time/residue: 0.3032 time to fit residues: 43.2807 Evaluate side-chains 129 residues out of total 628 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 109 time to evaluate : 0.230 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 501 SER Chi-restraints excluded: chain B residue 534 ILE Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 557 SER Chi-restraints excluded: chain C residue 5 VAL Chi-restraints excluded: chain C residue 31 HIS Chi-restraints excluded: chain C residue 38 ARG Chi-restraints excluded: chain C residue 69 THR Chi-restraints excluded: chain C residue 71 THR Chi-restraints excluded: chain C residue 72 ARG Chi-restraints excluded: chain C residue 83 LEU Chi-restraints excluded: chain D residue 19 VAL Chi-restraints excluded: chain D residue 28 ASP Chi-restraints excluded: chain H residue 7 SER Chi-restraints excluded: chain H residue 19 LYS Chi-restraints excluded: chain H residue 71 THR Chi-restraints excluded: chain L residue 19 VAL Chi-restraints excluded: chain L residue 72 THR Chi-restraints excluded: chain L residue 74 THR Chi-restraints excluded: chain L residue 85 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 38 optimal weight: 1.9990 chunk 14 optimal weight: 2.9990 chunk 34 optimal weight: 1.9990 chunk 42 optimal weight: 2.9990 chunk 25 optimal weight: 2.9990 chunk 6 optimal weight: 0.8980 chunk 59 optimal weight: 1.9990 chunk 47 optimal weight: 0.9990 chunk 50 optimal weight: 1.9990 chunk 66 optimal weight: 3.9990 chunk 73 optimal weight: 0.0070 overall best weight: 1.1804 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 31 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4166 r_free = 0.4166 target = 0.162836 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3937 r_free = 0.3937 target = 0.144200 restraints weight = 24874.756| |-----------------------------------------------------------------------------| r_work (start): 0.3919 rms_B_bonded: 3.64 r_work: 0.3729 rms_B_bonded: 4.33 restraints_weight: 0.5000 r_work (final): 0.3729 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3727 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3727 r_free = 0.3727 target_work(ls_wunit_k1) = 0.128 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 12 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3727 r_free = 0.3727 target_work(ls_wunit_k1) = 0.128 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| r_final: 0.3727 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7547 moved from start: 0.2040 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.051 6086 Z= 0.276 Angle : 0.673 5.825 8320 Z= 0.359 Chirality : 0.050 0.158 904 Planarity : 0.007 0.071 1058 Dihedral : 6.263 47.554 838 Min Nonbonded Distance : 2.589 Molprobity Statistics. All-atom Clashscore : 7.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.04 % Favored : 90.96 % Rotamer: Outliers : 4.87 % Allowed : 20.44 % Favored : 74.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 15.00 % 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: -0.98 (0.30), residues: 764 helix: None (None), residues: 0 sheet: 0.40 (0.27), residues: 351 loop : -1.66 (0.30), residues: 413 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 449 TYR 0.018 0.002 TYR L 91 PHE 0.013 0.003 PHE H 111 TRP 0.017 0.003 TRP B 505 HIS 0.006 0.001 HIS H 35 Details of bonding type rmsd covalent geometry : bond 0.00661 ( 6080) covalent geometry : angle 0.67161 ( 8308) SS BOND : bond 0.00807 ( 6) SS BOND : angle 1.45200 ( 12) hydrogen bonds : bond 0.04308 ( 202) hydrogen bonds : angle 6.23517 ( 546) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1528 Ramachandran restraints generated. 764 Oldfield, 0 Emsley, 764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1528 Ramachandran restraints generated. 764 Oldfield, 0 Emsley, 764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 628 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 112 time to evaluate : 0.221 Fit side-chains REVERT: B 534 ILE cc_start: 0.8166 (OUTLIER) cc_final: 0.7809 (tp) REVERT: C 38 ARG cc_start: 0.8296 (OUTLIER) cc_final: 0.7671 (ptm160) REVERT: H 19 LYS cc_start: 0.7580 (OUTLIER) cc_final: 0.6047 (tppp) REVERT: L 31 ASN cc_start: 0.8565 (m-40) cc_final: 0.8355 (m-40) outliers start: 31 outliers final: 21 residues processed: 131 average time/residue: 0.3114 time to fit residues: 44.3167 Evaluate side-chains 136 residues out of total 628 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 112 time to evaluate : 0.163 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 501 SER Chi-restraints excluded: chain B residue 534 ILE Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 557 SER Chi-restraints excluded: chain B residue 586 ILE Chi-restraints excluded: chain C residue 5 VAL Chi-restraints excluded: chain C residue 38 ARG Chi-restraints excluded: chain C residue 69 THR Chi-restraints excluded: chain C residue 72 ARG Chi-restraints excluded: chain C residue 83 LEU Chi-restraints excluded: chain D residue 19 VAL Chi-restraints excluded: chain D residue 22 THR Chi-restraints excluded: chain D residue 27 GLN Chi-restraints excluded: chain D residue 60 SER Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 7 SER Chi-restraints excluded: chain H residue 19 LYS Chi-restraints excluded: chain H residue 71 THR Chi-restraints excluded: chain H residue 72 ARG Chi-restraints excluded: chain H residue 83 LEU Chi-restraints excluded: chain L residue 19 VAL Chi-restraints excluded: chain L residue 72 THR Chi-restraints excluded: chain L residue 74 THR Chi-restraints excluded: chain L residue 85 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 66 optimal weight: 0.8980 chunk 4 optimal weight: 1.9990 chunk 45 optimal weight: 0.6980 chunk 18 optimal weight: 0.5980 chunk 23 optimal weight: 0.6980 chunk 17 optimal weight: 0.5980 chunk 1 optimal weight: 0.7980 chunk 12 optimal weight: 1.9990 chunk 70 optimal weight: 0.9980 chunk 47 optimal weight: 0.6980 chunk 34 optimal weight: 1.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 31 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4194 r_free = 0.4194 target = 0.164791 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3965 r_free = 0.3965 target = 0.146161 restraints weight = 24237.179| |-----------------------------------------------------------------------------| r_work (start): 0.3961 rms_B_bonded: 3.60 r_work: 0.3776 rms_B_bonded: 4.31 restraints_weight: 0.5000 r_work (final): 0.3776 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3777 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3777 r_free = 0.3777 target_work(ls_wunit_k1) = 0.132 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3777 r_free = 0.3777 target_work(ls_wunit_k1) = 0.132 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 12 | |-----------------------------------------------------------------------------| r_final: 0.3777 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7508 moved from start: 0.2093 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 6086 Z= 0.175 Angle : 0.597 5.539 8320 Z= 0.319 Chirality : 0.046 0.158 904 Planarity : 0.007 0.072 1058 Dihedral : 6.045 45.732 838 Min Nonbonded Distance : 2.599 Molprobity Statistics. All-atom Clashscore : 8.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.71 % Favored : 92.29 % Rotamer: Outliers : 5.35 % Allowed : 19.34 % Favored : 75.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 15.00 % 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: 764 helix: None (None), residues: 0 sheet: 0.48 (0.27), residues: 349 loop : -1.66 (0.30), residues: 415 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 449 TYR 0.014 0.002 TYR L 91 PHE 0.011 0.002 PHE A 536 TRP 0.016 0.002 TRP C 120 HIS 0.004 0.001 HIS H 35 Details of bonding type rmsd covalent geometry : bond 0.00418 ( 6080) covalent geometry : angle 0.59637 ( 8308) SS BOND : bond 0.00625 ( 6) SS BOND : angle 1.13294 ( 12) hydrogen bonds : bond 0.03691 ( 202) hydrogen bonds : angle 6.04701 ( 546) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1528 Ramachandran restraints generated. 764 Oldfield, 0 Emsley, 764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1528 Ramachandran restraints generated. 764 Oldfield, 0 Emsley, 764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 628 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 109 time to evaluate : 0.341 Fit side-chains REVERT: B 534 ILE cc_start: 0.8183 (OUTLIER) cc_final: 0.7841 (tp) REVERT: H 19 LYS cc_start: 0.7492 (OUTLIER) cc_final: 0.5983 (tppp) REVERT: L 31 ASN cc_start: 0.8562 (m-40) cc_final: 0.8357 (m-40) outliers start: 34 outliers final: 22 residues processed: 131 average time/residue: 0.3412 time to fit residues: 48.2562 Evaluate side-chains 133 residues out of total 628 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 109 time to evaluate : 0.168 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 501 SER Chi-restraints excluded: chain B residue 534 ILE Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 557 SER Chi-restraints excluded: chain C residue 5 VAL Chi-restraints excluded: chain C residue 7 SER Chi-restraints excluded: chain C residue 38 ARG Chi-restraints excluded: chain C residue 69 THR Chi-restraints excluded: chain C residue 71 THR Chi-restraints excluded: chain C residue 72 ARG Chi-restraints excluded: chain D residue 19 VAL Chi-restraints excluded: chain D residue 22 THR Chi-restraints excluded: chain D residue 27 GLN Chi-restraints excluded: chain D residue 60 SER Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 7 SER Chi-restraints excluded: chain H residue 19 LYS Chi-restraints excluded: chain H residue 71 THR Chi-restraints excluded: chain H residue 72 ARG Chi-restraints excluded: chain H residue 83 LEU Chi-restraints excluded: chain L residue 19 VAL Chi-restraints excluded: chain L residue 72 THR Chi-restraints excluded: chain L residue 74 THR Chi-restraints excluded: chain L residue 85 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 51 optimal weight: 0.7980 chunk 47 optimal weight: 0.9990 chunk 32 optimal weight: 1.9990 chunk 4 optimal weight: 2.9990 chunk 55 optimal weight: 0.9990 chunk 13 optimal weight: 1.9990 chunk 61 optimal weight: 1.9990 chunk 39 optimal weight: 0.5980 chunk 1 optimal weight: 0.8980 chunk 65 optimal weight: 1.9990 chunk 8 optimal weight: 1.9990 overall best weight: 0.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 31 ASN D 55 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4177 r_free = 0.4177 target = 0.163855 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3946 r_free = 0.3946 target = 0.144948 restraints weight = 26285.342| |-----------------------------------------------------------------------------| r_work (start): 0.3927 rms_B_bonded: 3.78 r_work: 0.3733 rms_B_bonded: 4.47 restraints_weight: 0.5000 r_work (final): 0.3733 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3733 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3733 r_free = 0.3733 target_work(ls_wunit_k1) = 0.129 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 12 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3733 r_free = 0.3733 target_work(ls_wunit_k1) = 0.128 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 12 | |-----------------------------------------------------------------------------| r_final: 0.3733 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7542 moved from start: 0.2183 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 6086 Z= 0.215 Angle : 0.633 4.949 8320 Z= 0.338 Chirality : 0.047 0.154 904 Planarity : 0.007 0.072 1058 Dihedral : 6.201 47.029 838 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 7.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.91 % Favored : 91.09 % Rotamer: Outliers : 4.87 % Allowed : 19.50 % Favored : 75.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 15.00 % 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: -1.02 (0.30), residues: 764 helix: None (None), residues: 0 sheet: 0.41 (0.27), residues: 349 loop : -1.73 (0.30), residues: 415 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 449 TYR 0.016 0.002 TYR L 91 PHE 0.011 0.002 PHE A 536 TRP 0.016 0.002 TRP B 505 HIS 0.005 0.001 HIS C 35 Details of bonding type rmsd covalent geometry : bond 0.00515 ( 6080) covalent geometry : angle 0.63141 ( 8308) SS BOND : bond 0.00743 ( 6) SS BOND : angle 1.20078 ( 12) hydrogen bonds : bond 0.03933 ( 202) hydrogen bonds : angle 6.07551 ( 546) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1528 Ramachandran restraints generated. 764 Oldfield, 0 Emsley, 764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1528 Ramachandran restraints generated. 764 Oldfield, 0 Emsley, 764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 628 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 110 time to evaluate : 0.223 Fit side-chains REVERT: B 534 ILE cc_start: 0.8200 (OUTLIER) cc_final: 0.7857 (tp) REVERT: C 38 ARG cc_start: 0.8298 (OUTLIER) cc_final: 0.7689 (ptm160) REVERT: C 39 GLN cc_start: 0.8590 (OUTLIER) cc_final: 0.7246 (tt0) REVERT: D 55 GLN cc_start: 0.8063 (OUTLIER) cc_final: 0.7423 (mm110) REVERT: H 19 LYS cc_start: 0.7562 (OUTLIER) cc_final: 0.6102 (tppp) REVERT: H 39 GLN cc_start: 0.8677 (OUTLIER) cc_final: 0.6798 (tt0) REVERT: L 31 ASN cc_start: 0.8552 (m-40) cc_final: 0.8341 (m-40) outliers start: 31 outliers final: 23 residues processed: 130 average time/residue: 0.3222 time to fit residues: 45.1271 Evaluate side-chains 140 residues out of total 628 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 111 time to evaluate : 0.219 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 584 VAL Chi-restraints excluded: chain B residue 501 SER Chi-restraints excluded: chain B residue 534 ILE Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 557 SER Chi-restraints excluded: chain B residue 586 ILE Chi-restraints excluded: chain C residue 5 VAL Chi-restraints excluded: chain C residue 7 SER Chi-restraints excluded: chain C residue 38 ARG Chi-restraints excluded: chain C residue 39 GLN Chi-restraints excluded: chain C residue 69 THR Chi-restraints excluded: chain C residue 72 ARG Chi-restraints excluded: chain C residue 83 LEU Chi-restraints excluded: chain D residue 19 VAL Chi-restraints excluded: chain D residue 22 THR Chi-restraints excluded: chain D residue 27 GLN Chi-restraints excluded: chain D residue 55 GLN Chi-restraints excluded: chain D residue 60 SER Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 7 SER Chi-restraints excluded: chain H residue 19 LYS Chi-restraints excluded: chain H residue 39 GLN Chi-restraints excluded: chain H residue 71 THR Chi-restraints excluded: chain H residue 72 ARG Chi-restraints excluded: chain H residue 83 LEU Chi-restraints excluded: chain L residue 19 VAL Chi-restraints excluded: chain L residue 72 THR Chi-restraints excluded: chain L residue 74 THR Chi-restraints excluded: chain L residue 85 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 15 optimal weight: 1.9990 chunk 66 optimal weight: 0.0670 chunk 2 optimal weight: 2.9990 chunk 48 optimal weight: 0.9990 chunk 23 optimal weight: 0.9990 chunk 27 optimal weight: 0.5980 chunk 43 optimal weight: 0.7980 chunk 73 optimal weight: 1.9990 chunk 18 optimal weight: 0.9980 chunk 44 optimal weight: 1.9990 chunk 55 optimal weight: 0.6980 overall best weight: 0.6318 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 31 ASN D 55 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4194 r_free = 0.4194 target = 0.164943 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3969 r_free = 0.3969 target = 0.146625 restraints weight = 22804.195| |-----------------------------------------------------------------------------| r_work (start): 0.3953 rms_B_bonded: 3.47 r_work: 0.3771 rms_B_bonded: 4.20 restraints_weight: 0.5000 r_work (final): 0.3771 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3774 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3774 r_free = 0.3774 target_work(ls_wunit_k1) = 0.131 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 12 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3774 r_free = 0.3774 target_work(ls_wunit_k1) = 0.131 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 12 | |-----------------------------------------------------------------------------| r_final: 0.3774 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7499 moved from start: 0.2222 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 6086 Z= 0.171 Angle : 0.598 4.941 8320 Z= 0.319 Chirality : 0.046 0.154 904 Planarity : 0.007 0.074 1058 Dihedral : 6.074 45.766 838 Min Nonbonded Distance : 2.570 Molprobity Statistics. All-atom Clashscore : 7.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.85 % Favored : 92.15 % Rotamer: Outliers : 4.87 % Allowed : 19.81 % Favored : 75.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 15.00 % 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: -0.96 (0.30), residues: 764 helix: None (None), residues: 0 sheet: 0.45 (0.27), residues: 349 loop : -1.68 (0.30), residues: 415 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 449 TYR 0.014 0.002 TYR L 91 PHE 0.010 0.002 PHE A 536 TRP 0.015 0.002 TRP B 505 HIS 0.004 0.001 HIS C 35 Details of bonding type rmsd covalent geometry : bond 0.00410 ( 6080) covalent geometry : angle 0.59686 ( 8308) SS BOND : bond 0.00631 ( 6) SS BOND : angle 1.10484 ( 12) hydrogen bonds : bond 0.03624 ( 202) hydrogen bonds : angle 5.97578 ( 546) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1528 Ramachandran restraints generated. 764 Oldfield, 0 Emsley, 764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1528 Ramachandran restraints generated. 764 Oldfield, 0 Emsley, 764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 628 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 111 time to evaluate : 0.224 Fit side-chains REVERT: B 534 ILE cc_start: 0.8186 (OUTLIER) cc_final: 0.7856 (tp) REVERT: C 38 ARG cc_start: 0.8220 (OUTLIER) cc_final: 0.7638 (ptm160) REVERT: C 39 GLN cc_start: 0.8542 (OUTLIER) cc_final: 0.7135 (tt0) REVERT: D 55 GLN cc_start: 0.8040 (OUTLIER) cc_final: 0.7356 (mm110) REVERT: H 19 LYS cc_start: 0.7472 (OUTLIER) cc_final: 0.5982 (tppp) REVERT: H 39 GLN cc_start: 0.8644 (OUTLIER) cc_final: 0.6683 (tt0) outliers start: 31 outliers final: 23 residues processed: 131 average time/residue: 0.3166 time to fit residues: 44.9012 Evaluate side-chains 139 residues out of total 628 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 110 time to evaluate : 0.203 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 584 VAL Chi-restraints excluded: chain B residue 501 SER Chi-restraints excluded: chain B residue 534 ILE Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 557 SER Chi-restraints excluded: chain B residue 586 ILE Chi-restraints excluded: chain C residue 5 VAL Chi-restraints excluded: chain C residue 7 SER Chi-restraints excluded: chain C residue 38 ARG Chi-restraints excluded: chain C residue 39 GLN Chi-restraints excluded: chain C residue 69 THR Chi-restraints excluded: chain C residue 72 ARG Chi-restraints excluded: chain C residue 83 LEU Chi-restraints excluded: chain D residue 19 VAL Chi-restraints excluded: chain D residue 22 THR Chi-restraints excluded: chain D residue 27 GLN Chi-restraints excluded: chain D residue 55 GLN Chi-restraints excluded: chain D residue 60 SER Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 7 SER Chi-restraints excluded: chain H residue 19 LYS Chi-restraints excluded: chain H residue 39 GLN Chi-restraints excluded: chain H residue 71 THR Chi-restraints excluded: chain H residue 72 ARG Chi-restraints excluded: chain H residue 83 LEU Chi-restraints excluded: chain L residue 19 VAL Chi-restraints excluded: chain L residue 72 THR Chi-restraints excluded: chain L residue 74 THR Chi-restraints excluded: chain L residue 85 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 71 optimal weight: 1.9990 chunk 33 optimal weight: 1.9990 chunk 22 optimal weight: 0.6980 chunk 8 optimal weight: 1.9990 chunk 25 optimal weight: 1.9990 chunk 55 optimal weight: 0.8980 chunk 16 optimal weight: 1.9990 chunk 63 optimal weight: 0.5980 chunk 21 optimal weight: 0.0000 chunk 39 optimal weight: 0.7980 chunk 15 optimal weight: 1.9990 overall best weight: 0.5984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 31 ASN D 55 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4196 r_free = 0.4196 target = 0.165235 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3966 r_free = 0.3966 target = 0.146500 restraints weight = 26776.746| |-----------------------------------------------------------------------------| r_work (start): 0.3962 rms_B_bonded: 3.90 r_work: 0.3771 rms_B_bonded: 4.43 restraints_weight: 0.5000 r_work (final): 0.3771 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3771 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3771 r_free = 0.3771 target_work(ls_wunit_k1) = 0.132 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 12 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3771 r_free = 0.3771 target_work(ls_wunit_k1) = 0.132 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 12 | |-----------------------------------------------------------------------------| r_final: 0.3771 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7510 moved from start: 0.2234 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 6086 Z= 0.164 Angle : 0.589 4.943 8320 Z= 0.314 Chirality : 0.045 0.154 904 Planarity : 0.007 0.073 1058 Dihedral : 6.022 46.138 838 Min Nonbonded Distance : 2.577 Molprobity Statistics. All-atom Clashscore : 7.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.64 % Favored : 91.36 % Rotamer: Outliers : 4.72 % Allowed : 20.28 % Favored : 75.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 15.00 % 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: -0.99 (0.30), residues: 764 helix: None (None), residues: 0 sheet: 0.38 (0.27), residues: 359 loop : -1.70 (0.31), residues: 405 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 449 TYR 0.013 0.002 TYR L 91 PHE 0.010 0.001 PHE A 536 TRP 0.015 0.002 TRP C 120 HIS 0.004 0.001 HIS C 35 Details of bonding type rmsd covalent geometry : bond 0.00394 ( 6080) covalent geometry : angle 0.58762 ( 8308) SS BOND : bond 0.00619 ( 6) SS BOND : angle 1.04929 ( 12) hydrogen bonds : bond 0.03541 ( 202) hydrogen bonds : angle 5.91603 ( 546) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1528 Ramachandran restraints generated. 764 Oldfield, 0 Emsley, 764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1528 Ramachandran restraints generated. 764 Oldfield, 0 Emsley, 764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 628 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 111 time to evaluate : 0.242 Fit side-chains REVERT: B 534 ILE cc_start: 0.8196 (OUTLIER) cc_final: 0.7861 (tp) REVERT: C 38 ARG cc_start: 0.8220 (OUTLIER) cc_final: 0.7624 (ptm160) REVERT: C 39 GLN cc_start: 0.8537 (OUTLIER) cc_final: 0.7115 (tt0) REVERT: H 19 LYS cc_start: 0.7490 (OUTLIER) cc_final: 0.5951 (tppp) REVERT: H 39 GLN cc_start: 0.8637 (OUTLIER) cc_final: 0.6665 (tt0) outliers start: 30 outliers final: 23 residues processed: 131 average time/residue: 0.3247 time to fit residues: 45.9636 Evaluate side-chains 138 residues out of total 628 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 110 time to evaluate : 0.212 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 584 VAL Chi-restraints excluded: chain B residue 501 SER Chi-restraints excluded: chain B residue 534 ILE Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 557 SER Chi-restraints excluded: chain B residue 586 ILE Chi-restraints excluded: chain C residue 5 VAL Chi-restraints excluded: chain C residue 7 SER Chi-restraints excluded: chain C residue 38 ARG Chi-restraints excluded: chain C residue 39 GLN Chi-restraints excluded: chain C residue 69 THR Chi-restraints excluded: chain C residue 72 ARG Chi-restraints excluded: chain C residue 83 LEU Chi-restraints excluded: chain D residue 19 VAL Chi-restraints excluded: chain D residue 22 THR Chi-restraints excluded: chain D residue 27 GLN Chi-restraints excluded: chain D residue 60 SER Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 7 SER Chi-restraints excluded: chain H residue 19 LYS Chi-restraints excluded: chain H residue 39 GLN Chi-restraints excluded: chain H residue 71 THR Chi-restraints excluded: chain H residue 72 ARG Chi-restraints excluded: chain H residue 83 LEU Chi-restraints excluded: chain L residue 19 VAL Chi-restraints excluded: chain L residue 72 THR Chi-restraints excluded: chain L residue 74 THR Chi-restraints excluded: chain L residue 85 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 63 optimal weight: 0.9980 chunk 36 optimal weight: 0.4980 chunk 53 optimal weight: 0.3980 chunk 69 optimal weight: 0.6980 chunk 24 optimal weight: 0.7980 chunk 39 optimal weight: 1.9990 chunk 18 optimal weight: 0.7980 chunk 6 optimal weight: 0.8980 chunk 72 optimal weight: 0.7980 chunk 9 optimal weight: 0.0980 chunk 25 optimal weight: 1.9990 overall best weight: 0.4980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 31 ASN D 55 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4209 r_free = 0.4209 target = 0.166439 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3964 r_free = 0.3964 target = 0.146462 restraints weight = 31277.733| |-----------------------------------------------------------------------------| r_work (start): 0.3956 rms_B_bonded: 4.85 r_work (final): 0.3956 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3959 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3959 r_free = 0.3959 target_work(ls_wunit_k1) = 0.145 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 12 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3959 r_free = 0.3959 target_work(ls_wunit_k1) = 0.145 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 12 | |-----------------------------------------------------------------------------| r_final: 0.3959 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7302 moved from start: 0.2284 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 6086 Z= 0.145 Angle : 0.567 4.955 8320 Z= 0.302 Chirality : 0.045 0.151 904 Planarity : 0.007 0.072 1058 Dihedral : 5.865 45.486 838 Min Nonbonded Distance : 2.586 Molprobity Statistics. All-atom Clashscore : 7.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.45 % Favored : 92.55 % Rotamer: Outliers : 4.56 % Allowed : 20.60 % Favored : 74.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 15.00 % 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 (0.31), residues: 764 helix: None (None), residues: 0 sheet: 0.47 (0.27), residues: 357 loop : -1.68 (0.31), residues: 407 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 449 TYR 0.012 0.001 TYR L 91 PHE 0.010 0.001 PHE A 536 TRP 0.014 0.002 TRP C 120 HIS 0.004 0.001 HIS C 35 Details of bonding type rmsd covalent geometry : bond 0.00348 ( 6080) covalent geometry : angle 0.56649 ( 8308) SS BOND : bond 0.00555 ( 6) SS BOND : angle 0.95914 ( 12) hydrogen bonds : bond 0.03351 ( 202) hydrogen bonds : angle 5.76261 ( 546) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2189.96 seconds wall clock time: 38 minutes 13.39 seconds (2293.39 seconds total)