Starting phenix.real_space_refine on Tue Feb 11 12:25:47 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8d48_27177/02_2025/8d48_27177.cif Found real_map, /net/cci-nas-00/data/ceres_data/8d48_27177/02_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_27177/02_2025/8d48_27177.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8d48_27177/02_2025/8d48_27177.map" model { file = "/net/cci-nas-00/data/ceres_data/8d48_27177/02_2025/8d48_27177.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8d48_27177/02_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): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/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: 6.58, per 1000 atoms: 1.19 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: 1.40 Conformation dependent library (CDL) restraints added in 1.3 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: 0.72 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: 1.89 Time building geometry restraints manager: 1.62 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: 5.220 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: 0.020 Extract box with map and model: 0.210 Check model and map are aligned: 0.050 Set scattering table: 0.080 Process input model: 20.920 Find NCS groups from input model: 0.070 Set up NCS constraints: 0.040 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:2.730 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.340 ------------------------------------------------------------------------------- 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 5683 Z= 0.302 Angle : 0.807 15.589 7742 Z= 0.472 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 *********************** 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 : 0.583 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: 0.1991 time to fit residues: 21.7057 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 : 0.606 ------------------------------------------------------------------------------- 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: 2.9990 chunk 18 optimal weight: 0.9980 chunk 36 optimal weight: 0.7980 chunk 28 optimal weight: 1.9990 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: 0.4214 ------------------------------------------------------------------------------- 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 = 0.3885 r_free = 0.3885 target = 0.164098 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.129629 restraints weight = 20788.575| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.131349 restraints weight = 23763.010| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.131226 restraints weight = 10838.418| |-----------------------------------------------------------------------------| r_work (final): 0.3413 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3413 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3413 r_free = 0.3413 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 = 0.3412 r_free = 0.3412 target_work(ls_wunit_k1) = 0.123 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.3412 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7762 moved from start: 0.1119 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.067 5683 Z= 0.216 Angle : 0.706 13.847 7742 Z= 0.359 Chirality : 0.047 0.165 864 Planarity : 0.007 0.108 1002 Dihedral : 6.816 69.605 821 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 6.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.21 % Favored : 93.79 % Rotamer: Outliers : 2.57 % Allowed : 19.74 % Favored : 77.69 % 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: -0.91 (0.31), residues: 713 helix: -3.15 (0.89), residues: 21 sheet: 0.55 (0.35), residues: 226 loop : -1.13 (0.28), residues: 466 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 0.017 0.001 TYR L 92 ARG 0.007 0.001 ARG A 509 *********************** 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 89 residues out of total 619 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 73 time to evaluate : 0.492 Fit side-chains revert: symmetry clash REVERT: A 409 GLN cc_start: 0.7545 (tp-100) cc_final: 0.7299 (tp40) REVERT: H 178 LEU cc_start: 0.8568 (OUTLIER) cc_final: 0.8338 (tt) REVERT: L 81 GLU cc_start: 0.8318 (pp20) cc_final: 0.8009 (pp20) outliers start: 16 outliers final: 8 residues processed: 86 average time/residue: 0.2068 time to fit residues: 22.9741 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 : 0.640 ------------------------------------------------------------------------------- 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 35 HIS Chi-restraints excluded: chain H residue 67 VAL 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 109 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: 0.0980 chunk 55 optimal weight: 0.1980 chunk 32 optimal weight: 0.4980 chunk 59 optimal weight: 0.0980 chunk 9 optimal weight: 3.9990 chunk 21 optimal weight: 2.9990 chunk 37 optimal weight: 0.5980 chunk 46 optimal weight: 5.9990 chunk 24 optimal weight: 0.5980 chunk 48 optimal weight: 0.7980 chunk 66 optimal weight: 2.9990 overall best weight: 0.2980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 506 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 = 0.3887 r_free = 0.3887 target = 0.164127 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3506 r_free = 0.3506 target = 0.131512 restraints weight = 21924.547| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.132963 restraints weight = 25708.547| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.133370 restraints weight = 8589.707| |-----------------------------------------------------------------------------| r_work (final): 0.3468 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3468 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3468 r_free = 0.3468 target_work(ls_wunit_k1) = 0.127 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3468 r_free = 0.3468 target_work(ls_wunit_k1) = 0.127 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.3468 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7692 moved from start: 0.1341 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 5683 Z= 0.185 Angle : 0.654 13.571 7742 Z= 0.339 Chirality : 0.046 0.194 864 Planarity : 0.006 0.077 1002 Dihedral : 5.116 38.640 821 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 6.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.79 % Favored : 94.21 % Rotamer: Outliers : 2.25 % Allowed : 20.22 % 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: -0.85 (0.31), residues: 713 helix: -3.01 (0.91), residues: 21 sheet: 0.62 (0.35), residues: 226 loop : -1.10 (0.28), residues: 466 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 436 HIS 0.003 0.001 HIS H 35 PHE 0.012 0.001 PHE A 374 TYR 0.015 0.001 TYR L 49 ARG 0.005 0.001 ARG L 54 *********************** 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 : 0.562 Fit side-chains revert: symmetry clash REVERT: H 156 SER cc_start: 0.7991 (OUTLIER) cc_final: 0.7693 (m) REVERT: H 178 LEU cc_start: 0.8623 (OUTLIER) cc_final: 0.8419 (tt) REVERT: L 81 GLU cc_start: 0.8186 (pp20) cc_final: 0.7871 (pp20) outliers start: 14 outliers final: 8 residues processed: 80 average time/residue: 0.1854 time to fit residues: 19.1832 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 : 0.592 ------------------------------------------------------------------------------- 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 35 HIS Chi-restraints excluded: chain H residue 67 VAL 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 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: 0.0020 chunk 40 optimal weight: 5.9990 chunk 6 optimal weight: 0.9980 chunk 11 optimal weight: 0.7980 chunk 38 optimal weight: 0.2980 chunk 10 optimal weight: 1.9990 chunk 28 optimal weight: 0.9980 chunk 0 optimal weight: 2.9990 chunk 47 optimal weight: 0.9990 chunk 60 optimal weight: 3.9990 chunk 58 optimal weight: 1.9990 overall best weight: 0.6188 ------------------------------------------------------------------------------- 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 = 0.3831 r_free = 0.3831 target = 0.158885 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.124679 restraints weight = 24799.403| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.126159 restraints weight = 23423.945| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.126095 restraints weight = 10059.123| |-----------------------------------------------------------------------------| r_work (final): 0.3355 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3360 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3360 r_free = 0.3360 target_work(ls_wunit_k1) = 0.119 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3360 r_free = 0.3360 target_work(ls_wunit_k1) = 0.119 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.3360 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7821 moved from start: 0.1703 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.068 5683 Z= 0.237 Angle : 0.686 13.693 7742 Z= 0.354 Chirality : 0.047 0.168 864 Planarity : 0.006 0.061 1002 Dihedral : 5.176 35.638 821 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 6.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.21 % Favored : 93.79 % Rotamer: Outliers : 3.37 % Allowed : 18.78 % 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: -0.93 (0.32), residues: 713 helix: -3.04 (0.91), residues: 21 sheet: 0.40 (0.35), residues: 237 loop : -1.10 (0.29), residues: 455 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 0.016 0.002 PHE A 543 TYR 0.023 0.001 TYR L 92 ARG 0.004 0.001 ARG A 509 *********************** 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 91 residues out of total 619 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 70 time to evaluate : 0.592 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 69 MET cc_start: 0.8293 (mtm) cc_final: 0.8021 (mtt) REVERT: H 86 ASP cc_start: 0.8495 (t0) cc_final: 0.8244 (t0) REVERT: H 156 SER cc_start: 0.8116 (OUTLIER) cc_final: 0.7869 (m) REVERT: L 81 GLU cc_start: 0.8301 (pp20) cc_final: 0.7966 (pp20) outliers start: 21 outliers final: 15 residues processed: 85 average time/residue: 0.2026 time to fit residues: 21.7816 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 : 0.771 ------------------------------------------------------------------------------- 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 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 80 MET Chi-restraints excluded: chain H residue 94 ARG 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 196 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 71 random chunks: chunk 50 optimal weight: 0.0970 chunk 13 optimal weight: 3.9990 chunk 54 optimal weight: 0.7980 chunk 56 optimal weight: 0.9980 chunk 60 optimal weight: 1.9990 chunk 11 optimal weight: 2.9990 chunk 33 optimal weight: 0.9990 chunk 9 optimal weight: 1.9990 chunk 5 optimal weight: 0.9980 chunk 51 optimal weight: 0.5980 chunk 24 optimal weight: 0.9990 overall best weight: 0.6978 ------------------------------------------------------------------------------- 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 = 0.3967 r_free = 0.3967 target = 0.169682 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.134550 restraints weight = 22006.342| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.137141 restraints weight = 21727.532| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3555 r_free = 0.3555 target = 0.138023 restraints weight = 15468.546| |-----------------------------------------------------------------------------| r_work (final): 0.3313 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3312 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3312 r_free = 0.3312 target_work(ls_wunit_k1) = 0.115 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3312 r_free = 0.3312 target_work(ls_wunit_k1) = 0.115 | | occupancies: max = 1.00 min = 0.01 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.3312 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7905 moved from start: 0.1808 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.068 5683 Z= 0.248 Angle : 0.690 13.682 7742 Z= 0.358 Chirality : 0.046 0.163 864 Planarity : 0.005 0.054 1002 Dihedral : 5.152 33.221 821 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 6.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.93 % Favored : 94.07 % Rotamer: Outliers : 4.17 % Allowed : 18.30 % 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: -0.99 (0.31), residues: 713 helix: -3.05 (0.93), residues: 21 sheet: 0.34 (0.34), residues: 238 loop : -1.14 (0.29), residues: 454 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 436 HIS 0.002 0.001 HIS H 35 PHE 0.015 0.002 PHE A 562 TYR 0.019 0.001 TYR L 49 ARG 0.003 0.000 ARG A 357 *********************** 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 95 residues out of total 619 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 69 time to evaluate : 0.640 Fit side-chains revert: symmetry clash REVERT: H 86 ASP cc_start: 0.8434 (t0) cc_final: 0.8183 (t0) REVERT: H 156 SER cc_start: 0.8114 (OUTLIER) cc_final: 0.7905 (m) REVERT: L 81 GLU cc_start: 0.8278 (pp20) cc_final: 0.8047 (pp20) outliers start: 26 outliers final: 20 residues processed: 89 average time/residue: 0.2094 time to fit residues: 24.1199 Evaluate side-chains 89 residues out of total 619 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 68 time to evaluate : 0.673 ------------------------------------------------------------------------------- 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 94 ARG Chi-restraints excluded: chain H residue 107 THR 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 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 135 LEU Chi-restraints excluded: chain L residue 150 VAL 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: 0.1980 chunk 59 optimal weight: 0.1980 chunk 10 optimal weight: 2.9990 chunk 6 optimal weight: 1.9990 chunk 48 optimal weight: 0.1980 chunk 3 optimal weight: 0.6980 chunk 55 optimal weight: 0.8980 chunk 42 optimal weight: 0.2980 chunk 16 optimal weight: 7.9990 chunk 20 optimal weight: 0.0470 chunk 9 optimal weight: 0.9990 overall best weight: 0.1878 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 506 GLN A 580 GLN ** L 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3861 r_free = 0.3861 target = 0.162043 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.127246 restraints weight = 20578.753| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.127951 restraints weight = 23202.952| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.128758 restraints weight = 13514.422| |-----------------------------------------------------------------------------| r_work (final): 0.3376 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3378 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3378 r_free = 0.3378 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 = 0.3378 r_free = 0.3378 target_work(ls_wunit_k1) = 0.120 | | occupancies: max = 1.00 min = 0.01 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.3378 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7788 moved from start: 0.1975 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.067 5683 Z= 0.161 Angle : 0.638 13.065 7742 Z= 0.328 Chirality : 0.045 0.149 864 Planarity : 0.005 0.049 1002 Dihedral : 4.687 26.298 821 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 6.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.51 % Favored : 94.49 % Rotamer: Outliers : 2.89 % Allowed : 19.26 % 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: -0.75 (0.31), residues: 713 helix: -2.88 (0.93), residues: 21 sheet: 0.71 (0.35), residues: 226 loop : -1.06 (0.28), 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 0.012 0.001 TYR L 91 ARG 0.003 0.000 ARG A 509 *********************** 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 87 residues out of total 619 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 69 time to evaluate : 0.684 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 156 SER cc_start: 0.7990 (OUTLIER) cc_final: 0.7765 (m) REVERT: L 81 GLU cc_start: 0.8246 (pp20) cc_final: 0.7926 (pp20) outliers start: 18 outliers final: 14 residues processed: 84 average time/residue: 0.1971 time to fit residues: 21.3312 Evaluate side-chains 83 residues out of total 619 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 68 time to evaluate : 0.606 ------------------------------------------------------------------------------- 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 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 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 L residue 52 SER Chi-restraints excluded: chain L residue 97 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 71 random chunks: chunk 55 optimal weight: 0.4980 chunk 65 optimal weight: 0.9990 chunk 18 optimal weight: 4.9990 chunk 5 optimal weight: 0.9990 chunk 3 optimal weight: 0.6980 chunk 67 optimal weight: 0.5980 chunk 0 optimal weight: 2.9990 chunk 60 optimal weight: 3.9990 chunk 17 optimal weight: 0.9990 chunk 21 optimal weight: 0.9980 chunk 66 optimal weight: 0.4980 overall best weight: 0.6580 ------------------------------------------------------------------------------- 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** A 580 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 = 0.3822 r_free = 0.3822 target = 0.158537 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.124213 restraints weight = 24536.817| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.125165 restraints weight = 25248.048| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.125821 restraints weight = 9328.679| |-----------------------------------------------------------------------------| r_work (final): 0.3342 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3342 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3342 r_free = 0.3342 target_work(ls_wunit_k1) = 0.117 | | occupancies: max = 1.00 min = 0.01 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3342 r_free = 0.3342 target_work(ls_wunit_k1) = 0.117 | | occupancies: max = 1.00 min = 0.01 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.3342 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7841 moved from start: 0.2017 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.068 5683 Z= 0.240 Angle : 0.668 13.429 7742 Z= 0.345 Chirality : 0.046 0.154 864 Planarity : 0.005 0.050 1002 Dihedral : 4.814 27.236 821 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 6.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.79 % Favored : 94.21 % Rotamer: Outliers : 3.69 % Allowed : 18.62 % Favored : 77.69 % 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: -0.80 (0.31), residues: 713 helix: -2.99 (0.92), residues: 21 sheet: 0.77 (0.35), residues: 226 loop : -1.14 (0.28), residues: 466 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 436 HIS 0.002 0.001 HIS H 35 PHE 0.012 0.001 PHE A 562 TYR 0.018 0.002 TYR L 49 ARG 0.004 0.000 ARG A 509 *********************** 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 94 residues out of total 619 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 71 time to evaluate : 0.639 Fit side-chains revert: symmetry clash REVERT: L 81 GLU cc_start: 0.8303 (pp20) cc_final: 0.7952 (pp20) REVERT: L 134 CYS cc_start: 0.7034 (OUTLIER) cc_final: 0.6683 (t) outliers start: 23 outliers final: 19 residues processed: 89 average time/residue: 0.2020 time to fit residues: 23.1617 Evaluate side-chains 90 residues out of total 619 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 70 time to evaluate : 0.571 ------------------------------------------------------------------------------- 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 11 VAL Chi-restraints excluded: chain H residue 35 HIS Chi-restraints excluded: chain H residue 37 VAL 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 94 ARG 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 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: 0.8980 chunk 24 optimal weight: 0.9990 chunk 47 optimal weight: 4.9990 chunk 38 optimal weight: 0.3980 chunk 62 optimal weight: 6.9990 chunk 39 optimal weight: 0.8980 chunk 29 optimal weight: 0.8980 chunk 59 optimal weight: 0.9980 chunk 2 optimal weight: 0.3980 chunk 1 optimal weight: 0.3980 overall best weight: 0.5980 ------------------------------------------------------------------------------- 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 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 = 0.3807 r_free = 0.3807 target = 0.157196 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.121722 restraints weight = 18599.331| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.123189 restraints weight = 21456.527| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.123189 restraints weight = 12267.022| |-----------------------------------------------------------------------------| r_work (final): 0.3282 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3285 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3285 r_free = 0.3285 target_work(ls_wunit_k1) = 0.113 | | occupancies: max = 1.00 min = 0.01 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3285 r_free = 0.3285 target_work(ls_wunit_k1) = 0.113 | | occupancies: max = 1.00 min = 0.01 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.3285 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7906 moved from start: 0.2226 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.068 5683 Z= 0.223 Angle : 0.673 13.523 7742 Z= 0.348 Chirality : 0.046 0.157 864 Planarity : 0.005 0.048 1002 Dihedral : 4.833 26.677 821 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 6.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.79 % Favored : 94.21 % Rotamer: Outliers : 2.57 % Allowed : 20.55 % 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: -0.87 (0.31), residues: 713 helix: -3.10 (0.89), residues: 21 sheet: 0.63 (0.34), residues: 235 loop : -1.16 (0.28), residues: 457 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 436 HIS 0.002 0.001 HIS H 35 PHE 0.013 0.002 PHE A 347 TYR 0.018 0.001 TYR L 49 ARG 0.003 0.000 ARG L 142 *********************** 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 84 residues out of total 619 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 68 time to evaluate : 0.636 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: L 81 GLU cc_start: 0.8380 (pp20) cc_final: 0.8012 (pp20) outliers start: 16 outliers final: 15 residues processed: 82 average time/residue: 0.2058 time to fit residues: 21.7213 Evaluate side-chains 79 residues out of total 619 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 64 time to evaluate : 0.614 ------------------------------------------------------------------------------- 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 506 GLN Chi-restraints excluded: chain H residue 11 VAL Chi-restraints excluded: chain H residue 35 HIS Chi-restraints excluded: chain H residue 67 VAL Chi-restraints excluded: chain H residue 143 LEU Chi-restraints excluded: chain H residue 208 CYS Chi-restraints excluded: chain L residue 52 SER Chi-restraints excluded: chain L residue 97 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: 0.6980 chunk 41 optimal weight: 0.9990 chunk 18 optimal weight: 3.9990 chunk 66 optimal weight: 1.9990 chunk 46 optimal weight: 3.9990 chunk 13 optimal weight: 1.9990 chunk 40 optimal weight: 4.9990 chunk 36 optimal weight: 0.9980 chunk 70 optimal weight: 0.9990 chunk 10 optimal weight: 1.9990 chunk 65 optimal weight: 0.3980 overall best weight: 0.8184 ------------------------------------------------------------------------------- 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 = 0.3795 r_free = 0.3795 target = 0.155923 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.3580 r_free = 0.3580 target = 0.136686 restraints weight = 11954.694| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.130990 restraints weight = 19591.010| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.130521 restraints weight = 9709.598| |-----------------------------------------------------------------------------| r_work (final): 0.3438 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3439 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3439 r_free = 0.3439 target_work(ls_wunit_k1) = 0.125 | | occupancies: max = 1.00 min = 0.01 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3439 r_free = 0.3439 target_work(ls_wunit_k1) = 0.125 | | occupancies: max = 1.00 min = 0.01 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.3439 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7740 moved from start: 0.2308 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.069 5683 Z= 0.278 Angle : 0.707 13.705 7742 Z= 0.365 Chirality : 0.047 0.168 864 Planarity : 0.005 0.049 1002 Dihedral : 4.978 27.220 821 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 6.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.93 % Favored : 94.07 % Rotamer: Outliers : 3.53 % Allowed : 20.06 % Favored : 76.40 % 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: -0.91 (0.31), residues: 713 helix: -3.17 (0.87), residues: 21 sheet: 0.58 (0.34), residues: 235 loop : -1.17 (0.28), residues: 457 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 0.023 0.002 PHE A 456 TYR 0.021 0.002 TYR L 92 ARG 0.003 0.000 ARG A 509 *********************** 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 89 residues out of total 619 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 67 time to evaluate : 0.597 Fit side-chains revert: symmetry clash REVERT: L 81 GLU cc_start: 0.8224 (pp20) cc_final: 0.7901 (pp20) outliers start: 22 outliers final: 20 residues processed: 84 average time/residue: 0.2041 time to fit residues: 21.7474 Evaluate side-chains 84 residues out of total 619 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 64 time to evaluate : 0.590 ------------------------------------------------------------------------------- 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 557 LYS Chi-restraints excluded: chain H residue 35 HIS Chi-restraints excluded: chain H residue 37 VAL 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 94 ARG 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 71 random chunks: chunk 16 optimal weight: 0.0060 chunk 17 optimal weight: 0.6980 chunk 36 optimal weight: 0.5980 chunk 68 optimal weight: 5.9990 chunk 62 optimal weight: 6.9990 chunk 41 optimal weight: 1.9990 chunk 28 optimal weight: 1.9990 chunk 37 optimal weight: 0.4980 chunk 34 optimal weight: 0.9980 chunk 2 optimal weight: 0.8980 chunk 24 optimal weight: 0.9980 overall best weight: 0.5396 ------------------------------------------------------------------------------- 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 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 = 0.3797 r_free = 0.3797 target = 0.156593 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.133072 restraints weight = 17711.971| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.133081 restraints weight = 23039.452| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.131671 restraints weight = 7352.140| |-----------------------------------------------------------------------------| r_work (final): 0.3479 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3480 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3480 r_free = 0.3480 target_work(ls_wunit_k1) = 0.128 | | occupancies: max = 1.00 min = 0.01 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3480 r_free = 0.3480 target_work(ls_wunit_k1) = 0.128 | | occupancies: max = 1.00 min = 0.01 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.3480 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7666 moved from start: 0.2409 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.070 5683 Z= 0.213 Angle : 0.679 13.616 7742 Z= 0.351 Chirality : 0.046 0.162 864 Planarity : 0.005 0.047 1002 Dihedral : 4.866 27.007 821 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 6.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.65 % Favored : 94.35 % Rotamer: Outliers : 3.69 % Allowed : 20.39 % Favored : 75.92 % 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: -3.18 (0.87), residues: 21 sheet: 0.38 (0.33), residues: 260 loop : -1.14 (0.29), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 436 HIS 0.002 0.001 HIS H 35 PHE 0.015 0.002 PHE A 497 TYR 0.017 0.002 TYR L 49 ARG 0.003 0.000 ARG A 357 ********************** 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 88 residues out of total 619 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 65 time to evaluate : 0.625 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 23 outliers final: 21 residues processed: 83 average time/residue: 0.2135 time to fit residues: 22.4690 Evaluate side-chains 85 residues out of total 619 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 64 time to evaluate : 0.577 ------------------------------------------------------------------------------- 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 506 GLN Chi-restraints excluded: chain A residue 557 LYS 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 71 random chunks: chunk 64 optimal weight: 4.9990 chunk 38 optimal weight: 0.5980 chunk 67 optimal weight: 4.9990 chunk 31 optimal weight: 1.9990 chunk 68 optimal weight: 4.9990 chunk 45 optimal weight: 0.0270 chunk 42 optimal weight: 0.9980 chunk 32 optimal weight: 0.1980 chunk 2 optimal weight: 3.9990 chunk 15 optimal weight: 0.0970 chunk 28 optimal weight: 0.5980 overall best weight: 0.3036 ------------------------------------------------------------------------------- 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 ** 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 = 0.3951 r_free = 0.3951 target = 0.168680 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3572 r_free = 0.3572 target = 0.137058 restraints weight = 27736.980| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3579 r_free = 0.3579 target = 0.138337 restraints weight = 25127.856| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3588 r_free = 0.3588 target = 0.138951 restraints weight = 12208.185| |-----------------------------------------------------------------------------| r_work (final): 0.3401 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3401 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3401 r_free = 0.3401 target_work(ls_wunit_k1) = 0.122 | | occupancies: max = 1.00 min = 0.01 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3401 r_free = 0.3401 target_work(ls_wunit_k1) = 0.122 | | occupancies: max = 1.00 min = 0.01 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.3401 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7793 moved from start: 0.2440 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.069 5683 Z= 0.180 Angle : 0.667 13.521 7742 Z= 0.343 Chirality : 0.046 0.154 864 Planarity : 0.006 0.098 1002 Dihedral : 4.778 27.921 821 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 6.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.07 % Favored : 93.93 % Rotamer: Outliers : 2.73 % Allowed : 21.35 % Favored : 75.92 % 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: -0.88 (0.31), residues: 713 helix: -3.14 (0.87), residues: 21 sheet: 0.59 (0.34), residues: 237 loop : -1.17 (0.28), residues: 455 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 436 HIS 0.002 0.000 HIS H 35 PHE 0.024 0.001 PHE A 456 TYR 0.015 0.001 TYR L 91 ARG 0.004 0.000 ARG A 509 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2437.45 seconds wall clock time: 44 minutes 29.34 seconds (2669.34 seconds total)