Starting phenix.real_space_refine on Wed Sep 17 20:17:54 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8xs4_38614/09_2025/8xs4_38614.cif Found real_map, /net/cci-nas-00/data/ceres_data/8xs4_38614/09_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_38614/09_2025/8xs4_38614.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8xs4_38614/09_2025/8xs4_38614.map" model { file = "/net/cci-nas-00/data/ceres_data/8xs4_38614/09_2025/8xs4_38614.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8xs4_38614/09_2025/8xs4_38614.cif" } resolution = 3.23 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= 0.007 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): 0.01s 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: 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: {'ARG:plan': 2, 'ASN:plan1': 2, 'GLN:plan1': 2, 'PHE:plan': 1, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 39 Restraints were copied for chains: B Time building chain proxies: 4.47, per 1000 atoms: 0.40 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: 0.82 Conformation dependent library (CDL) restraints added in 398.6 milliseconds Enol-peptide restraints added in 238.4 nanoseconds 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: 0.32 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: 1.73 Time building geometry restraints manager: 1.06 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: 0.02 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: 0.910 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.200 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 12.140 Find NCS groups from input model: 0.070 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:1.290 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.670 ------------------------------------------------------------------------------- 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= 0.175 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 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: -0.41 (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 ARG 0.004 0.001 ARG A 630 TYR 0.045 0.002 TYR A 181 PHE 0.036 0.002 PHE A 33 TRP 0.016 0.002 TRP A 75 HIS 0.003 0.001 HIS B 628 Details of bonding type rmsd covalent geometry : bond 0.00390 (11444) covalent geometry : angle 0.79688 (15576) hydrogen bonds : bond 0.12757 ( 693) hydrogen bonds : angle 5.90154 ( 2043) *********************** 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 : 0.398 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: 0.0835 time to fit residues: 25.1802 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 : 0.418 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 98 optimal weight: 3.9990 chunk 107 optimal weight: 5.9990 chunk 10 optimal weight: 0.0050 chunk 66 optimal weight: 1.9990 chunk 130 optimal weight: 0.9980 chunk 124 optimal weight: 0.9990 chunk 103 optimal weight: 0.7980 chunk 77 optimal weight: 0.5980 chunk 122 optimal weight: 7.9990 chunk 91 optimal weight: 0.8980 chunk 55 optimal weight: 1.9990 overall best weight: 0.6594 ------------------------------------------------------------------------------- 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 = 0.4062 r_free = 0.4062 target = 0.187253 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3507 r_free = 0.3507 target = 0.134396 restraints weight = 12736.789| |-----------------------------------------------------------------------------| r_work (start): 0.3381 rms_B_bonded: 2.67 r_work: 0.3057 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.3057 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7849 moved from start: 0.1195 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= 0.149 Angle : 0.691 10.492 15576 Z= 0.341 Chirality : 0.044 0.202 1764 Planarity : 0.006 0.060 1946 Dihedral : 5.035 20.688 1494 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 7.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.15 % Favored : 92.85 % Rotamer: Outliers : 0.94 % Allowed : 8.02 % Favored : 91.04 % 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: -0.02 (0.24), residues: 1384 helix: 1.46 (0.18), residues: 886 sheet: -2.61 (0.74), residues: 42 loop : -2.86 (0.28), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 374 TYR 0.029 0.001 TYR B 181 PHE 0.028 0.001 PHE B 33 TRP 0.018 0.001 TRP A 624 HIS 0.004 0.001 HIS A 628 Details of bonding type rmsd covalent geometry : bond 0.00347 (11444) covalent geometry : angle 0.69148 (15576) hydrogen bonds : bond 0.04220 ( 693) hydrogen bonds : angle 4.56710 ( 2043) *********************** 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 180 residues out of total 1206 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 169 time to evaluate : 0.308 Fit side-chains REVERT: A 98 TYR cc_start: 0.8830 (t80) cc_final: 0.8469 (t80) REVERT: A 422 LYS cc_start: 0.7490 (mmtt) cc_final: 0.7175 (mmtt) REVERT: A 613 TYR cc_start: 0.8353 (m-10) cc_final: 0.8095 (m-10) REVERT: B 315 ASP cc_start: 0.7652 (t0) cc_final: 0.7354 (t0) REVERT: B 395 PHE cc_start: 0.9040 (t80) cc_final: 0.8797 (t80) REVERT: B 422 LYS cc_start: 0.7232 (mmtt) cc_final: 0.6983 (mmtt) REVERT: B 452 GLU cc_start: 0.3964 (mt-10) cc_final: 0.3365 (mt-10) REVERT: B 511 MET cc_start: 0.7439 (mtm) cc_final: 0.7173 (mpp) REVERT: B 709 GLN cc_start: 0.8512 (pt0) cc_final: 0.8286 (tt0) outliers start: 11 outliers final: 7 residues processed: 171 average time/residue: 0.0837 time to fit residues: 22.1891 Evaluate side-chains 164 residues out of total 1206 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 157 time to evaluate : 0.379 ------------------------------------------------------------------------------- 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 94 optimal weight: 20.0000 chunk 55 optimal weight: 1.9990 chunk 42 optimal weight: 1.9990 chunk 68 optimal weight: 4.9990 chunk 20 optimal weight: 0.6980 chunk 106 optimal weight: 0.7980 chunk 82 optimal weight: 0.0570 chunk 74 optimal weight: 0.9990 chunk 80 optimal weight: 30.0000 chunk 29 optimal weight: 3.9990 chunk 61 optimal weight: 0.8980 overall best weight: 0.6900 ------------------------------------------------------------------------------- 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 = 0.4057 r_free = 0.4057 target = 0.187060 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.134332 restraints weight = 12780.012| |-----------------------------------------------------------------------------| r_work (start): 0.3390 rms_B_bonded: 2.71 r_work: 0.3066 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.3066 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7844 moved from start: 0.1515 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 11444 Z= 0.141 Angle : 0.646 9.890 15576 Z= 0.320 Chirality : 0.043 0.186 1764 Planarity : 0.006 0.059 1946 Dihedral : 4.775 19.188 1494 Min Nonbonded Distance : 2.558 Molprobity Statistics. All-atom Clashscore : 6.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.01 % Favored : 92.99 % Rotamer: Outliers : 1.54 % Allowed : 12.46 % Favored : 86.01 % 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: 0.23 (0.24), residues: 1384 helix: 1.61 (0.18), residues: 894 sheet: -3.04 (0.67), residues: 42 loop : -2.68 (0.29), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 29 TYR 0.022 0.001 TYR A 181 PHE 0.025 0.001 PHE B 33 TRP 0.017 0.001 TRP A 624 HIS 0.004 0.001 HIS A 628 Details of bonding type rmsd covalent geometry : bond 0.00334 (11444) covalent geometry : angle 0.64602 (15576) hydrogen bonds : bond 0.03943 ( 693) hydrogen bonds : angle 4.39193 ( 2043) *********************** 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 181 residues out of total 1206 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 163 time to evaluate : 0.344 Fit side-chains REVERT: A 98 TYR cc_start: 0.8791 (t80) cc_final: 0.8533 (t80) REVERT: A 257 ASN cc_start: 0.8737 (m110) cc_final: 0.8340 (m110) REVERT: A 422 LYS cc_start: 0.7489 (mmtt) cc_final: 0.7152 (mmtt) REVERT: A 583 TYR cc_start: 0.7541 (m-80) cc_final: 0.7309 (m-10) REVERT: A 613 TYR cc_start: 0.8397 (m-10) cc_final: 0.8185 (m-10) REVERT: B 422 LYS cc_start: 0.7336 (mmtt) cc_final: 0.7101 (mmtt) REVERT: B 511 MET cc_start: 0.7475 (mtm) cc_final: 0.7234 (mpp) REVERT: B 578 LEU cc_start: 0.7953 (OUTLIER) cc_final: 0.7517 (tt) REVERT: B 709 GLN cc_start: 0.8393 (pt0) cc_final: 0.8175 (tt0) outliers start: 18 outliers final: 6 residues processed: 172 average time/residue: 0.0844 time to fit residues: 22.6295 Evaluate side-chains 160 residues out of total 1206 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 153 time to evaluate : 0.410 ------------------------------------------------------------------------------- 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 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 34 optimal weight: 0.8980 chunk 115 optimal weight: 9.9990 chunk 74 optimal weight: 0.9990 chunk 133 optimal weight: 0.5980 chunk 71 optimal weight: 2.9990 chunk 81 optimal weight: 10.0000 chunk 31 optimal weight: 0.9980 chunk 122 optimal weight: 6.9990 chunk 116 optimal weight: 30.0000 chunk 68 optimal weight: 4.9990 chunk 67 optimal weight: 2.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- 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 = 0.4045 r_free = 0.4045 target = 0.185875 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.132059 restraints weight = 12881.437| |-----------------------------------------------------------------------------| r_work (start): 0.3340 rms_B_bonded: 3.18 r_work: 0.3004 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work (final): 0.3004 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7869 moved from start: 0.1759 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 11444 Z= 0.187 Angle : 0.663 10.341 15576 Z= 0.328 Chirality : 0.044 0.184 1764 Planarity : 0.006 0.058 1946 Dihedral : 4.730 18.805 1494 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 6.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.23 % Favored : 92.77 % Rotamer: Outliers : 1.54 % Allowed : 14.85 % Favored : 83.62 % 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: 0.29 (0.24), residues: 1384 helix: 1.62 (0.18), residues: 894 sheet: -3.39 (0.59), residues: 46 loop : -2.50 (0.30), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 36 TYR 0.026 0.002 TYR A 181 PHE 0.022 0.001 PHE B 33 TRP 0.019 0.001 TRP A 624 HIS 0.005 0.001 HIS A 628 Details of bonding type rmsd covalent geometry : bond 0.00462 (11444) covalent geometry : angle 0.66254 (15576) hydrogen bonds : bond 0.04219 ( 693) hydrogen bonds : angle 4.37861 ( 2043) *********************** 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 179 residues out of total 1206 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 161 time to evaluate : 0.336 Fit side-chains REVERT: A 165 MET cc_start: 0.7969 (mmm) cc_final: 0.7711 (mmp) REVERT: A 257 ASN cc_start: 0.8745 (m110) cc_final: 0.8338 (m110) REVERT: A 422 LYS cc_start: 0.7477 (mmtt) cc_final: 0.7165 (mmtt) REVERT: A 523 ASP cc_start: 0.7791 (t0) cc_final: 0.7545 (t0) REVERT: A 531 GLU cc_start: 0.7848 (tp30) cc_final: 0.7065 (mm-30) REVERT: A 613 TYR cc_start: 0.8517 (m-10) cc_final: 0.8228 (m-10) REVERT: B 256 GLN cc_start: 0.8351 (tp40) cc_final: 0.8146 (tp40) REVERT: B 315 ASP cc_start: 0.7819 (t0) cc_final: 0.7547 (t0) REVERT: B 511 MET cc_start: 0.7524 (mtm) cc_final: 0.7281 (mpp) REVERT: B 559 MET cc_start: 0.5600 (mtm) cc_final: 0.5400 (mtm) REVERT: B 578 LEU cc_start: 0.7941 (OUTLIER) cc_final: 0.7444 (tt) REVERT: B 709 GLN cc_start: 0.8559 (pt0) cc_final: 0.8210 (tt0) outliers start: 18 outliers final: 11 residues processed: 171 average time/residue: 0.0807 time to fit residues: 21.8427 Evaluate side-chains 166 residues out of total 1206 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 154 time to evaluate : 0.359 ------------------------------------------------------------------------------- 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 482 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 399 LEU 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 48 optimal weight: 6.9990 chunk 21 optimal weight: 3.9990 chunk 131 optimal weight: 10.0000 chunk 116 optimal weight: 9.9990 chunk 82 optimal weight: 0.1980 chunk 73 optimal weight: 9.9990 chunk 120 optimal weight: 5.9990 chunk 66 optimal weight: 1.9990 chunk 110 optimal weight: 0.9990 chunk 67 optimal weight: 3.9990 chunk 122 optimal weight: 0.2980 overall best weight: 1.4986 ------------------------------------------------------------------------------- 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** B 340 GLN B 472 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4039 r_free = 0.4039 target = 0.185218 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.132933 restraints weight = 12750.236| |-----------------------------------------------------------------------------| r_work (start): 0.3360 rms_B_bonded: 2.51 r_work: 0.3015 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.3015 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7903 moved from start: 0.1870 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.059 11444 Z= 0.201 Angle : 0.660 10.436 15576 Z= 0.328 Chirality : 0.045 0.186 1764 Planarity : 0.006 0.060 1946 Dihedral : 4.729 18.996 1494 Min Nonbonded Distance : 2.564 Molprobity Statistics. All-atom Clashscore : 7.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.15 % Favored : 92.85 % Rotamer: Outliers : 2.13 % Allowed : 16.04 % Favored : 81.83 % 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: 0.29 (0.24), residues: 1384 helix: 1.63 (0.18), residues: 892 sheet: -3.45 (0.57), residues: 46 loop : -2.50 (0.29), residues: 446 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 48 TYR 0.020 0.002 TYR A 181 PHE 0.022 0.001 PHE A 383 TRP 0.019 0.001 TRP A 624 HIS 0.005 0.001 HIS A 628 Details of bonding type rmsd covalent geometry : bond 0.00499 (11444) covalent geometry : angle 0.66041 (15576) hydrogen bonds : bond 0.04266 ( 693) hydrogen bonds : angle 4.38783 ( 2043) *********************** 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 181 residues out of total 1206 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 156 time to evaluate : 0.427 Fit side-chains REVERT: A 181 TYR cc_start: 0.8704 (OUTLIER) cc_final: 0.8467 (t80) REVERT: A 256 GLN cc_start: 0.8436 (tp40) cc_final: 0.8222 (tp40) REVERT: A 257 ASN cc_start: 0.8797 (m110) cc_final: 0.8333 (m110) REVERT: A 422 LYS cc_start: 0.7519 (mmtt) cc_final: 0.7187 (mmtt) REVERT: A 523 ASP cc_start: 0.7815 (t0) cc_final: 0.7565 (t0) REVERT: A 531 GLU cc_start: 0.7842 (tp30) cc_final: 0.7063 (mm-30) REVERT: A 613 TYR cc_start: 0.8509 (m-10) cc_final: 0.8188 (m-10) REVERT: B 315 ASP cc_start: 0.7788 (t0) cc_final: 0.7529 (t0) REVERT: B 422 LYS cc_start: 0.7308 (mmtt) cc_final: 0.7071 (mmtt) REVERT: B 578 LEU cc_start: 0.8037 (OUTLIER) cc_final: 0.7554 (tt) REVERT: B 709 GLN cc_start: 0.8515 (pt0) cc_final: 0.8175 (tt0) outliers start: 25 outliers final: 13 residues processed: 169 average time/residue: 0.0818 time to fit residues: 21.6006 Evaluate side-chains 165 residues out of total 1206 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 150 time to evaluate : 0.362 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 LEU Chi-restraints excluded: chain A residue 132 MET Chi-restraints excluded: chain A residue 181 TYR 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 472 ASN 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 73 optimal weight: 8.9990 chunk 86 optimal weight: 0.0970 chunk 105 optimal weight: 0.5980 chunk 29 optimal weight: 6.9990 chunk 60 optimal weight: 0.5980 chunk 62 optimal weight: 0.5980 chunk 68 optimal weight: 0.8980 chunk 1 optimal weight: 2.9990 chunk 77 optimal weight: 0.8980 chunk 48 optimal weight: 2.9990 chunk 65 optimal weight: 0.9990 overall best weight: 0.5578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 90 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4066 r_free = 0.4066 target = 0.188066 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.134917 restraints weight = 12738.572| |-----------------------------------------------------------------------------| r_work (start): 0.3374 rms_B_bonded: 2.75 r_work: 0.3048 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.3048 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7826 moved from start: 0.2015 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 11444 Z= 0.130 Angle : 0.639 14.701 15576 Z= 0.310 Chirality : 0.043 0.185 1764 Planarity : 0.005 0.061 1946 Dihedral : 4.622 19.879 1494 Min Nonbonded Distance : 2.571 Molprobity Statistics. All-atom Clashscore : 7.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.65 % Favored : 93.35 % Rotamer: Outliers : 2.05 % Allowed : 16.47 % Favored : 81.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 0.52 (0.24), residues: 1384 helix: 1.85 (0.18), residues: 882 sheet: -3.30 (0.60), residues: 46 loop : -2.41 (0.29), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 48 TYR 0.015 0.001 TYR B 294 PHE 0.020 0.001 PHE B 33 TRP 0.019 0.001 TRP B 624 HIS 0.004 0.001 HIS A 628 Details of bonding type rmsd covalent geometry : bond 0.00301 (11444) covalent geometry : angle 0.63932 (15576) hydrogen bonds : bond 0.03726 ( 693) hydrogen bonds : angle 4.23511 ( 2043) *********************** 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 184 residues out of total 1206 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 160 time to evaluate : 0.421 Fit side-chains REVERT: A 76 MET cc_start: 0.8345 (mtt) cc_final: 0.8044 (mtt) REVERT: A 82 MET cc_start: 0.8285 (ttp) cc_final: 0.7919 (ttt) REVERT: A 181 TYR cc_start: 0.8636 (OUTLIER) cc_final: 0.8282 (t80) REVERT: A 257 ASN cc_start: 0.8790 (m110) cc_final: 0.8367 (m110) REVERT: A 523 ASP cc_start: 0.7783 (t0) cc_final: 0.7512 (t0) REVERT: A 531 GLU cc_start: 0.7791 (tp30) cc_final: 0.6908 (mm-30) REVERT: A 613 TYR cc_start: 0.8447 (m-10) cc_final: 0.8200 (m-10) REVERT: B 4 LEU cc_start: 0.7267 (tt) cc_final: 0.6556 (tp) REVERT: B 256 GLN cc_start: 0.8317 (tp40) cc_final: 0.8110 (tp40) REVERT: B 447 ILE cc_start: 0.8530 (mm) cc_final: 0.8281 (mt) REVERT: B 531 GLU cc_start: 0.7869 (tp30) cc_final: 0.7275 (mm-30) REVERT: B 578 LEU cc_start: 0.7935 (OUTLIER) cc_final: 0.7443 (tt) REVERT: B 709 GLN cc_start: 0.8531 (pt0) cc_final: 0.8177 (tt0) outliers start: 24 outliers final: 10 residues processed: 174 average time/residue: 0.0788 time to fit residues: 21.4664 Evaluate side-chains 165 residues out of total 1206 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 153 time to evaluate : 0.410 ------------------------------------------------------------------------------- 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 181 TYR 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 645 LEU Chi-restraints excluded: chain B residue 37 VAL Chi-restraints excluded: chain B residue 132 MET Chi-restraints excluded: chain B residue 474 VAL 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 28 optimal weight: 2.9990 chunk 120 optimal weight: 0.3980 chunk 7 optimal weight: 0.6980 chunk 38 optimal weight: 40.0000 chunk 27 optimal weight: 0.9980 chunk 15 optimal weight: 0.6980 chunk 19 optimal weight: 0.8980 chunk 26 optimal weight: 20.0000 chunk 2 optimal weight: 0.8980 chunk 118 optimal weight: 3.9990 chunk 76 optimal weight: 0.9990 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 = 0.4069 r_free = 0.4069 target = 0.188024 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.135649 restraints weight = 12617.263| |-----------------------------------------------------------------------------| r_work (start): 0.3387 rms_B_bonded: 2.85 r_work: 0.3043 rms_B_bonded: 3.50 restraints_weight: 0.5000 r_work (final): 0.3043 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7909 moved from start: 0.2109 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= 0.139 Angle : 0.642 14.112 15576 Z= 0.311 Chirality : 0.043 0.229 1764 Planarity : 0.005 0.061 1946 Dihedral : 4.554 20.671 1494 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 7.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.79 % Favored : 93.21 % Rotamer: Outliers : 1.62 % Allowed : 17.32 % 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 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: 0.57 (0.24), residues: 1384 helix: 1.89 (0.18), residues: 882 sheet: -3.29 (0.60), residues: 46 loop : -2.39 (0.29), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 343 TYR 0.014 0.001 TYR A 181 PHE 0.020 0.001 PHE B 33 TRP 0.018 0.001 TRP B 624 HIS 0.004 0.001 HIS A 628 Details of bonding type rmsd covalent geometry : bond 0.00331 (11444) covalent geometry : angle 0.64213 (15576) hydrogen bonds : bond 0.03686 ( 693) hydrogen bonds : angle 4.20281 ( 2043) *********************** 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 173 residues out of total 1206 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 154 time to evaluate : 0.417 Fit side-chains REVERT: A 76 MET cc_start: 0.8486 (mtt) cc_final: 0.8282 (mtt) REVERT: A 257 ASN cc_start: 0.8795 (m110) cc_final: 0.8361 (m110) REVERT: A 388 PHE cc_start: 0.7860 (t80) cc_final: 0.7246 (m-10) REVERT: A 422 LYS cc_start: 0.7731 (mptt) cc_final: 0.7487 (mptt) REVERT: A 523 ASP cc_start: 0.7815 (t0) cc_final: 0.7589 (t0) REVERT: A 531 GLU cc_start: 0.7796 (tp30) cc_final: 0.6924 (mm-30) REVERT: A 613 TYR cc_start: 0.8439 (m-10) cc_final: 0.8205 (m-10) REVERT: B 4 LEU cc_start: 0.7112 (tt) cc_final: 0.6519 (tp) REVERT: B 256 GLN cc_start: 0.8378 (tp40) cc_final: 0.8173 (tp40) REVERT: B 315 ASP cc_start: 0.7656 (t0) cc_final: 0.7436 (t0) REVERT: B 447 ILE cc_start: 0.8649 (mm) cc_final: 0.8384 (mt) REVERT: B 531 GLU cc_start: 0.7892 (tp30) cc_final: 0.7323 (mm-30) REVERT: B 560 ASP cc_start: 0.7180 (t0) cc_final: 0.6277 (p0) REVERT: B 578 LEU cc_start: 0.7965 (OUTLIER) cc_final: 0.7474 (tt) REVERT: B 709 GLN cc_start: 0.8498 (pt0) cc_final: 0.8173 (tt0) outliers start: 19 outliers final: 9 residues processed: 163 average time/residue: 0.0834 time to fit residues: 21.1259 Evaluate side-chains 159 residues out of total 1206 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 149 time to evaluate : 0.404 ------------------------------------------------------------------------------- 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 538 LEU 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 474 VAL 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 74 optimal weight: 2.9990 chunk 126 optimal weight: 0.9980 chunk 86 optimal weight: 0.6980 chunk 121 optimal weight: 6.9990 chunk 41 optimal weight: 3.9990 chunk 120 optimal weight: 2.9990 chunk 28 optimal weight: 1.9990 chunk 64 optimal weight: 0.5980 chunk 136 optimal weight: 0.7980 chunk 39 optimal weight: 0.6980 chunk 17 optimal weight: 0.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 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 = 0.4070 r_free = 0.4070 target = 0.188240 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.135368 restraints weight = 12684.497| |-----------------------------------------------------------------------------| r_work (start): 0.3389 rms_B_bonded: 2.80 r_work: 0.3049 rms_B_bonded: 3.53 restraints_weight: 0.5000 r_work (final): 0.3049 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7912 moved from start: 0.2237 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= 0.139 Angle : 0.654 14.020 15576 Z= 0.313 Chirality : 0.043 0.236 1764 Planarity : 0.005 0.060 1946 Dihedral : 4.513 21.455 1494 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 6.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.43 % Favored : 93.57 % Rotamer: Outliers : 1.96 % Allowed : 17.15 % 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 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: 0.62 (0.24), residues: 1384 helix: 1.90 (0.18), residues: 884 sheet: -3.26 (0.60), residues: 46 loop : -2.33 (0.29), residues: 454 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 48 TYR 0.014 0.001 TYR A 181 PHE 0.028 0.001 PHE A 383 TRP 0.019 0.001 TRP B 624 HIS 0.004 0.001 HIS A 628 Details of bonding type rmsd covalent geometry : bond 0.00332 (11444) covalent geometry : angle 0.65367 (15576) hydrogen bonds : bond 0.03664 ( 693) hydrogen bonds : angle 4.16916 ( 2043) *********************** 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 176 residues out of total 1206 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 153 time to evaluate : 0.360 Fit side-chains REVERT: A 43 TYR cc_start: 0.8238 (m-80) cc_final: 0.8038 (m-80) REVERT: A 98 TYR cc_start: 0.8959 (t80) cc_final: 0.8624 (t80) REVERT: A 257 ASN cc_start: 0.8808 (m110) cc_final: 0.8411 (m110) REVERT: A 388 PHE cc_start: 0.7832 (t80) cc_final: 0.7249 (m-10) REVERT: A 422 LYS cc_start: 0.7694 (mptt) cc_final: 0.7298 (mmtt) REVERT: A 523 ASP cc_start: 0.7811 (t0) cc_final: 0.7573 (t0) REVERT: A 531 GLU cc_start: 0.7628 (tp30) cc_final: 0.6827 (mm-30) REVERT: B 4 LEU cc_start: 0.7223 (tt) cc_final: 0.6636 (tp) REVERT: B 256 GLN cc_start: 0.8424 (tp40) cc_final: 0.8179 (tp40) REVERT: B 315 ASP cc_start: 0.7642 (t0) cc_final: 0.7439 (t0) REVERT: B 422 LYS cc_start: 0.7246 (mmtt) cc_final: 0.6989 (mmtt) REVERT: B 447 ILE cc_start: 0.8631 (mm) cc_final: 0.8367 (mt) REVERT: B 531 GLU cc_start: 0.7830 (tp30) cc_final: 0.7276 (mm-30) REVERT: B 578 LEU cc_start: 0.7995 (OUTLIER) cc_final: 0.7491 (tt) REVERT: B 709 GLN cc_start: 0.8497 (pt0) cc_final: 0.8166 (tt0) outliers start: 23 outliers final: 10 residues processed: 165 average time/residue: 0.0792 time to fit residues: 20.2554 Evaluate side-chains 157 residues out of total 1206 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 146 time to evaluate : 0.293 ------------------------------------------------------------------------------- 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 389 PHE 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 37 VAL Chi-restraints excluded: chain B residue 474 VAL 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 89 optimal weight: 0.0470 chunk 113 optimal weight: 1.9990 chunk 49 optimal weight: 0.6980 chunk 15 optimal weight: 0.6980 chunk 71 optimal weight: 4.9990 chunk 37 optimal weight: 0.8980 chunk 91 optimal weight: 4.9990 chunk 11 optimal weight: 40.0000 chunk 100 optimal weight: 0.7980 chunk 12 optimal weight: 3.9990 chunk 48 optimal weight: 2.9990 overall best weight: 0.6278 ------------------------------------------------------------------------------- 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 = 0.4079 r_free = 0.4079 target = 0.189063 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3525 r_free = 0.3525 target = 0.136639 restraints weight = 12468.862| |-----------------------------------------------------------------------------| r_work (start): 0.3408 rms_B_bonded: 2.85 r_work: 0.3075 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.3075 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7833 moved from start: 0.2339 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= 0.131 Angle : 0.652 13.876 15576 Z= 0.312 Chirality : 0.043 0.285 1764 Planarity : 0.005 0.059 1946 Dihedral : 4.451 21.526 1494 Min Nonbonded Distance : 2.569 Molprobity Statistics. All-atom Clashscore : 6.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.36 % Favored : 93.64 % Rotamer: Outliers : 1.37 % Allowed : 17.58 % 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 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: 0.70 (0.24), residues: 1384 helix: 1.92 (0.18), residues: 884 sheet: -2.51 (0.77), residues: 34 loop : -2.32 (0.29), residues: 466 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 48 TYR 0.012 0.001 TYR A 181 PHE 0.019 0.001 PHE B 33 TRP 0.018 0.001 TRP B 624 HIS 0.004 0.001 HIS A 628 Details of bonding type rmsd covalent geometry : bond 0.00309 (11444) covalent geometry : angle 0.65211 (15576) hydrogen bonds : bond 0.03548 ( 693) hydrogen bonds : angle 4.11714 ( 2043) *********************** 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 166 residues out of total 1206 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 150 time to evaluate : 0.413 Fit side-chains REVERT: A 82 MET cc_start: 0.8204 (ttp) cc_final: 0.7795 (ttt) REVERT: A 98 TYR cc_start: 0.8953 (t80) cc_final: 0.8700 (t80) REVERT: A 257 ASN cc_start: 0.8823 (m110) cc_final: 0.8422 (m110) REVERT: A 388 PHE cc_start: 0.7832 (t80) cc_final: 0.7256 (m-10) REVERT: A 422 LYS cc_start: 0.7723 (mptt) cc_final: 0.7362 (mmtt) REVERT: A 523 ASP cc_start: 0.7774 (t0) cc_final: 0.7491 (t0) REVERT: A 531 GLU cc_start: 0.7601 (tp30) cc_final: 0.6783 (mm-30) REVERT: B 4 LEU cc_start: 0.7225 (tt) cc_final: 0.6618 (tp) REVERT: B 315 ASP cc_start: 0.7664 (t0) cc_final: 0.7459 (t0) REVERT: B 447 ILE cc_start: 0.8505 (mm) cc_final: 0.8259 (mt) REVERT: B 531 GLU cc_start: 0.7700 (tp30) cc_final: 0.7155 (mm-30) REVERT: B 578 LEU cc_start: 0.7921 (OUTLIER) cc_final: 0.7429 (tt) REVERT: B 709 GLN cc_start: 0.8430 (pt0) cc_final: 0.8149 (tt0) outliers start: 16 outliers final: 10 residues processed: 157 average time/residue: 0.0826 time to fit residues: 20.4431 Evaluate side-chains 160 residues out of total 1206 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 149 time to evaluate : 0.436 ------------------------------------------------------------------------------- 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 389 PHE 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 28 optimal weight: 1.9990 chunk 77 optimal weight: 0.0270 chunk 43 optimal weight: 0.5980 chunk 35 optimal weight: 1.9990 chunk 122 optimal weight: 0.8980 chunk 128 optimal weight: 0.7980 chunk 12 optimal weight: 9.9990 chunk 136 optimal weight: 1.9990 chunk 68 optimal weight: 0.6980 chunk 73 optimal weight: 3.9990 chunk 58 optimal weight: 0.7980 overall best weight: 0.5838 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 489 GLN ** B 162 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.4083 r_free = 0.4083 target = 0.189511 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.137053 restraints weight = 12690.319| |-----------------------------------------------------------------------------| r_work (start): 0.3413 rms_B_bonded: 2.87 r_work: 0.3078 rms_B_bonded: 3.41 restraints_weight: 0.5000 r_work (final): 0.3078 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7827 moved from start: 0.2434 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= 0.129 Angle : 0.663 13.818 15576 Z= 0.314 Chirality : 0.043 0.267 1764 Planarity : 0.005 0.058 1946 Dihedral : 4.421 20.913 1494 Min Nonbonded Distance : 2.570 Molprobity Statistics. All-atom Clashscore : 6.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.21 % Favored : 93.79 % Rotamer: Outliers : 1.11 % Allowed : 17.83 % 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 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 (0.24), residues: 1384 helix: 1.90 (0.18), residues: 888 sheet: -2.44 (0.78), residues: 34 loop : -2.39 (0.29), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 48 TYR 0.016 0.001 TYR B 583 PHE 0.026 0.001 PHE A 383 TRP 0.018 0.001 TRP A 624 HIS 0.004 0.001 HIS A 628 Details of bonding type rmsd covalent geometry : bond 0.00302 (11444) covalent geometry : angle 0.66266 (15576) hydrogen bonds : bond 0.03492 ( 693) hydrogen bonds : angle 4.07727 ( 2043) ********************** 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 157 residues out of total 1206 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 144 time to evaluate : 0.417 Fit side-chains REVERT: A 98 TYR cc_start: 0.8941 (t80) cc_final: 0.8603 (t80) REVERT: A 257 ASN cc_start: 0.8838 (m110) cc_final: 0.8445 (m110) REVERT: A 388 PHE cc_start: 0.7828 (t80) cc_final: 0.7241 (m-10) REVERT: A 422 LYS cc_start: 0.7724 (mptt) cc_final: 0.6921 (mmtt) REVERT: A 511 MET cc_start: 0.7429 (mpp) cc_final: 0.7149 (mpp) REVERT: A 523 ASP cc_start: 0.7822 (t0) cc_final: 0.7508 (t0) REVERT: A 531 GLU cc_start: 0.7631 (tp30) cc_final: 0.6808 (mm-30) REVERT: B 4 LEU cc_start: 0.7114 (tt) cc_final: 0.6508 (tp) REVERT: B 260 ASP cc_start: 0.8188 (m-30) cc_final: 0.7812 (t0) REVERT: B 447 ILE cc_start: 0.8484 (mm) cc_final: 0.8261 (mt) REVERT: B 531 GLU cc_start: 0.7669 (tp30) cc_final: 0.7114 (mm-30) REVERT: B 578 LEU cc_start: 0.7924 (OUTLIER) cc_final: 0.7439 (tt) REVERT: B 709 GLN cc_start: 0.8352 (pt0) cc_final: 0.8070 (tt0) outliers start: 13 outliers final: 7 residues processed: 153 average time/residue: 0.0832 time to fit residues: 20.2016 Evaluate side-chains 151 residues out of total 1206 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 143 time to evaluate : 0.441 ------------------------------------------------------------------------------- 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 645 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 118 optimal weight: 0.9990 chunk 72 optimal weight: 0.8980 chunk 134 optimal weight: 0.0040 chunk 34 optimal weight: 3.9990 chunk 64 optimal weight: 0.7980 chunk 12 optimal weight: 9.9990 chunk 101 optimal weight: 0.8980 chunk 2 optimal weight: 1.9990 chunk 105 optimal weight: 0.6980 chunk 15 optimal weight: 0.5980 chunk 71 optimal weight: 0.5980 overall best weight: 0.5392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 162 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.4087 r_free = 0.4087 target = 0.189779 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3569 r_free = 0.3569 target = 0.139957 restraints weight = 12637.266| |-----------------------------------------------------------------------------| r_work (start): 0.3442 rms_B_bonded: 2.54 r_work: 0.3082 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.3082 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7824 moved from start: 0.2545 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= 0.127 Angle : 0.666 16.747 15576 Z= 0.313 Chirality : 0.042 0.163 1764 Planarity : 0.005 0.057 1946 Dihedral : 4.385 21.262 1494 Min Nonbonded Distance : 2.572 Molprobity Statistics. All-atom Clashscore : 6.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.21 % Favored : 93.79 % Rotamer: Outliers : 0.77 % Allowed : 17.75 % Favored : 81.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 0.70 (0.24), residues: 1384 helix: 1.93 (0.18), residues: 888 sheet: -2.37 (0.79), residues: 34 loop : -2.39 (0.29), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 198 TYR 0.011 0.001 TYR B 583 PHE 0.019 0.001 PHE A 33 TRP 0.018 0.001 TRP A 624 HIS 0.004 0.001 HIS A 628 Details of bonding type rmsd covalent geometry : bond 0.00296 (11444) covalent geometry : angle 0.66609 (15576) hydrogen bonds : bond 0.03447 ( 693) hydrogen bonds : angle 4.06954 ( 2043) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2497.35 seconds wall clock time: 43 minutes 33.19 seconds (2613.19 seconds total)