Starting phenix.real_space_refine on Tue Mar 3 11:23:49 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8cv3_27007/03_2026/8cv3_27007.cif Found real_map, /net/cci-nas-00/data/ceres_data/8cv3_27007/03_2026/8cv3_27007.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.04 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8cv3_27007/03_2026/8cv3_27007.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8cv3_27007/03_2026/8cv3_27007.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8cv3_27007/03_2026/8cv3_27007.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8cv3_27007/03_2026/8cv3_27007.map" } resolution = 3.04 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.004 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 21 5.16 5 Na 2 4.78 5 C 2076 2.51 5 N 504 2.21 5 O 565 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-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 3168 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 3166 Number of conformers: 1 Conformer: "" Number of residues, atoms: 416, 3166 Classifications: {'peptide': 416} Link IDs: {'PTRANS': 11, 'TRANS': 404} Chain breaks: 2 Chain: "A" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' NA': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 0.93, per 1000 atoms: 0.29 Number of scatterers: 3168 At special positions: 0 Unit cell: (67.308, 61.344, 77.532, 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 21 16.00 Na 2 11.00 O 565 8.00 N 504 7.00 C 2076 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: 0.19 Conformation dependent library (CDL) restraints added in 115.1 milliseconds 820 Ramachandran restraints generated. 410 Oldfield, 0 Emsley, 410 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 770 Finding SS restraints... Secondary structure from input PDB file: 23 helices and 1 sheets defined 85.3% alpha, 3.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.10 Creating SS restraints... Processing helix chain 'A' and resid 18 through 42 removed outlier: 3.634A pdb=" N LEU A 22 " --> pdb=" O ASN A 18 " (cutoff:3.500A) Processing helix chain 'A' and resid 45 through 53 removed outlier: 3.694A pdb=" N ALA A 53 " --> pdb=" O LYS A 49 " (cutoff:3.500A) Processing helix chain 'A' and resid 53 through 82 removed outlier: 4.403A pdb=" N LEU A 68 " --> pdb=" O LYS A 64 " (cutoff:3.500A) Proline residue: A 69 - end of helix removed outlier: 3.857A pdb=" N LEU A 82 " --> pdb=" O GLY A 78 " (cutoff:3.500A) Processing helix chain 'A' and resid 86 through 117 removed outlier: 3.594A pdb=" N ILE A 90 " --> pdb=" O VAL A 86 " (cutoff:3.500A) Processing helix chain 'A' and resid 138 through 148 Processing helix chain 'A' and resid 153 through 158 removed outlier: 3.533A pdb=" N ALA A 158 " --> pdb=" O LEU A 154 " (cutoff:3.500A) Processing helix chain 'A' and resid 211 through 230 removed outlier: 3.629A pdb=" N LEU A 215 " --> pdb=" O ASN A 211 " (cutoff:3.500A) removed outlier: 4.281A pdb=" N GLY A 230 " --> pdb=" O ILE A 226 " (cutoff:3.500A) Processing helix chain 'A' and resid 233 through 273 removed outlier: 3.556A pdb=" N VAL A 237 " --> pdb=" O GLY A 233 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N TYR A 257 " --> pdb=" O ILE A 253 " (cutoff:3.500A) Proline residue: A 259 - end of helix removed outlier: 4.285A pdb=" N VAL A 273 " --> pdb=" O CYS A 269 " (cutoff:3.500A) Processing helix chain 'A' and resid 277 through 282 Processing helix chain 'A' and resid 282 through 299 removed outlier: 3.554A pdb=" N VAL A 289 " --> pdb=" O TYR A 285 " (cutoff:3.500A) Processing helix chain 'A' and resid 299 through 309 Processing helix chain 'A' and resid 312 through 320 removed outlier: 3.755A pdb=" N PHE A 316 " --> pdb=" O ASN A 312 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ALA A 317 " --> pdb=" O PRO A 313 " (cutoff:3.500A) Processing helix chain 'A' and resid 320 through 331 Processing helix chain 'A' and resid 333 through 335 No H-bonds generated for 'chain 'A' and resid 333 through 335' Processing helix chain 'A' and resid 336 through 347 Processing helix chain 'A' and resid 351 through 366 removed outlier: 3.794A pdb=" N PHE A 357 " --> pdb=" O ARG A 353 " (cutoff:3.500A) Proline residue: A 360 - end of helix Processing helix chain 'A' and resid 367 through 385 Processing helix chain 'A' and resid 390 through 404 Processing helix chain 'A' and resid 416 through 427 removed outlier: 3.716A pdb=" N VAL A 422 " --> pdb=" O THR A 418 " (cutoff:3.500A) Processing helix chain 'A' and resid 429 through 431 No H-bonds generated for 'chain 'A' and resid 429 through 431' Processing helix chain 'A' and resid 432 through 437 removed outlier: 4.252A pdb=" N ILE A 436 " --> pdb=" O ASP A 432 " (cutoff:3.500A) Processing helix chain 'A' and resid 439 through 466 removed outlier: 4.717A pdb=" N ARG A 445 " --> pdb=" O CYS A 441 " (cutoff:3.500A) removed outlier: 4.177A pdb=" N PHE A 446 " --> pdb=" O LEU A 442 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N GLY A 460 " --> pdb=" O ALA A 456 " (cutoff:3.500A) Processing helix chain 'A' and resid 466 through 476 removed outlier: 3.782A pdb=" N VAL A 475 " --> pdb=" O GLU A 471 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N SER A 476 " --> pdb=" O GLN A 472 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 160 through 167 242 hydrogen bonds defined for protein. 723 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: 0.47 Time building geometry restraints manager: 0.28 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 946 1.34 - 1.45: 356 1.45 - 1.57: 1872 1.57 - 1.69: 0 1.69 - 1.81: 39 Bond restraints: 3213 Sorted by residual: bond pdb=" N ILE A 421 " pdb=" CA ILE A 421 " ideal model delta sigma weight residual 1.461 1.493 -0.032 1.17e-02 7.31e+03 7.46e+00 bond pdb=" N VAL A 411 " pdb=" CA VAL A 411 " ideal model delta sigma weight residual 1.461 1.494 -0.033 1.23e-02 6.61e+03 7.18e+00 bond pdb=" N GLY A 410 " pdb=" CA GLY A 410 " ideal model delta sigma weight residual 1.447 1.476 -0.028 1.58e-02 4.01e+03 3.21e+00 bond pdb=" C GLN A 413 " pdb=" O GLN A 413 " ideal model delta sigma weight residual 1.234 1.255 -0.021 1.20e-02 6.94e+03 3.13e+00 bond pdb=" CB GLN A 413 " pdb=" CG GLN A 413 " ideal model delta sigma weight residual 1.520 1.570 -0.050 3.00e-02 1.11e+03 2.75e+00 ... (remaining 3208 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.56: 4281 1.56 - 3.11: 57 3.11 - 4.67: 14 4.67 - 6.22: 4 6.22 - 7.78: 4 Bond angle restraints: 4360 Sorted by residual: angle pdb=" CA GLN A 413 " pdb=" CB GLN A 413 " pdb=" CG GLN A 413 " ideal model delta sigma weight residual 114.10 120.85 -6.75 2.00e+00 2.50e-01 1.14e+01 angle pdb=" CA PRO A 412 " pdb=" C PRO A 412 " pdb=" O PRO A 412 " ideal model delta sigma weight residual 121.77 118.13 3.64 1.14e+00 7.69e-01 1.02e+01 angle pdb=" CA ILE A 421 " pdb=" C ILE A 421 " pdb=" O ILE A 421 " ideal model delta sigma weight residual 121.17 118.11 3.06 1.06e+00 8.90e-01 8.35e+00 angle pdb=" CB LEU A 265 " pdb=" CG LEU A 265 " pdb=" CD1 LEU A 265 " ideal model delta sigma weight residual 110.70 103.30 7.40 3.00e+00 1.11e-01 6.08e+00 angle pdb=" O ILE A 421 " pdb=" C ILE A 421 " pdb=" N VAL A 422 " ideal model delta sigma weight residual 121.91 124.32 -2.41 9.80e-01 1.04e+00 6.06e+00 ... (remaining 4355 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 11.87: 1592 11.87 - 23.75: 209 23.75 - 35.62: 82 35.62 - 47.49: 23 47.49 - 59.36: 15 Dihedral angle restraints: 1921 sinusoidal: 728 harmonic: 1193 Sorted by residual: dihedral pdb=" CA ASP A 351 " pdb=" CB ASP A 351 " pdb=" CG ASP A 351 " pdb=" OD1 ASP A 351 " ideal model delta sinusoidal sigma weight residual -30.00 -83.34 53.34 1 2.00e+01 2.50e-03 9.67e+00 dihedral pdb=" CB ARG A 445 " pdb=" CG ARG A 445 " pdb=" CD ARG A 445 " pdb=" NE ARG A 445 " ideal model delta sinusoidal sigma weight residual 60.00 119.36 -59.36 3 1.50e+01 4.44e-03 9.48e+00 dihedral pdb=" CG LYS A 201 " pdb=" CD LYS A 201 " pdb=" CE LYS A 201 " pdb=" NZ LYS A 201 " ideal model delta sinusoidal sigma weight residual 60.00 1.95 58.05 3 1.50e+01 4.44e-03 9.46e+00 ... (remaining 1918 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.038: 403 0.038 - 0.076: 120 0.076 - 0.114: 26 0.114 - 0.152: 2 0.152 - 0.190: 2 Chirality restraints: 553 Sorted by residual: chirality pdb=" CA ILE A 421 " pdb=" N ILE A 421 " pdb=" C ILE A 421 " pdb=" CB ILE A 421 " both_signs ideal model delta sigma weight residual False 2.43 2.62 -0.19 2.00e-01 2.50e+01 9.03e-01 chirality pdb=" CA VAL A 411 " pdb=" N VAL A 411 " pdb=" C VAL A 411 " pdb=" CB VAL A 411 " both_signs ideal model delta sigma weight residual False 2.44 2.61 -0.17 2.00e-01 2.50e+01 6.82e-01 chirality pdb=" CA MET A 367 " pdb=" N MET A 367 " pdb=" C MET A 367 " pdb=" CB MET A 367 " both_signs ideal model delta sigma weight residual False 2.51 2.65 -0.14 2.00e-01 2.50e+01 5.22e-01 ... (remaining 550 not shown) Planarity restraints: 531 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA VAL A 417 " -0.026 2.00e-02 2.50e+03 5.13e-02 2.63e+01 pdb=" C VAL A 417 " 0.089 2.00e-02 2.50e+03 pdb=" O VAL A 417 " -0.033 2.00e-02 2.50e+03 pdb=" N THR A 418 " -0.030 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR A 326 " -0.008 2.00e-02 2.50e+03 1.61e-02 2.59e+00 pdb=" C THR A 326 " 0.028 2.00e-02 2.50e+03 pdb=" O THR A 326 " -0.010 2.00e-02 2.50e+03 pdb=" N ALA A 327 " -0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C MET A 258 " -0.026 5.00e-02 4.00e+02 3.86e-02 2.39e+00 pdb=" N PRO A 259 " 0.067 5.00e-02 4.00e+02 pdb=" CA PRO A 259 " -0.019 5.00e-02 4.00e+02 pdb=" CD PRO A 259 " -0.022 5.00e-02 4.00e+02 ... (remaining 528 not shown) Histogram of nonbonded interaction distances: 2.31 - 2.83: 933 2.83 - 3.35: 3144 3.35 - 3.86: 4984 3.86 - 4.38: 5450 4.38 - 4.90: 9882 Nonbonded interactions: 24393 Sorted by model distance: nonbonded pdb=" O THR A 336 " pdb=" OG1 THR A 340 " model vdw 2.310 3.040 nonbonded pdb=" O PRO A 69 " pdb=" OG SER A 73 " model vdw 2.323 3.040 nonbonded pdb=" OD1 ASP A 368 " pdb="NA NA A 602 " model vdw 2.366 2.470 nonbonded pdb=" OG1 THR A 101 " pdb="NA NA A 602 " model vdw 2.386 2.470 nonbonded pdb=" O THR A 396 " pdb=" OG1 THR A 400 " model vdw 2.396 3.040 ... (remaining 24388 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: 1.020 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: 0.050 Check model and map are aligned: 0.010 Set scattering table: 0.020 Process input model: 5.270 Find NCS groups from input model: 0.020 Set up NCS constraints: 0.000 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.390 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 7.780 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8094 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 3213 Z= 0.146 Angle : 0.513 7.776 4360 Z= 0.277 Chirality : 0.038 0.190 553 Planarity : 0.004 0.051 531 Dihedral : 14.071 59.364 1151 Min Nonbonded Distance : 2.310 Molprobity Statistics. All-atom Clashscore : 2.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 0.00 % Allowed : 19.60 % Favored : 80.40 % 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 (0.42), residues: 410 helix: 1.97 (0.29), residues: 325 sheet: 0.18 (1.38), residues: 18 loop : -1.91 (0.65), residues: 67 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 445 TYR 0.012 0.001 TYR A 200 PHE 0.003 0.000 PHE A 14 TRP 0.003 0.001 TRP A 276 HIS 0.000 0.000 HIS A 296 Details of bonding type rmsd covalent geometry : bond 0.00282 ( 3213) covalent geometry : angle 0.51338 ( 4360) hydrogen bonds : bond 0.16787 ( 242) hydrogen bonds : angle 5.84430 ( 723) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 820 Ramachandran restraints generated. 410 Oldfield, 0 Emsley, 410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 820 Ramachandran restraints generated. 410 Oldfield, 0 Emsley, 410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 49 residues out of total 347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 49 time to evaluate : 0.123 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 49 average time/residue: 0.0497 time to fit residues: 3.1606 Evaluate side-chains 47 residues out of total 347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 47 time to evaluate : 0.096 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 24 optimal weight: 3.9990 chunk 26 optimal weight: 0.9990 chunk 2 optimal weight: 0.6980 chunk 16 optimal weight: 0.6980 chunk 32 optimal weight: 4.9990 chunk 31 optimal weight: 0.8980 chunk 25 optimal weight: 0.9990 chunk 19 optimal weight: 0.6980 chunk 30 optimal weight: 6.9990 chunk 22 optimal weight: 0.5980 chunk 37 optimal weight: 1.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- 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 = 0.3734 r_free = 0.3734 target = 0.155321 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.122907 restraints weight = 3809.154| |-----------------------------------------------------------------------------| r_work (start): 0.3262 rms_B_bonded: 1.54 r_work: 0.3150 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.3030 rms_B_bonded: 3.78 restraints_weight: 0.2500 r_work (final): 0.3030 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8110 moved from start: 0.1037 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 3213 Z= 0.136 Angle : 0.477 7.137 4360 Z= 0.254 Chirality : 0.037 0.133 553 Planarity : 0.004 0.067 531 Dihedral : 3.665 15.281 436 Min Nonbonded Distance : 2.207 Molprobity Statistics. All-atom Clashscore : 2.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 2.02 % Allowed : 17.29 % Favored : 80.69 % 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: 2.48 (0.42), residues: 410 helix: 2.33 (0.28), residues: 327 sheet: 0.31 (1.43), residues: 18 loop : -1.68 (0.65), residues: 65 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 147 TYR 0.007 0.001 TYR A 305 PHE 0.009 0.001 PHE A 240 TRP 0.005 0.001 TRP A 19 HIS 0.001 0.000 HIS A 296 Details of bonding type rmsd covalent geometry : bond 0.00270 ( 3213) covalent geometry : angle 0.47654 ( 4360) hydrogen bonds : bond 0.05722 ( 242) hydrogen bonds : angle 4.41221 ( 723) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 820 Ramachandran restraints generated. 410 Oldfield, 0 Emsley, 410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 820 Ramachandran restraints generated. 410 Oldfield, 0 Emsley, 410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 52 residues out of total 347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 45 time to evaluate : 0.079 Fit side-chains revert: symmetry clash REVERT: A 255 MET cc_start: 0.8484 (mmt) cc_final: 0.8071 (mmt) outliers start: 7 outliers final: 3 residues processed: 49 average time/residue: 0.0446 time to fit residues: 2.8893 Evaluate side-chains 46 residues out of total 347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 43 time to evaluate : 0.120 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 LEU Chi-restraints excluded: chain A residue 67 ILE Chi-restraints excluded: chain A residue 265 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 25 optimal weight: 0.0060 chunk 32 optimal weight: 6.9990 chunk 20 optimal weight: 3.9990 chunk 9 optimal weight: 0.8980 chunk 4 optimal weight: 0.8980 chunk 2 optimal weight: 0.9980 chunk 24 optimal weight: 0.0470 chunk 36 optimal weight: 2.9990 chunk 7 optimal weight: 3.9990 chunk 33 optimal weight: 0.9990 chunk 17 optimal weight: 1.9990 overall best weight: 0.5694 ------------------------------------------------------------------------------- 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 = 0.3691 r_free = 0.3691 target = 0.152135 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3286 r_free = 0.3286 target = 0.118279 restraints weight = 3774.196| |-----------------------------------------------------------------------------| r_work (start): 0.3270 rms_B_bonded: 1.63 r_work: 0.3154 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.3033 rms_B_bonded: 4.04 restraints_weight: 0.2500 r_work (final): 0.3033 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8064 moved from start: 0.1316 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 3213 Z= 0.122 Angle : 0.444 6.548 4360 Z= 0.236 Chirality : 0.036 0.132 553 Planarity : 0.004 0.067 531 Dihedral : 3.577 14.613 436 Min Nonbonded Distance : 2.234 Molprobity Statistics. All-atom Clashscore : 2.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 1.44 % Allowed : 18.73 % Favored : 79.83 % 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: 2.72 (0.42), residues: 410 helix: 2.51 (0.28), residues: 327 sheet: 0.32 (1.41), residues: 18 loop : -1.69 (0.64), residues: 65 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 147 TYR 0.005 0.001 TYR A 97 PHE 0.007 0.001 PHE A 240 TRP 0.003 0.001 TRP A 19 HIS 0.001 0.000 HIS A 41 Details of bonding type rmsd covalent geometry : bond 0.00237 ( 3213) covalent geometry : angle 0.44353 ( 4360) hydrogen bonds : bond 0.05037 ( 242) hydrogen bonds : angle 4.17540 ( 723) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 820 Ramachandran restraints generated. 410 Oldfield, 0 Emsley, 410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 820 Ramachandran restraints generated. 410 Oldfield, 0 Emsley, 410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 51 residues out of total 347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 46 time to evaluate : 0.112 Fit side-chains revert: symmetry clash REVERT: A 21 LEU cc_start: 0.5782 (OUTLIER) cc_final: 0.5232 (tp) REVERT: A 255 MET cc_start: 0.8504 (mmt) cc_final: 0.8175 (mmt) REVERT: A 262 ILE cc_start: 0.7927 (mm) cc_final: 0.7726 (mt) REVERT: A 373 TYR cc_start: 0.6479 (t80) cc_final: 0.5738 (t80) outliers start: 5 outliers final: 2 residues processed: 49 average time/residue: 0.0393 time to fit residues: 2.5842 Evaluate side-chains 46 residues out of total 347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 43 time to evaluate : 0.114 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 LEU Chi-restraints excluded: chain A residue 21 LEU Chi-restraints excluded: chain A residue 67 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 24 optimal weight: 2.9990 chunk 9 optimal weight: 0.7980 chunk 31 optimal weight: 0.9980 chunk 36 optimal weight: 6.9990 chunk 8 optimal weight: 0.7980 chunk 3 optimal weight: 1.9990 chunk 19 optimal weight: 1.9990 chunk 37 optimal weight: 0.8980 chunk 30 optimal weight: 3.9990 chunk 29 optimal weight: 0.6980 chunk 38 optimal weight: 2.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- 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 = 0.3666 r_free = 0.3666 target = 0.149523 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3234 r_free = 0.3234 target = 0.114655 restraints weight = 3770.268| |-----------------------------------------------------------------------------| r_work (start): 0.3239 rms_B_bonded: 1.65 r_work: 0.3120 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.3000 rms_B_bonded: 4.10 restraints_weight: 0.2500 r_work (final): 0.3000 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8111 moved from start: 0.1355 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 3213 Z= 0.133 Angle : 0.463 6.683 4360 Z= 0.246 Chirality : 0.037 0.134 553 Planarity : 0.004 0.069 531 Dihedral : 3.599 15.361 436 Min Nonbonded Distance : 2.213 Molprobity Statistics. All-atom Clashscore : 2.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 2.31 % Allowed : 17.87 % Favored : 79.83 % 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: 2.66 (0.42), residues: 410 helix: 2.48 (0.28), residues: 327 sheet: 0.26 (1.41), residues: 18 loop : -1.77 (0.62), residues: 65 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 447 TYR 0.005 0.001 TYR A 97 PHE 0.012 0.001 PHE A 240 TRP 0.003 0.001 TRP A 276 HIS 0.001 0.000 HIS A 41 Details of bonding type rmsd covalent geometry : bond 0.00278 ( 3213) covalent geometry : angle 0.46307 ( 4360) hydrogen bonds : bond 0.05520 ( 242) hydrogen bonds : angle 4.17497 ( 723) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 820 Ramachandran restraints generated. 410 Oldfield, 0 Emsley, 410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 820 Ramachandran restraints generated. 410 Oldfield, 0 Emsley, 410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 54 residues out of total 347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 46 time to evaluate : 0.097 Fit side-chains revert: symmetry clash REVERT: A 21 LEU cc_start: 0.5928 (OUTLIER) cc_final: 0.5322 (tp) REVERT: A 255 MET cc_start: 0.8480 (mmt) cc_final: 0.8145 (mmt) REVERT: A 262 ILE cc_start: 0.8037 (mm) cc_final: 0.7825 (mt) REVERT: A 373 TYR cc_start: 0.6469 (t80) cc_final: 0.5758 (t80) outliers start: 8 outliers final: 5 residues processed: 52 average time/residue: 0.0426 time to fit residues: 3.0246 Evaluate side-chains 51 residues out of total 347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 45 time to evaluate : 0.112 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 LEU Chi-restraints excluded: chain A residue 21 LEU Chi-restraints excluded: chain A residue 67 ILE Chi-restraints excluded: chain A residue 265 LEU Chi-restraints excluded: chain A residue 269 CYS Chi-restraints excluded: chain A residue 391 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 22 optimal weight: 0.6980 chunk 0 optimal weight: 10.0000 chunk 9 optimal weight: 0.6980 chunk 12 optimal weight: 0.1980 chunk 15 optimal weight: 0.7980 chunk 2 optimal weight: 0.8980 chunk 1 optimal weight: 2.9990 chunk 16 optimal weight: 0.7980 chunk 11 optimal weight: 0.7980 chunk 36 optimal weight: 8.9990 chunk 28 optimal weight: 1.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- 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 = 0.3707 r_free = 0.3707 target = 0.152983 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.119105 restraints weight = 3786.752| |-----------------------------------------------------------------------------| r_work (start): 0.3257 rms_B_bonded: 1.64 r_work: 0.3142 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.3024 rms_B_bonded: 3.99 restraints_weight: 0.2500 r_work (final): 0.3024 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8078 moved from start: 0.1434 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.046 3213 Z= 0.124 Angle : 0.447 6.425 4360 Z= 0.238 Chirality : 0.036 0.132 553 Planarity : 0.004 0.056 531 Dihedral : 3.582 15.068 436 Min Nonbonded Distance : 2.228 Molprobity Statistics. All-atom Clashscore : 3.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 2.02 % Allowed : 17.29 % Favored : 80.69 % 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: 2.76 (0.42), residues: 410 helix: 2.57 (0.28), residues: 327 sheet: 0.24 (1.41), residues: 18 loop : -1.84 (0.61), residues: 65 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 447 TYR 0.005 0.001 TYR A 97 PHE 0.009 0.001 PHE A 240 TRP 0.003 0.001 TRP A 19 HIS 0.001 0.000 HIS A 41 Details of bonding type rmsd covalent geometry : bond 0.00247 ( 3213) covalent geometry : angle 0.44660 ( 4360) hydrogen bonds : bond 0.05094 ( 242) hydrogen bonds : angle 4.17309 ( 723) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 820 Ramachandran restraints generated. 410 Oldfield, 0 Emsley, 410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 820 Ramachandran restraints generated. 410 Oldfield, 0 Emsley, 410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 52 residues out of total 347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 45 time to evaluate : 0.083 Fit side-chains revert: symmetry clash REVERT: A 21 LEU cc_start: 0.5911 (OUTLIER) cc_final: 0.5310 (tp) REVERT: A 255 MET cc_start: 0.8481 (mmt) cc_final: 0.8122 (mmt) REVERT: A 262 ILE cc_start: 0.7885 (mm) cc_final: 0.7652 (mt) REVERT: A 373 TYR cc_start: 0.6450 (t80) cc_final: 0.5750 (t80) outliers start: 7 outliers final: 5 residues processed: 50 average time/residue: 0.0403 time to fit residues: 2.6902 Evaluate side-chains 50 residues out of total 347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 44 time to evaluate : 0.121 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 LEU Chi-restraints excluded: chain A residue 21 LEU Chi-restraints excluded: chain A residue 67 ILE Chi-restraints excluded: chain A residue 265 LEU Chi-restraints excluded: chain A residue 269 CYS Chi-restraints excluded: chain A residue 391 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 5 optimal weight: 0.9990 chunk 27 optimal weight: 0.7980 chunk 35 optimal weight: 9.9990 chunk 16 optimal weight: 2.9990 chunk 12 optimal weight: 0.9990 chunk 8 optimal weight: 0.9980 chunk 9 optimal weight: 0.6980 chunk 23 optimal weight: 0.6980 chunk 40 optimal weight: 2.9990 chunk 31 optimal weight: 1.9990 chunk 22 optimal weight: 0.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- 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 = 0.3663 r_free = 0.3663 target = 0.149411 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3237 r_free = 0.3237 target = 0.114801 restraints weight = 3731.574| |-----------------------------------------------------------------------------| r_work (start): 0.3247 rms_B_bonded: 1.63 r_work: 0.3129 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.3011 rms_B_bonded: 4.05 restraints_weight: 0.2500 r_work (final): 0.3011 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8136 moved from start: 0.1450 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 3213 Z= 0.134 Angle : 0.462 6.478 4360 Z= 0.246 Chirality : 0.037 0.134 553 Planarity : 0.004 0.050 531 Dihedral : 3.612 15.684 436 Min Nonbonded Distance : 2.213 Molprobity Statistics. All-atom Clashscore : 3.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 3.17 % Allowed : 15.56 % Favored : 81.27 % 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: 2.68 (0.42), residues: 410 helix: 2.54 (0.28), residues: 326 sheet: 0.18 (1.40), residues: 18 loop : -1.91 (0.61), residues: 66 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 447 TYR 0.005 0.001 TYR A 97 PHE 0.012 0.001 PHE A 240 TRP 0.003 0.001 TRP A 256 HIS 0.001 0.000 HIS A 41 Details of bonding type rmsd covalent geometry : bond 0.00279 ( 3213) covalent geometry : angle 0.46182 ( 4360) hydrogen bonds : bond 0.05499 ( 242) hydrogen bonds : angle 4.24051 ( 723) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 820 Ramachandran restraints generated. 410 Oldfield, 0 Emsley, 410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 820 Ramachandran restraints generated. 410 Oldfield, 0 Emsley, 410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 55 residues out of total 347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 44 time to evaluate : 0.121 Fit side-chains revert: symmetry clash REVERT: A 21 LEU cc_start: 0.6011 (OUTLIER) cc_final: 0.5380 (tp) REVERT: A 262 ILE cc_start: 0.7997 (mm) cc_final: 0.7760 (mt) REVERT: A 373 TYR cc_start: 0.6496 (t80) cc_final: 0.5772 (t80) outliers start: 11 outliers final: 6 residues processed: 53 average time/residue: 0.0440 time to fit residues: 3.1466 Evaluate side-chains 51 residues out of total 347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 44 time to evaluate : 0.114 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 LEU Chi-restraints excluded: chain A residue 21 LEU Chi-restraints excluded: chain A residue 67 ILE Chi-restraints excluded: chain A residue 265 LEU Chi-restraints excluded: chain A residue 269 CYS Chi-restraints excluded: chain A residue 391 ILE Chi-restraints excluded: chain A residue 475 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 4 optimal weight: 4.9990 chunk 22 optimal weight: 2.9990 chunk 0 optimal weight: 9.9990 chunk 8 optimal weight: 0.9990 chunk 28 optimal weight: 9.9990 chunk 20 optimal weight: 3.9990 chunk 33 optimal weight: 0.3980 chunk 35 optimal weight: 3.9990 chunk 5 optimal weight: 0.9980 chunk 3 optimal weight: 0.8980 chunk 17 optimal weight: 1.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- 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 = 0.3651 r_free = 0.3651 target = 0.148411 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3211 r_free = 0.3211 target = 0.112956 restraints weight = 3849.377| |-----------------------------------------------------------------------------| r_work (start): 0.3214 rms_B_bonded: 1.69 r_work: 0.3097 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.2976 rms_B_bonded: 4.09 restraints_weight: 0.2500 r_work (final): 0.2976 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8139 moved from start: 0.1438 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 3213 Z= 0.149 Angle : 0.495 8.924 4360 Z= 0.261 Chirality : 0.038 0.136 553 Planarity : 0.004 0.046 531 Dihedral : 3.703 15.977 436 Min Nonbonded Distance : 2.194 Molprobity Statistics. All-atom Clashscore : 3.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 3.17 % Allowed : 16.43 % Favored : 80.40 % 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: 2.50 (0.41), residues: 410 helix: 2.38 (0.28), residues: 326 sheet: 1.09 (1.36), residues: 16 loop : -2.04 (0.61), residues: 68 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 447 TYR 0.005 0.001 TYR A 97 PHE 0.013 0.001 PHE A 240 TRP 0.005 0.001 TRP A 256 HIS 0.001 0.000 HIS A 41 Details of bonding type rmsd covalent geometry : bond 0.00326 ( 3213) covalent geometry : angle 0.49453 ( 4360) hydrogen bonds : bond 0.05999 ( 242) hydrogen bonds : angle 4.35101 ( 723) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 820 Ramachandran restraints generated. 410 Oldfield, 0 Emsley, 410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 820 Ramachandran restraints generated. 410 Oldfield, 0 Emsley, 410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 57 residues out of total 347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 46 time to evaluate : 0.122 Fit side-chains revert: symmetry clash REVERT: A 21 LEU cc_start: 0.5978 (OUTLIER) cc_final: 0.5429 (tp) REVERT: A 373 TYR cc_start: 0.6503 (t80) cc_final: 0.5810 (t80) outliers start: 11 outliers final: 7 residues processed: 54 average time/residue: 0.0499 time to fit residues: 3.5475 Evaluate side-chains 54 residues out of total 347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 46 time to evaluate : 0.103 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 LEU Chi-restraints excluded: chain A residue 21 LEU Chi-restraints excluded: chain A residue 67 ILE Chi-restraints excluded: chain A residue 265 LEU Chi-restraints excluded: chain A residue 269 CYS Chi-restraints excluded: chain A residue 365 ILE Chi-restraints excluded: chain A residue 391 ILE Chi-restraints excluded: chain A residue 475 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 3 optimal weight: 1.9990 chunk 35 optimal weight: 0.0470 chunk 28 optimal weight: 0.9980 chunk 23 optimal weight: 0.9990 chunk 37 optimal weight: 0.1980 chunk 26 optimal weight: 0.9980 chunk 13 optimal weight: 0.9980 chunk 15 optimal weight: 1.9990 chunk 19 optimal weight: 0.6980 chunk 20 optimal weight: 0.5980 chunk 40 optimal weight: 1.9990 overall best weight: 0.5078 ------------------------------------------------------------------------------- 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 = 0.3703 r_free = 0.3703 target = 0.153161 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.119238 restraints weight = 3823.487| |-----------------------------------------------------------------------------| r_work (start): 0.3275 rms_B_bonded: 1.63 r_work: 0.3159 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.3040 rms_B_bonded: 4.10 restraints_weight: 0.2500 r_work (final): 0.3040 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8097 moved from start: 0.1575 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 3213 Z= 0.121 Angle : 0.464 9.011 4360 Z= 0.241 Chirality : 0.036 0.133 553 Planarity : 0.004 0.046 531 Dihedral : 3.580 14.869 436 Min Nonbonded Distance : 2.233 Molprobity Statistics. All-atom Clashscore : 3.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 2.02 % Allowed : 16.71 % Favored : 81.27 % 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: 2.73 (0.42), residues: 410 helix: 2.58 (0.28), residues: 326 sheet: 0.07 (1.38), residues: 18 loop : -1.89 (0.61), residues: 66 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 147 TYR 0.007 0.001 TYR A 305 PHE 0.007 0.001 PHE A 264 TRP 0.003 0.001 TRP A 19 HIS 0.001 0.000 HIS A 41 Details of bonding type rmsd covalent geometry : bond 0.00239 ( 3213) covalent geometry : angle 0.46433 ( 4360) hydrogen bonds : bond 0.04868 ( 242) hydrogen bonds : angle 4.20291 ( 723) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 820 Ramachandran restraints generated. 410 Oldfield, 0 Emsley, 410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 820 Ramachandran restraints generated. 410 Oldfield, 0 Emsley, 410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 53 residues out of total 347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 46 time to evaluate : 0.123 Fit side-chains revert: symmetry clash REVERT: A 21 LEU cc_start: 0.5830 (OUTLIER) cc_final: 0.5276 (tp) REVERT: A 41 HIS cc_start: 0.6800 (m90) cc_final: 0.6515 (m170) REVERT: A 255 MET cc_start: 0.8442 (mmt) cc_final: 0.8138 (mmt) REVERT: A 262 ILE cc_start: 0.7985 (mm) cc_final: 0.7755 (mt) REVERT: A 373 TYR cc_start: 0.6477 (t80) cc_final: 0.5777 (t80) outliers start: 7 outliers final: 6 residues processed: 51 average time/residue: 0.0497 time to fit residues: 3.3602 Evaluate side-chains 52 residues out of total 347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 45 time to evaluate : 0.122 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 LEU Chi-restraints excluded: chain A residue 21 LEU Chi-restraints excluded: chain A residue 67 ILE Chi-restraints excluded: chain A residue 265 LEU Chi-restraints excluded: chain A residue 269 CYS Chi-restraints excluded: chain A residue 391 ILE Chi-restraints excluded: chain A residue 475 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 8 optimal weight: 0.9990 chunk 37 optimal weight: 3.9990 chunk 3 optimal weight: 1.9990 chunk 1 optimal weight: 3.9990 chunk 27 optimal weight: 4.9990 chunk 11 optimal weight: 0.8980 chunk 25 optimal weight: 3.9990 chunk 39 optimal weight: 0.9990 chunk 28 optimal weight: 0.9980 chunk 17 optimal weight: 0.6980 chunk 33 optimal weight: 0.8980 overall best weight: 0.8982 ------------------------------------------------------------------------------- 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 = 0.3670 r_free = 0.3670 target = 0.150043 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3242 r_free = 0.3242 target = 0.115224 restraints weight = 3851.859| |-----------------------------------------------------------------------------| r_work (start): 0.3223 rms_B_bonded: 1.66 r_work: 0.3107 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.2986 rms_B_bonded: 4.03 restraints_weight: 0.2500 r_work (final): 0.2986 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8115 moved from start: 0.1502 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 3213 Z= 0.139 Angle : 0.493 9.124 4360 Z= 0.256 Chirality : 0.037 0.135 553 Planarity : 0.004 0.046 531 Dihedral : 3.634 16.006 436 Min Nonbonded Distance : 2.209 Molprobity Statistics. All-atom Clashscore : 3.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 2.02 % Allowed : 17.00 % Favored : 80.98 % 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: 2.55 (0.42), residues: 410 helix: 2.46 (0.28), residues: 326 sheet: -0.01 (1.36), residues: 18 loop : -1.93 (0.61), residues: 66 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 447 TYR 0.008 0.001 TYR A 305 PHE 0.012 0.001 PHE A 240 TRP 0.004 0.001 TRP A 256 HIS 0.001 0.000 HIS A 41 Details of bonding type rmsd covalent geometry : bond 0.00296 ( 3213) covalent geometry : angle 0.49324 ( 4360) hydrogen bonds : bond 0.05640 ( 242) hydrogen bonds : angle 4.25900 ( 723) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 820 Ramachandran restraints generated. 410 Oldfield, 0 Emsley, 410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 820 Ramachandran restraints generated. 410 Oldfield, 0 Emsley, 410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 53 residues out of total 347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 46 time to evaluate : 0.100 Fit side-chains revert: symmetry clash REVERT: A 21 LEU cc_start: 0.5939 (OUTLIER) cc_final: 0.5370 (tp) REVERT: A 41 HIS cc_start: 0.6853 (m90) cc_final: 0.6579 (m170) REVERT: A 320 MET cc_start: 0.7481 (mmm) cc_final: 0.7279 (mmm) REVERT: A 373 TYR cc_start: 0.6489 (t80) cc_final: 0.5745 (t80) outliers start: 7 outliers final: 6 residues processed: 51 average time/residue: 0.0566 time to fit residues: 3.7023 Evaluate side-chains 53 residues out of total 347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 46 time to evaluate : 0.116 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 LEU Chi-restraints excluded: chain A residue 21 LEU Chi-restraints excluded: chain A residue 67 ILE Chi-restraints excluded: chain A residue 265 LEU Chi-restraints excluded: chain A residue 269 CYS Chi-restraints excluded: chain A residue 391 ILE Chi-restraints excluded: chain A residue 475 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 9 optimal weight: 0.8980 chunk 8 optimal weight: 0.8980 chunk 27 optimal weight: 3.9990 chunk 28 optimal weight: 0.8980 chunk 25 optimal weight: 0.0050 chunk 21 optimal weight: 0.0770 chunk 17 optimal weight: 0.7980 chunk 35 optimal weight: 0.0050 chunk 31 optimal weight: 5.9990 chunk 12 optimal weight: 0.0040 chunk 11 optimal weight: 0.9990 overall best weight: 0.1778 ------------------------------------------------------------------------------- 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 = 0.3740 r_free = 0.3740 target = 0.157267 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.124086 restraints weight = 3805.346| |-----------------------------------------------------------------------------| r_work (start): 0.3335 rms_B_bonded: 1.69 r_work: 0.3227 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.3106 rms_B_bonded: 4.14 restraints_weight: 0.2500 r_work (final): 0.3106 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7922 moved from start: 0.1906 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 3213 Z= 0.106 Angle : 0.454 9.109 4360 Z= 0.231 Chirality : 0.036 0.130 553 Planarity : 0.004 0.046 531 Dihedral : 3.470 15.807 436 Min Nonbonded Distance : 2.230 Molprobity Statistics. All-atom Clashscore : 3.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 1.73 % Allowed : 17.29 % Favored : 80.98 % 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: 2.98 (0.42), residues: 410 helix: 2.78 (0.29), residues: 326 sheet: 0.18 (1.39), residues: 18 loop : -1.92 (0.60), residues: 66 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 61 TYR 0.006 0.001 TYR A 305 PHE 0.005 0.001 PHE A 239 TRP 0.008 0.001 TRP A 256 HIS 0.000 0.000 HIS A 41 Details of bonding type rmsd covalent geometry : bond 0.00201 ( 3213) covalent geometry : angle 0.45384 ( 4360) hydrogen bonds : bond 0.03773 ( 242) hydrogen bonds : angle 4.06773 ( 723) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 820 Ramachandran restraints generated. 410 Oldfield, 0 Emsley, 410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 820 Ramachandran restraints generated. 410 Oldfield, 0 Emsley, 410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 49 residues out of total 347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 43 time to evaluate : 0.124 Fit side-chains revert: symmetry clash REVERT: A 21 LEU cc_start: 0.5649 (OUTLIER) cc_final: 0.5226 (tp) REVERT: A 41 HIS cc_start: 0.6557 (m90) cc_final: 0.6342 (m170) REVERT: A 255 MET cc_start: 0.8284 (mmt) cc_final: 0.7920 (mmt) REVERT: A 262 ILE cc_start: 0.7740 (mm) cc_final: 0.7476 (mt) REVERT: A 320 MET cc_start: 0.7308 (mmm) cc_final: 0.7097 (mmm) REVERT: A 373 TYR cc_start: 0.6222 (t80) cc_final: 0.5600 (t80) outliers start: 6 outliers final: 5 residues processed: 47 average time/residue: 0.0462 time to fit residues: 2.8321 Evaluate side-chains 47 residues out of total 347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 41 time to evaluate : 0.119 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 LEU Chi-restraints excluded: chain A residue 21 LEU Chi-restraints excluded: chain A residue 67 ILE Chi-restraints excluded: chain A residue 265 LEU Chi-restraints excluded: chain A residue 269 CYS Chi-restraints excluded: chain A residue 475 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 40 optimal weight: 4.9990 chunk 30 optimal weight: 4.9990 chunk 20 optimal weight: 2.9990 chunk 36 optimal weight: 5.9990 chunk 4 optimal weight: 0.9990 chunk 3 optimal weight: 0.6980 chunk 18 optimal weight: 0.9990 chunk 28 optimal weight: 2.9990 chunk 0 optimal weight: 9.9990 chunk 24 optimal weight: 3.9990 chunk 15 optimal weight: 0.5980 overall best weight: 1.2586 ------------------------------------------------------------------------------- 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 = 0.3646 r_free = 0.3646 target = 0.148235 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3209 r_free = 0.3209 target = 0.112942 restraints weight = 3848.351| |-----------------------------------------------------------------------------| r_work (start): 0.3206 rms_B_bonded: 1.67 r_work: 0.3087 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.2968 rms_B_bonded: 4.09 restraints_weight: 0.2500 r_work (final): 0.2968 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8135 moved from start: 0.1520 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 3213 Z= 0.162 Angle : 0.546 10.032 4360 Z= 0.276 Chirality : 0.038 0.136 553 Planarity : 0.004 0.047 531 Dihedral : 3.637 15.972 436 Min Nonbonded Distance : 2.188 Molprobity Statistics. All-atom Clashscore : 3.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 1.73 % Allowed : 18.16 % Favored : 80.12 % 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: 2.48 (0.42), residues: 410 helix: 2.41 (0.28), residues: 326 sheet: -0.09 (1.34), residues: 18 loop : -1.95 (0.61), residues: 66 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 147 TYR 0.008 0.001 TYR A 305 PHE 0.014 0.001 PHE A 240 TRP 0.009 0.001 TRP A 256 HIS 0.002 0.001 HIS A 41 Details of bonding type rmsd covalent geometry : bond 0.00369 ( 3213) covalent geometry : angle 0.54560 ( 4360) hydrogen bonds : bond 0.06087 ( 242) hydrogen bonds : angle 4.30233 ( 723) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 989.17 seconds wall clock time: 17 minutes 33.43 seconds (1053.43 seconds total)