Starting phenix.real_space_refine on Wed Jul 1 22:15:26 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7zcf_14629/07_2026/7zcf_14629.cif Found real_map, /net/cci-nas-00/data/ceres_data/7zcf_14629/07_2026/7zcf_14629.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/7zcf_14629/07_2026/7zcf_14629.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7zcf_14629/07_2026/7zcf_14629.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7zcf_14629/07_2026/7zcf_14629.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7zcf_14629/07_2026/7zcf_14629.map" model { file = "/net/cci-nas-00/data/ceres_data/7zcf_14629/07_2026/7zcf_14629.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7zcf_14629/07_2026/7zcf_14629.cif" } resolution = 4.0 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= -0.004 sd= 0.044 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 14 5.16 5 C 2107 2.51 5 N 556 2.21 5 O 635 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 9 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: 3312 Number of models: 1 Model: "" Number of chains: 3 Chain: "C" Number of atoms: 1595 Number of conformers: 1 Conformer: "" Number of residues, atoms: 201, 1595 Classifications: {'peptide': 201} Link IDs: {'PTRANS': 12, 'TRANS': 188} Chain: "E" Number of atoms: 1703 Number of conformers: 1 Conformer: "" Number of residues, atoms: 225, 1703 Classifications: {'peptide': 225} Link IDs: {'PTRANS': 10, 'TRANS': 214} Chain breaks: 1 Chain: "C" 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: 1.07, per 1000 atoms: 0.32 Number of scatterers: 3312 At special positions: 0 Unit cell: (65.786, 91.567, 90.678, 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 14 16.00 O 635 8.00 N 556 7.00 C 2107 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.03 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.04 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.03 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " distance=2.03 Simple disulfide: pdb=" SG CYS E 22 " - pdb=" SG CYS E 95 " distance=2.03 Simple disulfide: pdb=" SG CYS E 156 " - pdb=" SG CYS E 222 " distance=2.03 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 C1301 " - " ASN C 343 " Time building additional restraints: 0.29 Conformation dependent library (CDL) restraints added in 128.2 milliseconds 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 774 Finding SS restraints... Secondary structure from input PDB file: 6 helices and 6 sheets defined 8.5% alpha, 16.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.09 Creating SS restraints... Processing helix chain 'C' and resid 337 through 343 removed outlier: 3.854A pdb=" N VAL C 341 " --> pdb=" O PRO C 337 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N PHE C 342 " --> pdb=" O PHE C 338 " (cutoff:3.500A) Processing helix chain 'C' and resid 365 through 370 removed outlier: 4.228A pdb=" N TYR C 369 " --> pdb=" O TYR C 365 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N ASN C 370 " --> pdb=" O SER C 366 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 365 through 370' Processing helix chain 'C' and resid 386 through 390 removed outlier: 3.676A pdb=" N LEU C 390 " --> pdb=" O LEU C 387 " (cutoff:3.500A) Processing helix chain 'C' and resid 403 through 410 removed outlier: 3.585A pdb=" N ARG C 408 " --> pdb=" O ASP C 405 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N GLN C 409 " --> pdb=" O GLU C 406 " (cutoff:3.500A) Processing helix chain 'C' and resid 439 through 443 removed outlier: 3.877A pdb=" N SER C 443 " --> pdb=" O ASN C 440 " (cutoff:3.500A) Processing helix chain 'E' and resid 213 through 217 removed outlier: 3.954A pdb=" N PHE E 217 " --> pdb=" O PRO E 214 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'C' and resid 354 through 358 removed outlier: 3.651A pdb=" N ASN C 354 " --> pdb=" O SER C 399 " (cutoff:3.500A) removed outlier: 4.669A pdb=" N VAL C 395 " --> pdb=" O ILE C 358 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 452 through 454 removed outlier: 3.640A pdb=" N GLN C 493 " --> pdb=" O TYR C 453 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'E' and resid 18 through 20 removed outlier: 3.639A pdb=" N LEU E 80 " --> pdb=" O LEU E 20 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N THR E 68 " --> pdb=" O GLN E 81 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'E' and resid 57 through 59 removed outlier: 5.179A pdb=" N TRP E 47 " --> pdb=" O ARG E 38 " (cutoff:3.500A) removed outlier: 5.462A pdb=" N ARG E 38 " --> pdb=" O TRP E 47 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N TYR E 33 " --> pdb=" O ASP E 98 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'E' and resid 137 through 139 Processing sheet with id=AA6, first strand: chain 'E' and resid 187 through 188 removed outlier: 3.778A pdb=" N SER E 187 " --> pdb=" O TYR E 183 " (cutoff:3.500A) removed outlier: 6.910A pdb=" N TRP E 169 " --> pdb=" O LEU E 181 " (cutoff:3.500A) removed outlier: 5.600A pdb=" N TYR E 183 " --> pdb=" O LEU E 167 " (cutoff:3.500A) removed outlier: 7.234A pdb=" N LEU E 167 " --> pdb=" O TYR E 183 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N THR E 231 " --> pdb=" O GLN E 224 " (cutoff:3.500A) 54 hydrogen bonds defined for protein. 132 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: 0.43 Time building geometry restraints manager: 0.40 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 1057 1.35 - 1.46: 899 1.46 - 1.58: 1423 1.58 - 1.70: 0 1.70 - 1.82: 16 Bond restraints: 3395 Sorted by residual: bond pdb=" C PRO E 174 " pdb=" O PRO E 174 " ideal model delta sigma weight residual 1.235 1.268 -0.033 1.30e-02 5.92e+03 6.36e+00 bond pdb=" C PRO E 174 " pdb=" N GLY E 175 " ideal model delta sigma weight residual 1.333 1.368 -0.036 1.57e-02 4.06e+03 5.19e+00 bond pdb=" C1 NAG C1301 " pdb=" O5 NAG C1301 " ideal model delta sigma weight residual 1.406 1.432 -0.026 2.00e-02 2.50e+03 1.75e+00 bond pdb=" C SER E 228 " pdb=" N PRO E 229 " ideal model delta sigma weight residual 1.334 1.364 -0.030 2.34e-02 1.83e+03 1.64e+00 bond pdb=" C5 NAG C1301 " pdb=" O5 NAG C1301 " ideal model delta sigma weight residual 1.413 1.434 -0.021 2.00e-02 2.50e+03 1.13e+00 ... (remaining 3390 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.33: 4379 1.33 - 2.66: 180 2.66 - 4.00: 46 4.00 - 5.33: 7 5.33 - 6.66: 2 Bond angle restraints: 4614 Sorted by residual: angle pdb=" N SER E 140 " pdb=" CA SER E 140 " pdb=" C SER E 140 " ideal model delta sigma weight residual 109.81 116.47 -6.66 2.21e+00 2.05e-01 9.08e+00 angle pdb=" N GLY C 526 " pdb=" CA GLY C 526 " pdb=" C GLY C 526 " ideal model delta sigma weight residual 112.34 118.46 -6.12 2.04e+00 2.40e-01 8.99e+00 angle pdb=" N GLN E 110 " pdb=" CA GLN E 110 " pdb=" C GLN E 110 " ideal model delta sigma weight residual 114.04 110.83 3.21 1.24e+00 6.50e-01 6.71e+00 angle pdb=" O PRO E 174 " pdb=" C PRO E 174 " pdb=" N GLY E 175 " ideal model delta sigma weight residual 122.64 126.13 -3.49 1.35e+00 5.49e-01 6.68e+00 angle pdb=" N PRO C 337 " pdb=" CA PRO C 337 " pdb=" C PRO C 337 " ideal model delta sigma weight residual 114.68 112.10 2.58 1.04e+00 9.25e-01 6.13e+00 ... (remaining 4609 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.95: 1795 17.95 - 35.91: 160 35.91 - 53.86: 31 53.86 - 71.82: 4 71.82 - 89.77: 4 Dihedral angle restraints: 1994 sinusoidal: 769 harmonic: 1225 Sorted by residual: dihedral pdb=" CB CYS C 379 " pdb=" SG CYS C 379 " pdb=" SG CYS C 432 " pdb=" CB CYS C 432 " ideal model delta sinusoidal sigma weight residual 93.00 47.90 45.10 1 1.00e+01 1.00e-02 2.82e+01 dihedral pdb=" CB CYS C 391 " pdb=" SG CYS C 391 " pdb=" SG CYS C 525 " pdb=" CB CYS C 525 " ideal model delta sinusoidal sigma weight residual 93.00 137.62 -44.62 1 1.00e+01 1.00e-02 2.77e+01 dihedral pdb=" CA SER E 140 " pdb=" C SER E 140 " pdb=" N PRO E 141 " pdb=" CA PRO E 141 " ideal model delta harmonic sigma weight residual -180.00 -156.22 -23.78 0 5.00e+00 4.00e-02 2.26e+01 ... (remaining 1991 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.049: 398 0.049 - 0.097: 80 0.097 - 0.146: 19 0.146 - 0.194: 2 0.194 - 0.243: 1 Chirality restraints: 500 Sorted by residual: chirality pdb=" CB ILE C 468 " pdb=" CA ILE C 468 " pdb=" CG1 ILE C 468 " pdb=" CG2 ILE C 468 " both_signs ideal model delta sigma weight residual False 2.64 2.40 0.24 2.00e-01 2.50e+01 1.47e+00 chirality pdb=" CA ILE C 472 " pdb=" N ILE C 472 " pdb=" C ILE C 472 " pdb=" CB ILE C 472 " both_signs ideal model delta sigma weight residual False 2.43 2.60 -0.17 2.00e-01 2.50e+01 7.30e-01 chirality pdb=" CB VAL E 116 " pdb=" CA VAL E 116 " pdb=" CG1 VAL E 116 " pdb=" CG2 VAL E 116 " both_signs ideal model delta sigma weight residual False -2.63 -2.48 -0.15 2.00e-01 2.50e+01 5.78e-01 ... (remaining 497 not shown) Planarity restraints: 598 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C CYS C 336 " 0.035 5.00e-02 4.00e+02 5.38e-02 4.63e+00 pdb=" N PRO C 337 " -0.093 5.00e-02 4.00e+02 pdb=" CA PRO C 337 " 0.028 5.00e-02 4.00e+02 pdb=" CD PRO C 337 " 0.030 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLN C 506 " -0.021 5.00e-02 4.00e+02 3.14e-02 1.57e+00 pdb=" N PRO C 507 " 0.054 5.00e-02 4.00e+02 pdb=" CA PRO C 507 " -0.016 5.00e-02 4.00e+02 pdb=" CD PRO C 507 " -0.017 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA C 411 " 0.021 5.00e-02 4.00e+02 3.14e-02 1.57e+00 pdb=" N PRO C 412 " -0.054 5.00e-02 4.00e+02 pdb=" CA PRO C 412 " 0.016 5.00e-02 4.00e+02 pdb=" CD PRO C 412 " 0.018 5.00e-02 4.00e+02 ... (remaining 595 not shown) Histogram of nonbonded interaction distances: 2.09 - 2.65: 42 2.65 - 3.21: 2931 3.21 - 3.78: 4503 3.78 - 4.34: 6072 4.34 - 4.90: 10024 Nonbonded interactions: 23572 Sorted by model distance: nonbonded pdb=" OD1 ASN C 354 " pdb=" OG SER C 399 " model vdw 2.089 3.040 nonbonded pdb=" O LEU C 455 " pdb=" OH TYR E 33 " model vdw 2.219 3.040 nonbonded pdb=" OD1 ASN C 331 " pdb=" N ILE C 332 " model vdw 2.228 3.120 nonbonded pdb=" OH TYR C 421 " pdb=" O PRO E 53 " model vdw 2.256 3.040 nonbonded pdb=" N GLN E 3 " pdb=" OG SER E 25 " model vdw 2.311 3.120 ... (remaining 23567 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== 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=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue 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: 5.600 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: 0.080 Check model and map are aligned: 0.010 Set scattering table: 0.020 Process input model: 5.270 Find NCS groups from input model: 0.020 Set up NCS constraints: 0.010 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:1.230 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 12.250 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7146 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 3402 Z= 0.143 Angle : 0.660 6.658 4629 Z= 0.371 Chirality : 0.045 0.243 500 Planarity : 0.005 0.054 597 Dihedral : 14.125 89.770 1202 Min Nonbonded Distance : 2.089 Molprobity Statistics. All-atom Clashscore : 10.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.76 % Favored : 85.24 % Rotamer: Outliers : 0.56 % Allowed : 0.28 % Favored : 99.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.45 (0.40), residues: 420 helix: -4.94 (0.47), residues: 8 sheet: -0.46 (0.55), residues: 104 loop : -2.12 (0.35), residues: 308 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG E 71 TYR 0.012 0.001 TYR C 473 PHE 0.015 0.001 PHE C 338 TRP 0.007 0.001 TRP C 353 HIS 0.001 0.001 HIS C 519 Details of bonding type rmsd/Z covalent geometry : bond 0.00265 / 0.14 ( 3395) covalent geometry : angle 0.65843 / 0.37 ( 4614) SS BOND : bond 0.00217 / 0.10 ( 6) SS BOND : angle 0.93469 / 0.58 ( 12) hydrogen bonds : bond 0.18437 / 10.71 ( 54) hydrogen bonds : angle 6.93570 / 4.74 ( 132) link_NAG-ASN : bond 0.00241 / 0.13 ( 1) link_NAG-ASN : angle 1.22629 / 0.72 ( 3) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 358 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 71 time to evaluate : 0.127 Fit side-chains revert: symmetry clash outliers start: 2 outliers final: 1 residues processed: 71 average time/residue: 0.0683 time to fit residues: 5.9886 Evaluate side-chains 58 residues out of total 358 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 57 time to evaluate : 0.120 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 139 GLN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 24 optimal weight: 1.9990 chunk 26 optimal weight: 0.1980 chunk 2 optimal weight: 2.9990 chunk 16 optimal weight: 0.0270 chunk 32 optimal weight: 0.8980 chunk 31 optimal weight: 0.8980 chunk 25 optimal weight: 0.8980 chunk 19 optimal weight: 0.9980 chunk 30 optimal weight: 0.3980 chunk 22 optimal weight: 1.9990 chunk 37 optimal weight: 0.9980 overall best weight: 0.4838 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** E 83 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3907 r_free = 0.3907 target = 0.168206 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3686 r_free = 0.3686 target = 0.148911 restraints weight = 5813.248| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3725 r_free = 0.3725 target = 0.152017 restraints weight = 3691.450| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3751 r_free = 0.3751 target = 0.154192 restraints weight = 2649.914| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3769 r_free = 0.3769 target = 0.155734 restraints weight = 2072.292| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3781 r_free = 0.3781 target = 0.156810 restraints weight = 1725.198| |-----------------------------------------------------------------------------| r_work (final): 0.3782 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3781 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3781 r_free = 0.3781 target_work(ls_wunit_k1) = 0.157 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3781 r_free = 0.3781 target_work(ls_wunit_k1) = 0.157 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (9 function evaluations) r_final: 0.3781 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7504 moved from start: 0.2280 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 3402 Z= 0.153 Angle : 0.668 7.036 4629 Z= 0.350 Chirality : 0.046 0.174 500 Planarity : 0.005 0.038 597 Dihedral : 5.526 29.720 475 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 9.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 17.14 % Favored : 82.86 % Rotamer: Outliers : 1.68 % Allowed : 12.29 % Favored : 86.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.59 (0.41), residues: 420 helix: -4.90 (0.49), residues: 8 sheet: -1.20 (0.49), residues: 123 loop : -1.97 (0.37), residues: 289 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG E 71 TYR 0.026 0.002 TYR E 183 PHE 0.015 0.002 PHE C 342 TRP 0.011 0.001 TRP C 436 HIS 0.002 0.002 HIS C 519 Details of bonding type rmsd/Z covalent geometry : bond 0.00349 / 0.15 ( 3395) covalent geometry : angle 0.66405 / 0.35 ( 4614) SS BOND : bond 0.00580 / 0.27 ( 6) SS BOND : angle 1.50120 / 0.82 ( 12) hydrogen bonds : bond 0.03695 / 2.07 ( 54) hydrogen bonds : angle 6.04687 / 4.22 ( 132) link_NAG-ASN : bond 0.00086 / 0.05 ( 1) link_NAG-ASN : angle 0.98677 / 0.76 ( 3) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 358 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 75 time to evaluate : 0.085 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 425 LEU cc_start: 0.8394 (mt) cc_final: 0.8121 (mt) outliers start: 6 outliers final: 5 residues processed: 77 average time/residue: 0.0563 time to fit residues: 5.5429 Evaluate side-chains 71 residues out of total 358 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 66 time to evaluate : 0.122 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 341 VAL Chi-restraints excluded: chain C residue 441 LEU Chi-restraints excluded: chain E residue 12 VAL Chi-restraints excluded: chain E residue 37 VAL Chi-restraints excluded: chain E residue 231 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 22 optimal weight: 1.9990 chunk 38 optimal weight: 3.9990 chunk 15 optimal weight: 0.7980 chunk 5 optimal weight: 2.9990 chunk 34 optimal weight: 2.9990 chunk 31 optimal weight: 0.4980 chunk 13 optimal weight: 0.9990 chunk 18 optimal weight: 0.5980 chunk 24 optimal weight: 0.0870 chunk 17 optimal weight: 1.9990 chunk 32 optimal weight: 0.6980 overall best weight: 0.5358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** E 83 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 139 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3902 r_free = 0.3902 target = 0.168374 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3687 r_free = 0.3687 target = 0.149651 restraints weight = 5713.261| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3724 r_free = 0.3724 target = 0.152711 restraints weight = 3557.229| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3748 r_free = 0.3748 target = 0.154824 restraints weight = 2530.067| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3763 r_free = 0.3763 target = 0.156154 restraints weight = 1963.067| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3777 r_free = 0.3777 target = 0.157342 restraints weight = 1643.395| |-----------------------------------------------------------------------------| r_work (final): 0.3764 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3757 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3757 r_free = 0.3757 target_work(ls_wunit_k1) = 0.155 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3757 r_free = 0.3757 target_work(ls_wunit_k1) = 0.155 | | occupancies: max = 1.00 min = 0.87 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3757 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7579 moved from start: 0.3042 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 3402 Z= 0.158 Angle : 0.686 7.033 4629 Z= 0.360 Chirality : 0.046 0.169 500 Planarity : 0.005 0.038 597 Dihedral : 5.352 25.396 472 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 10.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 17.14 % Favored : 82.86 % Rotamer: Outliers : 2.79 % Allowed : 18.16 % Favored : 79.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.69 (0.41), residues: 420 helix: -4.88 (0.50), residues: 8 sheet: -1.32 (0.49), residues: 120 loop : -2.02 (0.36), residues: 292 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 97 TYR 0.025 0.002 TYR E 183 PHE 0.013 0.002 PHE C 456 TRP 0.018 0.002 TRP C 353 HIS 0.002 0.001 HIS C 519 Details of bonding type rmsd/Z covalent geometry : bond 0.00363 / 0.16 ( 3395) covalent geometry : angle 0.68229 / 0.36 ( 4614) SS BOND : bond 0.00895 / 0.43 ( 6) SS BOND : angle 1.59914 / 0.88 ( 12) hydrogen bonds : bond 0.03849 / 2.20 ( 54) hydrogen bonds : angle 6.23430 / 4.34 ( 132) link_NAG-ASN : bond 0.00150 / 0.08 ( 1) link_NAG-ASN : angle 0.63552 / 0.42 ( 3) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 68 residues out of total 358 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 58 time to evaluate : 0.129 Fit side-chains REVERT: C 331 ASN cc_start: 0.6862 (OUTLIER) cc_final: 0.6625 (p0) REVERT: C 425 LEU cc_start: 0.8910 (mt) cc_final: 0.8662 (mt) REVERT: E 139 GLN cc_start: 0.7032 (pt0) cc_final: 0.6554 (pt0) outliers start: 10 outliers final: 6 residues processed: 65 average time/residue: 0.0581 time to fit residues: 4.8067 Evaluate side-chains 61 residues out of total 358 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 54 time to evaluate : 0.123 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 331 ASN Chi-restraints excluded: chain C residue 341 VAL Chi-restraints excluded: chain C residue 478 THR Chi-restraints excluded: chain E residue 69 ILE Chi-restraints excluded: chain E residue 167 LEU Chi-restraints excluded: chain E residue 182 ILE Chi-restraints excluded: chain E residue 199 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 40 optimal weight: 1.9990 chunk 32 optimal weight: 0.4980 chunk 26 optimal weight: 1.9990 chunk 8 optimal weight: 0.7980 chunk 35 optimal weight: 0.6980 chunk 34 optimal weight: 0.9990 chunk 2 optimal weight: 0.8980 chunk 12 optimal weight: 0.8980 chunk 18 optimal weight: 0.9980 chunk 13 optimal weight: 0.7980 chunk 16 optimal weight: 0.6980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** E 83 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3815 r_free = 0.3815 target = 0.160116 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3586 r_free = 0.3586 target = 0.141114 restraints weight = 5846.541| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3622 r_free = 0.3622 target = 0.144064 restraints weight = 3699.291| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3646 r_free = 0.3646 target = 0.146062 restraints weight = 2656.951| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3664 r_free = 0.3664 target = 0.147532 restraints weight = 2092.954| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3678 r_free = 0.3678 target = 0.148595 restraints weight = 1749.697| |-----------------------------------------------------------------------------| r_work (final): 0.3664 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3678 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3678 r_free = 0.3678 target_work(ls_wunit_k1) = 0.148 | | occupancies: max = 1.00 min = 0.87 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3677 r_free = 0.3677 target_work(ls_wunit_k1) = 0.148 | | occupancies: max = 1.00 min = 0.99 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (7 function evaluations) r_final: 0.3677 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7708 moved from start: 0.3865 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 3402 Z= 0.189 Angle : 0.720 7.337 4629 Z= 0.378 Chirality : 0.047 0.201 500 Planarity : 0.005 0.032 597 Dihedral : 5.691 25.472 472 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 13.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 19.29 % Favored : 80.71 % Rotamer: Outliers : 4.47 % Allowed : 19.27 % Favored : 76.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.81 (0.41), residues: 420 helix: -4.68 (0.68), residues: 8 sheet: -1.50 (0.48), residues: 125 loop : -2.06 (0.37), residues: 287 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 97 TYR 0.025 0.002 TYR E 183 PHE 0.014 0.002 PHE C 342 TRP 0.026 0.002 TRP C 353 HIS 0.002 0.001 HIS C 519 Details of bonding type rmsd/Z covalent geometry : bond 0.00438 / 0.19 ( 3395) covalent geometry : angle 0.71232 / 0.38 ( 4614) SS BOND : bond 0.00561 / 0.27 ( 6) SS BOND : angle 2.13912 / 1.30 ( 12) hydrogen bonds : bond 0.03840 / 2.19 ( 54) hydrogen bonds : angle 6.37227 / 4.44 ( 132) link_NAG-ASN : bond 0.00231 / 0.12 ( 1) link_NAG-ASN : angle 0.84565 / 0.45 ( 3) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 358 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 60 time to evaluate : 0.120 Fit side-chains REVERT: C 450 ASN cc_start: 0.8817 (p0) cc_final: 0.8242 (p0) REVERT: E 139 GLN cc_start: 0.7245 (pt0) cc_final: 0.6703 (pt0) outliers start: 16 outliers final: 13 residues processed: 68 average time/residue: 0.0557 time to fit residues: 4.7770 Evaluate side-chains 71 residues out of total 358 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 58 time to evaluate : 0.125 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 341 VAL Chi-restraints excluded: chain C residue 382 VAL Chi-restraints excluded: chain C residue 441 LEU Chi-restraints excluded: chain C residue 473 TYR Chi-restraints excluded: chain C residue 478 THR Chi-restraints excluded: chain C residue 518 LEU Chi-restraints excluded: chain E residue 35 SER Chi-restraints excluded: chain E residue 37 VAL Chi-restraints excluded: chain E residue 46 GLU Chi-restraints excluded: chain E residue 167 LEU Chi-restraints excluded: chain E residue 182 ILE Chi-restraints excluded: chain E residue 199 SER Chi-restraints excluded: chain E residue 240 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 33 optimal weight: 0.0030 chunk 21 optimal weight: 0.0770 chunk 41 optimal weight: 0.7980 chunk 30 optimal weight: 0.8980 chunk 27 optimal weight: 0.6980 chunk 34 optimal weight: 2.9990 chunk 17 optimal weight: 0.6980 chunk 39 optimal weight: 0.9990 chunk 2 optimal weight: 0.8980 chunk 4 optimal weight: 0.6980 chunk 5 optimal weight: 0.1980 overall best weight: 0.3348 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** E 83 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3839 r_free = 0.3839 target = 0.162616 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3627 r_free = 0.3627 target = 0.144436 restraints weight = 5758.377| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3663 r_free = 0.3663 target = 0.147403 restraints weight = 3604.376| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3688 r_free = 0.3688 target = 0.149409 restraints weight = 2557.104| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3705 r_free = 0.3705 target = 0.150825 restraints weight = 2001.705| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3717 r_free = 0.3717 target = 0.151878 restraints weight = 1671.120| |-----------------------------------------------------------------------------| r_work (final): 0.3716 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3729 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3729 r_free = 0.3729 target_work(ls_wunit_k1) = 0.153 | | occupancies: max = 1.00 min = 0.99 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3729 r_free = 0.3729 target_work(ls_wunit_k1) = 0.153 | | occupancies: max = 1.00 min = 0.83 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3729 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7614 moved from start: 0.3799 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 3402 Z= 0.129 Angle : 0.675 6.831 4629 Z= 0.352 Chirality : 0.045 0.181 500 Planarity : 0.005 0.031 597 Dihedral : 5.306 25.312 472 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 12.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 15.48 % Favored : 84.52 % Rotamer: Outliers : 3.35 % Allowed : 21.23 % Favored : 75.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.83 (0.41), residues: 420 helix: -4.61 (0.73), residues: 8 sheet: -1.57 (0.49), residues: 124 loop : -2.05 (0.37), residues: 288 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG E 97 TYR 0.022 0.001 TYR E 183 PHE 0.011 0.001 PHE E 27 TRP 0.016 0.002 TRP C 353 HIS 0.000 0.000 HIS C 519 Details of bonding type rmsd/Z covalent geometry : bond 0.00297 / 0.13 ( 3395) covalent geometry : angle 0.67372 / 0.35 ( 4614) SS BOND : bond 0.00565 / 0.27 ( 6) SS BOND : angle 1.13543 / 0.64 ( 12) hydrogen bonds : bond 0.03277 / 1.86 ( 54) hydrogen bonds : angle 6.04233 / 4.20 ( 132) link_NAG-ASN : bond 0.00275 / 0.14 ( 1) link_NAG-ASN : angle 0.73130 / 0.44 ( 3) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 358 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 63 time to evaluate : 0.077 Fit side-chains REVERT: C 450 ASN cc_start: 0.8779 (p0) cc_final: 0.8218 (p0) REVERT: E 139 GLN cc_start: 0.7232 (pt0) cc_final: 0.6751 (pt0) REVERT: E 215 GLU cc_start: 0.7901 (tm-30) cc_final: 0.7653 (tm-30) REVERT: E 224 GLN cc_start: 0.8637 (pp30) cc_final: 0.8344 (pp30) outliers start: 12 outliers final: 11 residues processed: 68 average time/residue: 0.0475 time to fit residues: 4.0865 Evaluate side-chains 70 residues out of total 358 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 59 time to evaluate : 0.082 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 341 VAL Chi-restraints excluded: chain C residue 433 VAL Chi-restraints excluded: chain C residue 473 TYR Chi-restraints excluded: chain C residue 478 THR Chi-restraints excluded: chain C residue 492 LEU Chi-restraints excluded: chain E residue 35 SER Chi-restraints excluded: chain E residue 46 GLU Chi-restraints excluded: chain E residue 167 LEU Chi-restraints excluded: chain E residue 182 ILE Chi-restraints excluded: chain E residue 199 SER Chi-restraints excluded: chain E residue 240 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 17 optimal weight: 0.9980 chunk 40 optimal weight: 0.9980 chunk 34 optimal weight: 0.6980 chunk 1 optimal weight: 0.9980 chunk 4 optimal weight: 0.0010 chunk 3 optimal weight: 0.2980 chunk 8 optimal weight: 0.6980 chunk 19 optimal weight: 0.0970 chunk 25 optimal weight: 0.3980 chunk 6 optimal weight: 0.6980 chunk 27 optimal weight: 1.9990 overall best weight: 0.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** E 83 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3856 r_free = 0.3856 target = 0.164156 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3639 r_free = 0.3639 target = 0.145604 restraints weight = 5812.436| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3675 r_free = 0.3675 target = 0.148616 restraints weight = 3681.402| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3699 r_free = 0.3699 target = 0.150715 restraints weight = 2635.863| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3717 r_free = 0.3717 target = 0.152241 restraints weight = 2050.553| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3730 r_free = 0.3730 target = 0.153327 restraints weight = 1699.726| |-----------------------------------------------------------------------------| r_work (final): 0.3723 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3668 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3668 r_free = 0.3668 target_work(ls_wunit_k1) = 0.148 | | occupancies: max = 1.00 min = 0.83 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3668 r_free = 0.3668 target_work(ls_wunit_k1) = 0.148 | | occupancies: max = 1.00 min = 0.69 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3668 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7601 moved from start: 0.3878 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 3402 Z= 0.123 Angle : 0.659 6.970 4629 Z= 0.340 Chirality : 0.044 0.173 500 Planarity : 0.004 0.031 597 Dihedral : 5.115 22.790 472 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 9.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 15.95 % Favored : 84.05 % Rotamer: Outliers : 4.47 % Allowed : 20.67 % Favored : 74.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.76 (0.41), residues: 420 helix: -4.66 (0.69), residues: 8 sheet: -1.49 (0.48), residues: 126 loop : -2.01 (0.38), residues: 286 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG E 97 TYR 0.022 0.001 TYR E 183 PHE 0.008 0.001 PHE E 27 TRP 0.013 0.001 TRP C 436 HIS 0.000 0.000 HIS C 519 Details of bonding type rmsd/Z covalent geometry : bond 0.00286 / 0.12 ( 3395) covalent geometry : angle 0.65158 / 0.34 ( 4614) SS BOND : bond 0.00592 / 0.28 ( 6) SS BOND : angle 2.07758 / 1.31 ( 12) hydrogen bonds : bond 0.03154 / 1.76 ( 54) hydrogen bonds : angle 5.94318 / 4.12 ( 132) link_NAG-ASN : bond 0.00332 / 0.17 ( 1) link_NAG-ASN : angle 0.52651 / 0.32 ( 3) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 358 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 63 time to evaluate : 0.113 Fit side-chains REVERT: C 450 ASN cc_start: 0.8744 (p0) cc_final: 0.8198 (p0) REVERT: E 139 GLN cc_start: 0.7236 (pt0) cc_final: 0.6830 (pt0) REVERT: E 215 GLU cc_start: 0.7823 (tm-30) cc_final: 0.7471 (tm-30) REVERT: E 224 GLN cc_start: 0.8657 (pp30) cc_final: 0.8364 (pp30) outliers start: 16 outliers final: 15 residues processed: 69 average time/residue: 0.0550 time to fit residues: 4.8756 Evaluate side-chains 76 residues out of total 358 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 61 time to evaluate : 0.117 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 341 VAL Chi-restraints excluded: chain C residue 379 CYS Chi-restraints excluded: chain C residue 382 VAL Chi-restraints excluded: chain C residue 433 VAL Chi-restraints excluded: chain C residue 441 LEU Chi-restraints excluded: chain C residue 473 TYR Chi-restraints excluded: chain C residue 478 THR Chi-restraints excluded: chain C residue 492 LEU Chi-restraints excluded: chain E residue 35 SER Chi-restraints excluded: chain E residue 46 GLU Chi-restraints excluded: chain E residue 167 LEU Chi-restraints excluded: chain E residue 180 LEU Chi-restraints excluded: chain E residue 182 ILE Chi-restraints excluded: chain E residue 231 THR Chi-restraints excluded: chain E residue 240 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 41 optimal weight: 2.9990 chunk 13 optimal weight: 0.0970 chunk 9 optimal weight: 0.0050 chunk 15 optimal weight: 3.9990 chunk 40 optimal weight: 0.8980 chunk 35 optimal weight: 0.6980 chunk 29 optimal weight: 0.0770 chunk 32 optimal weight: 0.7980 chunk 23 optimal weight: 0.5980 chunk 11 optimal weight: 2.9990 chunk 14 optimal weight: 0.4980 overall best weight: 0.2550 ------------------------------------------------------------------------------- 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 = 0.3868 r_free = 0.3868 target = 0.165056 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3653 r_free = 0.3653 target = 0.146701 restraints weight = 5857.486| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3688 r_free = 0.3688 target = 0.149651 restraints weight = 3686.011| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3714 r_free = 0.3714 target = 0.151820 restraints weight = 2636.959| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3731 r_free = 0.3731 target = 0.153232 restraints weight = 2059.584| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3745 r_free = 0.3745 target = 0.154385 restraints weight = 1721.504| |-----------------------------------------------------------------------------| r_work (final): 0.3683 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3687 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3687 r_free = 0.3687 target_work(ls_wunit_k1) = 0.150 | | occupancies: max = 1.00 min = 0.69 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3687 r_free = 0.3687 target_work(ls_wunit_k1) = 0.150 | | occupancies: max = 1.00 min = 0.71 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3687 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7570 moved from start: 0.3847 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 3402 Z= 0.118 Angle : 0.652 6.897 4629 Z= 0.335 Chirality : 0.044 0.172 500 Planarity : 0.004 0.032 597 Dihedral : 5.021 22.373 472 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 9.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 15.24 % Favored : 84.76 % Rotamer: Outliers : 5.31 % Allowed : 21.51 % Favored : 73.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.72 (0.41), residues: 420 helix: -4.67 (0.68), residues: 8 sheet: -1.44 (0.50), residues: 118 loop : -1.99 (0.37), residues: 294 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG E 97 TYR 0.018 0.001 TYR C 473 PHE 0.010 0.001 PHE E 27 TRP 0.014 0.001 TRP C 436 HIS 0.000 0.000 HIS C 519 Details of bonding type rmsd/Z covalent geometry : bond 0.00273 / 0.12 ( 3395) covalent geometry : angle 0.64538 / 0.33 ( 4614) SS BOND : bond 0.00524 / 0.25 ( 6) SS BOND : angle 1.89513 / 1.21 ( 12) hydrogen bonds : bond 0.03065 / 1.73 ( 54) hydrogen bonds : angle 5.89350 / 4.09 ( 132) link_NAG-ASN : bond 0.00291 / 0.15 ( 1) link_NAG-ASN : angle 0.51659 / 0.33 ( 3) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 358 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 63 time to evaluate : 0.144 Fit side-chains REVERT: C 398 ASP cc_start: 0.8139 (m-30) cc_final: 0.7557 (m-30) REVERT: C 450 ASN cc_start: 0.8692 (p0) cc_final: 0.8154 (p0) REVERT: C 492 LEU cc_start: 0.8914 (OUTLIER) cc_final: 0.8601 (mp) REVERT: E 215 GLU cc_start: 0.7783 (tm-30) cc_final: 0.7412 (tm-30) REVERT: E 224 GLN cc_start: 0.8625 (pp30) cc_final: 0.8341 (pp30) outliers start: 19 outliers final: 14 residues processed: 71 average time/residue: 0.0688 time to fit residues: 6.0562 Evaluate side-chains 75 residues out of total 358 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 60 time to evaluate : 0.151 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 338 PHE Chi-restraints excluded: chain C residue 341 VAL Chi-restraints excluded: chain C residue 379 CYS Chi-restraints excluded: chain C residue 382 VAL Chi-restraints excluded: chain C residue 441 LEU Chi-restraints excluded: chain C residue 473 TYR Chi-restraints excluded: chain C residue 478 THR Chi-restraints excluded: chain C residue 492 LEU Chi-restraints excluded: chain E residue 35 SER Chi-restraints excluded: chain E residue 46 GLU Chi-restraints excluded: chain E residue 69 ILE Chi-restraints excluded: chain E residue 180 LEU Chi-restraints excluded: chain E residue 182 ILE Chi-restraints excluded: chain E residue 231 THR Chi-restraints excluded: chain E residue 240 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 5 optimal weight: 1.9990 chunk 37 optimal weight: 0.0670 chunk 38 optimal weight: 0.9980 chunk 10 optimal weight: 2.9990 chunk 18 optimal weight: 0.6980 chunk 35 optimal weight: 1.9990 chunk 28 optimal weight: 0.9980 chunk 0 optimal weight: 1.9990 chunk 33 optimal weight: 0.5980 chunk 6 optimal weight: 0.9990 chunk 41 optimal weight: 2.9990 overall best weight: 0.6718 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 139 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3803 r_free = 0.3803 target = 0.159274 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3571 r_free = 0.3571 target = 0.140233 restraints weight = 5923.433| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3608 r_free = 0.3608 target = 0.143156 restraints weight = 3756.776| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3633 r_free = 0.3633 target = 0.145154 restraints weight = 2713.517| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3650 r_free = 0.3650 target = 0.146579 restraints weight = 2139.189| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3662 r_free = 0.3662 target = 0.147526 restraints weight = 1798.561| |-----------------------------------------------------------------------------| r_work (final): 0.3654 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3654 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3654 r_free = 0.3654 target_work(ls_wunit_k1) = 0.147 | | occupancies: max = 1.00 min = 0.71 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3654 r_free = 0.3654 target_work(ls_wunit_k1) = 0.147 | | occupancies: max = 1.00 min = 0.83 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3654 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7715 moved from start: 0.4317 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 3402 Z= 0.181 Angle : 0.708 7.112 4629 Z= 0.368 Chirality : 0.045 0.180 500 Planarity : 0.005 0.032 597 Dihedral : 5.424 24.071 472 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 13.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 18.10 % Favored : 81.90 % Rotamer: Outliers : 5.03 % Allowed : 21.51 % Favored : 73.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.92 (0.41), residues: 420 helix: -4.59 (0.75), residues: 8 sheet: -1.72 (0.49), residues: 119 loop : -2.07 (0.37), residues: 293 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 97 TYR 0.019 0.002 TYR C 489 PHE 0.011 0.002 PHE E 205 TRP 0.016 0.002 TRP C 436 HIS 0.001 0.001 HIS C 519 Details of bonding type rmsd/Z covalent geometry : bond 0.00422 / 0.18 ( 3395) covalent geometry : angle 0.70225 / 0.37 ( 4614) SS BOND : bond 0.00595 / 0.28 ( 6) SS BOND : angle 1.93209 / 1.17 ( 12) hydrogen bonds : bond 0.03526 / 2.04 ( 54) hydrogen bonds : angle 6.30636 / 4.37 ( 132) link_NAG-ASN : bond 0.00255 / 0.13 ( 1) link_NAG-ASN : angle 0.77788 / 0.57 ( 3) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 358 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 62 time to evaluate : 0.125 Fit side-chains REVERT: C 353 TRP cc_start: 0.8391 (p-90) cc_final: 0.8184 (p-90) REVERT: C 450 ASN cc_start: 0.8873 (p0) cc_final: 0.8329 (p0) REVERT: E 139 GLN cc_start: 0.7131 (pt0) cc_final: 0.6810 (pt0) REVERT: E 215 GLU cc_start: 0.7792 (tm-30) cc_final: 0.7405 (tm-30) outliers start: 18 outliers final: 16 residues processed: 72 average time/residue: 0.0589 time to fit residues: 5.2379 Evaluate side-chains 75 residues out of total 358 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 59 time to evaluate : 0.073 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 338 PHE Chi-restraints excluded: chain C residue 341 VAL Chi-restraints excluded: chain C residue 382 VAL Chi-restraints excluded: chain C residue 433 VAL Chi-restraints excluded: chain C residue 441 LEU Chi-restraints excluded: chain C residue 473 TYR Chi-restraints excluded: chain C residue 478 THR Chi-restraints excluded: chain C residue 492 LEU Chi-restraints excluded: chain E residue 46 GLU Chi-restraints excluded: chain E residue 69 ILE Chi-restraints excluded: chain E residue 138 THR Chi-restraints excluded: chain E residue 167 LEU Chi-restraints excluded: chain E residue 180 LEU Chi-restraints excluded: chain E residue 182 ILE Chi-restraints excluded: chain E residue 231 THR Chi-restraints excluded: chain E residue 240 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 11 optimal weight: 3.9990 chunk 34 optimal weight: 0.0020 chunk 23 optimal weight: 0.2980 chunk 3 optimal weight: 0.5980 chunk 38 optimal weight: 0.6980 chunk 4 optimal weight: 0.9980 chunk 7 optimal weight: 0.0030 chunk 22 optimal weight: 0.5980 chunk 12 optimal weight: 0.7980 chunk 31 optimal weight: 1.9990 chunk 29 optimal weight: 0.7980 overall best weight: 0.2998 ------------------------------------------------------------------------------- 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 = 0.3838 r_free = 0.3838 target = 0.162491 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3621 r_free = 0.3621 target = 0.144191 restraints weight = 5867.049| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3658 r_free = 0.3658 target = 0.147137 restraints weight = 3678.806| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3684 r_free = 0.3684 target = 0.149185 restraints weight = 2620.038| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3700 r_free = 0.3700 target = 0.150589 restraints weight = 2044.545| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3713 r_free = 0.3713 target = 0.151752 restraints weight = 1711.317| |-----------------------------------------------------------------------------| r_work (final): 0.3699 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3710 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3710 r_free = 0.3710 target_work(ls_wunit_k1) = 0.151 | | occupancies: max = 1.00 min = 0.83 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3710 r_free = 0.3710 target_work(ls_wunit_k1) = 0.151 | | occupancies: max = 1.00 min = 0.82 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (7 function evaluations) r_final: 0.3710 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7619 moved from start: 0.4166 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 3402 Z= 0.125 Angle : 0.678 6.853 4629 Z= 0.348 Chirality : 0.045 0.176 500 Planarity : 0.004 0.032 597 Dihedral : 5.159 23.306 472 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 10.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.29 % Favored : 85.71 % Rotamer: Outliers : 5.03 % Allowed : 21.79 % Favored : 73.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.81 (0.41), residues: 420 helix: -4.58 (0.76), residues: 8 sheet: -1.57 (0.48), residues: 124 loop : -2.03 (0.37), residues: 288 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG E 97 TYR 0.018 0.001 TYR C 473 PHE 0.010 0.001 PHE E 27 TRP 0.016 0.001 TRP C 436 HIS 0.000 0.000 HIS C 519 Details of bonding type rmsd/Z covalent geometry : bond 0.00290 / 0.13 ( 3395) covalent geometry : angle 0.67581 / 0.35 ( 4614) SS BOND : bond 0.00451 / 0.21 ( 6) SS BOND : angle 1.20401 / 0.73 ( 12) hydrogen bonds : bond 0.03157 / 1.78 ( 54) hydrogen bonds : angle 6.09813 / 4.19 ( 132) link_NAG-ASN : bond 0.00353 / 0.19 ( 1) link_NAG-ASN : angle 0.86498 / 0.66 ( 3) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 358 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 60 time to evaluate : 0.141 Fit side-chains REVERT: C 353 TRP cc_start: 0.8362 (p-90) cc_final: 0.8150 (p-90) REVERT: C 450 ASN cc_start: 0.8782 (p0) cc_final: 0.8238 (p0) REVERT: E 139 GLN cc_start: 0.7129 (pt0) cc_final: 0.6829 (pt0) REVERT: E 215 GLU cc_start: 0.7741 (tm-30) cc_final: 0.7365 (tm-30) outliers start: 18 outliers final: 17 residues processed: 69 average time/residue: 0.0587 time to fit residues: 5.1624 Evaluate side-chains 75 residues out of total 358 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 58 time to evaluate : 0.122 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 338 PHE Chi-restraints excluded: chain C residue 341 VAL Chi-restraints excluded: chain C residue 382 VAL Chi-restraints excluded: chain C residue 433 VAL Chi-restraints excluded: chain C residue 441 LEU Chi-restraints excluded: chain C residue 473 TYR Chi-restraints excluded: chain C residue 478 THR Chi-restraints excluded: chain C residue 492 LEU Chi-restraints excluded: chain E residue 35 SER Chi-restraints excluded: chain E residue 46 GLU Chi-restraints excluded: chain E residue 69 ILE Chi-restraints excluded: chain E residue 138 THR Chi-restraints excluded: chain E residue 167 LEU Chi-restraints excluded: chain E residue 180 LEU Chi-restraints excluded: chain E residue 182 ILE Chi-restraints excluded: chain E residue 199 SER Chi-restraints excluded: chain E residue 240 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 36 optimal weight: 0.0770 chunk 24 optimal weight: 0.6980 chunk 13 optimal weight: 1.9990 chunk 38 optimal weight: 1.9990 chunk 34 optimal weight: 0.8980 chunk 16 optimal weight: 0.7980 chunk 26 optimal weight: 0.0770 chunk 11 optimal weight: 4.9990 chunk 10 optimal weight: 2.9990 chunk 1 optimal weight: 0.8980 chunk 35 optimal weight: 0.7980 overall best weight: 0.4896 ------------------------------------------------------------------------------- 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 = 0.3813 r_free = 0.3813 target = 0.160263 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3601 r_free = 0.3601 target = 0.142496 restraints weight = 5845.938| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3635 r_free = 0.3635 target = 0.145244 restraints weight = 3745.293| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3659 r_free = 0.3659 target = 0.147195 restraints weight = 2705.227| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3674 r_free = 0.3674 target = 0.148416 restraints weight = 2130.888| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3687 r_free = 0.3687 target = 0.149534 restraints weight = 1812.677| |-----------------------------------------------------------------------------| r_work (final): 0.3654 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3671 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3671 r_free = 0.3671 target_work(ls_wunit_k1) = 0.148 | | occupancies: max = 1.00 min = 0.82 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3671 r_free = 0.3671 target_work(ls_wunit_k1) = 0.148 | | occupancies: max = 1.00 min = 0.80 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3671 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7665 moved from start: 0.4343 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 3402 Z= 0.151 Angle : 0.703 6.957 4629 Z= 0.361 Chirality : 0.045 0.175 500 Planarity : 0.004 0.032 597 Dihedral : 5.249 23.207 472 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 12.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 18.10 % Favored : 81.90 % Rotamer: Outliers : 4.75 % Allowed : 21.79 % Favored : 73.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.84 (0.41), residues: 420 helix: -4.58 (0.77), residues: 8 sheet: -1.61 (0.48), residues: 124 loop : -2.04 (0.37), residues: 288 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 97 TYR 0.018 0.002 TYR C 473 PHE 0.010 0.001 PHE C 429 TRP 0.017 0.002 TRP C 436 HIS 0.001 0.001 HIS C 519 Details of bonding type rmsd/Z covalent geometry : bond 0.00355 / 0.15 ( 3395) covalent geometry : angle 0.69536 / 0.36 ( 4614) SS BOND : bond 0.00537 / 0.25 ( 6) SS BOND : angle 2.09754 / 1.29 ( 12) hydrogen bonds : bond 0.03355 / 1.89 ( 54) hydrogen bonds : angle 6.09992 / 4.21 ( 132) link_NAG-ASN : bond 0.00358 / 0.19 ( 1) link_NAG-ASN : angle 0.91365 / 0.71 ( 3) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 358 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 58 time to evaluate : 0.085 Fit side-chains REVERT: C 353 TRP cc_start: 0.8476 (p-90) cc_final: 0.7959 (p-90) REVERT: C 450 ASN cc_start: 0.8798 (p0) cc_final: 0.8320 (p0) REVERT: E 139 GLN cc_start: 0.7145 (pt0) cc_final: 0.6849 (pt0) REVERT: E 215 GLU cc_start: 0.7766 (tm-30) cc_final: 0.7396 (tm-30) outliers start: 17 outliers final: 17 residues processed: 67 average time/residue: 0.0469 time to fit residues: 3.9479 Evaluate side-chains 75 residues out of total 358 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 58 time to evaluate : 0.073 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 338 PHE Chi-restraints excluded: chain C residue 341 VAL Chi-restraints excluded: chain C residue 382 VAL Chi-restraints excluded: chain C residue 433 VAL Chi-restraints excluded: chain C residue 441 LEU Chi-restraints excluded: chain C residue 473 TYR Chi-restraints excluded: chain C residue 478 THR Chi-restraints excluded: chain C residue 492 LEU Chi-restraints excluded: chain E residue 35 SER Chi-restraints excluded: chain E residue 46 GLU Chi-restraints excluded: chain E residue 69 ILE Chi-restraints excluded: chain E residue 138 THR Chi-restraints excluded: chain E residue 167 LEU Chi-restraints excluded: chain E residue 180 LEU Chi-restraints excluded: chain E residue 182 ILE Chi-restraints excluded: chain E residue 199 SER Chi-restraints excluded: chain E residue 240 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 41 optimal weight: 1.9990 chunk 37 optimal weight: 1.9990 chunk 2 optimal weight: 0.2980 chunk 10 optimal weight: 1.9990 chunk 36 optimal weight: 0.9980 chunk 31 optimal weight: 0.7980 chunk 7 optimal weight: 0.9990 chunk 23 optimal weight: 0.9980 chunk 5 optimal weight: 1.9990 chunk 15 optimal weight: 3.9990 chunk 8 optimal weight: 0.6980 overall best weight: 0.7580 ------------------------------------------------------------------------------- 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 = 0.3756 r_free = 0.3756 target = 0.155470 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.136881 restraints weight = 5908.888| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.139787 restraints weight = 3744.826| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3592 r_free = 0.3592 target = 0.141798 restraints weight = 2685.395| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3609 r_free = 0.3609 target = 0.143200 restraints weight = 2102.846| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3619 r_free = 0.3619 target = 0.144016 restraints weight = 1763.382| |-----------------------------------------------------------------------------| r_work (final): 0.3611 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3625 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3625 r_free = 0.3625 target_work(ls_wunit_k1) = 0.144 | | occupancies: max = 1.00 min = 0.80 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3625 r_free = 0.3625 target_work(ls_wunit_k1) = 0.144 | | occupancies: max = 1.00 min = 0.89 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3625 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7777 moved from start: 0.4799 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 3402 Z= 0.198 Angle : 0.754 7.228 4629 Z= 0.394 Chirality : 0.047 0.182 500 Planarity : 0.005 0.032 597 Dihedral : 5.819 27.191 472 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 14.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 19.76 % Favored : 80.24 % Rotamer: Outliers : 4.75 % Allowed : 21.79 % Favored : 73.46 % 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: -3.01 (0.41), residues: 420 helix: -4.61 (0.73), residues: 8 sheet: -1.76 (0.49), residues: 119 loop : -2.14 (0.36), residues: 293 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 97 TYR 0.018 0.002 TYR C 489 PHE 0.011 0.002 PHE E 205 TRP 0.019 0.002 TRP C 436 HIS 0.002 0.001 HIS C 519 Details of bonding type rmsd/Z covalent geometry : bond 0.00464 / 0.20 ( 3395) covalent geometry : angle 0.74645 / 0.39 ( 4614) SS BOND : bond 0.00704 / 0.33 ( 6) SS BOND : angle 2.09804 / 1.25 ( 12) hydrogen bonds : bond 0.03751 / 2.14 ( 54) hydrogen bonds : angle 6.56932 / 4.50 ( 132) link_NAG-ASN : bond 0.00365 / 0.19 ( 1) link_NAG-ASN : angle 1.33591 / 1.11 ( 3) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 899.00 seconds wall clock time: 16 minutes 9.49 seconds (969.49 seconds total)