Starting phenix.real_space_refine on Wed Jul 1 20:45:13 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7tpk_26058/07_2026/7tpk_26058.cif Found real_map, /net/cci-nas-00/data/ceres_data/7tpk_26058/07_2026/7tpk_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 { restraint_files = "/net/cci-nas-00/data/ceres_data/7tpk_26058/07_2026/7tpk_26058.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7tpk_26058/07_2026/7tpk_26058.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7tpk_26058/07_2026/7tpk_26058.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7tpk_26058/07_2026/7tpk_26058.map" model { file = "/net/cci-nas-00/data/ceres_data/7tpk_26058/07_2026/7tpk_26058.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7tpk_26058/07_2026/7tpk_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-dev-6108/lib/python3.11/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 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: 0.20 Conformation dependent library (CDL) restraints added in 114.6 milliseconds 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: 0.21 Time building geometry restraints manager: 0.22 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: 828 14.18 - 28.36: 41 28.36 - 42.54: 4 42.54 - 56.72: 4 56.72 - 70.89: 2 Dihedral angle restraints: 879 sinusoidal: 313 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 876 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: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 10.240 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: 0.040 Check model and map are aligned: 0.000 Set scattering table: 0.010 Process input model: 4.600 Find NCS groups from input model: 0.000 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.800 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.710 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7232 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 : 9.693 70.895 509 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 are 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/Z covalent geometry : bond 0.01121 / 0.62 ( 1528) covalent geometry : angle 1.40277 / 0.96 ( 2084) SS BOND : bond 0.05115 / 2.17 ( 4) SS BOND : angle 1.95834 / 1.14 ( 8) hydrogen bonds : bond 0.15225 / 10.45 ( 44) hydrogen bonds : angle 9.84021 / 7.15 ( 105) link_NAG-ASN : bond 0.05197 / 2.74 ( 1) link_NAG-ASN : angle 15.31923 / 8.25 ( 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 : 0.070 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: 0.0864 time to fit residues: 3.1584 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 : 0.050 ------------------------------------------------------------------------------- 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: 0.9990 chunk 6 optimal weight: 0.0870 chunk 4 optimal weight: 0.7980 overall best weight: 0.2136 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3840 r_free = 0.3840 target = 0.166888 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3675 r_free = 0.3675 target = 0.152059 restraints weight = 2059.674| |-----------------------------------------------------------------------------| r_work (start): 0.3672 rms_B_bonded: 1.94 r_work: 0.3588 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.3470 rms_B_bonded: 4.12 restraints_weight: 0.2500 r_work (final): 0.3470 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7830 moved from start: 0.2859 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 1533 Z= 0.129 Angle : 0.547 4.835 2095 Z= 0.287 Chirality : 0.044 0.125 223 Planarity : 0.004 0.028 269 Dihedral : 4.240 12.954 217 Min Nonbonded Distance : 2.580 Molprobity Statistics. All-atom Clashscore : 3.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 0.72 % Allowed : 6.47 % Favored : 92.81 % 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: -1.51 (0.55), residues: 192 helix: -4.18 (0.48), residues: 24 sheet: 0.88 (0.78), residues: 39 loop : -1.00 (0.50), residues: 129 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG E 457 TYR 0.010 0.001 TYR E 421 PHE 0.008 0.002 PHE E 497 TRP 0.012 0.002 TRP E 436 Details of bonding type rmsd/Z covalent geometry : bond 0.00277 / 0.13 ( 1528) covalent geometry : angle 0.53219 / 0.28 ( 2084) SS BOND : bond 0.00329 / 0.13 ( 4) SS BOND : angle 0.57049 / 0.33 ( 8) hydrogen bonds : bond 0.04109 / 2.62 ( 44) hydrogen bonds : angle 7.23884 / 5.23 ( 105) link_NAG-ASN : bond 0.00662 / 0.35 ( 1) link_NAG-ASN : angle 3.30940 / 1.66 ( 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 : 0.055 Fit side-chains outliers start: 1 outliers final: 0 residues processed: 28 average time/residue: 0.0775 time to fit residues: 2.4066 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 : 0.070 ------------------------------------------------------------------------------- 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: 0.6980 chunk 15 optimal weight: 0.8980 chunk 12 optimal weight: 0.6980 chunk 13 optimal weight: 0.8980 chunk 5 optimal weight: 0.0050 chunk 0 optimal weight: 0.9990 chunk 4 optimal weight: 0.2980 chunk 18 optimal weight: 0.3980 chunk 1 optimal weight: 0.2980 chunk 14 optimal weight: 0.9990 chunk 8 optimal weight: 0.7980 overall best weight: 0.3394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 354 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3734 r_free = 0.3734 target = 0.157961 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3581 r_free = 0.3581 target = 0.144151 restraints weight = 2060.318| |-----------------------------------------------------------------------------| r_work (start): 0.3547 rms_B_bonded: 1.68 r_work: 0.3467 rms_B_bonded: 2.08 restraints_weight: 0.5000 r_work: 0.3351 rms_B_bonded: 3.70 restraints_weight: 0.2500 r_work (final): 0.3351 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7966 moved from start: 0.3912 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= 0.143 Angle : 0.537 4.804 2095 Z= 0.287 Chirality : 0.044 0.125 223 Planarity : 0.004 0.027 269 Dihedral : 4.245 12.902 217 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 3.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 1.44 % Allowed : 10.79 % Favored : 87.77 % 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: -1.52 (0.54), residues: 192 helix: -3.66 (0.54), residues: 31 sheet: 1.42 (0.84), residues: 37 loop : -1.10 (0.49), residues: 124 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.001 ARG E 509 TYR 0.010 0.001 TYR E 351 PHE 0.009 0.001 PHE E 497 TRP 0.008 0.001 TRP E 436 Details of bonding type rmsd/Z covalent geometry : bond 0.00329 / 0.14 ( 1528) covalent geometry : angle 0.52715 / 0.28 ( 2084) SS BOND : bond 0.00100 / 0.05 ( 4) SS BOND : angle 0.96106 / 0.49 ( 8) hydrogen bonds : bond 0.04327 / 2.82 ( 44) hydrogen bonds : angle 6.92067 / 4.82 ( 105) link_NAG-ASN : bond 0.00099 / 0.05 ( 1) link_NAG-ASN : angle 2.35729 / 1.24 ( 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 27 residues out of total 167 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 25 time to evaluate : 0.060 Fit side-chains outliers start: 2 outliers final: 2 residues processed: 25 average time/residue: 0.0597 time to fit residues: 1.7451 Evaluate side-chains 26 residues out of total 167 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 24 time to evaluate : 0.064 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 367 VAL 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: 0.4980 chunk 13 optimal weight: 0.0870 chunk 18 optimal weight: 0.0470 chunk 7 optimal weight: 0.2980 chunk 0 optimal weight: 0.9990 chunk 1 optimal weight: 0.5980 chunk 4 optimal weight: 0.5980 chunk 2 optimal weight: 0.6980 chunk 9 optimal weight: 0.2980 chunk 10 optimal weight: 0.5980 chunk 6 optimal weight: 0.2980 overall best weight: 0.2056 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3740 r_free = 0.3740 target = 0.158112 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3590 r_free = 0.3590 target = 0.144606 restraints weight = 2059.901| |-----------------------------------------------------------------------------| r_work (start): 0.3577 rms_B_bonded: 1.68 r_work: 0.3492 rms_B_bonded: 2.13 restraints_weight: 0.5000 r_work: 0.3381 rms_B_bonded: 3.79 restraints_weight: 0.2500 r_work (final): 0.3381 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7984 moved from start: 0.4223 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 1533 Z= 0.101 Angle : 0.499 6.341 2095 Z= 0.257 Chirality : 0.043 0.122 223 Planarity : 0.004 0.028 269 Dihedral : 3.881 12.694 217 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 2.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 1.44 % Allowed : 12.23 % Favored : 86.33 % 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: -1.41 (0.54), residues: 192 helix: -3.54 (0.58), residues: 31 sheet: 1.68 (0.85), residues: 37 loop : -1.10 (0.48), residues: 124 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 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/Z covalent geometry : bond 0.00227 / 0.10 ( 1528) covalent geometry : angle 0.49048 / 0.26 ( 2084) SS BOND : bond 0.00174 / 0.09 ( 4) SS BOND : angle 0.98191 / 0.49 ( 8) hydrogen bonds : bond 0.03593 / 2.33 ( 44) hydrogen bonds : angle 6.45966 / 4.49 ( 105) link_NAG-ASN : bond 0.00070 / 0.04 ( 1) link_NAG-ASN : angle 2.04914 / 1.12 ( 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 24 residues out of total 167 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 22 time to evaluate : 0.057 Fit side-chains outliers start: 2 outliers final: 2 residues processed: 23 average time/residue: 0.0597 time to fit residues: 1.6016 Evaluate side-chains 21 residues out of total 167 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 19 time to evaluate : 0.057 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 367 VAL Chi-restraints excluded: chain E residue 373 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 19 random chunks: chunk 10 optimal weight: 0.4980 chunk 14 optimal weight: 0.0980 chunk 4 optimal weight: 0.5980 chunk 15 optimal weight: 0.9980 chunk 8 optimal weight: 0.2980 chunk 16 optimal weight: 0.7980 chunk 7 optimal weight: 0.1980 chunk 1 optimal weight: 0.1980 chunk 11 optimal weight: 0.0470 chunk 12 optimal weight: 0.4980 chunk 17 optimal weight: 0.0980 overall best weight: 0.1278 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 506 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3748 r_free = 0.3748 target = 0.159111 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3605 r_free = 0.3605 target = 0.145902 restraints weight = 2035.047| |-----------------------------------------------------------------------------| r_work (start): 0.3609 rms_B_bonded: 1.63 r_work: 0.3529 rms_B_bonded: 2.08 restraints_weight: 0.5000 r_work: 0.3417 rms_B_bonded: 3.74 restraints_weight: 0.2500 r_work (final): 0.3417 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7952 moved from start: 0.4490 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.019 1533 Z= 0.083 Angle : 0.463 5.376 2095 Z= 0.239 Chirality : 0.043 0.123 223 Planarity : 0.004 0.027 269 Dihedral : 3.617 11.759 217 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 2.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % 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 are not related in a simple way. whole: -1.19 (0.55), residues: 192 helix: -3.16 (0.78), residues: 24 sheet: 1.89 (0.89), residues: 37 loop : -1.20 (0.46), residues: 131 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG E 457 TYR 0.006 0.001 TYR E 453 PHE 0.006 0.001 PHE E 377 TRP 0.007 0.001 TRP E 436 Details of bonding type rmsd/Z covalent geometry : bond 0.00179 / 0.08 ( 1528) covalent geometry : angle 0.45487 / 0.24 ( 2084) SS BOND : bond 0.00333 / 0.17 ( 4) SS BOND : angle 0.87824 / 0.43 ( 8) hydrogen bonds : bond 0.03268 / 2.09 ( 44) hydrogen bonds : angle 6.16435 / 4.29 ( 105) link_NAG-ASN : bond 0.00123 / 0.06 ( 1) link_NAG-ASN : angle 1.90801 / 1.06 ( 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 26 residues out of total 167 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 24 time to evaluate : 0.047 Fit side-chains revert: symmetry clash outliers start: 2 outliers final: 2 residues processed: 25 average time/residue: 0.0744 time to fit residues: 2.0727 Evaluate side-chains 21 residues out of total 167 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 19 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 19 random chunks: chunk 15 optimal weight: 0.3980 chunk 11 optimal weight: 0.3980 chunk 4 optimal weight: 0.0770 chunk 0 optimal weight: 0.9990 chunk 12 optimal weight: 0.0770 chunk 13 optimal weight: 0.5980 chunk 9 optimal weight: 0.3980 chunk 8 optimal weight: 0.1980 chunk 7 optimal weight: 0.0770 chunk 14 optimal weight: 1.9990 chunk 6 optimal weight: 0.9980 overall best weight: 0.1654 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3729 r_free = 0.3729 target = 0.156485 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3588 r_free = 0.3588 target = 0.143372 restraints weight = 2095.712| |-----------------------------------------------------------------------------| r_work (start): 0.3583 rms_B_bonded: 1.65 r_work: 0.3498 rms_B_bonded: 2.18 restraints_weight: 0.5000 r_work: 0.3387 rms_B_bonded: 3.91 restraints_weight: 0.2500 r_work (final): 0.3387 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7978 moved from start: 0.4702 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.019 1533 Z= 0.088 Angle : 0.455 4.453 2095 Z= 0.235 Chirality : 0.043 0.126 223 Planarity : 0.004 0.027 269 Dihedral : 3.570 11.726 217 Min Nonbonded Distance : 2.562 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 are not related in a simple way. whole: -0.78 (0.56), residues: 192 helix: -2.59 (1.09), residues: 18 sheet: 1.89 (0.90), residues: 37 loop : -0.98 (0.46), residues: 137 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG E 457 TYR 0.006 0.001 TYR E 351 PHE 0.006 0.001 PHE E 377 TRP 0.006 0.001 TRP E 436 Details of bonding type rmsd/Z covalent geometry : bond 0.00199 / 0.09 ( 1528) covalent geometry : angle 0.44668 / 0.23 ( 2084) SS BOND : bond 0.00157 / 0.08 ( 4) SS BOND : angle 0.98580 / 0.49 ( 8) hydrogen bonds : bond 0.03246 / 2.08 ( 44) hydrogen bonds : angle 6.08878 / 4.26 ( 105) link_NAG-ASN : bond 0.00083 / 0.04 ( 1) link_NAG-ASN : angle 1.87121 / 1.05 ( 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 23 residues out of total 167 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 21 time to evaluate : 0.050 Fit side-chains outliers start: 2 outliers final: 2 residues processed: 22 average time/residue: 0.0726 time to fit residues: 1.7939 Evaluate side-chains 21 residues out of total 167 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 19 time to evaluate : 0.052 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 367 VAL Chi-restraints excluded: chain E residue 373 SER 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: 0.5980 chunk 12 optimal weight: 0.2980 chunk 16 optimal weight: 0.1980 chunk 11 optimal weight: 0.0020 chunk 8 optimal weight: 0.5980 chunk 17 optimal weight: 0.9990 chunk 4 optimal weight: 0.4980 chunk 2 optimal weight: 1.9990 chunk 1 optimal weight: 0.0980 chunk 7 optimal weight: 0.4980 overall best weight: 0.2188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3712 r_free = 0.3712 target = 0.155155 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.142392 restraints weight = 2095.867| |-----------------------------------------------------------------------------| r_work (start): 0.3572 rms_B_bonded: 1.60 r_work: 0.3486 rms_B_bonded: 2.15 restraints_weight: 0.5000 r_work: 0.3378 rms_B_bonded: 3.80 restraints_weight: 0.2500 r_work (final): 0.3378 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8014 moved from start: 0.4869 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 : 0.466 3.951 2095 Z= 0.242 Chirality : 0.043 0.129 223 Planarity : 0.004 0.027 269 Dihedral : 3.726 13.218 217 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 1.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 2.16 % Allowed : 14.39 % Favored : 83.45 % 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: -1.29 (0.54), residues: 192 helix: -3.01 (0.69), residues: 31 sheet: 1.71 (0.88), residues: 37 loop : -1.13 (0.46), residues: 124 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 457 TYR 0.007 0.001 TYR E 351 PHE 0.006 0.001 PHE E 377 TRP 0.007 0.001 TRP E 436 Details of bonding type rmsd/Z covalent geometry : bond 0.00243 / 0.10 ( 1528) covalent geometry : angle 0.45716 / 0.24 ( 2084) SS BOND : bond 0.00128 / 0.07 ( 4) SS BOND : angle 1.08318 / 0.54 ( 8) hydrogen bonds : bond 0.03361 / 2.16 ( 44) hydrogen bonds : angle 6.06520 / 4.23 ( 105) link_NAG-ASN : bond 0.00075 / 0.04 ( 1) link_NAG-ASN : angle 1.90105 / 1.06 ( 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 28 residues out of total 167 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 25 time to evaluate : 0.060 Fit side-chains outliers start: 3 outliers final: 3 residues processed: 26 average time/residue: 0.0684 time to fit residues: 2.0200 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 : 0.054 ------------------------------------------------------------------------------- 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: 0.8980 chunk 17 optimal weight: 0.9990 chunk 9 optimal weight: 0.6980 chunk 15 optimal weight: 0.0070 chunk 14 optimal weight: 0.9990 chunk 10 optimal weight: 0.7980 chunk 18 optimal weight: 0.2980 chunk 2 optimal weight: 0.9980 chunk 3 optimal weight: 0.5980 chunk 7 optimal weight: 0.0980 chunk 0 optimal weight: 0.0980 overall best weight: 0.2198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3700 r_free = 0.3700 target = 0.154343 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3563 r_free = 0.3563 target = 0.141791 restraints weight = 2048.751| |-----------------------------------------------------------------------------| r_work (start): 0.3560 rms_B_bonded: 1.63 r_work: 0.3469 rms_B_bonded: 2.20 restraints_weight: 0.5000 r_work: 0.3361 rms_B_bonded: 3.87 restraints_weight: 0.2500 r_work (final): 0.3361 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8025 moved from start: 0.5019 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= 0.103 Angle : 0.466 3.804 2095 Z= 0.242 Chirality : 0.043 0.130 223 Planarity : 0.004 0.027 269 Dihedral : 3.683 12.832 217 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 1.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 2.16 % Allowed : 15.11 % Favored : 82.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.92 (0.55), residues: 192 helix: -2.72 (0.84), residues: 25 sheet: 1.61 (0.86), residues: 37 loop : -0.88 (0.47), residues: 130 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG E 457 TYR 0.006 0.001 TYR E 473 PHE 0.006 0.001 PHE E 377 TRP 0.007 0.001 TRP E 436 Details of bonding type rmsd/Z covalent geometry : bond 0.00240 / 0.10 ( 1528) covalent geometry : angle 0.45769 / 0.24 ( 2084) SS BOND : bond 0.00202 / 0.10 ( 4) SS BOND : angle 1.03729 / 0.51 ( 8) hydrogen bonds : bond 0.03316 / 2.12 ( 44) hydrogen bonds : angle 6.07009 / 4.25 ( 105) link_NAG-ASN : bond 0.00071 / 0.04 ( 1) link_NAG-ASN : angle 1.86718 / 1.04 ( 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 28 residues out of total 167 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 25 time to evaluate : 0.057 Fit side-chains revert: symmetry clash outliers start: 3 outliers final: 3 residues processed: 26 average time/residue: 0.0768 time to fit residues: 2.2528 Evaluate side-chains 28 residues out of total 167 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 25 time to evaluate : 0.065 ------------------------------------------------------------------------------- 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: 1.9990 chunk 13 optimal weight: 0.8980 chunk 2 optimal weight: 0.9990 chunk 11 optimal weight: 1.9990 chunk 0 optimal weight: 0.9990 chunk 17 optimal weight: 0.6980 chunk 15 optimal weight: 1.9990 chunk 9 optimal weight: 0.9990 chunk 12 optimal weight: 0.1980 chunk 18 optimal weight: 0.4980 chunk 14 optimal weight: 0.6980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3615 r_free = 0.3615 target = 0.147398 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.135006 restraints weight = 2127.113| |-----------------------------------------------------------------------------| r_work (start): 0.3489 rms_B_bonded: 1.62 r_work: 0.3402 rms_B_bonded: 2.16 restraints_weight: 0.5000 r_work: 0.3284 rms_B_bonded: 3.89 restraints_weight: 0.2500 r_work (final): 0.3284 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8129 moved from start: 0.5275 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 1533 Z= 0.223 Angle : 0.585 5.474 2095 Z= 0.300 Chirality : 0.047 0.139 223 Planarity : 0.005 0.027 269 Dihedral : 4.490 15.358 217 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 2.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.17 % Favored : 95.83 % Rotamer: Outliers : 2.88 % Allowed : 13.67 % Favored : 83.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.70 (0.52), residues: 192 helix: -2.85 (0.75), residues: 31 sheet: 1.28 (0.84), residues: 37 loop : -1.51 (0.44), residues: 124 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG E 466 TYR 0.012 0.001 TYR E 453 PHE 0.013 0.002 PHE E 429 TRP 0.005 0.001 TRP E 436 Details of bonding type rmsd/Z covalent geometry : bond 0.00547 / 0.22 ( 1528) covalent geometry : angle 0.57143 / 0.30 ( 2084) SS BOND : bond 0.00127 / 0.05 ( 4) SS BOND : angle 1.45912 / 0.74 ( 8) hydrogen bonds : bond 0.04173 / 2.67 ( 44) hydrogen bonds : angle 6.56233 / 4.59 ( 105) link_NAG-ASN : bond 0.00223 / 0.12 ( 1) link_NAG-ASN : angle 2.48545 / 1.33 ( 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 26 residues out of total 167 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 22 time to evaluate : 0.039 Fit side-chains outliers start: 4 outliers final: 3 residues processed: 24 average time/residue: 0.0644 time to fit residues: 1.7874 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 : 0.038 ------------------------------------------------------------------------------- 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 19 random chunks: chunk 10 optimal weight: 0.0870 chunk 4 optimal weight: 0.6980 chunk 14 optimal weight: 0.9990 chunk 3 optimal weight: 0.9980 chunk 17 optimal weight: 0.0980 chunk 12 optimal weight: 0.6980 chunk 15 optimal weight: 0.6980 chunk 9 optimal weight: 0.8980 chunk 6 optimal weight: 0.5980 chunk 13 optimal weight: 0.3980 chunk 0 optimal weight: 0.9990 overall best weight: 0.3758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3622 r_free = 0.3622 target = 0.148059 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.135189 restraints weight = 2097.254| |-----------------------------------------------------------------------------| r_work (start): 0.3512 rms_B_bonded: 1.66 r_work: 0.3422 rms_B_bonded: 2.20 restraints_weight: 0.5000 r_work: 0.3303 rms_B_bonded: 3.95 restraints_weight: 0.2500 r_work (final): 0.3303 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8096 moved from start: 0.5416 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 1533 Z= 0.152 Angle : 0.520 4.503 2095 Z= 0.267 Chirality : 0.045 0.136 223 Planarity : 0.004 0.027 269 Dihedral : 4.196 14.123 217 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 1.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % 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 are not related in a simple way. whole: -1.61 (0.53), residues: 192 helix: -2.73 (0.76), residues: 31 sheet: 1.29 (0.84), residues: 37 loop : -1.44 (0.45), residues: 124 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.001 ARG E 457 TYR 0.008 0.001 TYR E 351 PHE 0.018 0.002 PHE E 456 TRP 0.007 0.001 TRP E 436 Details of bonding type rmsd/Z covalent geometry : bond 0.00368 / 0.15 ( 1528) covalent geometry : angle 0.50772 / 0.26 ( 2084) SS BOND : bond 0.00191 / 0.10 ( 4) SS BOND : angle 1.22107 / 0.61 ( 8) hydrogen bonds : bond 0.03716 / 2.39 ( 44) hydrogen bonds : angle 6.43643 / 4.50 ( 105) link_NAG-ASN : bond 0.00108 / 0.06 ( 1) link_NAG-ASN : angle 2.32866 / 1.26 ( 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 26 residues out of total 167 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 23 time to evaluate : 0.078 Fit side-chains outliers start: 3 outliers final: 3 residues processed: 24 average time/residue: 0.0874 time to fit residues: 2.3429 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 : 0.033 ------------------------------------------------------------------------------- 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 19 random chunks: chunk 7 optimal weight: 0.5980 chunk 1 optimal weight: 0.5980 chunk 14 optimal weight: 0.0970 chunk 12 optimal weight: 0.7980 chunk 0 optimal weight: 0.9990 chunk 9 optimal weight: 0.9980 chunk 6 optimal weight: 0.7980 chunk 16 optimal weight: 0.5980 chunk 2 optimal weight: 0.7980 chunk 11 optimal weight: 0.8980 chunk 5 optimal weight: 0.0070 overall best weight: 0.3796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3618 r_free = 0.3618 target = 0.147469 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.134699 restraints weight = 2095.964| |-----------------------------------------------------------------------------| r_work (start): 0.3507 rms_B_bonded: 1.65 r_work: 0.3413 rms_B_bonded: 2.21 restraints_weight: 0.5000 r_work: 0.3298 rms_B_bonded: 3.92 restraints_weight: 0.2500 r_work (final): 0.3298 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8101 moved from start: 0.5441 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 1533 Z= 0.151 Angle : 0.525 4.558 2095 Z= 0.268 Chirality : 0.045 0.136 223 Planarity : 0.004 0.027 269 Dihedral : 4.188 13.619 217 Min Nonbonded Distance : 2.558 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 are not related in a simple way. whole: -1.65 (0.53), residues: 192 helix: -2.58 (0.79), residues: 31 sheet: 1.29 (0.85), residues: 37 loop : -1.54 (0.45), 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 0.009 0.002 PHE E 429 TRP 0.006 0.001 TRP E 436 Details of bonding type rmsd/Z covalent geometry : bond 0.00367 / 0.15 ( 1528) covalent geometry : angle 0.51275 / 0.26 ( 2084) SS BOND : bond 0.00184 / 0.09 ( 4) SS BOND : angle 1.26074 / 0.63 ( 8) hydrogen bonds : bond 0.03741 / 2.42 ( 44) hydrogen bonds : angle 6.41628 / 4.47 ( 105) link_NAG-ASN : bond 0.00080 / 0.04 ( 1) link_NAG-ASN : angle 2.32730 / 1.25 ( 3) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 879.40 seconds wall clock time: 16 minutes 11.13 seconds (971.13 seconds total)