Starting phenix.real_space_refine on Wed Feb 4 09:02:00 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9sgo_54875/02_2026/9sgo_54875.cif Found real_map, /net/cci-nas-00/data/ceres_data/9sgo_54875/02_2026/9sgo_54875.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.74 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9sgo_54875/02_2026/9sgo_54875.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9sgo_54875/02_2026/9sgo_54875.map" model { file = "/net/cci-nas-00/data/ceres_data/9sgo_54875/02_2026/9sgo_54875.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9sgo_54875/02_2026/9sgo_54875.cif" } resolution = 2.74 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= 0.006 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 1 7.16 5 S 32 5.16 5 C 6073 2.51 5 N 1633 2.21 5 O 1789 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 9528 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 4181 Number of conformers: 1 Conformer: "" Number of residues, atoms: 559, 4181 Classifications: {'peptide': 559} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 37} Link IDs: {'PTRANS': 29, 'TRANS': 529} Chain breaks: 4 Unresolved non-hydrogen bonds: 184 Unresolved non-hydrogen angles: 225 Unresolved non-hydrogen dihedrals: 165 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'TRP:plan': 2, 'ASP:plan': 4, 'TYR:plan': 2, 'ARG:plan': 6, 'GLU:plan': 10, 'HIS:plan': 1, 'ASN:plan1': 1, 'ARG%COO:plan': 1} Unresolved non-hydrogen planarities: 127 Chain: "B" Number of atoms: 5304 Number of conformers: 1 Conformer: "" Number of residues, atoms: 700, 5304 Classifications: {'peptide': 700} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 22} Link IDs: {'PTRANS': 44, 'TRANS': 655} Unresolved non-hydrogen bonds: 90 Unresolved non-hydrogen angles: 101 Unresolved non-hydrogen dihedrals: 79 Planarities with less than four sites: {'ARG:plan': 3, 'GLU:plan': 4, 'ASP:plan': 4} Unresolved non-hydrogen planarities: 43 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: 1.87, per 1000 atoms: 0.20 Number of scatterers: 9528 At special positions: 0 Unit cell: (82.4, 94.76, 124.424, 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 1 26.01 S 32 16.00 O 1789 8.00 N 1633 7.00 C 6073 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=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 0.56 Conformation dependent library (CDL) restraints added in 347.0 milliseconds 2494 Ramachandran restraints generated. 1247 Oldfield, 0 Emsley, 1247 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2266 Finding SS restraints... Secondary structure from input PDB file: 75 helices and 5 sheets defined 58.4% alpha, 2.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.33 Creating SS restraints... Processing helix chain 'A' and resid 28 through 32 Processing helix chain 'A' and resid 34 through 39 removed outlier: 4.292A pdb=" N TRP A 38 " --> pdb=" O GLY A 34 " (cutoff:3.500A) Processing helix chain 'A' and resid 44 through 48 removed outlier: 3.634A pdb=" N VAL A 47 " --> pdb=" O ASN A 44 " (cutoff:3.500A) Processing helix chain 'A' and resid 52 through 56 Processing helix chain 'A' and resid 63 through 69 Processing helix chain 'A' and resid 72 through 86 Processing helix chain 'A' and resid 98 through 111 Processing helix chain 'A' and resid 142 through 156 Proline residue: A 150 - end of helix removed outlier: 3.696A pdb=" N LYS A 154 " --> pdb=" O PRO A 150 " (cutoff:3.500A) Processing helix chain 'A' and resid 157 through 159 No H-bonds generated for 'chain 'A' and resid 157 through 159' Processing helix chain 'A' and resid 160 through 176 removed outlier: 3.586A pdb=" N VAL A 166 " --> pdb=" O ALA A 162 " (cutoff:3.500A) Processing helix chain 'A' and resid 244 through 254 Processing helix chain 'A' and resid 258 through 272 Processing helix chain 'A' and resid 330 through 337 removed outlier: 3.732A pdb=" N GLU A 334 " --> pdb=" O ASN A 330 " (cutoff:3.500A) Processing helix chain 'A' and resid 382 through 387 Processing helix chain 'A' and resid 387 through 400 removed outlier: 4.921A pdb=" N ARG A 396 " --> pdb=" O ARG A 392 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N TRP A 397 " --> pdb=" O ILE A 393 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N LEU A 398 " --> pdb=" O THR A 394 " (cutoff:3.500A) Processing helix chain 'A' and resid 400 through 418 removed outlier: 3.958A pdb=" N LEU A 404 " --> pdb=" O HIS A 400 " (cutoff:3.500A) Processing helix chain 'A' and resid 422 through 426 Processing helix chain 'A' and resid 436 through 440 Processing helix chain 'A' and resid 451 through 464 Processing helix chain 'A' and resid 468 through 481 Processing helix chain 'A' and resid 495 through 498 removed outlier: 4.087A pdb=" N ARG A 498 " --> pdb=" O GLY A 495 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 495 through 498' Processing helix chain 'A' and resid 499 through 504 removed outlier: 3.653A pdb=" N GLY A 504 " --> pdb=" O GLN A 500 " (cutoff:3.500A) Processing helix chain 'A' and resid 512 through 531 removed outlier: 3.642A pdb=" N LYS A 516 " --> pdb=" O GLY A 512 " (cutoff:3.500A) Processing helix chain 'A' and resid 539 through 560 Processing helix chain 'A' and resid 584 through 588 Processing helix chain 'A' and resid 605 through 617 Processing helix chain 'A' and resid 620 through 634 removed outlier: 4.060A pdb=" N VAL A 633 " --> pdb=" O GLY A 629 " (cutoff:3.500A) Processing helix chain 'A' and resid 637 through 641 Processing helix chain 'A' and resid 655 through 662 Processing helix chain 'A' and resid 693 through 701 removed outlier: 4.045A pdb=" N PHE A 698 " --> pdb=" O VAL A 694 " (cutoff:3.500A) removed outlier: 4.267A pdb=" N GLY A 699 " --> pdb=" O ASP A 695 " (cutoff:3.500A) Processing helix chain 'A' and resid 701 through 713 removed outlier: 3.705A pdb=" N LEU A 707 " --> pdb=" O GLU A 703 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ALA A 713 " --> pdb=" O GLU A 709 " (cutoff:3.500A) Processing helix chain 'A' and resid 716 through 733 Processing helix chain 'B' and resid 44 through 50 removed outlier: 3.528A pdb=" N HIS B 49 " --> pdb=" O LYS B 46 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N GLN B 50 " --> pdb=" O VAL B 47 " (cutoff:3.500A) Processing helix chain 'B' and resid 52 through 56 Processing helix chain 'B' and resid 63 through 69 Processing helix chain 'B' and resid 72 through 86 Processing helix chain 'B' and resid 93 through 97 Processing helix chain 'B' and resid 98 through 111 Processing helix chain 'B' and resid 125 through 128 removed outlier: 3.809A pdb=" N ARG B 128 " --> pdb=" O GLY B 125 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 125 through 128' Processing helix chain 'B' and resid 129 through 134 removed outlier: 3.951A pdb=" N SER B 134 " --> pdb=" O ALA B 130 " (cutoff:3.500A) Processing helix chain 'B' and resid 135 through 139 removed outlier: 3.509A pdb=" N ALA B 139 " --> pdb=" O PRO B 136 " (cutoff:3.500A) Processing helix chain 'B' and resid 140 through 148 removed outlier: 3.545A pdb=" N ALA B 144 " --> pdb=" O SER B 140 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N LEU B 148 " --> pdb=" O ALA B 144 " (cutoff:3.500A) Processing helix chain 'B' and resid 148 through 156 removed outlier: 3.609A pdb=" N LYS B 154 " --> pdb=" O PRO B 150 " (cutoff:3.500A) Processing helix chain 'B' and resid 157 through 159 No H-bonds generated for 'chain 'B' and resid 157 through 159' Processing helix chain 'B' and resid 160 through 176 removed outlier: 3.696A pdb=" N VAL B 166 " --> pdb=" O ALA B 162 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N GLY B 169 " --> pdb=" O ILE B 165 " (cutoff:3.500A) Processing helix chain 'B' and resid 234 through 238 Processing helix chain 'B' and resid 240 through 254 Processing helix chain 'B' and resid 258 through 271 Processing helix chain 'B' and resid 280 through 284 Processing helix chain 'B' and resid 287 through 291 Processing helix chain 'B' and resid 292 through 296 Processing helix chain 'B' and resid 308 through 312 Processing helix chain 'B' and resid 330 through 339 removed outlier: 3.584A pdb=" N TYR B 339 " --> pdb=" O ILE B 335 " (cutoff:3.500A) Processing helix chain 'B' and resid 357 through 359 No H-bonds generated for 'chain 'B' and resid 357 through 359' Processing helix chain 'B' and resid 379 through 381 No H-bonds generated for 'chain 'B' and resid 379 through 381' Processing helix chain 'B' and resid 382 through 387 Processing helix chain 'B' and resid 387 through 399 removed outlier: 4.122A pdb=" N GLU B 399 " --> pdb=" O ARG B 395 " (cutoff:3.500A) Processing helix chain 'B' and resid 400 through 417 Processing helix chain 'B' and resid 422 through 426 Processing helix chain 'B' and resid 436 through 440 Processing helix chain 'B' and resid 451 through 464 Processing helix chain 'B' and resid 468 through 481 Processing helix chain 'B' and resid 495 through 498 removed outlier: 3.796A pdb=" N ARG B 498 " --> pdb=" O GLY B 495 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 495 through 498' Processing helix chain 'B' and resid 499 through 504 removed outlier: 3.623A pdb=" N GLY B 504 " --> pdb=" O GLN B 500 " (cutoff:3.500A) Processing helix chain 'B' and resid 512 through 532 Processing helix chain 'B' and resid 539 through 560 Processing helix chain 'B' and resid 580 through 585 Processing helix chain 'B' and resid 586 through 588 No H-bonds generated for 'chain 'B' and resid 586 through 588' Processing helix chain 'B' and resid 605 through 617 Processing helix chain 'B' and resid 620 through 635 removed outlier: 3.656A pdb=" N VAL B 633 " --> pdb=" O GLY B 629 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N GLY B 635 " --> pdb=" O LEU B 631 " (cutoff:3.500A) Processing helix chain 'B' and resid 637 through 641 Processing helix chain 'B' and resid 656 through 662 Processing helix chain 'B' and resid 692 through 701 removed outlier: 3.895A pdb=" N PHE B 698 " --> pdb=" O VAL B 694 " (cutoff:3.500A) removed outlier: 4.300A pdb=" N GLY B 699 " --> pdb=" O ASP B 695 " (cutoff:3.500A) Processing helix chain 'B' and resid 701 through 712 Processing helix chain 'B' and resid 716 through 733 Processing sheet with id=AA1, first strand: chain 'A' and resid 667 through 670 Processing sheet with id=AA2, first strand: chain 'B' and resid 210 through 211 Processing sheet with id=AA3, first strand: chain 'B' and resid 341 through 345 Processing sheet with id=AA4, first strand: chain 'B' and resid 591 through 592 Processing sheet with id=AA5, first strand: chain 'B' and resid 667 through 670 450 hydrogen bonds defined for protein. 1227 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: 1.47 Time building geometry restraints manager: 0.75 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.39: 3999 1.39 - 1.55: 5716 1.55 - 1.72: 0 1.72 - 1.88: 60 1.88 - 2.05: 4 Bond restraints: 9779 Sorted by residual: bond pdb=" CA ASN A 330 " pdb=" CB ASN A 330 " ideal model delta sigma weight residual 1.526 1.546 -0.020 1.68e-02 3.54e+03 1.40e+00 bond pdb=" CD1 TYR B 229 " pdb=" CE1 TYR B 229 " ideal model delta sigma weight residual 1.382 1.348 0.034 3.00e-02 1.11e+03 1.27e+00 bond pdb=" CA THR A 394 " pdb=" C THR A 394 " ideal model delta sigma weight residual 1.523 1.537 -0.015 1.41e-02 5.03e+03 1.09e+00 bond pdb=" CB GLU A 526 " pdb=" CG GLU A 526 " ideal model delta sigma weight residual 1.520 1.551 -0.031 3.00e-02 1.11e+03 1.07e+00 bond pdb=" CB TYR B 229 " pdb=" CG TYR B 229 " ideal model delta sigma weight residual 1.512 1.490 0.022 2.20e-02 2.07e+03 9.91e-01 ... (remaining 9774 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.40: 13099 1.40 - 2.80: 171 2.80 - 4.20: 64 4.20 - 5.60: 18 5.60 - 7.00: 5 Bond angle restraints: 13357 Sorted by residual: angle pdb=" N ASN A 330 " pdb=" CA ASN A 330 " pdb=" C ASN A 330 " ideal model delta sigma weight residual 110.44 106.08 4.36 1.20e+00 6.94e-01 1.32e+01 angle pdb=" CA GLU A 526 " pdb=" CB GLU A 526 " pdb=" CG GLU A 526 " ideal model delta sigma weight residual 114.10 120.90 -6.80 2.00e+00 2.50e-01 1.16e+01 angle pdb=" CA THR A 394 " pdb=" C THR A 394 " pdb=" N ARG A 395 " ideal model delta sigma weight residual 118.44 122.14 -3.70 1.41e+00 5.03e-01 6.89e+00 angle pdb=" CB GLN A 722 " pdb=" CG GLN A 722 " pdb=" CD GLN A 722 " ideal model delta sigma weight residual 112.60 116.80 -4.20 1.70e+00 3.46e-01 6.11e+00 angle pdb=" C ASN A 330 " pdb=" CA ASN A 330 " pdb=" CB ASN A 330 " ideal model delta sigma weight residual 111.77 117.17 -5.40 2.28e+00 1.92e-01 5.61e+00 ... (remaining 13352 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.40: 5005 17.40 - 34.80: 488 34.80 - 52.21: 129 52.21 - 69.61: 37 69.61 - 87.01: 12 Dihedral angle restraints: 5671 sinusoidal: 2118 harmonic: 3553 Sorted by residual: dihedral pdb=" CA PHE B 129 " pdb=" C PHE B 129 " pdb=" N ALA B 130 " pdb=" CA ALA B 130 " ideal model delta harmonic sigma weight residual -180.00 -158.80 -21.20 0 5.00e+00 4.00e-02 1.80e+01 dihedral pdb=" CA MET A 664 " pdb=" C MET A 664 " pdb=" N GLY A 665 " pdb=" CA GLY A 665 " ideal model delta harmonic sigma weight residual 180.00 159.04 20.96 0 5.00e+00 4.00e-02 1.76e+01 dihedral pdb=" CA MET B 255 " pdb=" C MET B 255 " pdb=" N ALA B 256 " pdb=" CA ALA B 256 " ideal model delta harmonic sigma weight residual 180.00 160.22 19.78 0 5.00e+00 4.00e-02 1.56e+01 ... (remaining 5668 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.033: 961 0.033 - 0.067: 348 0.067 - 0.100: 93 0.100 - 0.134: 41 0.134 - 0.167: 2 Chirality restraints: 1445 Sorted by residual: chirality pdb=" CA MET B 255 " pdb=" N MET B 255 " pdb=" C MET B 255 " pdb=" CB MET B 255 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.17 2.00e-01 2.50e+01 6.96e-01 chirality pdb=" CA MET A 664 " pdb=" N MET A 664 " pdb=" C MET A 664 " pdb=" CB MET A 664 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.14 2.00e-01 2.50e+01 5.17e-01 chirality pdb=" CA TYR B 155 " pdb=" N TYR B 155 " pdb=" C TYR B 155 " pdb=" CB TYR B 155 " both_signs ideal model delta sigma weight residual False 2.51 2.38 0.13 2.00e-01 2.50e+01 4.16e-01 ... (remaining 1442 not shown) Planarity restraints: 1755 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C TRP A 149 " 0.036 5.00e-02 4.00e+02 5.46e-02 4.78e+00 pdb=" N PRO A 150 " -0.094 5.00e-02 4.00e+02 pdb=" CA PRO A 150 " 0.028 5.00e-02 4.00e+02 pdb=" CD PRO A 150 " 0.031 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ASN A 330 " -0.009 2.00e-02 2.50e+03 1.74e-02 3.02e+00 pdb=" C ASN A 330 " 0.030 2.00e-02 2.50e+03 pdb=" O ASN A 330 " -0.012 2.00e-02 2.50e+03 pdb=" N SER A 331 " -0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C TRP B 149 " -0.026 5.00e-02 4.00e+02 3.90e-02 2.43e+00 pdb=" N PRO B 150 " 0.067 5.00e-02 4.00e+02 pdb=" CA PRO B 150 " -0.020 5.00e-02 4.00e+02 pdb=" CD PRO B 150 " -0.022 5.00e-02 4.00e+02 ... (remaining 1752 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 1230 2.75 - 3.28: 9191 3.28 - 3.82: 16816 3.82 - 4.36: 19844 4.36 - 4.90: 34237 Nonbonded interactions: 81318 Sorted by model distance: nonbonded pdb=" O TRP A 91 " pdb=" OH TYR A 98 " model vdw 2.207 3.040 nonbonded pdb=" O ASN A 41 " pdb=" OH TYR A 608 " model vdw 2.229 3.040 nonbonded pdb=" O TRP B 91 " pdb=" OH TYR B 98 " model vdw 2.254 3.040 nonbonded pdb=" OH TYR B 337 " pdb=" OG1 THR B 394 " model vdw 2.297 3.040 nonbonded pdb=" NH2 ARG A 114 " pdb=" OD2 ASP A 117 " model vdw 2.314 3.120 ... (remaining 81313 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: 1.400 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.160 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 8.900 Find NCS groups from input model: 0.040 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:6.700 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.270 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8741 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.078 9780 Z= 0.144 Angle : 0.503 6.998 13357 Z= 0.248 Chirality : 0.040 0.167 1445 Planarity : 0.004 0.055 1755 Dihedral : 16.007 87.009 3405 Min Nonbonded Distance : 2.207 Molprobity Statistics. All-atom Clashscore : 5.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer: Outliers : 0.43 % Allowed : 19.91 % Favored : 79.66 % 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 are not related in a simple way. whole: 0.91 (0.23), residues: 1247 helix: 1.81 (0.22), residues: 571 sheet: 2.94 (1.64), residues: 10 loop : -0.51 (0.23), residues: 666 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 249 TYR 0.015 0.001 TYR B 155 PHE 0.009 0.001 PHE B 720 TRP 0.016 0.001 TRP B 191 HIS 0.005 0.001 HIS A 116 Details of bonding type rmsd covalent geometry : bond 0.00345 ( 9779) covalent geometry : angle 0.50349 (13357) hydrogen bonds : bond 0.15427 ( 450) hydrogen bonds : angle 5.04800 ( 1227) Misc. bond : bond 0.07824 ( 1) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2494 Ramachandran restraints generated. 1247 Oldfield, 0 Emsley, 1247 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2494 Ramachandran restraints generated. 1247 Oldfield, 0 Emsley, 1247 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 37 residues out of total 999 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 33 time to evaluate : 0.362 Fit side-chains outliers start: 4 outliers final: 2 residues processed: 37 average time/residue: 0.6288 time to fit residues: 25.1026 Evaluate side-chains 35 residues out of total 999 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 33 time to evaluate : 0.273 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 607 GLU Chi-restraints excluded: chain B residue 740 ARG Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 108 optimal weight: 6.9990 chunk 49 optimal weight: 5.9990 chunk 97 optimal weight: 3.9990 chunk 113 optimal weight: 1.9990 chunk 53 optimal weight: 0.9990 chunk 5 optimal weight: 2.9990 chunk 33 optimal weight: 0.8980 chunk 123 optimal weight: 2.9990 chunk 65 optimal weight: 3.9990 chunk 62 optimal weight: 0.5980 chunk 51 optimal weight: 0.0870 overall best weight: 0.9162 ------------------------------------------------------------------------------- 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 = 0.3047 r_free = 0.3047 target = 0.075931 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2703 r_free = 0.2703 target = 0.057858 restraints weight = 20067.394| |-----------------------------------------------------------------------------| r_work (start): 0.2667 rms_B_bonded: 2.89 r_work: 0.2532 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work (final): 0.2532 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8749 moved from start: 0.0639 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.084 9780 Z= 0.121 Angle : 0.491 7.980 13357 Z= 0.243 Chirality : 0.040 0.127 1445 Planarity : 0.004 0.052 1755 Dihedral : 4.711 67.765 1362 Min Nonbonded Distance : 2.575 Molprobity Statistics. All-atom Clashscore : 3.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 1.60 % Allowed : 17.47 % Favored : 80.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.98 (0.23), residues: 1247 helix: 1.68 (0.22), residues: 584 sheet: 3.07 (1.62), residues: 10 loop : -0.32 (0.24), residues: 653 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 396 TYR 0.016 0.001 TYR B 155 PHE 0.007 0.001 PHE B 720 TRP 0.010 0.001 TRP B 191 HIS 0.004 0.001 HIS A 116 Details of bonding type rmsd covalent geometry : bond 0.00284 ( 9779) covalent geometry : angle 0.49113 (13357) hydrogen bonds : bond 0.03965 ( 450) hydrogen bonds : angle 4.12578 ( 1227) Misc. bond : bond 0.08418 ( 1) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2494 Ramachandran restraints generated. 1247 Oldfield, 0 Emsley, 1247 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2494 Ramachandran restraints generated. 1247 Oldfield, 0 Emsley, 1247 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 51 residues out of total 999 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 36 time to evaluate : 0.222 Fit side-chains REVERT: A 58 MET cc_start: 0.8735 (mmt) cc_final: 0.8515 (mmm) REVERT: A 176 MET cc_start: 0.8995 (OUTLIER) cc_final: 0.8108 (mpt) REVERT: B 391 GLU cc_start: 0.8870 (OUTLIER) cc_final: 0.8647 (tp30) outliers start: 15 outliers final: 1 residues processed: 47 average time/residue: 0.5937 time to fit residues: 29.9833 Evaluate side-chains 37 residues out of total 999 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 34 time to evaluate : 0.326 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 176 MET Chi-restraints excluded: chain B residue 203 THR Chi-restraints excluded: chain B residue 391 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 27 optimal weight: 2.9990 chunk 34 optimal weight: 0.8980 chunk 104 optimal weight: 4.9990 chunk 23 optimal weight: 5.9990 chunk 89 optimal weight: 0.5980 chunk 15 optimal weight: 7.9990 chunk 84 optimal weight: 0.7980 chunk 28 optimal weight: 0.9990 chunk 17 optimal weight: 2.9990 chunk 10 optimal weight: 5.9990 chunk 57 optimal weight: 1.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- 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 = 0.3044 r_free = 0.3044 target = 0.075804 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2701 r_free = 0.2701 target = 0.057737 restraints weight = 20069.665| |-----------------------------------------------------------------------------| r_work (start): 0.2667 rms_B_bonded: 2.89 r_work: 0.2528 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work (final): 0.2528 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8750 moved from start: 0.0819 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.089 9780 Z= 0.127 Angle : 0.491 8.972 13357 Z= 0.237 Chirality : 0.040 0.139 1445 Planarity : 0.004 0.054 1755 Dihedral : 4.043 68.739 1355 Min Nonbonded Distance : 2.577 Molprobity Statistics. All-atom Clashscore : 3.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 1.17 % Allowed : 18.00 % Favored : 80.83 % 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 are not related in a simple way. whole: 1.00 (0.23), residues: 1247 helix: 1.71 (0.21), residues: 584 sheet: 3.19 (1.69), residues: 10 loop : -0.31 (0.24), residues: 653 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 253 TYR 0.016 0.001 TYR B 155 PHE 0.007 0.001 PHE B 272 TRP 0.010 0.001 TRP B 191 HIS 0.005 0.001 HIS B 49 Details of bonding type rmsd covalent geometry : bond 0.00303 ( 9779) covalent geometry : angle 0.49101 (13357) hydrogen bonds : bond 0.03761 ( 450) hydrogen bonds : angle 3.97679 ( 1227) Misc. bond : bond 0.08851 ( 1) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2494 Ramachandran restraints generated. 1247 Oldfield, 0 Emsley, 1247 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2494 Ramachandran restraints generated. 1247 Oldfield, 0 Emsley, 1247 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 47 residues out of total 999 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 36 time to evaluate : 0.267 Fit side-chains REVERT: A 58 MET cc_start: 0.8715 (mmt) cc_final: 0.8474 (mmm) REVERT: A 176 MET cc_start: 0.8826 (OUTLIER) cc_final: 0.7910 (mpt) REVERT: B 391 GLU cc_start: 0.8824 (OUTLIER) cc_final: 0.8600 (tp30) outliers start: 11 outliers final: 3 residues processed: 45 average time/residue: 0.6311 time to fit residues: 30.4880 Evaluate side-chains 40 residues out of total 999 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 35 time to evaluate : 0.356 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 GLU Chi-restraints excluded: chain A residue 176 MET Chi-restraints excluded: chain A residue 607 GLU Chi-restraints excluded: chain B residue 203 THR Chi-restraints excluded: chain B residue 391 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 41 optimal weight: 4.9990 chunk 46 optimal weight: 0.9980 chunk 49 optimal weight: 0.5980 chunk 117 optimal weight: 0.7980 chunk 100 optimal weight: 5.9990 chunk 70 optimal weight: 5.9990 chunk 87 optimal weight: 2.9990 chunk 102 optimal weight: 0.9990 chunk 27 optimal weight: 0.9980 chunk 88 optimal weight: 0.8980 chunk 18 optimal weight: 6.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- 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 = 0.3053 r_free = 0.3053 target = 0.076326 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2710 r_free = 0.2710 target = 0.058174 restraints weight = 20192.400| |-----------------------------------------------------------------------------| r_work (start): 0.2677 rms_B_bonded: 2.91 r_work: 0.2539 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work (final): 0.2539 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8736 moved from start: 0.0937 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.103 9780 Z= 0.110 Angle : 0.475 8.864 13357 Z= 0.229 Chirality : 0.039 0.127 1445 Planarity : 0.004 0.053 1755 Dihedral : 4.008 70.289 1355 Min Nonbonded Distance : 2.604 Molprobity Statistics. All-atom Clashscore : 3.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 1.17 % Allowed : 18.42 % Favored : 80.40 % 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 are not related in a simple way. whole: 1.06 (0.23), residues: 1247 helix: 1.76 (0.21), residues: 585 sheet: 3.18 (1.71), residues: 10 loop : -0.29 (0.24), residues: 652 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 253 TYR 0.016 0.001 TYR B 155 PHE 0.006 0.001 PHE B 720 TRP 0.010 0.001 TRP B 107 HIS 0.004 0.001 HIS B 49 Details of bonding type rmsd covalent geometry : bond 0.00262 ( 9779) covalent geometry : angle 0.47507 (13357) hydrogen bonds : bond 0.03484 ( 450) hydrogen bonds : angle 3.90449 ( 1227) Misc. bond : bond 0.10334 ( 1) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2494 Ramachandran restraints generated. 1247 Oldfield, 0 Emsley, 1247 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2494 Ramachandran restraints generated. 1247 Oldfield, 0 Emsley, 1247 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 48 residues out of total 999 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 37 time to evaluate : 0.271 Fit side-chains REVERT: A 58 MET cc_start: 0.8694 (mmt) cc_final: 0.8454 (mmm) REVERT: B 391 GLU cc_start: 0.8824 (OUTLIER) cc_final: 0.8606 (tp30) REVERT: B 664 MET cc_start: 0.9112 (mmm) cc_final: 0.8819 (tpt) outliers start: 11 outliers final: 4 residues processed: 46 average time/residue: 0.6010 time to fit residues: 29.7179 Evaluate side-chains 38 residues out of total 999 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 33 time to evaluate : 0.237 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 GLU Chi-restraints excluded: chain A residue 607 GLU Chi-restraints excluded: chain B residue 84 MET Chi-restraints excluded: chain B residue 203 THR Chi-restraints excluded: chain B residue 391 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 79 optimal weight: 0.9990 chunk 63 optimal weight: 4.9990 chunk 17 optimal weight: 4.9990 chunk 48 optimal weight: 0.9990 chunk 96 optimal weight: 0.9980 chunk 75 optimal weight: 0.9980 chunk 35 optimal weight: 0.8980 chunk 58 optimal weight: 2.9990 chunk 118 optimal weight: 0.0050 chunk 12 optimal weight: 0.5980 chunk 93 optimal weight: 1.9990 overall best weight: 0.6994 ------------------------------------------------------------------------------- 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 = 0.3065 r_free = 0.3065 target = 0.077004 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2727 r_free = 0.2727 target = 0.058993 restraints weight = 20089.894| |-----------------------------------------------------------------------------| r_work (start): 0.2694 rms_B_bonded: 2.88 r_work: 0.2563 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work (final): 0.2563 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8749 moved from start: 0.1059 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.110 9780 Z= 0.102 Angle : 0.471 8.543 13357 Z= 0.227 Chirality : 0.039 0.129 1445 Planarity : 0.004 0.052 1755 Dihedral : 3.960 70.636 1355 Min Nonbonded Distance : 2.613 Molprobity Statistics. All-atom Clashscore : 3.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 0.85 % Allowed : 19.06 % Favored : 80.09 % 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 are not related in a simple way. whole: 1.12 (0.23), residues: 1247 helix: 1.85 (0.21), residues: 584 sheet: 3.17 (1.72), residues: 10 loop : -0.30 (0.24), residues: 653 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 254 TYR 0.017 0.001 TYR B 229 PHE 0.006 0.001 PHE B 272 TRP 0.011 0.001 TRP B 107 HIS 0.004 0.001 HIS B 49 Details of bonding type rmsd covalent geometry : bond 0.00240 ( 9779) covalent geometry : angle 0.47075 (13357) hydrogen bonds : bond 0.03290 ( 450) hydrogen bonds : angle 3.86693 ( 1227) Misc. bond : bond 0.10985 ( 1) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2494 Ramachandran restraints generated. 1247 Oldfield, 0 Emsley, 1247 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2494 Ramachandran restraints generated. 1247 Oldfield, 0 Emsley, 1247 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 43 residues out of total 999 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 35 time to evaluate : 0.379 Fit side-chains REVERT: B 391 GLU cc_start: 0.8805 (OUTLIER) cc_final: 0.8583 (tp30) REVERT: B 664 MET cc_start: 0.9123 (mmm) cc_final: 0.8836 (tpt) outliers start: 8 outliers final: 4 residues processed: 42 average time/residue: 0.5577 time to fit residues: 25.1149 Evaluate side-chains 39 residues out of total 999 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 34 time to evaluate : 0.258 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 GLU Chi-restraints excluded: chain A residue 607 GLU Chi-restraints excluded: chain B residue 84 MET Chi-restraints excluded: chain B residue 203 THR Chi-restraints excluded: chain B residue 391 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 82 optimal weight: 0.7980 chunk 10 optimal weight: 5.9990 chunk 67 optimal weight: 0.7980 chunk 7 optimal weight: 0.9990 chunk 0 optimal weight: 6.9990 chunk 34 optimal weight: 0.9990 chunk 105 optimal weight: 3.9990 chunk 8 optimal weight: 5.9990 chunk 47 optimal weight: 2.9990 chunk 104 optimal weight: 2.9990 chunk 30 optimal weight: 5.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- 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 = 0.3037 r_free = 0.3037 target = 0.075478 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2690 r_free = 0.2690 target = 0.057311 restraints weight = 20145.472| |-----------------------------------------------------------------------------| r_work (start): 0.2640 rms_B_bonded: 2.90 r_work: 0.2496 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work (final): 0.2496 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8735 moved from start: 0.1031 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.078 9780 Z= 0.147 Angle : 0.495 8.326 13357 Z= 0.240 Chirality : 0.040 0.135 1445 Planarity : 0.004 0.052 1755 Dihedral : 4.103 72.189 1355 Min Nonbonded Distance : 2.593 Molprobity Statistics. All-atom Clashscore : 3.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.09 % Favored : 97.91 % Rotamer: Outliers : 1.28 % Allowed : 18.64 % Favored : 80.09 % 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 are not related in a simple way. whole: 1.11 (0.23), residues: 1247 helix: 1.83 (0.21), residues: 585 sheet: 3.28 (1.74), residues: 10 loop : -0.29 (0.24), residues: 652 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 146 TYR 0.017 0.001 TYR B 155 PHE 0.008 0.001 PHE B 720 TRP 0.008 0.001 TRP B 341 HIS 0.005 0.001 HIS B 49 Details of bonding type rmsd covalent geometry : bond 0.00353 ( 9779) covalent geometry : angle 0.49469 (13357) hydrogen bonds : bond 0.03648 ( 450) hydrogen bonds : angle 3.86642 ( 1227) Misc. bond : bond 0.07815 ( 1) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2494 Ramachandran restraints generated. 1247 Oldfield, 0 Emsley, 1247 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2494 Ramachandran restraints generated. 1247 Oldfield, 0 Emsley, 1247 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 44 residues out of total 999 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 32 time to evaluate : 0.223 Fit side-chains REVERT: B 107 TRP cc_start: 0.8701 (OUTLIER) cc_final: 0.7825 (t-100) outliers start: 12 outliers final: 5 residues processed: 42 average time/residue: 0.5809 time to fit residues: 26.0460 Evaluate side-chains 38 residues out of total 999 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 32 time to evaluate : 0.235 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 GLU Chi-restraints excluded: chain A residue 607 GLU Chi-restraints excluded: chain B residue 84 MET Chi-restraints excluded: chain B residue 107 TRP Chi-restraints excluded: chain B residue 203 THR Chi-restraints excluded: chain B residue 319 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 57 optimal weight: 1.9990 chunk 43 optimal weight: 0.9980 chunk 25 optimal weight: 2.9990 chunk 79 optimal weight: 0.9990 chunk 64 optimal weight: 0.8980 chunk 49 optimal weight: 4.9990 chunk 114 optimal weight: 0.9990 chunk 8 optimal weight: 3.9990 chunk 55 optimal weight: 0.2980 chunk 6 optimal weight: 3.9990 chunk 105 optimal weight: 3.9990 overall best weight: 0.8384 ------------------------------------------------------------------------------- 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 = 0.3055 r_free = 0.3055 target = 0.076412 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2712 r_free = 0.2712 target = 0.058294 restraints weight = 20102.781| |-----------------------------------------------------------------------------| r_work (start): 0.2680 rms_B_bonded: 2.91 r_work: 0.2543 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work (final): 0.2543 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8730 moved from start: 0.1106 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.095 9780 Z= 0.110 Angle : 0.478 8.788 13357 Z= 0.231 Chirality : 0.039 0.136 1445 Planarity : 0.004 0.052 1755 Dihedral : 4.024 71.209 1355 Min Nonbonded Distance : 2.613 Molprobity Statistics. All-atom Clashscore : 3.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 1.17 % Allowed : 18.64 % Favored : 80.19 % 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 are not related in a simple way. whole: 1.15 (0.23), residues: 1247 helix: 1.87 (0.21), residues: 584 sheet: 3.24 (1.73), residues: 10 loop : -0.29 (0.24), residues: 653 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 254 TYR 0.016 0.001 TYR B 155 PHE 0.006 0.001 PHE A 167 TRP 0.010 0.001 TRP B 191 HIS 0.004 0.001 HIS B 49 Details of bonding type rmsd covalent geometry : bond 0.00263 ( 9779) covalent geometry : angle 0.47848 (13357) hydrogen bonds : bond 0.03364 ( 450) hydrogen bonds : angle 3.85357 ( 1227) Misc. bond : bond 0.09471 ( 1) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2494 Ramachandran restraints generated. 1247 Oldfield, 0 Emsley, 1247 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2494 Ramachandran restraints generated. 1247 Oldfield, 0 Emsley, 1247 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 46 residues out of total 999 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 35 time to evaluate : 0.369 Fit side-chains REVERT: B 669 GLU cc_start: 0.8814 (OUTLIER) cc_final: 0.8275 (pp20) outliers start: 11 outliers final: 5 residues processed: 45 average time/residue: 0.5511 time to fit residues: 26.7749 Evaluate side-chains 38 residues out of total 999 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 32 time to evaluate : 0.384 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 GLU Chi-restraints excluded: chain A residue 607 GLU Chi-restraints excluded: chain B residue 84 MET Chi-restraints excluded: chain B residue 203 THR Chi-restraints excluded: chain B residue 319 VAL Chi-restraints excluded: chain B residue 669 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 41 optimal weight: 4.9990 chunk 1 optimal weight: 0.7980 chunk 78 optimal weight: 9.9990 chunk 73 optimal weight: 2.9990 chunk 10 optimal weight: 4.9990 chunk 30 optimal weight: 0.5980 chunk 29 optimal weight: 0.9980 chunk 84 optimal weight: 3.9990 chunk 38 optimal weight: 0.0570 chunk 42 optimal weight: 2.9990 chunk 79 optimal weight: 0.5980 overall best weight: 0.6098 ------------------------------------------------------------------------------- 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 = 0.3072 r_free = 0.3072 target = 0.077464 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2735 r_free = 0.2735 target = 0.059479 restraints weight = 19950.644| |-----------------------------------------------------------------------------| r_work (start): 0.2703 rms_B_bonded: 2.89 r_work: 0.2572 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work (final): 0.2572 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8739 moved from start: 0.1221 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.112 9780 Z= 0.096 Angle : 0.470 8.559 13357 Z= 0.226 Chirality : 0.039 0.162 1445 Planarity : 0.004 0.051 1755 Dihedral : 3.969 71.510 1355 Min Nonbonded Distance : 2.616 Molprobity Statistics. All-atom Clashscore : 3.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 1.06 % Allowed : 18.64 % Favored : 80.30 % 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 are not related in a simple way. whole: 1.24 (0.24), residues: 1247 helix: 1.96 (0.21), residues: 584 sheet: 3.38 (1.74), residues: 10 loop : -0.26 (0.24), residues: 653 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 254 TYR 0.023 0.001 TYR B 229 PHE 0.006 0.001 PHE A 167 TRP 0.014 0.001 TRP B 107 HIS 0.004 0.001 HIS B 49 Details of bonding type rmsd covalent geometry : bond 0.00227 ( 9779) covalent geometry : angle 0.47050 (13357) hydrogen bonds : bond 0.03161 ( 450) hydrogen bonds : angle 3.80824 ( 1227) Misc. bond : bond 0.11153 ( 1) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2494 Ramachandran restraints generated. 1247 Oldfield, 0 Emsley, 1247 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2494 Ramachandran restraints generated. 1247 Oldfield, 0 Emsley, 1247 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 47 residues out of total 999 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 37 time to evaluate : 0.317 Fit side-chains REVERT: B 669 GLU cc_start: 0.8803 (OUTLIER) cc_final: 0.8396 (pp20) outliers start: 10 outliers final: 6 residues processed: 46 average time/residue: 0.5906 time to fit residues: 29.2210 Evaluate side-chains 39 residues out of total 999 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 32 time to evaluate : 0.246 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 GLU Chi-restraints excluded: chain A residue 607 GLU Chi-restraints excluded: chain B residue 84 MET Chi-restraints excluded: chain B residue 189 ASP Chi-restraints excluded: chain B residue 203 THR Chi-restraints excluded: chain B residue 319 VAL Chi-restraints excluded: chain B residue 669 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 62 optimal weight: 3.9990 chunk 54 optimal weight: 4.9990 chunk 76 optimal weight: 0.8980 chunk 26 optimal weight: 2.9990 chunk 97 optimal weight: 2.9990 chunk 118 optimal weight: 6.9990 chunk 52 optimal weight: 3.9990 chunk 87 optimal weight: 4.9990 chunk 66 optimal weight: 0.2980 chunk 94 optimal weight: 3.9990 chunk 43 optimal weight: 4.9990 overall best weight: 2.2386 ------------------------------------------------------------------------------- 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 = 0.3007 r_free = 0.3007 target = 0.073821 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2655 r_free = 0.2655 target = 0.055668 restraints weight = 20234.945| |-----------------------------------------------------------------------------| r_work (start): 0.2602 rms_B_bonded: 2.88 r_work: 0.2458 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.2458 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8771 moved from start: 0.1120 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.055 9780 Z= 0.229 Angle : 0.557 9.211 13357 Z= 0.272 Chirality : 0.043 0.232 1445 Planarity : 0.004 0.052 1755 Dihedral : 4.305 73.616 1355 Min Nonbonded Distance : 2.575 Molprobity Statistics. All-atom Clashscore : 3.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 0.96 % Allowed : 19.17 % Favored : 79.87 % 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 are not related in a simple way. whole: 1.12 (0.23), residues: 1247 helix: 1.85 (0.21), residues: 584 sheet: 3.31 (1.74), residues: 10 loop : -0.31 (0.24), residues: 653 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 254 TYR 0.030 0.002 TYR B 229 PHE 0.012 0.001 PHE B 724 TRP 0.012 0.001 TRP B 107 HIS 0.007 0.001 HIS B 49 Details of bonding type rmsd covalent geometry : bond 0.00550 ( 9779) covalent geometry : angle 0.55745 (13357) hydrogen bonds : bond 0.04128 ( 450) hydrogen bonds : angle 3.92834 ( 1227) Misc. bond : bond 0.03916 ( 1) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2494 Ramachandran restraints generated. 1247 Oldfield, 0 Emsley, 1247 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2494 Ramachandran restraints generated. 1247 Oldfield, 0 Emsley, 1247 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 42 residues out of total 999 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 33 time to evaluate : 0.251 Fit side-chains REVERT: B 669 GLU cc_start: 0.8851 (OUTLIER) cc_final: 0.8256 (pp20) outliers start: 9 outliers final: 5 residues processed: 41 average time/residue: 0.6350 time to fit residues: 28.0284 Evaluate side-chains 39 residues out of total 999 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 33 time to evaluate : 0.428 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 GLU Chi-restraints excluded: chain A residue 607 GLU Chi-restraints excluded: chain B residue 84 MET Chi-restraints excluded: chain B residue 203 THR Chi-restraints excluded: chain B residue 436 LEU Chi-restraints excluded: chain B residue 669 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 78 optimal weight: 10.0000 chunk 72 optimal weight: 4.9990 chunk 65 optimal weight: 0.7980 chunk 82 optimal weight: 4.9990 chunk 45 optimal weight: 0.9990 chunk 77 optimal weight: 0.9980 chunk 57 optimal weight: 2.9990 chunk 30 optimal weight: 0.6980 chunk 23 optimal weight: 1.9990 chunk 63 optimal weight: 0.7980 chunk 109 optimal weight: 0.8980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 36 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3048 r_free = 0.3048 target = 0.076064 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2705 r_free = 0.2705 target = 0.058055 restraints weight = 20058.237| |-----------------------------------------------------------------------------| r_work (start): 0.2676 rms_B_bonded: 2.90 r_work: 0.2541 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work (final): 0.2541 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8739 moved from start: 0.1184 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.085 9780 Z= 0.112 Angle : 0.495 9.034 13357 Z= 0.237 Chirality : 0.039 0.214 1445 Planarity : 0.004 0.051 1755 Dihedral : 4.085 71.632 1355 Min Nonbonded Distance : 2.608 Molprobity Statistics. All-atom Clashscore : 3.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 0.64 % Allowed : 19.49 % Favored : 79.87 % 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 are not related in a simple way. whole: 1.18 (0.23), residues: 1247 helix: 1.91 (0.21), residues: 584 sheet: 3.32 (1.71), residues: 10 loop : -0.28 (0.24), residues: 653 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 254 TYR 0.020 0.001 TYR B 229 PHE 0.005 0.001 PHE A 724 TRP 0.013 0.001 TRP B 191 HIS 0.004 0.001 HIS B 49 Details of bonding type rmsd covalent geometry : bond 0.00266 ( 9779) covalent geometry : angle 0.49452 (13357) hydrogen bonds : bond 0.03357 ( 450) hydrogen bonds : angle 3.87630 ( 1227) Misc. bond : bond 0.08505 ( 1) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2494 Ramachandran restraints generated. 1247 Oldfield, 0 Emsley, 1247 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2494 Ramachandran restraints generated. 1247 Oldfield, 0 Emsley, 1247 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 41 residues out of total 999 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 35 time to evaluate : 0.257 Fit side-chains REVERT: B 391 GLU cc_start: 0.8760 (OUTLIER) cc_final: 0.7894 (tp30) REVERT: B 669 GLU cc_start: 0.8804 (OUTLIER) cc_final: 0.8345 (pp20) outliers start: 6 outliers final: 1 residues processed: 40 average time/residue: 0.6406 time to fit residues: 27.3618 Evaluate side-chains 35 residues out of total 999 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 32 time to evaluate : 0.244 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 607 GLU Chi-restraints excluded: chain B residue 391 GLU Chi-restraints excluded: chain B residue 669 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 64 optimal weight: 0.9980 chunk 16 optimal weight: 0.8980 chunk 55 optimal weight: 0.8980 chunk 102 optimal weight: 0.0770 chunk 108 optimal weight: 3.9990 chunk 80 optimal weight: 4.9990 chunk 15 optimal weight: 4.9990 chunk 18 optimal weight: 4.9990 chunk 83 optimal weight: 0.6980 chunk 69 optimal weight: 3.9990 chunk 58 optimal weight: 0.9980 overall best weight: 0.7138 ------------------------------------------------------------------------------- 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 = 0.3052 r_free = 0.3052 target = 0.076093 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2718 r_free = 0.2718 target = 0.058128 restraints weight = 19751.031| |-----------------------------------------------------------------------------| r_work (start): 0.2698 rms_B_bonded: 2.86 r_work: 0.2572 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work (final): 0.2572 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8750 moved from start: 0.1261 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.096 9780 Z= 0.106 Angle : 0.493 8.137 13357 Z= 0.235 Chirality : 0.039 0.224 1445 Planarity : 0.004 0.051 1755 Dihedral : 4.044 72.315 1355 Min Nonbonded Distance : 2.602 Molprobity Statistics. All-atom Clashscore : 3.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 0.32 % Allowed : 19.81 % Favored : 79.87 % 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 are not related in a simple way. whole: 1.27 (0.24), residues: 1247 helix: 2.00 (0.21), residues: 584 sheet: 3.34 (1.72), residues: 10 loop : -0.25 (0.24), residues: 653 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 254 TYR 0.015 0.001 TYR B 155 PHE 0.006 0.001 PHE A 167 TRP 0.016 0.001 TRP B 107 HIS 0.004 0.001 HIS B 49 Details of bonding type rmsd covalent geometry : bond 0.00251 ( 9779) covalent geometry : angle 0.49304 (13357) hydrogen bonds : bond 0.03254 ( 450) hydrogen bonds : angle 3.81442 ( 1227) Misc. bond : bond 0.09583 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1924.92 seconds wall clock time: 33 minutes 35.34 seconds (2015.34 seconds total)