Starting phenix.real_space_refine on Thu Mar 6 09:05:38 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8d48_27177/03_2025/8d48_27177.cif Found real_map, /net/cci-nas-00/data/ceres_data/8d48_27177/03_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_27177/03_2025/8d48_27177.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8d48_27177/03_2025/8d48_27177.map" model { file = "/net/cci-nas-00/data/ceres_data/8d48_27177/03_2025/8d48_27177.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8d48_27177/03_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-5624/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: 6.11, per 1000 atoms: 1.10 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: 1.43 Conformation dependent library (CDL) restraints added in 1.2 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: 0.85 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: 1.79 Time building geometry restraints manager: 1.72 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: 3.650 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.200 Check model and map are aligned: 0.040 Set scattering table: 0.050 Process input model: 20.520 Find NCS groups from input model: 0.090 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:2.850 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.450 ------------------------------------------------------------------------------- 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 : 0.559 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: 0.1822 time to fit residues: 19.9423 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 : 0.552 ------------------------------------------------------------------------------- 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 = 0.3883 r_free = 0.3883 target = 0.164028 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.129429 restraints weight = 20787.664| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.131107 restraints weight = 23686.529| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.130873 restraints weight = 11136.062| |-----------------------------------------------------------------------------| r_work (final): 0.3410 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3412 |-occupancy refinement: start-------------------------------------------------| | 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: 9 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3411 r_free = 0.3411 target_work(ls_wunit_k1) = 0.123 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.3411 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7767 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 69.604 821 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 : 0.580 Fit side-chains revert: symmetry clash REVERT: A 409 GLN cc_start: 0.7565 (tp-100) cc_final: 0.7318 (tp40) REVERT: H 178 LEU cc_start: 0.8577 (OUTLIER) cc_final: 0.8349 (tt) REVERT: L 81 GLU cc_start: 0.8316 (pp20) cc_final: 0.8007 (pp20) outliers start: 16 outliers final: 8 residues processed: 86 average time/residue: 0.1911 time to fit residues: 21.1336 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 : 0.602 ------------------------------------------------------------------------------- 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: 0.0770 chunk 55 optimal weight: 0.1980 chunk 32 optimal weight: 0.4980 chunk 59 optimal weight: 0.5980 chunk 9 optimal weight: 3.9990 chunk 21 optimal weight: 3.9990 chunk 37 optimal weight: 0.5980 chunk 46 optimal weight: 1.9990 chunk 24 optimal weight: 0.8980 chunk 48 optimal weight: 0.7980 chunk 66 optimal weight: 1.9990 overall best weight: 0.3938 ------------------------------------------------------------------------------- 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 = 0.3872 r_free = 0.3872 target = 0.162782 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.126429 restraints weight = 21917.532| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.127762 restraints weight = 23807.703| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.128387 restraints weight = 12403.312| |-----------------------------------------------------------------------------| r_work (final): 0.3368 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3367 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3367 r_free = 0.3367 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 = 0.3367 r_free = 0.3367 target_work(ls_wunit_k1) = 0.119 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.3367 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7820 moved from start: 0.1403 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= 0.196 Angle : 0.663 13.644 7742 Z= 0.343 Chirality : 0.046 0.198 864 Planarity : 0.006 0.075 1002 Dihedral : 5.264 44.789 821 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 6.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.79 % Favored : 94.21 % Rotamer: Outliers : 2.73 % Allowed : 19.74 % 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: -3.05 (0.89), residues: 21 sheet: 0.62 (0.35), residues: 226 loop : -1.13 (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 0.014 0.001 PHE A 497 TYR 0.017 0.001 TYR L 49 ARG 0.006 0.001 ARG H 83 *********************** 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 85 residues out of total 619 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 68 time to evaluate : 0.580 Fit side-chains revert: symmetry clash REVERT: H 156 SER cc_start: 0.7936 (OUTLIER) cc_final: 0.7674 (m) REVERT: H 178 LEU cc_start: 0.8565 (OUTLIER) cc_final: 0.8354 (tt) REVERT: L 81 GLU cc_start: 0.8335 (pp20) cc_final: 0.8026 (pp20) outliers start: 17 outliers final: 9 residues processed: 83 average time/residue: 0.1948 time to fit residues: 20.8318 Evaluate side-chains 78 residues out of total 619 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 67 time to evaluate : 0.556 ------------------------------------------------------------------------------- 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 52 SER 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: 0.0030 chunk 40 optimal weight: 4.9990 chunk 6 optimal weight: 0.0670 chunk 11 optimal weight: 0.5980 chunk 38 optimal weight: 1.9990 chunk 10 optimal weight: 0.0040 chunk 28 optimal weight: 0.5980 chunk 0 optimal weight: 2.9990 chunk 47 optimal weight: 3.9990 chunk 60 optimal weight: 2.9990 chunk 58 optimal weight: 0.6980 overall best weight: 0.2540 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3904 r_free = 0.3904 target = 0.165023 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.130849 restraints weight = 24606.617| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.132583 restraints weight = 24801.964| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.133480 restraints weight = 9948.711| |-----------------------------------------------------------------------------| r_work (final): 0.3430 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3430 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3430 r_free = 0.3430 target_work(ls_wunit_k1) = 0.124 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3430 r_free = 0.3430 target_work(ls_wunit_k1) = 0.124 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.3430 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7731 moved from start: 0.1657 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= 0.167 Angle : 0.632 13.214 7742 Z= 0.326 Chirality : 0.045 0.174 864 Planarity : 0.005 0.057 1002 Dihedral : 4.980 39.733 821 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 6.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.51 % Favored : 94.49 % Rotamer: Outliers : 3.37 % Allowed : 18.46 % Favored : 78.17 % 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: -0.77 (0.31), residues: 713 helix: -2.99 (0.92), residues: 21 sheet: 0.65 (0.35), residues: 226 loop : -1.03 (0.29), residues: 466 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 0.012 0.001 PHE A 374 TYR 0.012 0.001 TYR L 49 ARG 0.004 0.000 ARG A 357 *********************** 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 : 0.559 Fit side-chains revert: symmetry clash REVERT: H 156 SER cc_start: 0.7990 (OUTLIER) cc_final: 0.7732 (m) REVERT: H 178 LEU cc_start: 0.8601 (OUTLIER) cc_final: 0.8382 (tt) REVERT: L 81 GLU cc_start: 0.8265 (pp20) cc_final: 0.7934 (pp20) outliers start: 21 outliers final: 14 residues processed: 86 average time/residue: 0.1856 time to fit residues: 20.5650 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 : 0.637 ------------------------------------------------------------------------------- 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 156 SER Chi-restraints excluded: chain H residue 178 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 135 LEU Chi-restraints excluded: chain L residue 179 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: 0.3980 chunk 13 optimal weight: 2.9990 chunk 54 optimal weight: 0.8980 chunk 56 optimal weight: 1.9990 chunk 60 optimal weight: 7.9990 chunk 11 optimal weight: 0.9990 chunk 33 optimal weight: 0.0030 chunk 9 optimal weight: 0.1980 chunk 5 optimal weight: 0.5980 chunk 51 optimal weight: 0.0980 chunk 24 optimal weight: 0.9990 overall best weight: 0.2590 ------------------------------------------------------------------------------- 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** 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 = 0.3998 r_free = 0.3998 target = 0.172721 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.138337 restraints weight = 22221.881| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3604 r_free = 0.3604 target = 0.141376 restraints weight = 20917.546| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.141978 restraints weight = 14414.817| |-----------------------------------------------------------------------------| r_work (final): 0.3412 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3412 |-occupancy refinement: start-------------------------------------------------| | 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 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3412 r_free = 0.3412 target_work(ls_wunit_k1) = 0.123 | | occupancies: max = 1.00 min = 0.01 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.3412 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7779 moved from start: 0.1803 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= 0.164 Angle : 0.618 13.037 7742 Z= 0.319 Chirality : 0.045 0.146 864 Planarity : 0.005 0.050 1002 Dihedral : 4.825 39.082 821 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 6.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.37 % Favored : 94.63 % Rotamer: Outliers : 3.37 % Allowed : 18.62 % Favored : 78.01 % 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: -0.70 (0.31), residues: 713 helix: -2.82 (0.98), residues: 21 sheet: 0.69 (0.34), residues: 226 loop : -0.99 (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 0.010 0.001 PHE A 374 TYR 0.012 0.001 TYR L 49 ARG 0.004 0.000 ARG A 509 *********************** 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 91 residues out of total 619 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 70 time to evaluate : 0.632 Fit side-chains revert: symmetry clash REVERT: H 86 ASP cc_start: 0.7967 (t0) cc_final: 0.7693 (t0) REVERT: H 156 SER cc_start: 0.8054 (OUTLIER) cc_final: 0.7783 (m) REVERT: L 81 GLU cc_start: 0.8089 (pp20) cc_final: 0.7811 (pp20) outliers start: 21 outliers final: 13 residues processed: 86 average time/residue: 0.1993 time to fit residues: 22.0055 Evaluate side-chains 80 residues out of total 619 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 66 time to evaluate : 0.584 ------------------------------------------------------------------------------- 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 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 71 random chunks: chunk 37 optimal weight: 0.9990 chunk 59 optimal weight: 0.8980 chunk 10 optimal weight: 1.9990 chunk 6 optimal weight: 0.9980 chunk 48 optimal weight: 1.9990 chunk 3 optimal weight: 0.8980 chunk 55 optimal weight: 0.4980 chunk 42 optimal weight: 0.1980 chunk 16 optimal weight: 0.7980 chunk 20 optimal weight: 1.9990 chunk 9 optimal weight: 0.6980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3987 r_free = 0.3987 target = 0.171531 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.3597 r_free = 0.3597 target = 0.139074 restraints weight = 20004.461| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.140827 restraints weight = 22687.105| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.140902 restraints weight = 15108.879| |-----------------------------------------------------------------------------| r_work (final): 0.3393 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3393 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3393 r_free = 0.3393 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 = 0.3393 r_free = 0.3393 target_work(ls_wunit_k1) = 0.121 | | occupancies: max = 1.00 min = 0.01 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.3393 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7799 moved from start: 0.1983 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.067 5683 Z= 0.229 Angle : 0.687 13.377 7742 Z= 0.351 Chirality : 0.046 0.155 864 Planarity : 0.005 0.050 1002 Dihedral : 4.947 32.347 821 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 6.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.65 % Favored : 94.35 % Rotamer: Outliers : 3.21 % Allowed : 18.46 % 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: -0.74 (0.31), residues: 713 helix: -3.00 (0.94), residues: 21 sheet: 0.71 (0.34), residues: 226 loop : -1.04 (0.29), 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 0.015 0.002 PHE A 562 TYR 0.019 0.002 TYR L 49 ARG 0.004 0.001 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 92 residues out of total 619 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 72 time to evaluate : 0.669 Fit side-chains revert: symmetry clash REVERT: H 69 MET cc_start: 0.8444 (mtm) cc_final: 0.8235 (mtt) REVERT: H 156 SER cc_start: 0.8144 (OUTLIER) cc_final: 0.7904 (m) outliers start: 20 outliers final: 17 residues processed: 86 average time/residue: 0.1951 time to fit residues: 21.7911 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 : 0.675 ------------------------------------------------------------------------------- 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 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 196 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 71 random chunks: chunk 55 optimal weight: 0.3980 chunk 65 optimal weight: 0.7980 chunk 18 optimal weight: 0.8980 chunk 5 optimal weight: 0.8980 chunk 3 optimal weight: 0.9990 chunk 67 optimal weight: 0.5980 chunk 0 optimal weight: 2.9990 chunk 60 optimal weight: 0.0870 chunk 17 optimal weight: 6.9990 chunk 21 optimal weight: 0.8980 chunk 66 optimal weight: 0.9990 overall best weight: 0.5558 ------------------------------------------------------------------------------- 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 = 0.3945 r_free = 0.3945 target = 0.167786 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.132963 restraints weight = 23685.165| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.136155 restraints weight = 22395.242| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.136636 restraints weight = 14564.916| |-----------------------------------------------------------------------------| r_work (final): 0.3321 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3318 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3318 r_free = 0.3318 target_work(ls_wunit_k1) = 0.116 | | occupancies: max = 1.00 min = 0.01 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3318 r_free = 0.3318 target_work(ls_wunit_k1) = 0.116 | | occupancies: max = 1.00 min = 0.01 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.3318 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7897 moved from start: 0.2033 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.068 5683 Z= 0.214 Angle : 0.682 13.379 7742 Z= 0.350 Chirality : 0.046 0.155 864 Planarity : 0.005 0.048 1002 Dihedral : 4.924 26.694 821 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 6.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.79 % Favored : 94.21 % 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: -0.77 (0.31), residues: 713 helix: -3.06 (0.89), residues: 21 sheet: 0.72 (0.34), residues: 226 loop : -1.08 (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 0.013 0.001 PHE A 562 TYR 0.018 0.001 TYR L 49 ARG 0.003 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 92 residues out of total 619 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 69 time to evaluate : 0.609 Fit side-chains revert: symmetry clash REVERT: H 69 MET cc_start: 0.8444 (mtm) cc_final: 0.8234 (mtt) outliers start: 23 outliers final: 18 residues processed: 86 average time/residue: 0.1928 time to fit residues: 21.4336 Evaluate side-chains 86 residues out of total 619 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 68 time to evaluate : 0.604 ------------------------------------------------------------------------------- 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 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 Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 71 random chunks: chunk 8 optimal weight: 0.8980 chunk 57 optimal weight: 1.9990 chunk 24 optimal weight: 0.9990 chunk 47 optimal weight: 3.9990 chunk 38 optimal weight: 0.6980 chunk 62 optimal weight: 6.9990 chunk 39 optimal weight: 0.7980 chunk 29 optimal weight: 1.9990 chunk 59 optimal weight: 0.9980 chunk 2 optimal weight: 1.9990 chunk 1 optimal weight: 1.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3921 r_free = 0.3921 target = 0.165515 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.3587 r_free = 0.3587 target = 0.137590 restraints weight = 18179.059| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3590 r_free = 0.3590 target = 0.138317 restraints weight = 24236.990| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3591 r_free = 0.3591 target = 0.138347 restraints weight = 13178.868| |-----------------------------------------------------------------------------| r_work (final): 0.3412 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3412 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3412 r_free = 0.3412 target_work(ls_wunit_k1) = 0.123 | | occupancies: max = 1.00 min = 0.01 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3412 r_free = 0.3412 target_work(ls_wunit_k1) = 0.123 | | occupancies: max = 1.00 min = 0.01 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.3412 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7783 moved from start: 0.2312 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.069 5683 Z= 0.291 Angle : 0.742 13.827 7742 Z= 0.381 Chirality : 0.047 0.173 864 Planarity : 0.005 0.048 1002 Dihedral : 5.165 27.623 821 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 6.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.50 % Favored : 93.50 % 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: -0.95 (0.31), residues: 713 helix: -3.22 (0.87), residues: 21 sheet: 0.45 (0.34), residues: 237 loop : -1.14 (0.29), residues: 455 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 0.020 0.002 PHE A 456 TYR 0.023 0.002 TYR L 92 ARG 0.003 0.001 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 88 residues out of total 619 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 66 time to evaluate : 0.610 Fit side-chains revert: symmetry clash REVERT: H 69 MET cc_start: 0.8442 (mtm) cc_final: 0.8226 (mtt) REVERT: H 86 ASP cc_start: 0.8410 (t70) cc_final: 0.8181 (t0) outliers start: 22 outliers final: 18 residues processed: 83 average time/residue: 0.1983 time to fit residues: 21.1296 Evaluate side-chains 81 residues out of total 619 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 63 time to evaluate : 0.644 ------------------------------------------------------------------------------- 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 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 71 random chunks: chunk 5 optimal weight: 0.7980 chunk 41 optimal weight: 7.9990 chunk 18 optimal weight: 0.7980 chunk 66 optimal weight: 1.9990 chunk 46 optimal weight: 0.9990 chunk 13 optimal weight: 2.9990 chunk 40 optimal weight: 5.9990 chunk 36 optimal weight: 0.5980 chunk 70 optimal weight: 0.7980 chunk 10 optimal weight: 1.9990 chunk 65 optimal weight: 0.7980 overall best weight: 0.7580 ------------------------------------------------------------------------------- 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 = 0.3787 r_free = 0.3787 target = 0.155076 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3562 r_free = 0.3562 target = 0.134770 restraints weight = 11998.175| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.131831 restraints weight = 14781.795| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.129417 restraints weight = 13499.946| |-----------------------------------------------------------------------------| r_work (final): 0.3494 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3494 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3494 r_free = 0.3494 target_work(ls_wunit_k1) = 0.129 | | occupancies: max = 1.00 min = 0.01 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3494 r_free = 0.3494 target_work(ls_wunit_k1) = 0.129 | | occupancies: max = 1.00 min = 0.01 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.3494 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7686 moved from start: 0.2403 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.070 5683 Z= 0.261 Angle : 0.718 13.819 7742 Z= 0.370 Chirality : 0.047 0.174 864 Planarity : 0.006 0.097 1002 Dihedral : 5.143 27.781 821 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 6.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.79 % Favored : 94.21 % Rotamer: Outliers : 3.37 % Allowed : 18.94 % 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: -1.06 (0.31), residues: 713 helix: -3.28 (0.87), residues: 21 sheet: 0.29 (0.33), residues: 259 loop : -1.24 (0.29), residues: 433 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 0.018 0.002 PHE A 497 TYR 0.019 0.002 TYR L 92 ARG 0.004 0.001 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 85 residues out of total 619 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 64 time to evaluate : 0.559 Fit side-chains revert: symmetry clash REVERT: A 495 TYR cc_start: 0.4082 (OUTLIER) cc_final: 0.1870 (m-80) outliers start: 21 outliers final: 18 residues processed: 79 average time/residue: 0.1891 time to fit residues: 19.3000 Evaluate side-chains 81 residues out of total 619 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 62 time to evaluate : 0.561 ------------------------------------------------------------------------------- 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 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 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: 0.0670 chunk 17 optimal weight: 1.9990 chunk 36 optimal weight: 0.9980 chunk 68 optimal weight: 5.9990 chunk 62 optimal weight: 6.9990 chunk 41 optimal weight: 5.9990 chunk 28 optimal weight: 1.9990 chunk 37 optimal weight: 0.4980 chunk 34 optimal weight: 0.0870 chunk 2 optimal weight: 0.3980 chunk 24 optimal weight: 0.9990 overall best weight: 0.4096 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3940 r_free = 0.3940 target = 0.167675 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3801 r_free = 0.3801 target = 0.154423 restraints weight = 17106.366| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3644 r_free = 0.3644 target = 0.142425 restraints weight = 18576.575| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3568 r_free = 0.3568 target = 0.136777 restraints weight = 23471.325| |-----------------------------------------------------------------------------| r_work (final): 0.3388 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3388 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3388 r_free = 0.3388 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 = 0.3388 r_free = 0.3388 target_work(ls_wunit_k1) = 0.121 | | occupancies: max = 1.00 min = 0.01 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.3388 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7810 moved from start: 0.2510 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.069 5683 Z= 0.192 Angle : 0.682 13.494 7742 Z= 0.348 Chirality : 0.046 0.159 864 Planarity : 0.006 0.102 1002 Dihedral : 4.916 28.475 821 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 6.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.79 % Favored : 94.21 % Rotamer: Outliers : 2.57 % Allowed : 20.06 % Favored : 77.37 % 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: -3.29 (0.86), residues: 21 sheet: 0.49 (0.34), residues: 238 loop : -1.20 (0.28), residues: 454 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 0.029 0.002 PHE A 456 TYR 0.016 0.001 TYR L 49 ARG 0.003 0.000 ARG A 509 ********************** 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 79 residues out of total 619 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 63 time to evaluate : 0.567 Fit side-chains revert: symmetry clash REVERT: A 495 TYR cc_start: 0.4724 (OUTLIER) cc_final: 0.2144 (m-80) REVERT: L 134 CYS cc_start: 0.6891 (OUTLIER) cc_final: 0.6464 (t) outliers start: 16 outliers final: 12 residues processed: 75 average time/residue: 0.2013 time to fit residues: 19.4351 Evaluate side-chains 76 residues out of total 619 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 62 time to evaluate : 0.629 ------------------------------------------------------------------------------- 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 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 192 THR Chi-restraints excluded: chain H residue 208 CYS Chi-restraints excluded: chain H residue 210 VAL 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 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: 1.9990 chunk 67 optimal weight: 3.9990 chunk 31 optimal weight: 1.9990 chunk 68 optimal weight: 0.0970 chunk 45 optimal weight: 0.9990 chunk 42 optimal weight: 0.1980 chunk 32 optimal weight: 0.5980 chunk 2 optimal weight: 0.9990 chunk 15 optimal weight: 20.0000 chunk 28 optimal weight: 0.7980 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3918 r_free = 0.3918 target = 0.165549 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.133654 restraints weight = 27858.487| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3538 r_free = 0.3538 target = 0.135370 restraints weight = 24238.674| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.135705 restraints weight = 12838.610| |-----------------------------------------------------------------------------| r_work (final): 0.3363 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3363 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3363 r_free = 0.3363 target_work(ls_wunit_k1) = 0.119 | | occupancies: max = 1.00 min = 0.01 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3363 r_free = 0.3363 target_work(ls_wunit_k1) = 0.119 | | occupancies: max = 1.00 min = 0.01 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.3363 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7841 moved from start: 0.2557 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= 0.215 Angle : 0.692 13.724 7742 Z= 0.353 Chirality : 0.046 0.162 864 Planarity : 0.005 0.090 1002 Dihedral : 4.898 27.080 821 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 6.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.93 % Favored : 94.07 % Rotamer: Outliers : 2.41 % Allowed : 20.55 % Favored : 77.05 % 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 (0.31), residues: 713 helix: -3.33 (0.86), residues: 21 sheet: 0.57 (0.34), residues: 237 loop : -1.19 (0.28), residues: 455 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 0.021 0.002 PHE A 347 TYR 0.017 0.001 TYR L 92 ARG 0.003 0.000 ARG A 509 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2401.86 seconds wall clock time: 42 minutes 14.95 seconds (2534.95 seconds total)