Starting phenix.real_space_refine on Wed Jun 3 11:05:40 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9rwt_54347/06_2026/9rwt_54347.cif Found real_map, /net/cci-nas-00/data/ceres_data/9rwt_54347/06_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_54347/06_2026/9rwt_54347.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9rwt_54347/06_2026/9rwt_54347.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9rwt_54347/06_2026/9rwt_54347.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9rwt_54347/06_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-6079/lib/python3.9/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, 1 Unusual residues: {' NA': 1} Classifications: {'undetermined': 1} Time building chain proxies: 1.16, per 1000 atoms: 0.30 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 154.1 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: 0.63 Time building geometry restraints manager: 0.45 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: 1.170 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: 0.070 Check model and map are aligned: 0.020 Set scattering table: 0.010 Process input model: 5.700 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:6.050 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.040 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7459 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 : 0.146 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 73 average time/residue: 0.4155 time to fit residues: 31.6938 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 : 0.083 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: 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 = 0.223473 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4195 r_free = 0.4195 target = 0.202411 restraints weight = 4217.621| |-----------------------------------------------------------------------------| r_work (start): 0.4206 rms_B_bonded: 1.46 r_work: 0.4133 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.4038 rms_B_bonded: 4.31 restraints_weight: 0.2500 r_work (final): 0.4038 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7476 moved from start: 0.0898 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 4002 Z= 0.135 Angle : 0.553 6.345 5469 Z= 0.281 Chirality : 0.040 0.128 638 Planarity : 0.005 0.052 661 Dihedral : 3.790 12.852 548 Min Nonbonded Distance : 2.581 Molprobity Statistics. All-atom Clashscore : 8.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer: Outliers : 2.02 % Allowed : 8.59 % Favored : 89.39 % 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 : -0.89 (0.56), residues: 129 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 404 TYR 0.022 0.002 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 0.00312 / 0.14 ( 4002) covalent geometry : angle 0.55325 / 0.28 ( 5469) hydrogen bonds : bond 0.03962 / 2.67 ( 294) hydrogen bonds : angle 4.39659 / 3.18 ( 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 : 0.143 Fit side-chains outliers start: 8 outliers final: 2 residues processed: 70 average time/residue: 0.3853 time to fit residues: 28.3142 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 : 0.140 ------------------------------------------------------------------------------- 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: 1.9990 chunk 42 optimal weight: 2.9990 chunk 43 optimal weight: 5.9990 chunk 21 optimal weight: 0.5980 chunk 0 optimal weight: 5.9990 chunk 9 optimal weight: 0.5980 chunk 5 optimal weight: 0.4980 chunk 48 optimal weight: 0.5980 chunk 28 optimal weight: 1.9990 chunk 12 optimal weight: 1.9990 chunk 15 optimal weight: 0.8980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 299 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4389 r_free = 0.4389 target = 0.223301 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4196 r_free = 0.4196 target = 0.202107 restraints weight = 4154.188| |-----------------------------------------------------------------------------| r_work (start): 0.4211 rms_B_bonded: 1.47 r_work: 0.4137 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.4046 rms_B_bonded: 4.23 restraints_weight: 0.2500 r_work (final): 0.4046 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7486 moved from start: 0.1126 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= 0.131 Angle : 0.531 6.246 5469 Z= 0.270 Chirality : 0.039 0.132 638 Planarity : 0.005 0.050 661 Dihedral : 3.795 13.096 548 Min Nonbonded Distance : 2.618 Molprobity Statistics. All-atom Clashscore : 7.60 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: 1.85 (0.38), residues: 508 helix: 1.91 (0.27), residues: 379 sheet: None (None), residues: 0 loop : -0.86 (0.58), residues: 129 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 304 TYR 0.022 0.001 TYR A 446 PHE 0.011 0.001 PHE A 188 TRP 0.012 0.001 TRP A 298 Details of bonding type rmsd/Z covalent geometry : bond 0.00304 / 0.13 ( 4002) covalent geometry : angle 0.53052 / 0.27 ( 5469) hydrogen bonds : bond 0.03717 / 2.47 ( 294) hydrogen bonds : angle 4.23163 / 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 79 residues out of total 397 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 71 time to evaluate : 0.155 Fit side-chains REVERT: A 404 ARG cc_start: 0.6132 (mmt180) cc_final: 0.5888 (mmt180) REVERT: A 455 MET cc_start: 0.7643 (mtm) cc_final: 0.7410 (mtt) outliers start: 8 outliers final: 1 residues processed: 73 average time/residue: 0.3337 time to fit residues: 25.6915 Evaluate side-chains 63 residues out of total 397 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 62 time to evaluate : 0.167 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 234 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 51 random chunks: chunk 17 optimal weight: 3.9990 chunk 48 optimal weight: 0.9980 chunk 2 optimal weight: 0.1980 chunk 25 optimal weight: 0.8980 chunk 23 optimal weight: 0.9980 chunk 44 optimal weight: 3.9990 chunk 13 optimal weight: 0.6980 chunk 15 optimal weight: 0.7980 chunk 12 optimal weight: 2.9990 chunk 20 optimal weight: 0.8980 chunk 1 optimal weight: 0.9980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 299 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4384 r_free = 0.4384 target = 0.222628 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4188 r_free = 0.4188 target = 0.201342 restraints weight = 4137.336| |-----------------------------------------------------------------------------| r_work (start): 0.4201 rms_B_bonded: 1.47 r_work: 0.4127 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.4033 rms_B_bonded: 4.24 restraints_weight: 0.2500 r_work (final): 0.4033 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7497 moved from start: 0.1268 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 4002 Z= 0.134 Angle : 0.537 6.361 5469 Z= 0.272 Chirality : 0.039 0.133 638 Planarity : 0.005 0.051 661 Dihedral : 3.816 13.350 548 Min Nonbonded Distance : 2.615 Molprobity Statistics. All-atom Clashscore : 8.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 2.27 % Allowed : 12.88 % Favored : 84.85 % 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: 1.75 (0.26), residues: 390 sheet: None (None), residues: 0 loop : -0.66 (0.61), residues: 118 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 156 TYR 0.023 0.001 TYR A 446 PHE 0.010 0.001 PHE A 53 TRP 0.014 0.001 TRP A 298 Details of bonding type rmsd/Z covalent geometry : bond 0.00315 / 0.13 ( 4002) covalent geometry : angle 0.53684 / 0.27 ( 5469) hydrogen bonds : bond 0.03654 / 2.42 ( 294) hydrogen bonds : angle 4.19696 / 3.04 ( 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 79 residues out of total 397 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 70 time to evaluate : 0.090 Fit side-chains REVERT: A 404 ARG cc_start: 0.6089 (mmt180) cc_final: 0.5857 (mmt180) outliers start: 9 outliers final: 4 residues processed: 72 average time/residue: 0.3547 time to fit residues: 26.8288 Evaluate side-chains 67 residues out of total 397 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 63 time to evaluate : 0.162 ------------------------------------------------------------------------------- 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: 0.8980 chunk 29 optimal weight: 0.1980 chunk 15 optimal weight: 1.9990 chunk 49 optimal weight: 0.1980 chunk 37 optimal weight: 0.5980 chunk 6 optimal weight: 0.9980 chunk 34 optimal weight: 0.7980 chunk 35 optimal weight: 0.9980 chunk 3 optimal weight: 0.6980 chunk 38 optimal weight: 0.2980 chunk 41 optimal weight: 0.7980 overall best weight: 0.3980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.4403 r_free = 0.4403 target = 0.224761 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4210 r_free = 0.4210 target = 0.203670 restraints weight = 4159.446| |-----------------------------------------------------------------------------| r_work (start): 0.4218 rms_B_bonded: 1.46 r_work: 0.4145 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.4051 rms_B_bonded: 4.27 restraints_weight: 0.2500 r_work (final): 0.4051 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7461 moved from start: 0.1425 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 4002 Z= 0.114 Angle : 0.510 6.423 5469 Z= 0.259 Chirality : 0.039 0.128 638 Planarity : 0.005 0.051 661 Dihedral : 3.730 13.338 548 Min Nonbonded Distance : 2.593 Molprobity Statistics. All-atom Clashscore : 8.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 2.78 % Allowed : 15.15 % Favored : 82.07 % 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: 1.98 (0.38), residues: 508 helix: 1.89 (0.26), residues: 390 sheet: None (None), residues: 0 loop : -0.61 (0.62), residues: 118 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 514 TYR 0.020 0.001 TYR A 446 PHE 0.024 0.001 PHE A 28 TRP 0.012 0.001 TRP A 298 Details of bonding type rmsd/Z covalent geometry : bond 0.00258 / 0.11 ( 4002) covalent geometry : angle 0.51050 / 0.26 ( 5469) hydrogen bonds : bond 0.03394 / 2.24 ( 294) hydrogen bonds : angle 4.09906 / 2.95 ( 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 82 residues out of total 397 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 71 time to evaluate : 0.145 Fit side-chains REVERT: A 404 ARG cc_start: 0.6089 (mmt180) cc_final: 0.5371 (mtm180) outliers start: 11 outliers final: 5 residues processed: 74 average time/residue: 0.3269 time to fit residues: 25.5684 Evaluate side-chains 68 residues out of total 397 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 63 time to evaluate : 0.142 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 141 MET 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: 2.9990 chunk 25 optimal weight: 1.9990 chunk 32 optimal weight: 0.9980 chunk 46 optimal weight: 0.9980 chunk 44 optimal weight: 3.9990 chunk 28 optimal weight: 3.9990 chunk 33 optimal weight: 0.5980 chunk 39 optimal weight: 1.9990 chunk 36 optimal weight: 0.6980 chunk 24 optimal weight: 1.9990 chunk 12 optimal weight: 3.9990 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 299 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4369 r_free = 0.4369 target = 0.220867 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4168 r_free = 0.4168 target = 0.199152 restraints weight = 4210.185| |-----------------------------------------------------------------------------| r_work (start): 0.4193 rms_B_bonded: 1.47 r_work: 0.4120 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.4026 rms_B_bonded: 4.21 restraints_weight: 0.2500 r_work (final): 0.4026 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7521 moved from start: 0.1500 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 4002 Z= 0.165 Angle : 0.589 6.273 5469 Z= 0.297 Chirality : 0.041 0.145 638 Planarity : 0.005 0.053 661 Dihedral : 3.941 13.435 548 Min Nonbonded Distance : 2.579 Molprobity Statistics. All-atom Clashscore : 9.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 2.27 % Allowed : 16.41 % Favored : 81.31 % 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: 1.77 (0.26), residues: 385 sheet: None (None), residues: 0 loop : -0.90 (0.60), residues: 123 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 156 TYR 0.026 0.002 TYR A 446 PHE 0.017 0.002 PHE A 28 TRP 0.016 0.002 TRP A 298 Details of bonding type rmsd/Z covalent geometry : bond 0.00398 / 0.16 ( 4002) covalent geometry : angle 0.58853 / 0.30 ( 5469) hydrogen bonds : bond 0.03901 / 2.58 ( 294) hydrogen bonds : angle 4.25255 / 3.07 ( 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 76 residues out of total 397 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 67 time to evaluate : 0.186 Fit side-chains REVERT: A 188 PHE cc_start: 0.7264 (OUTLIER) cc_final: 0.6593 (m-10) outliers start: 9 outliers final: 6 residues processed: 70 average time/residue: 0.3695 time to fit residues: 27.1907 Evaluate side-chains 72 residues out of total 397 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 65 time to evaluate : 0.098 ------------------------------------------------------------------------------- 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 315 MET Chi-restraints excluded: chain A residue 370 LEU Chi-restraints excluded: chain A residue 388 ASP Chi-restraints excluded: chain A residue 455 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 51 random chunks: chunk 5 optimal weight: 0.6980 chunk 4 optimal weight: 1.9990 chunk 28 optimal weight: 0.5980 chunk 41 optimal weight: 2.9990 chunk 17 optimal weight: 1.9990 chunk 12 optimal weight: 3.9990 chunk 46 optimal weight: 0.9980 chunk 33 optimal weight: 6.9990 chunk 30 optimal weight: 1.9990 chunk 39 optimal weight: 0.6980 chunk 35 optimal weight: 0.8980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 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 = 0.222044 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4180 r_free = 0.4180 target = 0.200387 restraints weight = 4249.335| |-----------------------------------------------------------------------------| r_work (start): 0.4199 rms_B_bonded: 1.48 r_work: 0.4126 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.4034 rms_B_bonded: 4.22 restraints_weight: 0.2500 r_work (final): 0.4034 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7498 moved from start: 0.1545 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= 0.140 Angle : 0.558 6.351 5469 Z= 0.281 Chirality : 0.040 0.137 638 Planarity : 0.005 0.054 661 Dihedral : 3.905 13.705 548 Min Nonbonded Distance : 2.588 Molprobity Statistics. All-atom Clashscore : 8.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 2.78 % Allowed : 17.68 % Favored : 79.55 % 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: 1.78 (0.26), residues: 386 sheet: None (None), residues: 0 loop : -0.88 (0.60), residues: 122 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 0.00330 / 0.14 ( 4002) covalent geometry : angle 0.55834 / 0.28 ( 5469) hydrogen bonds : bond 0.03670 / 2.43 ( 294) hydrogen bonds : angle 4.20365 / 3.03 ( 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 81 residues out of total 397 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 70 time to evaluate : 0.150 Fit side-chains REVERT: A 188 PHE cc_start: 0.7278 (OUTLIER) cc_final: 0.6661 (m-10) REVERT: A 404 ARG cc_start: 0.6137 (mmt180) cc_final: 0.5407 (mtm180) outliers start: 11 outliers final: 5 residues processed: 73 average time/residue: 0.3718 time to fit residues: 28.4983 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 : 0.146 ------------------------------------------------------------------------------- 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 315 MET Chi-restraints excluded: chain A residue 370 LEU 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: 0.7980 chunk 37 optimal weight: 0.9980 chunk 46 optimal weight: 0.7980 chunk 6 optimal weight: 2.9990 chunk 23 optimal weight: 0.5980 chunk 44 optimal weight: 1.9990 chunk 27 optimal weight: 1.9990 chunk 47 optimal weight: 0.7980 chunk 42 optimal weight: 0.4980 chunk 1 optimal weight: 2.9990 chunk 29 optimal weight: 0.0980 overall best weight: 0.5580 ------------------------------------------------------------------------------- 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 = 0.4390 r_free = 0.4390 target = 0.223768 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4202 r_free = 0.4202 target = 0.202937 restraints weight = 4197.512| |-----------------------------------------------------------------------------| r_work (start): 0.4218 rms_B_bonded: 1.41 r_work: 0.4141 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.4047 rms_B_bonded: 4.27 restraints_weight: 0.2500 r_work (final): 0.4047 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7507 moved from start: 0.1585 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 4002 Z= 0.125 Angle : 0.540 6.392 5469 Z= 0.272 Chirality : 0.039 0.132 638 Planarity : 0.005 0.055 661 Dihedral : 3.843 14.082 548 Min Nonbonded Distance : 2.574 Molprobity Statistics. All-atom Clashscore : 8.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 3.03 % Allowed : 18.69 % 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: 1.88 (0.38), residues: 508 helix: 1.89 (0.26), residues: 386 sheet: None (None), residues: 0 loop : -0.85 (0.61), residues: 122 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 0.015 0.001 PHE A 28 TRP 0.015 0.001 TRP A 298 Details of bonding type rmsd/Z covalent geometry : bond 0.00288 / 0.12 ( 4002) covalent geometry : angle 0.54032 / 0.27 ( 5469) hydrogen bonds : bond 0.03491 / 2.31 ( 294) hydrogen bonds : angle 4.13762 / 2.97 ( 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 83 residues out of total 397 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 71 time to evaluate : 0.181 Fit side-chains REVERT: A 188 PHE cc_start: 0.7260 (OUTLIER) cc_final: 0.6619 (m-10) REVERT: A 404 ARG cc_start: 0.6244 (mmt180) cc_final: 0.5480 (mtm180) outliers start: 12 outliers final: 5 residues processed: 74 average time/residue: 0.3774 time to fit residues: 29.3625 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 : 0.138 ------------------------------------------------------------------------------- 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 51 random chunks: chunk 9 optimal weight: 0.7980 chunk 39 optimal weight: 0.8980 chunk 42 optimal weight: 0.7980 chunk 20 optimal weight: 0.7980 chunk 46 optimal weight: 1.9990 chunk 16 optimal weight: 0.4980 chunk 30 optimal weight: 0.5980 chunk 27 optimal weight: 0.6980 chunk 49 optimal weight: 2.9990 chunk 44 optimal weight: 1.9990 chunk 48 optimal weight: 0.9980 overall best weight: 0.6780 ------------------------------------------------------------------------------- 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 = 0.4387 r_free = 0.4387 target = 0.222837 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4189 r_free = 0.4189 target = 0.201218 restraints weight = 4225.872| |-----------------------------------------------------------------------------| r_work (start): 0.4199 rms_B_bonded: 1.48 r_work: 0.4123 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.4028 rms_B_bonded: 4.37 restraints_weight: 0.2500 r_work (final): 0.4028 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7502 moved from start: 0.1601 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 4002 Z= 0.134 Angle : 0.557 6.452 5469 Z= 0.281 Chirality : 0.040 0.150 638 Planarity : 0.005 0.055 661 Dihedral : 3.872 13.603 548 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 9.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 2.53 % Allowed : 19.44 % 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: 1.87 (0.38), residues: 508 helix: 1.87 (0.26), residues: 385 sheet: None (None), residues: 0 loop : -0.79 (0.61), residues: 123 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 0.014 0.001 PHE A 28 TRP 0.017 0.001 TRP A 298 Details of bonding type rmsd/Z covalent geometry : bond 0.00315 / 0.13 ( 4002) covalent geometry : angle 0.55662 / 0.28 ( 5469) hydrogen bonds : bond 0.03586 / 2.38 ( 294) hydrogen bonds : angle 4.16538 / 2.99 ( 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 79 residues out of total 397 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 69 time to evaluate : 0.091 Fit side-chains REVERT: A 188 PHE cc_start: 0.7260 (OUTLIER) cc_final: 0.6648 (m-10) REVERT: A 404 ARG cc_start: 0.6186 (mmt180) cc_final: 0.5430 (mtm180) outliers start: 10 outliers final: 5 residues processed: 72 average time/residue: 0.3623 time to fit residues: 27.4138 Evaluate side-chains 74 residues out of total 397 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 68 time to evaluate : 0.168 ------------------------------------------------------------------------------- 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 51 random chunks: chunk 47 optimal weight: 1.9990 chunk 17 optimal weight: 2.9990 chunk 27 optimal weight: 1.9990 chunk 43 optimal weight: 1.9990 chunk 15 optimal weight: 1.9990 chunk 46 optimal weight: 0.6980 chunk 30 optimal weight: 0.9990 chunk 49 optimal weight: 2.9990 chunk 32 optimal weight: 0.8980 chunk 34 optimal weight: 0.7980 chunk 50 optimal weight: 0.0870 overall best weight: 0.6960 ------------------------------------------------------------------------------- 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 = 0.4384 r_free = 0.4384 target = 0.222767 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4187 r_free = 0.4187 target = 0.201046 restraints weight = 4193.068| |-----------------------------------------------------------------------------| r_work (start): 0.4200 rms_B_bonded: 1.48 r_work: 0.4125 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.4031 rms_B_bonded: 4.24 restraints_weight: 0.2500 r_work (final): 0.4031 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7481 moved from start: 0.1635 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= 0.136 Angle : 0.570 6.506 5469 Z= 0.287 Chirality : 0.040 0.135 638 Planarity : 0.005 0.057 661 Dihedral : 3.892 13.485 548 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 9.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 1.77 % Allowed : 20.71 % 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: 1.85 (0.38), residues: 508 helix: 1.86 (0.26), residues: 385 sheet: None (None), residues: 0 loop : -0.78 (0.61), residues: 123 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 0.014 0.001 PHE A 28 TRP 0.017 0.001 TRP A 298 Details of bonding type rmsd/Z covalent geometry : bond 0.00319 / 0.14 ( 4002) covalent geometry : angle 0.57024 / 0.29 ( 5469) hydrogen bonds : bond 0.03610 / 2.40 ( 294) hydrogen bonds : angle 4.18243 / 3.00 ( 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: 7 poor density : 66 time to evaluate : 0.150 Fit side-chains REVERT: A 52 VAL cc_start: 0.7840 (p) cc_final: 0.7577 (m) REVERT: A 188 PHE cc_start: 0.7259 (OUTLIER) cc_final: 0.6648 (m-10) REVERT: A 404 ARG cc_start: 0.6166 (mmt180) cc_final: 0.5398 (mtm180) outliers start: 7 outliers final: 5 residues processed: 67 average time/residue: 0.3768 time to fit residues: 26.5223 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 : 0.137 ------------------------------------------------------------------------------- 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 51 random chunks: chunk 16 optimal weight: 0.8980 chunk 22 optimal weight: 0.9990 chunk 45 optimal weight: 0.5980 chunk 33 optimal weight: 0.8980 chunk 12 optimal weight: 0.8980 chunk 29 optimal weight: 2.9990 chunk 34 optimal weight: 1.9990 chunk 35 optimal weight: 0.9980 chunk 18 optimal weight: 0.0040 chunk 5 optimal weight: 0.0970 chunk 25 optimal weight: 2.9990 overall best weight: 0.4990 ------------------------------------------------------------------------------- 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 = 0.4401 r_free = 0.4401 target = 0.224903 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4218 r_free = 0.4218 target = 0.204324 restraints weight = 4201.668| |-----------------------------------------------------------------------------| r_work (start): 0.4220 rms_B_bonded: 1.39 r_work: 0.4144 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.4049 rms_B_bonded: 4.21 restraints_weight: 0.2500 r_work (final): 0.4049 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7486 moved from start: 0.1687 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= 0.123 Angle : 0.551 6.561 5469 Z= 0.279 Chirality : 0.040 0.150 638 Planarity : 0.005 0.053 661 Dihedral : 3.838 13.557 548 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 9.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 2.02 % Allowed : 20.96 % Favored : 77.02 % 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: 1.93 (0.38), residues: 508 helix: 1.91 (0.26), residues: 386 sheet: None (None), residues: 0 loop : -0.76 (0.62), residues: 122 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 0.015 0.001 TRP A 298 Details of bonding type rmsd/Z covalent geometry : bond 0.00281 / 0.12 ( 4002) covalent geometry : angle 0.55126 / 0.28 ( 5469) hydrogen bonds : bond 0.03482 / 2.31 ( 294) hydrogen bonds : angle 4.15900 / 2.97 ( 849) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1467.32 seconds wall clock time: 26 minutes 11.08 seconds (1571.08 seconds total)