Starting phenix.real_space_refine on Wed Jul 1 23:13:32 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9rwt_54347/07_2026/9rwt_54347.cif Found real_map, /net/cci-nas-00/data/ceres_data/9rwt_54347/07_2026/9rwt_54347.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.83 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9rwt_54347/07_2026/9rwt_54347.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9rwt_54347/07_2026/9rwt_54347.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9rwt_54347/07_2026/9rwt_54347.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9rwt_54347/07_2026/9rwt_54347.map" } resolution = 2.83 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= 0.001 sd= 0.039 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: 5 Type Number sf(0) Gaussians S 23 5.16 5 Na 1 4.78 5 C 2602 2.51 5 N 606 2.21 5 O 663 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 2 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 3895 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 3894 Number of conformers: 1 Conformer: "" Number of residues, atoms: 512, 3894 Classifications: {'peptide': 512} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 23, 'TRANS': 488} Chain breaks: 1 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'HIS:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 0 Ad-hoc single atom residues: {' NA': 1} Chain breaks: 1 Time building chain proxies: 1.13, per 1000 atoms: 0.29 Number of scatterers: 3895 At special positions: 0 Unit cell: (73.3182, 65.0802, 81.5562, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 23 16.00 Na 1 11.00 O 663 8.00 N 606 7.00 C 2602 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: 0.33 Conformation dependent library (CDL) restraints added in 154.9 milliseconds 1016 Ramachandran restraints generated. 508 Oldfield, 0 Emsley, 508 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 920 Finding SS restraints... Secondary structure from input PDB file: 28 helices and 1 sheets defined 82.4% alpha, 0.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.12 Creating SS restraints... Processing helix chain 'A' and resid 23 through 43 Processing helix chain 'A' and resid 47 through 69 removed outlier: 3.952A pdb=" N THR A 68 " --> pdb=" O ILE A 64 " (cutoff:3.500A) Processing helix chain 'A' and resid 87 through 97 Processing helix chain 'A' and resid 101 through 115 Processing helix chain 'A' and resid 116 through 120 Processing helix chain 'A' and resid 121 through 136 Processing helix chain 'A' and resid 136 through 144 removed outlier: 3.750A pdb=" N LYS A 140 " --> pdb=" O PHE A 136 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N TYR A 144 " --> pdb=" O LYS A 140 " (cutoff:3.500A) Processing helix chain 'A' and resid 150 through 158 removed outlier: 3.723A pdb=" N ARG A 156 " --> pdb=" O PRO A 152 " (cutoff:3.500A) Processing helix chain 'A' and resid 158 through 165 removed outlier: 3.545A pdb=" N ALA A 162 " --> pdb=" O GLY A 158 " (cutoff:3.500A) Processing helix chain 'A' and resid 165 through 193 removed outlier: 4.518A pdb=" N ALA A 169 " --> pdb=" O LEU A 165 " (cutoff:3.500A) Processing helix chain 'A' and resid 195 through 213 Processing helix chain 'A' and resid 220 through 246 removed outlier: 4.000A pdb=" N VAL A 224 " --> pdb=" O ALA A 220 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N ALA A 225 " --> pdb=" O LEU A 221 " (cutoff:3.500A) Proline residue: A 239 - end of helix Processing helix chain 'A' and resid 247 through 259 Processing helix chain 'A' and resid 270 through 274 Processing helix chain 'A' and resid 279 through 295 removed outlier: 3.596A pdb=" N ASN A 283 " --> pdb=" O ASN A 279 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N GLY A 295 " --> pdb=" O LEU A 291 " (cutoff:3.500A) Processing helix chain 'A' and resid 298 through 306 Processing helix chain 'A' and resid 310 through 341 removed outlier: 4.088A pdb=" N VAL A 330 " --> pdb=" O ILE A 326 " (cutoff:3.500A) Proline residue: A 331 - end of helix removed outlier: 3.733A pdb=" N SER A 341 " --> pdb=" O VAL A 337 " (cutoff:3.500A) Processing helix chain 'A' and resid 343 through 348 Processing helix chain 'A' and resid 354 through 356 No H-bonds generated for 'chain 'A' and resid 354 through 356' Processing helix chain 'A' and resid 357 through 366 Processing helix chain 'A' and resid 368 through 402 Processing helix chain 'A' and resid 412 through 415 Processing helix chain 'A' and resid 416 through 438 removed outlier: 3.539A pdb=" N ILE A 425 " --> pdb=" O ARG A 421 " (cutoff:3.500A) Processing helix chain 'A' and resid 440 through 455 removed outlier: 3.628A pdb=" N ALA A 449 " --> pdb=" O TRP A 445 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N LEU A 451 " --> pdb=" O LEU A 447 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N VAL A 452 " --> pdb=" O CYS A 448 " (cutoff:3.500A) Processing helix chain 'A' and resid 455 through 465 removed outlier: 3.821A pdb=" N GLN A 459 " --> pdb=" O MET A 455 " (cutoff:3.500A) Processing helix chain 'A' and resid 470 through 489 removed outlier: 3.776A pdb=" N GLY A 488 " --> pdb=" O LEU A 484 " (cutoff:3.500A) Processing helix chain 'A' and resid 490 through 494 Processing helix chain 'A' and resid 512 through 532 Processing sheet with id=AA1, first strand: chain 'A' and resid 504 through 505 294 hydrogen bonds defined for protein. 849 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: 0.86 Time building geometry restraints manager: 0.44 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 1151 1.34 - 1.46: 1016 1.46 - 1.58: 1793 1.58 - 1.70: 0 1.70 - 1.81: 42 Bond restraints: 4002 Sorted by residual: bond pdb=" CB MET A 518 " pdb=" CG MET A 518 " ideal model delta sigma weight residual 1.520 1.468 0.052 3.00e-02 1.11e+03 3.02e+00 bond pdb=" CB PRO A 540 " pdb=" CG PRO A 540 " ideal model delta sigma weight residual 1.492 1.575 -0.083 5.00e-02 4.00e+02 2.74e+00 bond pdb=" CG MET A 518 " pdb=" SD MET A 518 " ideal model delta sigma weight residual 1.803 1.763 0.040 2.50e-02 1.60e+03 2.51e+00 bond pdb=" SD MET A 518 " pdb=" CE MET A 518 " ideal model delta sigma weight residual 1.791 1.759 0.032 2.50e-02 1.60e+03 1.60e+00 bond pdb=" C ALA A 122 " pdb=" N PRO A 123 " ideal model delta sigma weight residual 1.334 1.360 -0.026 2.34e-02 1.83e+03 1.25e+00 ... (remaining 3997 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.50: 5412 2.50 - 4.99: 48 4.99 - 7.49: 7 7.49 - 9.99: 0 9.99 - 12.48: 2 Bond angle restraints: 5469 Sorted by residual: angle pdb=" CB MET A 518 " pdb=" CG MET A 518 " pdb=" SD MET A 518 " ideal model delta sigma weight residual 112.70 100.22 12.48 3.00e+00 1.11e-01 1.73e+01 angle pdb=" CB MET A 397 " pdb=" CG MET A 397 " pdb=" SD MET A 397 " ideal model delta sigma weight residual 112.70 102.65 10.05 3.00e+00 1.11e-01 1.12e+01 angle pdb=" CA TYR A 453 " pdb=" CB TYR A 453 " pdb=" CG TYR A 453 " ideal model delta sigma weight residual 113.90 119.05 -5.15 1.80e+00 3.09e-01 8.18e+00 angle pdb=" CA TYR A 446 " pdb=" CB TYR A 446 " pdb=" CG TYR A 446 " ideal model delta sigma weight residual 113.90 118.96 -5.06 1.80e+00 3.09e-01 7.90e+00 angle pdb=" N LEU A 265 " pdb=" CA LEU A 265 " pdb=" CB LEU A 265 " ideal model delta sigma weight residual 113.65 110.23 3.42 1.47e+00 4.63e-01 5.42e+00 ... (remaining 5464 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.33: 2057 17.33 - 34.65: 188 34.65 - 51.98: 23 51.98 - 69.30: 2 69.30 - 86.63: 2 Dihedral angle restraints: 2272 sinusoidal: 818 harmonic: 1454 Sorted by residual: dihedral pdb=" CG ARG A 143 " pdb=" CD ARG A 143 " pdb=" NE ARG A 143 " pdb=" CZ ARG A 143 " ideal model delta sinusoidal sigma weight residual 90.00 131.28 -41.28 2 1.50e+01 4.44e-03 9.28e+00 dihedral pdb=" CG ARG A 304 " pdb=" CD ARG A 304 " pdb=" NE ARG A 304 " pdb=" CZ ARG A 304 " ideal model delta sinusoidal sigma weight residual 180.00 -139.45 -40.55 2 1.50e+01 4.44e-03 9.02e+00 dihedral pdb=" CB ARG A 84 " pdb=" CG ARG A 84 " pdb=" CD ARG A 84 " pdb=" NE ARG A 84 " ideal model delta sinusoidal sigma weight residual 60.00 103.11 -43.11 3 1.50e+01 4.44e-03 7.74e+00 ... (remaining 2269 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.031: 398 0.031 - 0.062: 162 0.062 - 0.094: 59 0.094 - 0.125: 17 0.125 - 0.156: 2 Chirality restraints: 638 Sorted by residual: chirality pdb=" CG LEU A 522 " pdb=" CB LEU A 522 " pdb=" CD1 LEU A 522 " pdb=" CD2 LEU A 522 " both_signs ideal model delta sigma weight residual False -2.59 -2.75 0.16 2.00e-01 2.50e+01 6.07e-01 chirality pdb=" CA TYR A 446 " pdb=" N TYR A 446 " pdb=" C TYR A 446 " pdb=" CB TYR A 446 " both_signs ideal model delta sigma weight residual False 2.51 2.38 0.13 2.00e-01 2.50e+01 4.30e-01 chirality pdb=" CA MET A 86 " pdb=" N MET A 86 " pdb=" C MET A 86 " pdb=" CB MET A 86 " both_signs ideal model delta sigma weight residual False 2.51 2.63 -0.12 2.00e-01 2.50e+01 3.63e-01 ... (remaining 635 not shown) Planarity restraints: 661 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PRO A 537 " 0.029 5.00e-02 4.00e+02 4.52e-02 3.26e+00 pdb=" N PRO A 538 " -0.078 5.00e-02 4.00e+02 pdb=" CA PRO A 538 " 0.024 5.00e-02 4.00e+02 pdb=" CD PRO A 538 " 0.025 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE A 511 " -0.027 5.00e-02 4.00e+02 4.03e-02 2.60e+00 pdb=" N PRO A 512 " 0.070 5.00e-02 4.00e+02 pdb=" CA PRO A 512 " -0.021 5.00e-02 4.00e+02 pdb=" CD PRO A 512 " -0.023 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 453 " 0.016 2.00e-02 2.50e+03 9.81e-03 1.93e+00 pdb=" CG TYR A 453 " -0.021 2.00e-02 2.50e+03 pdb=" CD1 TYR A 453 " -0.006 2.00e-02 2.50e+03 pdb=" CD2 TYR A 453 " -0.001 2.00e-02 2.50e+03 pdb=" CE1 TYR A 453 " 0.006 2.00e-02 2.50e+03 pdb=" CE2 TYR A 453 " 0.002 2.00e-02 2.50e+03 pdb=" CZ TYR A 453 " 0.003 2.00e-02 2.50e+03 pdb=" OH TYR A 453 " 0.001 2.00e-02 2.50e+03 ... (remaining 658 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.79: 945 2.79 - 3.32: 3907 3.32 - 3.84: 6880 3.84 - 4.37: 7818 4.37 - 4.90: 13819 Nonbonded interactions: 33369 Sorted by model distance: nonbonded pdb=" O LEU A 130 " pdb=" OG SER A 318 " model vdw 2.258 3.040 nonbonded pdb=" O VAL A 363 " pdb=" OG SER A 367 " model vdw 2.262 3.040 nonbonded pdb=" OE2 GLU A 110 " pdb=" OG SER A 440 " model vdw 2.281 3.040 nonbonded pdb=" OG1 THR A 211 " pdb=" OD1 ASP A 388 " model vdw 2.327 3.040 nonbonded pdb=" O LYS A 468 " pdb=" NE2 GLN A 533 " model vdw 2.334 3.120 ... (remaining 33364 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: 1.640 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: 0.010 Set scattering table: 0.010 Process input model: 6.560 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:9.990 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.330 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7700 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 0.083 4002 Z= 0.145 Angle : 0.614 12.485 5469 Z= 0.304 Chirality : 0.040 0.156 638 Planarity : 0.005 0.045 661 Dihedral : 12.597 86.628 1352 Min Nonbonded Distance : 2.258 Molprobity Statistics. All-atom Clashscore : 9.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer: Outliers : 0.00 % Allowed : 0.25 % Favored : 99.75 % 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: 1.40 (0.38), residues: 508 helix: 1.60 (0.26), residues: 379 sheet: None (None), residues: 0 loop : -1.08 (0.56), residues: 129 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 156 TYR 0.023 0.002 TYR A 446 PHE 0.014 0.001 PHE A 188 TRP 0.010 0.001 TRP A 124 Details of bonding type rmsd/Z covalent geometry : bond 0.00353 / 0.15 ( 4002) covalent geometry : angle 0.61417 / 0.30 ( 5469) hydrogen bonds : bond 0.12610 / 9.31 ( 294) hydrogen bonds : angle 5.48199 / 3.88 ( 849) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1016 Ramachandran restraints generated. 508 Oldfield, 0 Emsley, 508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1016 Ramachandran restraints generated. 508 Oldfield, 0 Emsley, 508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 397 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 73 time to evaluate : 0.100 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 73 average time/residue: 0.3181 time to fit residues: 24.2537 Evaluate side-chains 63 residues out of total 397 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 63 time to evaluate : 0.130 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 51 random chunks: chunk 24 optimal weight: 2.9990 chunk 48 optimal weight: 2.9990 chunk 26 optimal weight: 0.6980 chunk 2 optimal weight: 3.9990 chunk 16 optimal weight: 0.0980 chunk 32 optimal weight: 0.7980 chunk 31 optimal weight: 0.5980 chunk 25 optimal weight: 0.7980 chunk 50 optimal weight: 9.9990 chunk 19 optimal weight: 0.9990 chunk 30 optimal weight: 0.9980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 299 GLN A 533 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4391 r_free = 0.4391 target = 0.223591 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4202 r_free = 0.4202 target = 0.203238 restraints weight = 4217.237| |-----------------------------------------------------------------------------| r_work (start): 0.4213 rms_B_bonded: 1.39 r_work: 0.4140 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.4046 rms_B_bonded: 4.17 restraints_weight: 0.2500 r_work (final): 0.4046 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7720 moved from start: 0.0920 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 4002 Z= 0.134 Angle : 0.551 6.322 5469 Z= 0.280 Chirality : 0.040 0.126 638 Planarity : 0.005 0.052 661 Dihedral : 3.799 12.801 548 Min Nonbonded Distance : 2.587 Molprobity Statistics. All-atom Clashscore : 8.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 2.02 % Allowed : 8.33 % Favored : 89.65 % 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: 1.68 (0.38), residues: 508 helix: 1.78 (0.26), residues: 379 sheet: None (None), residues: 0 loop : -0.88 (0.57), residues: 129 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 404 TYR 0.022 0.001 TYR A 446 PHE 0.012 0.001 PHE A 188 TRP 0.011 0.001 TRP A 298 Details of bonding type rmsd/Z covalent geometry : bond 0.00308 / 0.13 ( 4002) covalent geometry : angle 0.55139 / 0.28 ( 5469) hydrogen bonds : bond 0.03892 / 2.62 ( 294) hydrogen bonds : angle 4.38521 / 3.17 ( 849) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1016 Ramachandran restraints generated. 508 Oldfield, 0 Emsley, 508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1016 Ramachandran restraints generated. 508 Oldfield, 0 Emsley, 508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 397 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 68 time to evaluate : 0.109 Fit side-chains outliers start: 8 outliers final: 2 residues processed: 70 average time/residue: 0.3380 time to fit residues: 24.8021 Evaluate side-chains 63 residues out of total 397 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 61 time to evaluate : 0.093 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 141 MET Chi-restraints excluded: chain A residue 370 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 51 random chunks: chunk 35 optimal weight: 0.7980 chunk 42 optimal weight: 2.9990 chunk 43 optimal weight: 5.9990 chunk 21 optimal weight: 0.6980 chunk 0 optimal weight: 5.9990 chunk 9 optimal weight: 0.5980 chunk 5 optimal weight: 0.6980 chunk 48 optimal weight: 0.5980 chunk 28 optimal weight: 0.8980 chunk 12 optimal weight: 1.9990 chunk 15 optimal weight: 0.8980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 299 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4386 r_free = 0.4386 target = 0.222915 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4196 r_free = 0.4196 target = 0.202180 restraints weight = 4154.161| |-----------------------------------------------------------------------------| r_work (start): 0.4210 rms_B_bonded: 1.40 r_work: 0.4137 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.4042 rms_B_bonded: 4.15 restraints_weight: 0.2500 r_work (final): 0.4042 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7739 moved from start: 0.1141 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 4002 Z= 0.133 Angle : 0.536 6.307 5469 Z= 0.273 Chirality : 0.039 0.132 638 Planarity : 0.005 0.050 661 Dihedral : 3.809 13.194 548 Min Nonbonded Distance : 2.606 Molprobity Statistics. All-atom Clashscore : 7.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer: Outliers : 2.02 % Allowed : 10.10 % Favored : 87.88 % 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: 1.80 (0.38), residues: 508 helix: 1.84 (0.27), residues: 382 sheet: None (None), residues: 0 loop : -0.82 (0.59), residues: 126 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 304 TYR 0.023 0.002 TYR A 446 PHE 0.012 0.001 PHE A 188 TRP 0.013 0.001 TRP A 298 Details of bonding type rmsd/Z covalent geometry : bond 0.00311 / 0.13 ( 4002) covalent geometry : angle 0.53562 / 0.27 ( 5469) hydrogen bonds : bond 0.03731 / 2.48 ( 294) hydrogen bonds : angle 4.23457 / 3.06 ( 849) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1016 Ramachandran restraints generated. 508 Oldfield, 0 Emsley, 508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1016 Ramachandran restraints generated. 508 Oldfield, 0 Emsley, 508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 397 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 68 time to evaluate : 0.137 Fit side-chains REVERT: A 404 ARG cc_start: 0.6139 (mmt180) cc_final: 0.5901 (mmt180) REVERT: A 455 MET cc_start: 0.7630 (mtm) cc_final: 0.7409 (mtt) outliers start: 8 outliers final: 2 residues processed: 71 average time/residue: 0.2881 time to fit residues: 21.6297 Evaluate side-chains 64 residues out of total 397 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 62 time to evaluate : 0.130 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 234 MET Chi-restraints excluded: chain A residue 370 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 51 random chunks: chunk 17 optimal weight: 4.9990 chunk 48 optimal weight: 2.9990 chunk 2 optimal weight: 0.9990 chunk 25 optimal weight: 0.8980 chunk 23 optimal weight: 0.6980 chunk 44 optimal weight: 0.9990 chunk 13 optimal weight: 0.8980 chunk 15 optimal weight: 0.8980 chunk 12 optimal weight: 1.9990 chunk 20 optimal weight: 0.6980 chunk 1 optimal weight: 0.9980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 299 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4377 r_free = 0.4377 target = 0.221863 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4180 r_free = 0.4180 target = 0.200458 restraints weight = 4118.431| |-----------------------------------------------------------------------------| r_work (start): 0.4205 rms_B_bonded: 1.46 r_work: 0.4132 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.4043 rms_B_bonded: 4.11 restraints_weight: 0.2500 r_work (final): 0.4043 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7737 moved from start: 0.1281 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 4002 Z= 0.143 Angle : 0.545 6.353 5469 Z= 0.277 Chirality : 0.040 0.137 638 Planarity : 0.005 0.052 661 Dihedral : 3.865 13.327 548 Min Nonbonded Distance : 2.608 Molprobity Statistics. All-atom Clashscore : 8.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 2.53 % Allowed : 12.88 % Favored : 84.60 % 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: 1.73 (0.38), residues: 508 helix: 1.71 (0.26), residues: 390 sheet: None (None), residues: 0 loop : -0.69 (0.61), residues: 118 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 156 TYR 0.023 0.002 TYR A 446 PHE 0.011 0.001 PHE A 53 TRP 0.014 0.001 TRP A 298 Details of bonding type rmsd/Z covalent geometry : bond 0.00338 / 0.14 ( 4002) covalent geometry : angle 0.54514 / 0.28 ( 5469) hydrogen bonds : bond 0.03757 / 2.49 ( 294) hydrogen bonds : angle 4.22764 / 3.06 ( 849) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1016 Ramachandran restraints generated. 508 Oldfield, 0 Emsley, 508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1016 Ramachandran restraints generated. 508 Oldfield, 0 Emsley, 508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 397 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 70 time to evaluate : 0.137 Fit side-chains outliers start: 10 outliers final: 4 residues processed: 72 average time/residue: 0.3501 time to fit residues: 26.6046 Evaluate side-chains 68 residues out of total 397 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 64 time to evaluate : 0.124 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 141 MET Chi-restraints excluded: chain A residue 234 MET Chi-restraints excluded: chain A residue 370 LEU Chi-restraints excluded: chain A residue 388 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 51 random chunks: chunk 36 optimal weight: 0.9990 chunk 29 optimal weight: 0.8980 chunk 15 optimal weight: 1.9990 chunk 49 optimal weight: 1.9990 chunk 37 optimal weight: 0.4980 chunk 6 optimal weight: 0.6980 chunk 34 optimal weight: 0.6980 chunk 35 optimal weight: 0.6980 chunk 3 optimal weight: 0.6980 chunk 38 optimal weight: 1.9990 chunk 41 optimal weight: 0.5980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 299 GLN A 303 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4382 r_free = 0.4382 target = 0.222939 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4194 r_free = 0.4194 target = 0.202269 restraints weight = 4195.149| |-----------------------------------------------------------------------------| r_work (start): 0.4210 rms_B_bonded: 1.40 r_work: 0.4136 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.4041 rms_B_bonded: 4.22 restraints_weight: 0.2500 r_work (final): 0.4041 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7756 moved from start: 0.1391 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 4002 Z= 0.129 Angle : 0.532 6.374 5469 Z= 0.270 Chirality : 0.039 0.134 638 Planarity : 0.005 0.052 661 Dihedral : 3.826 13.312 548 Min Nonbonded Distance : 2.609 Molprobity Statistics. All-atom Clashscore : 8.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 3.03 % Allowed : 15.15 % Favored : 81.82 % 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: 1.81 (0.38), residues: 508 helix: 1.76 (0.26), residues: 390 sheet: None (None), residues: 0 loop : -0.62 (0.61), residues: 118 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 156 TYR 0.021 0.001 TYR A 446 PHE 0.020 0.001 PHE A 28 TRP 0.013 0.001 TRP A 298 Details of bonding type rmsd/Z covalent geometry : bond 0.00302 / 0.13 ( 4002) covalent geometry : angle 0.53238 / 0.27 ( 5469) hydrogen bonds : bond 0.03596 / 2.38 ( 294) hydrogen bonds : angle 4.17361 / 3.01 ( 849) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1016 Ramachandran restraints generated. 508 Oldfield, 0 Emsley, 508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1016 Ramachandran restraints generated. 508 Oldfield, 0 Emsley, 508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 397 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 72 time to evaluate : 0.140 Fit side-chains REVERT: A 404 ARG cc_start: 0.6192 (mmt180) cc_final: 0.5326 (mmm-85) outliers start: 12 outliers final: 6 residues processed: 75 average time/residue: 0.3308 time to fit residues: 26.2319 Evaluate side-chains 71 residues out of total 397 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 65 time to evaluate : 0.117 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 141 MET Chi-restraints excluded: chain A residue 173 GLU Chi-restraints excluded: chain A residue 216 MET Chi-restraints excluded: chain A residue 234 MET Chi-restraints excluded: chain A residue 370 LEU Chi-restraints excluded: chain A residue 388 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 51 random chunks: chunk 41 optimal weight: 0.7980 chunk 25 optimal weight: 1.9990 chunk 32 optimal weight: 1.9990 chunk 46 optimal weight: 0.5980 chunk 44 optimal weight: 1.9990 chunk 28 optimal weight: 2.9990 chunk 33 optimal weight: 0.7980 chunk 39 optimal weight: 0.9990 chunk 36 optimal weight: 0.7980 chunk 24 optimal weight: 0.7980 chunk 12 optimal weight: 3.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 299 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4380 r_free = 0.4380 target = 0.222139 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4180 r_free = 0.4180 target = 0.200439 restraints weight = 4219.579| |-----------------------------------------------------------------------------| r_work (start): 0.4200 rms_B_bonded: 1.48 r_work: 0.4127 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.4035 rms_B_bonded: 4.21 restraints_weight: 0.2500 r_work (final): 0.4035 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7738 moved from start: 0.1511 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 4002 Z= 0.139 Angle : 0.552 6.318 5469 Z= 0.278 Chirality : 0.040 0.137 638 Planarity : 0.005 0.052 661 Dihedral : 3.867 13.356 548 Min Nonbonded Distance : 2.582 Molprobity Statistics. All-atom Clashscore : 8.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 3.28 % Allowed : 16.41 % Favored : 80.30 % 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: 1.73 (0.38), residues: 508 helix: 1.71 (0.26), residues: 391 sheet: None (None), residues: 0 loop : -0.70 (0.62), residues: 117 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 156 TYR 0.022 0.001 TYR A 446 PHE 0.016 0.001 PHE A 28 TRP 0.015 0.001 TRP A 298 Details of bonding type rmsd/Z covalent geometry : bond 0.00329 / 0.14 ( 4002) covalent geometry : angle 0.55195 / 0.28 ( 5469) hydrogen bonds : bond 0.03648 / 2.41 ( 294) hydrogen bonds : angle 4.18671 / 3.02 ( 849) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1016 Ramachandran restraints generated. 508 Oldfield, 0 Emsley, 508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1016 Ramachandran restraints generated. 508 Oldfield, 0 Emsley, 508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 397 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 68 time to evaluate : 0.142 Fit side-chains REVERT: A 188 PHE cc_start: 0.7275 (OUTLIER) cc_final: 0.6644 (m-10) REVERT: A 404 ARG cc_start: 0.6228 (mmt180) cc_final: 0.5452 (mtm180) outliers start: 13 outliers final: 5 residues processed: 72 average time/residue: 0.3194 time to fit residues: 24.2869 Evaluate side-chains 72 residues out of total 397 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 66 time to evaluate : 0.139 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 141 MET Chi-restraints excluded: chain A residue 173 GLU Chi-restraints excluded: chain A residue 188 PHE Chi-restraints excluded: chain A residue 234 MET Chi-restraints excluded: chain A residue 370 LEU Chi-restraints excluded: chain A residue 388 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 51 random chunks: chunk 5 optimal weight: 0.4980 chunk 4 optimal weight: 0.9980 chunk 28 optimal weight: 1.9990 chunk 41 optimal weight: 0.5980 chunk 17 optimal weight: 0.0980 chunk 12 optimal weight: 3.9990 chunk 46 optimal weight: 1.9990 chunk 33 optimal weight: 0.7980 chunk 30 optimal weight: 2.9990 chunk 39 optimal weight: 0.6980 chunk 35 optimal weight: 0.6980 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 299 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4395 r_free = 0.4395 target = 0.224196 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4205 r_free = 0.4205 target = 0.203228 restraints weight = 4296.341| |-----------------------------------------------------------------------------| r_work (start): 0.4222 rms_B_bonded: 1.43 r_work: 0.4145 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.4052 rms_B_bonded: 4.28 restraints_weight: 0.2500 r_work (final): 0.4052 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7746 moved from start: 0.1567 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 4002 Z= 0.122 Angle : 0.538 6.388 5469 Z= 0.270 Chirality : 0.039 0.137 638 Planarity : 0.005 0.053 661 Dihedral : 3.808 13.382 548 Min Nonbonded Distance : 2.599 Molprobity Statistics. All-atom Clashscore : 9.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 2.27 % Allowed : 17.68 % Favored : 80.05 % 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: 1.86 (0.38), residues: 508 helix: 1.81 (0.26), residues: 391 sheet: None (None), residues: 0 loop : -0.69 (0.63), residues: 117 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 156 TYR 0.020 0.001 TYR A 446 PHE 0.015 0.001 PHE A 28 TRP 0.014 0.001 TRP A 298 Details of bonding type rmsd/Z covalent geometry : bond 0.00280 / 0.12 ( 4002) covalent geometry : angle 0.53756 / 0.27 ( 5469) hydrogen bonds : bond 0.03469 / 2.29 ( 294) hydrogen bonds : angle 4.11828 / 2.96 ( 849) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1016 Ramachandran restraints generated. 508 Oldfield, 0 Emsley, 508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1016 Ramachandran restraints generated. 508 Oldfield, 0 Emsley, 508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 397 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 74 time to evaluate : 0.139 Fit side-chains REVERT: A 188 PHE cc_start: 0.7263 (OUTLIER) cc_final: 0.6608 (m-10) REVERT: A 404 ARG cc_start: 0.6259 (mmt180) cc_final: 0.5497 (mtm180) outliers start: 9 outliers final: 4 residues processed: 77 average time/residue: 0.3242 time to fit residues: 26.3735 Evaluate side-chains 72 residues out of total 397 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 67 time to evaluate : 0.129 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 141 MET Chi-restraints excluded: chain A residue 188 PHE Chi-restraints excluded: chain A residue 216 MET Chi-restraints excluded: chain A residue 234 MET Chi-restraints excluded: chain A residue 388 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 51 random chunks: chunk 12 optimal weight: 0.2980 chunk 37 optimal weight: 0.9990 chunk 46 optimal weight: 0.8980 chunk 6 optimal weight: 1.9990 chunk 23 optimal weight: 0.2980 chunk 44 optimal weight: 2.9990 chunk 27 optimal weight: 0.8980 chunk 47 optimal weight: 0.9990 chunk 42 optimal weight: 1.9990 chunk 1 optimal weight: 2.9990 chunk 29 optimal weight: 1.9990 overall best weight: 0.6782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4388 r_free = 0.4388 target = 0.222991 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4190 r_free = 0.4190 target = 0.201384 restraints weight = 4158.164| |-----------------------------------------------------------------------------| r_work (start): 0.4204 rms_B_bonded: 1.46 r_work: 0.4129 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.4035 rms_B_bonded: 4.32 restraints_weight: 0.2500 r_work (final): 0.4035 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7744 moved from start: 0.1582 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 4002 Z= 0.134 Angle : 0.562 6.471 5469 Z= 0.282 Chirality : 0.040 0.151 638 Planarity : 0.005 0.053 661 Dihedral : 3.867 13.587 548 Min Nonbonded Distance : 2.585 Molprobity Statistics. All-atom Clashscore : 9.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 2.78 % Allowed : 18.43 % Favored : 78.79 % 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: 1.85 (0.38), residues: 508 helix: 1.86 (0.26), residues: 386 sheet: None (None), residues: 0 loop : -0.81 (0.61), residues: 122 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 156 TYR 0.022 0.002 TYR A 446 PHE 0.013 0.001 PHE A 28 TRP 0.015 0.001 TRP A 298 Details of bonding type rmsd/Z covalent geometry : bond 0.00315 / 0.13 ( 4002) covalent geometry : angle 0.56167 / 0.28 ( 5469) hydrogen bonds : bond 0.03596 / 2.38 ( 294) hydrogen bonds : angle 4.15883 / 2.99 ( 849) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1016 Ramachandran restraints generated. 508 Oldfield, 0 Emsley, 508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1016 Ramachandran restraints generated. 508 Oldfield, 0 Emsley, 508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 397 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 70 time to evaluate : 0.134 Fit side-chains REVERT: A 188 PHE cc_start: 0.7260 (OUTLIER) cc_final: 0.6611 (m-10) REVERT: A 404 ARG cc_start: 0.6193 (mmt180) cc_final: 0.5449 (mtm180) outliers start: 11 outliers final: 5 residues processed: 73 average time/residue: 0.3356 time to fit residues: 25.8125 Evaluate side-chains 73 residues out of total 397 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 67 time to evaluate : 0.134 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 141 MET Chi-restraints excluded: chain A residue 188 PHE Chi-restraints excluded: chain A residue 216 MET Chi-restraints excluded: chain A residue 234 MET Chi-restraints excluded: chain A residue 370 LEU Chi-restraints excluded: chain A residue 388 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 51 random chunks: chunk 9 optimal weight: 0.5980 chunk 39 optimal weight: 0.9980 chunk 42 optimal weight: 0.7980 chunk 20 optimal weight: 0.8980 chunk 46 optimal weight: 1.9990 chunk 16 optimal weight: 0.0980 chunk 30 optimal weight: 1.9990 chunk 27 optimal weight: 0.4980 chunk 49 optimal weight: 0.5980 chunk 44 optimal weight: 1.9990 chunk 48 optimal weight: 0.9980 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4401 r_free = 0.4401 target = 0.224930 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4215 r_free = 0.4215 target = 0.203992 restraints weight = 4260.920| |-----------------------------------------------------------------------------| r_work (start): 0.4219 rms_B_bonded: 1.42 r_work: 0.4143 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.4047 rms_B_bonded: 4.31 restraints_weight: 0.2500 r_work (final): 0.4047 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7726 moved from start: 0.1649 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 4002 Z= 0.124 Angle : 0.555 6.578 5469 Z= 0.279 Chirality : 0.039 0.134 638 Planarity : 0.005 0.052 661 Dihedral : 3.855 13.679 548 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 9.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer: Outliers : 2.27 % Allowed : 19.44 % Favored : 78.28 % 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: 1.91 (0.39), residues: 508 helix: 1.96 (0.27), residues: 381 sheet: None (None), residues: 0 loop : -0.89 (0.60), residues: 127 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 156 TYR 0.020 0.001 TYR A 446 PHE 0.014 0.001 PHE A 28 TRP 0.014 0.001 TRP A 298 Details of bonding type rmsd/Z covalent geometry : bond 0.00285 / 0.12 ( 4002) covalent geometry : angle 0.55519 / 0.28 ( 5469) hydrogen bonds : bond 0.03492 / 2.32 ( 294) hydrogen bonds : angle 4.13303 / 2.96 ( 849) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1016 Ramachandran restraints generated. 508 Oldfield, 0 Emsley, 508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1016 Ramachandran restraints generated. 508 Oldfield, 0 Emsley, 508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 397 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 68 time to evaluate : 0.140 Fit side-chains REVERT: A 188 PHE cc_start: 0.7193 (OUTLIER) cc_final: 0.6575 (m-10) REVERT: A 404 ARG cc_start: 0.6184 (mmt180) cc_final: 0.5445 (mtm180) outliers start: 9 outliers final: 5 residues processed: 71 average time/residue: 0.3345 time to fit residues: 25.0604 Evaluate side-chains 73 residues out of total 397 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 67 time to evaluate : 0.136 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 141 MET Chi-restraints excluded: chain A residue 188 PHE Chi-restraints excluded: chain A residue 216 MET Chi-restraints excluded: chain A residue 234 MET Chi-restraints excluded: chain A residue 259 MET Chi-restraints excluded: chain A residue 388 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 51 random chunks: chunk 47 optimal weight: 0.9990 chunk 17 optimal weight: 0.7980 chunk 27 optimal weight: 1.9990 chunk 43 optimal weight: 1.9990 chunk 15 optimal weight: 1.9990 chunk 46 optimal weight: 1.9990 chunk 30 optimal weight: 1.9990 chunk 49 optimal weight: 0.9990 chunk 32 optimal weight: 0.6980 chunk 34 optimal weight: 0.8980 chunk 50 optimal weight: 0.8980 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4383 r_free = 0.4383 target = 0.222406 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4192 r_free = 0.4192 target = 0.201181 restraints weight = 4171.298| |-----------------------------------------------------------------------------| r_work (start): 0.4198 rms_B_bonded: 1.43 r_work: 0.4123 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.4028 rms_B_bonded: 4.25 restraints_weight: 0.2500 r_work (final): 0.4028 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7763 moved from start: 0.1673 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 4002 Z= 0.152 Angle : 0.610 6.936 5469 Z= 0.304 Chirality : 0.041 0.146 638 Planarity : 0.005 0.052 661 Dihedral : 4.011 13.924 548 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 9.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 1.52 % Allowed : 20.45 % Favored : 78.03 % 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: 1.70 (0.38), residues: 508 helix: 1.81 (0.26), residues: 381 sheet: None (None), residues: 0 loop : -0.97 (0.59), residues: 127 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 156 TYR 0.023 0.002 TYR A 446 PHE 0.012 0.001 PHE A 498 TRP 0.018 0.001 TRP A 298 Details of bonding type rmsd/Z covalent geometry : bond 0.00363 / 0.15 ( 4002) covalent geometry : angle 0.61012 / 0.30 ( 5469) hydrogen bonds : bond 0.03789 / 2.51 ( 294) hydrogen bonds : angle 4.25508 / 3.06 ( 849) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1016 Ramachandran restraints generated. 508 Oldfield, 0 Emsley, 508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1016 Ramachandran restraints generated. 508 Oldfield, 0 Emsley, 508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 397 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 67 time to evaluate : 0.146 Fit side-chains REVERT: A 188 PHE cc_start: 0.7261 (OUTLIER) cc_final: 0.6662 (m-10) REVERT: A 404 ARG cc_start: 0.6194 (mmt180) cc_final: 0.5450 (mtm180) outliers start: 6 outliers final: 5 residues processed: 68 average time/residue: 0.3708 time to fit residues: 26.4663 Evaluate side-chains 71 residues out of total 397 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 65 time to evaluate : 0.130 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 141 MET Chi-restraints excluded: chain A residue 188 PHE Chi-restraints excluded: chain A residue 234 MET Chi-restraints excluded: chain A residue 259 MET Chi-restraints excluded: chain A residue 370 LEU Chi-restraints excluded: chain A residue 388 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 51 random chunks: chunk 16 optimal weight: 0.4980 chunk 22 optimal weight: 0.9990 chunk 45 optimal weight: 0.7980 chunk 33 optimal weight: 4.9990 chunk 12 optimal weight: 0.2980 chunk 29 optimal weight: 3.9990 chunk 34 optimal weight: 0.8980 chunk 35 optimal weight: 0.9990 chunk 18 optimal weight: 5.9990 chunk 5 optimal weight: 0.5980 chunk 25 optimal weight: 2.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 299 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4398 r_free = 0.4398 target = 0.224561 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4218 r_free = 0.4218 target = 0.204064 restraints weight = 4187.589| |-----------------------------------------------------------------------------| r_work (start): 0.4219 rms_B_bonded: 1.38 r_work: 0.4144 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.4049 rms_B_bonded: 4.14 restraints_weight: 0.2500 r_work (final): 0.4049 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7736 moved from start: 0.1717 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 4002 Z= 0.132 Angle : 0.580 6.798 5469 Z= 0.290 Chirality : 0.040 0.138 638 Planarity : 0.004 0.051 661 Dihedral : 3.947 13.847 548 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 9.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer: Outliers : 1.52 % Allowed : 20.96 % Favored : 77.53 % 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: 1.79 (0.38), residues: 508 helix: 1.87 (0.26), residues: 381 sheet: None (None), residues: 0 loop : -0.94 (0.60), residues: 127 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 156 TYR 0.021 0.001 TYR A 446 PHE 0.012 0.001 PHE A 28 TRP 0.015 0.001 TRP A 298 Details of bonding type rmsd/Z covalent geometry : bond 0.00306 / 0.13 ( 4002) covalent geometry : angle 0.57975 / 0.29 ( 5469) hydrogen bonds : bond 0.03599 / 2.38 ( 294) hydrogen bonds : angle 4.22772 / 3.03 ( 849) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1369.04 seconds wall clock time: 24 minutes 5.15 seconds (1445.15 seconds total)