Starting phenix.real_space_refine on Wed Jun 3 13:58:19 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9szw_55389/06_2026/9szw_55389.cif Found real_map, /net/cci-nas-00/data/ceres_data/9szw_55389/06_2026/9szw_55389.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.14 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9szw_55389/06_2026/9szw_55389.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9szw_55389/06_2026/9szw_55389.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9szw_55389/06_2026/9szw_55389.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9szw_55389/06_2026/9szw_55389.map" } resolution = 3.14 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= -0.000 sd= 0.001 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 Fe 2 7.16 5 S 10 5.16 5 C 3938 2.51 5 N 1012 2.21 5 O 1172 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 23 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6079/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 6134 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 1062 Number of conformers: 1 Conformer: "" Number of residues, atoms: 140, 1062 Classifications: {'peptide': 140} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 132} Chain: "B" Number of atoms: 1116 Number of conformers: 1 Conformer: "" Number of residues, atoms: 145, 1116 Classifications: {'peptide': 145} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 137} Chain: "C" Number of atoms: 3870 Number of conformers: 1 Conformer: "" Number of residues, atoms: 472, 3870 Classifications: {'peptide': 472} Link IDs: {'PCIS': 3, 'PTRANS': 21, 'TRANS': 447} Chain breaks: 1 Chain: "A" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'HEM': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'HEM': 1} Classifications: {'undetermined': 1} Time building chain proxies: 1.65, per 1000 atoms: 0.27 Number of scatterers: 6134 At special positions: 0 Unit cell: (104.426, 89.218, 95.3011, 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) Fe 2 26.01 S 10 16.00 O 1172 8.00 N 1012 7.00 C 3938 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=2, symmetry=0 Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 0.40 Conformation dependent library (CDL) restraints added in 316.2 milliseconds 1498 Ramachandran restraints generated. 749 Oldfield, 0 Emsley, 749 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1446 Finding SS restraints... Secondary structure from input PDB file: 30 helices and 6 sheets defined 45.6% alpha, 22.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.22 Creating SS restraints... Processing helix chain 'A' and resid 3 through 18 Processing helix chain 'A' and resid 20 through 36 removed outlier: 3.507A pdb=" N LEU A 34 " --> pdb=" O GLU A 30 " (cutoff:3.500A) Processing helix chain 'A' and resid 37 through 43 removed outlier: 3.527A pdb=" N TYR A 42 " --> pdb=" O THR A 39 " (cutoff:3.500A) Processing helix chain 'A' and resid 52 through 72 Processing helix chain 'A' and resid 75 through 80 Processing helix chain 'A' and resid 80 through 89 Processing helix chain 'A' and resid 94 through 113 removed outlier: 4.263A pdb=" N PHE A 98 " --> pdb=" O ASP A 94 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N LYS A 99 " --> pdb=" O PRO A 95 " (cutoff:3.500A) Processing helix chain 'A' and resid 118 through 138 Processing helix chain 'B' and resid 4 through 16 Processing helix chain 'B' and resid 22 through 35 Processing helix chain 'B' and resid 36 through 42 Processing helix chain 'B' and resid 50 through 56 Processing helix chain 'B' and resid 57 through 75 removed outlier: 3.513A pdb=" N LYS B 65 " --> pdb=" O LYS B 61 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N LYS B 66 " --> pdb=" O ALA B 62 " (cutoff:3.500A) Processing helix chain 'B' and resid 80 through 85 Processing helix chain 'B' and resid 85 through 95 removed outlier: 3.583A pdb=" N CYS B 93 " --> pdb=" O SER B 89 " (cutoff:3.500A) Processing helix chain 'B' and resid 99 through 119 removed outlier: 3.923A pdb=" N PHE B 103 " --> pdb=" O ASP B 99 " (cutoff:3.500A) removed outlier: 4.128A pdb=" N ARG B 104 " --> pdb=" O PRO B 100 " (cutoff:3.500A) Processing helix chain 'B' and resid 120 through 122 No H-bonds generated for 'chain 'B' and resid 120 through 122' Processing helix chain 'B' and resid 123 through 142 removed outlier: 3.567A pdb=" N LYS B 132 " --> pdb=" O ALA B 128 " (cutoff:3.500A) Processing helix chain 'C' and resid 89 through 94 removed outlier: 3.650A pdb=" N ILE C 94 " --> pdb=" O LEU C 90 " (cutoff:3.500A) Processing helix chain 'C' and resid 95 through 100 removed outlier: 6.142A pdb=" N ALA C 98 " --> pdb=" O LYS C 95 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N LEU C 99 " --> pdb=" O ASP C 96 " (cutoff:3.500A) Processing helix chain 'C' and resid 124 through 129 Processing helix chain 'C' and resid 329 through 334 Processing helix chain 'C' and resid 364 through 370 Processing helix chain 'C' and resid 392 through 394 No H-bonds generated for 'chain 'C' and resid 392 through 394' Processing helix chain 'C' and resid 465 through 469 removed outlier: 3.746A pdb=" N TYR C 469 " --> pdb=" O PRO C 466 " (cutoff:3.500A) Processing helix chain 'C' and resid 471 through 487 Proline residue: C 483 - end of helix Processing helix chain 'C' and resid 489 through 501 Processing helix chain 'C' and resid 508 through 534 removed outlier: 3.653A pdb=" N LYS C 514 " --> pdb=" O ALA C 510 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N VAL C 531 " --> pdb=" O VAL C 527 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N THR C 532 " --> pdb=" O LYS C 528 " (cutoff:3.500A) Processing helix chain 'C' and resid 563 through 569 Processing helix chain 'C' and resid 590 through 592 No H-bonds generated for 'chain 'C' and resid 590 through 592' Processing sheet with id=AA1, first strand: chain 'C' and resid 109 through 112 removed outlier: 3.771A pdb=" N ALA C 144 " --> pdb=" O VAL C 189 " (cutoff:3.500A) removed outlier: 6.550A pdb=" N HIS C 182 " --> pdb=" O TYR C 175 " (cutoff:3.500A) removed outlier: 4.576A pdb=" N TYR C 175 " --> pdb=" O HIS C 182 " (cutoff:3.500A) removed outlier: 6.833A pdb=" N TYR C 184 " --> pdb=" O VAL C 173 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 114 through 117 removed outlier: 5.364A pdb=" N ASN C 211 " --> pdb=" O THR C 202 " (cutoff:3.500A) removed outlier: 6.795A pdb=" N THR C 202 " --> pdb=" O ASN C 211 " (cutoff:3.500A) removed outlier: 4.693A pdb=" N ASP C 213 " --> pdb=" O SER C 200 " (cutoff:3.500A) removed outlier: 5.871A pdb=" N SER C 200 " --> pdb=" O ASP C 213 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 349 through 352 removed outlier: 6.056A pdb=" N GLY C 389 " --> pdb=" O PRO C 374 " (cutoff:3.500A) removed outlier: 6.964A pdb=" N TYR C 423 " --> pdb=" O VAL C 413 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 354 through 357 removed outlier: 5.192A pdb=" N HIS C 448 " --> pdb=" O TYR C 443 " (cutoff:3.500A) removed outlier: 7.571A pdb=" N TYR C 443 " --> pdb=" O HIS C 448 " (cutoff:3.500A) removed outlier: 5.488A pdb=" N ASP C 450 " --> pdb=" O ILE C 441 " (cutoff:3.500A) removed outlier: 7.043A pdb=" N ILE C 441 " --> pdb=" O ASP C 450 " (cutoff:3.500A) removed outlier: 4.417A pdb=" N ASP C 452 " --> pdb=" O SER C 439 " (cutoff:3.500A) removed outlier: 5.792A pdb=" N SER C 439 " --> pdb=" O ASP C 452 " (cutoff:3.500A) removed outlier: 6.509A pdb=" N ARG C 433 " --> pdb=" O PHE C 458 " (cutoff:3.500A) removed outlier: 5.739A pdb=" N GLU C 442 " --> pdb=" O TRP C 396 " (cutoff:3.500A) removed outlier: 5.127A pdb=" N TRP C 396 " --> pdb=" O GLU C 442 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N LYS C 406 " --> pdb=" O GLU C 403 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 545 through 550 removed outlier: 5.402A pdb=" N ASP C 546 " --> pdb=" O THR C 577 " (cutoff:3.500A) removed outlier: 4.775A pdb=" N THR C 577 " --> pdb=" O ASP C 546 " (cutoff:3.500A) removed outlier: 4.164A pdb=" N PHE C 573 " --> pdb=" O ALA C 550 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N SER C 608 " --> pdb=" O THR C 617 " (cutoff:3.500A) removed outlier: 6.556A pdb=" N ILE C 619 " --> pdb=" O THR C 606 " (cutoff:3.500A) removed outlier: 5.460A pdb=" N THR C 606 " --> pdb=" O ILE C 619 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 552 through 556 removed outlier: 7.020A pdb=" N ASN C 630 " --> pdb=" O VAL C 599 " (cutoff:3.500A) removed outlier: 4.807A pdb=" N VAL C 599 " --> pdb=" O ASN C 630 " (cutoff:3.500A) removed outlier: 6.657A pdb=" N ILE C 632 " --> pdb=" O LEU C 597 " (cutoff:3.500A) removed outlier: 4.250A pdb=" N LEU C 597 " --> pdb=" O ILE C 632 " (cutoff:3.500A) removed outlier: 6.350A pdb=" N LYS C 634 " --> pdb=" O LYS C 595 " (cutoff:3.500A) 313 hydrogen bonds defined for protein. 873 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: 1.09 Time building geometry restraints manager: 0.54 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.44: 2724 1.44 - 1.67: 3547 1.67 - 1.89: 19 1.89 - 2.12: 3 2.12 - 2.34: 3 Bond restraints: 6296 Sorted by residual: bond pdb=" ND HEM B 201 " pdb="FE HEM B 201 " ideal model delta sigma weight residual 2.080 1.726 0.354 7.00e-02 2.04e+02 2.55e+01 bond pdb=" ND HEM A 201 " pdb="FE HEM A 201 " ideal model delta sigma weight residual 2.080 1.744 0.336 7.00e-02 2.04e+02 2.31e+01 bond pdb=" NB HEM A 201 " pdb="FE HEM A 201 " ideal model delta sigma weight residual 2.080 2.343 -0.263 7.00e-02 2.04e+02 1.41e+01 bond pdb=" NB HEM B 201 " pdb="FE HEM B 201 " ideal model delta sigma weight residual 2.080 2.334 -0.254 7.00e-02 2.04e+02 1.31e+01 bond pdb=" CZ ARG C 425 " pdb=" NH2 ARG C 425 " ideal model delta sigma weight residual 1.330 1.285 0.045 1.30e-02 5.92e+03 1.22e+01 ... (remaining 6291 not shown) Histogram of bond angle deviations from ideal: 0.00 - 5.39: 8530 5.39 - 10.78: 46 10.78 - 16.18: 2 16.18 - 21.57: 1 21.57 - 26.96: 2 Bond angle restraints: 8581 Sorted by residual: angle pdb=" CA THR C 489 " pdb=" C THR C 489 " pdb=" N LEU C 490 " ideal model delta sigma weight residual 115.49 122.13 -6.64 1.24e+00 6.50e-01 2.87e+01 angle pdb=" CB HIS A 20 " pdb=" CG HIS A 20 " pdb=" CD2 HIS A 20 " ideal model delta sigma weight residual 131.20 124.94 6.26 1.30e+00 5.92e-01 2.32e+01 angle pdb=" CB HIS B 143 " pdb=" CG HIS B 143 " pdb=" CD2 HIS B 143 " ideal model delta sigma weight residual 131.20 124.95 6.25 1.30e+00 5.92e-01 2.31e+01 angle pdb=" N PRO B 124 " pdb=" CA PRO B 124 " pdb=" C PRO B 124 " ideal model delta sigma weight residual 110.70 116.47 -5.77 1.22e+00 6.72e-01 2.24e+01 angle pdb=" C LEU C 597 " pdb=" N ILE C 598 " pdb=" CA ILE C 598 " ideal model delta sigma weight residual 123.19 129.04 -5.85 1.24e+00 6.50e-01 2.23e+01 ... (remaining 8576 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.08: 3434 17.08 - 34.16: 225 34.16 - 51.24: 41 51.24 - 68.32: 18 68.32 - 85.40: 14 Dihedral angle restraints: 3732 sinusoidal: 1495 harmonic: 2237 Sorted by residual: dihedral pdb=" C2B HEM B 201 " pdb=" C3B HEM B 201 " pdb=" CAB HEM B 201 " pdb=" CBB HEM B 201 " ideal model delta sinusoidal sigma weight residual 0.00 85.40 -85.40 2 1.00e+01 1.00e-02 4.77e+01 dihedral pdb=" C2B HEM A 201 " pdb=" C3B HEM A 201 " pdb=" CAB HEM A 201 " pdb=" CBB HEM A 201 " ideal model delta sinusoidal sigma weight residual 0.00 -75.27 75.27 2 1.00e+01 1.00e-02 4.49e+01 dihedral pdb=" C2C HEM A 201 " pdb=" C3C HEM A 201 " pdb=" CAC HEM A 201 " pdb=" CBC HEM A 201 " ideal model delta sinusoidal sigma weight residual -0.00 -67.33 67.33 2 1.00e+01 1.00e-02 4.09e+01 ... (remaining 3729 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.094: 649 0.094 - 0.188: 233 0.188 - 0.282: 40 0.282 - 0.376: 9 0.376 - 0.470: 2 Chirality restraints: 933 Sorted by residual: chirality pdb=" CA GLU C 533 " pdb=" N GLU C 533 " pdb=" C GLU C 533 " pdb=" CB GLU C 533 " both_signs ideal model delta sigma weight residual False 2.51 2.04 0.47 2.00e-01 2.50e+01 5.52e+00 chirality pdb=" CA ASN C 446 " pdb=" N ASN C 446 " pdb=" C ASN C 446 " pdb=" CB ASN C 446 " both_signs ideal model delta sigma weight residual False 2.51 2.12 0.39 2.00e-01 2.50e+01 3.74e+00 chirality pdb=" CA LYS C 503 " pdb=" N LYS C 503 " pdb=" C LYS C 503 " pdb=" CB LYS C 503 " both_signs ideal model delta sigma weight residual False 2.51 2.18 0.33 2.00e-01 2.50e+01 2.69e+00 ... (remaining 930 not shown) Planarity restraints: 1100 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" ND HEM A 201 " 0.004 2.00e-02 2.50e+03 7.71e-02 1.34e+02 pdb=" C1D HEM A 201 " 0.004 2.00e-02 2.50e+03 pdb=" C2D HEM A 201 " -0.063 2.00e-02 2.50e+03 pdb=" C3D HEM A 201 " 0.006 2.00e-02 2.50e+03 pdb=" C4D HEM A 201 " -0.017 2.00e-02 2.50e+03 pdb=" CAD HEM A 201 " 0.145 2.00e-02 2.50e+03 pdb=" CHA HEM A 201 " -0.074 2.00e-02 2.50e+03 pdb=" CHD HEM A 201 " 0.104 2.00e-02 2.50e+03 pdb=" CMD HEM A 201 " -0.109 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP B 15 " 0.129 2.00e-02 2.50e+03 7.14e-02 1.27e+02 pdb=" CG TRP B 15 " -0.002 2.00e-02 2.50e+03 pdb=" CD1 TRP B 15 " -0.035 2.00e-02 2.50e+03 pdb=" CD2 TRP B 15 " -0.061 2.00e-02 2.50e+03 pdb=" NE1 TRP B 15 " -0.054 2.00e-02 2.50e+03 pdb=" CE2 TRP B 15 " -0.006 2.00e-02 2.50e+03 pdb=" CE3 TRP B 15 " -0.105 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 15 " 0.082 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 15 " -0.035 2.00e-02 2.50e+03 pdb=" CH2 TRP B 15 " 0.086 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 14 " 0.148 2.00e-02 2.50e+03 7.10e-02 1.26e+02 pdb=" CG TRP A 14 " -0.043 2.00e-02 2.50e+03 pdb=" CD1 TRP A 14 " -0.052 2.00e-02 2.50e+03 pdb=" CD2 TRP A 14 " -0.059 2.00e-02 2.50e+03 pdb=" NE1 TRP A 14 " -0.028 2.00e-02 2.50e+03 pdb=" CE2 TRP A 14 " 0.006 2.00e-02 2.50e+03 pdb=" CE3 TRP A 14 " -0.091 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 14 " 0.081 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 14 " -0.026 2.00e-02 2.50e+03 pdb=" CH2 TRP A 14 " 0.064 2.00e-02 2.50e+03 ... (remaining 1097 not shown) Histogram of nonbonded interaction distances: 2.57 - 3.03: 3201 3.03 - 3.50: 6087 3.50 - 3.97: 9701 3.97 - 4.43: 10861 4.43 - 4.90: 18218 Nonbonded interactions: 48068 Sorted by model distance: nonbonded pdb=" OG SER C 176 " pdb=" OE1 GLU C 180 " model vdw 2.565 3.040 nonbonded pdb=" OG1 THR B 50 " pdb=" OE2 GLU C 445 " model vdw 2.575 3.040 nonbonded pdb=" OG SER C 394 " pdb=" OD2 ASP C 420 " model vdw 2.583 3.040 nonbonded pdb=" OD1 ASP C 353 " pdb=" OH TYR C 475 " model vdw 2.584 3.040 nonbonded pdb=" OE2 GLU C 163 " pdb=" OG SER C 190 " model vdw 2.584 3.040 ... (remaining 48063 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 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: 10.130 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: 0.140 Check model and map are aligned: 0.010 Set scattering table: 0.020 Process input model: 7.760 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.380 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.480 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8206 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 : 0.014 0.354 6298 Z= 0.701 Angle : 1.845 26.959 8581 Z= 1.182 Chirality : 0.097 0.470 933 Planarity : 0.014 0.115 1100 Dihedral : 14.050 85.400 2286 Min Nonbonded Distance : 2.565 Molprobity Statistics. All-atom Clashscore : 0.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.47 % Favored : 96.53 % Rotamer: Outliers : 0.00 % Allowed : 1.66 % Favored : 98.34 % Cbeta Deviations : 0.28 % Peptide Plane: Cis-proline : 7.89 % 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 are not related in a simple way. whole: -0.36 (0.29), residues: 749 helix: -0.51 (0.26), residues: 288 sheet: 0.43 (0.39), residues: 146 loop : -0.08 (0.36), residues: 315 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.002 ARG C 603 TYR 0.123 0.018 TYR C 512 PHE 0.055 0.011 PHE C 365 TRP 0.148 0.041 TRP A 14 HIS 0.008 0.003 HIS C 448 Details of bonding type rmsd/Z covalent geometry : bond 0.01407 / 0.70 ( 6296) covalent geometry : angle 1.84461 / 1.18 ( 8581) hydrogen bonds : bond 0.18307 / 12.68 ( 313) hydrogen bonds : angle 7.42758 / 5.53 ( 873) Misc. bond : bond 0.07229 / 3.44 ( 2) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1498 Ramachandran restraints generated. 749 Oldfield, 0 Emsley, 749 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1498 Ramachandran restraints generated. 749 Oldfield, 0 Emsley, 749 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 661 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 90 time to evaluate : 0.239 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 90 average time/residue: 0.1041 time to fit residues: 11.9034 Evaluate side-chains 54 residues out of total 661 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 54 time to evaluate : 0.261 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 49 optimal weight: 0.6980 chunk 53 optimal weight: 3.9990 chunk 5 optimal weight: 0.8980 chunk 33 optimal weight: 0.9990 chunk 65 optimal weight: 0.9980 chunk 62 optimal weight: 0.9990 chunk 51 optimal weight: 0.7980 chunk 38 optimal weight: 0.4980 chunk 61 optimal weight: 0.9980 chunk 45 optimal weight: 0.8980 chunk 74 optimal weight: 0.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 139 ASN C 115 GLN C 460 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3180 r_free = 0.3180 target = 0.069429 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2873 r_free = 0.2873 target = 0.055618 restraints weight = 16822.113| |-----------------------------------------------------------------------------| r_work (start): 0.2861 rms_B_bonded: 2.92 r_work: 0.2725 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work (final): 0.2725 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8571 moved from start: 0.2405 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 6298 Z= 0.156 Angle : 0.607 8.918 8581 Z= 0.313 Chirality : 0.044 0.149 933 Planarity : 0.004 0.046 1100 Dihedral : 8.256 86.936 827 Min Nonbonded Distance : 2.622 Molprobity Statistics. All-atom Clashscore : 2.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Rotamer: Outliers : 0.30 % Allowed : 5.60 % Favored : 94.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.89 % 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 are not related in a simple way. whole: 1.57 (0.32), residues: 749 helix: 1.90 (0.30), residues: 291 sheet: 0.50 (0.39), residues: 146 loop : 0.64 (0.40), residues: 312 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG C 616 TYR 0.018 0.002 TYR C 583 PHE 0.013 0.002 PHE C 620 TRP 0.016 0.002 TRP A 14 HIS 0.005 0.001 HIS A 103 Details of bonding type rmsd/Z covalent geometry : bond 0.00376 / 0.16 ( 6296) covalent geometry : angle 0.60700 / 0.31 ( 8581) hydrogen bonds : bond 0.03795 / 2.66 ( 313) hydrogen bonds : angle 4.95448 / 3.76 ( 873) Misc. bond : bond 0.03857 / 1.84 ( 2) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1498 Ramachandran restraints generated. 749 Oldfield, 0 Emsley, 749 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1498 Ramachandran restraints generated. 749 Oldfield, 0 Emsley, 749 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 50 residues out of total 661 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 48 time to evaluate : 0.261 Fit side-chains REVERT: B 8 LYS cc_start: 0.8234 (mtpt) cc_final: 0.7958 (mttt) REVERT: B 26 GLU cc_start: 0.8847 (tt0) cc_final: 0.8585 (tt0) REVERT: B 73 ASP cc_start: 0.8973 (t70) cc_final: 0.8721 (t0) REVERT: B 89 SER cc_start: 0.9408 (t) cc_final: 0.9151 (p) REVERT: C 533 GLU cc_start: 0.8626 (tp30) cc_final: 0.8309 (tp30) outliers start: 2 outliers final: 0 residues processed: 49 average time/residue: 0.0960 time to fit residues: 6.2202 Evaluate side-chains 44 residues out of total 661 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 44 time to evaluate : 0.264 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 14 optimal weight: 0.5980 chunk 52 optimal weight: 0.0060 chunk 26 optimal weight: 0.3980 chunk 43 optimal weight: 1.9990 chunk 11 optimal weight: 0.8980 chunk 13 optimal weight: 1.9990 chunk 17 optimal weight: 0.8980 chunk 34 optimal weight: 3.9990 chunk 30 optimal weight: 4.9990 chunk 21 optimal weight: 0.9990 chunk 27 optimal weight: 1.9990 overall best weight: 0.5596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 225 ASN ** C 639 ASN ** 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 = 0.3203 r_free = 0.3203 target = 0.070017 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2899 r_free = 0.2899 target = 0.056114 restraints weight = 16802.244| |-----------------------------------------------------------------------------| r_work (start): 0.2889 rms_B_bonded: 2.95 r_work: 0.2752 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work (final): 0.2752 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8576 moved from start: 0.2763 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.067 6298 Z= 0.119 Angle : 0.529 6.061 8581 Z= 0.267 Chirality : 0.042 0.139 933 Planarity : 0.004 0.048 1100 Dihedral : 7.121 84.437 827 Min Nonbonded Distance : 2.602 Molprobity Statistics. All-atom Clashscore : 2.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 0.91 % Allowed : 4.99 % Favored : 94.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.89 % 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 are not related in a simple way. whole: 2.20 (0.33), residues: 749 helix: 2.60 (0.31), residues: 292 sheet: 0.67 (0.41), residues: 151 loop : 0.88 (0.42), residues: 306 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 30 TYR 0.012 0.001 TYR C 512 PHE 0.012 0.001 PHE C 426 TRP 0.015 0.001 TRP A 14 HIS 0.003 0.001 HIS A 103 Details of bonding type rmsd/Z covalent geometry : bond 0.00300 / 0.12 ( 6296) covalent geometry : angle 0.52948 / 0.27 ( 8581) hydrogen bonds : bond 0.03240 / 2.26 ( 313) hydrogen bonds : angle 4.51091 / 3.44 ( 873) Misc. bond : bond 0.04888 / 2.34 ( 2) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1498 Ramachandran restraints generated. 749 Oldfield, 0 Emsley, 749 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1498 Ramachandran restraints generated. 749 Oldfield, 0 Emsley, 749 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 53 residues out of total 661 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 47 time to evaluate : 0.297 Fit side-chains REVERT: A 30 GLU cc_start: 0.9093 (tp30) cc_final: 0.8776 (tt0) REVERT: A 92 ARG cc_start: 0.7724 (mtm110) cc_final: 0.7483 (mpp-170) REVERT: B 7 GLU cc_start: 0.8545 (tp30) cc_final: 0.8159 (mm-30) REVERT: B 8 LYS cc_start: 0.8170 (mtpt) cc_final: 0.7915 (mttt) REVERT: B 26 GLU cc_start: 0.8896 (tt0) cc_final: 0.8632 (tt0) REVERT: B 89 SER cc_start: 0.9410 (t) cc_final: 0.9080 (p) REVERT: C 533 GLU cc_start: 0.8737 (tp30) cc_final: 0.8232 (tp30) outliers start: 6 outliers final: 4 residues processed: 53 average time/residue: 0.0895 time to fit residues: 6.3525 Evaluate side-chains 49 residues out of total 661 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 45 time to evaluate : 0.177 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 105 LEU Chi-restraints excluded: chain C residue 382 THR Chi-restraints excluded: chain C residue 435 VAL Chi-restraints excluded: chain C residue 606 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 44 optimal weight: 0.6980 chunk 17 optimal weight: 0.8980 chunk 5 optimal weight: 0.6980 chunk 21 optimal weight: 0.8980 chunk 35 optimal weight: 1.9990 chunk 43 optimal weight: 1.9990 chunk 31 optimal weight: 0.0770 chunk 34 optimal weight: 1.9990 chunk 74 optimal weight: 1.9990 chunk 52 optimal weight: 0.6980 chunk 36 optimal weight: 0.9990 overall best weight: 0.6138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 143 HIS ** C 639 ASN ** 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 = 0.3197 r_free = 0.3197 target = 0.069663 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2894 r_free = 0.2894 target = 0.055834 restraints weight = 16707.938| |-----------------------------------------------------------------------------| r_work (start): 0.2884 rms_B_bonded: 2.93 r_work: 0.2745 rms_B_bonded: 3.45 restraints_weight: 0.5000 r_work (final): 0.2745 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8587 moved from start: 0.2990 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.072 6298 Z= 0.123 Angle : 0.514 6.028 8581 Z= 0.258 Chirality : 0.042 0.140 933 Planarity : 0.004 0.047 1100 Dihedral : 6.989 86.879 827 Min Nonbonded Distance : 2.599 Molprobity Statistics. All-atom Clashscore : 2.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 1.51 % Allowed : 5.30 % Favored : 93.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.89 % 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 are not related in a simple way. whole: 2.31 (0.33), residues: 749 helix: 2.81 (0.31), residues: 292 sheet: 0.62 (0.41), residues: 151 loop : 0.88 (0.42), residues: 306 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 104 TYR 0.012 0.001 TYR C 512 PHE 0.011 0.001 PHE C 426 TRP 0.014 0.001 TRP A 14 HIS 0.003 0.001 HIS A 103 Details of bonding type rmsd/Z covalent geometry : bond 0.00314 / 0.12 ( 6296) covalent geometry : angle 0.51417 / 0.26 ( 8581) hydrogen bonds : bond 0.03034 / 2.12 ( 313) hydrogen bonds : angle 4.36329 / 3.32 ( 873) Misc. bond : bond 0.05060 / 2.41 ( 2) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1498 Ramachandran restraints generated. 749 Oldfield, 0 Emsley, 749 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1498 Ramachandran restraints generated. 749 Oldfield, 0 Emsley, 749 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 55 residues out of total 661 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 45 time to evaluate : 0.242 Fit side-chains REVERT: A 30 GLU cc_start: 0.9122 (tp30) cc_final: 0.8768 (tt0) REVERT: B 7 GLU cc_start: 0.8552 (tp30) cc_final: 0.8167 (mm-30) REVERT: B 8 LYS cc_start: 0.8166 (mtpt) cc_final: 0.7911 (mttt) REVERT: B 26 GLU cc_start: 0.8920 (tt0) cc_final: 0.8698 (tt0) REVERT: B 89 SER cc_start: 0.9390 (t) cc_final: 0.9042 (p) REVERT: C 381 LYS cc_start: 0.8933 (mmmt) cc_final: 0.8510 (tptp) REVERT: C 533 GLU cc_start: 0.8734 (tp30) cc_final: 0.8093 (tp30) outliers start: 10 outliers final: 5 residues processed: 52 average time/residue: 0.0740 time to fit residues: 5.4322 Evaluate side-chains 49 residues out of total 661 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 44 time to evaluate : 0.237 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 ASP Chi-restraints excluded: chain B residue 73 ASP Chi-restraints excluded: chain C residue 382 THR Chi-restraints excluded: chain C residue 435 VAL Chi-restraints excluded: chain C residue 606 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 70 optimal weight: 0.9980 chunk 12 optimal weight: 0.8980 chunk 13 optimal weight: 0.5980 chunk 38 optimal weight: 0.6980 chunk 11 optimal weight: 0.9980 chunk 24 optimal weight: 1.9990 chunk 33 optimal weight: 0.9990 chunk 31 optimal weight: 1.9990 chunk 41 optimal weight: 2.9990 chunk 37 optimal weight: 0.4980 chunk 26 optimal weight: 0.8980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 143 HIS ** C 639 ASN ** 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 = 0.3183 r_free = 0.3183 target = 0.068933 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2875 r_free = 0.2875 target = 0.054992 restraints weight = 17121.252| |-----------------------------------------------------------------------------| r_work (start): 0.2860 rms_B_bonded: 3.01 r_work: 0.2717 rms_B_bonded: 3.51 restraints_weight: 0.5000 r_work (final): 0.2717 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8582 moved from start: 0.3133 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.067 6298 Z= 0.133 Angle : 0.514 5.732 8581 Z= 0.257 Chirality : 0.042 0.142 933 Planarity : 0.004 0.043 1100 Dihedral : 6.858 87.756 827 Min Nonbonded Distance : 2.568 Molprobity Statistics. All-atom Clashscore : 2.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 1.51 % Allowed : 5.45 % Favored : 93.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.89 % 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 are not related in a simple way. whole: 2.38 (0.33), residues: 749 helix: 2.85 (0.31), residues: 293 sheet: 0.58 (0.40), residues: 155 loop : 0.97 (0.42), residues: 301 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 30 TYR 0.012 0.001 TYR C 512 PHE 0.011 0.001 PHE C 365 TRP 0.012 0.001 TRP A 14 HIS 0.003 0.001 HIS A 103 Details of bonding type rmsd/Z covalent geometry : bond 0.00341 / 0.13 ( 6296) covalent geometry : angle 0.51377 / 0.26 ( 8581) hydrogen bonds : bond 0.03013 / 2.10 ( 313) hydrogen bonds : angle 4.33067 / 3.30 ( 873) Misc. bond : bond 0.04838 / 2.31 ( 2) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1498 Ramachandran restraints generated. 749 Oldfield, 0 Emsley, 749 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1498 Ramachandran restraints generated. 749 Oldfield, 0 Emsley, 749 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 52 residues out of total 661 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 42 time to evaluate : 0.178 Fit side-chains REVERT: A 30 GLU cc_start: 0.9150 (tp30) cc_final: 0.8772 (tt0) REVERT: B 7 GLU cc_start: 0.8596 (tp30) cc_final: 0.8208 (mm-30) REVERT: B 8 LYS cc_start: 0.8145 (mtpt) cc_final: 0.7907 (mttt) REVERT: B 26 GLU cc_start: 0.8902 (tt0) cc_final: 0.8533 (tt0) REVERT: B 89 SER cc_start: 0.9371 (t) cc_final: 0.8973 (p) REVERT: B 94 ASP cc_start: 0.8457 (t0) cc_final: 0.8211 (t0) REVERT: C 381 LYS cc_start: 0.8962 (mmmt) cc_final: 0.8633 (tptp) REVERT: C 533 GLU cc_start: 0.8773 (tp30) cc_final: 0.8071 (tp30) outliers start: 10 outliers final: 9 residues processed: 50 average time/residue: 0.0776 time to fit residues: 5.4141 Evaluate side-chains 50 residues out of total 661 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 41 time to evaluate : 0.238 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 GLN Chi-restraints excluded: chain A residue 105 LEU Chi-restraints excluded: chain B residue 4 THR Chi-restraints excluded: chain B residue 73 ASP Chi-restraints excluded: chain C residue 382 THR Chi-restraints excluded: chain C residue 435 VAL Chi-restraints excluded: chain C residue 606 THR Chi-restraints excluded: chain C residue 633 VAL Chi-restraints excluded: chain C residue 637 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 22 optimal weight: 3.9990 chunk 72 optimal weight: 0.9990 chunk 35 optimal weight: 1.9990 chunk 1 optimal weight: 0.4980 chunk 74 optimal weight: 1.9990 chunk 62 optimal weight: 2.9990 chunk 69 optimal weight: 0.9990 chunk 37 optimal weight: 0.0570 chunk 67 optimal weight: 5.9990 chunk 4 optimal weight: 0.8980 chunk 3 optimal weight: 0.5980 overall best weight: 0.6100 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 639 ASN ** 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 = 0.3187 r_free = 0.3187 target = 0.069178 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2883 r_free = 0.2883 target = 0.055311 restraints weight = 16851.102| |-----------------------------------------------------------------------------| r_work (start): 0.2872 rms_B_bonded: 2.99 r_work: 0.2729 rms_B_bonded: 3.51 restraints_weight: 0.5000 r_work (final): 0.2729 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8572 moved from start: 0.3289 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 6298 Z= 0.120 Angle : 0.508 8.496 8581 Z= 0.252 Chirality : 0.041 0.137 933 Planarity : 0.004 0.042 1100 Dihedral : 6.766 89.638 827 Min Nonbonded Distance : 2.603 Molprobity Statistics. All-atom Clashscore : 2.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 1.66 % Allowed : 6.20 % Favored : 92.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.89 % 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 are not related in a simple way. whole: 2.43 (0.33), residues: 749 helix: 2.93 (0.31), residues: 292 sheet: 0.62 (0.40), residues: 150 loop : 0.95 (0.41), residues: 307 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 30 TYR 0.012 0.001 TYR C 512 PHE 0.010 0.001 PHE C 426 TRP 0.012 0.001 TRP A 14 HIS 0.003 0.001 HIS A 103 Details of bonding type rmsd/Z covalent geometry : bond 0.00309 / 0.12 ( 6296) covalent geometry : angle 0.50783 / 0.25 ( 8581) hydrogen bonds : bond 0.02876 / 2.00 ( 313) hydrogen bonds : angle 4.25527 / 3.24 ( 873) Misc. bond : bond 0.04883 / 2.35 ( 2) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1498 Ramachandran restraints generated. 749 Oldfield, 0 Emsley, 749 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1498 Ramachandran restraints generated. 749 Oldfield, 0 Emsley, 749 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 53 residues out of total 661 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 42 time to evaluate : 0.252 Fit side-chains REVERT: B 7 GLU cc_start: 0.8624 (tp30) cc_final: 0.8224 (mm-30) REVERT: B 8 LYS cc_start: 0.8148 (mtpt) cc_final: 0.7927 (mttt) REVERT: B 26 GLU cc_start: 0.8913 (tt0) cc_final: 0.8551 (tt0) REVERT: B 52 ASP cc_start: 0.8998 (m-30) cc_final: 0.8732 (m-30) REVERT: B 89 SER cc_start: 0.9411 (t) cc_final: 0.8991 (p) REVERT: B 94 ASP cc_start: 0.8530 (t0) cc_final: 0.8270 (t0) REVERT: B 101 GLU cc_start: 0.8481 (tp30) cc_final: 0.8181 (tp30) REVERT: C 381 LYS cc_start: 0.8977 (mmmt) cc_final: 0.8649 (tptp) outliers start: 11 outliers final: 8 residues processed: 51 average time/residue: 0.0900 time to fit residues: 6.1578 Evaluate side-chains 48 residues out of total 661 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 40 time to evaluate : 0.251 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 GLN Chi-restraints excluded: chain A residue 105 LEU Chi-restraints excluded: chain B residue 4 THR Chi-restraints excluded: chain B residue 73 ASP Chi-restraints excluded: chain C residue 382 THR Chi-restraints excluded: chain C residue 435 VAL Chi-restraints excluded: chain C residue 633 VAL Chi-restraints excluded: chain C residue 637 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 18 optimal weight: 0.0980 chunk 28 optimal weight: 2.9990 chunk 44 optimal weight: 0.0370 chunk 47 optimal weight: 1.9990 chunk 65 optimal weight: 0.9990 chunk 37 optimal weight: 0.7980 chunk 59 optimal weight: 0.5980 chunk 35 optimal weight: 0.6980 chunk 2 optimal weight: 1.9990 chunk 10 optimal weight: 0.7980 chunk 62 optimal weight: 2.9990 overall best weight: 0.4458 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 639 ASN ** 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 = 0.3212 r_free = 0.3212 target = 0.069972 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2903 r_free = 0.2903 target = 0.055863 restraints weight = 16907.948| |-----------------------------------------------------------------------------| r_work (start): 0.2893 rms_B_bonded: 3.02 r_work: 0.2758 rms_B_bonded: 3.44 restraints_weight: 0.5000 r_work (final): 0.2758 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8560 moved from start: 0.3391 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.067 6298 Z= 0.105 Angle : 0.503 7.598 8581 Z= 0.249 Chirality : 0.041 0.131 933 Planarity : 0.004 0.042 1100 Dihedral : 6.626 87.892 827 Min Nonbonded Distance : 2.582 Molprobity Statistics. All-atom Clashscore : 3.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 1.66 % Allowed : 6.81 % Favored : 91.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.89 % 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 are not related in a simple way. whole: 2.46 (0.33), residues: 749 helix: 2.95 (0.31), residues: 294 sheet: 0.66 (0.41), residues: 150 loop : 0.95 (0.41), residues: 305 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 104 TYR 0.012 0.001 TYR C 512 PHE 0.011 0.001 PHE C 426 TRP 0.013 0.001 TRP A 14 HIS 0.002 0.000 HIS A 103 Details of bonding type rmsd/Z covalent geometry : bond 0.00271 / 0.10 ( 6296) covalent geometry : angle 0.50286 / 0.25 ( 8581) hydrogen bonds : bond 0.02709 / 1.88 ( 313) hydrogen bonds : angle 4.17462 / 3.18 ( 873) Misc. bond : bond 0.04969 / 2.39 ( 2) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1498 Ramachandran restraints generated. 749 Oldfield, 0 Emsley, 749 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1498 Ramachandran restraints generated. 749 Oldfield, 0 Emsley, 749 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 52 residues out of total 661 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 41 time to evaluate : 0.251 Fit side-chains REVERT: B 7 GLU cc_start: 0.8608 (tp30) cc_final: 0.8219 (mm-30) REVERT: B 8 LYS cc_start: 0.8156 (mtpt) cc_final: 0.7945 (mttt) REVERT: B 26 GLU cc_start: 0.8862 (tt0) cc_final: 0.8511 (tt0) REVERT: B 52 ASP cc_start: 0.8961 (m-30) cc_final: 0.8696 (m-30) REVERT: B 89 SER cc_start: 0.9395 (t) cc_final: 0.8951 (p) REVERT: B 94 ASP cc_start: 0.8546 (t0) cc_final: 0.8296 (t0) outliers start: 11 outliers final: 10 residues processed: 50 average time/residue: 0.0796 time to fit residues: 5.6075 Evaluate side-chains 50 residues out of total 661 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 40 time to evaluate : 0.262 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 GLN Chi-restraints excluded: chain A residue 105 LEU Chi-restraints excluded: chain B residue 3 LEU Chi-restraints excluded: chain B residue 4 THR Chi-restraints excluded: chain B residue 73 ASP Chi-restraints excluded: chain B residue 143 HIS Chi-restraints excluded: chain C residue 382 THR Chi-restraints excluded: chain C residue 435 VAL Chi-restraints excluded: chain C residue 633 VAL Chi-restraints excluded: chain C residue 637 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 33 optimal weight: 0.9980 chunk 60 optimal weight: 0.6980 chunk 25 optimal weight: 1.9990 chunk 35 optimal weight: 0.9990 chunk 49 optimal weight: 0.6980 chunk 55 optimal weight: 0.0040 chunk 29 optimal weight: 4.9990 chunk 14 optimal weight: 0.8980 chunk 34 optimal weight: 0.5980 chunk 59 optimal weight: 1.9990 chunk 11 optimal weight: 2.9990 overall best weight: 0.5792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 639 ASN ** 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 = 0.3202 r_free = 0.3202 target = 0.069435 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2892 r_free = 0.2892 target = 0.055366 restraints weight = 16955.711| |-----------------------------------------------------------------------------| r_work (start): 0.2873 rms_B_bonded: 3.01 r_work: 0.2736 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work (final): 0.2736 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8574 moved from start: 0.3447 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.067 6298 Z= 0.118 Angle : 0.512 8.647 8581 Z= 0.253 Chirality : 0.041 0.135 933 Planarity : 0.004 0.042 1100 Dihedral : 6.609 86.098 827 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 3.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 1.66 % Allowed : 7.11 % Favored : 91.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.89 % 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 are not related in a simple way. whole: 2.42 (0.33), residues: 749 helix: 2.80 (0.31), residues: 300 sheet: 0.55 (0.40), residues: 156 loop : 1.09 (0.42), residues: 293 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 104 TYR 0.013 0.001 TYR C 512 PHE 0.011 0.001 PHE C 573 TRP 0.011 0.001 TRP A 14 HIS 0.003 0.001 HIS A 103 Details of bonding type rmsd/Z covalent geometry : bond 0.00306 / 0.12 ( 6296) covalent geometry : angle 0.51240 / 0.25 ( 8581) hydrogen bonds : bond 0.02791 / 1.93 ( 313) hydrogen bonds : angle 4.17775 / 3.18 ( 873) Misc. bond : bond 0.05017 / 2.42 ( 2) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1498 Ramachandran restraints generated. 749 Oldfield, 0 Emsley, 749 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1498 Ramachandran restraints generated. 749 Oldfield, 0 Emsley, 749 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 51 residues out of total 661 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 40 time to evaluate : 0.262 Fit side-chains REVERT: B 7 GLU cc_start: 0.8589 (tp30) cc_final: 0.8216 (mm-30) REVERT: B 8 LYS cc_start: 0.8181 (mtpt) cc_final: 0.7949 (mttt) REVERT: B 26 GLU cc_start: 0.8893 (tt0) cc_final: 0.8543 (tt0) REVERT: B 52 ASP cc_start: 0.8970 (m-30) cc_final: 0.8697 (m-30) REVERT: B 89 SER cc_start: 0.9399 (t) cc_final: 0.8968 (p) REVERT: B 94 ASP cc_start: 0.8580 (t0) cc_final: 0.8339 (t0) REVERT: C 586 MET cc_start: 0.8306 (ptm) cc_final: 0.7975 (ptm) outliers start: 11 outliers final: 10 residues processed: 48 average time/residue: 0.0778 time to fit residues: 5.3029 Evaluate side-chains 48 residues out of total 661 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 38 time to evaluate : 0.259 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 GLN Chi-restraints excluded: chain A residue 105 LEU Chi-restraints excluded: chain B residue 3 LEU Chi-restraints excluded: chain B residue 4 THR Chi-restraints excluded: chain B residue 73 ASP Chi-restraints excluded: chain B residue 143 HIS Chi-restraints excluded: chain C residue 382 THR Chi-restraints excluded: chain C residue 435 VAL Chi-restraints excluded: chain C residue 633 VAL Chi-restraints excluded: chain C residue 637 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 25 optimal weight: 0.6980 chunk 28 optimal weight: 0.0770 chunk 74 optimal weight: 0.7980 chunk 46 optimal weight: 0.7980 chunk 8 optimal weight: 5.9990 chunk 57 optimal weight: 0.8980 chunk 42 optimal weight: 0.4980 chunk 61 optimal weight: 0.5980 chunk 67 optimal weight: 0.9990 chunk 10 optimal weight: 0.6980 chunk 64 optimal weight: 0.7980 overall best weight: 0.5138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 639 ASN ** 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 = 0.3208 r_free = 0.3208 target = 0.069685 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2898 r_free = 0.2898 target = 0.055617 restraints weight = 16925.414| |-----------------------------------------------------------------------------| r_work (start): 0.2881 rms_B_bonded: 3.02 r_work: 0.2745 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work (final): 0.2745 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8569 moved from start: 0.3496 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.070 6298 Z= 0.111 Angle : 0.513 9.247 8581 Z= 0.253 Chirality : 0.041 0.131 933 Planarity : 0.004 0.042 1100 Dihedral : 6.511 85.940 827 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 3.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.60 % Favored : 98.40 % Rotamer: Outliers : 1.66 % Allowed : 7.26 % Favored : 91.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.89 % 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 are not related in a simple way. whole: 2.46 (0.33), residues: 749 helix: 2.83 (0.31), residues: 300 sheet: 0.66 (0.41), residues: 150 loop : 1.04 (0.41), residues: 299 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 104 TYR 0.012 0.001 TYR C 512 PHE 0.010 0.001 PHE C 426 TRP 0.012 0.001 TRP A 14 HIS 0.003 0.001 HIS A 103 Details of bonding type rmsd/Z covalent geometry : bond 0.00290 / 0.11 ( 6296) covalent geometry : angle 0.51290 / 0.25 ( 8581) hydrogen bonds : bond 0.02704 / 1.87 ( 313) hydrogen bonds : angle 4.13683 / 3.14 ( 873) Misc. bond : bond 0.05250 / 2.53 ( 2) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1498 Ramachandran restraints generated. 749 Oldfield, 0 Emsley, 749 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1498 Ramachandran restraints generated. 749 Oldfield, 0 Emsley, 749 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 51 residues out of total 661 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 40 time to evaluate : 0.270 Fit side-chains REVERT: B 7 GLU cc_start: 0.8600 (tp30) cc_final: 0.8221 (mm-30) REVERT: B 8 LYS cc_start: 0.8178 (mtpt) cc_final: 0.7948 (mttt) REVERT: B 26 GLU cc_start: 0.8893 (tt0) cc_final: 0.8551 (tt0) REVERT: B 52 ASP cc_start: 0.8963 (m-30) cc_final: 0.8693 (m-30) REVERT: B 89 SER cc_start: 0.9395 (t) cc_final: 0.8961 (p) REVERT: B 94 ASP cc_start: 0.8586 (t0) cc_final: 0.8347 (t0) REVERT: C 586 MET cc_start: 0.8319 (ptm) cc_final: 0.7989 (ptm) outliers start: 11 outliers final: 11 residues processed: 48 average time/residue: 0.0731 time to fit residues: 5.1206 Evaluate side-chains 50 residues out of total 661 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 39 time to evaluate : 0.185 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 GLN Chi-restraints excluded: chain A residue 74 ASP Chi-restraints excluded: chain A residue 105 LEU Chi-restraints excluded: chain B residue 3 LEU Chi-restraints excluded: chain B residue 4 THR Chi-restraints excluded: chain B residue 73 ASP Chi-restraints excluded: chain B residue 143 HIS Chi-restraints excluded: chain C residue 382 THR Chi-restraints excluded: chain C residue 435 VAL Chi-restraints excluded: chain C residue 633 VAL Chi-restraints excluded: chain C residue 637 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 60 optimal weight: 2.9990 chunk 55 optimal weight: 0.8980 chunk 8 optimal weight: 6.9990 chunk 72 optimal weight: 0.0060 chunk 64 optimal weight: 0.0040 chunk 74 optimal weight: 0.6980 chunk 67 optimal weight: 1.9990 chunk 51 optimal weight: 2.9990 chunk 26 optimal weight: 0.4980 chunk 14 optimal weight: 1.9990 chunk 33 optimal weight: 0.3980 overall best weight: 0.3208 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 639 ASN ** 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 = 0.3228 r_free = 0.3228 target = 0.070673 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2921 r_free = 0.2921 target = 0.056556 restraints weight = 16723.177| |-----------------------------------------------------------------------------| r_work (start): 0.2901 rms_B_bonded: 3.03 r_work: 0.2766 rms_B_bonded: 3.47 restraints_weight: 0.5000 r_work (final): 0.2766 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8553 moved from start: 0.3646 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.071 6298 Z= 0.096 Angle : 0.508 9.503 8581 Z= 0.251 Chirality : 0.040 0.129 933 Planarity : 0.004 0.042 1100 Dihedral : 6.349 86.797 827 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 3.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Rotamer: Outliers : 1.36 % Allowed : 7.87 % Favored : 90.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.89 % 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 are not related in a simple way. whole: 2.49 (0.33), residues: 749 helix: 2.86 (0.31), residues: 300 sheet: 0.74 (0.41), residues: 150 loop : 1.02 (0.41), residues: 299 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 30 TYR 0.018 0.001 TYR C 175 PHE 0.010 0.001 PHE C 620 TRP 0.012 0.001 TRP A 14 HIS 0.002 0.000 HIS B 143 Details of bonding type rmsd/Z covalent geometry : bond 0.00248 / 0.10 ( 6296) covalent geometry : angle 0.50808 / 0.25 ( 8581) hydrogen bonds : bond 0.02514 / 1.74 ( 313) hydrogen bonds : angle 4.03800 / 3.07 ( 873) Misc. bond : bond 0.05259 / 2.53 ( 2) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1498 Ramachandran restraints generated. 749 Oldfield, 0 Emsley, 749 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1498 Ramachandran restraints generated. 749 Oldfield, 0 Emsley, 749 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 55 residues out of total 661 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 46 time to evaluate : 0.283 Fit side-chains REVERT: A 30 GLU cc_start: 0.9094 (tp30) cc_final: 0.8759 (tt0) REVERT: A 75 ASP cc_start: 0.8579 (t0) cc_final: 0.7786 (t0) REVERT: A 78 ASN cc_start: 0.9358 (m-40) cc_final: 0.8947 (m110) REVERT: B 7 GLU cc_start: 0.8596 (tp30) cc_final: 0.8201 (mm-30) REVERT: B 8 LYS cc_start: 0.8166 (mtpt) cc_final: 0.7955 (mttt) REVERT: B 26 GLU cc_start: 0.8847 (tt0) cc_final: 0.8534 (tt0) REVERT: B 52 ASP cc_start: 0.8956 (m-30) cc_final: 0.8685 (m-30) REVERT: B 89 SER cc_start: 0.9395 (t) cc_final: 0.8944 (p) REVERT: B 94 ASP cc_start: 0.8595 (t0) cc_final: 0.8352 (t0) REVERT: C 196 LEU cc_start: 0.8917 (pp) cc_final: 0.8579 (pp) REVERT: C 586 MET cc_start: 0.8285 (ptm) cc_final: 0.7940 (ptm) outliers start: 9 outliers final: 9 residues processed: 53 average time/residue: 0.0704 time to fit residues: 5.4195 Evaluate side-chains 53 residues out of total 661 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 44 time to evaluate : 0.266 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 GLN Chi-restraints excluded: chain A residue 105 LEU Chi-restraints excluded: chain B residue 3 LEU Chi-restraints excluded: chain B residue 4 THR Chi-restraints excluded: chain B residue 73 ASP Chi-restraints excluded: chain B residue 143 HIS Chi-restraints excluded: chain C residue 435 VAL Chi-restraints excluded: chain C residue 633 VAL Chi-restraints excluded: chain C residue 637 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 14 optimal weight: 0.9980 chunk 52 optimal weight: 0.9980 chunk 13 optimal weight: 0.8980 chunk 49 optimal weight: 0.7980 chunk 36 optimal weight: 0.3980 chunk 34 optimal weight: 0.5980 chunk 0 optimal weight: 2.9990 chunk 64 optimal weight: 0.9990 chunk 59 optimal weight: 0.0370 chunk 29 optimal weight: 1.9990 chunk 40 optimal weight: 0.7980 overall best weight: 0.5258 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 614 ASN ** C 639 ASN ** 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 = 0.3213 r_free = 0.3213 target = 0.069990 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2901 r_free = 0.2901 target = 0.055739 restraints weight = 16858.727| |-----------------------------------------------------------------------------| r_work (start): 0.2884 rms_B_bonded: 3.04 r_work: 0.2747 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work (final): 0.2747 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8571 moved from start: 0.3641 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.072 6298 Z= 0.115 Angle : 0.517 5.571 8581 Z= 0.260 Chirality : 0.041 0.178 933 Planarity : 0.004 0.042 1100 Dihedral : 6.385 88.707 827 Min Nonbonded Distance : 2.403 Molprobity Statistics. All-atom Clashscore : 3.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 1.36 % Allowed : 8.62 % Favored : 90.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.89 % 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 are not related in a simple way. whole: 2.45 (0.33), residues: 749 helix: 2.87 (0.31), residues: 300 sheet: 0.65 (0.41), residues: 151 loop : 0.99 (0.41), residues: 298 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 104 TYR 0.017 0.001 TYR C 175 PHE 0.010 0.001 PHE C 620 TRP 0.011 0.001 TRP A 14 HIS 0.003 0.001 HIS A 103 Details of bonding type rmsd/Z covalent geometry : bond 0.00297 / 0.11 ( 6296) covalent geometry : angle 0.51733 / 0.26 ( 8581) hydrogen bonds : bond 0.02684 / 1.85 ( 313) hydrogen bonds : angle 4.10733 / 3.12 ( 873) Misc. bond : bond 0.05274 / 2.53 ( 2) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1612.08 seconds wall clock time: 28 minutes 29.97 seconds (1709.97 seconds total)