Starting phenix.real_space_refine on Tue Feb 3 14:25:13 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9j72_61191/02_2026/9j72_61191_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/9j72_61191/02_2026/9j72_61191.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.47 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9j72_61191/02_2026/9j72_61191_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9j72_61191/02_2026/9j72_61191_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9j72_61191/02_2026/9j72_61191.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9j72_61191/02_2026/9j72_61191.map" } resolution = 3.47 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= 0.027 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 25 5.16 5 C 2364 2.51 5 N 629 2.21 5 O 618 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 5 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 3636 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 3624 Number of conformers: 1 Conformer: "" Number of residues, atoms: 472, 3624 Classifications: {'peptide': 472} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 24, 'TRANS': 447} Chain breaks: 3 Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'PHE:plan': 1} Unresolved non-hydrogen planarities: 6 Chain: "A" Number of atoms: 12 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 12 Unusual residues: {'URC': 1} Classifications: {'undetermined': 1} Time building chain proxies: 1.10, per 1000 atoms: 0.30 Number of scatterers: 3636 At special positions: 0 Unit cell: (99.45, 67.15, 73.95, 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 25 16.00 O 618 8.00 N 629 7.00 C 2364 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS A 49 " - pdb=" SG CYS A 116 " distance=2.03 Simple disulfide: pdb=" SG CYS A 88 " - pdb=" SG CYS A 139 " 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 Time building additional restraints: 0.36 Conformation dependent library (CDL) restraints added in 160.0 milliseconds 928 Ramachandran restraints generated. 464 Oldfield, 0 Emsley, 464 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 868 Finding SS restraints... Secondary structure from input PDB file: 22 helices and 2 sheets defined 71.8% alpha, 1.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.07 Creating SS restraints... Processing helix chain 'A' and resid 2 through 11 Processing helix chain 'A' and resid 15 through 37 removed outlier: 3.539A pdb=" N ALA A 21 " --> pdb=" O GLN A 17 " (cutoff:3.500A) Proline residue: A 27 - end of helix removed outlier: 4.279A pdb=" N TRP A 30 " --> pdb=" O THR A 26 " (cutoff:3.500A) Processing helix chain 'A' and resid 69 through 77 Processing helix chain 'A' and resid 130 through 136 Processing helix chain 'A' and resid 144 through 165 removed outlier: 4.231A pdb=" N GLN A 149 " --> pdb=" O ARG A 145 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N SER A 150 " --> pdb=" O PRO A 146 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N GLY A 164 " --> pdb=" O ALA A 160 " (cutoff:3.500A) removed outlier: 4.310A pdb=" N HIS A 165 " --> pdb=" O ALA A 161 " (cutoff:3.500A) Processing helix chain 'A' and resid 172 through 191 removed outlier: 3.645A pdb=" N LEU A 176 " --> pdb=" O ARG A 172 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ALA A 191 " --> pdb=" O GLY A 187 " (cutoff:3.500A) Processing helix chain 'A' and resid 195 through 225 removed outlier: 3.537A pdb=" N TRP A 224 " --> pdb=" O LEU A 220 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N THR A 225 " --> pdb=" O LEU A 221 " (cutoff:3.500A) Processing helix chain 'A' and resid 228 through 255 removed outlier: 4.221A pdb=" N LEU A 232 " --> pdb=" O GLN A 228 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N MET A 233 " --> pdb=" O ALA A 229 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N MET A 234 " --> pdb=" O GLY A 230 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N ALA A 238 " --> pdb=" O MET A 234 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N VAL A 246 " --> pdb=" O SER A 242 " (cutoff:3.500A) Processing helix chain 'A' and resid 258 through 276 removed outlier: 3.543A pdb=" N GLN A 262 " --> pdb=" O TRP A 258 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N LEU A 263 " --> pdb=" O ARG A 259 " (cutoff:3.500A) Proline residue: A 268 - end of helix removed outlier: 4.146A pdb=" N LEU A 271 " --> pdb=" O ALA A 267 " (cutoff:3.500A) Processing helix chain 'A' and resid 282 through 290 removed outlier: 3.767A pdb=" N LEU A 286 " --> pdb=" O SER A 282 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N THR A 288 " --> pdb=" O ARG A 284 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N VAL A 289 " --> pdb=" O TRP A 285 " (cutoff:3.500A) Processing helix chain 'A' and resid 291 through 307 Processing helix chain 'A' and resid 311 through 315 Processing helix chain 'A' and resid 317 through 324 Processing helix chain 'A' and resid 348 through 368 Processing helix chain 'A' and resid 389 through 402 removed outlier: 4.561A pdb=" N ARG A 402 " --> pdb=" O LEU A 398 " (cutoff:3.500A) Processing helix chain 'A' and resid 404 through 426 removed outlier: 3.943A pdb=" N LEU A 413 " --> pdb=" O GLN A 409 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N LEU A 415 " --> pdb=" O SER A 411 " (cutoff:3.500A) Proline residue: A 416 - end of helix removed outlier: 3.973A pdb=" N ASN A 423 " --> pdb=" O CYS A 419 " (cutoff:3.500A) removed outlier: 4.373A pdb=" N ILE A 424 " --> pdb=" O ILE A 420 " (cutoff:3.500A) removed outlier: 4.321A pdb=" N LEU A 425 " --> pdb=" O LEU A 421 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N VAL A 426 " --> pdb=" O ALA A 422 " (cutoff:3.500A) Processing helix chain 'A' and resid 430 through 447 removed outlier: 3.509A pdb=" N ARG A 434 " --> pdb=" O MET A 430 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N LEU A 437 " --> pdb=" O LEU A 433 " (cutoff:3.500A) removed outlier: 4.758A pdb=" N ALA A 438 " --> pdb=" O ARG A 434 " (cutoff:3.500A) Processing helix chain 'A' and resid 447 through 455 removed outlier: 4.208A pdb=" N THR A 453 " --> pdb=" O PHE A 449 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N PHE A 455 " --> pdb=" O CYS A 451 " (cutoff:3.500A) Processing helix chain 'A' and resid 465 through 480 removed outlier: 4.258A pdb=" N GLY A 470 " --> pdb=" O MET A 466 " (cutoff:3.500A) removed outlier: 4.678A pdb=" N LEU A 471 " --> pdb=" O THR A 467 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N ALA A 475 " --> pdb=" O LEU A 471 " (cutoff:3.500A) Processing helix chain 'A' and resid 481 through 483 No H-bonds generated for 'chain 'A' and resid 481 through 483' Processing helix chain 'A' and resid 485 through 491 removed outlier: 4.445A pdb=" N VAL A 491 " --> pdb=" O LEU A 488 " (cutoff:3.500A) Processing helix chain 'A' and resid 494 through 513 removed outlier: 4.763A pdb=" N LEU A 498 " --> pdb=" O SER A 494 " (cutoff:3.500A) Proline residue: A 505 - end of helix removed outlier: 3.625A pdb=" N LEU A 513 " --> pdb=" O GLY A 509 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 47 through 49 Processing sheet with id=AA2, first strand: chain 'A' and resid 90 through 91 207 hydrogen bonds defined for protein. 603 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: 0.32 Time building geometry restraints manager: 0.48 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 798 1.33 - 1.45: 806 1.45 - 1.57: 2076 1.57 - 1.70: 0 1.70 - 1.82: 40 Bond restraints: 3720 Sorted by residual: bond pdb=" C4 URC A 601 " pdb=" N9 URC A 601 " ideal model delta sigma weight residual 1.352 1.434 -0.082 2.00e-02 2.50e+03 1.66e+01 bond pdb=" CA THR A 453 " pdb=" C THR A 453 " ideal model delta sigma weight residual 1.523 1.499 0.025 8.40e-03 1.42e+04 8.55e+00 bond pdb=" N PRO A 280 " pdb=" CD PRO A 280 " ideal model delta sigma weight residual 1.473 1.511 -0.038 1.40e-02 5.10e+03 7.48e+00 bond pdb=" CA SER A 401 " pdb=" CB SER A 401 " ideal model delta sigma weight residual 1.528 1.486 0.042 1.59e-02 3.96e+03 6.96e+00 bond pdb=" N ARG A 477 " pdb=" CA ARG A 477 " ideal model delta sigma weight residual 1.457 1.489 -0.032 1.32e-02 5.74e+03 5.83e+00 ... (remaining 3715 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.42: 4791 1.42 - 2.84: 187 2.84 - 4.26: 58 4.26 - 5.67: 26 5.67 - 7.09: 6 Bond angle restraints: 5068 Sorted by residual: angle pdb=" N ALA A 383 " pdb=" CA ALA A 383 " pdb=" C ALA A 383 " ideal model delta sigma weight residual 114.09 108.23 5.86 1.55e+00 4.16e-01 1.43e+01 angle pdb=" N ALA A 166 " pdb=" CA ALA A 166 " pdb=" C ALA A 166 " ideal model delta sigma weight residual 114.75 110.09 4.66 1.26e+00 6.30e-01 1.37e+01 angle pdb=" CA THR A 453 " pdb=" CB THR A 453 " pdb=" OG1 THR A 453 " ideal model delta sigma weight residual 109.60 104.64 4.96 1.50e+00 4.44e-01 1.09e+01 angle pdb=" N THR A 126 " pdb=" CA THR A 126 " pdb=" C THR A 126 " ideal model delta sigma weight residual 113.43 109.70 3.73 1.26e+00 6.30e-01 8.75e+00 angle pdb=" C GLY A 479 " pdb=" N ALA A 480 " pdb=" CA ALA A 480 " ideal model delta sigma weight residual 120.60 115.93 4.67 1.60e+00 3.91e-01 8.50e+00 ... (remaining 5063 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.31: 1831 17.31 - 34.61: 259 34.61 - 51.92: 81 51.92 - 69.23: 10 69.23 - 86.53: 3 Dihedral angle restraints: 2184 sinusoidal: 841 harmonic: 1343 Sorted by residual: dihedral pdb=" CD ARG A 477 " pdb=" NE ARG A 477 " pdb=" CZ ARG A 477 " pdb=" NH1 ARG A 477 " ideal model delta sinusoidal sigma weight residual 0.00 86.53 -86.53 1 1.00e+01 1.00e-02 9.02e+01 dihedral pdb=" CB CYS A 49 " pdb=" SG CYS A 49 " pdb=" SG CYS A 116 " pdb=" CB CYS A 116 " ideal model delta sinusoidal sigma weight residual -86.00 -156.65 70.65 1 1.00e+01 1.00e-02 6.42e+01 dihedral pdb=" CB CYS A 88 " pdb=" SG CYS A 88 " pdb=" SG CYS A 139 " pdb=" CB CYS A 139 " ideal model delta sinusoidal sigma weight residual -86.00 -136.90 50.90 1 1.00e+01 1.00e-02 3.55e+01 ... (remaining 2181 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.024: 326 0.024 - 0.048: 154 0.048 - 0.072: 71 0.072 - 0.096: 32 0.096 - 0.120: 16 Chirality restraints: 599 Sorted by residual: chirality pdb=" CA VAL A 51 " pdb=" N VAL A 51 " pdb=" C VAL A 51 " pdb=" CB VAL A 51 " both_signs ideal model delta sigma weight residual False 2.44 2.56 -0.12 2.00e-01 2.50e+01 3.58e-01 chirality pdb=" CA PRO A 461 " pdb=" N PRO A 461 " pdb=" C PRO A 461 " pdb=" CB PRO A 461 " both_signs ideal model delta sigma weight residual False 2.72 2.60 0.12 2.00e-01 2.50e+01 3.50e-01 chirality pdb=" CA PRO A 231 " pdb=" N PRO A 231 " pdb=" C PRO A 231 " pdb=" CB PRO A 231 " both_signs ideal model delta sigma weight residual False 2.72 2.60 0.12 2.00e-01 2.50e+01 3.31e-01 ... (remaining 596 not shown) Planarity restraints: 628 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG A 477 " -1.098 9.50e-02 1.11e+02 4.92e-01 1.46e+02 pdb=" NE ARG A 477 " 0.067 2.00e-02 2.50e+03 pdb=" CZ ARG A 477 " 0.011 2.00e-02 2.50e+03 pdb=" NH1 ARG A 477 " -0.013 2.00e-02 2.50e+03 pdb=" NH2 ARG A 477 " -0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PHE A 460 " 0.031 5.00e-02 4.00e+02 4.65e-02 3.46e+00 pdb=" N PRO A 461 " -0.080 5.00e-02 4.00e+02 pdb=" CA PRO A 461 " 0.024 5.00e-02 4.00e+02 pdb=" CD PRO A 461 " 0.026 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA A 267 " 0.027 5.00e-02 4.00e+02 4.12e-02 2.72e+00 pdb=" N PRO A 268 " -0.071 5.00e-02 4.00e+02 pdb=" CA PRO A 268 " 0.021 5.00e-02 4.00e+02 pdb=" CD PRO A 268 " 0.023 5.00e-02 4.00e+02 ... (remaining 625 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 492 2.75 - 3.29: 3563 3.29 - 3.83: 5808 3.83 - 4.36: 6229 4.36 - 4.90: 11095 Nonbonded interactions: 27187 Sorted by model distance: nonbonded pdb=" NH1 ARG A 172 " pdb=" OE2 GLU A 223 " model vdw 2.214 3.120 nonbonded pdb=" OD1 ASP A 123 " pdb=" OG SER A 125 " model vdw 2.246 3.040 nonbonded pdb=" OH TYR A 122 " pdb=" OD1 ASP A 136 " model vdw 2.322 3.040 nonbonded pdb=" O ASN A 306 " pdb=" ND2 ASN A 306 " model vdw 2.351 3.120 nonbonded pdb=" N GLU A 117 " pdb=" OE1 GLU A 117 " model vdw 2.399 3.120 ... (remaining 27182 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== 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: 1.160 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: 0.100 Check model and map are aligned: 0.020 Set scattering table: 0.010 Process input model: 5.570 Find NCS groups from input model: 0.010 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:1.060 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 7.950 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7560 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.082 3722 Z= 0.225 Angle : 0.775 7.093 5072 Z= 0.426 Chirality : 0.039 0.120 599 Planarity : 0.020 0.492 628 Dihedral : 17.451 86.534 1310 Min Nonbonded Distance : 2.214 Molprobity Statistics. All-atom Clashscore : 9.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.68 % Favored : 93.32 % Rotamer: Outliers : 1.03 % Allowed : 29.97 % Favored : 68.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 are not related in a simple way. whole: -0.06 (0.40), residues: 464 helix: 0.89 (0.32), residues: 302 sheet: None (None), residues: 0 loop : -1.82 (0.46), residues: 162 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 92 TYR 0.005 0.001 TYR A 122 PHE 0.015 0.001 PHE A 272 TRP 0.006 0.001 TRP A 258 HIS 0.001 0.000 HIS A 165 Details of bonding type rmsd covalent geometry : bond 0.00405 ( 3720) covalent geometry : angle 0.77546 ( 5068) SS BOND : bond 0.00288 ( 2) SS BOND : angle 0.71940 ( 4) hydrogen bonds : bond 0.15530 ( 207) hydrogen bonds : angle 5.33796 ( 603) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 928 Ramachandran restraints generated. 464 Oldfield, 0 Emsley, 464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 928 Ramachandran restraints generated. 464 Oldfield, 0 Emsley, 464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 65 residues out of total 388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 61 time to evaluate : 0.138 Fit side-chains revert: symmetry clash REVERT: A 92 ARG cc_start: 0.7393 (ttm110) cc_final: 0.7090 (mmt90) outliers start: 4 outliers final: 2 residues processed: 63 average time/residue: 0.0637 time to fit residues: 5.0702 Evaluate side-chains 57 residues out of total 388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 55 time to evaluate : 0.134 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 425 LEU Chi-restraints excluded: chain A residue 477 ARG Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 47 random chunks: chunk 24 optimal weight: 0.5980 chunk 26 optimal weight: 3.9990 chunk 2 optimal weight: 0.9980 chunk 16 optimal weight: 1.9990 chunk 32 optimal weight: 1.9990 chunk 31 optimal weight: 0.6980 chunk 25 optimal weight: 0.7980 chunk 19 optimal weight: 0.7980 chunk 30 optimal weight: 0.7980 chunk 22 optimal weight: 2.9990 chunk 37 optimal weight: 1.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 306 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4300 r_free = 0.4300 target = 0.202479 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3875 r_free = 0.3875 target = 0.157634 restraints weight = 5128.318| |-----------------------------------------------------------------------------| r_work (start): 0.3854 rms_B_bonded: 2.95 r_work: 0.3740 rms_B_bonded: 3.63 restraints_weight: 0.5000 r_work (final): 0.3740 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7714 moved from start: 0.0843 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 3722 Z= 0.137 Angle : 0.611 5.985 5072 Z= 0.304 Chirality : 0.039 0.125 599 Planarity : 0.005 0.050 628 Dihedral : 4.301 27.687 515 Min Nonbonded Distance : 2.562 Molprobity Statistics. All-atom Clashscore : 6.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.03 % Favored : 93.97 % Rotamer: Outliers : 3.88 % Allowed : 28.42 % Favored : 67.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.02 (0.39), residues: 464 helix: 0.90 (0.30), residues: 314 sheet: None (None), residues: 0 loop : -1.98 (0.46), residues: 150 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 172 TYR 0.014 0.002 TYR A 275 PHE 0.015 0.001 PHE A 204 TRP 0.006 0.001 TRP A 50 HIS 0.001 0.000 HIS A 86 Details of bonding type rmsd covalent geometry : bond 0.00306 ( 3720) covalent geometry : angle 0.61080 ( 5068) SS BOND : bond 0.00352 ( 2) SS BOND : angle 0.19723 ( 4) hydrogen bonds : bond 0.04742 ( 207) hydrogen bonds : angle 4.23698 ( 603) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 928 Ramachandran restraints generated. 464 Oldfield, 0 Emsley, 464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 928 Ramachandran restraints generated. 464 Oldfield, 0 Emsley, 464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 62 time to evaluate : 0.173 Fit side-chains revert: symmetry clash REVERT: A 92 ARG cc_start: 0.7595 (ttm110) cc_final: 0.7074 (mmt90) REVERT: A 223 GLU cc_start: 0.6864 (mt-10) cc_final: 0.6418 (mt-10) REVERT: A 318 GLU cc_start: 0.7671 (mp0) cc_final: 0.7253 (mp0) outliers start: 15 outliers final: 11 residues processed: 74 average time/residue: 0.0591 time to fit residues: 5.6285 Evaluate side-chains 68 residues out of total 388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 57 time to evaluate : 0.130 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 ASP Chi-restraints excluded: chain A residue 114 GLU Chi-restraints excluded: chain A residue 210 VAL Chi-restraints excluded: chain A residue 219 SER Chi-restraints excluded: chain A residue 275 TYR Chi-restraints excluded: chain A residue 287 ILE Chi-restraints excluded: chain A residue 293 ASP Chi-restraints excluded: chain A residue 348 LEU Chi-restraints excluded: chain A residue 388 VAL Chi-restraints excluded: chain A residue 392 VAL Chi-restraints excluded: chain A residue 432 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 47 random chunks: chunk 20 optimal weight: 0.9990 chunk 43 optimal weight: 1.9990 chunk 46 optimal weight: 0.0050 chunk 4 optimal weight: 6.9990 chunk 23 optimal weight: 0.9990 chunk 12 optimal weight: 0.8980 chunk 18 optimal weight: 0.5980 chunk 33 optimal weight: 0.0970 chunk 44 optimal weight: 0.9990 chunk 27 optimal weight: 2.9990 chunk 41 optimal weight: 0.9990 overall best weight: 0.5194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4330 r_free = 0.4330 target = 0.206107 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3943 r_free = 0.3943 target = 0.163923 restraints weight = 4908.909| |-----------------------------------------------------------------------------| r_work (start): 0.3903 rms_B_bonded: 2.76 r_work: 0.3791 rms_B_bonded: 3.45 restraints_weight: 0.5000 r_work (final): 0.3791 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7697 moved from start: 0.1185 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 3722 Z= 0.118 Angle : 0.560 5.995 5072 Z= 0.277 Chirality : 0.038 0.154 599 Planarity : 0.005 0.050 628 Dihedral : 3.886 17.383 509 Min Nonbonded Distance : 2.587 Molprobity Statistics. All-atom Clashscore : 6.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.82 % Favored : 94.18 % Rotamer: Outliers : 4.39 % Allowed : 28.68 % Favored : 66.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 are not related in a simple way. whole: 0.18 (0.40), residues: 464 helix: 0.95 (0.30), residues: 327 sheet: None (None), residues: 0 loop : -1.89 (0.48), residues: 137 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 173 TYR 0.013 0.001 TYR A 275 PHE 0.016 0.001 PHE A 204 TRP 0.008 0.001 TRP A 285 HIS 0.001 0.000 HIS A 86 Details of bonding type rmsd covalent geometry : bond 0.00264 ( 3720) covalent geometry : angle 0.55994 ( 5068) SS BOND : bond 0.00222 ( 2) SS BOND : angle 0.22588 ( 4) hydrogen bonds : bond 0.04058 ( 207) hydrogen bonds : angle 3.98108 ( 603) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 928 Ramachandran restraints generated. 464 Oldfield, 0 Emsley, 464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 928 Ramachandran restraints generated. 464 Oldfield, 0 Emsley, 464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 65 time to evaluate : 0.080 Fit side-chains REVERT: A 318 GLU cc_start: 0.7768 (mp0) cc_final: 0.7334 (mp0) outliers start: 17 outliers final: 12 residues processed: 77 average time/residue: 0.0398 time to fit residues: 4.1164 Evaluate side-chains 68 residues out of total 388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 56 time to evaluate : 0.079 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 ASP Chi-restraints excluded: chain A residue 114 GLU Chi-restraints excluded: chain A residue 210 VAL Chi-restraints excluded: chain A residue 258 TRP Chi-restraints excluded: chain A residue 275 TYR Chi-restraints excluded: chain A residue 293 ASP Chi-restraints excluded: chain A residue 348 LEU Chi-restraints excluded: chain A residue 378 ILE Chi-restraints excluded: chain A residue 388 VAL Chi-restraints excluded: chain A residue 392 VAL Chi-restraints excluded: chain A residue 425 LEU Chi-restraints excluded: chain A residue 432 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 47 random chunks: chunk 23 optimal weight: 1.9990 chunk 13 optimal weight: 3.9990 chunk 5 optimal weight: 0.0870 chunk 20 optimal weight: 0.0040 chunk 0 optimal weight: 6.9990 chunk 24 optimal weight: 0.5980 chunk 26 optimal weight: 3.9990 chunk 37 optimal weight: 4.9990 chunk 27 optimal weight: 0.9980 chunk 15 optimal weight: 1.9990 chunk 41 optimal weight: 0.0470 overall best weight: 0.3468 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4352 r_free = 0.4352 target = 0.209071 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3955 r_free = 0.3955 target = 0.165337 restraints weight = 5026.037| |-----------------------------------------------------------------------------| r_work (start): 0.3935 rms_B_bonded: 2.83 r_work: 0.3818 rms_B_bonded: 3.55 restraints_weight: 0.5000 r_work (final): 0.3818 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7695 moved from start: 0.1555 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 3722 Z= 0.108 Angle : 0.549 6.334 5072 Z= 0.271 Chirality : 0.038 0.125 599 Planarity : 0.005 0.053 628 Dihedral : 3.787 15.961 509 Min Nonbonded Distance : 2.618 Molprobity Statistics. All-atom Clashscore : 5.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.03 % Favored : 93.97 % Rotamer: Outliers : 3.88 % Allowed : 30.23 % Favored : 65.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 are not related in a simple way. whole: 0.56 (0.41), residues: 464 helix: 1.29 (0.31), residues: 327 sheet: None (None), residues: 0 loop : -1.91 (0.48), residues: 137 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 92 TYR 0.014 0.001 TYR A 275 PHE 0.016 0.001 PHE A 204 TRP 0.009 0.001 TRP A 285 HIS 0.000 0.000 HIS A 46 Details of bonding type rmsd covalent geometry : bond 0.00240 ( 3720) covalent geometry : angle 0.54951 ( 5068) SS BOND : bond 0.00177 ( 2) SS BOND : angle 0.21253 ( 4) hydrogen bonds : bond 0.03577 ( 207) hydrogen bonds : angle 3.83042 ( 603) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 928 Ramachandran restraints generated. 464 Oldfield, 0 Emsley, 464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 928 Ramachandran restraints generated. 464 Oldfield, 0 Emsley, 464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 62 time to evaluate : 0.078 Fit side-chains revert: symmetry clash REVERT: A 92 ARG cc_start: 0.7573 (ttm110) cc_final: 0.7039 (mmt90) REVERT: A 318 GLU cc_start: 0.7717 (mp0) cc_final: 0.7291 (mp0) outliers start: 15 outliers final: 11 residues processed: 72 average time/residue: 0.0430 time to fit residues: 3.8899 Evaluate side-chains 70 residues out of total 388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 59 time to evaluate : 0.077 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 ASP Chi-restraints excluded: chain A residue 75 VAL Chi-restraints excluded: chain A residue 114 GLU Chi-restraints excluded: chain A residue 210 VAL Chi-restraints excluded: chain A residue 258 TRP Chi-restraints excluded: chain A residue 275 TYR Chi-restraints excluded: chain A residue 348 LEU Chi-restraints excluded: chain A residue 378 ILE Chi-restraints excluded: chain A residue 392 VAL Chi-restraints excluded: chain A residue 425 LEU Chi-restraints excluded: chain A residue 432 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 47 random chunks: chunk 16 optimal weight: 0.7980 chunk 18 optimal weight: 0.7980 chunk 31 optimal weight: 0.5980 chunk 38 optimal weight: 0.0170 chunk 6 optimal weight: 0.0770 chunk 44 optimal weight: 0.4980 chunk 3 optimal weight: 0.9990 chunk 0 optimal weight: 6.9990 chunk 17 optimal weight: 0.6980 chunk 24 optimal weight: 0.8980 chunk 33 optimal weight: 3.9990 overall best weight: 0.3776 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4354 r_free = 0.4354 target = 0.208824 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3950 r_free = 0.3950 target = 0.165298 restraints weight = 5084.468| |-----------------------------------------------------------------------------| r_work (start): 0.3905 rms_B_bonded: 2.86 r_work: 0.3794 rms_B_bonded: 3.51 restraints_weight: 0.5000 r_work (final): 0.3794 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7678 moved from start: 0.1822 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 3722 Z= 0.108 Angle : 0.547 6.816 5072 Z= 0.268 Chirality : 0.038 0.123 599 Planarity : 0.004 0.052 628 Dihedral : 3.717 15.047 509 Min Nonbonded Distance : 2.582 Molprobity Statistics. All-atom Clashscore : 5.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.82 % Favored : 94.18 % Rotamer: Outliers : 3.62 % Allowed : 30.23 % Favored : 66.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 are not related in a simple way. whole: 0.69 (0.41), residues: 464 helix: 1.38 (0.31), residues: 327 sheet: None (None), residues: 0 loop : -1.84 (0.49), residues: 137 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 434 TYR 0.013 0.001 TYR A 275 PHE 0.017 0.001 PHE A 204 TRP 0.008 0.001 TRP A 285 HIS 0.000 0.000 HIS A 86 Details of bonding type rmsd covalent geometry : bond 0.00246 ( 3720) covalent geometry : angle 0.54765 ( 5068) SS BOND : bond 0.00188 ( 2) SS BOND : angle 0.24873 ( 4) hydrogen bonds : bond 0.03477 ( 207) hydrogen bonds : angle 3.75181 ( 603) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 928 Ramachandran restraints generated. 464 Oldfield, 0 Emsley, 464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 928 Ramachandran restraints generated. 464 Oldfield, 0 Emsley, 464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 70 residues out of total 388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 56 time to evaluate : 0.079 Fit side-chains REVERT: A 318 GLU cc_start: 0.7702 (mp0) cc_final: 0.7282 (mp0) outliers start: 14 outliers final: 11 residues processed: 65 average time/residue: 0.0326 time to fit residues: 2.8335 Evaluate side-chains 68 residues out of total 388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 57 time to evaluate : 0.074 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 LEU Chi-restraints excluded: chain A residue 70 ASP Chi-restraints excluded: chain A residue 210 VAL Chi-restraints excluded: chain A residue 236 LEU Chi-restraints excluded: chain A residue 258 TRP Chi-restraints excluded: chain A residue 275 TYR Chi-restraints excluded: chain A residue 348 LEU Chi-restraints excluded: chain A residue 378 ILE Chi-restraints excluded: chain A residue 388 VAL Chi-restraints excluded: chain A residue 392 VAL Chi-restraints excluded: chain A residue 425 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 47 random chunks: chunk 6 optimal weight: 0.0030 chunk 31 optimal weight: 0.5980 chunk 33 optimal weight: 4.9990 chunk 21 optimal weight: 1.9990 chunk 26 optimal weight: 0.0570 chunk 38 optimal weight: 0.9980 chunk 23 optimal weight: 0.9980 chunk 22 optimal weight: 0.9990 chunk 30 optimal weight: 0.6980 chunk 29 optimal weight: 10.0000 chunk 19 optimal weight: 0.9980 overall best weight: 0.4708 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4326 r_free = 0.4326 target = 0.204881 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3935 r_free = 0.3935 target = 0.163363 restraints weight = 5000.680| |-----------------------------------------------------------------------------| r_work (start): 0.3904 rms_B_bonded: 2.76 r_work: 0.3793 rms_B_bonded: 3.43 restraints_weight: 0.5000 r_work (final): 0.3793 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7697 moved from start: 0.1986 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 3722 Z= 0.109 Angle : 0.548 5.969 5072 Z= 0.269 Chirality : 0.039 0.154 599 Planarity : 0.005 0.055 628 Dihedral : 3.718 14.974 509 Min Nonbonded Distance : 2.585 Molprobity Statistics. All-atom Clashscore : 5.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.82 % Favored : 94.18 % Rotamer: Outliers : 5.17 % Allowed : 28.42 % Favored : 66.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 are not related in a simple way. whole: 0.71 (0.41), residues: 464 helix: 1.37 (0.30), residues: 327 sheet: None (None), residues: 0 loop : -1.77 (0.49), residues: 137 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 434 TYR 0.013 0.001 TYR A 275 PHE 0.016 0.001 PHE A 204 TRP 0.006 0.001 TRP A 258 HIS 0.000 0.000 HIS A 86 Details of bonding type rmsd covalent geometry : bond 0.00248 ( 3720) covalent geometry : angle 0.54845 ( 5068) SS BOND : bond 0.00208 ( 2) SS BOND : angle 0.27277 ( 4) hydrogen bonds : bond 0.03544 ( 207) hydrogen bonds : angle 3.70471 ( 603) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 928 Ramachandran restraints generated. 464 Oldfield, 0 Emsley, 464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 928 Ramachandran restraints generated. 464 Oldfield, 0 Emsley, 464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 58 time to evaluate : 0.160 Fit side-chains revert: symmetry clash REVERT: A 318 GLU cc_start: 0.7763 (mp0) cc_final: 0.7314 (mp0) outliers start: 20 outliers final: 17 residues processed: 72 average time/residue: 0.0519 time to fit residues: 4.8269 Evaluate side-chains 74 residues out of total 388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 57 time to evaluate : 0.128 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 LEU Chi-restraints excluded: chain A residue 18 LEU Chi-restraints excluded: chain A residue 70 ASP Chi-restraints excluded: chain A residue 75 VAL Chi-restraints excluded: chain A residue 121 VAL Chi-restraints excluded: chain A residue 156 ILE Chi-restraints excluded: chain A residue 210 VAL Chi-restraints excluded: chain A residue 223 GLU Chi-restraints excluded: chain A residue 236 LEU Chi-restraints excluded: chain A residue 258 TRP Chi-restraints excluded: chain A residue 275 TYR Chi-restraints excluded: chain A residue 293 ASP Chi-restraints excluded: chain A residue 348 LEU Chi-restraints excluded: chain A residue 378 ILE Chi-restraints excluded: chain A residue 388 VAL Chi-restraints excluded: chain A residue 392 VAL Chi-restraints excluded: chain A residue 425 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 47 random chunks: chunk 29 optimal weight: 0.5980 chunk 38 optimal weight: 0.8980 chunk 15 optimal weight: 0.9990 chunk 39 optimal weight: 0.6980 chunk 27 optimal weight: 2.9990 chunk 35 optimal weight: 0.1980 chunk 23 optimal weight: 0.6980 chunk 25 optimal weight: 0.7980 chunk 36 optimal weight: 3.9990 chunk 42 optimal weight: 0.7980 chunk 17 optimal weight: 1.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 306 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4334 r_free = 0.4334 target = 0.205989 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3925 r_free = 0.3925 target = 0.162663 restraints weight = 5212.615| |-----------------------------------------------------------------------------| r_work (start): 0.3886 rms_B_bonded: 2.89 r_work: 0.3772 rms_B_bonded: 3.56 restraints_weight: 0.5000 r_work (final): 0.3772 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7732 moved from start: 0.2091 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 3722 Z= 0.115 Angle : 0.551 7.298 5072 Z= 0.271 Chirality : 0.038 0.136 599 Planarity : 0.005 0.066 628 Dihedral : 3.715 15.305 509 Min Nonbonded Distance : 2.403 Molprobity Statistics. All-atom Clashscore : 5.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.82 % Favored : 94.18 % Rotamer: Outliers : 4.65 % Allowed : 29.72 % Favored : 65.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 are not related in a simple way. whole: 0.81 (0.41), residues: 464 helix: 1.39 (0.30), residues: 332 sheet: None (None), residues: 0 loop : -1.67 (0.51), residues: 132 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 434 TYR 0.013 0.001 TYR A 275 PHE 0.016 0.001 PHE A 204 TRP 0.006 0.001 TRP A 50 HIS 0.001 0.000 HIS A 165 Details of bonding type rmsd covalent geometry : bond 0.00265 ( 3720) covalent geometry : angle 0.55145 ( 5068) SS BOND : bond 0.00242 ( 2) SS BOND : angle 0.30930 ( 4) hydrogen bonds : bond 0.03725 ( 207) hydrogen bonds : angle 3.73061 ( 603) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 928 Ramachandran restraints generated. 464 Oldfield, 0 Emsley, 464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 928 Ramachandran restraints generated. 464 Oldfield, 0 Emsley, 464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 57 time to evaluate : 0.133 Fit side-chains REVERT: A 92 ARG cc_start: 0.7514 (ttm110) cc_final: 0.7088 (mtt-85) REVERT: A 318 GLU cc_start: 0.7722 (mp0) cc_final: 0.7273 (mp0) outliers start: 18 outliers final: 16 residues processed: 71 average time/residue: 0.0554 time to fit residues: 5.1362 Evaluate side-chains 70 residues out of total 388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 54 time to evaluate : 0.130 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 LEU Chi-restraints excluded: chain A residue 70 ASP Chi-restraints excluded: chain A residue 75 VAL Chi-restraints excluded: chain A residue 156 ILE Chi-restraints excluded: chain A residue 210 VAL Chi-restraints excluded: chain A residue 219 SER Chi-restraints excluded: chain A residue 223 GLU Chi-restraints excluded: chain A residue 236 LEU Chi-restraints excluded: chain A residue 258 TRP Chi-restraints excluded: chain A residue 275 TYR Chi-restraints excluded: chain A residue 293 ASP Chi-restraints excluded: chain A residue 348 LEU Chi-restraints excluded: chain A residue 378 ILE Chi-restraints excluded: chain A residue 388 VAL Chi-restraints excluded: chain A residue 392 VAL Chi-restraints excluded: chain A residue 425 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 47 random chunks: chunk 24 optimal weight: 0.8980 chunk 10 optimal weight: 1.9990 chunk 4 optimal weight: 5.9990 chunk 31 optimal weight: 0.6980 chunk 14 optimal weight: 4.9990 chunk 46 optimal weight: 0.0010 chunk 9 optimal weight: 0.0070 chunk 3 optimal weight: 0.5980 chunk 38 optimal weight: 0.0870 chunk 23 optimal weight: 0.9990 chunk 30 optimal weight: 1.9990 overall best weight: 0.2782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 306 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4344 r_free = 0.4344 target = 0.206720 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3956 r_free = 0.3956 target = 0.165361 restraints weight = 5015.347| |-----------------------------------------------------------------------------| r_work (start): 0.3946 rms_B_bonded: 2.78 r_work: 0.3831 rms_B_bonded: 3.49 restraints_weight: 0.5000 r_work (final): 0.3831 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7671 moved from start: 0.2219 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 3722 Z= 0.103 Angle : 0.539 6.960 5072 Z= 0.264 Chirality : 0.038 0.130 599 Planarity : 0.005 0.054 628 Dihedral : 3.661 14.291 509 Min Nonbonded Distance : 2.607 Molprobity Statistics. All-atom Clashscore : 5.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.82 % Favored : 94.18 % Rotamer: Outliers : 3.88 % Allowed : 31.27 % Favored : 64.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 are not related in a simple way. whole: 0.93 (0.41), residues: 464 helix: 1.48 (0.30), residues: 332 sheet: None (None), residues: 0 loop : -1.63 (0.51), residues: 132 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 434 TYR 0.013 0.001 TYR A 275 PHE 0.017 0.001 PHE A 204 TRP 0.009 0.001 TRP A 285 HIS 0.000 0.000 HIS A 46 Details of bonding type rmsd covalent geometry : bond 0.00228 ( 3720) covalent geometry : angle 0.53946 ( 5068) SS BOND : bond 0.00170 ( 2) SS BOND : angle 0.09755 ( 4) hydrogen bonds : bond 0.03307 ( 207) hydrogen bonds : angle 3.65295 ( 603) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 928 Ramachandran restraints generated. 464 Oldfield, 0 Emsley, 464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 928 Ramachandran restraints generated. 464 Oldfield, 0 Emsley, 464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 57 time to evaluate : 0.081 Fit side-chains REVERT: A 318 GLU cc_start: 0.7760 (mp0) cc_final: 0.7264 (mp0) outliers start: 15 outliers final: 14 residues processed: 67 average time/residue: 0.0309 time to fit residues: 2.8308 Evaluate side-chains 70 residues out of total 388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 56 time to evaluate : 0.077 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 LEU Chi-restraints excluded: chain A residue 70 ASP Chi-restraints excluded: chain A residue 75 VAL Chi-restraints excluded: chain A residue 156 ILE Chi-restraints excluded: chain A residue 219 SER Chi-restraints excluded: chain A residue 223 GLU Chi-restraints excluded: chain A residue 258 TRP Chi-restraints excluded: chain A residue 275 TYR Chi-restraints excluded: chain A residue 293 ASP Chi-restraints excluded: chain A residue 348 LEU Chi-restraints excluded: chain A residue 378 ILE Chi-restraints excluded: chain A residue 388 VAL Chi-restraints excluded: chain A residue 392 VAL Chi-restraints excluded: chain A residue 425 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 47 random chunks: chunk 38 optimal weight: 1.9990 chunk 16 optimal weight: 2.9990 chunk 34 optimal weight: 0.7980 chunk 26 optimal weight: 4.9990 chunk 13 optimal weight: 3.9990 chunk 8 optimal weight: 4.9990 chunk 19 optimal weight: 3.9990 chunk 20 optimal weight: 0.5980 chunk 33 optimal weight: 1.9990 chunk 14 optimal weight: 0.6980 chunk 18 optimal weight: 0.9990 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 306 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4288 r_free = 0.4288 target = 0.200336 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3894 r_free = 0.3894 target = 0.159395 restraints weight = 4922.525| |-----------------------------------------------------------------------------| r_work (start): 0.3880 rms_B_bonded: 2.68 r_work: 0.3765 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.3765 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7791 moved from start: 0.2366 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 3722 Z= 0.144 Angle : 0.582 6.413 5072 Z= 0.290 Chirality : 0.040 0.138 599 Planarity : 0.005 0.054 628 Dihedral : 3.843 17.033 509 Min Nonbonded Distance : 2.345 Molprobity Statistics. All-atom Clashscore : 5.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.47 % Favored : 93.53 % Rotamer: Outliers : 4.13 % Allowed : 31.78 % Favored : 64.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 are not related in a simple way. whole: 0.74 (0.40), residues: 464 helix: 1.31 (0.30), residues: 332 sheet: None (None), residues: 0 loop : -1.62 (0.52), residues: 132 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 428 TYR 0.011 0.001 TYR A 275 PHE 0.017 0.002 PHE A 362 TRP 0.009 0.001 TRP A 278 HIS 0.001 0.000 HIS A 86 Details of bonding type rmsd covalent geometry : bond 0.00339 ( 3720) covalent geometry : angle 0.58209 ( 5068) SS BOND : bond 0.00331 ( 2) SS BOND : angle 0.53032 ( 4) hydrogen bonds : bond 0.04464 ( 207) hydrogen bonds : angle 3.87764 ( 603) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 928 Ramachandran restraints generated. 464 Oldfield, 0 Emsley, 464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 928 Ramachandran restraints generated. 464 Oldfield, 0 Emsley, 464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 70 residues out of total 388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 54 time to evaluate : 0.157 Fit side-chains REVERT: A 92 ARG cc_start: 0.7478 (ttm110) cc_final: 0.7061 (mtt-85) REVERT: A 318 GLU cc_start: 0.7788 (mp0) cc_final: 0.7324 (mp0) outliers start: 16 outliers final: 16 residues processed: 66 average time/residue: 0.0525 time to fit residues: 4.6468 Evaluate side-chains 66 residues out of total 388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 50 time to evaluate : 0.134 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 LEU Chi-restraints excluded: chain A residue 70 ASP Chi-restraints excluded: chain A residue 75 VAL Chi-restraints excluded: chain A residue 156 ILE Chi-restraints excluded: chain A residue 193 MET Chi-restraints excluded: chain A residue 210 VAL Chi-restraints excluded: chain A residue 219 SER Chi-restraints excluded: chain A residue 236 LEU Chi-restraints excluded: chain A residue 258 TRP Chi-restraints excluded: chain A residue 275 TYR Chi-restraints excluded: chain A residue 293 ASP Chi-restraints excluded: chain A residue 348 LEU Chi-restraints excluded: chain A residue 378 ILE Chi-restraints excluded: chain A residue 388 VAL Chi-restraints excluded: chain A residue 392 VAL Chi-restraints excluded: chain A residue 425 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 47 random chunks: chunk 24 optimal weight: 3.9990 chunk 6 optimal weight: 0.0670 chunk 35 optimal weight: 2.9990 chunk 13 optimal weight: 3.9990 chunk 37 optimal weight: 0.7980 chunk 40 optimal weight: 1.9990 chunk 0 optimal weight: 6.9990 chunk 41 optimal weight: 4.9990 chunk 1 optimal weight: 3.9990 chunk 34 optimal weight: 0.8980 chunk 8 optimal weight: 0.0040 overall best weight: 0.7532 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4282 r_free = 0.4282 target = 0.200104 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3887 r_free = 0.3887 target = 0.159087 restraints weight = 4965.703| |-----------------------------------------------------------------------------| r_work (start): 0.3859 rms_B_bonded: 2.74 r_work: 0.3745 rms_B_bonded: 3.41 restraints_weight: 0.5000 r_work (final): 0.3745 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7753 moved from start: 0.2461 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 3722 Z= 0.124 Angle : 0.570 7.477 5072 Z= 0.281 Chirality : 0.039 0.140 599 Planarity : 0.005 0.054 628 Dihedral : 3.858 17.076 509 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 5.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.68 % Favored : 93.32 % Rotamer: Outliers : 3.88 % Allowed : 32.30 % Favored : 63.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 are not related in a simple way. whole: 0.72 (0.40), residues: 464 helix: 1.23 (0.30), residues: 338 sheet: None (None), residues: 0 loop : -1.54 (0.53), residues: 126 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 428 TYR 0.011 0.001 TYR A 275 PHE 0.015 0.002 PHE A 204 TRP 0.008 0.001 TRP A 495 HIS 0.001 0.000 HIS A 86 Details of bonding type rmsd covalent geometry : bond 0.00287 ( 3720) covalent geometry : angle 0.57029 ( 5068) SS BOND : bond 0.00292 ( 2) SS BOND : angle 0.44044 ( 4) hydrogen bonds : bond 0.04075 ( 207) hydrogen bonds : angle 3.83580 ( 603) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 928 Ramachandran restraints generated. 464 Oldfield, 0 Emsley, 464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 928 Ramachandran restraints generated. 464 Oldfield, 0 Emsley, 464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 56 time to evaluate : 0.106 Fit side-chains REVERT: A 92 ARG cc_start: 0.7499 (ttm110) cc_final: 0.7072 (mtt-85) REVERT: A 318 GLU cc_start: 0.7751 (mp0) cc_final: 0.7307 (mp0) REVERT: A 434 ARG cc_start: 0.8034 (ttp80) cc_final: 0.7803 (ttm-80) outliers start: 15 outliers final: 15 residues processed: 68 average time/residue: 0.0398 time to fit residues: 3.5324 Evaluate side-chains 68 residues out of total 388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 53 time to evaluate : 0.078 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 LEU Chi-restraints excluded: chain A residue 70 ASP Chi-restraints excluded: chain A residue 75 VAL Chi-restraints excluded: chain A residue 156 ILE Chi-restraints excluded: chain A residue 210 VAL Chi-restraints excluded: chain A residue 219 SER Chi-restraints excluded: chain A residue 236 LEU Chi-restraints excluded: chain A residue 258 TRP Chi-restraints excluded: chain A residue 275 TYR Chi-restraints excluded: chain A residue 293 ASP Chi-restraints excluded: chain A residue 348 LEU Chi-restraints excluded: chain A residue 378 ILE Chi-restraints excluded: chain A residue 388 VAL Chi-restraints excluded: chain A residue 392 VAL Chi-restraints excluded: chain A residue 425 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 47 random chunks: chunk 29 optimal weight: 0.0060 chunk 3 optimal weight: 0.8980 chunk 8 optimal weight: 4.9990 chunk 41 optimal weight: 0.4980 chunk 24 optimal weight: 0.9980 chunk 28 optimal weight: 0.0770 chunk 45 optimal weight: 0.0870 chunk 12 optimal weight: 0.4980 chunk 2 optimal weight: 0.9990 chunk 33 optimal weight: 1.9990 chunk 14 optimal weight: 4.9990 overall best weight: 0.2332 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 306 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4334 r_free = 0.4334 target = 0.206324 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3941 r_free = 0.3941 target = 0.164527 restraints weight = 5007.616| |-----------------------------------------------------------------------------| r_work (start): 0.3929 rms_B_bonded: 2.77 r_work: 0.3818 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work (final): 0.3818 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7684 moved from start: 0.2594 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 3722 Z= 0.107 Angle : 0.555 7.988 5072 Z= 0.271 Chirality : 0.038 0.122 599 Planarity : 0.005 0.054 628 Dihedral : 3.758 14.811 509 Min Nonbonded Distance : 2.352 Molprobity Statistics. All-atom Clashscore : 5.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.60 % Favored : 94.40 % Rotamer: Outliers : 3.36 % Allowed : 32.82 % Favored : 63.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 are not related in a simple way. whole: 0.95 (0.41), residues: 464 helix: 1.40 (0.30), residues: 338 sheet: None (None), residues: 0 loop : -1.48 (0.54), residues: 126 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 428 TYR 0.013 0.001 TYR A 275 PHE 0.017 0.001 PHE A 204 TRP 0.009 0.001 TRP A 285 HIS 0.001 0.000 HIS A 165 Details of bonding type rmsd covalent geometry : bond 0.00234 ( 3720) covalent geometry : angle 0.55522 ( 5068) SS BOND : bond 0.00185 ( 2) SS BOND : angle 0.15586 ( 4) hydrogen bonds : bond 0.03299 ( 207) hydrogen bonds : angle 3.66557 ( 603) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 925.95 seconds wall clock time: 16 minutes 32.62 seconds (992.62 seconds total)