Starting phenix.real_space_refine on Wed Sep 17 09:55:56 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8y5z_38960/09_2025/8y5z_38960.cif Found real_map, /net/cci-nas-00/data/ceres_data/8y5z_38960/09_2025/8y5z_38960.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.35 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8y5z_38960/09_2025/8y5z_38960.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8y5z_38960/09_2025/8y5z_38960.map" model { file = "/net/cci-nas-00/data/ceres_data/8y5z_38960/09_2025/8y5z_38960.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8y5z_38960/09_2025/8y5z_38960.cif" } resolution = 3.35 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= 0.045 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: 5 Type Number sf(0) Gaussians S 54 5.16 5 Na 2 4.78 5 C 5314 2.51 5 N 1204 2.21 5 O 1344 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 15 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 7918 Number of models: 1 Model: "" Number of chains: 4 Chain: "B" Number of atoms: 3953 Number of conformers: 1 Conformer: "" Number of residues, atoms: 508, 3953 Classifications: {'peptide': 508} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 30, 'TRANS': 477} Chain breaks: 3 Unresolved non-hydrogen bonds: 33 Unresolved non-hydrogen angles: 42 Unresolved non-hydrogen dihedrals: 33 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1, 'PHE:plan': 1, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 19 Chain: "A" Number of atoms: 3953 Number of conformers: 1 Conformer: "" Number of residues, atoms: 508, 3953 Classifications: {'peptide': 508} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 30, 'TRANS': 477} Chain breaks: 3 Unresolved non-hydrogen bonds: 33 Unresolved non-hydrogen angles: 42 Unresolved non-hydrogen dihedrals: 33 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1, 'PHE:plan': 1, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 19 Chain: "B" Number of atoms: 6 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 6 Unusual residues: {' NA': 1, 'SO4': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "A" Number of atoms: 6 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 6 Unusual residues: {' NA': 1, 'SO4': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 2.08, per 1000 atoms: 0.26 Number of scatterers: 7918 At special positions: 0 Unit cell: (91.2766, 119.748, 80.3904, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 54 16.00 Na 2 11.00 O 1344 8.00 N 1204 7.00 C 5314 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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: 0.59 Conformation dependent library (CDL) restraints added in 391.7 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 2000 Ramachandran restraints generated. 1000 Oldfield, 0 Emsley, 1000 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1924 Finding SS restraints... Secondary structure from input PDB file: 60 helices and 0 sheets defined 79.4% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.26 Creating SS restraints... Processing helix chain 'B' and resid 2 through 10 Processing helix chain 'B' and resid 10 through 23 removed outlier: 4.044A pdb=" N LEU B 23 " --> pdb=" O THR B 19 " (cutoff:3.500A) Processing helix chain 'B' and resid 24 through 29 Processing helix chain 'B' and resid 32 through 51 Processing helix chain 'B' and resid 54 through 61 removed outlier: 3.610A pdb=" N LEU B 61 " --> pdb=" O VAL B 57 " (cutoff:3.500A) Processing helix chain 'B' and resid 64 through 69 removed outlier: 3.800A pdb=" N MET B 68 " --> pdb=" O LEU B 64 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N PHE B 69 " --> pdb=" O MET B 65 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 64 through 69' Processing helix chain 'B' and resid 83 through 102 removed outlier: 4.180A pdb=" N LEU B 87 " --> pdb=" O LYS B 83 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N LEU B 88 " --> pdb=" O ASP B 84 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N TRP B 102 " --> pdb=" O SER B 98 " (cutoff:3.500A) Processing helix chain 'B' and resid 103 through 117 removed outlier: 3.785A pdb=" N ARG B 107 " --> pdb=" O ASN B 103 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N GLY B 117 " --> pdb=" O VAL B 113 " (cutoff:3.500A) Processing helix chain 'B' and resid 119 through 138 removed outlier: 4.111A pdb=" N TRP B 137 " --> pdb=" O PHE B 133 " (cutoff:3.500A) Processing helix chain 'B' and resid 139 through 160 Proline residue: B 149 - end of helix Processing helix chain 'B' and resid 231 through 253 removed outlier: 3.872A pdb=" N THR B 249 " --> pdb=" O ALA B 245 " (cutoff:3.500A) Processing helix chain 'B' and resid 255 through 258 Processing helix chain 'B' and resid 259 through 273 Processing helix chain 'B' and resid 280 through 308 Proline residue: B 290 - end of helix Processing helix chain 'B' and resid 311 through 316 removed outlier: 3.507A pdb=" N PHE B 316 " --> pdb=" O PHE B 312 " (cutoff:3.500A) Processing helix chain 'B' and resid 323 through 341 removed outlier: 3.573A pdb=" N GLY B 341 " --> pdb=" O TYR B 337 " (cutoff:3.500A) Processing helix chain 'B' and resid 344 through 359 Processing helix chain 'B' and resid 384 through 394 removed outlier: 4.097A pdb=" N ILE B 392 " --> pdb=" O VAL B 388 " (cutoff:3.500A) Processing helix chain 'B' and resid 395 through 398 Processing helix chain 'B' and resid 413 through 417 removed outlier: 4.040A pdb=" N ASP B 417 " --> pdb=" O VAL B 414 " (cutoff:3.500A) Processing helix chain 'B' and resid 423 through 429 removed outlier: 3.740A pdb=" N SER B 429 " --> pdb=" O LYS B 425 " (cutoff:3.500A) Processing helix chain 'B' and resid 432 through 449 removed outlier: 3.950A pdb=" N ALA B 436 " --> pdb=" O PRO B 432 " (cutoff:3.500A) removed outlier: 4.230A pdb=" N ILE B 437 " --> pdb=" O TRP B 433 " (cutoff:3.500A) Processing helix chain 'B' and resid 453 through 460 Processing helix chain 'B' and resid 461 through 463 No H-bonds generated for 'chain 'B' and resid 461 through 463' Processing helix chain 'B' and resid 469 through 486 removed outlier: 3.505A pdb=" N GLU B 486 " --> pdb=" O THR B 482 " (cutoff:3.500A) Processing helix chain 'B' and resid 489 through 508 Proline residue: B 499 - end of helix Proline residue: B 503 - end of helix Processing helix chain 'B' and resid 511 through 524 removed outlier: 3.660A pdb=" N ILE B 515 " --> pdb=" O ASN B 511 " (cutoff:3.500A) Proline residue: B 518 - end of helix removed outlier: 4.013A pdb=" N SER B 524 " --> pdb=" O THR B 520 " (cutoff:3.500A) Processing helix chain 'B' and resid 533 through 542 removed outlier: 3.947A pdb=" N TYR B 542 " --> pdb=" O ILE B 538 " (cutoff:3.500A) Processing helix chain 'B' and resid 546 through 572 removed outlier: 3.780A pdb=" N GLY B 556 " --> pdb=" O LYS B 552 " (cutoff:3.500A) Processing helix chain 'B' and resid 572 through 578 removed outlier: 3.906A pdb=" N MET B 576 " --> pdb=" O TRP B 572 " (cutoff:3.500A) Processing helix chain 'A' and resid 3 through 10 Processing helix chain 'A' and resid 10 through 23 removed outlier: 4.045A pdb=" N LEU A 23 " --> pdb=" O THR A 19 " (cutoff:3.500A) Processing helix chain 'A' and resid 24 through 29 Processing helix chain 'A' and resid 32 through 51 Processing helix chain 'A' and resid 54 through 61 removed outlier: 3.552A pdb=" N LEU A 61 " --> pdb=" O VAL A 57 " (cutoff:3.500A) Processing helix chain 'A' and resid 64 through 69 removed outlier: 3.827A pdb=" N MET A 68 " --> pdb=" O LEU A 64 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N PHE A 69 " --> pdb=" O MET A 65 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 64 through 69' Processing helix chain 'A' and resid 83 through 102 removed outlier: 4.248A pdb=" N LEU A 87 " --> pdb=" O LYS A 83 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N LEU A 88 " --> pdb=" O ASP A 84 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N TRP A 102 " --> pdb=" O SER A 98 " (cutoff:3.500A) Processing helix chain 'A' and resid 103 through 117 removed outlier: 3.783A pdb=" N ARG A 107 " --> pdb=" O ASN A 103 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N GLY A 117 " --> pdb=" O VAL A 113 " (cutoff:3.500A) Processing helix chain 'A' and resid 119 through 138 removed outlier: 4.112A pdb=" N TRP A 137 " --> pdb=" O PHE A 133 " (cutoff:3.500A) Processing helix chain 'A' and resid 139 through 160 Proline residue: A 149 - end of helix Processing helix chain 'A' and resid 231 through 253 removed outlier: 3.888A pdb=" N THR A 249 " --> pdb=" O ALA A 245 " (cutoff:3.500A) Processing helix chain 'A' and resid 255 through 258 Processing helix chain 'A' and resid 259 through 273 Processing helix chain 'A' and resid 280 through 308 Proline residue: A 290 - end of helix Processing helix chain 'A' and resid 311 through 316 removed outlier: 3.508A pdb=" N PHE A 316 " --> pdb=" O PHE A 312 " (cutoff:3.500A) Processing helix chain 'A' and resid 323 through 341 removed outlier: 3.578A pdb=" N GLY A 341 " --> pdb=" O TYR A 337 " (cutoff:3.500A) Processing helix chain 'A' and resid 344 through 359 Processing helix chain 'A' and resid 384 through 394 removed outlier: 4.126A pdb=" N ILE A 392 " --> pdb=" O VAL A 388 " (cutoff:3.500A) Processing helix chain 'A' and resid 395 through 398 Processing helix chain 'A' and resid 413 through 417 removed outlier: 4.046A pdb=" N ASP A 417 " --> pdb=" O VAL A 414 " (cutoff:3.500A) Processing helix chain 'A' and resid 423 through 429 removed outlier: 3.735A pdb=" N SER A 429 " --> pdb=" O LYS A 425 " (cutoff:3.500A) Processing helix chain 'A' and resid 432 through 449 removed outlier: 3.950A pdb=" N ALA A 436 " --> pdb=" O PRO A 432 " (cutoff:3.500A) removed outlier: 4.230A pdb=" N ILE A 437 " --> pdb=" O TRP A 433 " (cutoff:3.500A) Processing helix chain 'A' and resid 453 through 460 Processing helix chain 'A' and resid 461 through 463 No H-bonds generated for 'chain 'A' and resid 461 through 463' Processing helix chain 'A' and resid 469 through 486 Processing helix chain 'A' and resid 489 through 508 Proline residue: A 499 - end of helix Proline residue: A 503 - end of helix Processing helix chain 'A' and resid 511 through 524 removed outlier: 3.668A pdb=" N ILE A 515 " --> pdb=" O ASN A 511 " (cutoff:3.500A) Proline residue: A 518 - end of helix removed outlier: 4.022A pdb=" N SER A 524 " --> pdb=" O THR A 520 " (cutoff:3.500A) Processing helix chain 'A' and resid 533 through 542 removed outlier: 3.902A pdb=" N TYR A 542 " --> pdb=" O ILE A 538 " (cutoff:3.500A) Processing helix chain 'A' and resid 546 through 572 removed outlier: 3.779A pdb=" N GLY A 556 " --> pdb=" O LYS A 552 " (cutoff:3.500A) Processing helix chain 'A' and resid 572 through 578 removed outlier: 3.908A pdb=" N MET A 576 " --> pdb=" O TRP A 572 " (cutoff:3.500A) 498 hydrogen bonds defined for protein. 1476 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: 1.08 Time building geometry restraints manager: 0.83 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 2284 1.34 - 1.46: 1512 1.46 - 1.57: 4260 1.57 - 1.69: 0 1.69 - 1.81: 86 Bond restraints: 8142 Sorted by residual: bond pdb=" O4 SO4 B 601 " pdb=" S SO4 B 601 " ideal model delta sigma weight residual 1.499 1.457 0.042 2.00e-02 2.50e+03 4.37e+00 bond pdb=" O4 SO4 A 601 " pdb=" S SO4 A 601 " ideal model delta sigma weight residual 1.499 1.458 0.041 2.00e-02 2.50e+03 4.17e+00 bond pdb=" O3 SO4 B 601 " pdb=" S SO4 B 601 " ideal model delta sigma weight residual 1.499 1.459 0.040 2.00e-02 2.50e+03 4.07e+00 bond pdb=" O3 SO4 A 601 " pdb=" S SO4 A 601 " ideal model delta sigma weight residual 1.499 1.459 0.040 2.00e-02 2.50e+03 4.00e+00 bond pdb=" O1 SO4 A 601 " pdb=" S SO4 A 601 " ideal model delta sigma weight residual 1.498 1.458 0.040 2.00e-02 2.50e+03 3.98e+00 ... (remaining 8137 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.45: 10780 1.45 - 2.90: 257 2.90 - 4.36: 65 4.36 - 5.81: 25 5.81 - 7.26: 5 Bond angle restraints: 11132 Sorted by residual: angle pdb=" C SER A 452 " pdb=" CA SER A 452 " pdb=" CB SER A 452 " ideal model delta sigma weight residual 116.63 111.31 5.32 1.16e+00 7.43e-01 2.10e+01 angle pdb=" C SER B 452 " pdb=" CA SER B 452 " pdb=" CB SER B 452 " ideal model delta sigma weight residual 116.63 111.33 5.30 1.16e+00 7.43e-01 2.09e+01 angle pdb=" N GLU A 450 " pdb=" CA GLU A 450 " pdb=" C GLU A 450 " ideal model delta sigma weight residual 114.56 109.22 5.34 1.27e+00 6.20e-01 1.77e+01 angle pdb=" N GLU B 450 " pdb=" CA GLU B 450 " pdb=" C GLU B 450 " ideal model delta sigma weight residual 114.56 109.23 5.33 1.27e+00 6.20e-01 1.76e+01 angle pdb=" CA GLU A 450 " pdb=" C GLU A 450 " pdb=" N GLU A 451 " ideal model delta sigma weight residual 119.26 116.32 2.94 1.14e+00 7.69e-01 6.66e+00 ... (remaining 11127 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.52: 4127 14.52 - 29.03: 453 29.03 - 43.55: 118 43.55 - 58.07: 14 58.07 - 72.58: 6 Dihedral angle restraints: 4718 sinusoidal: 1756 harmonic: 2962 Sorted by residual: dihedral pdb=" CA TRP B 361 " pdb=" C TRP B 361 " pdb=" N PHE B 362 " pdb=" CA PHE B 362 " ideal model delta harmonic sigma weight residual 180.00 159.69 20.31 0 5.00e+00 4.00e-02 1.65e+01 dihedral pdb=" CA TRP A 361 " pdb=" C TRP A 361 " pdb=" N PHE A 362 " pdb=" CA PHE A 362 " ideal model delta harmonic sigma weight residual 180.00 159.76 20.24 0 5.00e+00 4.00e-02 1.64e+01 dihedral pdb=" CA LEU A 360 " pdb=" C LEU A 360 " pdb=" N TRP A 361 " pdb=" CA TRP A 361 " ideal model delta harmonic sigma weight residual 180.00 162.82 17.18 0 5.00e+00 4.00e-02 1.18e+01 ... (remaining 4715 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.027: 732 0.027 - 0.054: 372 0.054 - 0.081: 130 0.081 - 0.108: 81 0.108 - 0.134: 27 Chirality restraints: 1342 Sorted by residual: chirality pdb=" CA ILE A 422 " pdb=" N ILE A 422 " pdb=" C ILE A 422 " pdb=" CB ILE A 422 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.52e-01 chirality pdb=" CA ILE B 422 " pdb=" N ILE B 422 " pdb=" C ILE B 422 " pdb=" CB ILE B 422 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.40e-01 chirality pdb=" CA GLN B 157 " pdb=" N GLN B 157 " pdb=" C GLN B 157 " pdb=" CB GLN B 157 " both_signs ideal model delta sigma weight residual False 2.51 2.38 0.13 2.00e-01 2.50e+01 4.27e-01 ... (remaining 1339 not shown) Planarity restraints: 1326 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU A 24 " -0.041 5.00e-02 4.00e+02 6.27e-02 6.28e+00 pdb=" N PRO A 25 " 0.108 5.00e-02 4.00e+02 pdb=" CA PRO A 25 " -0.032 5.00e-02 4.00e+02 pdb=" CD PRO A 25 " -0.035 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU B 24 " 0.041 5.00e-02 4.00e+02 6.22e-02 6.20e+00 pdb=" N PRO B 25 " -0.108 5.00e-02 4.00e+02 pdb=" CA PRO B 25 " 0.032 5.00e-02 4.00e+02 pdb=" CD PRO B 25 " 0.035 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C MET A 72 " 0.035 5.00e-02 4.00e+02 5.29e-02 4.47e+00 pdb=" N PRO A 73 " -0.091 5.00e-02 4.00e+02 pdb=" CA PRO A 73 " 0.028 5.00e-02 4.00e+02 pdb=" CD PRO A 73 " 0.029 5.00e-02 4.00e+02 ... (remaining 1323 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 771 2.74 - 3.28: 8360 3.28 - 3.82: 13396 3.82 - 4.36: 15038 4.36 - 4.90: 26476 Nonbonded interactions: 64041 Sorted by model distance: nonbonded pdb=" O CYS A 449 " pdb=" OG SER A 455 " model vdw 2.201 3.040 nonbonded pdb=" O CYS B 449 " pdb=" OG SER B 455 " model vdw 2.203 3.040 nonbonded pdb=" O MET B 136 " pdb=" OG1 THR B 255 " model vdw 2.355 3.040 nonbonded pdb=" O MET A 136 " pdb=" OG1 THR A 255 " model vdw 2.357 3.040 nonbonded pdb=" O LEU A 138 " pdb="NA NA A 602 " model vdw 2.361 2.470 ... (remaining 64036 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: 0.02 Found NCS groups: ncs_group { reference = chain 'B' selection = chain 'A' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.520 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 0.120 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 8.580 Find NCS groups from input model: 0.060 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.070 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 12.420 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8207 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 : 0.003 0.049 8142 Z= 0.146 Angle : 0.606 7.259 11132 Z= 0.320 Chirality : 0.042 0.134 1342 Planarity : 0.006 0.063 1326 Dihedral : 13.091 72.582 2794 Min Nonbonded Distance : 2.201 Molprobity Statistics. All-atom Clashscore : 8.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.70 % Favored : 95.30 % Rotamer: Outliers : 0.00 % Allowed : 0.12 % Favored : 99.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.63 (0.29), residues: 1000 helix: 2.10 (0.20), residues: 684 sheet: None (None), residues: 0 loop : -1.29 (0.39), residues: 316 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 277 TYR 0.010 0.001 TYR A 81 PHE 0.014 0.001 PHE B 287 TRP 0.022 0.001 TRP B 433 HIS 0.005 0.001 HIS A 544 Details of bonding type rmsd covalent geometry : bond 0.00330 ( 8142) covalent geometry : angle 0.60640 (11132) hydrogen bonds : bond 0.12072 ( 498) hydrogen bonds : angle 4.60006 ( 1476) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2000 Ramachandran restraints generated. 1000 Oldfield, 0 Emsley, 1000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2000 Ramachandran restraints generated. 1000 Oldfield, 0 Emsley, 1000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 876 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 129 time to evaluate : 0.258 Fit side-chains REVERT: B 375 LEU cc_start: 0.6527 (tp) cc_final: 0.6310 (tp) outliers start: 0 outliers final: 0 residues processed: 129 average time/residue: 0.0709 time to fit residues: 13.3524 Evaluate side-chains 115 residues out of total 876 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 115 time to evaluate : 0.220 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 49 optimal weight: 0.0970 chunk 97 optimal weight: 5.9990 chunk 53 optimal weight: 5.9990 chunk 5 optimal weight: 8.9990 chunk 33 optimal weight: 6.9990 chunk 65 optimal weight: 0.9980 chunk 62 optimal weight: 0.7980 chunk 51 optimal weight: 0.8980 chunk 38 optimal weight: 0.2980 chunk 61 optimal weight: 0.9990 chunk 45 optimal weight: 0.0770 overall best weight: 0.4336 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 536 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 490 ASN A 544 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3871 r_free = 0.3871 target = 0.141462 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3497 r_free = 0.3497 target = 0.112419 restraints weight = 13748.788| |-----------------------------------------------------------------------------| r_work (start): 0.3492 rms_B_bonded: 2.61 r_work: 0.3362 rms_B_bonded: 3.59 restraints_weight: 0.5000 r_work (final): 0.3362 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8382 moved from start: 0.0897 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 8142 Z= 0.115 Angle : 0.556 8.050 11132 Z= 0.279 Chirality : 0.040 0.139 1342 Planarity : 0.006 0.063 1326 Dihedral : 4.039 21.144 1054 Min Nonbonded Distance : 2.323 Molprobity Statistics. All-atom Clashscore : 6.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.40 % Favored : 95.60 % Rotamer: Outliers : 0.70 % Allowed : 9.51 % Favored : 89.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.71 (0.29), residues: 1000 helix: 2.12 (0.20), residues: 692 sheet: None (None), residues: 0 loop : -1.24 (0.40), residues: 308 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 277 TYR 0.009 0.001 TYR B 81 PHE 0.011 0.001 PHE B 287 TRP 0.010 0.001 TRP B 572 HIS 0.014 0.002 HIS B 544 Details of bonding type rmsd covalent geometry : bond 0.00247 ( 8142) covalent geometry : angle 0.55615 (11132) hydrogen bonds : bond 0.03959 ( 498) hydrogen bonds : angle 3.84001 ( 1476) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2000 Ramachandran restraints generated. 1000 Oldfield, 0 Emsley, 1000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2000 Ramachandran restraints generated. 1000 Oldfield, 0 Emsley, 1000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 876 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 116 time to evaluate : 0.210 Fit side-chains REVERT: B 390 LEU cc_start: 0.9071 (mt) cc_final: 0.8814 (mt) outliers start: 6 outliers final: 2 residues processed: 119 average time/residue: 0.0645 time to fit residues: 11.4085 Evaluate side-chains 117 residues out of total 876 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 115 time to evaluate : 0.309 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 112 MET Chi-restraints excluded: chain A residue 112 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 41 optimal weight: 0.9990 chunk 62 optimal weight: 4.9990 chunk 97 optimal weight: 0.9990 chunk 9 optimal weight: 2.9990 chunk 71 optimal weight: 0.9980 chunk 78 optimal weight: 0.0470 chunk 98 optimal weight: 2.9990 chunk 51 optimal weight: 1.9990 chunk 39 optimal weight: 0.9980 chunk 73 optimal weight: 0.6980 chunk 68 optimal weight: 0.7980 overall best weight: 0.7078 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 536 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 544 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3850 r_free = 0.3850 target = 0.139798 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.110451 restraints weight = 13637.033| |-----------------------------------------------------------------------------| r_work (start): 0.3478 rms_B_bonded: 2.59 r_work: 0.3356 rms_B_bonded: 3.51 restraints_weight: 0.5000 r_work (final): 0.3356 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8405 moved from start: 0.1173 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 8142 Z= 0.117 Angle : 0.538 8.205 11132 Z= 0.270 Chirality : 0.040 0.135 1342 Planarity : 0.005 0.060 1326 Dihedral : 3.985 20.980 1054 Min Nonbonded Distance : 2.297 Molprobity Statistics. All-atom Clashscore : 6.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.80 % Favored : 95.20 % Rotamer: Outliers : 1.28 % Allowed : 12.18 % Favored : 86.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.73 (0.28), residues: 1000 helix: 2.12 (0.20), residues: 694 sheet: None (None), residues: 0 loop : -1.22 (0.39), residues: 306 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 272 TYR 0.008 0.001 TYR B 81 PHE 0.013 0.001 PHE B 527 TRP 0.009 0.001 TRP B 572 HIS 0.007 0.001 HIS B 544 Details of bonding type rmsd covalent geometry : bond 0.00269 ( 8142) covalent geometry : angle 0.53751 (11132) hydrogen bonds : bond 0.03703 ( 498) hydrogen bonds : angle 3.68947 ( 1476) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2000 Ramachandran restraints generated. 1000 Oldfield, 0 Emsley, 1000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2000 Ramachandran restraints generated. 1000 Oldfield, 0 Emsley, 1000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 876 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 123 time to evaluate : 0.300 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 335 GLN cc_start: 0.8185 (pp30) cc_final: 0.7922 (pp30) REVERT: B 375 LEU cc_start: 0.6555 (tp) cc_final: 0.6347 (tp) REVERT: A 335 GLN cc_start: 0.8194 (pp30) cc_final: 0.7925 (pp30) REVERT: A 375 LEU cc_start: 0.6554 (tp) cc_final: 0.6336 (tp) outliers start: 11 outliers final: 7 residues processed: 125 average time/residue: 0.0660 time to fit residues: 12.2989 Evaluate side-chains 121 residues out of total 876 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 114 time to evaluate : 0.319 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 112 MET Chi-restraints excluded: chain B residue 157 GLN Chi-restraints excluded: chain B residue 158 ILE Chi-restraints excluded: chain B residue 394 LEU Chi-restraints excluded: chain A residue 112 MET Chi-restraints excluded: chain A residue 157 GLN Chi-restraints excluded: chain A residue 158 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 61 optimal weight: 2.9990 chunk 79 optimal weight: 7.9990 chunk 74 optimal weight: 10.0000 chunk 26 optimal weight: 4.9990 chunk 37 optimal weight: 0.8980 chunk 69 optimal weight: 1.9990 chunk 32 optimal weight: 2.9990 chunk 24 optimal weight: 7.9990 chunk 45 optimal weight: 0.0270 chunk 44 optimal weight: 0.4980 chunk 88 optimal weight: 8.9990 overall best weight: 1.2842 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 536 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3810 r_free = 0.3810 target = 0.136769 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.107636 restraints weight = 14010.135| |-----------------------------------------------------------------------------| r_work (start): 0.3397 rms_B_bonded: 2.57 r_work: 0.3277 rms_B_bonded: 3.45 restraints_weight: 0.5000 r_work (final): 0.3277 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8457 moved from start: 0.1405 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 8142 Z= 0.153 Angle : 0.568 9.163 11132 Z= 0.284 Chirality : 0.041 0.143 1342 Planarity : 0.005 0.060 1326 Dihedral : 4.119 21.823 1054 Min Nonbonded Distance : 2.272 Molprobity Statistics. All-atom Clashscore : 7.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.40 % Favored : 95.60 % Rotamer: Outliers : 1.86 % Allowed : 14.73 % Favored : 83.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.65 (0.28), residues: 1000 helix: 2.07 (0.20), residues: 692 sheet: None (None), residues: 0 loop : -1.23 (0.39), residues: 308 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 237 TYR 0.006 0.001 TYR B 81 PHE 0.018 0.001 PHE A 527 TRP 0.011 0.001 TRP A 424 HIS 0.003 0.001 HIS B 544 Details of bonding type rmsd covalent geometry : bond 0.00368 ( 8142) covalent geometry : angle 0.56823 (11132) hydrogen bonds : bond 0.04019 ( 498) hydrogen bonds : angle 3.71931 ( 1476) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2000 Ramachandran restraints generated. 1000 Oldfield, 0 Emsley, 1000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2000 Ramachandran restraints generated. 1000 Oldfield, 0 Emsley, 1000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 876 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 122 time to evaluate : 0.289 Fit side-chains revert: symmetry clash REVERT: B 335 GLN cc_start: 0.8255 (pp30) cc_final: 0.7934 (pp30) REVERT: A 375 LEU cc_start: 0.6723 (tp) cc_final: 0.6522 (tp) outliers start: 16 outliers final: 4 residues processed: 130 average time/residue: 0.0743 time to fit residues: 13.9156 Evaluate side-chains 119 residues out of total 876 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 115 time to evaluate : 0.287 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 112 MET Chi-restraints excluded: chain B residue 157 GLN Chi-restraints excluded: chain B residue 394 LEU Chi-restraints excluded: chain A residue 112 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 47 optimal weight: 2.9990 chunk 84 optimal weight: 2.9990 chunk 10 optimal weight: 1.9990 chunk 66 optimal weight: 8.9990 chunk 54 optimal weight: 0.9980 chunk 4 optimal weight: 0.9980 chunk 14 optimal weight: 0.5980 chunk 77 optimal weight: 0.6980 chunk 85 optimal weight: 0.2980 chunk 50 optimal weight: 5.9990 chunk 93 optimal weight: 0.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3830 r_free = 0.3830 target = 0.138374 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.108796 restraints weight = 13929.226| |-----------------------------------------------------------------------------| r_work (start): 0.3445 rms_B_bonded: 2.60 r_work: 0.3315 rms_B_bonded: 3.60 restraints_weight: 0.5000 r_work (final): 0.3315 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8446 moved from start: 0.1514 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 8142 Z= 0.117 Angle : 0.540 8.337 11132 Z= 0.271 Chirality : 0.040 0.140 1342 Planarity : 0.005 0.060 1326 Dihedral : 4.055 21.893 1054 Min Nonbonded Distance : 2.279 Molprobity Statistics. All-atom Clashscore : 7.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.70 % Favored : 95.30 % Rotamer: Outliers : 1.28 % Allowed : 15.78 % Favored : 82.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.81 (0.28), residues: 1000 helix: 2.20 (0.20), residues: 694 sheet: None (None), residues: 0 loop : -1.25 (0.39), residues: 306 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 237 TYR 0.006 0.001 TYR B 81 PHE 0.010 0.001 PHE A 527 TRP 0.011 0.001 TRP B 572 HIS 0.004 0.001 HIS A 544 Details of bonding type rmsd covalent geometry : bond 0.00268 ( 8142) covalent geometry : angle 0.54016 (11132) hydrogen bonds : bond 0.03618 ( 498) hydrogen bonds : angle 3.64965 ( 1476) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2000 Ramachandran restraints generated. 1000 Oldfield, 0 Emsley, 1000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2000 Ramachandran restraints generated. 1000 Oldfield, 0 Emsley, 1000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 876 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 120 time to evaluate : 0.312 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 375 LEU cc_start: 0.6729 (tp) cc_final: 0.6527 (tp) REVERT: A 458 ILE cc_start: 0.9398 (mm) cc_final: 0.9092 (tt) outliers start: 11 outliers final: 7 residues processed: 127 average time/residue: 0.0695 time to fit residues: 13.1073 Evaluate side-chains 122 residues out of total 876 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 115 time to evaluate : 0.253 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 112 MET Chi-restraints excluded: chain B residue 157 GLN Chi-restraints excluded: chain B residue 394 LEU Chi-restraints excluded: chain A residue 112 MET Chi-restraints excluded: chain A residue 157 GLN Chi-restraints excluded: chain A residue 158 ILE Chi-restraints excluded: chain A residue 394 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 65 optimal weight: 0.8980 chunk 0 optimal weight: 10.0000 chunk 91 optimal weight: 1.9990 chunk 9 optimal weight: 1.9990 chunk 48 optimal weight: 0.7980 chunk 45 optimal weight: 1.9990 chunk 47 optimal weight: 0.7980 chunk 50 optimal weight: 0.8980 chunk 87 optimal weight: 0.8980 chunk 27 optimal weight: 0.7980 chunk 16 optimal weight: 2.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3829 r_free = 0.3829 target = 0.138176 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.108644 restraints weight = 13778.051| |-----------------------------------------------------------------------------| r_work (start): 0.3443 rms_B_bonded: 2.58 r_work: 0.3320 rms_B_bonded: 3.55 restraints_weight: 0.5000 r_work (final): 0.3320 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8442 moved from start: 0.1611 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 8142 Z= 0.124 Angle : 0.567 8.305 11132 Z= 0.283 Chirality : 0.040 0.147 1342 Planarity : 0.005 0.060 1326 Dihedral : 4.020 21.726 1054 Min Nonbonded Distance : 2.267 Molprobity Statistics. All-atom Clashscore : 7.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.60 % Favored : 95.40 % Rotamer: Outliers : 1.62 % Allowed : 15.78 % Favored : 82.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.80 (0.28), residues: 1000 helix: 2.22 (0.20), residues: 696 sheet: None (None), residues: 0 loop : -1.34 (0.39), residues: 304 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 237 TYR 0.007 0.001 TYR B 379 PHE 0.012 0.001 PHE A 527 TRP 0.010 0.001 TRP B 424 HIS 0.003 0.001 HIS A 544 Details of bonding type rmsd covalent geometry : bond 0.00287 ( 8142) covalent geometry : angle 0.56682 (11132) hydrogen bonds : bond 0.03597 ( 498) hydrogen bonds : angle 3.60743 ( 1476) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2000 Ramachandran restraints generated. 1000 Oldfield, 0 Emsley, 1000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2000 Ramachandran restraints generated. 1000 Oldfield, 0 Emsley, 1000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 876 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 115 time to evaluate : 0.284 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 375 LEU cc_start: 0.6747 (tp) cc_final: 0.6546 (tp) REVERT: A 458 ILE cc_start: 0.9412 (mm) cc_final: 0.9094 (tt) outliers start: 14 outliers final: 8 residues processed: 125 average time/residue: 0.0677 time to fit residues: 12.5616 Evaluate side-chains 119 residues out of total 876 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 111 time to evaluate : 0.204 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 112 MET Chi-restraints excluded: chain B residue 157 GLN Chi-restraints excluded: chain B residue 158 ILE Chi-restraints excluded: chain B residue 394 LEU Chi-restraints excluded: chain A residue 112 MET Chi-restraints excluded: chain A residue 157 GLN Chi-restraints excluded: chain A residue 158 ILE Chi-restraints excluded: chain A residue 394 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 1 optimal weight: 0.0020 chunk 43 optimal weight: 0.9990 chunk 54 optimal weight: 0.6980 chunk 47 optimal weight: 2.9990 chunk 61 optimal weight: 0.8980 chunk 99 optimal weight: 0.0470 chunk 34 optimal weight: 0.8980 chunk 92 optimal weight: 0.9980 chunk 58 optimal weight: 1.9990 chunk 46 optimal weight: 0.9980 chunk 26 optimal weight: 0.3980 overall best weight: 0.4086 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 544 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3853 r_free = 0.3853 target = 0.140043 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.110877 restraints weight = 13870.111| |-----------------------------------------------------------------------------| r_work (start): 0.3474 rms_B_bonded: 2.59 r_work: 0.3347 rms_B_bonded: 3.60 restraints_weight: 0.5000 r_work (final): 0.3347 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8408 moved from start: 0.1719 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 8142 Z= 0.107 Angle : 0.551 7.423 11132 Z= 0.274 Chirality : 0.040 0.154 1342 Planarity : 0.005 0.061 1326 Dihedral : 3.953 21.315 1054 Min Nonbonded Distance : 2.285 Molprobity Statistics. All-atom Clashscore : 7.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.80 % Favored : 95.20 % Rotamer: Outliers : 1.97 % Allowed : 15.20 % Favored : 82.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.74 (0.28), residues: 1000 helix: 2.18 (0.20), residues: 706 sheet: None (None), residues: 0 loop : -1.53 (0.38), residues: 294 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG B 237 TYR 0.007 0.001 TYR B 379 PHE 0.008 0.001 PHE B 287 TRP 0.011 0.001 TRP B 572 HIS 0.007 0.001 HIS B 544 Details of bonding type rmsd covalent geometry : bond 0.00231 ( 8142) covalent geometry : angle 0.55084 (11132) hydrogen bonds : bond 0.03313 ( 498) hydrogen bonds : angle 3.57085 ( 1476) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2000 Ramachandran restraints generated. 1000 Oldfield, 0 Emsley, 1000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2000 Ramachandran restraints generated. 1000 Oldfield, 0 Emsley, 1000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 876 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 115 time to evaluate : 0.337 Fit side-chains revert: symmetry clash REVERT: A 375 LEU cc_start: 0.6693 (tp) cc_final: 0.6489 (tp) REVERT: A 458 ILE cc_start: 0.9408 (mm) cc_final: 0.9080 (tt) outliers start: 17 outliers final: 13 residues processed: 126 average time/residue: 0.0642 time to fit residues: 12.2131 Evaluate side-chains 123 residues out of total 876 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 110 time to evaluate : 0.273 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 23 LEU Chi-restraints excluded: chain B residue 28 ILE Chi-restraints excluded: chain B residue 112 MET Chi-restraints excluded: chain B residue 158 ILE Chi-restraints excluded: chain B residue 391 LEU Chi-restraints excluded: chain B residue 394 LEU Chi-restraints excluded: chain B residue 435 ILE Chi-restraints excluded: chain A residue 23 LEU Chi-restraints excluded: chain A residue 28 ILE Chi-restraints excluded: chain A residue 112 MET Chi-restraints excluded: chain A residue 157 GLN Chi-restraints excluded: chain A residue 158 ILE Chi-restraints excluded: chain A residue 394 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 96 optimal weight: 5.9990 chunk 18 optimal weight: 0.7980 chunk 24 optimal weight: 6.9990 chunk 94 optimal weight: 3.9990 chunk 12 optimal weight: 0.9990 chunk 22 optimal weight: 0.5980 chunk 2 optimal weight: 3.9990 chunk 75 optimal weight: 0.9980 chunk 45 optimal weight: 0.0970 chunk 47 optimal weight: 0.7980 chunk 81 optimal weight: 0.9990 overall best weight: 0.6578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 544 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3848 r_free = 0.3848 target = 0.139469 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.110302 restraints weight = 13892.483| |-----------------------------------------------------------------------------| r_work (start): 0.3466 rms_B_bonded: 2.59 r_work: 0.3338 rms_B_bonded: 3.60 restraints_weight: 0.5000 r_work (final): 0.3338 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8420 moved from start: 0.1788 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 8142 Z= 0.114 Angle : 0.550 7.523 11132 Z= 0.274 Chirality : 0.040 0.149 1342 Planarity : 0.005 0.060 1326 Dihedral : 3.936 21.065 1054 Min Nonbonded Distance : 2.270 Molprobity Statistics. All-atom Clashscore : 7.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.80 % Favored : 95.20 % Rotamer: Outliers : 1.97 % Allowed : 15.20 % Favored : 82.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.72 (0.28), residues: 1000 helix: 2.17 (0.20), residues: 706 sheet: None (None), residues: 0 loop : -1.54 (0.38), residues: 294 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 237 TYR 0.007 0.001 TYR A 379 PHE 0.011 0.001 PHE B 527 TRP 0.010 0.001 TRP A 572 HIS 0.007 0.001 HIS B 544 Details of bonding type rmsd covalent geometry : bond 0.00261 ( 8142) covalent geometry : angle 0.54981 (11132) hydrogen bonds : bond 0.03436 ( 498) hydrogen bonds : angle 3.56032 ( 1476) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2000 Ramachandran restraints generated. 1000 Oldfield, 0 Emsley, 1000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2000 Ramachandran restraints generated. 1000 Oldfield, 0 Emsley, 1000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 876 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 111 time to evaluate : 0.312 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 375 LEU cc_start: 0.6728 (tp) cc_final: 0.6523 (tp) outliers start: 17 outliers final: 13 residues processed: 122 average time/residue: 0.0641 time to fit residues: 11.8111 Evaluate side-chains 120 residues out of total 876 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 107 time to evaluate : 0.268 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 23 LEU Chi-restraints excluded: chain B residue 28 ILE Chi-restraints excluded: chain B residue 112 MET Chi-restraints excluded: chain B residue 157 GLN Chi-restraints excluded: chain B residue 158 ILE Chi-restraints excluded: chain B residue 391 LEU Chi-restraints excluded: chain B residue 394 LEU Chi-restraints excluded: chain A residue 23 LEU Chi-restraints excluded: chain A residue 28 ILE Chi-restraints excluded: chain A residue 112 MET Chi-restraints excluded: chain A residue 157 GLN Chi-restraints excluded: chain A residue 158 ILE Chi-restraints excluded: chain A residue 394 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 88 optimal weight: 7.9990 chunk 81 optimal weight: 0.9980 chunk 46 optimal weight: 6.9990 chunk 6 optimal weight: 0.9990 chunk 61 optimal weight: 0.6980 chunk 95 optimal weight: 0.7980 chunk 71 optimal weight: 2.9990 chunk 2 optimal weight: 0.9980 chunk 96 optimal weight: 0.8980 chunk 52 optimal weight: 0.9990 chunk 69 optimal weight: 0.6980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 544 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3842 r_free = 0.3842 target = 0.138803 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.109674 restraints weight = 13932.905| |-----------------------------------------------------------------------------| r_work (start): 0.3456 rms_B_bonded: 2.58 r_work: 0.3335 rms_B_bonded: 3.54 restraints_weight: 0.5000 r_work (final): 0.3335 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8428 moved from start: 0.1828 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 8142 Z= 0.122 Angle : 0.557 7.858 11132 Z= 0.278 Chirality : 0.041 0.158 1342 Planarity : 0.005 0.060 1326 Dihedral : 3.957 21.066 1054 Min Nonbonded Distance : 2.262 Molprobity Statistics. All-atom Clashscore : 7.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.90 % Favored : 95.10 % Rotamer: Outliers : 1.86 % Allowed : 15.08 % Favored : 83.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.80 (0.28), residues: 1000 helix: 2.24 (0.20), residues: 696 sheet: None (None), residues: 0 loop : -1.39 (0.38), residues: 304 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 237 TYR 0.007 0.001 TYR A 379 PHE 0.011 0.001 PHE A 527 TRP 0.009 0.001 TRP A 572 HIS 0.007 0.001 HIS B 544 Details of bonding type rmsd covalent geometry : bond 0.00286 ( 8142) covalent geometry : angle 0.55679 (11132) hydrogen bonds : bond 0.03527 ( 498) hydrogen bonds : angle 3.59535 ( 1476) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2000 Ramachandran restraints generated. 1000 Oldfield, 0 Emsley, 1000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2000 Ramachandran restraints generated. 1000 Oldfield, 0 Emsley, 1000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 876 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 107 time to evaluate : 0.311 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 375 LEU cc_start: 0.6729 (tp) cc_final: 0.6528 (tp) outliers start: 16 outliers final: 14 residues processed: 117 average time/residue: 0.0692 time to fit residues: 12.1646 Evaluate side-chains 121 residues out of total 876 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 107 time to evaluate : 0.253 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 23 LEU Chi-restraints excluded: chain B residue 28 ILE Chi-restraints excluded: chain B residue 112 MET Chi-restraints excluded: chain B residue 157 GLN Chi-restraints excluded: chain B residue 158 ILE Chi-restraints excluded: chain B residue 391 LEU Chi-restraints excluded: chain B residue 394 LEU Chi-restraints excluded: chain B residue 528 LEU Chi-restraints excluded: chain A residue 23 LEU Chi-restraints excluded: chain A residue 28 ILE Chi-restraints excluded: chain A residue 112 MET Chi-restraints excluded: chain A residue 157 GLN Chi-restraints excluded: chain A residue 158 ILE Chi-restraints excluded: chain A residue 394 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 43 optimal weight: 0.7980 chunk 23 optimal weight: 0.6980 chunk 55 optimal weight: 0.9990 chunk 96 optimal weight: 5.9990 chunk 69 optimal weight: 0.9990 chunk 77 optimal weight: 2.9990 chunk 62 optimal weight: 0.9990 chunk 0 optimal weight: 10.0000 chunk 51 optimal weight: 0.9980 chunk 68 optimal weight: 0.9980 chunk 61 optimal weight: 0.9980 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 335 GLN ** B 544 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3829 r_free = 0.3829 target = 0.137536 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.108062 restraints weight = 13825.066| |-----------------------------------------------------------------------------| r_work (start): 0.3440 rms_B_bonded: 2.58 r_work: 0.3323 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work (final): 0.3323 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8444 moved from start: 0.1871 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 8142 Z= 0.127 Angle : 0.563 8.060 11132 Z= 0.281 Chirality : 0.041 0.153 1342 Planarity : 0.005 0.060 1326 Dihedral : 3.992 21.269 1054 Min Nonbonded Distance : 2.255 Molprobity Statistics. All-atom Clashscore : 7.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.90 % Favored : 95.10 % Rotamer: Outliers : 2.09 % Allowed : 14.97 % Favored : 82.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.78 (0.28), residues: 1000 helix: 2.23 (0.20), residues: 696 sheet: None (None), residues: 0 loop : -1.40 (0.38), residues: 304 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 237 TYR 0.007 0.001 TYR B 379 PHE 0.012 0.001 PHE A 527 TRP 0.009 0.001 TRP A 424 HIS 0.007 0.001 HIS B 544 Details of bonding type rmsd covalent geometry : bond 0.00299 ( 8142) covalent geometry : angle 0.56264 (11132) hydrogen bonds : bond 0.03635 ( 498) hydrogen bonds : angle 3.60645 ( 1476) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2000 Ramachandran restraints generated. 1000 Oldfield, 0 Emsley, 1000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2000 Ramachandran restraints generated. 1000 Oldfield, 0 Emsley, 1000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 876 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 113 time to evaluate : 0.299 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 375 LEU cc_start: 0.6780 (tp) cc_final: 0.6479 (tp) REVERT: B 447 ASP cc_start: 0.8345 (t0) cc_final: 0.7969 (t0) REVERT: A 375 LEU cc_start: 0.6746 (tp) cc_final: 0.6545 (tp) REVERT: A 447 ASP cc_start: 0.8322 (t0) cc_final: 0.7954 (t0) outliers start: 18 outliers final: 13 residues processed: 125 average time/residue: 0.0709 time to fit residues: 13.1978 Evaluate side-chains 125 residues out of total 876 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 112 time to evaluate : 0.309 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 23 LEU Chi-restraints excluded: chain B residue 28 ILE Chi-restraints excluded: chain B residue 112 MET Chi-restraints excluded: chain B residue 157 GLN Chi-restraints excluded: chain B residue 391 LEU Chi-restraints excluded: chain B residue 394 LEU Chi-restraints excluded: chain B residue 528 LEU Chi-restraints excluded: chain A residue 23 LEU Chi-restraints excluded: chain A residue 28 ILE Chi-restraints excluded: chain A residue 112 MET Chi-restraints excluded: chain A residue 157 GLN Chi-restraints excluded: chain A residue 158 ILE Chi-restraints excluded: chain A residue 394 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 49 optimal weight: 0.0000 chunk 11 optimal weight: 2.9990 chunk 43 optimal weight: 0.7980 chunk 62 optimal weight: 2.9990 chunk 70 optimal weight: 0.9980 chunk 98 optimal weight: 2.9990 chunk 29 optimal weight: 0.4980 chunk 89 optimal weight: 0.9990 chunk 19 optimal weight: 2.9990 chunk 51 optimal weight: 2.9990 chunk 76 optimal weight: 0.0770 overall best weight: 0.4742 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 544 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3851 r_free = 0.3851 target = 0.139638 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.110516 restraints weight = 13873.457| |-----------------------------------------------------------------------------| r_work (start): 0.3475 rms_B_bonded: 2.58 r_work: 0.3349 rms_B_bonded: 3.57 restraints_weight: 0.5000 r_work (final): 0.3349 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8412 moved from start: 0.1928 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 8142 Z= 0.108 Angle : 0.548 7.472 11132 Z= 0.275 Chirality : 0.040 0.153 1342 Planarity : 0.005 0.061 1326 Dihedral : 3.913 20.862 1054 Min Nonbonded Distance : 2.281 Molprobity Statistics. All-atom Clashscore : 7.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.00 % Favored : 95.00 % Rotamer: Outliers : 1.74 % Allowed : 15.08 % Favored : 83.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.76 (0.28), residues: 1000 helix: 2.21 (0.20), residues: 704 sheet: None (None), residues: 0 loop : -1.52 (0.38), residues: 296 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 237 TYR 0.008 0.001 TYR A 379 PHE 0.009 0.001 PHE B 287 TRP 0.012 0.001 TRP B 572 HIS 0.006 0.001 HIS B 544 Details of bonding type rmsd covalent geometry : bond 0.00237 ( 8142) covalent geometry : angle 0.54810 (11132) hydrogen bonds : bond 0.03326 ( 498) hydrogen bonds : angle 3.56791 ( 1476) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1601.78 seconds wall clock time: 28 minutes 19.11 seconds (1699.11 seconds total)