Starting phenix.real_space_refine on Sat Jul 26 02:00:35 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8j74_36025/07_2025/8j74_36025.cif Found real_map, /net/cci-nas-00/data/ceres_data/8j74_36025/07_2025/8j74_36025.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8j74_36025/07_2025/8j74_36025.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8j74_36025/07_2025/8j74_36025.map" model { file = "/net/cci-nas-00/data/ceres_data/8j74_36025/07_2025/8j74_36025.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8j74_36025/07_2025/8j74_36025.cif" } resolution = 3.6 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= 0.004 sd= 0.061 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 40 5.16 5 C 5546 2.51 5 N 1214 2.21 5 O 1488 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 6 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib" Total number of atoms: 8288 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 3959 Number of conformers: 1 Conformer: "" Number of residues, atoms: 515, 3959 Classifications: {'peptide': 515} Link IDs: {'PTRANS': 22, 'TRANS': 492} Chain: "E" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "A" Number of atoms: 146 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 146 Unusual residues: {'AV0': 1, 'HC6': 1, 'R16': 1, 'Y01': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "B" Number of atoms: 116 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 116 Unusual residues: {'AV0': 1, 'R16': 1, 'Y01': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Restraints were copied for chains: B, F Time building chain proxies: 8.69, per 1000 atoms: 1.05 Number of scatterers: 8288 At special positions: 0 Unit cell: (100.86, 100.86, 95.94, 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 40 16.00 O 1488 8.00 N 1214 7.00 C 5546 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 Links applied BETA1-4 " NAG E 1 " - " NAG E 2 " " NAG E 2 " - " BMA E 3 " " NAG F 1 " - " NAG F 2 " " NAG F 2 " - " BMA F 3 " NAG-ASN " NAG E 1 " - " ASN A 301 " " NAG F 1 " - " ASN B 301 " Time building additional restraints: 2.81 Conformation dependent library (CDL) restraints added in 1.1 seconds 2052 Ramachandran restraints generated. 1026 Oldfield, 0 Emsley, 1026 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1872 Finding SS restraints... Secondary structure from input PDB file: 52 helices and 2 sheets defined 77.5% alpha, 0.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.71 Creating SS restraints... Processing helix chain 'A' and resid 4 through 29 removed outlier: 3.548A pdb=" N LEU A 8 " --> pdb=" O HIS A 4 " (cutoff:3.500A) Processing helix chain 'A' and resid 37 through 45 Processing helix chain 'A' and resid 46 through 48 No H-bonds generated for 'chain 'A' and resid 46 through 48' Processing helix chain 'A' and resid 50 through 63 removed outlier: 3.529A pdb=" N VAL A 63 " --> pdb=" O THR A 59 " (cutoff:3.500A) Processing helix chain 'A' and resid 65 through 77 removed outlier: 3.815A pdb=" N THR A 71 " --> pdb=" O TYR A 67 " (cutoff:3.500A) Processing helix chain 'A' and resid 86 through 102 Processing helix chain 'A' and resid 103 through 109 removed outlier: 3.645A pdb=" N ARG A 107 " --> pdb=" O ALA A 103 " (cutoff:3.500A) Processing helix chain 'A' and resid 114 through 122 removed outlier: 4.309A pdb=" N PHE A 118 " --> pdb=" O MET A 114 " (cutoff:3.500A) Processing helix chain 'A' and resid 123 through 130 Processing helix chain 'A' and resid 130 through 157 removed outlier: 4.235A pdb=" N ALA A 134 " --> pdb=" O LEU A 130 " (cutoff:3.500A) Processing helix chain 'A' and resid 160 through 179 removed outlier: 3.721A pdb=" N VAL A 178 " --> pdb=" O LEU A 174 " (cutoff:3.500A) Processing helix chain 'A' and resid 180 through 200 removed outlier: 3.714A pdb=" N VAL A 190 " --> pdb=" O TYR A 186 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N PHE A 193 " --> pdb=" O VAL A 189 " (cutoff:3.500A) Processing helix chain 'A' and resid 202 through 208 Processing helix chain 'A' and resid 233 through 235 No H-bonds generated for 'chain 'A' and resid 233 through 235' Processing helix chain 'A' and resid 236 through 250 Processing helix chain 'A' and resid 254 through 262 Processing helix chain 'A' and resid 266 through 297 removed outlier: 4.168A pdb=" N ALA A 270 " --> pdb=" O SER A 266 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N PHE A 275 " --> pdb=" O GLN A 271 " (cutoff:3.500A) Proline residue: A 287 - end of helix Processing helix chain 'A' and resid 309 through 314 Processing helix chain 'A' and resid 315 through 318 Processing helix chain 'A' and resid 319 through 327 removed outlier: 3.677A pdb=" N GLN A 325 " --> pdb=" O PRO A 321 " (cutoff:3.500A) Processing helix chain 'A' and resid 329 through 363 removed outlier: 3.871A pdb=" N PHE A 335 " --> pdb=" O TYR A 331 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N ARG A 361 " --> pdb=" O SER A 357 " (cutoff:3.500A) Processing helix chain 'A' and resid 373 through 399 removed outlier: 3.561A pdb=" N PHE A 386 " --> pdb=" O ARG A 382 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N THR A 399 " --> pdb=" O MET A 395 " (cutoff:3.500A) Processing helix chain 'A' and resid 401 through 426 Proline residue: A 419 - end of helix Processing helix chain 'A' and resid 431 through 448 removed outlier: 3.852A pdb=" N ALA A 437 " --> pdb=" O TYR A 433 " (cutoff:3.500A) Processing helix chain 'A' and resid 478 through 505 removed outlier: 4.106A pdb=" N MET A 484 " --> pdb=" O LYS A 480 " (cutoff:3.500A) Processing helix chain 'A' and resid 508 through 512 removed outlier: 3.725A pdb=" N LEU A 511 " --> pdb=" O PRO A 508 " (cutoff:3.500A) Processing helix chain 'B' and resid 4 through 29 removed outlier: 3.548A pdb=" N LEU B 8 " --> pdb=" O HIS B 4 " (cutoff:3.500A) Processing helix chain 'B' and resid 37 through 45 Processing helix chain 'B' and resid 46 through 48 No H-bonds generated for 'chain 'B' and resid 46 through 48' Processing helix chain 'B' and resid 50 through 63 removed outlier: 3.529A pdb=" N VAL B 63 " --> pdb=" O THR B 59 " (cutoff:3.500A) Processing helix chain 'B' and resid 65 through 77 removed outlier: 3.815A pdb=" N THR B 71 " --> pdb=" O TYR B 67 " (cutoff:3.500A) Processing helix chain 'B' and resid 86 through 102 Processing helix chain 'B' and resid 103 through 109 removed outlier: 3.645A pdb=" N ARG B 107 " --> pdb=" O ALA B 103 " (cutoff:3.500A) Processing helix chain 'B' and resid 114 through 122 removed outlier: 4.309A pdb=" N PHE B 118 " --> pdb=" O MET B 114 " (cutoff:3.500A) Processing helix chain 'B' and resid 123 through 130 Processing helix chain 'B' and resid 130 through 157 removed outlier: 4.235A pdb=" N ALA B 134 " --> pdb=" O LEU B 130 " (cutoff:3.500A) Processing helix chain 'B' and resid 160 through 179 removed outlier: 3.721A pdb=" N VAL B 178 " --> pdb=" O LEU B 174 " (cutoff:3.500A) Processing helix chain 'B' and resid 180 through 200 removed outlier: 3.714A pdb=" N VAL B 190 " --> pdb=" O TYR B 186 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N PHE B 193 " --> pdb=" O VAL B 189 " (cutoff:3.500A) Processing helix chain 'B' and resid 202 through 208 Processing helix chain 'B' and resid 233 through 235 No H-bonds generated for 'chain 'B' and resid 233 through 235' Processing helix chain 'B' and resid 236 through 250 Processing helix chain 'B' and resid 254 through 262 Processing helix chain 'B' and resid 266 through 297 removed outlier: 4.168A pdb=" N ALA B 270 " --> pdb=" O SER B 266 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N PHE B 275 " --> pdb=" O GLN B 271 " (cutoff:3.500A) Proline residue: B 287 - end of helix Processing helix chain 'B' and resid 309 through 314 Processing helix chain 'B' and resid 315 through 318 Processing helix chain 'B' and resid 319 through 327 removed outlier: 3.677A pdb=" N GLN B 325 " --> pdb=" O PRO B 321 " (cutoff:3.500A) Processing helix chain 'B' and resid 329 through 363 removed outlier: 3.871A pdb=" N PHE B 335 " --> pdb=" O TYR B 331 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N ARG B 361 " --> pdb=" O SER B 357 " (cutoff:3.500A) Processing helix chain 'B' and resid 373 through 399 removed outlier: 3.561A pdb=" N PHE B 386 " --> pdb=" O ARG B 382 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N THR B 399 " --> pdb=" O MET B 395 " (cutoff:3.500A) Processing helix chain 'B' and resid 401 through 426 Proline residue: B 419 - end of helix Processing helix chain 'B' and resid 431 through 448 removed outlier: 3.852A pdb=" N ALA B 437 " --> pdb=" O TYR B 433 " (cutoff:3.500A) Processing helix chain 'B' and resid 478 through 505 removed outlier: 4.106A pdb=" N MET B 484 " --> pdb=" O LYS B 480 " (cutoff:3.500A) Processing helix chain 'B' and resid 508 through 512 removed outlier: 3.725A pdb=" N LEU B 511 " --> pdb=" O PRO B 508 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 466 through 467 Processing sheet with id=AA2, first strand: chain 'B' and resid 466 through 467 552 hydrogen bonds defined for protein. 1638 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.41 Time building geometry restraints manager: 3.15 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 1255 1.32 - 1.45: 2473 1.45 - 1.57: 4730 1.57 - 1.69: 0 1.69 - 1.81: 70 Bond restraints: 8528 Sorted by residual: bond pdb=" CB ASP B 411 " pdb=" CG ASP B 411 " ideal model delta sigma weight residual 1.516 1.447 0.069 2.50e-02 1.60e+03 7.58e+00 bond pdb=" CB ASP A 411 " pdb=" CG ASP A 411 " ideal model delta sigma weight residual 1.516 1.447 0.069 2.50e-02 1.60e+03 7.58e+00 bond pdb=" CA ASP B 411 " pdb=" C ASP B 411 " ideal model delta sigma weight residual 1.524 1.497 0.027 1.27e-02 6.20e+03 4.39e+00 bond pdb=" CA ASP A 411 " pdb=" C ASP A 411 " ideal model delta sigma weight residual 1.524 1.497 0.027 1.27e-02 6.20e+03 4.39e+00 bond pdb=" N PHE A 477 " pdb=" CA PHE A 477 " ideal model delta sigma weight residual 1.457 1.484 -0.028 1.41e-02 5.03e+03 3.83e+00 ... (remaining 8523 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.68: 11209 1.68 - 3.36: 345 3.36 - 5.04: 70 5.04 - 6.72: 30 6.72 - 8.41: 6 Bond angle restraints: 11660 Sorted by residual: angle pdb=" N LEU A 482 " pdb=" CA LEU A 482 " pdb=" C LEU A 482 " ideal model delta sigma weight residual 111.28 105.66 5.62 1.09e+00 8.42e-01 2.65e+01 angle pdb=" N LEU B 482 " pdb=" CA LEU B 482 " pdb=" C LEU B 482 " ideal model delta sigma weight residual 111.28 105.67 5.61 1.09e+00 8.42e-01 2.65e+01 angle pdb=" N TYR A 364 " pdb=" CA TYR A 364 " pdb=" C TYR A 364 " ideal model delta sigma weight residual 112.04 118.40 -6.36 1.44e+00 4.82e-01 1.95e+01 angle pdb=" N TYR B 364 " pdb=" CA TYR B 364 " pdb=" C TYR B 364 " ideal model delta sigma weight residual 112.04 118.40 -6.36 1.44e+00 4.82e-01 1.95e+01 angle pdb=" N ILE B 332 " pdb=" CA ILE B 332 " pdb=" C ILE B 332 " ideal model delta sigma weight residual 111.81 108.01 3.80 8.60e-01 1.35e+00 1.95e+01 ... (remaining 11655 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 26.42: 4774 26.42 - 52.84: 300 52.84 - 79.26: 60 79.26 - 105.68: 72 105.68 - 132.10: 32 Dihedral angle restraints: 5238 sinusoidal: 2276 harmonic: 2962 Sorted by residual: dihedral pdb=" CCF AV0 B 601 " pdb=" CCQ AV0 B 601 " pdb=" OCB AV0 B 601 " pdb=" CCS AV0 B 601 " ideal model delta sinusoidal sigma weight residual -112.55 19.55 -132.10 1 3.00e+01 1.11e-03 1.78e+01 dihedral pdb=" CCF AV0 A 702 " pdb=" CCQ AV0 A 702 " pdb=" OCB AV0 A 702 " pdb=" CCS AV0 A 702 " ideal model delta sinusoidal sigma weight residual -112.55 19.55 -132.10 1 3.00e+01 1.11e-03 1.78e+01 dihedral pdb=" CCH AV0 B 601 " pdb=" CCQ AV0 B 601 " pdb=" OCB AV0 B 601 " pdb=" CCS AV0 B 601 " ideal model delta sinusoidal sigma weight residual 127.39 -100.76 -131.85 1 3.00e+01 1.11e-03 1.78e+01 ... (remaining 5235 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.055: 1105 0.055 - 0.110: 227 0.110 - 0.164: 28 0.164 - 0.219: 14 0.219 - 0.274: 2 Chirality restraints: 1376 Sorted by residual: chirality pdb=" C5 BMA F 3 " pdb=" C4 BMA F 3 " pdb=" C6 BMA F 3 " pdb=" O5 BMA F 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.55 0.27 2.00e-01 2.50e+01 1.88e+00 chirality pdb=" C5 BMA E 3 " pdb=" C4 BMA E 3 " pdb=" C6 BMA E 3 " pdb=" O5 BMA E 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.55 0.27 2.00e-01 2.50e+01 1.85e+00 chirality pdb=" CB ILE A 252 " pdb=" CA ILE A 252 " pdb=" CG1 ILE A 252 " pdb=" CG2 ILE A 252 " both_signs ideal model delta sigma weight residual False 2.64 2.44 0.21 2.00e-01 2.50e+01 1.07e+00 ... (remaining 1373 not shown) Planarity restraints: 1372 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR B 455 " -0.007 2.00e-02 2.50e+03 1.30e-02 3.40e+00 pdb=" CG TYR B 455 " 0.030 2.00e-02 2.50e+03 pdb=" CD1 TYR B 455 " -0.012 2.00e-02 2.50e+03 pdb=" CD2 TYR B 455 " -0.015 2.00e-02 2.50e+03 pdb=" CE1 TYR B 455 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 TYR B 455 " 0.003 2.00e-02 2.50e+03 pdb=" CZ TYR B 455 " 0.001 2.00e-02 2.50e+03 pdb=" OH TYR B 455 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 455 " -0.007 2.00e-02 2.50e+03 1.30e-02 3.40e+00 pdb=" CG TYR A 455 " 0.030 2.00e-02 2.50e+03 pdb=" CD1 TYR A 455 " -0.012 2.00e-02 2.50e+03 pdb=" CD2 TYR A 455 " -0.015 2.00e-02 2.50e+03 pdb=" CE1 TYR A 455 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 TYR A 455 " 0.003 2.00e-02 2.50e+03 pdb=" CZ TYR A 455 " 0.001 2.00e-02 2.50e+03 pdb=" OH TYR A 455 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA TYR A 455 " -0.008 2.00e-02 2.50e+03 1.58e-02 2.50e+00 pdb=" C TYR A 455 " 0.027 2.00e-02 2.50e+03 pdb=" O TYR A 455 " -0.010 2.00e-02 2.50e+03 pdb=" N LEU A 456 " -0.009 2.00e-02 2.50e+03 ... (remaining 1369 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 887 2.74 - 3.28: 8846 3.28 - 3.82: 14360 3.82 - 4.36: 15495 4.36 - 4.90: 27129 Nonbonded interactions: 66717 Sorted by model distance: nonbonded pdb=" OG SER B 34 " pdb=" OE1 GLU B 37 " model vdw 2.203 3.040 nonbonded pdb=" OG SER A 34 " pdb=" OE1 GLU A 37 " model vdw 2.204 3.040 nonbonded pdb=" OG SER A 34 " pdb=" OE1 GLU A 36 " model vdw 2.232 3.040 nonbonded pdb=" OG SER B 34 " pdb=" OE1 GLU B 36 " model vdw 2.232 3.040 nonbonded pdb=" O PHE A 444 " pdb=" OG1 THR A 448 " model vdw 2.281 3.040 ... (remaining 66712 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: 0.04 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 3 through 517 or resid 704)) selection = (chain 'B' and (resid 3 through 517 or resid 604)) } ncs_group { reference = chain 'E' selection = chain 'F' } 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 group one per residue 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: 2.270 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.390 Check model and map are aligned: 0.070 Set scattering table: 0.090 Process input model: 26.320 Find NCS groups from input model: 0.420 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: 0.000 Load rotamer database and sin/cos tables:3.130 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.730 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7994 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 0.069 8534 Z= 0.205 Angle : 0.744 8.405 11678 Z= 0.365 Chirality : 0.047 0.274 1376 Planarity : 0.004 0.037 1370 Dihedral : 24.907 132.103 3366 Min Nonbonded Distance : 2.203 Molprobity Statistics. All-atom Clashscore : 15.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.04 % Favored : 93.96 % Rotamer: Outliers : 0.00 % Allowed : 25.30 % Favored : 74.70 % 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: 0.74 (0.29), residues: 1026 helix: 1.49 (0.21), residues: 734 sheet: None (None), residues: 0 loop : -2.18 (0.39), residues: 292 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 300 HIS 0.005 0.001 HIS B 221 PHE 0.012 0.001 PHE A 118 TYR 0.030 0.002 TYR A 455 ARG 0.009 0.001 ARG A 38 Details of bonding type rmsd link_NAG-ASN : bond 0.00508 ( 2) link_NAG-ASN : angle 3.89095 ( 6) link_BETA1-4 : bond 0.00589 ( 4) link_BETA1-4 : angle 2.68435 ( 12) hydrogen bonds : bond 0.10692 ( 552) hydrogen bonds : angle 4.42392 ( 1638) covalent geometry : bond 0.00414 ( 8528) covalent geometry : angle 0.73438 (11660) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2052 Ramachandran restraints generated. 1026 Oldfield, 0 Emsley, 1026 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2052 Ramachandran restraints generated. 1026 Oldfield, 0 Emsley, 1026 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 157 time to evaluate : 0.832 Fit side-chains REVERT: A 130 LEU cc_start: 0.8802 (mp) cc_final: 0.8563 (mp) REVERT: A 455 TYR cc_start: 0.5322 (p90) cc_final: 0.5001 (p90) REVERT: B 130 LEU cc_start: 0.8787 (mp) cc_final: 0.8544 (mp) REVERT: B 455 TYR cc_start: 0.5323 (p90) cc_final: 0.5000 (p90) outliers start: 0 outliers final: 0 residues processed: 157 average time/residue: 0.1765 time to fit residues: 39.6889 Evaluate side-chains 144 residues out of total 830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 144 time to evaluate : 0.917 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 86 optimal weight: 6.9990 chunk 77 optimal weight: 1.9990 chunk 42 optimal weight: 0.6980 chunk 26 optimal weight: 3.9990 chunk 52 optimal weight: 0.9980 chunk 41 optimal weight: 0.4980 chunk 79 optimal weight: 0.9990 chunk 30 optimal weight: 4.9990 chunk 48 optimal weight: 2.9990 chunk 59 optimal weight: 3.9990 chunk 92 optimal weight: 0.9980 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 491 ASN B 491 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3790 r_free = 0.3790 target = 0.142049 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3613 r_free = 0.3613 target = 0.127671 restraints weight = 15238.316| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3648 r_free = 0.3648 target = 0.130463 restraints weight = 7921.602| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3669 r_free = 0.3669 target = 0.132169 restraints weight = 4922.708| |-----------------------------------------------------------------------------| r_work (final): 0.3653 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8012 moved from start: 0.1059 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 8534 Z= 0.142 Angle : 0.766 10.131 11678 Z= 0.338 Chirality : 0.046 0.236 1376 Planarity : 0.004 0.028 1370 Dihedral : 19.397 148.671 1716 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 11.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.07 % Favored : 94.93 % Rotamer: Outliers : 3.37 % Allowed : 22.65 % Favored : 73.98 % 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: 0.93 (0.29), residues: 1026 helix: 1.54 (0.20), residues: 742 sheet: None (None), residues: 0 loop : -1.92 (0.40), residues: 284 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 406 HIS 0.003 0.001 HIS A 221 PHE 0.010 0.001 PHE B 461 TYR 0.012 0.001 TYR A 414 ARG 0.005 0.001 ARG A 446 Details of bonding type rmsd link_NAG-ASN : bond 0.00871 ( 2) link_NAG-ASN : angle 4.22488 ( 6) link_BETA1-4 : bond 0.00914 ( 4) link_BETA1-4 : angle 3.11693 ( 12) hydrogen bonds : bond 0.03780 ( 552) hydrogen bonds : angle 4.13953 ( 1638) covalent geometry : bond 0.00312 ( 8528) covalent geometry : angle 0.75349 (11660) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2052 Ramachandran restraints generated. 1026 Oldfield, 0 Emsley, 1026 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2052 Ramachandran restraints generated. 1026 Oldfield, 0 Emsley, 1026 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 146 time to evaluate : 1.340 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 62 TRP cc_start: 0.7842 (m100) cc_final: 0.7384 (m100) REVERT: A 130 LEU cc_start: 0.9020 (OUTLIER) cc_final: 0.8807 (mp) REVERT: A 318 MET cc_start: 0.7124 (ppp) cc_final: 0.6437 (ppp) REVERT: A 455 TYR cc_start: 0.5459 (p90) cc_final: 0.5177 (p90) REVERT: B 62 TRP cc_start: 0.7844 (m100) cc_final: 0.7393 (m100) REVERT: B 130 LEU cc_start: 0.9017 (OUTLIER) cc_final: 0.8802 (mp) REVERT: B 318 MET cc_start: 0.7131 (ppp) cc_final: 0.6420 (ppp) REVERT: B 455 TYR cc_start: 0.5457 (p90) cc_final: 0.5179 (p90) outliers start: 28 outliers final: 10 residues processed: 170 average time/residue: 0.1669 time to fit residues: 41.3753 Evaluate side-chains 144 residues out of total 830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 132 time to evaluate : 0.867 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 116 ASP Chi-restraints excluded: chain A residue 130 LEU Chi-restraints excluded: chain A residue 184 VAL Chi-restraints excluded: chain A residue 368 PHE Chi-restraints excluded: chain A residue 383 ILE Chi-restraints excluded: chain A residue 431 ASN Chi-restraints excluded: chain B residue 116 ASP Chi-restraints excluded: chain B residue 130 LEU Chi-restraints excluded: chain B residue 184 VAL Chi-restraints excluded: chain B residue 368 PHE Chi-restraints excluded: chain B residue 383 ILE Chi-restraints excluded: chain B residue 431 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 98 optimal weight: 3.9990 chunk 93 optimal weight: 3.9990 chunk 100 optimal weight: 3.9990 chunk 95 optimal weight: 0.2980 chunk 22 optimal weight: 0.0070 chunk 97 optimal weight: 7.9990 chunk 7 optimal weight: 0.0980 chunk 28 optimal weight: 0.9980 chunk 80 optimal weight: 0.8980 chunk 101 optimal weight: 8.9990 chunk 11 optimal weight: 0.8980 overall best weight: 0.4398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 191 GLN ** 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 = 0.3797 r_free = 0.3797 target = 0.142787 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3621 r_free = 0.3621 target = 0.128582 restraints weight = 15569.898| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3657 r_free = 0.3657 target = 0.131340 restraints weight = 8092.150| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3681 r_free = 0.3681 target = 0.133216 restraints weight = 5072.193| |-----------------------------------------------------------------------------| r_work (final): 0.3668 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7976 moved from start: 0.1326 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 8534 Z= 0.120 Angle : 0.643 9.345 11678 Z= 0.298 Chirality : 0.042 0.240 1376 Planarity : 0.004 0.026 1370 Dihedral : 15.640 158.995 1716 Min Nonbonded Distance : 2.328 Molprobity Statistics. All-atom Clashscore : 11.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.26 % Favored : 94.74 % Rotamer: Outliers : 3.86 % Allowed : 20.96 % Favored : 75.18 % 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: 0.96 (0.29), residues: 1026 helix: 1.54 (0.20), residues: 748 sheet: None (None), residues: 0 loop : -1.92 (0.41), residues: 278 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 300 HIS 0.002 0.000 HIS B 221 PHE 0.006 0.001 PHE A 140 TYR 0.014 0.001 TYR A 439 ARG 0.005 0.001 ARG A 38 Details of bonding type rmsd link_NAG-ASN : bond 0.00658 ( 2) link_NAG-ASN : angle 4.14731 ( 6) link_BETA1-4 : bond 0.00953 ( 4) link_BETA1-4 : angle 2.64947 ( 12) hydrogen bonds : bond 0.03627 ( 552) hydrogen bonds : angle 4.06381 ( 1638) covalent geometry : bond 0.00258 ( 8528) covalent geometry : angle 0.63118 (11660) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2052 Ramachandran restraints generated. 1026 Oldfield, 0 Emsley, 1026 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2052 Ramachandran restraints generated. 1026 Oldfield, 0 Emsley, 1026 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 154 time to evaluate : 0.856 Fit side-chains REVERT: A 62 TRP cc_start: 0.7824 (m100) cc_final: 0.7350 (m100) REVERT: A 116 ASP cc_start: 0.7874 (OUTLIER) cc_final: 0.7588 (t0) REVERT: A 318 MET cc_start: 0.7257 (ppp) cc_final: 0.6977 (ppp) REVERT: A 455 TYR cc_start: 0.5494 (p90) cc_final: 0.5194 (p90) REVERT: B 62 TRP cc_start: 0.7823 (m100) cc_final: 0.7349 (m100) REVERT: B 116 ASP cc_start: 0.7868 (OUTLIER) cc_final: 0.7585 (t0) REVERT: B 318 MET cc_start: 0.7255 (ppp) cc_final: 0.6970 (ppp) REVERT: B 455 TYR cc_start: 0.5480 (p90) cc_final: 0.5186 (p90) outliers start: 32 outliers final: 15 residues processed: 180 average time/residue: 0.1684 time to fit residues: 44.4102 Evaluate side-chains 154 residues out of total 830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 137 time to evaluate : 0.894 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 93 LEU Chi-restraints excluded: chain A residue 116 ASP Chi-restraints excluded: chain A residue 153 ILE Chi-restraints excluded: chain A residue 157 ILE Chi-restraints excluded: chain A residue 184 VAL Chi-restraints excluded: chain A residue 252 ILE Chi-restraints excluded: chain A residue 330 VAL Chi-restraints excluded: chain A residue 368 PHE Chi-restraints excluded: chain B residue 93 LEU Chi-restraints excluded: chain B residue 116 ASP Chi-restraints excluded: chain B residue 153 ILE Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain B residue 184 VAL Chi-restraints excluded: chain B residue 252 ILE Chi-restraints excluded: chain B residue 330 VAL Chi-restraints excluded: chain B residue 358 MET Chi-restraints excluded: chain B residue 368 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 96 optimal weight: 0.8980 chunk 43 optimal weight: 4.9990 chunk 76 optimal weight: 0.7980 chunk 70 optimal weight: 3.9990 chunk 18 optimal weight: 0.9990 chunk 53 optimal weight: 1.9990 chunk 2 optimal weight: 1.9990 chunk 57 optimal weight: 5.9990 chunk 64 optimal weight: 0.9980 chunk 59 optimal weight: 4.9990 chunk 12 optimal weight: 1.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 191 GLN A 365 GLN B 191 GLN B 365 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3778 r_free = 0.3778 target = 0.140998 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3604 r_free = 0.3604 target = 0.126930 restraints weight = 15450.204| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3639 r_free = 0.3639 target = 0.129697 restraints weight = 7908.944| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3659 r_free = 0.3659 target = 0.131324 restraints weight = 4903.972| |-----------------------------------------------------------------------------| r_work (final): 0.3642 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8024 moved from start: 0.1502 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 8534 Z= 0.141 Angle : 0.660 9.390 11678 Z= 0.306 Chirality : 0.042 0.238 1376 Planarity : 0.003 0.025 1370 Dihedral : 14.654 156.131 1716 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 11.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.26 % Favored : 94.74 % Rotamer: Outliers : 3.37 % Allowed : 21.57 % Favored : 75.06 % 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: 0.98 (0.29), residues: 1026 helix: 1.54 (0.20), residues: 748 sheet: None (None), residues: 0 loop : -1.86 (0.42), residues: 278 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 406 HIS 0.001 0.000 HIS B 221 PHE 0.006 0.001 PHE B 140 TYR 0.012 0.001 TYR B 439 ARG 0.005 0.001 ARG A 38 Details of bonding type rmsd link_NAG-ASN : bond 0.00711 ( 2) link_NAG-ASN : angle 4.09789 ( 6) link_BETA1-4 : bond 0.00877 ( 4) link_BETA1-4 : angle 2.79796 ( 12) hydrogen bonds : bond 0.03712 ( 552) hydrogen bonds : angle 4.13158 ( 1638) covalent geometry : bond 0.00328 ( 8528) covalent geometry : angle 0.64780 (11660) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2052 Ramachandran restraints generated. 1026 Oldfield, 0 Emsley, 1026 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2052 Ramachandran restraints generated. 1026 Oldfield, 0 Emsley, 1026 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 148 time to evaluate : 0.826 Fit side-chains REVERT: A 62 TRP cc_start: 0.7844 (m100) cc_final: 0.7562 (m100) REVERT: A 116 ASP cc_start: 0.7806 (OUTLIER) cc_final: 0.7549 (t0) REVERT: A 229 LEU cc_start: 0.8580 (OUTLIER) cc_final: 0.8284 (mp) REVERT: A 318 MET cc_start: 0.7023 (ppp) cc_final: 0.6702 (ppp) REVERT: A 455 TYR cc_start: 0.5543 (p90) cc_final: 0.5227 (p90) REVERT: B 62 TRP cc_start: 0.7843 (m100) cc_final: 0.7561 (m100) REVERT: B 116 ASP cc_start: 0.7807 (OUTLIER) cc_final: 0.7548 (t0) REVERT: B 229 LEU cc_start: 0.8571 (OUTLIER) cc_final: 0.8278 (mp) REVERT: B 318 MET cc_start: 0.7036 (ppp) cc_final: 0.6702 (ppp) REVERT: B 455 TYR cc_start: 0.5538 (p90) cc_final: 0.5221 (p90) outliers start: 28 outliers final: 20 residues processed: 169 average time/residue: 0.1632 time to fit residues: 40.1030 Evaluate side-chains 156 residues out of total 830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 132 time to evaluate : 0.822 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 93 LEU Chi-restraints excluded: chain A residue 100 LEU Chi-restraints excluded: chain A residue 116 ASP Chi-restraints excluded: chain A residue 157 ILE Chi-restraints excluded: chain A residue 184 VAL Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 241 LEU Chi-restraints excluded: chain A residue 252 ILE Chi-restraints excluded: chain A residue 330 VAL Chi-restraints excluded: chain A residue 368 PHE Chi-restraints excluded: chain A residue 427 VAL Chi-restraints excluded: chain A residue 431 ASN Chi-restraints excluded: chain B residue 93 LEU Chi-restraints excluded: chain B residue 100 LEU Chi-restraints excluded: chain B residue 116 ASP Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain B residue 184 VAL Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 241 LEU Chi-restraints excluded: chain B residue 252 ILE Chi-restraints excluded: chain B residue 330 VAL Chi-restraints excluded: chain B residue 368 PHE Chi-restraints excluded: chain B residue 427 VAL Chi-restraints excluded: chain B residue 431 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 41 optimal weight: 1.9990 chunk 35 optimal weight: 3.9990 chunk 28 optimal weight: 0.9990 chunk 72 optimal weight: 2.9990 chunk 62 optimal weight: 5.9990 chunk 19 optimal weight: 6.9990 chunk 76 optimal weight: 0.6980 chunk 10 optimal weight: 1.9990 chunk 63 optimal weight: 0.7980 chunk 13 optimal weight: 0.5980 chunk 79 optimal weight: 0.9990 overall best weight: 0.8184 ------------------------------------------------------------------------------- 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 = 0.3786 r_free = 0.3786 target = 0.141608 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3617 r_free = 0.3617 target = 0.127748 restraints weight = 15352.206| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3650 r_free = 0.3650 target = 0.130467 restraints weight = 7828.604| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3675 r_free = 0.3675 target = 0.132343 restraints weight = 4840.397| |-----------------------------------------------------------------------------| r_work (final): 0.3657 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8006 moved from start: 0.1558 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 8534 Z= 0.127 Angle : 0.633 9.372 11678 Z= 0.298 Chirality : 0.041 0.238 1376 Planarity : 0.003 0.025 1370 Dihedral : 13.997 156.035 1716 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 11.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.87 % Favored : 95.13 % Rotamer: Outliers : 3.61 % Allowed : 24.34 % Favored : 72.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.01 (0.29), residues: 1026 helix: 1.55 (0.20), residues: 748 sheet: None (None), residues: 0 loop : -1.83 (0.42), residues: 278 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 406 HIS 0.001 0.000 HIS A 209 PHE 0.005 0.001 PHE B 131 TYR 0.014 0.001 TYR A 439 ARG 0.006 0.001 ARG B 38 Details of bonding type rmsd link_NAG-ASN : bond 0.00661 ( 2) link_NAG-ASN : angle 4.10617 ( 6) link_BETA1-4 : bond 0.00837 ( 4) link_BETA1-4 : angle 2.66899 ( 12) hydrogen bonds : bond 0.03669 ( 552) hydrogen bonds : angle 4.10731 ( 1638) covalent geometry : bond 0.00288 ( 8528) covalent geometry : angle 0.62100 (11660) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2052 Ramachandran restraints generated. 1026 Oldfield, 0 Emsley, 1026 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2052 Ramachandran restraints generated. 1026 Oldfield, 0 Emsley, 1026 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 144 time to evaluate : 0.893 Fit side-chains REVERT: A 116 ASP cc_start: 0.7853 (OUTLIER) cc_final: 0.7553 (t0) REVERT: A 229 LEU cc_start: 0.8566 (OUTLIER) cc_final: 0.8286 (mp) REVERT: A 318 MET cc_start: 0.7105 (ppp) cc_final: 0.6800 (ppp) REVERT: A 455 TYR cc_start: 0.5564 (p90) cc_final: 0.5254 (p90) REVERT: B 116 ASP cc_start: 0.7857 (OUTLIER) cc_final: 0.7563 (t0) REVERT: B 229 LEU cc_start: 0.8560 (OUTLIER) cc_final: 0.8284 (mp) REVERT: B 318 MET cc_start: 0.7109 (ppp) cc_final: 0.6799 (ppp) REVERT: B 455 TYR cc_start: 0.5556 (p90) cc_final: 0.5251 (p90) outliers start: 30 outliers final: 19 residues processed: 170 average time/residue: 0.1748 time to fit residues: 43.4089 Evaluate side-chains 166 residues out of total 830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 143 time to evaluate : 0.994 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 116 ASP Chi-restraints excluded: chain A residue 130 LEU Chi-restraints excluded: chain A residue 157 ILE Chi-restraints excluded: chain A residue 184 VAL Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 241 LEU Chi-restraints excluded: chain A residue 252 ILE Chi-restraints excluded: chain A residue 330 VAL Chi-restraints excluded: chain A residue 368 PHE Chi-restraints excluded: chain A residue 427 VAL Chi-restraints excluded: chain A residue 431 ASN Chi-restraints excluded: chain B residue 93 LEU Chi-restraints excluded: chain B residue 116 ASP Chi-restraints excluded: chain B residue 130 LEU Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain B residue 184 VAL Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 241 LEU Chi-restraints excluded: chain B residue 252 ILE Chi-restraints excluded: chain B residue 330 VAL Chi-restraints excluded: chain B residue 368 PHE Chi-restraints excluded: chain B residue 427 VAL Chi-restraints excluded: chain B residue 431 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 40 optimal weight: 0.9990 chunk 38 optimal weight: 2.9990 chunk 42 optimal weight: 4.9990 chunk 4 optimal weight: 0.9980 chunk 20 optimal weight: 0.9980 chunk 93 optimal weight: 5.9990 chunk 48 optimal weight: 0.9980 chunk 97 optimal weight: 0.0770 chunk 87 optimal weight: 0.8980 chunk 43 optimal weight: 1.9990 chunk 10 optimal weight: 0.0770 overall best weight: 0.6096 ------------------------------------------------------------------------------- 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 = 0.3792 r_free = 0.3792 target = 0.142034 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3621 r_free = 0.3621 target = 0.128201 restraints weight = 15208.852| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3655 r_free = 0.3655 target = 0.130923 restraints weight = 7799.803| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3678 r_free = 0.3678 target = 0.132765 restraints weight = 4841.560| |-----------------------------------------------------------------------------| r_work (final): 0.3659 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7992 moved from start: 0.1659 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 8534 Z= 0.121 Angle : 0.628 9.378 11678 Z= 0.296 Chirality : 0.041 0.238 1376 Planarity : 0.003 0.026 1370 Dihedral : 13.052 156.304 1716 Min Nonbonded Distance : 2.410 Molprobity Statistics. All-atom Clashscore : 11.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.68 % Favored : 95.32 % Rotamer: Outliers : 3.86 % Allowed : 24.10 % Favored : 72.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.06 (0.29), residues: 1026 helix: 1.59 (0.20), residues: 748 sheet: None (None), residues: 0 loop : -1.81 (0.42), residues: 278 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 300 HIS 0.001 0.000 HIS A 209 PHE 0.005 0.001 PHE B 140 TYR 0.014 0.001 TYR B 439 ARG 0.007 0.001 ARG A 38 Details of bonding type rmsd link_NAG-ASN : bond 0.00661 ( 2) link_NAG-ASN : angle 4.07439 ( 6) link_BETA1-4 : bond 0.00808 ( 4) link_BETA1-4 : angle 2.56063 ( 12) hydrogen bonds : bond 0.03523 ( 552) hydrogen bonds : angle 4.08594 ( 1638) covalent geometry : bond 0.00271 ( 8528) covalent geometry : angle 0.61661 (11660) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2052 Ramachandran restraints generated. 1026 Oldfield, 0 Emsley, 1026 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2052 Ramachandran restraints generated. 1026 Oldfield, 0 Emsley, 1026 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 150 time to evaluate : 0.806 Fit side-chains REVERT: A 116 ASP cc_start: 0.7840 (OUTLIER) cc_final: 0.7539 (t0) REVERT: A 318 MET cc_start: 0.7159 (ppp) cc_final: 0.6857 (ppp) REVERT: A 455 TYR cc_start: 0.5673 (p90) cc_final: 0.5356 (p90) REVERT: B 116 ASP cc_start: 0.7831 (OUTLIER) cc_final: 0.7539 (t0) REVERT: B 318 MET cc_start: 0.7163 (ppp) cc_final: 0.6851 (ppp) outliers start: 32 outliers final: 19 residues processed: 177 average time/residue: 0.1664 time to fit residues: 42.9043 Evaluate side-chains 159 residues out of total 830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 138 time to evaluate : 0.849 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 93 LEU Chi-restraints excluded: chain A residue 116 ASP Chi-restraints excluded: chain A residue 130 LEU Chi-restraints excluded: chain A residue 157 ILE Chi-restraints excluded: chain A residue 184 VAL Chi-restraints excluded: chain A residue 252 ILE Chi-restraints excluded: chain A residue 330 VAL Chi-restraints excluded: chain A residue 368 PHE Chi-restraints excluded: chain A residue 427 VAL Chi-restraints excluded: chain A residue 431 ASN Chi-restraints excluded: chain B residue 93 LEU Chi-restraints excluded: chain B residue 116 ASP Chi-restraints excluded: chain B residue 130 LEU Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain B residue 184 VAL Chi-restraints excluded: chain B residue 241 LEU Chi-restraints excluded: chain B residue 252 ILE Chi-restraints excluded: chain B residue 330 VAL Chi-restraints excluded: chain B residue 368 PHE Chi-restraints excluded: chain B residue 427 VAL Chi-restraints excluded: chain B residue 431 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 12 optimal weight: 1.9990 chunk 76 optimal weight: 0.2980 chunk 31 optimal weight: 0.8980 chunk 86 optimal weight: 0.8980 chunk 48 optimal weight: 2.9990 chunk 19 optimal weight: 5.9990 chunk 59 optimal weight: 4.9990 chunk 17 optimal weight: 0.0970 chunk 24 optimal weight: 0.9980 chunk 23 optimal weight: 3.9990 chunk 25 optimal weight: 0.9990 overall best weight: 0.6378 ------------------------------------------------------------------------------- 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 = 0.3791 r_free = 0.3791 target = 0.142036 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3622 r_free = 0.3622 target = 0.128318 restraints weight = 15262.459| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3656 r_free = 0.3656 target = 0.131042 restraints weight = 7788.864| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3676 r_free = 0.3676 target = 0.132657 restraints weight = 4818.667| |-----------------------------------------------------------------------------| r_work (final): 0.3652 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8000 moved from start: 0.1688 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 8534 Z= 0.123 Angle : 0.643 9.385 11678 Z= 0.301 Chirality : 0.042 0.238 1376 Planarity : 0.003 0.027 1370 Dihedral : 12.219 156.645 1716 Min Nonbonded Distance : 2.410 Molprobity Statistics. All-atom Clashscore : 11.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.97 % Favored : 95.03 % Rotamer: Outliers : 3.49 % Allowed : 25.66 % Favored : 70.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.04 (0.29), residues: 1026 helix: 1.58 (0.20), residues: 748 sheet: None (None), residues: 0 loop : -1.83 (0.42), residues: 278 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 62 HIS 0.004 0.001 HIS A 221 PHE 0.008 0.001 PHE B 131 TYR 0.033 0.001 TYR B 455 ARG 0.007 0.001 ARG A 38 Details of bonding type rmsd link_NAG-ASN : bond 0.00657 ( 2) link_NAG-ASN : angle 4.04963 ( 6) link_BETA1-4 : bond 0.00817 ( 4) link_BETA1-4 : angle 2.51586 ( 12) hydrogen bonds : bond 0.03512 ( 552) hydrogen bonds : angle 4.06451 ( 1638) covalent geometry : bond 0.00277 ( 8528) covalent geometry : angle 0.63216 (11660) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2052 Ramachandran restraints generated. 1026 Oldfield, 0 Emsley, 1026 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2052 Ramachandran restraints generated. 1026 Oldfield, 0 Emsley, 1026 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 147 time to evaluate : 0.965 Fit side-chains REVERT: A 116 ASP cc_start: 0.7833 (OUTLIER) cc_final: 0.7547 (t0) REVERT: A 229 LEU cc_start: 0.8512 (OUTLIER) cc_final: 0.8228 (mp) REVERT: A 318 MET cc_start: 0.7173 (ppp) cc_final: 0.6900 (ppp) REVERT: A 455 TYR cc_start: 0.5763 (p90) cc_final: 0.5420 (p90) REVERT: B 116 ASP cc_start: 0.7857 (OUTLIER) cc_final: 0.7599 (t0) REVERT: B 229 LEU cc_start: 0.8520 (OUTLIER) cc_final: 0.8234 (mp) REVERT: B 318 MET cc_start: 0.7180 (ppp) cc_final: 0.6906 (ppp) REVERT: B 455 TYR cc_start: 0.5866 (p90) cc_final: 0.5474 (p90) outliers start: 29 outliers final: 21 residues processed: 166 average time/residue: 0.1712 time to fit residues: 41.2291 Evaluate side-chains 167 residues out of total 830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 142 time to evaluate : 0.917 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 93 LEU Chi-restraints excluded: chain A residue 116 ASP Chi-restraints excluded: chain A residue 130 LEU Chi-restraints excluded: chain A residue 157 ILE Chi-restraints excluded: chain A residue 184 VAL Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 241 LEU Chi-restraints excluded: chain A residue 252 ILE Chi-restraints excluded: chain A residue 330 VAL Chi-restraints excluded: chain A residue 368 PHE Chi-restraints excluded: chain A residue 427 VAL Chi-restraints excluded: chain A residue 431 ASN Chi-restraints excluded: chain B residue 93 LEU Chi-restraints excluded: chain B residue 100 LEU Chi-restraints excluded: chain B residue 116 ASP Chi-restraints excluded: chain B residue 130 LEU Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain B residue 184 VAL Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 241 LEU Chi-restraints excluded: chain B residue 252 ILE Chi-restraints excluded: chain B residue 330 VAL Chi-restraints excluded: chain B residue 368 PHE Chi-restraints excluded: chain B residue 427 VAL Chi-restraints excluded: chain B residue 431 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 18 optimal weight: 0.6980 chunk 57 optimal weight: 5.9990 chunk 7 optimal weight: 0.9980 chunk 100 optimal weight: 4.9990 chunk 19 optimal weight: 0.6980 chunk 69 optimal weight: 2.9990 chunk 90 optimal weight: 4.9990 chunk 13 optimal weight: 0.7980 chunk 24 optimal weight: 6.9990 chunk 40 optimal weight: 1.9990 chunk 49 optimal weight: 2.9990 overall best weight: 1.0382 ------------------------------------------------------------------------------- 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 = 0.3778 r_free = 0.3778 target = 0.140901 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3607 r_free = 0.3607 target = 0.127141 restraints weight = 15481.315| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3642 r_free = 0.3642 target = 0.129887 restraints weight = 7853.486| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3663 r_free = 0.3663 target = 0.131554 restraints weight = 4843.342| |-----------------------------------------------------------------------------| r_work (final): 0.3634 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8032 moved from start: 0.1729 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 8534 Z= 0.136 Angle : 0.643 9.359 11678 Z= 0.304 Chirality : 0.042 0.237 1376 Planarity : 0.004 0.033 1370 Dihedral : 11.659 156.982 1716 Min Nonbonded Distance : 2.404 Molprobity Statistics. All-atom Clashscore : 12.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.97 % Favored : 95.03 % Rotamer: Outliers : 3.37 % Allowed : 24.82 % Favored : 71.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.00 (0.29), residues: 1026 helix: 1.55 (0.20), residues: 748 sheet: None (None), residues: 0 loop : -1.84 (0.43), residues: 278 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 62 HIS 0.005 0.001 HIS A 221 PHE 0.006 0.001 PHE B 131 TYR 0.030 0.001 TYR B 455 ARG 0.008 0.001 ARG A 38 Details of bonding type rmsd link_NAG-ASN : bond 0.00697 ( 2) link_NAG-ASN : angle 4.01522 ( 6) link_BETA1-4 : bond 0.00737 ( 4) link_BETA1-4 : angle 2.53745 ( 12) hydrogen bonds : bond 0.03672 ( 552) hydrogen bonds : angle 4.13919 ( 1638) covalent geometry : bond 0.00313 ( 8528) covalent geometry : angle 0.63146 (11660) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2052 Ramachandran restraints generated. 1026 Oldfield, 0 Emsley, 1026 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2052 Ramachandran restraints generated. 1026 Oldfield, 0 Emsley, 1026 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 151 time to evaluate : 0.931 Fit side-chains REVERT: A 116 ASP cc_start: 0.7760 (OUTLIER) cc_final: 0.7488 (t0) REVERT: A 229 LEU cc_start: 0.8600 (OUTLIER) cc_final: 0.8321 (mp) REVERT: A 318 MET cc_start: 0.7253 (ppp) cc_final: 0.7014 (ppp) REVERT: B 116 ASP cc_start: 0.7901 (OUTLIER) cc_final: 0.7600 (t0) REVERT: B 229 LEU cc_start: 0.8600 (OUTLIER) cc_final: 0.8312 (mp) REVERT: B 318 MET cc_start: 0.7266 (ppp) cc_final: 0.6995 (ppp) REVERT: B 455 TYR cc_start: 0.5972 (p90) cc_final: 0.5580 (p90) outliers start: 28 outliers final: 21 residues processed: 165 average time/residue: 0.1813 time to fit residues: 43.3121 Evaluate side-chains 169 residues out of total 830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 144 time to evaluate : 0.898 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 93 LEU Chi-restraints excluded: chain A residue 116 ASP Chi-restraints excluded: chain A residue 130 LEU Chi-restraints excluded: chain A residue 157 ILE Chi-restraints excluded: chain A residue 184 VAL Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 241 LEU Chi-restraints excluded: chain A residue 252 ILE Chi-restraints excluded: chain A residue 330 VAL Chi-restraints excluded: chain A residue 368 PHE Chi-restraints excluded: chain A residue 427 VAL Chi-restraints excluded: chain A residue 431 ASN Chi-restraints excluded: chain B residue 93 LEU Chi-restraints excluded: chain B residue 100 LEU Chi-restraints excluded: chain B residue 116 ASP Chi-restraints excluded: chain B residue 130 LEU Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain B residue 184 VAL Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 241 LEU Chi-restraints excluded: chain B residue 252 ILE Chi-restraints excluded: chain B residue 330 VAL Chi-restraints excluded: chain B residue 368 PHE Chi-restraints excluded: chain B residue 427 VAL Chi-restraints excluded: chain B residue 431 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 15 optimal weight: 3.9990 chunk 57 optimal weight: 5.9990 chunk 34 optimal weight: 0.9990 chunk 37 optimal weight: 0.6980 chunk 58 optimal weight: 0.5980 chunk 39 optimal weight: 9.9990 chunk 60 optimal weight: 4.9990 chunk 42 optimal weight: 4.9990 chunk 100 optimal weight: 4.9990 chunk 29 optimal weight: 10.0000 chunk 33 optimal weight: 1.9990 overall best weight: 1.6586 ------------------------------------------------------------------------------- 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 = 0.3740 r_free = 0.3740 target = 0.138003 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.124187 restraints weight = 15644.673| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3602 r_free = 0.3602 target = 0.126918 restraints weight = 7941.325| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3623 r_free = 0.3623 target = 0.128560 restraints weight = 4900.991| |-----------------------------------------------------------------------------| r_work (final): 0.3606 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8086 moved from start: 0.1846 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 8534 Z= 0.170 Angle : 0.717 12.194 11678 Z= 0.335 Chirality : 0.043 0.235 1376 Planarity : 0.004 0.032 1370 Dihedral : 11.612 157.053 1716 Min Nonbonded Distance : 2.398 Molprobity Statistics. All-atom Clashscore : 12.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.85 % Favored : 94.15 % Rotamer: Outliers : 3.01 % Allowed : 26.63 % Favored : 70.36 % 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: 0.92 (0.29), residues: 1026 helix: 1.48 (0.20), residues: 748 sheet: None (None), residues: 0 loop : -1.83 (0.44), residues: 278 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 406 HIS 0.005 0.001 HIS B 221 PHE 0.008 0.001 PHE A 140 TYR 0.028 0.002 TYR A 455 ARG 0.009 0.001 ARG A 38 Details of bonding type rmsd link_NAG-ASN : bond 0.00691 ( 2) link_NAG-ASN : angle 4.00835 ( 6) link_BETA1-4 : bond 0.00751 ( 4) link_BETA1-4 : angle 2.68353 ( 12) hydrogen bonds : bond 0.04025 ( 552) hydrogen bonds : angle 4.30467 ( 1638) covalent geometry : bond 0.00401 ( 8528) covalent geometry : angle 0.70632 (11660) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2052 Ramachandran restraints generated. 1026 Oldfield, 0 Emsley, 1026 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2052 Ramachandran restraints generated. 1026 Oldfield, 0 Emsley, 1026 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 137 time to evaluate : 0.847 Fit side-chains REVERT: A 229 LEU cc_start: 0.8666 (OUTLIER) cc_final: 0.8363 (mp) REVERT: A 318 MET cc_start: 0.7311 (ppp) cc_final: 0.7053 (ppp) REVERT: A 455 TYR cc_start: 0.5883 (p90) cc_final: 0.5567 (p90) REVERT: B 229 LEU cc_start: 0.8662 (OUTLIER) cc_final: 0.8364 (mp) REVERT: B 318 MET cc_start: 0.7304 (ppp) cc_final: 0.7048 (ppp) REVERT: B 455 TYR cc_start: 0.6022 (p90) cc_final: 0.5661 (p90) outliers start: 25 outliers final: 19 residues processed: 153 average time/residue: 0.1693 time to fit residues: 37.5380 Evaluate side-chains 156 residues out of total 830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 135 time to evaluate : 0.896 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 93 LEU Chi-restraints excluded: chain A residue 130 LEU Chi-restraints excluded: chain A residue 157 ILE Chi-restraints excluded: chain A residue 184 VAL Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 241 LEU Chi-restraints excluded: chain A residue 252 ILE Chi-restraints excluded: chain A residue 330 VAL Chi-restraints excluded: chain A residue 368 PHE Chi-restraints excluded: chain A residue 431 ASN Chi-restraints excluded: chain B residue 93 LEU Chi-restraints excluded: chain B residue 100 LEU Chi-restraints excluded: chain B residue 130 LEU Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain B residue 184 VAL Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 241 LEU Chi-restraints excluded: chain B residue 252 ILE Chi-restraints excluded: chain B residue 330 VAL Chi-restraints excluded: chain B residue 368 PHE Chi-restraints excluded: chain B residue 431 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 31 optimal weight: 0.0050 chunk 98 optimal weight: 0.9980 chunk 65 optimal weight: 0.9990 chunk 81 optimal weight: 0.8980 chunk 80 optimal weight: 3.9990 chunk 34 optimal weight: 0.9990 chunk 72 optimal weight: 0.7980 chunk 4 optimal weight: 3.9990 chunk 70 optimal weight: 1.9990 chunk 66 optimal weight: 2.9990 chunk 36 optimal weight: 0.9980 overall best weight: 0.7394 ------------------------------------------------------------------------------- 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 = 0.3773 r_free = 0.3773 target = 0.140479 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3600 r_free = 0.3600 target = 0.126650 restraints weight = 15437.955| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3634 r_free = 0.3634 target = 0.129376 restraints weight = 7909.675| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3656 r_free = 0.3656 target = 0.131071 restraints weight = 4896.777| |-----------------------------------------------------------------------------| r_work (final): 0.3641 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8038 moved from start: 0.1894 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 8534 Z= 0.131 Angle : 0.686 12.054 11678 Z= 0.319 Chirality : 0.042 0.235 1376 Planarity : 0.004 0.032 1370 Dihedral : 11.424 156.883 1716 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 12.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.07 % Favored : 94.93 % Rotamer: Outliers : 2.53 % Allowed : 27.59 % Favored : 69.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.03 (0.29), residues: 1026 helix: 1.55 (0.20), residues: 750 sheet: None (None), residues: 0 loop : -1.79 (0.44), residues: 276 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 254 HIS 0.005 0.001 HIS A 221 PHE 0.007 0.001 PHE B 131 TYR 0.031 0.001 TYR A 455 ARG 0.009 0.001 ARG A 38 Details of bonding type rmsd link_NAG-ASN : bond 0.00651 ( 2) link_NAG-ASN : angle 3.99123 ( 6) link_BETA1-4 : bond 0.00717 ( 4) link_BETA1-4 : angle 2.47172 ( 12) hydrogen bonds : bond 0.03764 ( 552) hydrogen bonds : angle 4.18960 ( 1638) covalent geometry : bond 0.00300 ( 8528) covalent geometry : angle 0.67556 (11660) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2052 Ramachandran restraints generated. 1026 Oldfield, 0 Emsley, 1026 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2052 Ramachandran restraints generated. 1026 Oldfield, 0 Emsley, 1026 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 147 time to evaluate : 0.875 Fit side-chains REVERT: A 229 LEU cc_start: 0.8573 (OUTLIER) cc_final: 0.8282 (mp) REVERT: A 305 TYR cc_start: 0.6582 (t80) cc_final: 0.6282 (t80) REVERT: A 318 MET cc_start: 0.7321 (ppp) cc_final: 0.7033 (ppp) REVERT: A 368 PHE cc_start: 0.6327 (OUTLIER) cc_final: 0.5817 (t80) REVERT: A 455 TYR cc_start: 0.5961 (p90) cc_final: 0.5617 (p90) REVERT: B 229 LEU cc_start: 0.8559 (OUTLIER) cc_final: 0.8273 (mp) REVERT: B 305 TYR cc_start: 0.6581 (t80) cc_final: 0.6294 (t80) REVERT: B 318 MET cc_start: 0.7334 (ppp) cc_final: 0.7039 (ppp) REVERT: B 368 PHE cc_start: 0.6341 (OUTLIER) cc_final: 0.5844 (t80) REVERT: B 455 TYR cc_start: 0.6138 (p90) cc_final: 0.5756 (p90) outliers start: 21 outliers final: 17 residues processed: 157 average time/residue: 0.1701 time to fit residues: 38.6926 Evaluate side-chains 165 residues out of total 830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 144 time to evaluate : 0.827 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 93 LEU Chi-restraints excluded: chain A residue 130 LEU Chi-restraints excluded: chain A residue 157 ILE Chi-restraints excluded: chain A residue 184 VAL Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 241 LEU Chi-restraints excluded: chain A residue 252 ILE Chi-restraints excluded: chain A residue 330 VAL Chi-restraints excluded: chain A residue 368 PHE Chi-restraints excluded: chain A residue 431 ASN Chi-restraints excluded: chain B residue 93 LEU Chi-restraints excluded: chain B residue 100 LEU Chi-restraints excluded: chain B residue 130 LEU Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain B residue 184 VAL Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 241 LEU Chi-restraints excluded: chain B residue 252 ILE Chi-restraints excluded: chain B residue 330 VAL Chi-restraints excluded: chain B residue 368 PHE Chi-restraints excluded: chain B residue 431 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 74 optimal weight: 0.8980 chunk 43 optimal weight: 3.9990 chunk 51 optimal weight: 10.0000 chunk 81 optimal weight: 0.7980 chunk 88 optimal weight: 2.9990 chunk 66 optimal weight: 6.9990 chunk 28 optimal weight: 0.7980 chunk 40 optimal weight: 8.9990 chunk 98 optimal weight: 0.0980 chunk 68 optimal weight: 5.9990 chunk 87 optimal weight: 4.9990 overall best weight: 1.1182 ------------------------------------------------------------------------------- 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 = 0.3761 r_free = 0.3761 target = 0.139499 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3587 r_free = 0.3587 target = 0.125608 restraints weight = 15680.229| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3623 r_free = 0.3623 target = 0.128406 restraints weight = 7949.422| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3645 r_free = 0.3645 target = 0.130162 restraints weight = 4876.266| |-----------------------------------------------------------------------------| r_work (final): 0.3632 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8054 moved from start: 0.1933 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 8534 Z= 0.148 Angle : 0.710 11.924 11678 Z= 0.330 Chirality : 0.043 0.236 1376 Planarity : 0.004 0.041 1370 Dihedral : 11.338 158.001 1716 Min Nonbonded Distance : 2.406 Molprobity Statistics. All-atom Clashscore : 12.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.65 % Favored : 94.35 % Rotamer: Outliers : 3.01 % Allowed : 26.51 % Favored : 70.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.97 (0.29), residues: 1026 helix: 1.52 (0.20), residues: 748 sheet: None (None), residues: 0 loop : -1.84 (0.44), residues: 278 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 254 HIS 0.005 0.001 HIS B 221 PHE 0.009 0.001 PHE A 258 TYR 0.031 0.001 TYR A 455 ARG 0.008 0.001 ARG B 38 Details of bonding type rmsd link_NAG-ASN : bond 0.00679 ( 2) link_NAG-ASN : angle 3.94050 ( 6) link_BETA1-4 : bond 0.00702 ( 4) link_BETA1-4 : angle 2.51745 ( 12) hydrogen bonds : bond 0.03850 ( 552) hydrogen bonds : angle 4.22367 ( 1638) covalent geometry : bond 0.00348 ( 8528) covalent geometry : angle 0.70056 (11660) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2521.99 seconds wall clock time: 45 minutes 8.10 seconds (2708.10 seconds total)