Starting phenix.real_space_refine on Wed Sep 17 12:40:09 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8xs5_38615/09_2025/8xs5_38615.cif Found real_map, /net/cci-nas-00/data/ceres_data/8xs5_38615/09_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_38615/09_2025/8xs5_38615.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8xs5_38615/09_2025/8xs5_38615.map" model { file = "/net/cci-nas-00/data/ceres_data/8xs5_38615/09_2025/8xs5_38615.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8xs5_38615/09_2025/8xs5_38615.cif" } resolution = 3.33 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= 0.006 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 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: {'ARG:plan': 2, 'ASN:plan1': 2, 'GLN:plan1': 2, 'PHE:plan': 1, '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: {'ARG:plan': 2, 'ASN:plan1': 2, 'GLN:plan1': 2, 'PHE:plan': 1, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 39 Time building chain proxies: 1.98, per 1000 atoms: 0.23 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: 0.65 Conformation dependent library (CDL) restraints added in 229.3 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 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: 0.28 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: 1.37 Time building geometry restraints manager: 0.86 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: 0.840 Set stop_for_unknowns flag: 0.010 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.140 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 8.560 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.270 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 10.920 ------------------------------------------------------------------------------- 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.34 (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 ARG 0.012 0.001 ARG A 197 TYR 0.112 0.004 TYR B 181 PHE 0.023 0.002 PHE A 225 TRP 0.031 0.003 TRP A 624 HIS 0.010 0.002 HIS A 379 Details of bonding type rmsd covalent geometry : bond 0.01103 ( 8952) covalent geometry : angle 0.88206 (12181) hydrogen bonds : bond 0.12586 ( 573) hydrogen bonds : angle 5.49024 ( 1701) *********************** 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 : 0.327 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: 0.1020 time to fit residues: 19.0256 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 : 0.340 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 49 optimal weight: 0.6980 chunk 97 optimal weight: 0.9990 chunk 53 optimal weight: 0.7980 chunk 5 optimal weight: 0.7980 chunk 33 optimal weight: 5.9990 chunk 65 optimal weight: 1.9990 chunk 62 optimal weight: 0.8980 chunk 51 optimal weight: 0.6980 chunk 100 optimal weight: 0.5980 chunk 106 optimal weight: 0.8980 chunk 38 optimal weight: 0.7980 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 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 = 0.3981 r_free = 0.3981 target = 0.173728 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3202 r_free = 0.3202 target = 0.110387 restraints weight = 11067.142| |-----------------------------------------------------------------------------| r_work (start): 0.3174 rms_B_bonded: 2.60 r_work: 0.2945 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work: 0.2791 rms_B_bonded: 4.79 restraints_weight: 0.2500 r_work (final): 0.2791 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8272 moved from start: 0.1192 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 8952 Z= 0.147 Angle : 0.619 8.753 12181 Z= 0.320 Chirality : 0.043 0.185 1378 Planarity : 0.006 0.059 1513 Dihedral : 4.838 24.936 1168 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 6.02 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.87 % Favored : 95.04 % Rotamer: Outliers : 0.78 % Allowed : 6.20 % Favored : 93.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.43 (0.26), residues: 1068 helix: 1.47 (0.19), residues: 720 sheet: -2.41 (0.75), residues: 44 loop : -2.25 (0.34), residues: 304 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 343 TYR 0.047 0.002 TYR B 181 PHE 0.025 0.001 PHE B 428 TRP 0.026 0.001 TRP A 624 HIS 0.004 0.001 HIS A 714 Details of bonding type rmsd covalent geometry : bond 0.00339 ( 8952) covalent geometry : angle 0.61909 (12181) hydrogen bonds : bond 0.04266 ( 573) hydrogen bonds : angle 4.32942 ( 1701) *********************** 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 : 0.308 Fit side-chains REVERT: A 200 ASP cc_start: 0.8478 (p0) cc_final: 0.8202 (p0) REVERT: A 212 ASP cc_start: 0.8748 (t0) cc_final: 0.8512 (t0) REVERT: A 683 TYR cc_start: 0.8756 (m-80) cc_final: 0.8454 (m-80) REVERT: A 709 GLN cc_start: 0.8557 (pp30) cc_final: 0.8213 (pp30) REVERT: B 159 PHE cc_start: 0.8058 (t80) cc_final: 0.7774 (t80) outliers start: 7 outliers final: 4 residues processed: 126 average time/residue: 0.1058 time to fit residues: 18.1371 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 : 0.331 ------------------------------------------------------------------------------- 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 77 optimal weight: 1.9990 chunk 107 optimal weight: 0.5980 chunk 23 optimal weight: 0.2980 chunk 65 optimal weight: 1.9990 chunk 76 optimal weight: 2.9990 chunk 50 optimal weight: 0.0470 chunk 40 optimal weight: 1.9990 chunk 13 optimal weight: 7.9990 chunk 21 optimal weight: 0.9980 chunk 15 optimal weight: 10.0000 chunk 70 optimal weight: 0.7980 overall best weight: 0.5478 ------------------------------------------------------------------------------- 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 = 0.3994 r_free = 0.3994 target = 0.174957 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3207 r_free = 0.3207 target = 0.109699 restraints weight = 10948.921| |-----------------------------------------------------------------------------| r_work (start): 0.3162 rms_B_bonded: 2.55 r_work: 0.2960 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work: 0.2804 rms_B_bonded: 4.86 restraints_weight: 0.2500 r_work (final): 0.2804 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8243 moved from start: 0.1579 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 8952 Z= 0.129 Angle : 0.576 7.716 12181 Z= 0.296 Chirality : 0.041 0.195 1378 Planarity : 0.005 0.055 1513 Dihedral : 4.544 21.489 1168 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 5.74 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.87 % Favored : 95.04 % Rotamer: Outliers : 1.11 % Allowed : 8.97 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.67 (0.26), residues: 1068 helix: 1.71 (0.19), residues: 720 sheet: -2.36 (0.76), residues: 44 loop : -2.30 (0.34), residues: 304 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 357 TYR 0.031 0.001 TYR B 181 PHE 0.021 0.001 PHE B 428 TRP 0.023 0.001 TRP A 103 HIS 0.004 0.001 HIS A 628 Details of bonding type rmsd covalent geometry : bond 0.00290 ( 8952) covalent geometry : angle 0.57578 (12181) hydrogen bonds : bond 0.03822 ( 573) hydrogen bonds : angle 4.11724 ( 1701) *********************** 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 140 residues out of total 937 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 130 time to evaluate : 0.284 Fit side-chains REVERT: A 200 ASP cc_start: 0.8379 (p0) cc_final: 0.8093 (p0) REVERT: A 212 ASP cc_start: 0.8924 (t0) cc_final: 0.8484 (t0) REVERT: A 340 GLN cc_start: 0.8785 (OUTLIER) cc_final: 0.8454 (tt0) REVERT: A 709 GLN cc_start: 0.8409 (pp30) cc_final: 0.8195 (pp30) REVERT: B 159 PHE cc_start: 0.7942 (t80) cc_final: 0.7594 (t80) REVERT: B 395 PHE cc_start: 0.8973 (t80) cc_final: 0.8730 (t80) outliers start: 10 outliers final: 4 residues processed: 136 average time/residue: 0.0918 time to fit residues: 17.4246 Evaluate side-chains 117 residues out of total 937 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 112 time to evaluate : 0.240 ------------------------------------------------------------------------------- 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 0 optimal weight: 20.0000 chunk 86 optimal weight: 0.8980 chunk 71 optimal weight: 1.9990 chunk 101 optimal weight: 4.9990 chunk 80 optimal weight: 1.9990 chunk 99 optimal weight: 0.5980 chunk 3 optimal weight: 0.8980 chunk 30 optimal weight: 4.9990 chunk 48 optimal weight: 0.9990 chunk 2 optimal weight: 0.0980 chunk 100 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 = 0.3992 r_free = 0.3992 target = 0.174685 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3243 r_free = 0.3243 target = 0.112945 restraints weight = 11099.044| |-----------------------------------------------------------------------------| r_work (start): 0.3204 rms_B_bonded: 2.51 r_work: 0.2959 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work: 0.2804 rms_B_bonded: 4.73 restraints_weight: 0.2500 r_work (final): 0.2804 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8261 moved from start: 0.1813 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= 0.134 Angle : 0.567 6.859 12181 Z= 0.290 Chirality : 0.042 0.192 1378 Planarity : 0.005 0.061 1513 Dihedral : 4.443 20.874 1168 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 5.33 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.96 % Favored : 94.94 % Rotamer: Outliers : 1.44 % Allowed : 10.19 % Favored : 88.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.85 (0.26), residues: 1068 helix: 1.87 (0.19), residues: 721 sheet: -2.35 (0.76), residues: 44 loop : -2.32 (0.33), residues: 303 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 357 TYR 0.026 0.001 TYR B 181 PHE 0.018 0.001 PHE B 428 TRP 0.021 0.001 TRP A 624 HIS 0.004 0.001 HIS A 628 Details of bonding type rmsd covalent geometry : bond 0.00311 ( 8952) covalent geometry : angle 0.56703 (12181) hydrogen bonds : bond 0.03691 ( 573) hydrogen bonds : angle 4.04793 ( 1701) *********************** 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 134 residues out of total 937 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 121 time to evaluate : 0.352 Fit side-chains REVERT: A 190 GLN cc_start: 0.8321 (mm-40) cc_final: 0.8024 (mt0) REVERT: A 200 ASP cc_start: 0.8337 (p0) cc_final: 0.8014 (p0) REVERT: A 212 ASP cc_start: 0.8915 (t0) cc_final: 0.8406 (t0) REVERT: A 320 MET cc_start: 0.8108 (ttp) cc_final: 0.7843 (ttm) REVERT: A 340 GLN cc_start: 0.8755 (OUTLIER) cc_final: 0.8506 (tt0) REVERT: B 159 PHE cc_start: 0.7938 (t80) cc_final: 0.7706 (t80) REVERT: B 395 PHE cc_start: 0.9006 (t80) cc_final: 0.8710 (t80) REVERT: B 545 ASN cc_start: 0.8967 (OUTLIER) cc_final: 0.8588 (m-40) outliers start: 13 outliers final: 5 residues processed: 129 average time/residue: 0.0898 time to fit residues: 16.4778 Evaluate side-chains 122 residues out of total 937 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 115 time to evaluate : 0.278 ------------------------------------------------------------------------------- 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 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 52 optimal weight: 1.9990 chunk 67 optimal weight: 0.0270 chunk 45 optimal weight: 4.9990 chunk 81 optimal weight: 0.9990 chunk 25 optimal weight: 10.0000 chunk 59 optimal weight: 2.9990 chunk 68 optimal weight: 8.9990 chunk 102 optimal weight: 2.9990 chunk 39 optimal weight: 0.8980 chunk 64 optimal weight: 3.9990 chunk 23 optimal weight: 0.8980 overall best weight: 0.9642 ------------------------------------------------------------------------------- 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 = 0.3984 r_free = 0.3984 target = 0.174071 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 74)----------------| | r_work = 0.3165 r_free = 0.3165 target = 0.106136 restraints weight = 11053.888| |-----------------------------------------------------------------------------| r_work (start): 0.3125 rms_B_bonded: 2.14 r_work: 0.2957 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.2805 rms_B_bonded: 4.41 restraints_weight: 0.2500 r_work (final): 0.2805 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8239 moved from start: 0.1874 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 8952 Z= 0.152 Angle : 0.578 6.637 12181 Z= 0.294 Chirality : 0.042 0.187 1378 Planarity : 0.005 0.063 1513 Dihedral : 4.365 20.569 1168 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 5.28 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.34 % Favored : 94.57 % Rotamer: Outliers : 1.33 % Allowed : 12.29 % Favored : 86.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.99 (0.26), residues: 1068 helix: 1.93 (0.19), residues: 723 sheet: -1.93 (0.84), residues: 38 loop : -2.24 (0.33), residues: 307 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 555 TYR 0.027 0.001 TYR B 181 PHE 0.024 0.001 PHE A 471 TRP 0.019 0.001 TRP A 624 HIS 0.004 0.001 HIS A 628 Details of bonding type rmsd covalent geometry : bond 0.00365 ( 8952) covalent geometry : angle 0.57806 (12181) hydrogen bonds : bond 0.03755 ( 573) hydrogen bonds : angle 4.02367 ( 1701) *********************** 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 : 0.341 Fit side-chains REVERT: A 200 ASP cc_start: 0.8362 (p0) cc_final: 0.8013 (p0) REVERT: A 212 ASP cc_start: 0.8924 (t0) cc_final: 0.8376 (t0) REVERT: A 320 MET cc_start: 0.8018 (ttp) cc_final: 0.7809 (ttm) REVERT: A 340 GLN cc_start: 0.8858 (OUTLIER) cc_final: 0.8625 (tt0) REVERT: B 159 PHE cc_start: 0.7944 (t80) cc_final: 0.7664 (t80) REVERT: B 378 MET cc_start: 0.8497 (mmt) cc_final: 0.8098 (mmt) REVERT: B 545 ASN cc_start: 0.9000 (OUTLIER) cc_final: 0.8693 (m-40) outliers start: 12 outliers final: 7 residues processed: 128 average time/residue: 0.0867 time to fit residues: 15.9694 Evaluate side-chains 123 residues out of total 937 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 114 time to evaluate : 0.266 ------------------------------------------------------------------------------- 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 340 GLN 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 10 optimal weight: 3.9990 chunk 103 optimal weight: 0.5980 chunk 59 optimal weight: 1.9990 chunk 30 optimal weight: 8.9990 chunk 49 optimal weight: 0.9980 chunk 96 optimal weight: 0.5980 chunk 67 optimal weight: 6.9990 chunk 82 optimal weight: 1.9990 chunk 87 optimal weight: 3.9990 chunk 43 optimal weight: 0.8980 chunk 4 optimal weight: 6.9990 overall best weight: 1.0182 ------------------------------------------------------------------------------- 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 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 = 0.173810 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3158 r_free = 0.3158 target = 0.105570 restraints weight = 11100.265| |-----------------------------------------------------------------------------| r_work (start): 0.3118 rms_B_bonded: 2.15 r_work: 0.2942 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.2791 rms_B_bonded: 4.56 restraints_weight: 0.2500 r_work (final): 0.2791 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8292 moved from start: 0.1956 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 8952 Z= 0.156 Angle : 0.578 6.828 12181 Z= 0.294 Chirality : 0.042 0.187 1378 Planarity : 0.005 0.064 1513 Dihedral : 4.331 20.521 1168 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 5.45 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.43 % Favored : 94.48 % Rotamer: Outliers : 1.55 % Allowed : 14.06 % Favored : 84.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.09 (0.27), residues: 1068 helix: 2.01 (0.19), residues: 723 sheet: -2.01 (0.83), residues: 38 loop : -2.16 (0.34), residues: 307 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 555 TYR 0.024 0.001 TYR B 181 PHE 0.020 0.001 PHE B 395 TRP 0.018 0.001 TRP A 624 HIS 0.004 0.001 HIS A 628 Details of bonding type rmsd covalent geometry : bond 0.00376 ( 8952) covalent geometry : angle 0.57791 (12181) hydrogen bonds : bond 0.03752 ( 573) hydrogen bonds : angle 4.00693 ( 1701) *********************** 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 133 residues out of total 937 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 119 time to evaluate : 0.253 Fit side-chains REVERT: A 200 ASP cc_start: 0.8393 (p0) cc_final: 0.7998 (p0) REVERT: A 212 ASP cc_start: 0.8926 (t0) cc_final: 0.8385 (t0) REVERT: B 159 PHE cc_start: 0.7976 (t80) cc_final: 0.7699 (t80) REVERT: B 378 MET cc_start: 0.8586 (mmt) cc_final: 0.8195 (mmt) outliers start: 14 outliers final: 8 residues processed: 128 average time/residue: 0.0835 time to fit residues: 15.3517 Evaluate side-chains 124 residues out of total 937 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 116 time to evaluate : 0.360 ------------------------------------------------------------------------------- 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 A residue 665 THR Chi-restraints excluded: chain B residue 452 GLU Chi-restraints excluded: chain B residue 567 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 64 optimal weight: 3.9990 chunk 28 optimal weight: 10.0000 chunk 102 optimal weight: 0.9990 chunk 50 optimal weight: 0.0570 chunk 34 optimal weight: 9.9990 chunk 7 optimal weight: 0.7980 chunk 47 optimal weight: 0.4980 chunk 63 optimal weight: 3.9990 chunk 46 optimal weight: 1.9990 chunk 100 optimal weight: 0.5980 chunk 96 optimal weight: 0.6980 overall best weight: 0.5298 ------------------------------------------------------------------------------- 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 = 0.4005 r_free = 0.4005 target = 0.175872 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3234 r_free = 0.3234 target = 0.112786 restraints weight = 11183.141| |-----------------------------------------------------------------------------| r_work (start): 0.3198 rms_B_bonded: 2.61 r_work: 0.2959 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work (final): 0.2959 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8138 moved from start: 0.2195 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= 0.120 Angle : 0.556 7.485 12181 Z= 0.282 Chirality : 0.041 0.180 1378 Planarity : 0.005 0.062 1513 Dihedral : 4.226 20.247 1168 Min Nonbonded Distance : 2.566 Molprobity Statistics. All-atom Clashscore : 4.82 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.15 % Favored : 94.76 % Rotamer: Outliers : 1.11 % Allowed : 14.40 % Favored : 84.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.31 (0.27), residues: 1068 helix: 2.13 (0.19), residues: 726 sheet: -1.93 (0.85), residues: 38 loop : -2.01 (0.35), residues: 304 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 555 TYR 0.019 0.001 TYR A 261 PHE 0.018 0.001 PHE B 383 TRP 0.022 0.001 TRP A 103 HIS 0.004 0.000 HIS A 628 Details of bonding type rmsd covalent geometry : bond 0.00274 ( 8952) covalent geometry : angle 0.55599 (12181) hydrogen bonds : bond 0.03433 ( 573) hydrogen bonds : angle 3.95315 ( 1701) *********************** 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 143 residues out of total 937 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 133 time to evaluate : 0.225 Fit side-chains REVERT: A 200 ASP cc_start: 0.8205 (p0) cc_final: 0.7781 (p0) REVERT: A 212 ASP cc_start: 0.8890 (t0) cc_final: 0.8428 (t0) REVERT: B 159 PHE cc_start: 0.7783 (t80) cc_final: 0.7563 (t80) REVERT: B 531 GLU cc_start: 0.7372 (mt-10) cc_final: 0.6875 (mm-30) outliers start: 10 outliers final: 8 residues processed: 139 average time/residue: 0.0793 time to fit residues: 16.1390 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 : 0.318 ------------------------------------------------------------------------------- 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 42 optimal weight: 3.9990 chunk 70 optimal weight: 1.9990 chunk 106 optimal weight: 0.0870 chunk 55 optimal weight: 1.9990 chunk 101 optimal weight: 0.1980 chunk 79 optimal weight: 1.9990 chunk 50 optimal weight: 0.4980 chunk 7 optimal weight: 0.7980 chunk 76 optimal weight: 4.9990 chunk 53 optimal weight: 0.9980 chunk 38 optimal weight: 0.5980 overall best weight: 0.4358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 639 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4015 r_free = 0.4015 target = 0.176817 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.114925 restraints weight = 10948.037| |-----------------------------------------------------------------------------| r_work (start): 0.3237 rms_B_bonded: 2.50 r_work: 0.2980 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work: 0.2825 rms_B_bonded: 4.77 restraints_weight: 0.2500 r_work (final): 0.2825 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8232 moved from start: 0.2360 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= 0.116 Angle : 0.566 7.733 12181 Z= 0.285 Chirality : 0.041 0.194 1378 Planarity : 0.005 0.063 1513 Dihedral : 4.185 19.717 1168 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 5.05 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.06 % Favored : 94.85 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.37 (0.27), residues: 1068 helix: 2.16 (0.19), residues: 727 sheet: -1.96 (0.85), residues: 38 loop : -1.96 (0.35), residues: 303 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 357 TYR 0.018 0.001 TYR A 261 PHE 0.023 0.001 PHE B 395 TRP 0.018 0.001 TRP B 624 HIS 0.004 0.000 HIS A 628 Details of bonding type rmsd covalent geometry : bond 0.00263 ( 8952) covalent geometry : angle 0.56578 (12181) hydrogen bonds : bond 0.03337 ( 573) hydrogen bonds : angle 3.91294 ( 1701) *********************** 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 138 residues out of total 937 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 129 time to evaluate : 0.308 Fit side-chains REVERT: A 200 ASP cc_start: 0.8249 (p0) cc_final: 0.7846 (p0) REVERT: A 212 ASP cc_start: 0.8915 (t0) cc_final: 0.8413 (t0) REVERT: B 159 PHE cc_start: 0.7889 (t80) cc_final: 0.7615 (t80) REVERT: B 378 MET cc_start: 0.8341 (mmt) cc_final: 0.7992 (mmt) REVERT: B 531 GLU cc_start: 0.7624 (mt-10) cc_final: 0.6939 (mm-30) REVERT: B 576 TYR cc_start: 0.8903 (m-10) cc_final: 0.8693 (m-10) outliers start: 9 outliers final: 6 residues processed: 133 average time/residue: 0.0881 time to fit residues: 16.9261 Evaluate side-chains 127 residues out of total 937 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 121 time to evaluate : 0.344 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 99 LEU 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 79 optimal weight: 1.9990 chunk 33 optimal weight: 20.0000 chunk 51 optimal weight: 0.0980 chunk 77 optimal weight: 1.9990 chunk 73 optimal weight: 2.9990 chunk 85 optimal weight: 0.5980 chunk 48 optimal weight: 0.5980 chunk 47 optimal weight: 0.6980 chunk 38 optimal weight: 0.8980 chunk 34 optimal weight: 10.0000 chunk 86 optimal weight: 6.9990 overall best weight: 0.5780 ------------------------------------------------------------------------------- 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** A 710 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4012 r_free = 0.4012 target = 0.176628 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.115258 restraints weight = 11106.265| |-----------------------------------------------------------------------------| r_work (start): 0.3241 rms_B_bonded: 2.60 r_work: 0.2966 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work: 0.2810 rms_B_bonded: 4.90 restraints_weight: 0.2500 r_work (final): 0.2810 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8245 moved from start: 0.2466 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 8952 Z= 0.122 Angle : 0.568 7.702 12181 Z= 0.285 Chirality : 0.041 0.192 1378 Planarity : 0.005 0.064 1513 Dihedral : 4.142 19.641 1168 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 5.10 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.78 % Favored : 95.13 % Rotamer: Outliers : 1.00 % Allowed : 15.50 % Favored : 83.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.36 (0.27), residues: 1068 helix: 2.17 (0.20), residues: 727 sheet: -2.02 (0.83), residues: 38 loop : -1.99 (0.34), residues: 303 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 357 TYR 0.018 0.001 TYR A 261 PHE 0.019 0.001 PHE B 383 TRP 0.030 0.001 TRP A 103 HIS 0.004 0.000 HIS A 628 Details of bonding type rmsd covalent geometry : bond 0.00280 ( 8952) covalent geometry : angle 0.56792 (12181) hydrogen bonds : bond 0.03375 ( 573) hydrogen bonds : angle 3.91041 ( 1701) *********************** 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 137 residues out of total 937 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 128 time to evaluate : 0.337 Fit side-chains REVERT: A 200 ASP cc_start: 0.8249 (p0) cc_final: 0.7842 (p0) REVERT: A 212 ASP cc_start: 0.8926 (t0) cc_final: 0.8424 (t0) REVERT: B 159 PHE cc_start: 0.7885 (t80) cc_final: 0.7602 (t80) REVERT: B 397 GLN cc_start: 0.8834 (mm-40) cc_final: 0.8598 (mm-40) REVERT: B 531 GLU cc_start: 0.7675 (mt-10) cc_final: 0.7024 (mm-30) REVERT: B 576 TYR cc_start: 0.8924 (m-10) cc_final: 0.8706 (m-10) outliers start: 9 outliers final: 7 residues processed: 132 average time/residue: 0.0856 time to fit residues: 16.4454 Evaluate side-chains 131 residues out of total 937 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 124 time to evaluate : 0.347 ------------------------------------------------------------------------------- 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 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 20 optimal weight: 0.1980 chunk 76 optimal weight: 0.7980 chunk 29 optimal weight: 2.9990 chunk 49 optimal weight: 0.0000 chunk 97 optimal weight: 0.8980 chunk 61 optimal weight: 0.0970 chunk 15 optimal weight: 6.9990 chunk 11 optimal weight: 4.9990 chunk 59 optimal weight: 0.4980 chunk 5 optimal weight: 1.9990 chunk 57 optimal weight: 0.9980 overall best weight: 0.3182 ------------------------------------------------------------------------------- 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 B 363 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4027 r_free = 0.4027 target = 0.178055 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3263 r_free = 0.3263 target = 0.114482 restraints weight = 11031.591| |-----------------------------------------------------------------------------| r_work (start): 0.3235 rms_B_bonded: 2.46 r_work: 0.2998 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work: 0.2843 rms_B_bonded: 4.91 restraints_weight: 0.2500 r_work (final): 0.2843 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8217 moved from start: 0.2640 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 8952 Z= 0.109 Angle : 0.567 8.787 12181 Z= 0.282 Chirality : 0.041 0.196 1378 Planarity : 0.005 0.065 1513 Dihedral : 4.067 18.954 1168 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 4.76 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.06 % Favored : 94.85 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.44 (0.27), residues: 1068 helix: 2.23 (0.20), residues: 727 sheet: -1.94 (0.84), residues: 38 loop : -1.98 (0.34), residues: 303 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 357 TYR 0.021 0.001 TYR A 181 PHE 0.014 0.001 PHE B 428 TRP 0.018 0.001 TRP B 624 HIS 0.004 0.000 HIS A 628 Details of bonding type rmsd covalent geometry : bond 0.00240 ( 8952) covalent geometry : angle 0.56679 (12181) hydrogen bonds : bond 0.03179 ( 573) hydrogen bonds : angle 3.86327 ( 1701) ********************** 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 132 residues out of total 937 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 124 time to evaluate : 0.351 Fit side-chains REVERT: A 200 ASP cc_start: 0.8212 (p0) cc_final: 0.7789 (p0) REVERT: A 212 ASP cc_start: 0.8920 (t0) cc_final: 0.8451 (t0) REVERT: B 159 PHE cc_start: 0.7836 (t80) cc_final: 0.7573 (t80) REVERT: B 263 GLN cc_start: 0.8431 (mt0) cc_final: 0.8131 (mt0) REVERT: B 531 GLU cc_start: 0.7575 (mt-10) cc_final: 0.6908 (mm-30) outliers start: 8 outliers final: 8 residues processed: 127 average time/residue: 0.0848 time to fit residues: 15.7532 Evaluate side-chains 125 residues out of total 937 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 117 time to evaluate : 0.336 ------------------------------------------------------------------------------- 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 43 optimal weight: 0.2980 chunk 77 optimal weight: 0.9990 chunk 14 optimal weight: 0.8980 chunk 37 optimal weight: 0.0980 chunk 86 optimal weight: 0.3980 chunk 6 optimal weight: 1.9990 chunk 61 optimal weight: 2.9990 chunk 2 optimal weight: 7.9990 chunk 90 optimal weight: 1.9990 chunk 107 optimal weight: 0.0470 chunk 56 optimal weight: 0.8980 overall best weight: 0.3478 ------------------------------------------------------------------------------- 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 = 0.4027 r_free = 0.4027 target = 0.178119 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3236 r_free = 0.3236 target = 0.112136 restraints weight = 10946.147| |-----------------------------------------------------------------------------| r_work (start): 0.3186 rms_B_bonded: 2.54 r_work: 0.3014 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work: 0.2859 rms_B_bonded: 4.78 restraints_weight: 0.2500 r_work (final): 0.2859 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8231 moved from start: 0.2681 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 8952 Z= 0.110 Angle : 0.568 8.947 12181 Z= 0.282 Chirality : 0.041 0.190 1378 Planarity : 0.005 0.065 1513 Dihedral : 4.049 18.753 1168 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 4.65 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.68 % Favored : 95.22 % Rotamer: Outliers : 0.78 % Allowed : 15.84 % Favored : 83.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.46 (0.27), residues: 1068 helix: 2.24 (0.20), residues: 727 sheet: -1.92 (0.83), residues: 38 loop : -1.95 (0.35), residues: 303 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 357 TYR 0.020 0.001 TYR A 181 PHE 0.018 0.001 PHE B 383 TRP 0.018 0.001 TRP A 103 HIS 0.004 0.000 HIS A 628 Details of bonding type rmsd covalent geometry : bond 0.00244 ( 8952) covalent geometry : angle 0.56802 (12181) hydrogen bonds : bond 0.03174 ( 573) hydrogen bonds : angle 3.86279 ( 1701) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2961.74 seconds wall clock time: 51 minutes 8.82 seconds (3068.82 seconds total)