Starting phenix.real_space_refine on Fri Aug 22 14:39:25 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8hsb_34992/08_2025/8hsb_34992.cif Found real_map, /net/cci-nas-00/data/ceres_data/8hsb_34992/08_2025/8hsb_34992.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8hsb_34992/08_2025/8hsb_34992.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8hsb_34992/08_2025/8hsb_34992.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8hsb_34992/08_2025/8hsb_34992.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8hsb_34992/08_2025/8hsb_34992.map" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.012 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 10 5.16 5 C 2714 2.51 5 N 766 2.21 5 O 788 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 12 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 4278 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 2973 Number of conformers: 1 Conformer: "" Number of residues, atoms: 374, 2973 Classifications: {'peptide': 374} Link IDs: {'PTRANS': 18, 'TRANS': 355} Chain breaks: 2 Chain: "B" Number of atoms: 1305 Number of conformers: 1 Conformer: "" Number of residues, atoms: 159, 1305 Classifications: {'peptide': 159} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 145} Time building chain proxies: 1.04, per 1000 atoms: 0.24 Number of scatterers: 4278 At special positions: 0 Unit cell: (63.65, 69.68, 121.27, 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 10 16.00 O 788 8.00 N 766 7.00 C 2714 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.52 Conformation dependent library (CDL) restraints added in 173.2 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 1050 Ramachandran restraints generated. 525 Oldfield, 0 Emsley, 525 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1002 Finding SS restraints... Secondary structure from input PDB file: 19 helices and 5 sheets defined 48.4% alpha, 10.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.16 Creating SS restraints... Processing helix chain 'A' and resid 11 through 30 removed outlier: 3.806A pdb=" N THR A 28 " --> pdb=" O GLN A 24 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N LEU A 29 " --> pdb=" O ILE A 25 " (cutoff:3.500A) Processing helix chain 'A' and resid 32 through 52 Processing helix chain 'A' and resid 98 through 113 removed outlier: 3.556A pdb=" N VAL A 102 " --> pdb=" O ASP A 98 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N ARG A 109 " --> pdb=" O ALA A 105 " (cutoff:3.500A) Processing helix chain 'A' and resid 113 through 119 removed outlier: 4.675A pdb=" N THR A 118 " --> pdb=" O LYS A 114 " (cutoff:3.500A) removed outlier: 4.402A pdb=" N LEU A 119 " --> pdb=" O THR A 115 " (cutoff:3.500A) Processing helix chain 'A' and resid 168 through 182 removed outlier: 3.949A pdb=" N TYR A 172 " --> pdb=" O ASN A 168 " (cutoff:3.500A) removed outlier: 4.193A pdb=" N VAL A 182 " --> pdb=" O SER A 178 " (cutoff:3.500A) Processing helix chain 'A' and resid 212 through 232 removed outlier: 3.939A pdb=" N ALA A 230 " --> pdb=" O ASP A 226 " (cutoff:3.500A) removed outlier: 4.440A pdb=" N GLU A 231 " --> pdb=" O GLU A 227 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N GLN A 232 " --> pdb=" O TRP A 228 " (cutoff:3.500A) Processing helix chain 'A' and resid 233 through 239 Processing helix chain 'A' and resid 242 through 260 Processing helix chain 'A' and resid 266 through 278 removed outlier: 3.989A pdb=" N LEU A 271 " --> pdb=" O ASP A 267 " (cutoff:3.500A) Processing helix chain 'A' and resid 279 through 282 removed outlier: 3.552A pdb=" N ILE A 282 " --> pdb=" O PRO A 279 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 279 through 282' Processing helix chain 'A' and resid 302 through 307 removed outlier: 3.523A pdb=" N ARG A 307 " --> pdb=" O GLU A 303 " (cutoff:3.500A) Processing helix chain 'A' and resid 308 through 310 No H-bonds generated for 'chain 'A' and resid 308 through 310' Processing helix chain 'A' and resid 311 through 337 removed outlier: 3.606A pdb=" N ARG A 316 " --> pdb=" O GLU A 312 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N PHE A 320 " --> pdb=" O ARG A 316 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N TYR A 321 " --> pdb=" O SER A 317 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N PHE A 331 " --> pdb=" O ALA A 327 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N ASN A 332 " --> pdb=" O GLN A 328 " (cutoff:3.500A) Processing helix chain 'A' and resid 339 through 352 removed outlier: 3.547A pdb=" N PHE A 344 " --> pdb=" O GLU A 340 " (cutoff:3.500A) Processing helix chain 'A' and resid 352 through 374 removed outlier: 3.603A pdb=" N VAL A 356 " --> pdb=" O GLY A 352 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N VAL A 358 " --> pdb=" O THR A 354 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N VAL A 359 " --> pdb=" O PRO A 355 " (cutoff:3.500A) Processing helix chain 'B' and resid 14 through 25 removed outlier: 4.347A pdb=" N GLN B 18 " --> pdb=" O THR B 14 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ARG B 20 " --> pdb=" O ALA B 16 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N ALA B 21 " --> pdb=" O GLN B 17 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N LEU B 22 " --> pdb=" O GLN B 18 " (cutoff:3.500A) removed outlier: 4.663A pdb=" N LYS B 23 " --> pdb=" O TYR B 19 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N ALA B 24 " --> pdb=" O ARG B 20 " (cutoff:3.500A) removed outlier: 4.153A pdb=" N GLY B 25 " --> pdb=" O ALA B 21 " (cutoff:3.500A) Processing helix chain 'B' and resid 77 through 81 Processing helix chain 'B' and resid 90 through 94 removed outlier: 3.763A pdb=" N HIS B 94 " --> pdb=" O ALA B 91 " (cutoff:3.500A) Processing helix chain 'B' and resid 125 through 144 removed outlier: 3.686A pdb=" N LEU B 141 " --> pdb=" O PHE B 137 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N HIS B 142 " --> pdb=" O GLU B 138 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 62 through 66 removed outlier: 3.866A pdb=" N TYR A 64 " --> pdb=" O ILE A 88 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N ILE A 88 " --> pdb=" O TYR A 64 " (cutoff:3.500A) removed outlier: 4.629A pdb=" N ASP A 86 " --> pdb=" O GLN A 66 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N GLY A 142 " --> pdb=" O CYS A 89 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N LEU A 91 " --> pdb=" O GLY A 142 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 155 through 157 Processing sheet with id=AA3, first strand: chain 'A' and resid 283 through 285 removed outlier: 4.032A pdb=" N VAL A 283 " --> pdb=" O HIS A 290 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 377 through 378 Processing sheet with id=AA5, first strand: chain 'B' and resid 30 through 34 removed outlier: 4.341A pdb=" N ARG B 30 " --> pdb=" O GLU B 43 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N GLU B 43 " --> pdb=" O ARG B 30 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N ARG B 60 " --> pdb=" O ILE B 68 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N ILE B 68 " --> pdb=" O ARG B 60 " (cutoff:3.500A) removed outlier: 5.527A pdb=" N SER B 62 " --> pdb=" O PRO B 66 " (cutoff:3.500A) removed outlier: 4.638A pdb=" N CYS B 69 " --> pdb=" O LEU B 100 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N ALA B 98 " --> pdb=" O VAL B 71 " (cutoff:3.500A) 190 hydrogen bonds defined for protein. 534 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: 0.63 Time building geometry restraints manager: 0.66 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 1389 1.34 - 1.45: 602 1.45 - 1.57: 2384 1.57 - 1.69: 0 1.69 - 1.81: 14 Bond restraints: 4389 Sorted by residual: bond pdb=" C GLN A 153 " pdb=" N PRO A 154 " ideal model delta sigma weight residual 1.334 1.379 -0.045 2.34e-02 1.83e+03 3.72e+00 bond pdb=" N ARG B 83 " pdb=" CA ARG B 83 " ideal model delta sigma weight residual 1.457 1.480 -0.022 1.29e-02 6.01e+03 3.01e+00 bond pdb=" C ILE B 85 " pdb=" N PRO B 86 " ideal model delta sigma weight residual 1.334 1.368 -0.034 2.34e-02 1.83e+03 2.08e+00 bond pdb=" CB LYS A 15 " pdb=" CG LYS A 15 " ideal model delta sigma weight residual 1.520 1.481 0.039 3.00e-02 1.11e+03 1.73e+00 bond pdb=" N THR B 82 " pdb=" CA THR B 82 " ideal model delta sigma weight residual 1.457 1.473 -0.016 1.29e-02 6.01e+03 1.51e+00 ... (remaining 4384 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.13: 5835 2.13 - 4.25: 116 4.25 - 6.38: 17 6.38 - 8.51: 1 8.51 - 10.63: 1 Bond angle restraints: 5970 Sorted by residual: angle pdb=" CA LEU B 79 " pdb=" CB LEU B 79 " pdb=" CG LEU B 79 " ideal model delta sigma weight residual 116.30 126.93 -10.63 3.50e+00 8.16e-02 9.23e+00 angle pdb=" CB ARG B 83 " pdb=" CG ARG B 83 " pdb=" CD ARG B 83 " ideal model delta sigma weight residual 111.30 118.07 -6.77 2.30e+00 1.89e-01 8.65e+00 angle pdb=" C THR B 82 " pdb=" CA THR B 82 " pdb=" CB THR B 82 " ideal model delta sigma weight residual 110.42 115.98 -5.56 1.99e+00 2.53e-01 7.79e+00 angle pdb=" C GLN A 59 " pdb=" N ASP A 60 " pdb=" CA ASP A 60 " ideal model delta sigma weight residual 122.74 126.75 -4.01 1.44e+00 4.82e-01 7.77e+00 angle pdb=" C ARG B 83 " pdb=" CA ARG B 83 " pdb=" CB ARG B 83 " ideal model delta sigma weight residual 110.42 115.90 -5.48 1.99e+00 2.53e-01 7.59e+00 ... (remaining 5965 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.84: 2389 16.84 - 33.68: 180 33.68 - 50.52: 34 50.52 - 67.37: 7 67.37 - 84.21: 5 Dihedral angle restraints: 2615 sinusoidal: 1064 harmonic: 1551 Sorted by residual: dihedral pdb=" CA ASN A 266 " pdb=" C ASN A 266 " pdb=" N ASP A 267 " pdb=" CA ASP A 267 " ideal model delta harmonic sigma weight residual -180.00 -155.53 -24.47 0 5.00e+00 4.00e-02 2.40e+01 dihedral pdb=" CA PRO A 297 " pdb=" C PRO A 297 " pdb=" N GLU A 298 " pdb=" CA GLU A 298 " ideal model delta harmonic sigma weight residual -180.00 -158.35 -21.65 0 5.00e+00 4.00e-02 1.87e+01 dihedral pdb=" CA ASN A 292 " pdb=" C ASN A 292 " pdb=" N ASN A 293 " pdb=" CA ASN A 293 " ideal model delta harmonic sigma weight residual 180.00 160.35 19.65 0 5.00e+00 4.00e-02 1.54e+01 ... (remaining 2612 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.038: 457 0.038 - 0.076: 128 0.076 - 0.115: 50 0.115 - 0.153: 12 0.153 - 0.191: 2 Chirality restraints: 649 Sorted by residual: chirality pdb=" CG LEU A 87 " pdb=" CB LEU A 87 " pdb=" CD1 LEU A 87 " pdb=" CD2 LEU A 87 " both_signs ideal model delta sigma weight residual False -2.59 -2.40 -0.19 2.00e-01 2.50e+01 9.11e-01 chirality pdb=" CA THR B 82 " pdb=" N THR B 82 " pdb=" C THR B 82 " pdb=" CB THR B 82 " both_signs ideal model delta sigma weight residual False 2.53 2.37 0.15 2.00e-01 2.50e+01 5.93e-01 chirality pdb=" CA ILE A 85 " pdb=" N ILE A 85 " pdb=" C ILE A 85 " pdb=" CB ILE A 85 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.48e-01 ... (remaining 646 not shown) Planarity restraints: 775 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLY A 313 " -0.029 5.00e-02 4.00e+02 4.45e-02 3.17e+00 pdb=" N PRO A 314 " 0.077 5.00e-02 4.00e+02 pdb=" CA PRO A 314 " -0.023 5.00e-02 4.00e+02 pdb=" CD PRO A 314 " -0.025 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C HIS A 150 " -0.029 5.00e-02 4.00e+02 4.37e-02 3.05e+00 pdb=" N PRO A 151 " 0.076 5.00e-02 4.00e+02 pdb=" CA PRO A 151 " -0.022 5.00e-02 4.00e+02 pdb=" CD PRO A 151 " -0.024 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLN A 153 " 0.029 5.00e-02 4.00e+02 4.34e-02 3.01e+00 pdb=" N PRO A 154 " -0.075 5.00e-02 4.00e+02 pdb=" CA PRO A 154 " 0.022 5.00e-02 4.00e+02 pdb=" CD PRO A 154 " 0.025 5.00e-02 4.00e+02 ... (remaining 772 not shown) Histogram of nonbonded interaction distances: 2.16 - 2.70: 112 2.70 - 3.25: 4283 3.25 - 3.80: 6489 3.80 - 4.35: 8357 4.35 - 4.90: 13598 Nonbonded interactions: 32839 Sorted by model distance: nonbonded pdb=" O PHE A 49 " pdb=" NH2 ARG A 109 " model vdw 2.156 3.120 nonbonded pdb=" O LEU A 50 " pdb=" NH1 ARG A 109 " model vdw 2.259 3.120 nonbonded pdb=" O SER A 243 " pdb=" OG1 THR A 247 " model vdw 2.320 3.040 nonbonded pdb=" N ILE A 289 " pdb=" OD1 ASN A 306 " model vdw 2.325 3.120 nonbonded pdb=" NZ LYS A 15 " pdb=" OD1 ASP A 269 " model vdw 2.345 3.120 ... (remaining 32834 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=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.110 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.090 Check model and map are aligned: 0.020 Set scattering table: 0.010 Process input model: 5.910 Find NCS groups from input model: 0.020 Set up NCS constraints: 0.010 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:6.900 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.070 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5576 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 : 0.003 0.045 4389 Z= 0.156 Angle : 0.713 10.633 5970 Z= 0.398 Chirality : 0.044 0.191 649 Planarity : 0.006 0.044 775 Dihedral : 12.902 84.208 1613 Min Nonbonded Distance : 2.156 Molprobity Statistics. All-atom Clashscore : 10.62 Ramachandran Plot: Outliers : 0.38 % Allowed : 3.81 % Favored : 95.81 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.19 (0.36), residues: 525 helix: 0.94 (0.37), residues: 207 sheet: 0.54 (0.66), residues: 51 loop : -0.57 (0.37), residues: 267 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 109 TYR 0.014 0.001 TYR A 43 PHE 0.017 0.002 PHE B 135 TRP 0.018 0.001 TRP B 140 HIS 0.003 0.001 HIS A 256 Details of bonding type rmsd covalent geometry : bond 0.00310 ( 4389) covalent geometry : angle 0.71346 ( 5970) hydrogen bonds : bond 0.21232 ( 190) hydrogen bonds : angle 6.90662 ( 534) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1050 Ramachandran restraints generated. 525 Oldfield, 0 Emsley, 525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1050 Ramachandran restraints generated. 525 Oldfield, 0 Emsley, 525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 57 residues out of total 457 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 57 time to evaluate : 0.172 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 57 average time/residue: 0.6034 time to fit residues: 35.5859 Evaluate side-chains 44 residues out of total 457 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 44 time to evaluate : 0.165 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 24 optimal weight: 0.5980 chunk 48 optimal weight: 8.9990 chunk 26 optimal weight: 3.9990 chunk 2 optimal weight: 0.8980 chunk 16 optimal weight: 1.9990 chunk 32 optimal weight: 1.9990 chunk 31 optimal weight: 0.8980 chunk 25 optimal weight: 0.3980 chunk 50 optimal weight: 2.9990 chunk 19 optimal weight: 1.9990 chunk 30 optimal weight: 0.6980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 66 GLN A 153 GLN A 216 HIS ** A 293 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 87 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5047 r_free = 0.5047 target = 0.282479 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4822 r_free = 0.4822 target = 0.252873 restraints weight = 5244.372| |-----------------------------------------------------------------------------| r_work (start): 0.4826 rms_B_bonded: 2.52 r_work: 0.4718 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work (final): 0.4718 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5878 moved from start: 0.1443 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 4389 Z= 0.158 Angle : 0.676 8.216 5970 Z= 0.345 Chirality : 0.045 0.154 649 Planarity : 0.006 0.049 775 Dihedral : 5.225 23.401 584 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 10.15 Ramachandran Plot: Outliers : 0.19 % Allowed : 4.00 % Favored : 95.81 % Rotamer: Outliers : 0.88 % Allowed : 7.88 % Favored : 91.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.53 (0.36), residues: 525 helix: 1.30 (0.36), residues: 217 sheet: 0.61 (0.61), residues: 62 loop : -0.54 (0.39), residues: 246 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 236 TYR 0.024 0.002 TYR A 43 PHE 0.013 0.002 PHE B 135 TRP 0.012 0.001 TRP A 323 HIS 0.006 0.001 HIS A 324 Details of bonding type rmsd covalent geometry : bond 0.00342 ( 4389) covalent geometry : angle 0.67567 ( 5970) hydrogen bonds : bond 0.05473 ( 190) hydrogen bonds : angle 5.16896 ( 534) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1050 Ramachandran restraints generated. 525 Oldfield, 0 Emsley, 525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1050 Ramachandran restraints generated. 525 Oldfield, 0 Emsley, 525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 53 residues out of total 457 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 49 time to evaluate : 0.168 Fit side-chains revert: symmetry clash REVERT: B 60 ARG cc_start: 0.7248 (ptm160) cc_final: 0.6632 (ttp-110) outliers start: 4 outliers final: 3 residues processed: 53 average time/residue: 0.4797 time to fit residues: 26.4569 Evaluate side-chains 46 residues out of total 457 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 43 time to evaluate : 0.154 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 LEU Chi-restraints excluded: chain A residue 256 HIS Chi-restraints excluded: chain A residue 338 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 8 optimal weight: 2.9990 chunk 2 optimal weight: 0.7980 chunk 11 optimal weight: 0.0070 chunk 42 optimal weight: 0.6980 chunk 22 optimal weight: 0.0970 chunk 47 optimal weight: 9.9990 chunk 20 optimal weight: 0.0010 chunk 12 optimal weight: 0.8980 chunk 40 optimal weight: 1.9990 chunk 6 optimal weight: 0.9990 chunk 32 optimal weight: 0.9980 overall best weight: 0.3202 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 94 HIS ** 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 = 0.5066 r_free = 0.5066 target = 0.285331 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.4849 r_free = 0.4849 target = 0.256154 restraints weight = 5233.825| |-----------------------------------------------------------------------------| r_work (start): 0.4856 rms_B_bonded: 2.50 r_work: 0.4756 rms_B_bonded: 3.39 restraints_weight: 0.5000 r_work (final): 0.4756 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5812 moved from start: 0.1753 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 4389 Z= 0.133 Angle : 0.602 7.313 5970 Z= 0.309 Chirality : 0.043 0.137 649 Planarity : 0.006 0.049 775 Dihedral : 4.923 23.096 584 Min Nonbonded Distance : 2.583 Molprobity Statistics. All-atom Clashscore : 7.91 Ramachandran Plot: Outliers : 0.19 % Allowed : 4.00 % Favored : 95.81 % Rotamer: Outliers : 1.31 % Allowed : 9.41 % Favored : 89.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.75 (0.37), residues: 525 helix: 1.84 (0.36), residues: 212 sheet: 0.99 (0.66), residues: 55 loop : -0.77 (0.39), residues: 258 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 54 TYR 0.022 0.001 TYR A 43 PHE 0.008 0.001 PHE A 351 TRP 0.011 0.001 TRP A 323 HIS 0.003 0.000 HIS A 324 Details of bonding type rmsd covalent geometry : bond 0.00283 ( 4389) covalent geometry : angle 0.60244 ( 5970) hydrogen bonds : bond 0.04460 ( 190) hydrogen bonds : angle 4.65490 ( 534) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1050 Ramachandran restraints generated. 525 Oldfield, 0 Emsley, 525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1050 Ramachandran restraints generated. 525 Oldfield, 0 Emsley, 525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 47 residues out of total 457 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 41 time to evaluate : 0.218 Fit side-chains REVERT: A 364 MET cc_start: 0.6091 (tpt) cc_final: 0.5754 (mmm) REVERT: B 60 ARG cc_start: 0.7130 (ptm160) cc_final: 0.6761 (ttp-110) outliers start: 6 outliers final: 1 residues processed: 45 average time/residue: 0.5347 time to fit residues: 25.0582 Evaluate side-chains 40 residues out of total 457 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 39 time to evaluate : 0.165 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 29 optimal weight: 2.9990 chunk 42 optimal weight: 1.9990 chunk 27 optimal weight: 1.9990 chunk 48 optimal weight: 0.2980 chunk 12 optimal weight: 4.9990 chunk 41 optimal weight: 0.2980 chunk 47 optimal weight: 7.9990 chunk 15 optimal weight: 0.8980 chunk 5 optimal weight: 0.2980 chunk 7 optimal weight: 0.0770 chunk 26 optimal weight: 0.7980 overall best weight: 0.3538 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 94 HIS ** 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 = 0.5058 r_free = 0.5058 target = 0.284865 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4843 r_free = 0.4843 target = 0.255946 restraints weight = 5157.695| |-----------------------------------------------------------------------------| r_work (start): 0.4846 rms_B_bonded: 2.44 r_work: 0.4743 rms_B_bonded: 3.39 restraints_weight: 0.5000 r_work (final): 0.4743 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5812 moved from start: 0.2059 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 4389 Z= 0.131 Angle : 0.601 7.612 5970 Z= 0.308 Chirality : 0.043 0.156 649 Planarity : 0.006 0.050 775 Dihedral : 4.784 19.120 584 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 8.62 Ramachandran Plot: Outliers : 0.19 % Allowed : 4.19 % Favored : 95.62 % Rotamer: Outliers : 1.53 % Allowed : 11.16 % Favored : 87.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.88 (0.37), residues: 525 helix: 1.79 (0.36), residues: 218 sheet: 1.09 (0.67), residues: 55 loop : -0.62 (0.39), residues: 252 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 30 TYR 0.022 0.001 TYR A 43 PHE 0.012 0.001 PHE B 135 TRP 0.010 0.001 TRP A 323 HIS 0.003 0.000 HIS A 324 Details of bonding type rmsd covalent geometry : bond 0.00286 ( 4389) covalent geometry : angle 0.60110 ( 5970) hydrogen bonds : bond 0.04011 ( 190) hydrogen bonds : angle 4.49413 ( 534) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1050 Ramachandran restraints generated. 525 Oldfield, 0 Emsley, 525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1050 Ramachandran restraints generated. 525 Oldfield, 0 Emsley, 525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 50 residues out of total 457 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 43 time to evaluate : 0.163 Fit side-chains REVERT: B 54 ARG cc_start: 0.7103 (ttm-80) cc_final: 0.6601 (pmm150) REVERT: B 60 ARG cc_start: 0.7140 (ptm160) cc_final: 0.6787 (ttp-110) outliers start: 7 outliers final: 1 residues processed: 47 average time/residue: 0.4682 time to fit residues: 22.9761 Evaluate side-chains 41 residues out of total 457 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 40 time to evaluate : 0.102 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 47 optimal weight: 3.9990 chunk 15 optimal weight: 0.0770 chunk 48 optimal weight: 0.9980 chunk 51 optimal weight: 0.0030 chunk 25 optimal weight: 0.9990 chunk 8 optimal weight: 0.9980 chunk 16 optimal weight: 1.9990 chunk 36 optimal weight: 0.0070 chunk 33 optimal weight: 0.0470 chunk 44 optimal weight: 0.9980 chunk 30 optimal weight: 0.6980 overall best weight: 0.1664 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 108 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5073 r_free = 0.5073 target = 0.287129 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4866 r_free = 0.4866 target = 0.258745 restraints weight = 5220.818| |-----------------------------------------------------------------------------| r_work (start): 0.4871 rms_B_bonded: 2.45 r_work: 0.4767 rms_B_bonded: 3.43 restraints_weight: 0.5000 r_work (final): 0.4767 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5761 moved from start: 0.2331 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 4389 Z= 0.120 Angle : 0.573 7.993 5970 Z= 0.293 Chirality : 0.043 0.154 649 Planarity : 0.005 0.050 775 Dihedral : 4.576 23.872 584 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 7.44 Ramachandran Plot: Outliers : 0.19 % Allowed : 3.81 % Favored : 96.00 % Rotamer: Outliers : 0.88 % Allowed : 15.10 % Favored : 84.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.04 (0.37), residues: 525 helix: 2.00 (0.36), residues: 221 sheet: 1.09 (0.68), residues: 55 loop : -0.62 (0.39), residues: 249 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 30 TYR 0.021 0.001 TYR A 43 PHE 0.008 0.001 PHE B 135 TRP 0.010 0.001 TRP A 323 HIS 0.002 0.000 HIS A 324 Details of bonding type rmsd covalent geometry : bond 0.00262 ( 4389) covalent geometry : angle 0.57344 ( 5970) hydrogen bonds : bond 0.03526 ( 190) hydrogen bonds : angle 4.25798 ( 534) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1050 Ramachandran restraints generated. 525 Oldfield, 0 Emsley, 525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1050 Ramachandran restraints generated. 525 Oldfield, 0 Emsley, 525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 46 residues out of total 457 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 42 time to evaluate : 0.165 Fit side-chains REVERT: B 54 ARG cc_start: 0.7067 (ttm-80) cc_final: 0.6581 (pmm150) REVERT: B 60 ARG cc_start: 0.7146 (ptm160) cc_final: 0.6813 (ttp-110) outliers start: 4 outliers final: 0 residues processed: 45 average time/residue: 0.4154 time to fit residues: 19.5539 Evaluate side-chains 41 residues out of total 457 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 41 time to evaluate : 0.158 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 15 optimal weight: 2.9990 chunk 48 optimal weight: 3.9990 chunk 45 optimal weight: 0.9990 chunk 50 optimal weight: 0.8980 chunk 30 optimal weight: 0.5980 chunk 51 optimal weight: 0.0980 chunk 22 optimal weight: 0.5980 chunk 5 optimal weight: 2.9990 chunk 39 optimal weight: 0.0270 chunk 20 optimal weight: 3.9990 chunk 8 optimal weight: 0.4980 overall best weight: 0.3638 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 94 HIS ** 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 = 0.5063 r_free = 0.5063 target = 0.285564 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4848 r_free = 0.4848 target = 0.256638 restraints weight = 5305.776| |-----------------------------------------------------------------------------| r_work (start): 0.4851 rms_B_bonded: 2.49 r_work: 0.4745 rms_B_bonded: 3.45 restraints_weight: 0.5000 r_work (final): 0.4745 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5799 moved from start: 0.2465 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 4389 Z= 0.123 Angle : 0.573 7.927 5970 Z= 0.292 Chirality : 0.043 0.138 649 Planarity : 0.005 0.050 775 Dihedral : 4.469 18.390 584 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 8.14 Ramachandran Plot: Outliers : 0.19 % Allowed : 4.19 % Favored : 95.62 % Rotamer: Outliers : 0.66 % Allowed : 15.54 % Favored : 83.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.03 (0.37), residues: 525 helix: 2.00 (0.37), residues: 218 sheet: 1.29 (0.69), residues: 55 loop : -0.65 (0.38), residues: 252 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 30 TYR 0.020 0.001 TYR A 43 PHE 0.008 0.001 PHE B 135 TRP 0.011 0.001 TRP A 323 HIS 0.004 0.000 HIS A 324 Details of bonding type rmsd covalent geometry : bond 0.00276 ( 4389) covalent geometry : angle 0.57297 ( 5970) hydrogen bonds : bond 0.03545 ( 190) hydrogen bonds : angle 4.25330 ( 534) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1050 Ramachandran restraints generated. 525 Oldfield, 0 Emsley, 525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1050 Ramachandran restraints generated. 525 Oldfield, 0 Emsley, 525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 43 residues out of total 457 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 40 time to evaluate : 0.152 Fit side-chains REVERT: B 54 ARG cc_start: 0.7089 (ttm-80) cc_final: 0.6611 (pmm150) REVERT: B 60 ARG cc_start: 0.7144 (ptm160) cc_final: 0.6812 (ttp-110) outliers start: 3 outliers final: 1 residues processed: 43 average time/residue: 0.4683 time to fit residues: 21.1054 Evaluate side-chains 40 residues out of total 457 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 39 time to evaluate : 0.128 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 48 optimal weight: 3.9990 chunk 38 optimal weight: 0.9990 chunk 17 optimal weight: 0.5980 chunk 28 optimal weight: 0.0870 chunk 23 optimal weight: 0.7980 chunk 44 optimal weight: 0.5980 chunk 46 optimal weight: 0.9990 chunk 13 optimal weight: 0.2980 chunk 29 optimal weight: 0.9980 chunk 31 optimal weight: 1.9990 chunk 2 optimal weight: 0.7980 overall best weight: 0.4758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 94 HIS ** 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 = 0.5054 r_free = 0.5054 target = 0.284279 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.4836 r_free = 0.4836 target = 0.254939 restraints weight = 5271.736| |-----------------------------------------------------------------------------| r_work (start): 0.4838 rms_B_bonded: 2.50 r_work: 0.4730 rms_B_bonded: 3.49 restraints_weight: 0.5000 r_work (final): 0.4730 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5831 moved from start: 0.2552 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 4389 Z= 0.128 Angle : 0.581 7.637 5970 Z= 0.298 Chirality : 0.043 0.159 649 Planarity : 0.005 0.050 775 Dihedral : 4.506 18.553 584 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 8.14 Ramachandran Plot: Outliers : 0.19 % Allowed : 4.19 % Favored : 95.62 % Rotamer: Outliers : 0.66 % Allowed : 15.54 % Favored : 83.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.00 (0.37), residues: 525 helix: 1.93 (0.37), residues: 215 sheet: 1.04 (0.65), residues: 63 loop : -0.59 (0.38), residues: 247 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 30 TYR 0.020 0.001 TYR A 43 PHE 0.011 0.001 PHE B 135 TRP 0.012 0.001 TRP A 323 HIS 0.004 0.001 HIS A 324 Details of bonding type rmsd covalent geometry : bond 0.00290 ( 4389) covalent geometry : angle 0.58125 ( 5970) hydrogen bonds : bond 0.03627 ( 190) hydrogen bonds : angle 4.28949 ( 534) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1050 Ramachandran restraints generated. 525 Oldfield, 0 Emsley, 525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1050 Ramachandran restraints generated. 525 Oldfield, 0 Emsley, 525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 45 residues out of total 457 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 42 time to evaluate : 0.101 Fit side-chains REVERT: B 54 ARG cc_start: 0.7080 (ttm-80) cc_final: 0.6635 (pmm150) REVERT: B 60 ARG cc_start: 0.7088 (ptm160) cc_final: 0.6768 (ttp-110) outliers start: 3 outliers final: 1 residues processed: 45 average time/residue: 0.4888 time to fit residues: 22.9926 Evaluate side-chains 41 residues out of total 457 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 40 time to evaluate : 0.196 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 21 optimal weight: 0.9980 chunk 6 optimal weight: 0.1980 chunk 19 optimal weight: 0.6980 chunk 46 optimal weight: 1.9990 chunk 28 optimal weight: 2.9990 chunk 17 optimal weight: 2.9990 chunk 14 optimal weight: 3.9990 chunk 49 optimal weight: 0.9990 chunk 40 optimal weight: 0.8980 chunk 20 optimal weight: 0.9980 chunk 12 optimal weight: 0.0870 overall best weight: 0.5758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 293 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 94 HIS ** 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 = 0.5050 r_free = 0.5050 target = 0.283466 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.4828 r_free = 0.4828 target = 0.253872 restraints weight = 5268.470| |-----------------------------------------------------------------------------| r_work (start): 0.4829 rms_B_bonded: 2.51 r_work: 0.4723 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work (final): 0.4723 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5856 moved from start: 0.2645 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 4389 Z= 0.134 Angle : 0.594 7.642 5970 Z= 0.305 Chirality : 0.044 0.143 649 Planarity : 0.006 0.050 775 Dihedral : 4.567 18.140 584 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 8.50 Ramachandran Plot: Outliers : 0.19 % Allowed : 4.19 % Favored : 95.62 % Rotamer: Outliers : 0.44 % Allowed : 16.41 % Favored : 83.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.92 (0.37), residues: 525 helix: 1.87 (0.37), residues: 215 sheet: 0.98 (0.65), residues: 63 loop : -0.62 (0.38), residues: 247 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 30 TYR 0.020 0.001 TYR A 43 PHE 0.015 0.001 PHE B 135 TRP 0.012 0.001 TRP A 323 HIS 0.006 0.001 HIS A 136 Details of bonding type rmsd covalent geometry : bond 0.00304 ( 4389) covalent geometry : angle 0.59371 ( 5970) hydrogen bonds : bond 0.03830 ( 190) hydrogen bonds : angle 4.34758 ( 534) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1050 Ramachandran restraints generated. 525 Oldfield, 0 Emsley, 525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1050 Ramachandran restraints generated. 525 Oldfield, 0 Emsley, 525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 45 residues out of total 457 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 43 time to evaluate : 0.110 Fit side-chains REVERT: A 347 LEU cc_start: 0.6886 (OUTLIER) cc_final: 0.6494 (mp) REVERT: B 54 ARG cc_start: 0.7114 (ttm-80) cc_final: 0.6663 (pmm150) REVERT: B 60 ARG cc_start: 0.7081 (ptm160) cc_final: 0.6636 (ttp-110) outliers start: 2 outliers final: 1 residues processed: 45 average time/residue: 0.4715 time to fit residues: 22.1372 Evaluate side-chains 43 residues out of total 457 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 41 time to evaluate : 0.146 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 LEU Chi-restraints excluded: chain A residue 347 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 13 optimal weight: 0.6980 chunk 41 optimal weight: 0.9980 chunk 34 optimal weight: 0.9990 chunk 11 optimal weight: 2.9990 chunk 38 optimal weight: 0.2980 chunk 26 optimal weight: 0.9990 chunk 20 optimal weight: 3.9990 chunk 6 optimal weight: 1.9990 chunk 17 optimal weight: 0.8980 chunk 7 optimal weight: 3.9990 chunk 16 optimal weight: 0.9980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 290 HIS ** B 94 HIS ** 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 = 0.5038 r_free = 0.5038 target = 0.281211 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.4811 r_free = 0.4811 target = 0.251126 restraints weight = 5312.362| |-----------------------------------------------------------------------------| r_work (start): 0.4809 rms_B_bonded: 2.56 r_work: 0.4698 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work (final): 0.4698 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5916 moved from start: 0.2743 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 4389 Z= 0.153 Angle : 0.633 7.431 5970 Z= 0.328 Chirality : 0.045 0.153 649 Planarity : 0.006 0.050 775 Dihedral : 4.766 18.646 584 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 8.73 Ramachandran Plot: Outliers : 0.19 % Allowed : 4.19 % Favored : 95.62 % Rotamer: Outliers : 0.88 % Allowed : 16.41 % Favored : 82.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.72 (0.37), residues: 525 helix: 1.68 (0.37), residues: 219 sheet: 0.43 (0.62), residues: 70 loop : -0.64 (0.39), residues: 236 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 30 TYR 0.020 0.001 TYR A 43 PHE 0.016 0.001 PHE B 135 TRP 0.013 0.002 TRP B 140 HIS 0.005 0.001 HIS A 324 Details of bonding type rmsd covalent geometry : bond 0.00350 ( 4389) covalent geometry : angle 0.63308 ( 5970) hydrogen bonds : bond 0.04268 ( 190) hydrogen bonds : angle 4.55385 ( 534) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1050 Ramachandran restraints generated. 525 Oldfield, 0 Emsley, 525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1050 Ramachandran restraints generated. 525 Oldfield, 0 Emsley, 525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 44 residues out of total 457 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 40 time to evaluate : 0.169 Fit side-chains REVERT: B 60 ARG cc_start: 0.7013 (ptm160) cc_final: 0.6588 (ttp-110) outliers start: 4 outliers final: 3 residues processed: 43 average time/residue: 0.4414 time to fit residues: 19.8913 Evaluate side-chains 41 residues out of total 457 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 38 time to evaluate : 0.095 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 LEU Chi-restraints excluded: chain A residue 347 LEU Chi-restraints excluded: chain B residue 33 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 51 optimal weight: 7.9990 chunk 8 optimal weight: 1.9990 chunk 32 optimal weight: 0.4980 chunk 0 optimal weight: 4.9990 chunk 27 optimal weight: 0.0060 chunk 2 optimal weight: 0.3980 chunk 45 optimal weight: 0.1980 chunk 17 optimal weight: 0.5980 chunk 18 optimal weight: 1.9990 chunk 39 optimal weight: 0.0470 chunk 12 optimal weight: 4.9990 overall best weight: 0.2294 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 66 GLN ** B 94 HIS ** 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 = 0.5069 r_free = 0.5069 target = 0.286252 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4851 r_free = 0.4851 target = 0.256731 restraints weight = 5235.238| |-----------------------------------------------------------------------------| r_work (start): 0.4853 rms_B_bonded: 2.48 r_work: 0.4744 rms_B_bonded: 3.52 restraints_weight: 0.5000 r_work (final): 0.4744 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5815 moved from start: 0.2903 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 4389 Z= 0.121 Angle : 0.576 7.627 5970 Z= 0.297 Chirality : 0.043 0.137 649 Planarity : 0.005 0.051 775 Dihedral : 4.527 17.814 584 Min Nonbonded Distance : 2.580 Molprobity Statistics. All-atom Clashscore : 7.08 Ramachandran Plot: Outliers : 0.19 % Allowed : 3.62 % Favored : 96.19 % Rotamer: Outliers : 0.44 % Allowed : 17.29 % Favored : 82.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.78 (0.37), residues: 525 helix: 1.88 (0.37), residues: 215 sheet: 0.46 (0.63), residues: 70 loop : -0.74 (0.38), residues: 240 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 30 TYR 0.021 0.001 TYR A 43 PHE 0.041 0.001 PHE B 135 TRP 0.010 0.001 TRP A 323 HIS 0.002 0.000 HIS A 324 Details of bonding type rmsd covalent geometry : bond 0.00272 ( 4389) covalent geometry : angle 0.57582 ( 5970) hydrogen bonds : bond 0.03499 ( 190) hydrogen bonds : angle 4.31023 ( 534) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1050 Ramachandran restraints generated. 525 Oldfield, 0 Emsley, 525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1050 Ramachandran restraints generated. 525 Oldfield, 0 Emsley, 525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 42 residues out of total 457 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 40 time to evaluate : 0.117 Fit side-chains REVERT: A 367 MET cc_start: 0.4820 (mtp) cc_final: 0.4598 (mtp) outliers start: 2 outliers final: 1 residues processed: 41 average time/residue: 0.3604 time to fit residues: 15.5448 Evaluate side-chains 37 residues out of total 457 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 36 time to evaluate : 0.096 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 13 optimal weight: 1.9990 chunk 0 optimal weight: 4.9990 chunk 46 optimal weight: 0.9990 chunk 51 optimal weight: 2.9990 chunk 40 optimal weight: 0.9980 chunk 47 optimal weight: 1.9990 chunk 27 optimal weight: 0.5980 chunk 15 optimal weight: 0.9990 chunk 25 optimal weight: 0.0970 chunk 17 optimal weight: 0.0870 chunk 20 optimal weight: 3.9990 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 145 HIS ** B 94 HIS ** 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 = 0.5050 r_free = 0.5050 target = 0.283803 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.4829 r_free = 0.4829 target = 0.254230 restraints weight = 5339.736| |-----------------------------------------------------------------------------| r_work (start): 0.4830 rms_B_bonded: 2.52 r_work: 0.4724 rms_B_bonded: 3.44 restraints_weight: 0.5000 r_work (final): 0.4724 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5866 moved from start: 0.2952 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 4389 Z= 0.135 Angle : 0.611 7.532 5970 Z= 0.315 Chirality : 0.044 0.143 649 Planarity : 0.005 0.049 775 Dihedral : 4.605 17.981 584 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 8.73 Ramachandran Plot: Outliers : 0.19 % Allowed : 4.19 % Favored : 95.62 % Rotamer: Outliers : 0.44 % Allowed : 17.94 % Favored : 81.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.78 (0.37), residues: 525 helix: 1.83 (0.37), residues: 219 sheet: 0.47 (0.63), residues: 68 loop : -0.72 (0.39), residues: 238 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 30 TYR 0.020 0.001 TYR A 43 PHE 0.032 0.002 PHE B 135 TRP 0.012 0.001 TRP A 323 HIS 0.004 0.001 HIS A 324 Details of bonding type rmsd covalent geometry : bond 0.00310 ( 4389) covalent geometry : angle 0.61053 ( 5970) hydrogen bonds : bond 0.03787 ( 190) hydrogen bonds : angle 4.38516 ( 534) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1497.13 seconds wall clock time: 26 minutes 14.18 seconds (1574.18 seconds total)