Starting phenix.real_space_refine on Fri Aug 22 12:38:31 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7tpk_26058/08_2025/7tpk_26058.cif Found real_map, /net/cci-nas-00/data/ceres_data/7tpk_26058/08_2025/7tpk_26058.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7tpk_26058/08_2025/7tpk_26058.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7tpk_26058/08_2025/7tpk_26058.map" model { file = "/net/cci-nas-00/data/ceres_data/7tpk_26058/08_2025/7tpk_26058.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7tpk_26058/08_2025/7tpk_26058.cif" } resolution = 3.4 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= 0.052 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 8 5.16 5 C 966 2.51 5 N 247 2.21 5 O 263 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 17 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 1484 Number of models: 1 Model: "" Number of chains: 2 Chain: "E" Number of atoms: 1470 Number of conformers: 1 Conformer: "" Number of residues, atoms: 194, 1470 Classifications: {'peptide': 194} Incomplete info: {'truncation_to_alanine': 28} Link IDs: {'PTRANS': 10, 'TRANS': 183} Unresolved non-hydrogen bonds: 72 Unresolved non-hydrogen angles: 95 Unresolved non-hydrogen dihedrals: 51 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'ASP:plan': 4, 'ASN:plan1': 7, 'GLN:plan1': 1, 'GLU:plan': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 46 Chain: "E" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 0.80, per 1000 atoms: 0.54 Number of scatterers: 1484 At special positions: 0 Unit cell: (51, 71, 63, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 8 16.00 O 263 8.00 N 247 7.00 C 966 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS E 336 " - pdb=" SG CYS E 361 " distance=2.03 Simple disulfide: pdb=" SG CYS E 379 " - pdb=" SG CYS E 432 " distance=2.05 Simple disulfide: pdb=" SG CYS E 391 " - pdb=" SG CYS E 525 " distance=2.11 Simple disulfide: pdb=" SG CYS E 480 " - pdb=" SG CYS E 488 " distance=2.09 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 Links applied NAG-ASN " NAG E 601 " - " ASN E 343 " Time building additional restraints: 0.13 Conformation dependent library (CDL) restraints added in 67.6 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 384 Ramachandran restraints generated. 192 Oldfield, 0 Emsley, 192 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 358 Finding SS restraints... Secondary structure from input PDB file: 6 helices and 4 sheets defined 17.5% alpha, 21.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.05 Creating SS restraints... Processing helix chain 'E' and resid 338 through 343 Processing helix chain 'E' and resid 349 through 353 removed outlier: 3.906A pdb=" N TRP E 353 " --> pdb=" O VAL E 350 " (cutoff:3.500A) Processing helix chain 'E' and resid 365 through 370 Processing helix chain 'E' and resid 386 through 389 Processing helix chain 'E' and resid 405 through 410 removed outlier: 4.736A pdb=" N ARG E 408 " --> pdb=" O ASP E 405 " (cutoff:3.500A) Processing helix chain 'E' and resid 416 through 422 Processing sheet with id=AA1, first strand: chain 'E' and resid 354 through 358 removed outlier: 3.504A pdb=" N ASN E 394 " --> pdb=" O GLU E 516 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'E' and resid 361 through 362 removed outlier: 6.629A pdb=" N CYS E 361 " --> pdb=" O CYS E 525 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'E' and resid 452 through 454 Processing sheet with id=AA4, first strand: chain 'E' and resid 473 through 474 44 hydrogen bonds defined for protein. 105 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: 0.19 Time building geometry restraints manager: 0.17 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 425 1.34 - 1.47: 475 1.47 - 1.60: 620 1.60 - 1.73: 0 1.73 - 1.86: 8 Bond restraints: 1528 Sorted by residual: bond pdb=" NE ARG E 403 " pdb=" CZ ARG E 403 " ideal model delta sigma weight residual 1.326 1.359 -0.033 1.10e-02 8.26e+03 8.93e+00 bond pdb=" NE ARG E 509 " pdb=" CZ ARG E 509 " ideal model delta sigma weight residual 1.326 1.356 -0.030 1.10e-02 8.26e+03 7.45e+00 bond pdb=" NE ARG E 346 " pdb=" CZ ARG E 346 " ideal model delta sigma weight residual 1.326 1.352 -0.026 1.10e-02 8.26e+03 5.45e+00 bond pdb=" CD GLU E 471 " pdb=" OE2 GLU E 471 " ideal model delta sigma weight residual 1.249 1.206 0.043 1.90e-02 2.77e+03 5.18e+00 bond pdb=" CA ASN E 422 " pdb=" CB ASN E 422 " ideal model delta sigma weight residual 1.537 1.498 0.040 1.76e-02 3.23e+03 5.06e+00 ... (remaining 1523 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.46: 1629 1.46 - 2.93: 360 2.93 - 4.39: 62 4.39 - 5.85: 23 5.85 - 7.31: 10 Bond angle restraints: 2084 Sorted by residual: angle pdb=" C LEU E 425 " pdb=" N PRO E 426 " pdb=" CA PRO E 426 " ideal model delta sigma weight residual 120.03 126.94 -6.91 9.90e-01 1.02e+00 4.88e+01 angle pdb=" C SER E 383 " pdb=" N PRO E 384 " pdb=" CA PRO E 384 " ideal model delta sigma weight residual 119.56 126.59 -7.03 1.02e+00 9.61e-01 4.74e+01 angle pdb=" C GLN E 506 " pdb=" N PRO E 507 " pdb=" CA PRO E 507 " ideal model delta sigma weight residual 119.83 126.64 -6.81 1.08e+00 8.57e-01 3.97e+01 angle pdb=" C PHE E 490 " pdb=" N PRO E 491 " pdb=" CA PRO E 491 " ideal model delta sigma weight residual 119.56 125.64 -6.08 1.02e+00 9.61e-01 3.55e+01 angle pdb=" C ALA E 411 " pdb=" N PRO E 412 " pdb=" CA PRO E 412 " ideal model delta sigma weight residual 119.85 125.61 -5.76 1.01e+00 9.80e-01 3.25e+01 ... (remaining 2079 not shown) Histogram of dihedral angle deviations from ideal: 0.01 - 14.18: 847 14.18 - 28.36: 41 28.36 - 42.54: 6 42.54 - 56.72: 4 56.72 - 70.89: 2 Dihedral angle restraints: 900 sinusoidal: 334 harmonic: 566 Sorted by residual: dihedral pdb=" CB CYS E 480 " pdb=" SG CYS E 480 " pdb=" SG CYS E 488 " pdb=" CB CYS E 488 " ideal model delta sinusoidal sigma weight residual 93.00 140.69 -47.69 1 1.00e+01 1.00e-02 3.14e+01 dihedral pdb=" N ASN E 501 " pdb=" C ASN E 501 " pdb=" CA ASN E 501 " pdb=" CB ASN E 501 " ideal model delta harmonic sigma weight residual 122.80 134.30 -11.50 0 2.50e+00 1.60e-01 2.12e+01 dihedral pdb=" C ASN E 501 " pdb=" N ASN E 501 " pdb=" CA ASN E 501 " pdb=" CB ASN E 501 " ideal model delta harmonic sigma weight residual -122.60 -132.07 9.47 0 2.50e+00 1.60e-01 1.43e+01 ... (remaining 897 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.079: 154 0.079 - 0.157: 59 0.157 - 0.236: 7 0.236 - 0.314: 1 0.314 - 0.393: 2 Chirality restraints: 223 Sorted by residual: chirality pdb=" CA ASN E 501 " pdb=" N ASN E 501 " pdb=" C ASN E 501 " pdb=" CB ASN E 501 " both_signs ideal model delta sigma weight residual False 2.51 2.12 0.39 2.00e-01 2.50e+01 3.86e+00 chirality pdb=" C1 NAG E 601 " pdb=" ND2 ASN E 343 " pdb=" C2 NAG E 601 " pdb=" O5 NAG E 601 " both_signs ideal model delta sigma weight residual False -2.40 -2.06 -0.34 2.00e-01 2.50e+01 2.95e+00 chirality pdb=" CA PHE E 497 " pdb=" N PHE E 497 " pdb=" C PHE E 497 " pdb=" CB PHE E 497 " both_signs ideal model delta sigma weight residual False 2.51 2.21 0.30 2.00e-01 2.50e+01 2.32e+00 ... (remaining 220 not shown) Planarity restraints: 270 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR E 495 " -0.062 2.00e-02 2.50e+03 3.46e-02 2.40e+01 pdb=" CG TYR E 495 " 0.019 2.00e-02 2.50e+03 pdb=" CD1 TYR E 495 " 0.028 2.00e-02 2.50e+03 pdb=" CD2 TYR E 495 " 0.025 2.00e-02 2.50e+03 pdb=" CE1 TYR E 495 " 0.019 2.00e-02 2.50e+03 pdb=" CE2 TYR E 495 " 0.021 2.00e-02 2.50e+03 pdb=" CZ TYR E 495 " 0.006 2.00e-02 2.50e+03 pdb=" OH TYR E 495 " -0.056 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN E 343 " 0.034 2.00e-02 2.50e+03 3.47e-02 1.50e+01 pdb=" CG ASN E 343 " -0.019 2.00e-02 2.50e+03 pdb=" OD1 ASN E 343 " -0.005 2.00e-02 2.50e+03 pdb=" ND2 ASN E 343 " -0.052 2.00e-02 2.50e+03 pdb=" C1 NAG E 601 " 0.042 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE E 497 " 0.019 2.00e-02 2.50e+03 1.22e-02 2.60e+00 pdb=" CG PHE E 497 " -0.016 2.00e-02 2.50e+03 pdb=" CD1 PHE E 497 " -0.008 2.00e-02 2.50e+03 pdb=" CD2 PHE E 497 " -0.013 2.00e-02 2.50e+03 pdb=" CE1 PHE E 497 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 PHE E 497 " 0.005 2.00e-02 2.50e+03 pdb=" CZ PHE E 497 " 0.012 2.00e-02 2.50e+03 ... (remaining 267 not shown) Histogram of nonbonded interaction distances: 2.53 - 3.00: 766 3.00 - 3.48: 1263 3.48 - 3.95: 2399 3.95 - 4.43: 2662 4.43 - 4.90: 4278 Nonbonded interactions: 11368 Sorted by model distance: nonbonded pdb=" O PHE E 497 " pdb=" C GLN E 498 " model vdw 2.528 3.270 nonbonded pdb=" N ASN E 440 " pdb=" N LEU E 441 " model vdw 2.602 2.560 nonbonded pdb=" N LYS E 462 " pdb=" O LYS E 462 " model vdw 2.608 2.496 nonbonded pdb=" N ASP E 389 " pdb=" N LEU E 390 " model vdw 2.626 2.560 nonbonded pdb=" N ALA E 411 " pdb=" O ALA E 411 " model vdw 2.627 2.496 ... (remaining 11363 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: 15.310 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.040 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 4.610 Find NCS groups from input model: 0.010 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:1.380 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.380 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7002 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 : 0.012 0.080 1533 Z= 0.634 Angle : 1.519 20.084 2095 Z= 0.974 Chirality : 0.084 0.393 223 Planarity : 0.006 0.035 269 Dihedral : 9.829 70.895 530 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 2.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.69 % Favored : 95.31 % Rotamer: Outliers : 0.00 % Allowed : 0.72 % Favored : 99.28 % Cbeta Deviations : 0.56 % 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 aren not related in a simple way. whole: -0.98 (0.57), residues: 192 helix: -4.18 (0.54), residues: 25 sheet: 1.35 (0.79), residues: 38 loop : -0.52 (0.52), residues: 129 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG E 403 TYR 0.062 0.004 TYR E 495 PHE 0.019 0.003 PHE E 497 TRP 0.014 0.006 TRP E 353 Details of bonding type rmsd covalent geometry : bond 0.01121 ( 1528) covalent geometry : angle 1.40277 ( 2084) SS BOND : bond 0.05115 ( 4) SS BOND : angle 1.95834 ( 8) hydrogen bonds : bond 0.15225 ( 44) hydrogen bonds : angle 9.84021 ( 105) link_NAG-ASN : bond 0.05197 ( 1) link_NAG-ASN : angle 15.31923 ( 3) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 384 Ramachandran restraints generated. 192 Oldfield, 0 Emsley, 192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 384 Ramachandran restraints generated. 192 Oldfield, 0 Emsley, 192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 33 residues out of total 167 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 33 time to evaluate : 0.060 Fit side-chains REVERT: E 438 SER cc_start: 0.7257 (t) cc_final: 0.7019 (t) outliers start: 0 outliers final: 0 residues processed: 33 average time/residue: 0.0916 time to fit residues: 3.3289 Evaluate side-chains 20 residues out of total 167 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 20 time to evaluate : 0.066 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 19 random chunks: chunk 12 optimal weight: 0.3980 chunk 13 optimal weight: 0.8980 chunk 1 optimal weight: 0.3980 chunk 8 optimal weight: 0.0870 chunk 16 optimal weight: 0.0980 chunk 15 optimal weight: 0.7980 chunk 9 optimal weight: 0.6980 chunk 11 optimal weight: 0.6980 chunk 18 optimal weight: 0.5980 chunk 6 optimal weight: 0.0970 chunk 4 optimal weight: 0.7980 overall best weight: 0.2156 ------------------------------------------------------------------------------- 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 = 0.3838 r_free = 0.3838 target = 0.166708 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3672 r_free = 0.3672 target = 0.151831 restraints weight = 2062.082| |-----------------------------------------------------------------------------| r_work (start): 0.3667 rms_B_bonded: 1.94 r_work: 0.3584 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.3465 rms_B_bonded: 4.13 restraints_weight: 0.2500 r_work (final): 0.3465 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7643 moved from start: 0.2868 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 1533 Z= 0.129 Angle : 0.539 4.922 2095 Z= 0.284 Chirality : 0.044 0.127 223 Planarity : 0.004 0.028 269 Dihedral : 5.277 35.480 238 Min Nonbonded Distance : 2.585 Molprobity Statistics. All-atom Clashscore : 3.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 0.72 % Allowed : 7.19 % Favored : 92.09 % 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 aren not related in a simple way. whole: -1.50 (0.55), residues: 192 helix: -4.21 (0.46), residues: 24 sheet: 0.92 (0.78), residues: 39 loop : -0.99 (0.50), residues: 129 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG E 457 TYR 0.011 0.001 TYR E 421 PHE 0.008 0.002 PHE E 490 TRP 0.012 0.002 TRP E 436 Details of bonding type rmsd covalent geometry : bond 0.00285 ( 1528) covalent geometry : angle 0.52970 ( 2084) SS BOND : bond 0.00383 ( 4) SS BOND : angle 0.49535 ( 8) hydrogen bonds : bond 0.03949 ( 44) hydrogen bonds : angle 7.28225 ( 105) link_NAG-ASN : bond 0.00337 ( 1) link_NAG-ASN : angle 2.75015 ( 3) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 384 Ramachandran restraints generated. 192 Oldfield, 0 Emsley, 192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 384 Ramachandran restraints generated. 192 Oldfield, 0 Emsley, 192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 28 residues out of total 167 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 27 time to evaluate : 0.062 Fit side-chains outliers start: 1 outliers final: 0 residues processed: 28 average time/residue: 0.0908 time to fit residues: 2.8142 Evaluate side-chains 20 residues out of total 167 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 20 time to evaluate : 0.060 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 19 random chunks: chunk 10 optimal weight: 0.8980 chunk 15 optimal weight: 0.0670 chunk 12 optimal weight: 0.5980 chunk 13 optimal weight: 0.5980 chunk 5 optimal weight: 0.0670 chunk 0 optimal weight: 0.9990 chunk 4 optimal weight: 0.1980 chunk 18 optimal weight: 0.5980 chunk 1 optimal weight: 0.0870 chunk 14 optimal weight: 0.6980 chunk 8 optimal weight: 0.7980 overall best weight: 0.2034 ------------------------------------------------------------------------------- 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 = 0.3776 r_free = 0.3776 target = 0.161399 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3623 r_free = 0.3623 target = 0.147483 restraints weight = 2070.677| |-----------------------------------------------------------------------------| r_work (start): 0.3620 rms_B_bonded: 1.72 r_work: 0.3543 rms_B_bonded: 2.10 restraints_weight: 0.5000 r_work: 0.3426 rms_B_bonded: 3.81 restraints_weight: 0.2500 r_work (final): 0.3426 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7737 moved from start: 0.3740 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 1533 Z= 0.104 Angle : 0.484 3.674 2095 Z= 0.258 Chirality : 0.043 0.121 223 Planarity : 0.003 0.027 269 Dihedral : 4.399 26.436 238 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 2.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 2.16 % Allowed : 9.35 % Favored : 88.49 % 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 aren not related in a simple way. whole: -1.53 (0.53), residues: 192 helix: -3.68 (0.51), residues: 31 sheet: 1.26 (0.82), residues: 37 loop : -1.04 (0.49), residues: 124 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG E 457 TYR 0.008 0.001 TYR E 351 PHE 0.008 0.001 PHE E 497 TRP 0.007 0.001 TRP E 436 Details of bonding type rmsd covalent geometry : bond 0.00230 ( 1528) covalent geometry : angle 0.47369 ( 2084) SS BOND : bond 0.00243 ( 4) SS BOND : angle 0.89957 ( 8) hydrogen bonds : bond 0.04017 ( 44) hydrogen bonds : angle 6.74086 ( 105) link_NAG-ASN : bond 0.00117 ( 1) link_NAG-ASN : angle 2.35329 ( 3) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 384 Ramachandran restraints generated. 192 Oldfield, 0 Emsley, 192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 384 Ramachandran restraints generated. 192 Oldfield, 0 Emsley, 192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 24 residues out of total 167 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 21 time to evaluate : 0.058 Fit side-chains REVERT: E 506 GLN cc_start: 0.7328 (mm-40) cc_final: 0.6982 (mp10) outliers start: 3 outliers final: 3 residues processed: 22 average time/residue: 0.0859 time to fit residues: 2.1207 Evaluate side-chains 23 residues out of total 167 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 20 time to evaluate : 0.053 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 367 VAL Chi-restraints excluded: chain E residue 373 SER Chi-restraints excluded: chain E residue 407 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 19 random chunks: chunk 16 optimal weight: 1.9990 chunk 13 optimal weight: 0.6980 chunk 18 optimal weight: 0.6980 chunk 7 optimal weight: 0.4980 chunk 0 optimal weight: 0.9990 chunk 1 optimal weight: 0.3980 chunk 4 optimal weight: 0.5980 chunk 2 optimal weight: 0.6980 chunk 9 optimal weight: 0.2980 chunk 10 optimal weight: 0.9990 chunk 6 optimal weight: 0.5980 overall best weight: 0.4780 ------------------------------------------------------------------------------- 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 = 0.3659 r_free = 0.3659 target = 0.150968 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3516 r_free = 0.3516 target = 0.138101 restraints weight = 2136.988| |-----------------------------------------------------------------------------| r_work (start): 0.3513 rms_B_bonded: 1.60 r_work: 0.3427 rms_B_bonded: 2.16 restraints_weight: 0.5000 r_work: 0.3313 rms_B_bonded: 3.85 restraints_weight: 0.2500 r_work (final): 0.3313 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7891 moved from start: 0.4449 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 1533 Z= 0.186 Angle : 0.575 6.732 2095 Z= 0.295 Chirality : 0.046 0.129 223 Planarity : 0.004 0.029 269 Dihedral : 5.125 29.740 238 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 2.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.17 % Favored : 95.83 % Rotamer: Outliers : 1.44 % Allowed : 12.95 % Favored : 85.61 % 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 aren not related in a simple way. whole: -1.52 (0.54), residues: 192 helix: -3.42 (0.62), residues: 31 sheet: 1.54 (0.86), residues: 37 loop : -1.22 (0.47), residues: 124 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.001 ARG E 457 TYR 0.011 0.001 TYR E 351 PHE 0.012 0.002 PHE E 429 TRP 0.008 0.001 TRP E 436 Details of bonding type rmsd covalent geometry : bond 0.00448 ( 1528) covalent geometry : angle 0.56561 ( 2084) SS BOND : bond 0.00081 ( 4) SS BOND : angle 1.07551 ( 8) hydrogen bonds : bond 0.04153 ( 44) hydrogen bonds : angle 6.86728 ( 105) link_NAG-ASN : bond 0.00074 ( 1) link_NAG-ASN : angle 2.39560 ( 3) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 384 Ramachandran restraints generated. 192 Oldfield, 0 Emsley, 192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 384 Ramachandran restraints generated. 192 Oldfield, 0 Emsley, 192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 22 residues out of total 167 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 20 time to evaluate : 0.063 Fit side-chains outliers start: 2 outliers final: 2 residues processed: 20 average time/residue: 0.0778 time to fit residues: 1.7876 Evaluate side-chains 20 residues out of total 167 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 18 time to evaluate : 0.053 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 367 VAL Chi-restraints excluded: chain E residue 407 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 19 random chunks: chunk 10 optimal weight: 0.6980 chunk 14 optimal weight: 0.9980 chunk 4 optimal weight: 0.2980 chunk 15 optimal weight: 0.9990 chunk 8 optimal weight: 0.0050 chunk 16 optimal weight: 0.3980 chunk 7 optimal weight: 0.5980 chunk 1 optimal weight: 0.3980 chunk 11 optimal weight: 0.9980 chunk 12 optimal weight: 0.3980 chunk 17 optimal weight: 0.1980 overall best weight: 0.2594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 506 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3699 r_free = 0.3699 target = 0.155293 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3555 r_free = 0.3555 target = 0.142099 restraints weight = 2039.446| |-----------------------------------------------------------------------------| r_work (start): 0.3548 rms_B_bonded: 1.64 r_work: 0.3461 rms_B_bonded: 2.12 restraints_weight: 0.5000 r_work: 0.3349 rms_B_bonded: 3.73 restraints_weight: 0.2500 r_work (final): 0.3349 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7850 moved from start: 0.4618 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 1533 Z= 0.114 Angle : 0.488 4.348 2095 Z= 0.253 Chirality : 0.044 0.126 223 Planarity : 0.004 0.027 269 Dihedral : 4.737 28.733 238 Min Nonbonded Distance : 2.591 Molprobity Statistics. All-atom Clashscore : 1.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 2.16 % Allowed : 12.23 % Favored : 85.61 % 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 aren not related in a simple way. whole: -1.47 (0.54), residues: 192 helix: -3.14 (0.70), residues: 31 sheet: 1.72 (0.88), residues: 37 loop : -1.31 (0.46), residues: 124 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG E 457 TYR 0.007 0.001 TYR E 351 PHE 0.007 0.001 PHE E 377 TRP 0.008 0.001 TRP E 436 Details of bonding type rmsd covalent geometry : bond 0.00267 ( 1528) covalent geometry : angle 0.47812 ( 2084) SS BOND : bond 0.00251 ( 4) SS BOND : angle 1.01229 ( 8) hydrogen bonds : bond 0.03570 ( 44) hydrogen bonds : angle 6.54198 ( 105) link_NAG-ASN : bond 0.00056 ( 1) link_NAG-ASN : angle 2.22503 ( 3) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 384 Ramachandran restraints generated. 192 Oldfield, 0 Emsley, 192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 384 Ramachandran restraints generated. 192 Oldfield, 0 Emsley, 192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 25 residues out of total 167 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 22 time to evaluate : 0.055 Fit side-chains outliers start: 3 outliers final: 2 residues processed: 24 average time/residue: 0.0611 time to fit residues: 1.6992 Evaluate side-chains 22 residues out of total 167 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 20 time to evaluate : 0.053 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 367 VAL Chi-restraints excluded: chain E residue 373 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 19 random chunks: chunk 15 optimal weight: 0.0000 chunk 11 optimal weight: 1.9990 chunk 4 optimal weight: 0.5980 chunk 0 optimal weight: 0.9990 chunk 12 optimal weight: 0.0970 chunk 13 optimal weight: 0.3980 chunk 9 optimal weight: 0.5980 chunk 8 optimal weight: 0.5980 chunk 7 optimal weight: 0.5980 chunk 14 optimal weight: 0.8980 chunk 6 optimal weight: 0.6980 overall best weight: 0.3382 ------------------------------------------------------------------------------- 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 = 0.151395 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.138483 restraints weight = 2121.278| |-----------------------------------------------------------------------------| r_work (start): 0.3518 rms_B_bonded: 1.65 r_work: 0.3423 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.3310 rms_B_bonded: 3.97 restraints_weight: 0.2500 r_work (final): 0.3310 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7898 moved from start: 0.4902 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 1533 Z= 0.137 Angle : 0.496 3.674 2095 Z= 0.259 Chirality : 0.044 0.128 223 Planarity : 0.004 0.027 269 Dihedral : 4.886 30.797 238 Min Nonbonded Distance : 2.575 Molprobity Statistics. All-atom Clashscore : 1.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 2.16 % Allowed : 12.95 % Favored : 84.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.55 (0.53), residues: 192 helix: -2.86 (0.74), residues: 31 sheet: 1.56 (0.87), residues: 37 loop : -1.43 (0.45), residues: 124 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.001 ARG E 457 TYR 0.007 0.001 TYR E 351 PHE 0.007 0.001 PHE E 377 TRP 0.008 0.001 TRP E 436 Details of bonding type rmsd covalent geometry : bond 0.00328 ( 1528) covalent geometry : angle 0.48507 ( 2084) SS BOND : bond 0.00203 ( 4) SS BOND : angle 1.12497 ( 8) hydrogen bonds : bond 0.03712 ( 44) hydrogen bonds : angle 6.51687 ( 105) link_NAG-ASN : bond 0.00037 ( 1) link_NAG-ASN : angle 2.21311 ( 3) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 384 Ramachandran restraints generated. 192 Oldfield, 0 Emsley, 192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 384 Ramachandran restraints generated. 192 Oldfield, 0 Emsley, 192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 26 residues out of total 167 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 23 time to evaluate : 0.057 Fit side-chains outliers start: 3 outliers final: 3 residues processed: 24 average time/residue: 0.0992 time to fit residues: 2.6101 Evaluate side-chains 24 residues out of total 167 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 21 time to evaluate : 0.058 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 367 VAL Chi-restraints excluded: chain E residue 373 SER Chi-restraints excluded: chain E residue 407 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 19 random chunks: chunk 15 optimal weight: 1.9990 chunk 18 optimal weight: 0.0000 chunk 12 optimal weight: 0.2980 chunk 16 optimal weight: 0.1980 chunk 11 optimal weight: 0.6980 chunk 8 optimal weight: 0.9980 chunk 17 optimal weight: 0.0870 chunk 4 optimal weight: 0.6980 chunk 2 optimal weight: 0.5980 chunk 1 optimal weight: 0.9990 chunk 7 optimal weight: 0.5980 overall best weight: 0.2362 ------------------------------------------------------------------------------- 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 = 0.154731 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3554 r_free = 0.3554 target = 0.142534 restraints weight = 2050.400| |-----------------------------------------------------------------------------| r_work (start): 0.3553 rms_B_bonded: 1.49 r_work: 0.3471 rms_B_bonded: 1.95 restraints_weight: 0.5000 r_work: 0.3363 rms_B_bonded: 3.48 restraints_weight: 0.2500 r_work (final): 0.3363 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7853 moved from start: 0.5079 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 1533 Z= 0.107 Angle : 0.473 3.767 2095 Z= 0.246 Chirality : 0.043 0.129 223 Planarity : 0.004 0.027 269 Dihedral : 4.729 30.251 238 Min Nonbonded Distance : 2.592 Molprobity Statistics. All-atom Clashscore : 1.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 2.16 % Allowed : 13.67 % Favored : 84.17 % 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 aren not related in a simple way. whole: -1.49 (0.53), residues: 192 helix: -2.90 (0.71), residues: 31 sheet: 1.56 (0.86), residues: 37 loop : -1.35 (0.46), residues: 124 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.001 ARG E 346 TYR 0.007 0.001 TYR E 351 PHE 0.006 0.001 PHE E 377 TRP 0.008 0.001 TRP E 436 Details of bonding type rmsd covalent geometry : bond 0.00252 ( 1528) covalent geometry : angle 0.46257 ( 2084) SS BOND : bond 0.00205 ( 4) SS BOND : angle 1.04770 ( 8) hydrogen bonds : bond 0.03382 ( 44) hydrogen bonds : angle 6.34121 ( 105) link_NAG-ASN : bond 0.00080 ( 1) link_NAG-ASN : angle 2.11707 ( 3) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 384 Ramachandran restraints generated. 192 Oldfield, 0 Emsley, 192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 384 Ramachandran restraints generated. 192 Oldfield, 0 Emsley, 192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 26 residues out of total 167 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 23 time to evaluate : 0.066 Fit side-chains outliers start: 3 outliers final: 3 residues processed: 24 average time/residue: 0.0790 time to fit residues: 2.1230 Evaluate side-chains 25 residues out of total 167 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 22 time to evaluate : 0.054 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 367 VAL Chi-restraints excluded: chain E residue 373 SER Chi-restraints excluded: chain E residue 407 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 19 random chunks: chunk 13 optimal weight: 0.0770 chunk 17 optimal weight: 0.9980 chunk 9 optimal weight: 0.9980 chunk 15 optimal weight: 1.9990 chunk 14 optimal weight: 0.6980 chunk 10 optimal weight: 1.9990 chunk 18 optimal weight: 0.5980 chunk 2 optimal weight: 0.9980 chunk 3 optimal weight: 0.5980 chunk 7 optimal weight: 0.2980 chunk 0 optimal weight: 0.0980 overall best weight: 0.3338 ------------------------------------------------------------------------------- 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 = 0.3658 r_free = 0.3658 target = 0.150591 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3513 r_free = 0.3513 target = 0.137865 restraints weight = 2059.519| |-----------------------------------------------------------------------------| r_work (start): 0.3515 rms_B_bonded: 1.65 r_work: 0.3420 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.3305 rms_B_bonded: 3.94 restraints_weight: 0.2500 r_work (final): 0.3305 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7909 moved from start: 0.5198 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 1533 Z= 0.135 Angle : 0.494 4.349 2095 Z= 0.257 Chirality : 0.044 0.134 223 Planarity : 0.004 0.028 269 Dihedral : 4.889 31.808 238 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 1.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.65 % Favored : 96.35 % Rotamer: Outliers : 2.16 % Allowed : 13.67 % Favored : 84.17 % 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 aren not related in a simple way. whole: -1.52 (0.53), residues: 192 helix: -2.75 (0.73), residues: 31 sheet: 1.44 (0.86), residues: 37 loop : -1.39 (0.46), residues: 124 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG E 466 TYR 0.009 0.001 TYR E 351 PHE 0.007 0.001 PHE E 429 TRP 0.008 0.001 TRP E 436 Details of bonding type rmsd covalent geometry : bond 0.00323 ( 1528) covalent geometry : angle 0.48297 ( 2084) SS BOND : bond 0.00183 ( 4) SS BOND : angle 1.13938 ( 8) hydrogen bonds : bond 0.03558 ( 44) hydrogen bonds : angle 6.38903 ( 105) link_NAG-ASN : bond 0.00004 ( 1) link_NAG-ASN : angle 2.21691 ( 3) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 384 Ramachandran restraints generated. 192 Oldfield, 0 Emsley, 192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 384 Ramachandran restraints generated. 192 Oldfield, 0 Emsley, 192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 25 residues out of total 167 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 22 time to evaluate : 0.059 Fit side-chains outliers start: 3 outliers final: 3 residues processed: 23 average time/residue: 0.0853 time to fit residues: 2.1892 Evaluate side-chains 25 residues out of total 167 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 22 time to evaluate : 0.057 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 367 VAL Chi-restraints excluded: chain E residue 373 SER Chi-restraints excluded: chain E residue 407 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 19 random chunks: chunk 3 optimal weight: 0.5980 chunk 13 optimal weight: 0.4980 chunk 2 optimal weight: 0.0030 chunk 11 optimal weight: 1.9990 chunk 0 optimal weight: 0.0970 chunk 17 optimal weight: 0.9990 chunk 15 optimal weight: 0.0170 chunk 9 optimal weight: 0.0870 chunk 12 optimal weight: 0.6980 chunk 18 optimal weight: 0.9980 chunk 14 optimal weight: 0.1980 overall best weight: 0.0804 ------------------------------------------------------------------------------- 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 = 0.3721 r_free = 0.3721 target = 0.155990 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3579 r_free = 0.3579 target = 0.143186 restraints weight = 2071.956| |-----------------------------------------------------------------------------| r_work (start): 0.3583 rms_B_bonded: 1.63 r_work: 0.3496 rms_B_bonded: 2.14 restraints_weight: 0.5000 r_work: 0.3385 rms_B_bonded: 3.78 restraints_weight: 0.2500 r_work (final): 0.3385 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7802 moved from start: 0.5283 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.017 1533 Z= 0.077 Angle : 0.442 4.083 2095 Z= 0.231 Chirality : 0.042 0.124 223 Planarity : 0.004 0.028 269 Dihedral : 4.307 28.387 238 Min Nonbonded Distance : 2.559 Molprobity Statistics. All-atom Clashscore : 1.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 1.44 % Allowed : 14.39 % Favored : 84.17 % 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 aren not related in a simple way. whole: -0.85 (0.55), residues: 192 helix: -2.39 (1.11), residues: 18 sheet: 1.64 (0.87), residues: 37 loop : -1.01 (0.46), residues: 137 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 457 TYR 0.005 0.001 TYR E 351 PHE 0.005 0.001 PHE E 377 TRP 0.009 0.001 TRP E 436 Details of bonding type rmsd covalent geometry : bond 0.00164 ( 1528) covalent geometry : angle 0.43340 ( 2084) SS BOND : bond 0.00312 ( 4) SS BOND : angle 0.92299 ( 8) hydrogen bonds : bond 0.02900 ( 44) hydrogen bonds : angle 5.96996 ( 105) link_NAG-ASN : bond 0.00138 ( 1) link_NAG-ASN : angle 1.93088 ( 3) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 384 Ramachandran restraints generated. 192 Oldfield, 0 Emsley, 192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 384 Ramachandran restraints generated. 192 Oldfield, 0 Emsley, 192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 28 residues out of total 167 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 26 time to evaluate : 0.062 Fit side-chains outliers start: 2 outliers final: 2 residues processed: 27 average time/residue: 0.0799 time to fit residues: 2.4157 Evaluate side-chains 25 residues out of total 167 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 23 time to evaluate : 0.054 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 367 VAL Chi-restraints excluded: chain E residue 373 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 19 random chunks: chunk 10 optimal weight: 0.9990 chunk 4 optimal weight: 0.0980 chunk 14 optimal weight: 0.6980 chunk 3 optimal weight: 0.7980 chunk 17 optimal weight: 0.5980 chunk 12 optimal weight: 0.2980 chunk 15 optimal weight: 0.8980 chunk 9 optimal weight: 0.0980 chunk 6 optimal weight: 0.6980 chunk 13 optimal weight: 0.5980 chunk 0 optimal weight: 0.9990 overall best weight: 0.3380 ------------------------------------------------------------------------------- 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 = 0.3657 r_free = 0.3657 target = 0.150762 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.138752 restraints weight = 2100.343| |-----------------------------------------------------------------------------| r_work (start): 0.3524 rms_B_bonded: 1.53 r_work: 0.3439 rms_B_bonded: 2.02 restraints_weight: 0.5000 r_work: 0.3329 rms_B_bonded: 3.65 restraints_weight: 0.2500 r_work (final): 0.3329 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7887 moved from start: 0.5292 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 1533 Z= 0.137 Angle : 0.492 4.112 2095 Z= 0.256 Chirality : 0.044 0.137 223 Planarity : 0.004 0.028 269 Dihedral : 4.742 31.240 238 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 1.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.17 % Favored : 95.83 % Rotamer: Outliers : 1.44 % Allowed : 14.39 % Favored : 84.17 % 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 aren not related in a simple way. whole: -1.35 (0.54), residues: 192 helix: -2.53 (0.77), residues: 31 sheet: 1.56 (0.85), residues: 37 loop : -1.30 (0.46), residues: 124 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.001 ARG E 357 TYR 0.010 0.001 TYR E 453 PHE 0.007 0.001 PHE E 429 TRP 0.007 0.001 TRP E 436 Details of bonding type rmsd covalent geometry : bond 0.00332 ( 1528) covalent geometry : angle 0.48010 ( 2084) SS BOND : bond 0.00152 ( 4) SS BOND : angle 1.24127 ( 8) hydrogen bonds : bond 0.03573 ( 44) hydrogen bonds : angle 6.25659 ( 105) link_NAG-ASN : bond 0.00000 ( 1) link_NAG-ASN : angle 2.11500 ( 3) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 384 Ramachandran restraints generated. 192 Oldfield, 0 Emsley, 192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 384 Ramachandran restraints generated. 192 Oldfield, 0 Emsley, 192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 24 residues out of total 167 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 22 time to evaluate : 0.073 Fit side-chains outliers start: 2 outliers final: 2 residues processed: 23 average time/residue: 0.0821 time to fit residues: 2.1102 Evaluate side-chains 23 residues out of total 167 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 21 time to evaluate : 0.063 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 367 VAL Chi-restraints excluded: chain E residue 373 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 19 random chunks: chunk 7 optimal weight: 0.3980 chunk 1 optimal weight: 0.0370 chunk 14 optimal weight: 0.9990 chunk 12 optimal weight: 0.8980 chunk 0 optimal weight: 0.9990 chunk 9 optimal weight: 0.3980 chunk 6 optimal weight: 0.8980 chunk 16 optimal weight: 0.0980 chunk 2 optimal weight: 0.7980 chunk 11 optimal weight: 0.5980 chunk 5 optimal weight: 0.0050 overall best weight: 0.1872 ------------------------------------------------------------------------------- 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 = 0.3683 r_free = 0.3683 target = 0.153053 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.140920 restraints weight = 2072.573| |-----------------------------------------------------------------------------| r_work (start): 0.3547 rms_B_bonded: 1.53 r_work: 0.3463 rms_B_bonded: 2.05 restraints_weight: 0.5000 r_work: 0.3355 rms_B_bonded: 3.61 restraints_weight: 0.2500 r_work (final): 0.3355 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7853 moved from start: 0.5345 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.020 1533 Z= 0.096 Angle : 0.460 3.316 2095 Z= 0.241 Chirality : 0.043 0.128 223 Planarity : 0.004 0.028 269 Dihedral : 4.545 29.688 238 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 1.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 1.44 % Allowed : 14.39 % Favored : 84.17 % 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 aren not related in a simple way. whole: -0.81 (0.56), residues: 192 helix: -2.08 (0.94), residues: 25 sheet: 1.75 (0.87), residues: 37 loop : -0.96 (0.48), residues: 130 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG E 457 TYR 0.008 0.001 TYR E 453 PHE 0.011 0.001 PHE E 456 TRP 0.008 0.001 TRP E 436 Details of bonding type rmsd covalent geometry : bond 0.00224 ( 1528) covalent geometry : angle 0.45075 ( 2084) SS BOND : bond 0.00175 ( 4) SS BOND : angle 1.03910 ( 8) hydrogen bonds : bond 0.03168 ( 44) hydrogen bonds : angle 6.09806 ( 105) link_NAG-ASN : bond 0.00077 ( 1) link_NAG-ASN : angle 1.97349 ( 3) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 967.52 seconds wall clock time: 17 minutes 47.68 seconds (1067.68 seconds total)