Starting phenix.real_space_refine on Tue Apr 29 14:01:13 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8xs5_38615/04_2025/8xs5_38615.cif Found real_map, /net/cci-nas-00/data/ceres_data/8xs5_38615/04_2025/8xs5_38615.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.33 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8xs5_38615/04_2025/8xs5_38615.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8xs5_38615/04_2025/8xs5_38615.map" model { file = "/net/cci-nas-00/data/ceres_data/8xs5_38615/04_2025/8xs5_38615.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8xs5_38615/04_2025/8xs5_38615.cif" } resolution = 3.33 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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= 0.006 sd= 0.068 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 39 5.16 5 C 5775 2.51 5 N 1425 2.21 5 O 1466 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 28 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/chem_data/mon_lib" Total number of atoms: 8705 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 3630 Number of conformers: 1 Conformer: "" Number of residues, atoms: 454, 3630 Classifications: {'peptide': 454} Incomplete info: {'truncation_to_alanine': 17} Link IDs: {'PTRANS': 23, 'TRANS': 430} Chain breaks: 4 Unresolved non-hydrogen bonds: 70 Unresolved non-hydrogen angles: 88 Unresolved non-hydrogen dihedrals: 61 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLN:plan1': 2, 'PHE:plan': 1, 'ARG:plan': 2, 'ASN:plan1': 2, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 39 Chain: "B" Number of atoms: 5075 Number of conformers: 1 Conformer: "" Number of residues, atoms: 634, 5075 Classifications: {'peptide': 634} Incomplete info: {'truncation_to_alanine': 17} Link IDs: {'PTRANS': 34, 'TRANS': 599} Chain breaks: 4 Unresolved non-hydrogen bonds: 70 Unresolved non-hydrogen angles: 88 Unresolved non-hydrogen dihedrals: 61 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLN:plan1': 2, 'PHE:plan': 1, 'ARG:plan': 2, 'ASN:plan1': 2, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 39 Time building chain proxies: 5.14, per 1000 atoms: 0.59 Number of scatterers: 8705 At special positions: 0 Unit cell: (97.06, 127.655, 98.115, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 39 16.00 O 1466 8.00 N 1425 7.00 C 5775 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.25 Conformation dependent library (CDL) restraints added in 1.0 seconds 2136 Ramachandran restraints generated. 1068 Oldfield, 0 Emsley, 1068 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2092 Finding SS restraints... Secondary structure from input PDB file: 50 helices and 2 sheets defined 73.3% alpha, 3.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.84 Creating SS restraints... Processing helix chain 'A' and resid 93 through 121 removed outlier: 3.986A pdb=" N ILE A 101 " --> pdb=" O VAL A 97 " (cutoff:3.500A) removed outlier: 4.570A pdb=" N TYR A 102 " --> pdb=" O TYR A 98 " (cutoff:3.500A) removed outlier: 4.154A pdb=" N GLY A 105 " --> pdb=" O ILE A 101 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N LEU A 106 " --> pdb=" O TYR A 102 " (cutoff:3.500A) Proline residue: A 111 - end of helix removed outlier: 3.723A pdb=" N VAL A 114 " --> pdb=" O THR A 110 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N ALA A 118 " --> pdb=" O VAL A 114 " (cutoff:3.500A) removed outlier: 4.361A pdb=" N VAL A 119 " --> pdb=" O LEU A 115 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N VAL A 121 " --> pdb=" O TRP A 117 " (cutoff:3.500A) Processing helix chain 'A' and resid 158 through 191 Processing helix chain 'A' and resid 216 through 228 Processing helix chain 'A' and resid 241 through 269 removed outlier: 3.929A pdb=" N LEU A 245 " --> pdb=" O ASN A 241 " (cutoff:3.500A) Processing helix chain 'A' and resid 291 through 313 removed outlier: 3.513A pdb=" N LYS A 303 " --> pdb=" O ASP A 299 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N VAL A 313 " --> pdb=" O ARG A 309 " (cutoff:3.500A) Processing helix chain 'A' and resid 329 through 339 removed outlier: 3.593A pdb=" N THR A 339 " --> pdb=" O VAL A 335 " (cutoff:3.500A) Processing helix chain 'A' and resid 360 through 366 removed outlier: 3.672A pdb=" N LEU A 364 " --> pdb=" O TRP A 361 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N ALA A 365 " --> pdb=" O SER A 362 " (cutoff:3.500A) Processing helix chain 'A' and resid 370 through 400 Proline residue: A 392 - end of helix Processing helix chain 'A' and resid 428 through 437 removed outlier: 3.763A pdb=" N ILE A 432 " --> pdb=" O PHE A 428 " (cutoff:3.500A) Processing helix chain 'A' and resid 440 through 451 Processing helix chain 'A' and resid 456 through 489 removed outlier: 3.911A pdb=" N PHE A 477 " --> pdb=" O LEU A 473 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ALA A 479 " --> pdb=" O ASN A 475 " (cutoff:3.500A) removed outlier: 4.785A pdb=" N SER A 480 " --> pdb=" O VAL A 476 " (cutoff:3.500A) Processing helix chain 'A' and resid 568 through 583 removed outlier: 3.770A pdb=" N ARG A 572 " --> pdb=" O THR A 568 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N TYR A 583 " --> pdb=" O LEU A 579 " (cutoff:3.500A) Processing helix chain 'A' and resid 623 through 647 Processing helix chain 'A' and resid 654 through 659 Processing helix chain 'A' and resid 659 through 677 removed outlier: 4.279A pdb=" N VAL A 663 " --> pdb=" O ILE A 659 " (cutoff:3.500A) Processing helix chain 'A' and resid 678 through 680 No H-bonds generated for 'chain 'A' and resid 678 through 680' Processing helix chain 'A' and resid 684 through 699 Processing helix chain 'A' and resid 703 through 709 Processing helix chain 'B' and resid 4 through 30 removed outlier: 4.074A pdb=" N LEU B 30 " --> pdb=" O ALA B 26 " (cutoff:3.500A) Processing helix chain 'B' and resid 31 through 33 No H-bonds generated for 'chain 'B' and resid 31 through 33' Processing helix chain 'B' and resid 34 through 39 removed outlier: 3.672A pdb=" N TYR B 38 " --> pdb=" O ASN B 34 " (cutoff:3.500A) Processing helix chain 'B' and resid 74 through 79 Processing helix chain 'B' and resid 83 through 91 Processing helix chain 'B' and resid 92 through 120 removed outlier: 3.545A pdb=" N VAL B 96 " --> pdb=" O GLY B 92 " (cutoff:3.500A) removed outlier: 4.346A pdb=" N TYR B 102 " --> pdb=" O TYR B 98 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N TRP B 103 " --> pdb=" O LEU B 99 " (cutoff:3.500A) Proline residue: B 111 - end of helix Processing helix chain 'B' and resid 157 through 195 Processing helix chain 'B' and resid 198 through 201 Processing helix chain 'B' and resid 216 through 229 Processing helix chain 'B' and resid 242 through 269 Processing helix chain 'B' and resid 291 through 315 removed outlier: 3.626A pdb=" N VAL B 313 " --> pdb=" O ARG B 309 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N ASN B 314 " --> pdb=" O GLU B 310 " (cutoff:3.500A) Processing helix chain 'B' and resid 329 through 337 Processing helix chain 'B' and resid 360 through 364 Processing helix chain 'B' and resid 367 through 369 No H-bonds generated for 'chain 'B' and resid 367 through 369' Processing helix chain 'B' and resid 370 through 388 Processing helix chain 'B' and resid 389 through 399 removed outlier: 3.772A pdb=" N ILE B 393 " --> pdb=" O PHE B 389 " (cutoff:3.500A) Processing helix chain 'B' and resid 421 through 438 removed outlier: 3.615A pdb=" N ILE B 425 " --> pdb=" O MET B 421 " (cutoff:3.500A) Proline residue: B 430 - end of helix Processing helix chain 'B' and resid 440 through 452 removed outlier: 3.620A pdb=" N ILE B 444 " --> pdb=" O PHE B 440 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N GLU B 452 " --> pdb=" O MET B 448 " (cutoff:3.500A) Processing helix chain 'B' and resid 456 through 476 Processing helix chain 'B' and resid 477 through 489 Processing helix chain 'B' and resid 504 through 509 Processing helix chain 'B' and resid 512 through 532 removed outlier: 3.814A pdb=" N ALA B 526 " --> pdb=" O VAL B 522 " (cutoff:3.500A) removed outlier: 4.445A pdb=" N GLY B 527 " --> pdb=" O ASP B 523 " (cutoff:3.500A) Processing helix chain 'B' and resid 534 through 548 Processing helix chain 'B' and resid 554 through 559 removed outlier: 3.782A pdb=" N ALA B 558 " --> pdb=" O ASP B 554 " (cutoff:3.500A) Processing helix chain 'B' and resid 565 through 584 Proline residue: B 571 - end of helix Processing helix chain 'B' and resid 590 through 612 removed outlier: 3.661A pdb=" N ILE B 594 " --> pdb=" O LEU B 590 " (cutoff:3.500A) Processing helix chain 'B' and resid 623 through 647 Processing helix chain 'B' and resid 654 through 659 Processing helix chain 'B' and resid 659 through 677 removed outlier: 3.810A pdb=" N VAL B 663 " --> pdb=" O ILE B 659 " (cutoff:3.500A) Processing helix chain 'B' and resid 677 through 682 Processing helix chain 'B' and resid 684 through 699 Processing helix chain 'B' and resid 703 through 709 Processing sheet with id=AA1, first strand: chain 'A' and resid 203 through 207 removed outlier: 5.725A pdb=" N ALA A 322 " --> pdb=" O VAL A 239 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 233 through 240 removed outlier: 5.416A pdb=" N ALA B 322 " --> pdb=" O VAL B 239 " (cutoff:3.500A) 573 hydrogen bonds defined for protein. 1701 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: 2.67 Time building geometry restraints manager: 2.66 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2457 1.33 - 1.45: 1626 1.45 - 1.57: 4799 1.57 - 1.69: 0 1.69 - 1.81: 70 Bond restraints: 8952 Sorted by residual: bond pdb=" C ARG A 198 " pdb=" N PRO A 199 " ideal model delta sigma weight residual 1.331 1.302 0.029 1.28e-02 6.10e+03 5.26e+00 bond pdb=" CE1 TYR B 181 " pdb=" CZ TYR B 181 " ideal model delta sigma weight residual 1.378 1.323 0.055 2.40e-02 1.74e+03 5.17e+00 bond pdb=" CA GLY B 524 " pdb=" C GLY B 524 " ideal model delta sigma weight residual 1.515 1.501 0.014 6.20e-03 2.60e+04 4.98e+00 bond pdb=" CB ILE B 594 " pdb=" CG2 ILE B 594 " ideal model delta sigma weight residual 1.521 1.452 0.069 3.30e-02 9.18e+02 4.39e+00 bond pdb=" CG1 ILE B 532 " pdb=" CD1 ILE B 532 " ideal model delta sigma weight residual 1.513 1.434 0.079 3.90e-02 6.57e+02 4.09e+00 ... (remaining 8947 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.86: 11636 1.86 - 3.71: 427 3.71 - 5.57: 96 5.57 - 7.42: 19 7.42 - 9.28: 3 Bond angle restraints: 12181 Sorted by residual: angle pdb=" C ASN A 257 " pdb=" N TRP A 258 " pdb=" CA TRP A 258 " ideal model delta sigma weight residual 120.44 126.03 -5.59 1.30e+00 5.92e-01 1.85e+01 angle pdb=" N VAL A 119 " pdb=" CA VAL A 119 " pdb=" C VAL A 119 " ideal model delta sigma weight residual 113.47 109.59 3.88 1.01e+00 9.80e-01 1.48e+01 angle pdb=" C PHE B 109 " pdb=" N THR B 110 " pdb=" CA THR B 110 " ideal model delta sigma weight residual 121.80 112.52 9.28 2.44e+00 1.68e-01 1.45e+01 angle pdb=" CA TYR B 181 " pdb=" CB TYR B 181 " pdb=" CG TYR B 181 " ideal model delta sigma weight residual 113.90 120.38 -6.48 1.80e+00 3.09e-01 1.30e+01 angle pdb=" N ILE B 659 " pdb=" CA ILE B 659 " pdb=" C ILE B 659 " ideal model delta sigma weight residual 113.22 109.10 4.12 1.23e+00 6.61e-01 1.12e+01 ... (remaining 12176 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.87: 4728 16.87 - 33.74: 413 33.74 - 50.60: 93 50.60 - 67.47: 11 67.47 - 84.34: 5 Dihedral angle restraints: 5250 sinusoidal: 2035 harmonic: 3215 Sorted by residual: dihedral pdb=" CA GLU B 618 " pdb=" C GLU B 618 " pdb=" N SER B 619 " pdb=" CA SER B 619 " ideal model delta harmonic sigma weight residual 180.00 152.16 27.84 0 5.00e+00 4.00e-02 3.10e+01 dihedral pdb=" CA GLU B 452 " pdb=" C GLU B 452 " pdb=" N GLY B 453 " pdb=" CA GLY B 453 " ideal model delta harmonic sigma weight residual -180.00 -153.06 -26.94 0 5.00e+00 4.00e-02 2.90e+01 dihedral pdb=" CA VAL B 276 " pdb=" C VAL B 276 " pdb=" N LYS B 277 " pdb=" CA LYS B 277 " ideal model delta harmonic sigma weight residual 180.00 154.67 25.33 0 5.00e+00 4.00e-02 2.57e+01 ... (remaining 5247 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.039: 772 0.039 - 0.077: 417 0.077 - 0.116: 145 0.116 - 0.155: 35 0.155 - 0.194: 9 Chirality restraints: 1378 Sorted by residual: chirality pdb=" CA THR A 110 " pdb=" N THR A 110 " pdb=" C THR A 110 " pdb=" CB THR A 110 " both_signs ideal model delta sigma weight residual False 2.53 2.33 0.19 2.00e-01 2.50e+01 9.36e-01 chirality pdb=" CB THR B 587 " pdb=" CA THR B 587 " pdb=" OG1 THR B 587 " pdb=" CG2 THR B 587 " both_signs ideal model delta sigma weight residual False 2.55 2.36 0.19 2.00e-01 2.50e+01 8.91e-01 chirality pdb=" CA LEU B 661 " pdb=" N LEU B 661 " pdb=" C LEU B 661 " pdb=" CB LEU B 661 " both_signs ideal model delta sigma weight residual False 2.51 2.33 0.18 2.00e-01 2.50e+01 8.20e-01 ... (remaining 1375 not shown) Planarity restraints: 1513 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR B 181 " 0.059 2.00e-02 2.50e+03 4.62e-02 4.26e+01 pdb=" CG TYR B 181 " -0.112 2.00e-02 2.50e+03 pdb=" CD1 TYR B 181 " 0.027 2.00e-02 2.50e+03 pdb=" CD2 TYR B 181 " 0.005 2.00e-02 2.50e+03 pdb=" CE1 TYR B 181 " -0.008 2.00e-02 2.50e+03 pdb=" CE2 TYR B 181 " 0.015 2.00e-02 2.50e+03 pdb=" CZ TYR B 181 " 0.008 2.00e-02 2.50e+03 pdb=" OH TYR B 181 " 0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 181 " 0.036 2.00e-02 2.50e+03 3.26e-02 2.12e+01 pdb=" CG TYR A 181 " -0.080 2.00e-02 2.50e+03 pdb=" CD1 TYR A 181 " 0.023 2.00e-02 2.50e+03 pdb=" CD2 TYR A 181 " 0.006 2.00e-02 2.50e+03 pdb=" CE1 TYR A 181 " -0.002 2.00e-02 2.50e+03 pdb=" CE2 TYR A 181 " 0.015 2.00e-02 2.50e+03 pdb=" CZ TYR A 181 " 0.002 2.00e-02 2.50e+03 pdb=" OH TYR A 181 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR B 468 " -0.024 2.00e-02 2.50e+03 2.71e-02 1.47e+01 pdb=" CG TYR B 468 " 0.067 2.00e-02 2.50e+03 pdb=" CD1 TYR B 468 " -0.024 2.00e-02 2.50e+03 pdb=" CD2 TYR B 468 " -0.015 2.00e-02 2.50e+03 pdb=" CE1 TYR B 468 " 0.003 2.00e-02 2.50e+03 pdb=" CE2 TYR B 468 " -0.006 2.00e-02 2.50e+03 pdb=" CZ TYR B 468 " -0.002 2.00e-02 2.50e+03 pdb=" OH TYR B 468 " 0.001 2.00e-02 2.50e+03 ... (remaining 1510 not shown) Histogram of nonbonded interaction distances: 2.08 - 2.64: 100 2.64 - 3.21: 8448 3.21 - 3.77: 13376 3.77 - 4.34: 17513 4.34 - 4.90: 29241 Nonbonded interactions: 68678 Sorted by model distance: nonbonded pdb=" NH1 ARG A 198 " pdb=" OE2 GLU A 355 " model vdw 2.081 3.120 nonbonded pdb=" ND2 ASN B 208 " pdb=" O THR B 346 " model vdw 2.181 3.120 nonbonded pdb=" O MET A 157 " pdb=" OG1 THR A 161 " model vdw 2.224 3.040 nonbonded pdb=" ND2 ASN A 208 " pdb=" O THR A 346 " model vdw 2.235 3.120 nonbonded pdb=" O GLU A 180 " pdb=" OG1 THR A 183 " model vdw 2.243 3.040 ... (remaining 68673 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=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.780 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: 0.330 Check model and map are aligned: 0.060 Set scattering table: 0.080 Process input model: 23.110 Find NCS groups from input model: 0.080 Set up NCS constraints: 0.040 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:3.740 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.230 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8210 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 : 0.011 0.081 8952 Z= 0.458 Angle : 0.882 9.275 12181 Z= 0.493 Chirality : 0.053 0.194 1378 Planarity : 0.007 0.065 1513 Dihedral : 13.490 84.338 3158 Min Nonbonded Distance : 2.081 Molprobity Statistics. All-atom Clashscore : 9.41 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.74 % Favored : 93.16 % Rotamer: Outliers : 0.00 % Allowed : 0.22 % Favored : 99.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.34 (0.25), residues: 1068 helix: 0.85 (0.19), residues: 715 sheet: -2.25 (0.79), residues: 38 loop : -2.49 (0.32), residues: 315 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.003 TRP A 624 HIS 0.010 0.002 HIS A 379 PHE 0.023 0.002 PHE A 225 TYR 0.112 0.004 TYR B 181 ARG 0.012 0.001 ARG A 197 Details of bonding type rmsd hydrogen bonds : bond 0.12586 ( 573) hydrogen bonds : angle 5.49024 ( 1701) covalent geometry : bond 0.01103 ( 8952) covalent geometry : angle 0.88206 (12181) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2136 Ramachandran restraints generated. 1068 Oldfield, 0 Emsley, 1068 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2136 Ramachandran restraints generated. 1068 Oldfield, 0 Emsley, 1068 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 937 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 137 time to evaluate : 1.547 Fit side-chains REVERT: A 200 ASP cc_start: 0.8281 (p0) cc_final: 0.7935 (p0) REVERT: A 212 ASP cc_start: 0.8651 (t0) cc_final: 0.7838 (t0) REVERT: A 214 ASP cc_start: 0.8847 (m-30) cc_final: 0.8461 (m-30) REVERT: A 215 GLU cc_start: 0.8058 (mp0) cc_final: 0.7466 (mp0) REVERT: B 159 PHE cc_start: 0.8241 (t80) cc_final: 0.7932 (t80) REVERT: B 387 PHE cc_start: 0.8032 (t80) cc_final: 0.7700 (t80) REVERT: B 556 GLU cc_start: 0.7738 (pm20) cc_final: 0.7128 (tm-30) outliers start: 0 outliers final: 0 residues processed: 137 average time/residue: 0.2987 time to fit residues: 57.0940 Evaluate side-chains 116 residues out of total 937 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 116 time to evaluate : 0.889 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 91 optimal weight: 2.9990 chunk 81 optimal weight: 0.8980 chunk 45 optimal weight: 0.6980 chunk 27 optimal weight: 9.9990 chunk 55 optimal weight: 0.9990 chunk 43 optimal weight: 0.6980 chunk 84 optimal weight: 0.6980 chunk 32 optimal weight: 9.9990 chunk 51 optimal weight: 0.6980 chunk 63 optimal weight: 0.9980 chunk 98 optimal weight: 0.6980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 340 GLN B 14 ASN B 545 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3982 r_free = 0.3982 target = 0.173799 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3204 r_free = 0.3204 target = 0.110545 restraints weight = 10989.280| |-----------------------------------------------------------------------------| r_work (start): 0.3170 rms_B_bonded: 2.66 r_work: 0.2914 rms_B_bonded: 3.32 restraints_weight: 0.5000 r_work (final): 0.2914 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8183 moved from start: 0.1186 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 8952 Z= 0.149 Angle : 0.620 8.533 12181 Z= 0.321 Chirality : 0.043 0.177 1378 Planarity : 0.006 0.059 1513 Dihedral : 4.842 24.875 1168 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 5.85 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.96 % Favored : 94.94 % Rotamer: Outliers : 0.78 % Allowed : 6.31 % Favored : 92.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.42 (0.26), residues: 1068 helix: 1.47 (0.19), residues: 720 sheet: -2.30 (0.75), residues: 46 loop : -2.27 (0.35), residues: 302 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP A 624 HIS 0.004 0.001 HIS A 714 PHE 0.024 0.001 PHE B 428 TYR 0.045 0.002 TYR B 181 ARG 0.003 0.000 ARG A 198 Details of bonding type rmsd hydrogen bonds : bond 0.04326 ( 573) hydrogen bonds : angle 4.33543 ( 1701) covalent geometry : bond 0.00343 ( 8952) covalent geometry : angle 0.61965 (12181) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2136 Ramachandran restraints generated. 1068 Oldfield, 0 Emsley, 1068 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2136 Ramachandran restraints generated. 1068 Oldfield, 0 Emsley, 1068 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 937 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 122 time to evaluate : 0.914 Fit side-chains REVERT: A 200 ASP cc_start: 0.8378 (p0) cc_final: 0.8115 (p0) REVERT: A 683 TYR cc_start: 0.8698 (m-80) cc_final: 0.8405 (m-80) REVERT: A 709 GLN cc_start: 0.8476 (pp30) cc_final: 0.8126 (pp30) REVERT: B 159 PHE cc_start: 0.7972 (t80) cc_final: 0.7724 (t80) outliers start: 7 outliers final: 4 residues processed: 126 average time/residue: 0.2280 time to fit residues: 39.1675 Evaluate side-chains 113 residues out of total 937 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 109 time to evaluate : 1.000 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 99 LEU Chi-restraints excluded: chain A residue 340 GLN Chi-restraints excluded: chain A residue 637 ILE Chi-restraints excluded: chain B residue 545 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 63 optimal weight: 0.9990 chunk 62 optimal weight: 1.9990 chunk 49 optimal weight: 0.5980 chunk 34 optimal weight: 4.9990 chunk 29 optimal weight: 4.9990 chunk 79 optimal weight: 0.0000 chunk 81 optimal weight: 0.5980 chunk 88 optimal weight: 0.8980 chunk 35 optimal weight: 9.9990 chunk 92 optimal weight: 2.9990 chunk 17 optimal weight: 20.0000 overall best weight: 0.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 340 GLN B 545 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3985 r_free = 0.3985 target = 0.174099 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 75)----------------| | r_work = 0.3188 r_free = 0.3188 target = 0.107519 restraints weight = 11028.705| |-----------------------------------------------------------------------------| r_work (start): 0.3137 rms_B_bonded: 2.11 r_work: 0.2964 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.2811 rms_B_bonded: 4.54 restraints_weight: 0.2500 r_work (final): 0.2811 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8278 moved from start: 0.1556 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 8952 Z= 0.133 Angle : 0.580 8.211 12181 Z= 0.298 Chirality : 0.042 0.190 1378 Planarity : 0.005 0.056 1513 Dihedral : 4.559 21.626 1168 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 5.79 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.96 % Favored : 94.94 % Rotamer: Outliers : 1.00 % Allowed : 9.08 % Favored : 89.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.67 (0.26), residues: 1068 helix: 1.69 (0.19), residues: 720 sheet: -2.36 (0.76), residues: 44 loop : -2.28 (0.34), residues: 304 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP A 103 HIS 0.004 0.001 HIS A 628 PHE 0.021 0.001 PHE B 428 TYR 0.032 0.001 TYR B 181 ARG 0.003 0.000 ARG B 555 Details of bonding type rmsd hydrogen bonds : bond 0.03872 ( 573) hydrogen bonds : angle 4.12576 ( 1701) covalent geometry : bond 0.00305 ( 8952) covalent geometry : angle 0.58038 (12181) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2136 Ramachandran restraints generated. 1068 Oldfield, 0 Emsley, 1068 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2136 Ramachandran restraints generated. 1068 Oldfield, 0 Emsley, 1068 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 937 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 127 time to evaluate : 0.926 Fit side-chains REVERT: A 200 ASP cc_start: 0.8357 (p0) cc_final: 0.8074 (p0) REVERT: A 212 ASP cc_start: 0.8614 (t0) cc_final: 0.8397 (t0) REVERT: A 340 GLN cc_start: 0.8758 (OUTLIER) cc_final: 0.8476 (tt0) REVERT: A 709 GLN cc_start: 0.8401 (pp30) cc_final: 0.8179 (pp30) REVERT: B 159 PHE cc_start: 0.7939 (t80) cc_final: 0.7613 (t80) REVERT: B 395 PHE cc_start: 0.8964 (t80) cc_final: 0.8708 (t80) outliers start: 9 outliers final: 4 residues processed: 132 average time/residue: 0.2047 time to fit residues: 37.7854 Evaluate side-chains 119 residues out of total 937 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 114 time to evaluate : 0.943 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 99 LEU Chi-restraints excluded: chain A residue 340 GLN Chi-restraints excluded: chain A residue 637 ILE Chi-restraints excluded: chain A residue 663 VAL Chi-restraints excluded: chain B residue 545 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 21 optimal weight: 1.9990 chunk 83 optimal weight: 0.8980 chunk 44 optimal weight: 5.9990 chunk 38 optimal weight: 5.9990 chunk 50 optimal weight: 0.0980 chunk 86 optimal weight: 7.9990 chunk 97 optimal weight: 0.9980 chunk 19 optimal weight: 1.9990 chunk 106 optimal weight: 5.9990 chunk 87 optimal weight: 0.4980 chunk 89 optimal weight: 0.9990 overall best weight: 0.6982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 228 ASN A 340 GLN ** A 363 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 545 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3994 r_free = 0.3994 target = 0.174831 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3183 r_free = 0.3183 target = 0.107220 restraints weight = 11055.754| |-----------------------------------------------------------------------------| r_work (start): 0.3132 rms_B_bonded: 2.18 r_work: 0.2974 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.2823 rms_B_bonded: 4.51 restraints_weight: 0.2500 r_work (final): 0.2823 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8255 moved from start: 0.1791 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 8952 Z= 0.133 Angle : 0.565 6.907 12181 Z= 0.290 Chirality : 0.042 0.186 1378 Planarity : 0.005 0.061 1513 Dihedral : 4.440 20.897 1168 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 5.28 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.96 % Favored : 94.94 % Rotamer: Outliers : 1.22 % Allowed : 10.30 % Favored : 88.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.86 (0.27), residues: 1068 helix: 1.88 (0.19), residues: 721 sheet: -2.36 (0.76), residues: 44 loop : -2.32 (0.34), residues: 303 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP A 624 HIS 0.004 0.001 HIS A 628 PHE 0.018 0.001 PHE B 428 TYR 0.026 0.001 TYR B 181 ARG 0.003 0.000 ARG A 357 Details of bonding type rmsd hydrogen bonds : bond 0.03697 ( 573) hydrogen bonds : angle 4.05112 ( 1701) covalent geometry : bond 0.00308 ( 8952) covalent geometry : angle 0.56491 (12181) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2136 Ramachandran restraints generated. 1068 Oldfield, 0 Emsley, 1068 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2136 Ramachandran restraints generated. 1068 Oldfield, 0 Emsley, 1068 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 937 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 124 time to evaluate : 1.029 Fit side-chains REVERT: A 190 GLN cc_start: 0.8286 (mm-40) cc_final: 0.8012 (mt0) REVERT: A 200 ASP cc_start: 0.8328 (p0) cc_final: 0.8002 (p0) REVERT: A 212 ASP cc_start: 0.8694 (t0) cc_final: 0.8342 (t0) REVERT: A 320 MET cc_start: 0.8105 (ttp) cc_final: 0.7868 (ttm) REVERT: A 340 GLN cc_start: 0.8773 (OUTLIER) cc_final: 0.8564 (tt0) REVERT: B 159 PHE cc_start: 0.7924 (t80) cc_final: 0.7694 (t80) REVERT: B 395 PHE cc_start: 0.9015 (t80) cc_final: 0.8725 (t80) REVERT: B 545 ASN cc_start: 0.8980 (OUTLIER) cc_final: 0.8653 (m-40) outliers start: 11 outliers final: 6 residues processed: 131 average time/residue: 0.1961 time to fit residues: 36.4994 Evaluate side-chains 122 residues out of total 937 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 114 time to evaluate : 0.979 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 99 LEU Chi-restraints excluded: chain A residue 169 PHE Chi-restraints excluded: chain A residue 340 GLN Chi-restraints excluded: chain A residue 637 ILE Chi-restraints excluded: chain A residue 663 VAL Chi-restraints excluded: chain B residue 452 GLU Chi-restraints excluded: chain B residue 545 ASN Chi-restraints excluded: chain B residue 567 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 98 optimal weight: 0.0370 chunk 77 optimal weight: 1.9990 chunk 61 optimal weight: 2.9990 chunk 50 optimal weight: 0.2980 chunk 24 optimal weight: 8.9990 chunk 103 optimal weight: 1.9990 chunk 37 optimal weight: 6.9990 chunk 72 optimal weight: 0.6980 chunk 41 optimal weight: 0.9980 chunk 69 optimal weight: 0.8980 chunk 45 optimal weight: 4.9990 overall best weight: 0.5858 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 340 GLN ** A 363 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 545 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4001 r_free = 0.4001 target = 0.175515 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.3190 r_free = 0.3190 target = 0.107775 restraints weight = 11022.589| |-----------------------------------------------------------------------------| r_work (start): 0.3141 rms_B_bonded: 2.18 r_work: 0.2984 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.2834 rms_B_bonded: 4.51 restraints_weight: 0.2500 r_work (final): 0.2834 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8237 moved from start: 0.1967 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 8952 Z= 0.125 Angle : 0.564 6.680 12181 Z= 0.286 Chirality : 0.041 0.186 1378 Planarity : 0.005 0.063 1513 Dihedral : 4.314 20.435 1168 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 4.99 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.24 % Favored : 94.66 % Rotamer: Outliers : 1.33 % Allowed : 11.96 % Favored : 86.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.07 (0.27), residues: 1068 helix: 1.99 (0.19), residues: 724 sheet: -1.89 (0.84), residues: 38 loop : -2.22 (0.33), residues: 306 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 624 HIS 0.004 0.001 HIS A 628 PHE 0.025 0.001 PHE A 471 TYR 0.022 0.001 TYR A 261 ARG 0.003 0.000 ARG A 357 Details of bonding type rmsd hydrogen bonds : bond 0.03552 ( 573) hydrogen bonds : angle 3.99208 ( 1701) covalent geometry : bond 0.00287 ( 8952) covalent geometry : angle 0.56393 (12181) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2136 Ramachandran restraints generated. 1068 Oldfield, 0 Emsley, 1068 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2136 Ramachandran restraints generated. 1068 Oldfield, 0 Emsley, 1068 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 937 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 120 time to evaluate : 0.952 Fit side-chains REVERT: A 200 ASP cc_start: 0.8283 (p0) cc_final: 0.7946 (p0) REVERT: A 212 ASP cc_start: 0.8714 (t0) cc_final: 0.8307 (t0) REVERT: B 159 PHE cc_start: 0.7899 (t80) cc_final: 0.7645 (t80) REVERT: B 545 ASN cc_start: 0.8978 (OUTLIER) cc_final: 0.8627 (m-40) outliers start: 12 outliers final: 7 residues processed: 127 average time/residue: 0.1971 time to fit residues: 35.7498 Evaluate side-chains 121 residues out of total 937 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 113 time to evaluate : 0.992 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 99 LEU Chi-restraints excluded: chain A residue 169 PHE Chi-restraints excluded: chain A residue 181 TYR Chi-restraints excluded: chain A residue 359 VAL Chi-restraints excluded: chain A residue 637 ILE Chi-restraints excluded: chain B residue 452 GLU Chi-restraints excluded: chain B residue 545 ASN Chi-restraints excluded: chain B residue 567 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 25 optimal weight: 8.9990 chunk 91 optimal weight: 0.9990 chunk 84 optimal weight: 0.6980 chunk 54 optimal weight: 0.9980 chunk 33 optimal weight: 5.9990 chunk 59 optimal weight: 0.0170 chunk 67 optimal weight: 0.0010 chunk 2 optimal weight: 0.0020 chunk 88 optimal weight: 0.7980 chunk 96 optimal weight: 1.9990 chunk 51 optimal weight: 0.7980 overall best weight: 0.3032 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 363 ASN B 363 ASN B 545 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4015 r_free = 0.4015 target = 0.176831 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 76)----------------| | r_work = 0.3220 r_free = 0.3220 target = 0.109953 restraints weight = 10948.209| |-----------------------------------------------------------------------------| r_work (start): 0.3178 rms_B_bonded: 2.16 r_work: 0.3007 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.2858 rms_B_bonded: 4.54 restraints_weight: 0.2500 r_work (final): 0.2858 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8229 moved from start: 0.2223 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 8952 Z= 0.110 Angle : 0.547 6.588 12181 Z= 0.278 Chirality : 0.040 0.190 1378 Planarity : 0.005 0.064 1513 Dihedral : 4.209 19.894 1168 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 4.53 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.96 % Favored : 94.94 % Rotamer: Outliers : 1.33 % Allowed : 13.84 % Favored : 84.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.26 (0.27), residues: 1068 helix: 2.12 (0.19), residues: 725 sheet: -1.89 (0.86), residues: 38 loop : -2.08 (0.34), residues: 305 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A 103 HIS 0.004 0.000 HIS A 628 PHE 0.020 0.001 PHE B 395 TYR 0.020 0.001 TYR A 261 ARG 0.004 0.000 ARG B 555 Details of bonding type rmsd hydrogen bonds : bond 0.03317 ( 573) hydrogen bonds : angle 3.93358 ( 1701) covalent geometry : bond 0.00239 ( 8952) covalent geometry : angle 0.54678 (12181) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2136 Ramachandran restraints generated. 1068 Oldfield, 0 Emsley, 1068 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2136 Ramachandran restraints generated. 1068 Oldfield, 0 Emsley, 1068 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 937 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 131 time to evaluate : 0.849 Fit side-chains REVERT: A 200 ASP cc_start: 0.8218 (p0) cc_final: 0.7990 (p0) REVERT: A 320 MET cc_start: 0.7852 (ttm) cc_final: 0.7630 (ttm) REVERT: B 159 PHE cc_start: 0.7853 (t80) cc_final: 0.7630 (t80) REVERT: B 531 GLU cc_start: 0.7578 (mt-10) cc_final: 0.7012 (mm-30) REVERT: B 576 TYR cc_start: 0.8883 (m-10) cc_final: 0.8664 (m-10) outliers start: 12 outliers final: 8 residues processed: 137 average time/residue: 0.1963 time to fit residues: 38.8530 Evaluate side-chains 133 residues out of total 937 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 125 time to evaluate : 1.042 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 99 LEU Chi-restraints excluded: chain A residue 169 PHE Chi-restraints excluded: chain A residue 181 TYR Chi-restraints excluded: chain A residue 359 VAL Chi-restraints excluded: chain A residue 637 ILE Chi-restraints excluded: chain B residue 452 GLU Chi-restraints excluded: chain B residue 567 ASN Chi-restraints excluded: chain B residue 658 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 97 optimal weight: 0.9990 chunk 52 optimal weight: 0.9990 chunk 25 optimal weight: 7.9990 chunk 8 optimal weight: 0.0060 chunk 62 optimal weight: 2.9990 chunk 12 optimal weight: 5.9990 chunk 0 optimal weight: 20.0000 chunk 23 optimal weight: 2.9990 chunk 99 optimal weight: 0.5980 chunk 102 optimal weight: 0.3980 chunk 16 optimal weight: 40.0000 overall best weight: 0.6000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 228 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4011 r_free = 0.4011 target = 0.176446 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3257 r_free = 0.3257 target = 0.114251 restraints weight = 11131.013| |-----------------------------------------------------------------------------| r_work (start): 0.3228 rms_B_bonded: 2.56 r_work: 0.2986 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work: 0.2833 rms_B_bonded: 4.70 restraints_weight: 0.2500 r_work (final): 0.2833 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8233 moved from start: 0.2290 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 8952 Z= 0.123 Angle : 0.557 7.282 12181 Z= 0.282 Chirality : 0.041 0.179 1378 Planarity : 0.005 0.063 1513 Dihedral : 4.155 19.553 1168 Min Nonbonded Distance : 2.567 Molprobity Statistics. All-atom Clashscore : 5.10 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.06 % Favored : 94.85 % Rotamer: Outliers : 1.44 % Allowed : 13.95 % Favored : 84.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.36 (0.27), residues: 1068 helix: 2.17 (0.19), residues: 725 sheet: -1.92 (0.86), residues: 38 loop : -1.99 (0.35), residues: 305 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 624 HIS 0.004 0.001 HIS A 628 PHE 0.017 0.001 PHE B 383 TYR 0.019 0.001 TYR A 261 ARG 0.004 0.000 ARG B 555 Details of bonding type rmsd hydrogen bonds : bond 0.03401 ( 573) hydrogen bonds : angle 3.91606 ( 1701) covalent geometry : bond 0.00283 ( 8952) covalent geometry : angle 0.55738 (12181) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2136 Ramachandran restraints generated. 1068 Oldfield, 0 Emsley, 1068 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2136 Ramachandran restraints generated. 1068 Oldfield, 0 Emsley, 1068 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 937 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 132 time to evaluate : 0.929 Fit side-chains revert: symmetry clash REVERT: A 200 ASP cc_start: 0.8249 (p0) cc_final: 0.7884 (p0) REVERT: A 212 ASP cc_start: 0.8804 (t0) cc_final: 0.8350 (t0) REVERT: B 159 PHE cc_start: 0.7923 (t80) cc_final: 0.7668 (t80) REVERT: B 397 GLN cc_start: 0.8844 (mm-40) cc_final: 0.8580 (mm-40) REVERT: B 531 GLU cc_start: 0.7626 (mt-10) cc_final: 0.7018 (mm-30) REVERT: B 576 TYR cc_start: 0.8917 (m-10) cc_final: 0.8694 (m-10) outliers start: 13 outliers final: 7 residues processed: 139 average time/residue: 0.1812 time to fit residues: 36.3535 Evaluate side-chains 128 residues out of total 937 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 121 time to evaluate : 0.889 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 99 LEU Chi-restraints excluded: chain A residue 181 TYR Chi-restraints excluded: chain A residue 359 VAL Chi-restraints excluded: chain A residue 637 ILE Chi-restraints excluded: chain B residue 452 GLU Chi-restraints excluded: chain B residue 567 ASN Chi-restraints excluded: chain B residue 658 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 28 optimal weight: 4.9990 chunk 91 optimal weight: 0.5980 chunk 1 optimal weight: 3.9990 chunk 55 optimal weight: 1.9990 chunk 97 optimal weight: 0.8980 chunk 10 optimal weight: 3.9990 chunk 67 optimal weight: 20.0000 chunk 107 optimal weight: 0.7980 chunk 21 optimal weight: 1.9990 chunk 56 optimal weight: 0.6980 chunk 47 optimal weight: 0.5980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 228 ASN ** A 639 GLN ** 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 = 0.4005 r_free = 0.4005 target = 0.175974 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3235 r_free = 0.3235 target = 0.113335 restraints weight = 11180.372| |-----------------------------------------------------------------------------| r_work (start): 0.3199 rms_B_bonded: 2.67 r_work: 0.2951 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.2951 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8169 moved from start: 0.2368 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 8952 Z= 0.131 Angle : 0.570 7.819 12181 Z= 0.287 Chirality : 0.042 0.194 1378 Planarity : 0.005 0.064 1513 Dihedral : 4.171 19.521 1168 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 5.39 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.06 % Favored : 94.85 % Rotamer: Outliers : 1.11 % Allowed : 14.73 % Favored : 84.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.36 (0.27), residues: 1068 helix: 2.18 (0.19), residues: 725 sheet: -1.92 (0.85), residues: 38 loop : -1.98 (0.34), residues: 305 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP A 103 HIS 0.003 0.001 HIS A 628 PHE 0.022 0.001 PHE B 395 TYR 0.019 0.001 TYR B 181 ARG 0.004 0.000 ARG A 357 Details of bonding type rmsd hydrogen bonds : bond 0.03471 ( 573) hydrogen bonds : angle 3.93197 ( 1701) covalent geometry : bond 0.00307 ( 8952) covalent geometry : angle 0.57029 (12181) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2136 Ramachandran restraints generated. 1068 Oldfield, 0 Emsley, 1068 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2136 Ramachandran restraints generated. 1068 Oldfield, 0 Emsley, 1068 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 937 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 125 time to evaluate : 0.952 Fit side-chains revert: symmetry clash REVERT: A 200 ASP cc_start: 0.8186 (p0) cc_final: 0.7765 (p0) REVERT: A 212 ASP cc_start: 0.8784 (t0) cc_final: 0.8375 (t0) REVERT: B 159 PHE cc_start: 0.7775 (t80) cc_final: 0.7545 (t80) REVERT: B 397 GLN cc_start: 0.8816 (mm-40) cc_final: 0.8549 (mm-40) REVERT: B 531 GLU cc_start: 0.7325 (mt-10) cc_final: 0.6873 (mm-30) REVERT: B 576 TYR cc_start: 0.8841 (m-10) cc_final: 0.8605 (m-10) outliers start: 10 outliers final: 8 residues processed: 130 average time/residue: 0.1858 time to fit residues: 34.9127 Evaluate side-chains 123 residues out of total 937 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 115 time to evaluate : 0.977 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 99 LEU Chi-restraints excluded: chain A residue 169 PHE Chi-restraints excluded: chain A residue 181 TYR Chi-restraints excluded: chain A residue 359 VAL Chi-restraints excluded: chain A residue 637 ILE Chi-restraints excluded: chain B residue 452 GLU Chi-restraints excluded: chain B residue 567 ASN Chi-restraints excluded: chain B residue 658 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 3 optimal weight: 20.0000 chunk 102 optimal weight: 0.5980 chunk 22 optimal weight: 0.7980 chunk 21 optimal weight: 0.9990 chunk 81 optimal weight: 0.8980 chunk 53 optimal weight: 0.9990 chunk 51 optimal weight: 0.6980 chunk 70 optimal weight: 1.9990 chunk 59 optimal weight: 0.4980 chunk 98 optimal weight: 1.9990 chunk 15 optimal weight: 50.0000 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 228 ASN A 639 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4007 r_free = 0.4007 target = 0.176282 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 73)----------------| | r_work = 0.3199 r_free = 0.3199 target = 0.108465 restraints weight = 11063.748| |-----------------------------------------------------------------------------| r_work (start): 0.3171 rms_B_bonded: 2.13 r_work: 0.3002 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.2854 rms_B_bonded: 4.39 restraints_weight: 0.2500 r_work (final): 0.2854 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8212 moved from start: 0.2457 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 8952 Z= 0.129 Angle : 0.576 8.025 12181 Z= 0.286 Chirality : 0.041 0.196 1378 Planarity : 0.005 0.064 1513 Dihedral : 4.137 19.666 1168 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 5.16 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.78 % Favored : 95.13 % Rotamer: Outliers : 1.22 % Allowed : 14.62 % Favored : 84.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.39 (0.27), residues: 1068 helix: 2.20 (0.19), residues: 726 sheet: -1.99 (0.84), residues: 38 loop : -1.99 (0.34), residues: 304 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 624 HIS 0.003 0.001 HIS A 628 PHE 0.019 0.001 PHE B 383 TYR 0.018 0.001 TYR A 261 ARG 0.004 0.000 ARG A 357 Details of bonding type rmsd hydrogen bonds : bond 0.03442 ( 573) hydrogen bonds : angle 3.90918 ( 1701) covalent geometry : bond 0.00303 ( 8952) covalent geometry : angle 0.57568 (12181) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2136 Ramachandran restraints generated. 1068 Oldfield, 0 Emsley, 1068 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2136 Ramachandran restraints generated. 1068 Oldfield, 0 Emsley, 1068 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 937 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 125 time to evaluate : 0.977 Fit side-chains revert: symmetry clash REVERT: A 200 ASP cc_start: 0.8251 (p0) cc_final: 0.7815 (p0) REVERT: A 212 ASP cc_start: 0.8830 (t0) cc_final: 0.8379 (t0) REVERT: B 159 PHE cc_start: 0.7879 (t80) cc_final: 0.7583 (t80) REVERT: B 531 GLU cc_start: 0.7607 (mt-10) cc_final: 0.6994 (mm-30) REVERT: B 576 TYR cc_start: 0.8901 (m-10) cc_final: 0.8665 (m-10) outliers start: 11 outliers final: 8 residues processed: 130 average time/residue: 0.2080 time to fit residues: 39.2747 Evaluate side-chains 128 residues out of total 937 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 120 time to evaluate : 0.911 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 99 LEU Chi-restraints excluded: chain A residue 169 PHE Chi-restraints excluded: chain A residue 359 VAL Chi-restraints excluded: chain A residue 637 ILE Chi-restraints excluded: chain A residue 639 GLN Chi-restraints excluded: chain B residue 452 GLU Chi-restraints excluded: chain B residue 567 ASN Chi-restraints excluded: chain B residue 658 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 41 optimal weight: 3.9990 chunk 46 optimal weight: 3.9990 chunk 12 optimal weight: 20.0000 chunk 87 optimal weight: 3.9990 chunk 62 optimal weight: 0.5980 chunk 102 optimal weight: 0.5980 chunk 1 optimal weight: 20.0000 chunk 40 optimal weight: 0.9980 chunk 3 optimal weight: 20.0000 chunk 99 optimal weight: 0.8980 chunk 94 optimal weight: 0.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 228 ASN A 639 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4001 r_free = 0.4001 target = 0.175698 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.112915 restraints weight = 11068.986| |-----------------------------------------------------------------------------| r_work (start): 0.3212 rms_B_bonded: 2.54 r_work: 0.2984 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.2830 rms_B_bonded: 4.65 restraints_weight: 0.2500 r_work (final): 0.2830 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8242 moved from start: 0.2457 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 8952 Z= 0.138 Angle : 0.587 8.129 12181 Z= 0.292 Chirality : 0.042 0.192 1378 Planarity : 0.005 0.064 1513 Dihedral : 4.143 19.966 1168 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 5.28 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.87 % Favored : 95.04 % Rotamer: Outliers : 1.00 % Allowed : 15.17 % Favored : 83.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.37 (0.27), residues: 1068 helix: 2.19 (0.20), residues: 727 sheet: -2.00 (0.84), residues: 38 loop : -2.03 (0.34), residues: 303 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 624 HIS 0.003 0.001 HIS A 628 PHE 0.014 0.001 PHE B 395 TYR 0.020 0.001 TYR B 181 ARG 0.004 0.000 ARG A 357 Details of bonding type rmsd hydrogen bonds : bond 0.03504 ( 573) hydrogen bonds : angle 3.92630 ( 1701) covalent geometry : bond 0.00329 ( 8952) covalent geometry : angle 0.58744 (12181) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2136 Ramachandran restraints generated. 1068 Oldfield, 0 Emsley, 1068 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2136 Ramachandran restraints generated. 1068 Oldfield, 0 Emsley, 1068 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 937 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 120 time to evaluate : 2.114 Fit side-chains revert: symmetry clash REVERT: A 200 ASP cc_start: 0.8275 (p0) cc_final: 0.7847 (p0) REVERT: A 212 ASP cc_start: 0.8821 (t0) cc_final: 0.8379 (t0) REVERT: B 159 PHE cc_start: 0.7903 (t80) cc_final: 0.7611 (t80) REVERT: B 531 GLU cc_start: 0.7626 (mt-10) cc_final: 0.7017 (mm-30) outliers start: 9 outliers final: 8 residues processed: 124 average time/residue: 0.2175 time to fit residues: 39.9515 Evaluate side-chains 127 residues out of total 937 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 119 time to evaluate : 1.563 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 99 LEU Chi-restraints excluded: chain A residue 169 PHE Chi-restraints excluded: chain A residue 359 VAL Chi-restraints excluded: chain A residue 637 ILE Chi-restraints excluded: chain A residue 639 GLN Chi-restraints excluded: chain B residue 452 GLU Chi-restraints excluded: chain B residue 567 ASN Chi-restraints excluded: chain B residue 658 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 91 optimal weight: 2.9990 chunk 40 optimal weight: 6.9990 chunk 24 optimal weight: 8.9990 chunk 38 optimal weight: 0.0570 chunk 105 optimal weight: 2.9990 chunk 25 optimal weight: 3.9990 chunk 101 optimal weight: 0.0270 chunk 104 optimal weight: 0.6980 chunk 73 optimal weight: 0.9990 chunk 85 optimal weight: 1.9990 chunk 64 optimal weight: 3.9990 overall best weight: 0.7560 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 228 ASN A 639 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4006 r_free = 0.4006 target = 0.176090 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3263 r_free = 0.3263 target = 0.114207 restraints weight = 11090.049| |-----------------------------------------------------------------------------| r_work (start): 0.3237 rms_B_bonded: 2.52 r_work: 0.2955 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work: 0.2798 rms_B_bonded: 4.95 restraints_weight: 0.2500 r_work (final): 0.2798 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8272 moved from start: 0.2488 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 8952 Z= 0.133 Angle : 0.582 8.237 12181 Z= 0.289 Chirality : 0.041 0.192 1378 Planarity : 0.005 0.065 1513 Dihedral : 4.129 19.799 1168 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 5.10 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.87 % Favored : 95.04 % Rotamer: Outliers : 0.89 % Allowed : 15.50 % Favored : 83.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.37 (0.27), residues: 1068 helix: 2.20 (0.20), residues: 727 sheet: -2.02 (0.84), residues: 38 loop : -2.03 (0.34), residues: 303 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 624 HIS 0.003 0.001 HIS A 628 PHE 0.019 0.001 PHE B 383 TYR 0.025 0.001 TYR A 181 ARG 0.004 0.000 ARG A 357 Details of bonding type rmsd hydrogen bonds : bond 0.03474 ( 573) hydrogen bonds : angle 3.92049 ( 1701) covalent geometry : bond 0.00315 ( 8952) covalent geometry : angle 0.58166 (12181) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6009.45 seconds wall clock time: 105 minutes 32.99 seconds (6332.99 seconds total)