Starting phenix.real_space_refine on Fri Jan 17 17:04:20 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8xs4_38614/01_2025/8xs4_38614.cif Found real_map, /net/cci-nas-00/data/ceres_data/8xs4_38614/01_2025/8xs4_38614.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.23 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8xs4_38614/01_2025/8xs4_38614.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8xs4_38614/01_2025/8xs4_38614.map" model { file = "/net/cci-nas-00/data/ceres_data/8xs4_38614/01_2025/8xs4_38614.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8xs4_38614/01_2025/8xs4_38614.cif" } resolution = 3.23 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= 0.007 sd= 0.093 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 50 5.16 5 C 7366 2.51 5 N 1814 2.21 5 O 1902 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 32 residue(s): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/chem_data/mon_lib" Total number of atoms: 11132 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 5566 Number of conformers: 1 Conformer: "" Number of residues, atoms: 696, 5566 Classifications: {'peptide': 696} Incomplete info: {'truncation_to_alanine': 17} Link IDs: {'PTRANS': 36, 'TRANS': 659} Chain breaks: 1 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 Restraints were copied for chains: B Time building chain proxies: 10.79, per 1000 atoms: 0.97 Number of scatterers: 11132 At special positions: 0 Unit cell: (87.565, 145.59, 101.28, 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 50 16.00 O 1902 8.00 N 1814 7.00 C 7366 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: 2.72 Conformation dependent library (CDL) restraints added in 1.4 seconds 2768 Ramachandran restraints generated. 1384 Oldfield, 0 Emsley, 1384 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2676 Finding SS restraints... Secondary structure from input PDB file: 66 helices and 2 sheets defined 69.6% alpha, 3.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.97 Creating SS restraints... Processing helix chain 'A' and resid 3 through 31 Processing helix chain 'A' and resid 34 through 39 removed outlier: 3.536A pdb=" N TYR A 38 " --> pdb=" O ASN A 34 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N PHE A 39 " --> pdb=" O ASP A 35 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 34 through 39' Processing helix chain 'A' and resid 74 through 80 removed outlier: 4.121A pdb=" N GLU A 78 " --> pdb=" O ASN A 74 " (cutoff:3.500A) Processing helix chain 'A' and resid 83 through 92 Processing helix chain 'A' and resid 92 through 120 removed outlier: 3.678A pdb=" N VAL A 96 " --> pdb=" O GLY A 92 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N GLY A 105 " --> pdb=" O ILE A 101 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N LEU A 106 " --> pdb=" O TYR A 102 " (cutoff:3.500A) Proline residue: A 111 - end of helix Processing helix chain 'A' and resid 157 through 195 Processing helix chain 'A' and resid 216 through 228 Processing helix chain 'A' and resid 229 through 231 No H-bonds generated for 'chain 'A' and resid 229 through 231' Processing helix chain 'A' and resid 242 through 269 Processing helix chain 'A' and resid 289 through 314 removed outlier: 3.711A pdb=" N ASN A 314 " --> pdb=" O GLU A 310 " (cutoff:3.500A) Processing helix chain 'A' and resid 315 through 317 No H-bonds generated for 'chain 'A' and resid 315 through 317' Processing helix chain 'A' and resid 329 through 338 Processing helix chain 'A' and resid 360 through 364 Processing helix chain 'A' and resid 367 through 369 No H-bonds generated for 'chain 'A' and resid 367 through 369' Processing helix chain 'A' and resid 370 through 389 removed outlier: 3.541A pdb=" N ARG A 374 " --> pdb=" O SER A 370 " (cutoff:3.500A) Processing helix chain 'A' and resid 389 through 401 removed outlier: 3.521A pdb=" N ILE A 393 " --> pdb=" O PHE A 389 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 409 removed outlier: 3.728A pdb=" N ALA A 408 " --> pdb=" O ILE A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 418 through 428 Processing helix chain 'A' and resid 428 through 438 Processing helix chain 'A' and resid 440 through 451 Processing helix chain 'A' and resid 456 through 475 Processing helix chain 'A' and resid 477 through 486 Processing helix chain 'A' and resid 504 through 532 Proline residue: A 510 - end of helix removed outlier: 3.882A pdb=" N THR A 518 " --> pdb=" O THR A 514 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N ALA A 526 " --> pdb=" O VAL A 522 " (cutoff:3.500A) removed outlier: 4.686A pdb=" N GLY A 527 " --> pdb=" O ASP A 523 " (cutoff:3.500A) Processing helix chain 'A' and resid 534 through 549 removed outlier: 3.991A pdb=" N VAL A 549 " --> pdb=" O ASN A 545 " (cutoff:3.500A) Processing helix chain 'A' and resid 551 through 555 Processing helix chain 'A' and resid 565 through 584 Proline residue: A 571 - end of helix Processing helix chain 'A' and resid 590 through 612 removed outlier: 3.548A pdb=" N ILE A 594 " --> pdb=" O LEU A 590 " (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: 4.119A pdb=" N VAL A 663 " --> pdb=" O ILE A 659 " (cutoff:3.500A) Processing helix chain 'A' and resid 677 through 682 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 31 Processing helix chain 'B' and resid 34 through 39 removed outlier: 3.536A pdb=" N TYR B 38 " --> pdb=" O ASN B 34 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N PHE B 39 " --> pdb=" O ASP B 35 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 34 through 39' Processing helix chain 'B' and resid 74 through 80 removed outlier: 4.121A pdb=" N GLU B 78 " --> pdb=" O ASN B 74 " (cutoff:3.500A) Processing helix chain 'B' and resid 83 through 92 Processing helix chain 'B' and resid 92 through 120 removed outlier: 3.679A pdb=" N VAL B 96 " --> pdb=" O GLY B 92 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N GLY B 105 " --> pdb=" O ILE B 101 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N LEU B 106 " --> pdb=" O TYR B 102 " (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 216 through 228 Processing helix chain 'B' and resid 229 through 231 No H-bonds generated for 'chain 'B' and resid 229 through 231' Processing helix chain 'B' and resid 242 through 269 Processing helix chain 'B' and resid 289 through 314 removed outlier: 3.711A pdb=" N ASN B 314 " --> pdb=" O GLU B 310 " (cutoff:3.500A) Processing helix chain 'B' and resid 315 through 317 No H-bonds generated for 'chain 'B' and resid 315 through 317' Processing helix chain 'B' and resid 329 through 338 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 389 removed outlier: 3.542A pdb=" N ARG B 374 " --> pdb=" O SER B 370 " (cutoff:3.500A) Processing helix chain 'B' and resid 389 through 401 removed outlier: 3.522A pdb=" N ILE B 393 " --> pdb=" O PHE B 389 " (cutoff:3.500A) Processing helix chain 'B' and resid 405 through 409 removed outlier: 3.729A pdb=" N ALA B 408 " --> pdb=" O ILE B 405 " (cutoff:3.500A) Processing helix chain 'B' and resid 418 through 428 Processing helix chain 'B' and resid 428 through 438 Processing helix chain 'B' and resid 440 through 451 Processing helix chain 'B' and resid 456 through 475 Processing helix chain 'B' and resid 477 through 486 Processing helix chain 'B' and resid 504 through 532 Proline residue: B 510 - end of helix removed outlier: 3.882A pdb=" N THR B 518 " --> pdb=" O THR B 514 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N ALA B 526 " --> pdb=" O VAL B 522 " (cutoff:3.500A) removed outlier: 4.686A pdb=" N GLY B 527 " --> pdb=" O ASP B 523 " (cutoff:3.500A) Processing helix chain 'B' and resid 534 through 549 removed outlier: 3.990A pdb=" N VAL B 549 " --> pdb=" O ASN B 545 " (cutoff:3.500A) Processing helix chain 'B' and resid 551 through 555 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: 3.548A 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: 4.119A 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 233 through 240 removed outlier: 5.447A 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: 5.448A pdb=" N ALA B 322 " --> pdb=" O VAL B 239 " (cutoff:3.500A) 693 hydrogen bonds defined for protein. 2043 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: 3.38 Time building geometry restraints manager: 3.10 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 3426 1.34 - 1.46: 2762 1.46 - 1.58: 5164 1.58 - 1.70: 0 1.70 - 1.82: 92 Bond restraints: 11444 Sorted by residual: bond pdb=" CG GLU B 452 " pdb=" CD GLU B 452 " ideal model delta sigma weight residual 1.516 1.465 0.051 2.50e-02 1.60e+03 4.13e+00 bond pdb=" CG GLU A 452 " pdb=" CD GLU A 452 " ideal model delta sigma weight residual 1.516 1.466 0.050 2.50e-02 1.60e+03 4.07e+00 bond pdb=" CA GLU A 452 " pdb=" CB GLU A 452 " ideal model delta sigma weight residual 1.532 1.515 0.017 1.62e-02 3.81e+03 1.12e+00 bond pdb=" CB PRO A 392 " pdb=" CG PRO A 392 " ideal model delta sigma weight residual 1.492 1.439 0.053 5.00e-02 4.00e+02 1.12e+00 bond pdb=" CA GLU B 452 " pdb=" CB GLU B 452 " ideal model delta sigma weight residual 1.532 1.515 0.017 1.62e-02 3.81e+03 1.11e+00 ... (remaining 11439 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.19: 15206 2.19 - 4.38: 294 4.38 - 6.57: 54 6.57 - 8.76: 16 8.76 - 10.95: 6 Bond angle restraints: 15576 Sorted by residual: angle pdb=" C PHE A 454 " pdb=" N THR A 455 " pdb=" CA THR A 455 " ideal model delta sigma weight residual 122.08 127.12 -5.04 1.47e+00 4.63e-01 1.18e+01 angle pdb=" C PHE B 454 " pdb=" N THR B 455 " pdb=" CA THR B 455 " ideal model delta sigma weight residual 122.08 127.10 -5.02 1.47e+00 4.63e-01 1.17e+01 angle pdb=" CA GLU A 452 " pdb=" CB GLU A 452 " pdb=" CG GLU A 452 " ideal model delta sigma weight residual 114.10 107.74 6.36 2.00e+00 2.50e-01 1.01e+01 angle pdb=" CA GLU B 452 " pdb=" CB GLU B 452 " pdb=" CG GLU B 452 " ideal model delta sigma weight residual 114.10 107.75 6.35 2.00e+00 2.50e-01 1.01e+01 angle pdb=" CA LEU B 73 " pdb=" CB LEU B 73 " pdb=" CG LEU B 73 " ideal model delta sigma weight residual 116.30 127.25 -10.95 3.50e+00 8.16e-02 9.80e+00 ... (remaining 15571 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.41: 6086 17.41 - 34.81: 538 34.81 - 52.22: 100 52.22 - 69.62: 8 69.62 - 87.03: 16 Dihedral angle restraints: 6748 sinusoidal: 2630 harmonic: 4118 Sorted by residual: dihedral pdb=" CA VAL A 119 " pdb=" C VAL A 119 " pdb=" N LEU A 120 " pdb=" CA LEU A 120 " ideal model delta harmonic sigma weight residual -180.00 -155.99 -24.01 0 5.00e+00 4.00e-02 2.31e+01 dihedral pdb=" CA VAL B 119 " pdb=" C VAL B 119 " pdb=" N LEU B 120 " pdb=" CA LEU B 120 " ideal model delta harmonic sigma weight residual 180.00 -156.03 -23.97 0 5.00e+00 4.00e-02 2.30e+01 dihedral pdb=" CA LYS B 413 " pdb=" C LYS B 413 " pdb=" N PHE B 414 " pdb=" CA PHE B 414 " ideal model delta harmonic sigma weight residual 180.00 156.15 23.85 0 5.00e+00 4.00e-02 2.28e+01 ... (remaining 6745 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.043: 1244 0.043 - 0.087: 388 0.087 - 0.130: 113 0.130 - 0.174: 15 0.174 - 0.217: 4 Chirality restraints: 1764 Sorted by residual: chirality pdb=" CA PRO A 32 " pdb=" N PRO A 32 " pdb=" C PRO A 32 " pdb=" CB PRO A 32 " both_signs ideal model delta sigma weight residual False 2.72 2.50 0.22 2.00e-01 2.50e+01 1.18e+00 chirality pdb=" CA PRO B 32 " pdb=" N PRO B 32 " pdb=" C PRO B 32 " pdb=" CB PRO B 32 " both_signs ideal model delta sigma weight residual False 2.72 2.50 0.22 2.00e-01 2.50e+01 1.18e+00 chirality pdb=" CG LEU A 47 " pdb=" CB LEU A 47 " pdb=" CD1 LEU A 47 " pdb=" CD2 LEU A 47 " both_signs ideal model delta sigma weight residual False -2.59 -2.40 -0.19 2.00e-01 2.50e+01 9.29e-01 ... (remaining 1761 not shown) Planarity restraints: 1946 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C MET B 76 " -0.043 5.00e-02 4.00e+02 6.55e-02 6.86e+00 pdb=" N PRO B 77 " 0.113 5.00e-02 4.00e+02 pdb=" CA PRO B 77 " -0.033 5.00e-02 4.00e+02 pdb=" CD PRO B 77 " -0.037 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C MET A 76 " 0.043 5.00e-02 4.00e+02 6.53e-02 6.82e+00 pdb=" N PRO A 77 " -0.113 5.00e-02 4.00e+02 pdb=" CA PRO A 77 " 0.033 5.00e-02 4.00e+02 pdb=" CD PRO A 77 " 0.037 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 181 " 0.022 2.00e-02 2.50e+03 1.83e-02 6.73e+00 pdb=" CG TYR A 181 " -0.045 2.00e-02 2.50e+03 pdb=" CD1 TYR A 181 " 0.011 2.00e-02 2.50e+03 pdb=" CD2 TYR A 181 " 0.004 2.00e-02 2.50e+03 pdb=" CE1 TYR A 181 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 TYR A 181 " 0.005 2.00e-02 2.50e+03 pdb=" CZ TYR A 181 " 0.002 2.00e-02 2.50e+03 pdb=" OH TYR A 181 " 0.002 2.00e-02 2.50e+03 ... (remaining 1943 not shown) Histogram of nonbonded interaction distances: 2.15 - 2.70: 262 2.70 - 3.25: 11490 3.25 - 3.80: 17976 3.80 - 4.35: 22645 4.35 - 4.90: 38125 Nonbonded interactions: 90498 Sorted by model distance: nonbonded pdb=" OE1 GLU B 222 " pdb=" OH TYR B 233 " model vdw 2.149 3.040 nonbonded pdb=" OE1 GLU A 222 " pdb=" OH TYR A 233 " model vdw 2.149 3.040 nonbonded pdb=" NH1 ARG A 374 " pdb=" O PHE A 451 " model vdw 2.209 3.120 nonbonded pdb=" NH1 ARG B 374 " pdb=" O PHE B 451 " model vdw 2.210 3.120 nonbonded pdb=" OD1 ASP A 143 " pdb=" OG1 THR A 514 " model vdw 2.235 3.040 ... (remaining 90493 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: 0.06 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } 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: 1.130 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.400 Check model and map are aligned: 0.070 Set scattering table: 0.090 Process input model: 30.150 Find NCS groups from input model: 0.220 Set up NCS constraints: 0.030 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: 0.010 Load rotamer database and sin/cos tables:3.070 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.190 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7662 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 11444 Z= 0.256 Angle : 0.797 10.954 15576 Z= 0.424 Chirality : 0.046 0.217 1764 Planarity : 0.006 0.065 1946 Dihedral : 13.899 87.027 4072 Min Nonbonded Distance : 2.149 Molprobity Statistics. All-atom Clashscore : 11.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.08 % Favored : 92.92 % Rotamer: Outliers : 0.00 % Allowed : 0.17 % Favored : 99.83 % 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: -0.41 (0.24), residues: 1384 helix: 1.14 (0.18), residues: 882 sheet: -2.18 (0.85), residues: 42 loop : -3.03 (0.28), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 75 HIS 0.003 0.001 HIS B 628 PHE 0.036 0.002 PHE A 33 TYR 0.045 0.002 TYR A 181 ARG 0.004 0.001 ARG A 630 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2768 Ramachandran restraints generated. 1384 Oldfield, 0 Emsley, 1384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2768 Ramachandran restraints generated. 1384 Oldfield, 0 Emsley, 1384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 1206 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 196 time to evaluate : 1.137 Fit side-chains REVERT: A 98 TYR cc_start: 0.8736 (t80) cc_final: 0.8492 (t80) REVERT: A 117 TRP cc_start: 0.7700 (m100) cc_final: 0.7478 (m100) REVERT: A 422 LYS cc_start: 0.7426 (mmtt) cc_final: 0.7132 (mmtt) REVERT: A 521 MET cc_start: 0.7883 (mtm) cc_final: 0.7471 (mtp) REVERT: A 547 PHE cc_start: 0.8080 (m-10) cc_final: 0.7833 (m-10) REVERT: A 613 TYR cc_start: 0.7996 (m-10) cc_final: 0.7640 (m-10) REVERT: B 395 PHE cc_start: 0.9086 (t80) cc_final: 0.8886 (t80) REVERT: B 422 LYS cc_start: 0.7504 (mmtt) cc_final: 0.7278 (mmtt) outliers start: 0 outliers final: 0 residues processed: 196 average time/residue: 0.2005 time to fit residues: 59.3762 Evaluate side-chains 164 residues out of total 1206 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 164 time to evaluate : 1.231 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 116 optimal weight: 0.0170 chunk 104 optimal weight: 2.9990 chunk 58 optimal weight: 0.7980 chunk 35 optimal weight: 0.8980 chunk 70 optimal weight: 2.9990 chunk 55 optimal weight: 1.9990 chunk 108 optimal weight: 20.0000 chunk 41 optimal weight: 0.0670 chunk 65 optimal weight: 0.9980 chunk 80 optimal weight: 0.3980 chunk 125 optimal weight: 0.8980 overall best weight: 0.4356 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 615 GLN ** B 472 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 615 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4070 r_free = 0.4070 target = 0.188163 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3535 r_free = 0.3535 target = 0.136734 restraints weight = 12675.553| |-----------------------------------------------------------------------------| r_work (start): 0.3426 rms_B_bonded: 2.42 r_work: 0.3098 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.3098 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7832 moved from start: 0.1196 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 11444 Z= 0.209 Angle : 0.686 10.336 15576 Z= 0.338 Chirality : 0.043 0.203 1764 Planarity : 0.006 0.060 1946 Dihedral : 5.022 20.751 1494 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 7.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.72 % Favored : 93.28 % Rotamer: Outliers : 0.85 % Allowed : 7.85 % Favored : 91.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.01 (0.24), residues: 1384 helix: 1.46 (0.18), residues: 888 sheet: -2.54 (0.76), residues: 42 loop : -2.83 (0.28), residues: 454 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 624 HIS 0.004 0.001 HIS B 90 PHE 0.028 0.001 PHE B 33 TYR 0.025 0.001 TYR B 181 ARG 0.003 0.000 ARG B 29 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2768 Ramachandran restraints generated. 1384 Oldfield, 0 Emsley, 1384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2768 Ramachandran restraints generated. 1384 Oldfield, 0 Emsley, 1384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 1206 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 171 time to evaluate : 1.167 Fit side-chains REVERT: A 98 TYR cc_start: 0.8821 (t80) cc_final: 0.8462 (t80) REVERT: A 422 LYS cc_start: 0.7500 (mmtt) cc_final: 0.7182 (mmtt) REVERT: A 613 TYR cc_start: 0.8326 (m-10) cc_final: 0.8079 (m-10) REVERT: B 315 ASP cc_start: 0.7612 (t0) cc_final: 0.7311 (t0) REVERT: B 395 PHE cc_start: 0.9047 (t80) cc_final: 0.8802 (t80) REVERT: B 422 LYS cc_start: 0.7245 (mmtt) cc_final: 0.6996 (mmtt) REVERT: B 511 MET cc_start: 0.7422 (mtm) cc_final: 0.7189 (mpp) REVERT: B 583 TYR cc_start: 0.7668 (m-80) cc_final: 0.7333 (m-10) REVERT: B 709 GLN cc_start: 0.8478 (pt0) cc_final: 0.8269 (tt0) outliers start: 10 outliers final: 7 residues processed: 173 average time/residue: 0.1931 time to fit residues: 50.7167 Evaluate side-chains 166 residues out of total 1206 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 159 time to evaluate : 1.128 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 393 ILE Chi-restraints excluded: chain A residue 482 ILE Chi-restraints excluded: chain A residue 543 LEU Chi-restraints excluded: chain A residue 645 LEU Chi-restraints excluded: chain B residue 37 VAL Chi-restraints excluded: chain B residue 190 GLN Chi-restraints excluded: chain B residue 645 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 13 optimal weight: 0.4980 chunk 85 optimal weight: 0.7980 chunk 115 optimal weight: 10.0000 chunk 135 optimal weight: 0.9990 chunk 21 optimal weight: 1.9990 chunk 106 optimal weight: 0.7980 chunk 8 optimal weight: 0.5980 chunk 71 optimal weight: 4.9990 chunk 0 optimal weight: 10.0000 chunk 17 optimal weight: 0.0070 chunk 109 optimal weight: 6.9990 overall best weight: 0.5398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 472 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4076 r_free = 0.4076 target = 0.188875 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.138205 restraints weight = 12773.203| |-----------------------------------------------------------------------------| r_work (start): 0.3437 rms_B_bonded: 2.14 r_work: 0.3112 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work: 0.2974 rms_B_bonded: 4.84 restraints_weight: 0.2500 r_work (final): 0.2974 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7929 moved from start: 0.1544 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 11444 Z= 0.201 Angle : 0.641 9.920 15576 Z= 0.316 Chirality : 0.043 0.187 1764 Planarity : 0.006 0.061 1946 Dihedral : 4.738 19.196 1494 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 6.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.79 % Favored : 93.21 % Rotamer: Outliers : 1.62 % Allowed : 11.77 % Favored : 86.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.27 (0.24), residues: 1384 helix: 1.64 (0.18), residues: 894 sheet: -2.98 (0.68), residues: 42 loop : -2.67 (0.29), residues: 448 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 0.025 0.001 PHE B 33 TYR 0.021 0.001 TYR B 181 ARG 0.003 0.000 ARG A 375 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2768 Ramachandran restraints generated. 1384 Oldfield, 0 Emsley, 1384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2768 Ramachandran restraints generated. 1384 Oldfield, 0 Emsley, 1384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 1206 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 164 time to evaluate : 1.138 Fit side-chains REVERT: A 422 LYS cc_start: 0.7493 (mmtt) cc_final: 0.7150 (mmtt) REVERT: A 613 TYR cc_start: 0.8474 (m-10) cc_final: 0.8269 (m-10) REVERT: B 422 LYS cc_start: 0.7341 (mmtt) cc_final: 0.7101 (mmtt) REVERT: B 511 MET cc_start: 0.7533 (mtm) cc_final: 0.7269 (mpp) REVERT: B 578 LEU cc_start: 0.7993 (OUTLIER) cc_final: 0.7597 (tt) REVERT: B 709 GLN cc_start: 0.8521 (pt0) cc_final: 0.8285 (tt0) outliers start: 19 outliers final: 7 residues processed: 173 average time/residue: 0.2014 time to fit residues: 52.9751 Evaluate side-chains 161 residues out of total 1206 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 153 time to evaluate : 1.206 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 132 MET Chi-restraints excluded: chain A residue 393 ILE Chi-restraints excluded: chain A residue 543 LEU Chi-restraints excluded: chain A residue 645 LEU Chi-restraints excluded: chain B residue 30 LEU Chi-restraints excluded: chain B residue 37 VAL Chi-restraints excluded: chain B residue 578 LEU Chi-restraints excluded: chain B residue 645 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 71 optimal weight: 2.9990 chunk 24 optimal weight: 9.9990 chunk 41 optimal weight: 1.9990 chunk 58 optimal weight: 0.6980 chunk 112 optimal weight: 0.8980 chunk 9 optimal weight: 3.9990 chunk 117 optimal weight: 1.9990 chunk 25 optimal weight: 50.0000 chunk 11 optimal weight: 8.9990 chunk 63 optimal weight: 0.8980 chunk 39 optimal weight: 0.0470 overall best weight: 0.9080 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 472 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4059 r_free = 0.4059 target = 0.186974 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.137391 restraints weight = 12599.192| |-----------------------------------------------------------------------------| r_work (start): 0.3429 rms_B_bonded: 2.31 r_work: 0.3075 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.3075 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7861 moved from start: 0.1769 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 11444 Z= 0.242 Angle : 0.639 10.199 15576 Z= 0.315 Chirality : 0.043 0.179 1764 Planarity : 0.005 0.060 1946 Dihedral : 4.646 19.870 1494 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 6.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.65 % Favored : 93.35 % Rotamer: Outliers : 1.37 % Allowed : 14.08 % Favored : 84.56 % 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: 0.45 (0.24), residues: 1384 helix: 1.77 (0.18), residues: 884 sheet: -3.08 (0.66), residues: 42 loop : -2.46 (0.29), residues: 458 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 624 HIS 0.004 0.001 HIS A 628 PHE 0.023 0.001 PHE B 33 TYR 0.022 0.001 TYR A 181 ARG 0.003 0.000 ARG B 29 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2768 Ramachandran restraints generated. 1384 Oldfield, 0 Emsley, 1384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2768 Ramachandran restraints generated. 1384 Oldfield, 0 Emsley, 1384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 1206 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 166 time to evaluate : 1.201 Fit side-chains REVERT: A 257 ASN cc_start: 0.8718 (m110) cc_final: 0.8319 (m110) REVERT: A 422 LYS cc_start: 0.7478 (mmtt) cc_final: 0.7155 (mmtt) REVERT: A 523 ASP cc_start: 0.7781 (t0) cc_final: 0.7567 (t0) REVERT: A 531 GLU cc_start: 0.7826 (tp30) cc_final: 0.7052 (mm-30) REVERT: A 613 TYR cc_start: 0.8453 (m-10) cc_final: 0.8190 (m-10) REVERT: B 315 ASP cc_start: 0.7724 (t0) cc_final: 0.7497 (t0) REVERT: B 422 LYS cc_start: 0.7430 (mmtt) cc_final: 0.7225 (mmtt) REVERT: B 511 MET cc_start: 0.7535 (mtm) cc_final: 0.7308 (mpp) REVERT: B 531 GLU cc_start: 0.7767 (tp30) cc_final: 0.7143 (mm-30) REVERT: B 578 LEU cc_start: 0.7946 (OUTLIER) cc_final: 0.7481 (tt) REVERT: B 709 GLN cc_start: 0.8427 (pt0) cc_final: 0.8189 (tt0) outliers start: 16 outliers final: 8 residues processed: 174 average time/residue: 0.1883 time to fit residues: 51.0785 Evaluate side-chains 166 residues out of total 1206 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 157 time to evaluate : 1.165 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 132 MET Chi-restraints excluded: chain A residue 393 ILE Chi-restraints excluded: chain A residue 543 LEU Chi-restraints excluded: chain A residue 563 SER Chi-restraints excluded: chain A residue 645 LEU Chi-restraints excluded: chain B residue 37 VAL Chi-restraints excluded: chain B residue 472 ASN Chi-restraints excluded: chain B residue 578 LEU Chi-restraints excluded: chain B residue 645 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 57 optimal weight: 0.5980 chunk 136 optimal weight: 0.9990 chunk 73 optimal weight: 3.9990 chunk 44 optimal weight: 0.9980 chunk 49 optimal weight: 0.6980 chunk 31 optimal weight: 0.9990 chunk 70 optimal weight: 2.9990 chunk 108 optimal weight: 8.9990 chunk 26 optimal weight: 20.0000 chunk 14 optimal weight: 1.9990 chunk 1 optimal weight: 0.9980 overall best weight: 0.8582 ------------------------------------------------------------------------------- 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 = 0.4062 r_free = 0.4062 target = 0.187332 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.137904 restraints weight = 12541.648| |-----------------------------------------------------------------------------| r_work (start): 0.3482 rms_B_bonded: 2.19 r_work: 0.3131 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work: 0.2992 rms_B_bonded: 4.94 restraints_weight: 0.2500 r_work (final): 0.2992 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7976 moved from start: 0.1908 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 11444 Z= 0.233 Angle : 0.630 10.119 15576 Z= 0.311 Chirality : 0.043 0.208 1764 Planarity : 0.005 0.061 1946 Dihedral : 4.608 19.364 1494 Min Nonbonded Distance : 2.576 Molprobity Statistics. All-atom Clashscore : 6.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.50 % Favored : 93.50 % Rotamer: Outliers : 1.79 % Allowed : 15.78 % Favored : 82.42 % 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: 0.54 (0.24), residues: 1384 helix: 1.86 (0.18), residues: 882 sheet: -3.16 (0.65), residues: 42 loop : -2.42 (0.29), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 624 HIS 0.004 0.001 HIS A 628 PHE 0.023 0.001 PHE A 383 TYR 0.017 0.001 TYR A 583 ARG 0.002 0.000 ARG B 48 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2768 Ramachandran restraints generated. 1384 Oldfield, 0 Emsley, 1384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2768 Ramachandran restraints generated. 1384 Oldfield, 0 Emsley, 1384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 1206 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 161 time to evaluate : 1.235 Fit side-chains REVERT: A 98 TYR cc_start: 0.9035 (t80) cc_final: 0.8695 (t80) REVERT: A 256 GLN cc_start: 0.8496 (tp40) cc_final: 0.8235 (tp40) REVERT: A 257 ASN cc_start: 0.8828 (m110) cc_final: 0.8402 (m110) REVERT: A 422 LYS cc_start: 0.7489 (mmtt) cc_final: 0.7112 (mmtt) REVERT: A 523 ASP cc_start: 0.7888 (t0) cc_final: 0.7655 (t0) REVERT: A 531 GLU cc_start: 0.7997 (tp30) cc_final: 0.7215 (mm-30) REVERT: A 613 TYR cc_start: 0.8555 (m-10) cc_final: 0.8267 (m-10) REVERT: B 315 ASP cc_start: 0.7843 (t0) cc_final: 0.7591 (t0) REVERT: B 511 MET cc_start: 0.7685 (mtm) cc_final: 0.7453 (mpp) REVERT: B 531 GLU cc_start: 0.7939 (tp30) cc_final: 0.7317 (mm-30) REVERT: B 578 LEU cc_start: 0.8054 (OUTLIER) cc_final: 0.7614 (tt) REVERT: B 709 GLN cc_start: 0.8608 (pt0) cc_final: 0.8311 (tt0) outliers start: 21 outliers final: 11 residues processed: 172 average time/residue: 0.1821 time to fit residues: 48.7901 Evaluate side-chains 168 residues out of total 1206 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 156 time to evaluate : 1.170 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 132 MET Chi-restraints excluded: chain A residue 204 VAL Chi-restraints excluded: chain A residue 393 ILE Chi-restraints excluded: chain A residue 399 LEU Chi-restraints excluded: chain A residue 482 ILE Chi-restraints excluded: chain A residue 543 LEU Chi-restraints excluded: chain A residue 645 LEU Chi-restraints excluded: chain B residue 37 VAL Chi-restraints excluded: chain B residue 132 MET Chi-restraints excluded: chain B residue 399 LEU Chi-restraints excluded: chain B residue 578 LEU Chi-restraints excluded: chain B residue 645 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 84 optimal weight: 1.9990 chunk 102 optimal weight: 0.9980 chunk 92 optimal weight: 8.9990 chunk 9 optimal weight: 1.9990 chunk 51 optimal weight: 4.9990 chunk 48 optimal weight: 0.0270 chunk 65 optimal weight: 0.3980 chunk 123 optimal weight: 0.6980 chunk 87 optimal weight: 0.9990 chunk 37 optimal weight: 0.8980 chunk 33 optimal weight: 0.6980 overall best weight: 0.5438 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 472 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4084 r_free = 0.4084 target = 0.189427 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.136670 restraints weight = 12708.241| |-----------------------------------------------------------------------------| r_work (start): 0.3400 rms_B_bonded: 2.60 r_work: 0.3080 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.3080 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7807 moved from start: 0.2093 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 11444 Z= 0.189 Angle : 0.632 15.240 15576 Z= 0.304 Chirality : 0.043 0.175 1764 Planarity : 0.005 0.060 1946 Dihedral : 4.501 19.957 1494 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 6.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.29 % Favored : 93.71 % Rotamer: Outliers : 1.88 % Allowed : 16.47 % Favored : 81.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.68 (0.24), residues: 1384 helix: 1.93 (0.18), residues: 884 sheet: -2.58 (0.77), residues: 34 loop : -2.38 (0.29), residues: 466 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 624 HIS 0.004 0.001 HIS A 628 PHE 0.021 0.001 PHE B 33 TYR 0.012 0.001 TYR A 181 ARG 0.002 0.000 ARG B 198 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2768 Ramachandran restraints generated. 1384 Oldfield, 0 Emsley, 1384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2768 Ramachandran restraints generated. 1384 Oldfield, 0 Emsley, 1384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 1206 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 164 time to evaluate : 1.135 Fit side-chains REVERT: A 98 TYR cc_start: 0.8921 (t80) cc_final: 0.8569 (t80) REVERT: A 257 ASN cc_start: 0.8796 (m110) cc_final: 0.8348 (m110) REVERT: A 388 PHE cc_start: 0.7781 (t80) cc_final: 0.7070 (m-10) REVERT: A 523 ASP cc_start: 0.7763 (t0) cc_final: 0.7495 (t0) REVERT: A 531 GLU cc_start: 0.7721 (tp30) cc_final: 0.6854 (mm-30) REVERT: A 613 TYR cc_start: 0.8389 (m-10) cc_final: 0.8168 (m-10) REVERT: B 4 LEU cc_start: 0.7182 (tt) cc_final: 0.6459 (tp) REVERT: B 422 LYS cc_start: 0.7216 (mmtt) cc_final: 0.6998 (mmtt) REVERT: B 487 PHE cc_start: 0.6894 (t80) cc_final: 0.6588 (m-80) REVERT: B 531 GLU cc_start: 0.7626 (tp30) cc_final: 0.6986 (mm-30) REVERT: B 560 ASP cc_start: 0.7069 (t0) cc_final: 0.6230 (p0) REVERT: B 578 LEU cc_start: 0.7898 (OUTLIER) cc_final: 0.7435 (tt) REVERT: B 709 GLN cc_start: 0.8341 (pt0) cc_final: 0.8076 (tt0) outliers start: 22 outliers final: 12 residues processed: 172 average time/residue: 0.2157 time to fit residues: 56.9175 Evaluate side-chains 168 residues out of total 1206 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 155 time to evaluate : 1.284 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 PHE Chi-restraints excluded: chain A residue 132 MET Chi-restraints excluded: chain A residue 393 ILE Chi-restraints excluded: chain A residue 399 LEU Chi-restraints excluded: chain A residue 543 LEU Chi-restraints excluded: chain A residue 563 SER Chi-restraints excluded: chain A residue 645 LEU Chi-restraints excluded: chain B residue 37 VAL Chi-restraints excluded: chain B residue 132 MET Chi-restraints excluded: chain B residue 399 LEU Chi-restraints excluded: chain B residue 538 LEU Chi-restraints excluded: chain B residue 578 LEU Chi-restraints excluded: chain B residue 645 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 109 optimal weight: 0.9990 chunk 6 optimal weight: 0.7980 chunk 39 optimal weight: 6.9990 chunk 134 optimal weight: 0.8980 chunk 8 optimal weight: 0.8980 chunk 89 optimal weight: 0.8980 chunk 85 optimal weight: 0.5980 chunk 126 optimal weight: 0.3980 chunk 46 optimal weight: 7.9990 chunk 27 optimal weight: 4.9990 chunk 101 optimal weight: 0.8980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 472 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4073 r_free = 0.4073 target = 0.188464 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.136477 restraints weight = 12718.722| |-----------------------------------------------------------------------------| r_work (start): 0.3434 rms_B_bonded: 2.77 r_work: 0.3118 rms_B_bonded: 3.38 restraints_weight: 0.5000 r_work (final): 0.3118 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7882 moved from start: 0.2183 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 11444 Z= 0.212 Angle : 0.630 14.000 15576 Z= 0.306 Chirality : 0.043 0.296 1764 Planarity : 0.005 0.063 1946 Dihedral : 4.463 21.108 1494 Min Nonbonded Distance : 2.571 Molprobity Statistics. All-atom Clashscore : 6.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.65 % Favored : 93.35 % Rotamer: Outliers : 1.79 % Allowed : 17.15 % Favored : 81.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.69 (0.24), residues: 1384 helix: 1.97 (0.18), residues: 884 sheet: -3.20 (0.61), residues: 46 loop : -2.34 (0.29), residues: 454 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 0.027 0.001 PHE A 383 TYR 0.014 0.001 TYR A 181 ARG 0.002 0.000 ARG B 48 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2768 Ramachandran restraints generated. 1384 Oldfield, 0 Emsley, 1384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2768 Ramachandran restraints generated. 1384 Oldfield, 0 Emsley, 1384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 1206 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 157 time to evaluate : 1.233 Fit side-chains REVERT: A 82 MET cc_start: 0.8123 (ttp) cc_final: 0.7706 (ttt) REVERT: A 257 ASN cc_start: 0.8792 (m110) cc_final: 0.8397 (m110) REVERT: A 388 PHE cc_start: 0.7822 (t80) cc_final: 0.7197 (m-10) REVERT: A 422 LYS cc_start: 0.7674 (mptt) cc_final: 0.6770 (mmtt) REVERT: A 523 ASP cc_start: 0.7778 (t0) cc_final: 0.7546 (t0) REVERT: A 531 GLU cc_start: 0.7606 (tp30) cc_final: 0.6810 (mm-30) REVERT: A 613 TYR cc_start: 0.8406 (m-10) cc_final: 0.8177 (m-10) REVERT: B 4 LEU cc_start: 0.7183 (tt) cc_final: 0.6581 (tp) REVERT: B 256 GLN cc_start: 0.8414 (tp40) cc_final: 0.8212 (tp40) REVERT: B 422 LYS cc_start: 0.7308 (mmtt) cc_final: 0.7096 (mmtt) REVERT: B 531 GLU cc_start: 0.7632 (tp30) cc_final: 0.7007 (mm-30) REVERT: B 547 PHE cc_start: 0.7292 (m-10) cc_final: 0.7087 (m-10) REVERT: B 559 MET cc_start: 0.5505 (mmm) cc_final: 0.4993 (mtt) REVERT: B 578 LEU cc_start: 0.7970 (OUTLIER) cc_final: 0.7520 (tt) REVERT: B 709 GLN cc_start: 0.8311 (pt0) cc_final: 0.8064 (tt0) outliers start: 21 outliers final: 10 residues processed: 169 average time/residue: 0.1932 time to fit residues: 50.1065 Evaluate side-chains 162 residues out of total 1206 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 151 time to evaluate : 1.222 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 PHE Chi-restraints excluded: chain A residue 132 MET Chi-restraints excluded: chain A residue 204 VAL Chi-restraints excluded: chain A residue 393 ILE Chi-restraints excluded: chain A residue 543 LEU Chi-restraints excluded: chain A residue 563 SER Chi-restraints excluded: chain A residue 645 LEU Chi-restraints excluded: chain B residue 37 VAL Chi-restraints excluded: chain B residue 538 LEU Chi-restraints excluded: chain B residue 578 LEU Chi-restraints excluded: chain B residue 645 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 43 optimal weight: 1.9990 chunk 95 optimal weight: 20.0000 chunk 136 optimal weight: 1.9990 chunk 1 optimal weight: 2.9990 chunk 26 optimal weight: 20.0000 chunk 102 optimal weight: 1.9990 chunk 124 optimal weight: 0.9980 chunk 17 optimal weight: 0.8980 chunk 91 optimal weight: 1.9990 chunk 20 optimal weight: 0.9980 chunk 3 optimal weight: 0.0970 overall best weight: 0.9980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 611 ASN ** B 472 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4063 r_free = 0.4063 target = 0.187575 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3513 r_free = 0.3513 target = 0.135399 restraints weight = 12698.511| |-----------------------------------------------------------------------------| r_work (start): 0.3400 rms_B_bonded: 2.77 r_work: 0.3059 rms_B_bonded: 3.53 restraints_weight: 0.5000 r_work (final): 0.3059 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7921 moved from start: 0.2250 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 11444 Z= 0.251 Angle : 0.668 13.956 15576 Z= 0.320 Chirality : 0.044 0.408 1764 Planarity : 0.005 0.063 1946 Dihedral : 4.481 20.825 1494 Min Nonbonded Distance : 2.572 Molprobity Statistics. All-atom Clashscore : 6.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.43 % Favored : 93.57 % Rotamer: Outliers : 2.05 % Allowed : 16.55 % Favored : 81.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.61 (0.24), residues: 1384 helix: 1.89 (0.18), residues: 888 sheet: -3.25 (0.60), residues: 46 loop : -2.38 (0.29), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 624 HIS 0.004 0.001 HIS A 628 PHE 0.020 0.001 PHE B 33 TYR 0.015 0.001 TYR A 181 ARG 0.003 0.000 ARG B 48 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2768 Ramachandran restraints generated. 1384 Oldfield, 0 Emsley, 1384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2768 Ramachandran restraints generated. 1384 Oldfield, 0 Emsley, 1384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 1206 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 150 time to evaluate : 1.160 Fit side-chains REVERT: A 48 ARG cc_start: 0.8212 (ttm-80) cc_final: 0.7587 (ttt180) REVERT: A 257 ASN cc_start: 0.8821 (m110) cc_final: 0.8425 (m110) REVERT: A 388 PHE cc_start: 0.7822 (t80) cc_final: 0.7238 (m-10) REVERT: A 422 LYS cc_start: 0.7716 (mptt) cc_final: 0.7324 (mmtt) REVERT: A 523 ASP cc_start: 0.7795 (t0) cc_final: 0.7553 (t0) REVERT: A 531 GLU cc_start: 0.7635 (tp30) cc_final: 0.6828 (mm-30) REVERT: A 613 TYR cc_start: 0.8463 (m-10) cc_final: 0.8219 (m-10) REVERT: B 4 LEU cc_start: 0.7295 (tt) cc_final: 0.6707 (tp) REVERT: B 256 GLN cc_start: 0.8386 (tp40) cc_final: 0.8151 (tp40) REVERT: B 422 LYS cc_start: 0.7334 (mmtt) cc_final: 0.7087 (mmtt) REVERT: B 531 GLU cc_start: 0.7651 (tp30) cc_final: 0.7015 (mm-30) REVERT: B 559 MET cc_start: 0.5087 (mmm) cc_final: 0.4738 (mtt) REVERT: B 578 LEU cc_start: 0.7939 (OUTLIER) cc_final: 0.7483 (tt) REVERT: B 709 GLN cc_start: 0.8416 (pt0) cc_final: 0.8154 (tt0) outliers start: 24 outliers final: 12 residues processed: 163 average time/residue: 0.1968 time to fit residues: 49.6831 Evaluate side-chains 159 residues out of total 1206 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 146 time to evaluate : 1.249 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 PHE Chi-restraints excluded: chain A residue 132 MET Chi-restraints excluded: chain A residue 204 VAL Chi-restraints excluded: chain A residue 393 ILE Chi-restraints excluded: chain A residue 473 LEU Chi-restraints excluded: chain A residue 543 LEU Chi-restraints excluded: chain A residue 563 SER Chi-restraints excluded: chain A residue 645 LEU Chi-restraints excluded: chain B residue 30 LEU Chi-restraints excluded: chain B residue 37 VAL Chi-restraints excluded: chain B residue 132 MET Chi-restraints excluded: chain B residue 578 LEU Chi-restraints excluded: chain B residue 645 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 68 optimal weight: 0.7980 chunk 60 optimal weight: 0.9980 chunk 43 optimal weight: 0.6980 chunk 52 optimal weight: 7.9990 chunk 103 optimal weight: 0.0040 chunk 56 optimal weight: 0.7980 chunk 23 optimal weight: 5.9990 chunk 109 optimal weight: 0.9990 chunk 87 optimal weight: 0.9990 chunk 79 optimal weight: 2.9990 chunk 39 optimal weight: 6.9990 overall best weight: 0.6592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 489 GLN ** B 472 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4076 r_free = 0.4076 target = 0.188826 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3568 r_free = 0.3568 target = 0.139511 restraints weight = 12502.218| |-----------------------------------------------------------------------------| r_work (start): 0.3431 rms_B_bonded: 2.32 r_work: 0.3067 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.3067 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7830 moved from start: 0.2369 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 11444 Z= 0.207 Angle : 0.667 18.730 15576 Z= 0.314 Chirality : 0.043 0.239 1764 Planarity : 0.005 0.063 1946 Dihedral : 4.437 21.650 1494 Min Nonbonded Distance : 2.572 Molprobity Statistics. All-atom Clashscore : 6.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.43 % Favored : 93.57 % Rotamer: Outliers : 1.45 % Allowed : 17.49 % Favored : 81.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.64 (0.24), residues: 1384 helix: 1.91 (0.18), residues: 888 sheet: -3.12 (0.62), residues: 46 loop : -2.36 (0.29), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 624 HIS 0.004 0.001 HIS A 628 PHE 0.027 0.001 PHE A 383 TYR 0.011 0.001 TYR A 181 ARG 0.002 0.000 ARG B 48 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2768 Ramachandran restraints generated. 1384 Oldfield, 0 Emsley, 1384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2768 Ramachandran restraints generated. 1384 Oldfield, 0 Emsley, 1384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 1206 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 152 time to evaluate : 1.196 Fit side-chains REVERT: A 257 ASN cc_start: 0.8840 (m110) cc_final: 0.8458 (m110) REVERT: A 388 PHE cc_start: 0.7752 (t80) cc_final: 0.7197 (m-10) REVERT: A 422 LYS cc_start: 0.7701 (mptt) cc_final: 0.7280 (mmtt) REVERT: A 523 ASP cc_start: 0.7776 (t0) cc_final: 0.7488 (t0) REVERT: A 531 GLU cc_start: 0.7499 (tp30) cc_final: 0.6742 (mm-30) REVERT: B 4 LEU cc_start: 0.7164 (tt) cc_final: 0.6539 (tp) REVERT: B 256 GLN cc_start: 0.8353 (tp40) cc_final: 0.8152 (tp40) REVERT: B 422 LYS cc_start: 0.7290 (mmtt) cc_final: 0.7074 (mmtt) REVERT: B 511 MET cc_start: 0.7434 (mpp) cc_final: 0.7179 (mpp) REVERT: B 531 GLU cc_start: 0.7518 (tp30) cc_final: 0.6876 (mm-30) REVERT: B 578 LEU cc_start: 0.7948 (OUTLIER) cc_final: 0.7508 (tt) REVERT: B 709 GLN cc_start: 0.8336 (pt0) cc_final: 0.8074 (tt0) outliers start: 17 outliers final: 8 residues processed: 162 average time/residue: 0.1985 time to fit residues: 49.6833 Evaluate side-chains 160 residues out of total 1206 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 151 time to evaluate : 1.226 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 PHE Chi-restraints excluded: chain A residue 204 VAL Chi-restraints excluded: chain A residue 393 ILE Chi-restraints excluded: chain A residue 473 LEU Chi-restraints excluded: chain A residue 645 LEU Chi-restraints excluded: chain B residue 30 LEU Chi-restraints excluded: chain B residue 37 VAL Chi-restraints excluded: chain B residue 578 LEU Chi-restraints excluded: chain B residue 645 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 137 optimal weight: 2.9990 chunk 47 optimal weight: 0.7980 chunk 66 optimal weight: 0.7980 chunk 130 optimal weight: 0.9990 chunk 27 optimal weight: 4.9990 chunk 116 optimal weight: 30.0000 chunk 55 optimal weight: 0.9980 chunk 16 optimal weight: 0.9980 chunk 112 optimal weight: 0.6980 chunk 125 optimal weight: 0.6980 chunk 132 optimal weight: 6.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 472 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4072 r_free = 0.4072 target = 0.188191 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.136300 restraints weight = 12634.755| |-----------------------------------------------------------------------------| r_work (start): 0.3432 rms_B_bonded: 2.66 r_work: 0.3102 rms_B_bonded: 3.44 restraints_weight: 0.5000 r_work (final): 0.3102 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7891 moved from start: 0.2425 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 11444 Z= 0.227 Angle : 0.683 20.914 15576 Z= 0.322 Chirality : 0.043 0.184 1764 Planarity : 0.005 0.062 1946 Dihedral : 4.452 20.824 1494 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 7.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.00 % Favored : 94.00 % Rotamer: Outliers : 0.94 % Allowed : 17.92 % Favored : 81.14 % 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: 0.62 (0.24), residues: 1384 helix: 1.89 (0.18), residues: 888 sheet: -3.20 (0.60), residues: 46 loop : -2.35 (0.29), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 624 HIS 0.004 0.001 HIS A 628 PHE 0.019 0.001 PHE B 33 TYR 0.013 0.001 TYR A 181 ARG 0.005 0.000 ARG B 36 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2768 Ramachandran restraints generated. 1384 Oldfield, 0 Emsley, 1384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2768 Ramachandran restraints generated. 1384 Oldfield, 0 Emsley, 1384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 1206 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 150 time to evaluate : 1.282 Fit side-chains REVERT: A 257 ASN cc_start: 0.8845 (m110) cc_final: 0.8462 (m110) REVERT: A 388 PHE cc_start: 0.7833 (t80) cc_final: 0.7247 (m-10) REVERT: A 422 LYS cc_start: 0.7742 (mptt) cc_final: 0.6940 (mmtt) REVERT: A 523 ASP cc_start: 0.7831 (t0) cc_final: 0.7594 (t0) REVERT: A 531 GLU cc_start: 0.7546 (tp30) cc_final: 0.6805 (mm-30) REVERT: B 4 LEU cc_start: 0.7166 (tt) cc_final: 0.6518 (tp) REVERT: B 256 GLN cc_start: 0.8396 (tp40) cc_final: 0.8027 (tp40) REVERT: B 315 ASP cc_start: 0.7696 (t0) cc_final: 0.7485 (t0) REVERT: B 422 LYS cc_start: 0.7270 (mmtt) cc_final: 0.7056 (mmtt) REVERT: B 511 MET cc_start: 0.7457 (mpp) cc_final: 0.7196 (mpp) REVERT: B 531 GLU cc_start: 0.7543 (tp30) cc_final: 0.6904 (mm-30) REVERT: B 578 LEU cc_start: 0.7975 (OUTLIER) cc_final: 0.7519 (tt) REVERT: B 709 GLN cc_start: 0.8324 (pt0) cc_final: 0.8065 (tt0) outliers start: 11 outliers final: 9 residues processed: 157 average time/residue: 0.1798 time to fit residues: 44.2746 Evaluate side-chains 156 residues out of total 1206 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 146 time to evaluate : 1.189 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 PHE Chi-restraints excluded: chain A residue 204 VAL Chi-restraints excluded: chain A residue 389 PHE Chi-restraints excluded: chain A residue 393 ILE Chi-restraints excluded: chain A residue 473 LEU Chi-restraints excluded: chain A residue 645 LEU Chi-restraints excluded: chain B residue 30 LEU Chi-restraints excluded: chain B residue 37 VAL Chi-restraints excluded: chain B residue 578 LEU Chi-restraints excluded: chain B residue 645 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 60 optimal weight: 0.7980 chunk 25 optimal weight: 20.0000 chunk 42 optimal weight: 1.9990 chunk 117 optimal weight: 0.0980 chunk 74 optimal weight: 8.9990 chunk 26 optimal weight: 20.0000 chunk 125 optimal weight: 0.5980 chunk 31 optimal weight: 0.9980 chunk 70 optimal weight: 1.9990 chunk 37 optimal weight: 0.6980 chunk 131 optimal weight: 3.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 472 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4085 r_free = 0.4085 target = 0.189575 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.140398 restraints weight = 12465.702| |-----------------------------------------------------------------------------| r_work (start): 0.3443 rms_B_bonded: 2.29 r_work: 0.3079 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.3079 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7832 moved from start: 0.2510 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 11444 Z= 0.204 Angle : 0.669 20.037 15576 Z= 0.315 Chirality : 0.043 0.182 1764 Planarity : 0.005 0.062 1946 Dihedral : 4.414 20.984 1494 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 6.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.21 % Favored : 93.79 % Rotamer: Outliers : 1.37 % Allowed : 17.75 % Favored : 80.89 % 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: 0.70 (0.24), residues: 1384 helix: 1.92 (0.18), residues: 888 sheet: -2.43 (0.77), residues: 34 loop : -2.36 (0.29), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 624 HIS 0.004 0.001 HIS A 628 PHE 0.027 0.001 PHE A 383 TYR 0.011 0.001 TYR A 181 ARG 0.002 0.000 ARG B 36 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5016.70 seconds wall clock time: 91 minutes 47.71 seconds (5507.71 seconds total)