Starting phenix.real_space_refine on Thu Jul 24 07:35:08 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8d48_27177/07_2025/8d48_27177.cif Found real_map, /net/cci-nas-00/data/ceres_data/8d48_27177/07_2025/8d48_27177.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8d48_27177/07_2025/8d48_27177.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8d48_27177/07_2025/8d48_27177.map" model { file = "/net/cci-nas-00/data/ceres_data/8d48_27177/07_2025/8d48_27177.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8d48_27177/07_2025/8d48_27177.cif" } resolution = 3.7 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= -0.000 sd= 0.015 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 24 5.16 5 C 3498 2.51 5 N 926 2.21 5 O 1097 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 15 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib" Total number of atoms: 5545 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 2143 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 271, 2134 Classifications: {'peptide': 271} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 16, 'TRANS': 254} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Conformer: "B" Number of residues, atoms: 271, 2134 Classifications: {'peptide': 271} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 16, 'TRANS': 254} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 bond proxies already assigned to first conformer: 2178 Chain: "H" Number of atoms: 1663 Number of conformers: 1 Conformer: "" Number of residues, atoms: 223, 1663 Classifications: {'peptide': 223} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 208} Chain: "L" Number of atoms: 1711 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 220, 1708 Classifications: {'peptide': 220} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 2, 'PTRANS': 9, 'TRANS': 208} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Conformer: "B" Number of residues, atoms: 220, 1708 Classifications: {'peptide': 220} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 2, 'PTRANS': 9, 'TRANS': 208} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 bond proxies already assigned to first conformer: 1742 Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Time building chain proxies: 6.05, per 1000 atoms: 1.09 Number of scatterers: 5545 At special positions: 0 Unit cell: (77.5411, 115.886, 113.329, 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 24 16.00 O 1097 8.00 N 926 7.00 C 3498 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=10, symmetry=0 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.05 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.03 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.03 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.04 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 92 " distance=2.03 Simple disulfide: pdb=" SG CYS H 142 " - pdb=" SG CYS H 208 " distance=2.04 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.03 Simple disulfide: pdb=" SG CYS L 134 " - pdb=" SG ACYS L 194 " distance=2.03 Simple disulfide: pdb=" SG CYS L 134 " - pdb=" SG BCYS L 194 " distance=2.03 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 B 1 " - " NAG B 2 " NAG-ASN " NAG B 1 " - " ASN A 331 " Time building additional restraints: 1.39 Conformation dependent library (CDL) restraints added in 1.4 seconds 1426 Ramachandran restraints generated. 713 Oldfield, 0 Emsley, 713 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1330 Finding SS restraints... Secondary structure from input PDB file: 10 helices and 16 sheets defined 6.9% alpha, 32.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.91 Creating SS restraints... Processing helix chain 'A' and resid 338 through 343 removed outlier: 3.692A pdb=" N PHE A 342 " --> pdb=" O PHE A 338 " (cutoff:3.500A) Processing helix chain 'A' and resid 349 through 353 Processing helix chain 'A' and resid 364 through 370 removed outlier: 4.046A pdb=" N LEU A 368 " --> pdb=" O ASP A 364 " (cutoff:3.500A) Processing helix chain 'A' and resid 386 through 390 removed outlier: 3.675A pdb=" N LEU A 390 " --> pdb=" O LEU A 387 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 407 No H-bonds generated for 'chain 'A' and resid 405 through 407' Processing helix chain 'A' and resid 438 through 443 Processing helix chain 'H' and resid 60 through 64 Processing helix chain 'H' and resid 163 through 165 No H-bonds generated for 'chain 'H' and resid 163 through 165' Processing helix chain 'H' and resid 196 through 198 No H-bonds generated for 'chain 'H' and resid 196 through 198' Processing helix chain 'L' and resid 121 through 126 removed outlier: 3.688A pdb=" N LEU L 125 " --> pdb=" O SER L 121 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N LYS L 126 " --> pdb=" O ASP L 122 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 121 through 126' Processing sheet with id=AA1, first strand: chain 'A' and resid 325 through 328 removed outlier: 5.757A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N THR A 572 " --> pdb=" O ASP A 568 " (cutoff:3.500A) removed outlier: 7.397A pdb=" N GLY A 566 " --> pdb=" O ASP A 574 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 354 through 358 removed outlier: 4.079A pdb=" N ASN A 354 " --> pdb=" O SER A 399 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N SER A 399 " --> pdb=" O ASN A 354 " (cutoff:3.500A) removed outlier: 4.316A pdb=" N ASN A 394 " --> pdb=" O GLU A 516 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N GLU A 516 " --> pdb=" O ASN A 394 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 361 through 362 removed outlier: 6.757A pdb=" N CYS A 361 " --> pdb=" O CYS A 525 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'A' and resid 452 through 454 removed outlier: 3.628A pdb=" N TYR A 453 " --> pdb=" O GLN A 493 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N GLN A 493 " --> pdb=" O TYR A 453 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'H' and resid 3 through 6 Processing sheet with id=AA6, first strand: chain 'H' and resid 10 through 12 removed outlier: 3.506A pdb=" N SER H 58 " --> pdb=" O ILE H 50 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'H' and resid 67 through 68 Processing sheet with id=AA8, first strand: chain 'H' and resid 120 through 124 removed outlier: 4.403A pdb=" N GLY H 141 " --> pdb=" O LEU H 124 " (cutoff:3.500A) removed outlier: 6.116A pdb=" N TYR H 185 " --> pdb=" O ASP H 146 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'H' and resid 120 through 124 removed outlier: 4.403A pdb=" N GLY H 141 " --> pdb=" O LEU H 124 " (cutoff:3.500A) removed outlier: 6.116A pdb=" N TYR H 185 " --> pdb=" O ASP H 146 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N SER H 186 " --> pdb=" O VAL H 177 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'H' and resid 153 through 157 Processing sheet with id=AB2, first strand: chain 'L' and resid 5 through 7 removed outlier: 4.096A pdb=" N ASP L 70 " --> pdb=" O SER L 67 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N SER L 67 " --> pdb=" O ASP L 70 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'L' and resid 10 through 13 removed outlier: 3.641A pdb=" N LEU L 11 " --> pdb=" O LYS L 103 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N VAL L 13 " --> pdb=" O GLU L 105 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N TYR L 86 " --> pdb=" O THR L 102 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'L' and resid 53 through 54 removed outlier: 5.727A pdb=" N LEU L 46 " --> pdb=" O GLN L 37 " (cutoff:3.500A) removed outlier: 6.288A pdb=" N GLN L 37 " --> pdb=" O LEU L 46 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'L' and resid 114 through 118 removed outlier: 3.942A pdb=" N VAL L 133 " --> pdb=" O PHE L 118 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N SER L 177 " --> pdb=" O CYS L 134 " (cutoff:3.500A) removed outlier: 6.196A pdb=" N TYR L 173 " --> pdb=" O ASN L 138 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'L' and resid 153 through 154 removed outlier: 4.083A pdb=" N VAL L 196 " --> pdb=" O VAL L 205 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N VAL L 205 " --> pdb=" O VAL L 196 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'L' and resid 153 through 154 166 hydrogen bonds defined for protein. 402 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: 1.83 Time building geometry restraints manager: 1.67 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 1687 1.33 - 1.47: 1544 1.47 - 1.61: 2423 1.61 - 1.74: 1 1.74 - 1.88: 28 Bond restraints: 5683 Sorted by residual: bond pdb=" C1 NAG B 2 " pdb=" O5 NAG B 2 " ideal model delta sigma weight residual 1.406 1.482 -0.076 2.00e-02 2.50e+03 1.46e+01 bond pdb=" CB PRO H 214 " pdb=" CG PRO H 214 " ideal model delta sigma weight residual 1.492 1.658 -0.166 5.00e-02 4.00e+02 1.11e+01 bond pdb=" N VAL L 27B" pdb=" CA VAL L 27B" ideal model delta sigma weight residual 1.459 1.499 -0.040 1.25e-02 6.40e+03 1.02e+01 bond pdb=" CA SER L 27F" pdb=" CB SER L 27F" ideal model delta sigma weight residual 1.541 1.505 0.036 1.20e-02 6.94e+03 9.10e+00 bond pdb=" CA TYR A 351 " pdb=" C TYR A 351 " ideal model delta sigma weight residual 1.523 1.577 -0.053 1.80e-02 3.09e+03 8.81e+00 ... (remaining 5678 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.12: 7657 3.12 - 6.24: 73 6.24 - 9.35: 10 9.35 - 12.47: 0 12.47 - 15.59: 2 Bond angle restraints: 7742 Sorted by residual: angle pdb=" CA PRO H 214 " pdb=" N PRO H 214 " pdb=" CD PRO H 214 " ideal model delta sigma weight residual 112.00 96.41 15.59 1.40e+00 5.10e-01 1.24e+02 angle pdb=" N VAL A 350 " pdb=" CA VAL A 350 " pdb=" C VAL A 350 " ideal model delta sigma weight residual 110.42 117.99 -7.57 9.60e-01 1.09e+00 6.22e+01 angle pdb=" CA CYS A 379 " pdb=" CB CYS A 379 " pdb=" SG CYS A 379 " ideal model delta sigma weight residual 114.40 128.65 -14.25 2.30e+00 1.89e-01 3.84e+01 angle pdb=" N ALA A 352 " pdb=" CA ALA A 352 " pdb=" CB ALA A 352 " ideal model delta sigma weight residual 111.65 120.29 -8.64 1.40e+00 5.10e-01 3.81e+01 angle pdb=" N PRO H 214 " pdb=" CD PRO H 214 " pdb=" CG PRO H 214 " ideal model delta sigma weight residual 103.20 96.03 7.17 1.50e+00 4.44e-01 2.28e+01 ... (remaining 7737 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.18: 3130 23.18 - 46.36: 260 46.36 - 69.54: 34 69.54 - 92.72: 6 92.72 - 115.90: 2 Dihedral angle restraints: 3432 sinusoidal: 1348 harmonic: 2084 Sorted by residual: dihedral pdb=" CB CYS A 379 " pdb=" SG CYS A 379 " pdb=" SG CYS A 432 " pdb=" CB CYS A 432 " ideal model delta sinusoidal sigma weight residual 93.00 33.62 59.38 1 1.00e+01 1.00e-02 4.71e+01 dihedral pdb=" CB CYS A 538 " pdb=" SG CYS A 538 " pdb=" SG CYS A 590 " pdb=" CB CYS A 590 " ideal model delta sinusoidal sigma weight residual -86.00 -32.29 -53.71 1 1.00e+01 1.00e-02 3.92e+01 dihedral pdb=" CA GLU H 150 " pdb=" C GLU H 150 " pdb=" N PRO H 151 " pdb=" CA PRO H 151 " ideal model delta harmonic sigma weight residual 180.00 150.62 29.38 0 5.00e+00 4.00e-02 3.45e+01 ... (remaining 3429 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.058: 699 0.058 - 0.116: 141 0.116 - 0.173: 19 0.173 - 0.231: 3 0.231 - 0.289: 2 Chirality restraints: 864 Sorted by residual: chirality pdb=" CA ALA A 352 " pdb=" N ALA A 352 " pdb=" C ALA A 352 " pdb=" CB ALA A 352 " both_signs ideal model delta sigma weight residual False 2.48 2.20 0.29 2.00e-01 2.50e+01 2.08e+00 chirality pdb=" CA VAL A 350 " pdb=" N VAL A 350 " pdb=" C VAL A 350 " pdb=" CB VAL A 350 " both_signs ideal model delta sigma weight residual False 2.44 2.20 0.24 2.00e-01 2.50e+01 1.42e+00 chirality pdb=" CA VAL H 223 " pdb=" N VAL H 223 " pdb=" C VAL H 223 " pdb=" CB VAL H 223 " both_signs ideal model delta sigma weight residual False 2.44 2.66 -0.22 2.00e-01 2.50e+01 1.18e+00 ... (remaining 861 not shown) Planarity restraints: 1003 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLU H 150 " -0.092 5.00e-02 4.00e+02 1.41e-01 3.20e+01 pdb=" N PRO H 151 " 0.245 5.00e-02 4.00e+02 pdb=" CA PRO H 151 " -0.077 5.00e-02 4.00e+02 pdb=" CD PRO H 151 " -0.075 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS H 213 " -0.092 5.00e-02 4.00e+02 1.27e-01 2.59e+01 pdb=" N PRO H 214 " 0.219 5.00e-02 4.00e+02 pdb=" CA PRO H 214 " -0.060 5.00e-02 4.00e+02 pdb=" CD PRO H 214 " -0.068 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ASN L 27A" 0.017 2.00e-02 2.50e+03 3.45e-02 1.19e+01 pdb=" C ASN L 27A" -0.060 2.00e-02 2.50e+03 pdb=" O ASN L 27A" 0.023 2.00e-02 2.50e+03 pdb=" N VAL L 27B" 0.020 2.00e-02 2.50e+03 ... (remaining 1000 not shown) Histogram of nonbonded interaction distances: 1.57 - 2.23: 3 2.23 - 2.90: 2320 2.90 - 3.57: 7034 3.57 - 4.23: 11297 4.23 - 4.90: 19319 Nonbonded interactions: 39973 Sorted by model distance: nonbonded pdb=" NH2 ARG H 222 " pdb=" OE2 GLU H 226 " model vdw 1.565 3.120 nonbonded pdb=" OD1 ASP H 86 " pdb=" OH TYR H 90 " model vdw 2.179 3.040 nonbonded pdb=" OD1 ASP A 568 " pdb=" N ILE A 569 " model vdw 2.219 3.120 nonbonded pdb=" OG SER H 156 " pdb=" OD1 ASN H 209 " model vdw 2.235 3.040 nonbonded pdb=" OG SER A 383 " pdb=" O THR A 385 " model vdw 2.247 3.040 ... (remaining 39968 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 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: 4.440 Set stop_for_unknowns flag: 0.010 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.220 Check model and map are aligned: 0.040 Set scattering table: 0.050 Process input model: 20.780 Find NCS groups from input model: 0.080 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:2.900 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.550 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7690 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 : 0.005 0.166 5695 Z= 0.238 Angle : 0.818 15.589 7768 Z= 0.475 Chirality : 0.049 0.289 864 Planarity : 0.008 0.141 1002 Dihedral : 16.279 115.898 2072 Min Nonbonded Distance : 1.565 Molprobity Statistics. All-atom Clashscore : 11.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.20 % Favored : 92.80 % Rotamer: Outliers : 0.00 % Allowed : 19.74 % Favored : 80.26 % Cbeta Deviations : 0.15 % Peptide Plane: Cis-proline : 7.32 % 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: -1.11 (0.31), residues: 713 helix: -3.19 (0.78), residues: 27 sheet: 0.49 (0.36), residues: 214 loop : -1.25 (0.28), residues: 472 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 436 HIS 0.002 0.001 HIS H 212 PHE 0.015 0.001 PHE A 374 TYR 0.011 0.001 TYR L 49 ARG 0.006 0.001 ARG A 509 Details of bonding type rmsd link_NAG-ASN : bond 0.00896 ( 1) link_NAG-ASN : angle 4.52327 ( 3) link_BETA1-4 : bond 0.00201 ( 1) link_BETA1-4 : angle 4.03111 ( 3) hydrogen bonds : bond 0.20058 ( 144) hydrogen bonds : angle 6.89286 ( 402) SS BOND : bond 0.00759 ( 10) SS BOND : angle 1.55202 ( 20) covalent geometry : bond 0.00464 ( 5683) covalent geometry : angle 0.80680 ( 7742) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1426 Ramachandran restraints generated. 713 Oldfield, 0 Emsley, 713 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1426 Ramachandran restraints generated. 713 Oldfield, 0 Emsley, 713 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 619 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 85 time to evaluate : 0.593 Fit side-chains REVERT: A 409 GLN cc_start: 0.7561 (tp40) cc_final: 0.7253 (tp40) REVERT: L 81 GLU cc_start: 0.8154 (pp20) cc_final: 0.7945 (pp20) outliers start: 0 outliers final: 0 residues processed: 85 average time/residue: 0.1998 time to fit residues: 21.8745 Evaluate side-chains 74 residues out of total 619 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 74 time to evaluate : 0.609 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 71 random chunks: chunk 59 optimal weight: 0.0060 chunk 53 optimal weight: 0.0070 chunk 29 optimal weight: 1.9990 chunk 18 optimal weight: 0.9980 chunk 36 optimal weight: 0.9990 chunk 28 optimal weight: 0.0570 chunk 55 optimal weight: 0.3980 chunk 21 optimal weight: 3.9990 chunk 33 optimal weight: 0.9980 chunk 41 optimal weight: 0.8980 chunk 64 optimal weight: 6.9990 overall best weight: 0.2732 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 370 ASN A 409 GLN A 437 ASN A 450 ASN ** A 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 172 HIS L 37 GLN ** L 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3906 r_free = 0.3906 target = 0.166034 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.130381 restraints weight = 20793.238| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.131994 restraints weight = 23497.500| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.132253 restraints weight = 13718.767| |-----------------------------------------------------------------------------| r_work (final): 0.3418 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3415 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3415 r_free = 0.3415 target_work(ls_wunit_k1) = 0.123 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3414 r_free = 0.3414 target_work(ls_wunit_k1) = 0.123 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.3414 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7758 moved from start: 0.1129 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 5695 Z= 0.133 Angle : 0.708 13.680 7768 Z= 0.357 Chirality : 0.046 0.161 864 Planarity : 0.007 0.107 1002 Dihedral : 6.655 67.180 821 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 6.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.93 % Favored : 94.07 % Rotamer: Outliers : 2.57 % Allowed : 19.90 % Favored : 77.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.32 % 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: -0.87 (0.31), residues: 713 helix: -3.08 (0.91), residues: 21 sheet: 0.52 (0.35), residues: 228 loop : -1.08 (0.29), residues: 464 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A 436 HIS 0.002 0.001 HIS H 35 PHE 0.015 0.001 PHE A 456 TYR 0.014 0.001 TYR L 49 ARG 0.007 0.001 ARG A 509 Details of bonding type rmsd link_NAG-ASN : bond 0.01311 ( 1) link_NAG-ASN : angle 4.33138 ( 3) link_BETA1-4 : bond 0.00597 ( 1) link_BETA1-4 : angle 4.61388 ( 3) hydrogen bonds : bond 0.04084 ( 144) hydrogen bonds : angle 5.94350 ( 402) SS BOND : bond 0.00794 ( 10) SS BOND : angle 1.53156 ( 20) covalent geometry : bond 0.00302 ( 5683) covalent geometry : angle 0.69380 ( 7742) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1426 Ramachandran restraints generated. 713 Oldfield, 0 Emsley, 713 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1426 Ramachandran restraints generated. 713 Oldfield, 0 Emsley, 713 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 619 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 74 time to evaluate : 0.616 Fit side-chains revert: symmetry clash REVERT: A 409 GLN cc_start: 0.7618 (tp-100) cc_final: 0.7379 (tp40) REVERT: H 86 ASP cc_start: 0.8026 (t0) cc_final: 0.7795 (t0) REVERT: H 156 SER cc_start: 0.7841 (OUTLIER) cc_final: 0.7600 (m) REVERT: H 178 LEU cc_start: 0.8458 (OUTLIER) cc_final: 0.8252 (tt) REVERT: L 81 GLU cc_start: 0.8074 (pp20) cc_final: 0.7701 (pp20) outliers start: 16 outliers final: 7 residues processed: 88 average time/residue: 0.1901 time to fit residues: 21.6271 Evaluate side-chains 77 residues out of total 619 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 68 time to evaluate : 0.557 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 495 TYR Chi-restraints excluded: chain H residue 11 VAL Chi-restraints excluded: chain H residue 35 HIS Chi-restraints excluded: chain H residue 156 SER Chi-restraints excluded: chain H residue 178 LEU Chi-restraints excluded: chain H residue 208 CYS Chi-restraints excluded: chain L residue 97 THR Chi-restraints excluded: chain L residue 135 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 71 random chunks: chunk 6 optimal weight: 0.8980 chunk 55 optimal weight: 1.9990 chunk 32 optimal weight: 0.6980 chunk 59 optimal weight: 0.0270 chunk 9 optimal weight: 0.4980 chunk 21 optimal weight: 2.9990 chunk 37 optimal weight: 0.6980 chunk 46 optimal weight: 7.9990 chunk 24 optimal weight: 1.9990 chunk 48 optimal weight: 0.8980 chunk 66 optimal weight: 0.0010 overall best weight: 0.3844 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 506 GLN ** L 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3880 r_free = 0.3880 target = 0.163380 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.127373 restraints weight = 21919.922| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.128549 restraints weight = 23878.625| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.128539 restraints weight = 10045.395| |-----------------------------------------------------------------------------| r_work (final): 0.3352 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3352 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3352 r_free = 0.3352 target_work(ls_wunit_k1) = 0.118 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3352 r_free = 0.3352 target_work(ls_wunit_k1) = 0.118 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.3352 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7818 moved from start: 0.1372 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 5695 Z= 0.132 Angle : 0.673 13.527 7768 Z= 0.344 Chirality : 0.046 0.191 864 Planarity : 0.006 0.075 1002 Dihedral : 5.155 42.193 821 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 5.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.37 % Favored : 94.63 % Rotamer: Outliers : 2.25 % Allowed : 19.90 % Favored : 77.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.32 % 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: -0.82 (0.31), residues: 713 helix: -2.98 (0.93), residues: 21 sheet: 0.63 (0.35), residues: 226 loop : -1.09 (0.28), residues: 466 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 436 HIS 0.003 0.001 HIS H 35 PHE 0.013 0.001 PHE A 374 TYR 0.016 0.001 TYR L 92 ARG 0.008 0.001 ARG H 83 Details of bonding type rmsd link_NAG-ASN : bond 0.01403 ( 1) link_NAG-ASN : angle 4.81393 ( 3) link_BETA1-4 : bond 0.00345 ( 1) link_BETA1-4 : angle 4.25748 ( 3) hydrogen bonds : bond 0.03840 ( 144) hydrogen bonds : angle 5.76743 ( 402) SS BOND : bond 0.00790 ( 10) SS BOND : angle 1.54422 ( 20) covalent geometry : bond 0.00307 ( 5683) covalent geometry : angle 0.65722 ( 7742) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1426 Ramachandran restraints generated. 713 Oldfield, 0 Emsley, 713 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1426 Ramachandran restraints generated. 713 Oldfield, 0 Emsley, 713 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 619 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 68 time to evaluate : 0.523 Fit side-chains revert: symmetry clash REVERT: A 506 GLN cc_start: 0.6846 (OUTLIER) cc_final: 0.6640 (mp10) REVERT: H 86 ASP cc_start: 0.8512 (t0) cc_final: 0.8240 (t0) REVERT: L 81 GLU cc_start: 0.8312 (pp20) cc_final: 0.7951 (pp20) outliers start: 14 outliers final: 9 residues processed: 79 average time/residue: 0.1999 time to fit residues: 20.3888 Evaluate side-chains 78 residues out of total 619 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 68 time to evaluate : 0.602 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 495 TYR Chi-restraints excluded: chain A residue 506 GLN Chi-restraints excluded: chain H residue 35 HIS Chi-restraints excluded: chain H residue 67 VAL Chi-restraints excluded: chain H residue 208 CYS Chi-restraints excluded: chain L residue 97 THR Chi-restraints excluded: chain L residue 109 THR Chi-restraints excluded: chain L residue 135 LEU Chi-restraints excluded: chain L residue 196 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 71 random chunks: chunk 33 optimal weight: 0.0470 chunk 40 optimal weight: 4.9990 chunk 6 optimal weight: 2.9990 chunk 11 optimal weight: 0.8980 chunk 38 optimal weight: 0.6980 chunk 10 optimal weight: 1.9990 chunk 28 optimal weight: 0.6980 chunk 0 optimal weight: 2.9990 chunk 47 optimal weight: 0.8980 chunk 60 optimal weight: 3.9990 chunk 58 optimal weight: 0.4980 overall best weight: 0.5678 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 506 GLN ** L 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3852 r_free = 0.3852 target = 0.160730 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.128069 restraints weight = 24737.336| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.129811 restraints weight = 25323.865| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.129627 restraints weight = 8400.026| |-----------------------------------------------------------------------------| r_work (final): 0.3416 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3416 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3416 r_free = 0.3416 target_work(ls_wunit_k1) = 0.123 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3416 r_free = 0.3416 target_work(ls_wunit_k1) = 0.123 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.3416 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7753 moved from start: 0.1589 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.067 5695 Z= 0.151 Angle : 0.684 13.558 7768 Z= 0.351 Chirality : 0.046 0.176 864 Planarity : 0.006 0.062 1002 Dihedral : 5.114 38.856 821 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 6.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.93 % Favored : 94.07 % Rotamer: Outliers : 3.53 % Allowed : 18.14 % Favored : 78.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.32 % 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: -0.84 (0.31), residues: 713 helix: -3.02 (0.93), residues: 21 sheet: 0.64 (0.35), residues: 226 loop : -1.11 (0.28), residues: 466 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 436 HIS 0.002 0.000 HIS H 35 PHE 0.012 0.001 PHE A 374 TYR 0.019 0.001 TYR L 92 ARG 0.006 0.001 ARG H 83 Details of bonding type rmsd link_NAG-ASN : bond 0.01379 ( 1) link_NAG-ASN : angle 4.52075 ( 3) link_BETA1-4 : bond 0.00667 ( 1) link_BETA1-4 : angle 3.75934 ( 3) hydrogen bonds : bond 0.03754 ( 144) hydrogen bonds : angle 5.73775 ( 402) SS BOND : bond 0.00841 ( 10) SS BOND : angle 1.64674 ( 20) covalent geometry : bond 0.00358 ( 5683) covalent geometry : angle 0.67035 ( 7742) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1426 Ramachandran restraints generated. 713 Oldfield, 0 Emsley, 713 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1426 Ramachandran restraints generated. 713 Oldfield, 0 Emsley, 713 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 619 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 68 time to evaluate : 0.576 Fit side-chains revert: symmetry clash REVERT: H 86 ASP cc_start: 0.8498 (t0) cc_final: 0.7881 (t0) REVERT: H 156 SER cc_start: 0.8108 (OUTLIER) cc_final: 0.7830 (m) REVERT: L 81 GLU cc_start: 0.8225 (pp20) cc_final: 0.7908 (pp20) outliers start: 22 outliers final: 15 residues processed: 84 average time/residue: 0.1952 time to fit residues: 20.9766 Evaluate side-chains 82 residues out of total 619 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 66 time to evaluate : 0.564 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 495 TYR Chi-restraints excluded: chain H residue 35 HIS Chi-restraints excluded: chain H residue 67 VAL Chi-restraints excluded: chain H residue 80 MET Chi-restraints excluded: chain H residue 94 ARG Chi-restraints excluded: chain H residue 143 LEU Chi-restraints excluded: chain H residue 156 SER Chi-restraints excluded: chain H residue 208 CYS Chi-restraints excluded: chain H residue 210 VAL Chi-restraints excluded: chain H residue 222 ARG Chi-restraints excluded: chain L residue 97 THR Chi-restraints excluded: chain L residue 109 THR Chi-restraints excluded: chain L residue 135 LEU Chi-restraints excluded: chain L residue 196 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 71 random chunks: chunk 50 optimal weight: 0.9980 chunk 13 optimal weight: 2.9990 chunk 54 optimal weight: 0.5980 chunk 56 optimal weight: 1.9990 chunk 60 optimal weight: 1.9990 chunk 11 optimal weight: 0.9980 chunk 33 optimal weight: 0.0870 chunk 9 optimal weight: 0.0040 chunk 5 optimal weight: 0.6980 chunk 51 optimal weight: 0.5980 chunk 24 optimal weight: 0.9980 overall best weight: 0.3970 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 147 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 = 0.3862 r_free = 0.3862 target = 0.161604 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.124725 restraints weight = 22838.283| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.127440 restraints weight = 21446.573| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.127054 restraints weight = 12216.922| |-----------------------------------------------------------------------------| r_work (final): 0.3323 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3323 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3323 r_free = 0.3323 target_work(ls_wunit_k1) = 0.116 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3323 r_free = 0.3323 target_work(ls_wunit_k1) = 0.116 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.3323 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7876 moved from start: 0.1731 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.067 5695 Z= 0.128 Angle : 0.658 13.376 7768 Z= 0.337 Chirality : 0.045 0.154 864 Planarity : 0.005 0.051 1002 Dihedral : 4.955 36.308 821 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 6.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.08 % Favored : 94.92 % Rotamer: Outliers : 3.69 % Allowed : 17.50 % Favored : 78.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.32 % 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: -0.75 (0.31), residues: 713 helix: -2.93 (0.96), residues: 21 sheet: 0.69 (0.35), residues: 226 loop : -1.04 (0.29), residues: 466 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 436 HIS 0.002 0.000 HIS H 35 PHE 0.011 0.001 PHE A 374 TYR 0.014 0.001 TYR L 49 ARG 0.008 0.000 ARG H 83 Details of bonding type rmsd link_NAG-ASN : bond 0.01347 ( 1) link_NAG-ASN : angle 4.59569 ( 3) link_BETA1-4 : bond 0.00472 ( 1) link_BETA1-4 : angle 3.46596 ( 3) hydrogen bonds : bond 0.03454 ( 144) hydrogen bonds : angle 5.63623 ( 402) SS BOND : bond 0.00780 ( 10) SS BOND : angle 1.54435 ( 20) covalent geometry : bond 0.00301 ( 5683) covalent geometry : angle 0.64476 ( 7742) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1426 Ramachandran restraints generated. 713 Oldfield, 0 Emsley, 713 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1426 Ramachandran restraints generated. 713 Oldfield, 0 Emsley, 713 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 619 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 69 time to evaluate : 0.548 Fit side-chains revert: symmetry clash REVERT: H 86 ASP cc_start: 0.8507 (t0) cc_final: 0.7893 (t0) REVERT: H 156 SER cc_start: 0.7983 (OUTLIER) cc_final: 0.7768 (m) REVERT: H 228 LYS cc_start: 0.8105 (ttpp) cc_final: 0.7877 (ttpp) REVERT: L 81 GLU cc_start: 0.8340 (pp20) cc_final: 0.8023 (pp20) outliers start: 23 outliers final: 15 residues processed: 86 average time/residue: 0.1907 time to fit residues: 21.1300 Evaluate side-chains 83 residues out of total 619 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 67 time to evaluate : 0.607 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 495 TYR Chi-restraints excluded: chain H residue 35 HIS Chi-restraints excluded: chain H residue 67 VAL Chi-restraints excluded: chain H residue 80 MET Chi-restraints excluded: chain H residue 143 LEU Chi-restraints excluded: chain H residue 156 SER Chi-restraints excluded: chain H residue 208 CYS Chi-restraints excluded: chain H residue 210 VAL Chi-restraints excluded: chain L residue 52 SER Chi-restraints excluded: chain L residue 97 THR Chi-restraints excluded: chain L residue 109 THR Chi-restraints excluded: chain L residue 135 LEU Chi-restraints excluded: chain L residue 179 LEU Chi-restraints excluded: chain L residue 196 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 71 random chunks: chunk 37 optimal weight: 0.9980 chunk 59 optimal weight: 0.9990 chunk 10 optimal weight: 0.8980 chunk 6 optimal weight: 1.9990 chunk 48 optimal weight: 0.6980 chunk 3 optimal weight: 0.9990 chunk 55 optimal weight: 0.0170 chunk 42 optimal weight: 0.7980 chunk 16 optimal weight: 0.0370 chunk 20 optimal weight: 0.9980 chunk 9 optimal weight: 1.9990 overall best weight: 0.4896 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 147 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 = 0.3985 r_free = 0.3985 target = 0.171367 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.3586 r_free = 0.3586 target = 0.138393 restraints weight = 19832.346| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3597 r_free = 0.3597 target = 0.140077 restraints weight = 23010.452| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3609 r_free = 0.3609 target = 0.141015 restraints weight = 13541.983| |-----------------------------------------------------------------------------| r_work (final): 0.3400 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3400 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3400 r_free = 0.3400 target_work(ls_wunit_k1) = 0.122 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3400 r_free = 0.3400 target_work(ls_wunit_k1) = 0.122 | | occupancies: max = 1.00 min = 0.01 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.3400 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7796 moved from start: 0.1909 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.068 5695 Z= 0.138 Angle : 0.687 13.425 7768 Z= 0.347 Chirality : 0.046 0.155 864 Planarity : 0.005 0.050 1002 Dihedral : 4.895 30.857 821 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 6.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.51 % Favored : 94.49 % Rotamer: Outliers : 3.37 % Allowed : 17.82 % Favored : 78.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.32 % 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: -0.75 (0.31), residues: 713 helix: -2.96 (0.95), residues: 21 sheet: 0.72 (0.35), residues: 226 loop : -1.06 (0.28), residues: 466 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 436 HIS 0.002 0.000 HIS H 35 PHE 0.011 0.001 PHE A 374 TYR 0.016 0.001 TYR L 49 ARG 0.009 0.001 ARG H 83 Details of bonding type rmsd link_NAG-ASN : bond 0.01281 ( 1) link_NAG-ASN : angle 4.54507 ( 3) link_BETA1-4 : bond 0.00477 ( 1) link_BETA1-4 : angle 3.33370 ( 3) hydrogen bonds : bond 0.03547 ( 144) hydrogen bonds : angle 5.62301 ( 402) SS BOND : bond 0.00821 ( 10) SS BOND : angle 1.60151 ( 20) covalent geometry : bond 0.00328 ( 5683) covalent geometry : angle 0.67382 ( 7742) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1426 Ramachandran restraints generated. 713 Oldfield, 0 Emsley, 713 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1426 Ramachandran restraints generated. 713 Oldfield, 0 Emsley, 713 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 619 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 71 time to evaluate : 0.586 Fit side-chains revert: symmetry clash REVERT: H 86 ASP cc_start: 0.8403 (t0) cc_final: 0.7891 (t0) REVERT: H 156 SER cc_start: 0.8140 (OUTLIER) cc_final: 0.7900 (m) outliers start: 21 outliers final: 19 residues processed: 86 average time/residue: 0.1961 time to fit residues: 21.6292 Evaluate side-chains 88 residues out of total 619 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 68 time to evaluate : 0.588 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 495 TYR Chi-restraints excluded: chain H residue 11 VAL Chi-restraints excluded: chain H residue 35 HIS Chi-restraints excluded: chain H residue 52 ASP Chi-restraints excluded: chain H residue 67 VAL Chi-restraints excluded: chain H residue 80 MET Chi-restraints excluded: chain H residue 143 LEU Chi-restraints excluded: chain H residue 156 SER Chi-restraints excluded: chain H residue 208 CYS Chi-restraints excluded: chain H residue 210 VAL Chi-restraints excluded: chain L residue 52 SER Chi-restraints excluded: chain L residue 97 THR Chi-restraints excluded: chain L residue 109 THR Chi-restraints excluded: chain L residue 134 CYS Chi-restraints excluded: chain L residue 135 LEU Chi-restraints excluded: chain L residue 150 VAL Chi-restraints excluded: chain L residue 179 LEU Chi-restraints excluded: chain L residue 196 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 71 random chunks: chunk 55 optimal weight: 0.9980 chunk 65 optimal weight: 2.9990 chunk 18 optimal weight: 1.9990 chunk 5 optimal weight: 0.5980 chunk 3 optimal weight: 0.9990 chunk 67 optimal weight: 0.8980 chunk 0 optimal weight: 2.9990 chunk 60 optimal weight: 3.9990 chunk 17 optimal weight: 4.9990 chunk 21 optimal weight: 0.9990 chunk 66 optimal weight: 0.9980 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 147 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 = 0.3796 r_free = 0.3796 target = 0.155691 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.121444 restraints weight = 24651.571| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.122922 restraints weight = 24517.214| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.122860 restraints weight = 10183.719| |-----------------------------------------------------------------------------| r_work (final): 0.3306 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3307 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3307 r_free = 0.3307 target_work(ls_wunit_k1) = 0.115 | | occupancies: max = 1.00 min = 0.01 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3307 r_free = 0.3307 target_work(ls_wunit_k1) = 0.115 | | occupancies: max = 1.00 min = 0.01 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.3307 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7892 moved from start: 0.2137 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.070 5695 Z= 0.189 Angle : 0.742 13.780 7768 Z= 0.381 Chirality : 0.047 0.171 864 Planarity : 0.005 0.051 1002 Dihedral : 5.236 29.120 821 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 6.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.50 % Favored : 93.50 % Rotamer: Outliers : 3.21 % Allowed : 18.30 % Favored : 78.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.32 % 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: -0.94 (0.31), residues: 713 helix: -3.19 (0.89), residues: 21 sheet: 0.43 (0.34), residues: 238 loop : -1.13 (0.29), residues: 454 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A 436 HIS 0.002 0.001 HIS H 35 PHE 0.018 0.002 PHE A 562 TYR 0.024 0.002 TYR L 92 ARG 0.007 0.001 ARG H 83 Details of bonding type rmsd link_NAG-ASN : bond 0.01334 ( 1) link_NAG-ASN : angle 4.37061 ( 3) link_BETA1-4 : bond 0.00467 ( 1) link_BETA1-4 : angle 3.24342 ( 3) hydrogen bonds : bond 0.04116 ( 144) hydrogen bonds : angle 5.83731 ( 402) SS BOND : bond 0.00913 ( 10) SS BOND : angle 1.83466 ( 20) covalent geometry : bond 0.00457 ( 5683) covalent geometry : angle 0.72920 ( 7742) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1426 Ramachandran restraints generated. 713 Oldfield, 0 Emsley, 713 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1426 Ramachandran restraints generated. 713 Oldfield, 0 Emsley, 713 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 619 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 69 time to evaluate : 0.589 Fit side-chains revert: symmetry clash REVERT: A 586 ASP cc_start: 0.7807 (t0) cc_final: 0.7602 (t0) REVERT: H 86 ASP cc_start: 0.8759 (t0) cc_final: 0.8262 (t0) outliers start: 20 outliers final: 17 residues processed: 84 average time/residue: 0.1987 time to fit residues: 21.5606 Evaluate side-chains 83 residues out of total 619 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 66 time to evaluate : 0.745 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain H residue 35 HIS Chi-restraints excluded: chain H residue 52 ASP Chi-restraints excluded: chain H residue 67 VAL Chi-restraints excluded: chain H residue 107 THR Chi-restraints excluded: chain H residue 143 LEU Chi-restraints excluded: chain H residue 208 CYS Chi-restraints excluded: chain H residue 210 VAL Chi-restraints excluded: chain L residue 52 SER Chi-restraints excluded: chain L residue 97 THR Chi-restraints excluded: chain L residue 109 THR Chi-restraints excluded: chain L residue 134 CYS Chi-restraints excluded: chain L residue 135 LEU Chi-restraints excluded: chain L residue 150 VAL Chi-restraints excluded: chain L residue 196 VAL Chi-restraints excluded: chain L residue 197 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 71 random chunks: chunk 8 optimal weight: 1.9990 chunk 57 optimal weight: 0.9990 chunk 24 optimal weight: 0.9980 chunk 47 optimal weight: 3.9990 chunk 38 optimal weight: 0.6980 chunk 62 optimal weight: 6.9990 chunk 39 optimal weight: 1.9990 chunk 29 optimal weight: 0.9990 chunk 59 optimal weight: 0.9980 chunk 2 optimal weight: 4.9990 chunk 1 optimal weight: 0.8980 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 212 HIS ** L 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3924 r_free = 0.3924 target = 0.165856 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.137054 restraints weight = 18155.753| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3581 r_free = 0.3581 target = 0.137896 restraints weight = 23835.975| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3583 r_free = 0.3583 target = 0.138084 restraints weight = 13748.579| |-----------------------------------------------------------------------------| r_work (final): 0.3390 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3390 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3390 r_free = 0.3390 target_work(ls_wunit_k1) = 0.121 | | occupancies: max = 1.00 min = 0.01 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3390 r_free = 0.3390 target_work(ls_wunit_k1) = 0.121 | | occupancies: max = 1.00 min = 0.01 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.3390 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7814 moved from start: 0.2369 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.070 5695 Z= 0.195 Angle : 0.771 13.987 7768 Z= 0.395 Chirality : 0.048 0.182 864 Planarity : 0.005 0.051 1002 Dihedral : 5.311 27.924 821 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 7.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.93 % Favored : 94.07 % Rotamer: Outliers : 3.53 % Allowed : 19.26 % Favored : 77.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.32 % 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: -1.05 (0.31), residues: 713 helix: -3.33 (0.88), residues: 21 sheet: 0.37 (0.34), residues: 238 loop : -1.21 (0.28), residues: 454 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A 436 HIS 0.002 0.001 HIS H 35 PHE 0.019 0.002 PHE A 562 TYR 0.023 0.002 TYR L 92 ARG 0.008 0.001 ARG H 83 Details of bonding type rmsd link_NAG-ASN : bond 0.01397 ( 1) link_NAG-ASN : angle 4.31737 ( 3) link_BETA1-4 : bond 0.00482 ( 1) link_BETA1-4 : angle 3.22125 ( 3) hydrogen bonds : bond 0.04105 ( 144) hydrogen bonds : angle 5.90866 ( 402) SS BOND : bond 0.00919 ( 10) SS BOND : angle 1.87397 ( 20) covalent geometry : bond 0.00475 ( 5683) covalent geometry : angle 0.75918 ( 7742) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1426 Ramachandran restraints generated. 713 Oldfield, 0 Emsley, 713 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1426 Ramachandran restraints generated. 713 Oldfield, 0 Emsley, 713 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 619 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 64 time to evaluate : 0.629 Fit side-chains revert: symmetry clash REVERT: H 86 ASP cc_start: 0.8659 (t0) cc_final: 0.8227 (t0) outliers start: 22 outliers final: 20 residues processed: 81 average time/residue: 0.1957 time to fit residues: 20.5610 Evaluate side-chains 81 residues out of total 619 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 61 time to evaluate : 0.623 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain H residue 35 HIS Chi-restraints excluded: chain H residue 52 ASP Chi-restraints excluded: chain H residue 67 VAL Chi-restraints excluded: chain H residue 80 MET Chi-restraints excluded: chain H residue 107 THR Chi-restraints excluded: chain H residue 143 LEU Chi-restraints excluded: chain H residue 192 THR Chi-restraints excluded: chain H residue 208 CYS Chi-restraints excluded: chain H residue 210 VAL Chi-restraints excluded: chain L residue 50 TRP Chi-restraints excluded: chain L residue 52 SER Chi-restraints excluded: chain L residue 97 THR Chi-restraints excluded: chain L residue 109 THR Chi-restraints excluded: chain L residue 134 CYS Chi-restraints excluded: chain L residue 135 LEU Chi-restraints excluded: chain L residue 150 VAL Chi-restraints excluded: chain L residue 196 VAL Chi-restraints excluded: chain L residue 197 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 71 random chunks: chunk 5 optimal weight: 0.9980 chunk 41 optimal weight: 6.9990 chunk 18 optimal weight: 0.0770 chunk 66 optimal weight: 0.8980 chunk 46 optimal weight: 0.5980 chunk 13 optimal weight: 6.9990 chunk 40 optimal weight: 4.9990 chunk 36 optimal weight: 0.8980 chunk 70 optimal weight: 0.0370 chunk 10 optimal weight: 0.8980 chunk 65 optimal weight: 0.4980 overall best weight: 0.4216 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 147 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 = 0.3953 r_free = 0.3953 target = 0.168816 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3799 r_free = 0.3799 target = 0.154054 restraints weight = 11535.518| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3720 r_free = 0.3720 target = 0.147199 restraints weight = 14052.309| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3700 r_free = 0.3700 target = 0.145912 restraints weight = 20857.103| |-----------------------------------------------------------------------------| r_work (final): 0.3544 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3546 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3546 r_free = 0.3546 target_work(ls_wunit_k1) = 0.134 | | occupancies: max = 1.00 min = 0.01 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3546 r_free = 0.3546 target_work(ls_wunit_k1) = 0.134 | | occupancies: max = 1.00 min = 0.01 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.3546 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7599 moved from start: 0.2417 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.069 5695 Z= 0.133 Angle : 0.704 13.577 7768 Z= 0.358 Chirality : 0.046 0.159 864 Planarity : 0.006 0.097 1002 Dihedral : 4.958 27.536 821 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 7.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.51 % Favored : 94.49 % Rotamer: Outliers : 3.05 % Allowed : 20.06 % Favored : 76.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.32 % 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 (0.31), residues: 713 helix: -3.30 (0.86), residues: 21 sheet: 0.47 (0.34), residues: 238 loop : -1.19 (0.28), residues: 454 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 436 HIS 0.002 0.001 HIS H 35 PHE 0.025 0.002 PHE A 456 TYR 0.016 0.001 TYR L 91 ARG 0.008 0.001 ARG H 83 Details of bonding type rmsd link_NAG-ASN : bond 0.01322 ( 1) link_NAG-ASN : angle 4.44708 ( 3) link_BETA1-4 : bond 0.00423 ( 1) link_BETA1-4 : angle 3.11581 ( 3) hydrogen bonds : bond 0.03348 ( 144) hydrogen bonds : angle 5.67149 ( 402) SS BOND : bond 0.00793 ( 10) SS BOND : angle 1.63055 ( 20) covalent geometry : bond 0.00311 ( 5683) covalent geometry : angle 0.69208 ( 7742) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1426 Ramachandran restraints generated. 713 Oldfield, 0 Emsley, 713 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1426 Ramachandran restraints generated. 713 Oldfield, 0 Emsley, 713 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 619 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 64 time to evaluate : 0.571 Fit side-chains revert: symmetry clash REVERT: A 495 TYR cc_start: 0.4139 (OUTLIER) cc_final: 0.1828 (m-80) REVERT: H 86 ASP cc_start: 0.8395 (t0) cc_final: 0.8017 (t0) outliers start: 19 outliers final: 17 residues processed: 78 average time/residue: 0.2031 time to fit residues: 20.1924 Evaluate side-chains 80 residues out of total 619 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 62 time to evaluate : 0.581 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 495 TYR Chi-restraints excluded: chain H residue 35 HIS Chi-restraints excluded: chain H residue 67 VAL Chi-restraints excluded: chain H residue 80 MET Chi-restraints excluded: chain H residue 107 THR Chi-restraints excluded: chain H residue 143 LEU Chi-restraints excluded: chain H residue 192 THR Chi-restraints excluded: chain H residue 208 CYS Chi-restraints excluded: chain H residue 210 VAL Chi-restraints excluded: chain L residue 52 SER Chi-restraints excluded: chain L residue 97 THR Chi-restraints excluded: chain L residue 109 THR Chi-restraints excluded: chain L residue 135 LEU Chi-restraints excluded: chain L residue 150 VAL Chi-restraints excluded: chain L residue 196 VAL Chi-restraints excluded: chain L residue 197 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 71 random chunks: chunk 16 optimal weight: 0.8980 chunk 17 optimal weight: 0.1980 chunk 36 optimal weight: 0.9990 chunk 68 optimal weight: 5.9990 chunk 62 optimal weight: 0.9980 chunk 41 optimal weight: 7.9990 chunk 28 optimal weight: 0.0670 chunk 37 optimal weight: 0.2980 chunk 34 optimal weight: 0.9990 chunk 2 optimal weight: 1.9990 chunk 24 optimal weight: 0.0970 overall best weight: 0.3116 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 147 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 = 0.3939 r_free = 0.3939 target = 0.167627 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3813 r_free = 0.3813 target = 0.155515 restraints weight = 17139.588| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3664 r_free = 0.3664 target = 0.143644 restraints weight = 16016.014| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3617 r_free = 0.3617 target = 0.139979 restraints weight = 22794.514| |-----------------------------------------------------------------------------| r_work (final): 0.3471 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3471 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3471 r_free = 0.3471 target_work(ls_wunit_k1) = 0.127 | | occupancies: max = 1.00 min = 0.01 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3471 r_free = 0.3471 target_work(ls_wunit_k1) = 0.127 | | occupancies: max = 1.00 min = 0.01 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.3471 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7710 moved from start: 0.2477 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.069 5695 Z= 0.125 Angle : 0.689 13.520 7768 Z= 0.350 Chirality : 0.046 0.155 864 Planarity : 0.006 0.100 1002 Dihedral : 4.759 28.751 821 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 6.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.36 % Favored : 93.64 % Rotamer: Outliers : 2.57 % Allowed : 20.71 % Favored : 76.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.32 % 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: -0.81 (0.31), residues: 713 helix: -3.15 (0.88), residues: 21 sheet: 0.74 (0.35), residues: 228 loop : -1.14 (0.28), residues: 464 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 436 HIS 0.002 0.001 HIS H 35 PHE 0.012 0.001 PHE A 456 TYR 0.015 0.001 TYR L 91 ARG 0.004 0.000 ARG A 509 Details of bonding type rmsd link_NAG-ASN : bond 0.01284 ( 1) link_NAG-ASN : angle 4.49220 ( 3) link_BETA1-4 : bond 0.00403 ( 1) link_BETA1-4 : angle 3.01503 ( 3) hydrogen bonds : bond 0.03208 ( 144) hydrogen bonds : angle 5.48730 ( 402) SS BOND : bond 0.00736 ( 10) SS BOND : angle 1.94187 ( 20) covalent geometry : bond 0.00290 ( 5683) covalent geometry : angle 0.67508 ( 7742) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1426 Ramachandran restraints generated. 713 Oldfield, 0 Emsley, 713 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1426 Ramachandran restraints generated. 713 Oldfield, 0 Emsley, 713 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 619 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 65 time to evaluate : 0.574 Fit side-chains revert: symmetry clash REVERT: A 495 TYR cc_start: 0.4344 (OUTLIER) cc_final: 0.1983 (m-80) REVERT: H 86 ASP cc_start: 0.8320 (t0) cc_final: 0.7945 (t0) outliers start: 16 outliers final: 13 residues processed: 76 average time/residue: 0.1976 time to fit residues: 19.5000 Evaluate side-chains 78 residues out of total 619 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 64 time to evaluate : 0.654 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 495 TYR Chi-restraints excluded: chain H residue 35 HIS Chi-restraints excluded: chain H residue 67 VAL Chi-restraints excluded: chain H residue 80 MET Chi-restraints excluded: chain H residue 143 LEU Chi-restraints excluded: chain H residue 192 THR Chi-restraints excluded: chain H residue 208 CYS Chi-restraints excluded: chain H residue 210 VAL Chi-restraints excluded: chain L residue 52 SER Chi-restraints excluded: chain L residue 97 THR Chi-restraints excluded: chain L residue 109 THR Chi-restraints excluded: chain L residue 150 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 71 random chunks: chunk 64 optimal weight: 4.9990 chunk 38 optimal weight: 0.8980 chunk 67 optimal weight: 3.9990 chunk 31 optimal weight: 2.9990 chunk 68 optimal weight: 0.9990 chunk 45 optimal weight: 0.2980 chunk 42 optimal weight: 0.7980 chunk 32 optimal weight: 0.7980 chunk 2 optimal weight: 6.9990 chunk 15 optimal weight: 0.8980 chunk 28 optimal weight: 0.5980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 147 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 = 0.3926 r_free = 0.3926 target = 0.166328 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3557 r_free = 0.3557 target = 0.135962 restraints weight = 27610.379| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3572 r_free = 0.3572 target = 0.137974 restraints weight = 24083.787| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3579 r_free = 0.3579 target = 0.138181 restraints weight = 12422.868| |-----------------------------------------------------------------------------| r_work (final): 0.3383 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3383 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3383 r_free = 0.3383 target_work(ls_wunit_k1) = 0.120 | | occupancies: max = 1.00 min = 0.01 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3383 r_free = 0.3383 target_work(ls_wunit_k1) = 0.120 | | occupancies: max = 1.00 min = 0.01 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.3383 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7823 moved from start: 0.2578 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.069 5695 Z= 0.161 Angle : 0.727 13.828 7768 Z= 0.370 Chirality : 0.047 0.165 864 Planarity : 0.006 0.092 1002 Dihedral : 4.931 27.796 821 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 6.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.93 % Favored : 94.07 % Rotamer: Outliers : 3.05 % Allowed : 20.06 % Favored : 76.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.32 % 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 (0.31), residues: 713 helix: -3.26 (0.86), residues: 21 sheet: 0.55 (0.35), residues: 238 loop : -1.18 (0.28), residues: 454 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 436 HIS 0.002 0.001 HIS H 212 PHE 0.023 0.002 PHE A 456 TYR 0.021 0.002 TYR L 92 ARG 0.004 0.001 ARG A 509 Details of bonding type rmsd link_NAG-ASN : bond 0.01293 ( 1) link_NAG-ASN : angle 4.38188 ( 3) link_BETA1-4 : bond 0.00446 ( 1) link_BETA1-4 : angle 2.96546 ( 3) hydrogen bonds : bond 0.03565 ( 144) hydrogen bonds : angle 5.58803 ( 402) SS BOND : bond 0.00828 ( 10) SS BOND : angle 2.24804 ( 20) covalent geometry : bond 0.00390 ( 5683) covalent geometry : angle 0.71203 ( 7742) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2564.40 seconds wall clock time: 45 minutes 25.75 seconds (2725.75 seconds total)