Starting phenix.real_space_refine on Wed Jul 23 06:57:42 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7tpk_26058/07_2025/7tpk_26058.cif Found real_map, /net/cci-nas-00/data/ceres_data/7tpk_26058/07_2025/7tpk_26058.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7tpk_26058/07_2025/7tpk_26058.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7tpk_26058/07_2025/7tpk_26058.map" model { file = "/net/cci-nas-00/data/ceres_data/7tpk_26058/07_2025/7tpk_26058.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7tpk_26058/07_2025/7tpk_26058.cif" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/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: {'GLN:plan1': 1, 'GLU:plan': 1, 'HIS:plan': 1, 'ASN:plan1': 7, 'ASP:plan': 4} Unresolved non-hydrogen planarities: 46 Chain: "E" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 5.64, per 1000 atoms: 3.80 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: 0.31 Conformation dependent library (CDL) restraints added in 173.4 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: 0.22 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: 0.38 Time building geometry restraints manager: 0.39 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 425 1.34 - 1.47: 475 1.47 - 1.60: 620 1.60 - 1.73: 0 1.73 - 1.86: 8 Bond restraints: 1528 Sorted by residual: bond pdb=" NE ARG E 403 " pdb=" CZ ARG E 403 " ideal model delta sigma weight residual 1.326 1.359 -0.033 1.10e-02 8.26e+03 8.93e+00 bond pdb=" NE ARG E 509 " pdb=" CZ ARG E 509 " ideal model delta sigma weight residual 1.326 1.356 -0.030 1.10e-02 8.26e+03 7.45e+00 bond pdb=" NE ARG E 346 " pdb=" CZ ARG E 346 " ideal model delta sigma weight residual 1.326 1.352 -0.026 1.10e-02 8.26e+03 5.45e+00 bond pdb=" CD GLU E 471 " pdb=" OE2 GLU E 471 " ideal model delta sigma weight residual 1.249 1.206 0.043 1.90e-02 2.77e+03 5.18e+00 bond pdb=" CA ASN E 422 " pdb=" CB ASN E 422 " ideal model delta sigma weight residual 1.537 1.498 0.040 1.76e-02 3.23e+03 5.06e+00 ... (remaining 1523 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.46: 1629 1.46 - 2.93: 360 2.93 - 4.39: 62 4.39 - 5.85: 23 5.85 - 7.31: 10 Bond angle restraints: 2084 Sorted by residual: angle pdb=" C LEU E 425 " pdb=" N PRO E 426 " pdb=" CA PRO E 426 " ideal model delta sigma weight residual 120.03 126.94 -6.91 9.90e-01 1.02e+00 4.88e+01 angle pdb=" C SER E 383 " pdb=" N PRO E 384 " pdb=" CA PRO E 384 " ideal model delta sigma weight residual 119.56 126.59 -7.03 1.02e+00 9.61e-01 4.74e+01 angle pdb=" C GLN E 506 " pdb=" N PRO E 507 " pdb=" CA PRO E 507 " ideal model delta sigma weight residual 119.83 126.64 -6.81 1.08e+00 8.57e-01 3.97e+01 angle pdb=" C PHE E 490 " pdb=" N PRO E 491 " pdb=" CA PRO E 491 " ideal model delta sigma weight residual 119.56 125.64 -6.08 1.02e+00 9.61e-01 3.55e+01 angle pdb=" C ALA E 411 " pdb=" N PRO E 412 " pdb=" CA PRO E 412 " ideal model delta sigma weight residual 119.85 125.61 -5.76 1.01e+00 9.80e-01 3.25e+01 ... (remaining 2079 not shown) Histogram of dihedral angle deviations from ideal: 0.01 - 14.18: 847 14.18 - 28.36: 41 28.36 - 42.54: 6 42.54 - 56.72: 4 56.72 - 70.89: 2 Dihedral angle restraints: 900 sinusoidal: 334 harmonic: 566 Sorted by residual: dihedral pdb=" CB CYS E 480 " pdb=" SG CYS E 480 " pdb=" SG CYS E 488 " pdb=" CB CYS E 488 " ideal model delta sinusoidal sigma weight residual 93.00 140.69 -47.69 1 1.00e+01 1.00e-02 3.14e+01 dihedral pdb=" N ASN E 501 " pdb=" C ASN E 501 " pdb=" CA ASN E 501 " pdb=" CB ASN E 501 " ideal model delta harmonic sigma weight residual 122.80 134.30 -11.50 0 2.50e+00 1.60e-01 2.12e+01 dihedral pdb=" C ASN E 501 " pdb=" N ASN E 501 " pdb=" CA ASN E 501 " pdb=" CB ASN E 501 " ideal model delta harmonic sigma weight residual -122.60 -132.07 9.47 0 2.50e+00 1.60e-01 1.43e+01 ... (remaining 897 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.079: 154 0.079 - 0.157: 59 0.157 - 0.236: 7 0.236 - 0.314: 1 0.314 - 0.393: 2 Chirality restraints: 223 Sorted by residual: chirality pdb=" CA ASN E 501 " pdb=" N ASN E 501 " pdb=" C ASN E 501 " pdb=" CB ASN E 501 " both_signs ideal model delta sigma weight residual False 2.51 2.12 0.39 2.00e-01 2.50e+01 3.86e+00 chirality pdb=" C1 NAG E 601 " pdb=" ND2 ASN E 343 " pdb=" C2 NAG E 601 " pdb=" O5 NAG E 601 " both_signs ideal model delta sigma weight residual False -2.40 -2.06 -0.34 2.00e-01 2.50e+01 2.95e+00 chirality pdb=" CA PHE E 497 " pdb=" N PHE E 497 " pdb=" C PHE E 497 " pdb=" CB PHE E 497 " both_signs ideal model delta sigma weight residual False 2.51 2.21 0.30 2.00e-01 2.50e+01 2.32e+00 ... (remaining 220 not shown) Planarity restraints: 270 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR E 495 " -0.062 2.00e-02 2.50e+03 3.46e-02 2.40e+01 pdb=" CG TYR E 495 " 0.019 2.00e-02 2.50e+03 pdb=" CD1 TYR E 495 " 0.028 2.00e-02 2.50e+03 pdb=" CD2 TYR E 495 " 0.025 2.00e-02 2.50e+03 pdb=" CE1 TYR E 495 " 0.019 2.00e-02 2.50e+03 pdb=" CE2 TYR E 495 " 0.021 2.00e-02 2.50e+03 pdb=" CZ TYR E 495 " 0.006 2.00e-02 2.50e+03 pdb=" OH TYR E 495 " -0.056 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN E 343 " 0.034 2.00e-02 2.50e+03 3.47e-02 1.50e+01 pdb=" CG ASN E 343 " -0.019 2.00e-02 2.50e+03 pdb=" OD1 ASN E 343 " -0.005 2.00e-02 2.50e+03 pdb=" ND2 ASN E 343 " -0.052 2.00e-02 2.50e+03 pdb=" C1 NAG E 601 " 0.042 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE E 497 " 0.019 2.00e-02 2.50e+03 1.22e-02 2.60e+00 pdb=" CG PHE E 497 " -0.016 2.00e-02 2.50e+03 pdb=" CD1 PHE E 497 " -0.008 2.00e-02 2.50e+03 pdb=" CD2 PHE E 497 " -0.013 2.00e-02 2.50e+03 pdb=" CE1 PHE E 497 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 PHE E 497 " 0.005 2.00e-02 2.50e+03 pdb=" CZ PHE E 497 " 0.012 2.00e-02 2.50e+03 ... (remaining 267 not shown) Histogram of nonbonded interaction distances: 2.53 - 3.00: 766 3.00 - 3.48: 1263 3.48 - 3.95: 2399 3.95 - 4.43: 2662 4.43 - 4.90: 4278 Nonbonded interactions: 11368 Sorted by model distance: nonbonded pdb=" O PHE E 497 " pdb=" C GLN E 498 " model vdw 2.528 3.270 nonbonded pdb=" N ASN E 440 " pdb=" N LEU E 441 " model vdw 2.602 2.560 nonbonded pdb=" N LYS E 462 " pdb=" O LYS E 462 " model vdw 2.608 2.496 nonbonded pdb=" N ASP E 389 " pdb=" N LEU E 390 " model vdw 2.626 2.560 nonbonded pdb=" N ALA E 411 " pdb=" O ALA E 411 " model vdw 2.627 2.496 ... (remaining 11363 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 5.370 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: 0.070 Check model and map are aligned: 0.010 Set scattering table: 0.020 Process input model: 13.940 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:2.950 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.400 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7002 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.012 0.080 1533 Z= 0.634 Angle : 1.519 20.084 2095 Z= 0.974 Chirality : 0.084 0.393 223 Planarity : 0.006 0.035 269 Dihedral : 9.829 70.895 530 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 2.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.69 % Favored : 95.31 % Rotamer: Outliers : 0.00 % Allowed : 0.72 % Favored : 99.28 % Cbeta Deviations : 0.56 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.014 0.006 TRP E 353 PHE 0.019 0.003 PHE E 497 TYR 0.062 0.004 TYR E 495 ARG 0.002 0.000 ARG E 403 Details of bonding type rmsd link_NAG-ASN : bond 0.05197 ( 1) link_NAG-ASN : angle 15.31923 ( 3) hydrogen bonds : bond 0.15225 ( 44) hydrogen bonds : angle 9.84021 ( 105) SS BOND : bond 0.05115 ( 4) SS BOND : angle 1.95834 ( 8) covalent geometry : bond 0.01121 ( 1528) covalent geometry : angle 1.40277 ( 2084) *********************** 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 : 0.135 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: 0.1855 time to fit residues: 6.7776 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 : 0.139 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 19 random chunks: chunk 16 optimal weight: 0.0170 chunk 14 optimal weight: 0.6980 chunk 7 optimal weight: 0.6980 chunk 4 optimal weight: 0.4980 chunk 9 optimal weight: 0.7980 chunk 5 optimal weight: 0.0770 chunk 11 optimal weight: 0.4980 chunk 17 optimal weight: 0.6980 chunk 18 optimal weight: 0.7980 chunk 15 optimal weight: 0.2980 chunk 13 optimal weight: 0.9990 overall best weight: 0.2776 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3813 r_free = 0.3813 target = 0.164530 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3650 r_free = 0.3650 target = 0.149918 restraints weight = 2023.874| |-----------------------------------------------------------------------------| r_work (start): 0.3644 rms_B_bonded: 1.88 r_work: 0.3561 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.3442 rms_B_bonded: 4.05 restraints_weight: 0.2500 r_work (final): 0.3442 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7685 moved from start: 0.2927 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 1533 Z= 0.144 Angle : 0.557 5.500 2095 Z= 0.297 Chirality : 0.045 0.126 223 Planarity : 0.004 0.026 269 Dihedral : 5.327 34.978 238 Min Nonbonded Distance : 2.573 Molprobity Statistics. All-atom Clashscore : 2.83 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.64 (0.54), residues: 192 helix: -4.00 (0.52), residues: 31 sheet: 0.93 (0.78), residues: 39 loop : -0.98 (0.50), residues: 122 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP E 436 PHE 0.009 0.002 PHE E 429 TYR 0.011 0.001 TYR E 351 ARG 0.002 0.000 ARG E 457 Details of bonding type rmsd link_NAG-ASN : bond 0.00244 ( 1) link_NAG-ASN : angle 2.87116 ( 3) hydrogen bonds : bond 0.04394 ( 44) hydrogen bonds : angle 7.33071 ( 105) SS BOND : bond 0.00315 ( 4) SS BOND : angle 0.56441 ( 8) covalent geometry : bond 0.00316 ( 1528) covalent geometry : angle 0.54615 ( 2084) *********************** 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 26 residues out of total 167 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 25 time to evaluate : 0.168 Fit side-chains outliers start: 1 outliers final: 1 residues processed: 26 average time/residue: 0.1902 time to fit residues: 5.6243 Evaluate side-chains 21 residues out of total 167 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 20 time to evaluate : 0.228 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 434 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 19 random chunks: chunk 8 optimal weight: 0.3980 chunk 6 optimal weight: 0.9990 chunk 4 optimal weight: 0.5980 chunk 3 optimal weight: 0.5980 chunk 18 optimal weight: 0.3980 chunk 9 optimal weight: 0.0970 chunk 2 optimal weight: 0.5980 chunk 7 optimal weight: 0.0980 chunk 10 optimal weight: 0.9980 chunk 11 optimal weight: 0.5980 chunk 12 optimal weight: 0.9980 overall best weight: 0.3178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 354 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3726 r_free = 0.3726 target = 0.157069 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.143363 restraints weight = 2037.152| |-----------------------------------------------------------------------------| r_work (start): 0.3566 rms_B_bonded: 1.66 r_work: 0.3483 rms_B_bonded: 2.11 restraints_weight: 0.5000 r_work: 0.3364 rms_B_bonded: 3.77 restraints_weight: 0.2500 r_work (final): 0.3364 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7805 moved from start: 0.4026 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 1533 Z= 0.137 Angle : 0.528 4.637 2095 Z= 0.282 Chirality : 0.044 0.123 223 Planarity : 0.004 0.027 269 Dihedral : 4.818 28.283 238 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 2.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 1.44 % Allowed : 11.51 % Favored : 87.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.55 (0.55), residues: 192 helix: -3.76 (0.53), residues: 31 sheet: 1.56 (0.86), residues: 37 loop : -1.16 (0.49), residues: 124 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP E 436 PHE 0.010 0.001 PHE E 497 TYR 0.010 0.001 TYR E 351 ARG 0.003 0.001 ARG E 457 Details of bonding type rmsd link_NAG-ASN : bond 0.00098 ( 1) link_NAG-ASN : angle 2.43604 ( 3) hydrogen bonds : bond 0.04260 ( 44) hydrogen bonds : angle 6.95236 ( 105) SS BOND : bond 0.00161 ( 4) SS BOND : angle 0.64196 ( 8) covalent geometry : bond 0.00312 ( 1528) covalent geometry : angle 0.51932 ( 2084) *********************** 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 25 residues out of total 167 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 23 time to evaluate : 0.159 Fit side-chains outliers start: 2 outliers final: 2 residues processed: 23 average time/residue: 0.1281 time to fit residues: 3.4725 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 : 0.151 ------------------------------------------------------------------------------- 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 5 optimal weight: 0.1980 chunk 8 optimal weight: 0.9980 chunk 13 optimal weight: 0.7980 chunk 2 optimal weight: 0.9980 chunk 14 optimal weight: 0.8980 chunk 16 optimal weight: 0.9980 chunk 9 optimal weight: 0.6980 chunk 18 optimal weight: 0.1980 chunk 6 optimal weight: 0.5980 chunk 7 optimal weight: 0.5980 chunk 10 optimal weight: 0.1980 overall best weight: 0.3580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 506 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3702 r_free = 0.3702 target = 0.155270 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.142776 restraints weight = 1988.406| |-----------------------------------------------------------------------------| r_work (start): 0.3521 rms_B_bonded: 1.52 r_work: 0.3442 rms_B_bonded: 1.91 restraints_weight: 0.5000 r_work: 0.3335 rms_B_bonded: 3.38 restraints_weight: 0.2500 r_work (final): 0.3335 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7824 moved from start: 0.4550 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 1533 Z= 0.147 Angle : 0.511 3.598 2095 Z= 0.273 Chirality : 0.044 0.128 223 Planarity : 0.004 0.028 269 Dihedral : 4.940 29.260 238 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 1.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.65 % Favored : 96.35 % Rotamer: Outliers : 2.88 % Allowed : 10.79 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.45 (0.55), residues: 192 helix: -3.45 (0.62), residues: 31 sheet: 1.85 (0.88), residues: 37 loop : -1.25 (0.48), residues: 124 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP E 436 PHE 0.008 0.001 PHE E 429 TYR 0.008 0.001 TYR E 351 ARG 0.002 0.001 ARG E 457 Details of bonding type rmsd link_NAG-ASN : bond 0.00043 ( 1) link_NAG-ASN : angle 2.27433 ( 3) hydrogen bonds : bond 0.03966 ( 44) hydrogen bonds : angle 6.68282 ( 105) SS BOND : bond 0.00097 ( 4) SS BOND : angle 1.16445 ( 8) covalent geometry : bond 0.00348 ( 1528) covalent geometry : angle 0.50007 ( 2084) *********************** 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 26 residues out of total 167 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 22 time to evaluate : 0.171 Fit side-chains outliers start: 4 outliers final: 3 residues processed: 24 average time/residue: 0.1600 time to fit residues: 4.4216 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 : 0.164 ------------------------------------------------------------------------------- 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 19 random chunks: chunk 11 optimal weight: 0.9990 chunk 13 optimal weight: 0.5980 chunk 16 optimal weight: 0.9990 chunk 12 optimal weight: 0.6980 chunk 10 optimal weight: 0.5980 chunk 5 optimal weight: 0.2980 chunk 7 optimal weight: 0.6980 chunk 15 optimal weight: 0.6980 chunk 6 optimal weight: 0.8980 chunk 0 optimal weight: 0.9990 chunk 1 optimal weight: 0.8980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3608 r_free = 0.3608 target = 0.146733 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.134038 restraints weight = 2099.062| |-----------------------------------------------------------------------------| r_work (start): 0.3486 rms_B_bonded: 1.60 r_work: 0.3395 rms_B_bonded: 2.15 restraints_weight: 0.5000 r_work: 0.3282 rms_B_bonded: 3.80 restraints_weight: 0.2500 r_work (final): 0.3282 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7930 moved from start: 0.4932 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= 0.214 Angle : 0.569 5.439 2095 Z= 0.301 Chirality : 0.046 0.133 223 Planarity : 0.005 0.030 269 Dihedral : 5.387 31.694 238 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 2.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.69 % Favored : 95.31 % Rotamer: Outliers : 2.16 % Allowed : 12.95 % Favored : 84.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.61 (0.54), residues: 192 helix: -2.98 (0.71), residues: 31 sheet: 1.61 (0.90), residues: 37 loop : -1.49 (0.46), residues: 124 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP E 436 PHE 0.012 0.002 PHE E 429 TYR 0.010 0.001 TYR E 351 ARG 0.003 0.001 ARG E 509 Details of bonding type rmsd link_NAG-ASN : bond 0.00090 ( 1) link_NAG-ASN : angle 2.53775 ( 3) hydrogen bonds : bond 0.04262 ( 44) hydrogen bonds : angle 6.86592 ( 105) SS BOND : bond 0.00119 ( 4) SS BOND : angle 1.33210 ( 8) covalent geometry : bond 0.00519 ( 1528) covalent geometry : angle 0.55638 ( 2084) *********************** 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 31 residues out of total 167 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 28 time to evaluate : 0.150 Fit side-chains REVERT: E 449 TYR cc_start: 0.7085 (m-80) cc_final: 0.6710 (m-80) outliers start: 3 outliers final: 3 residues processed: 29 average time/residue: 0.2065 time to fit residues: 6.6087 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 : 0.152 ------------------------------------------------------------------------------- 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 19 random chunks: chunk 8 optimal weight: 0.9990 chunk 12 optimal weight: 0.7980 chunk 10 optimal weight: 0.6980 chunk 13 optimal weight: 0.9980 chunk 16 optimal weight: 0.0770 chunk 6 optimal weight: 0.9990 chunk 0 optimal weight: 0.9990 chunk 5 optimal weight: 0.1980 chunk 1 optimal weight: 0.2980 chunk 4 optimal weight: 0.2980 chunk 2 optimal weight: 0.7980 overall best weight: 0.3138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3634 r_free = 0.3634 target = 0.149506 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.136920 restraints weight = 2068.725| |-----------------------------------------------------------------------------| r_work (start): 0.3529 rms_B_bonded: 1.52 r_work: 0.3449 rms_B_bonded: 1.98 restraints_weight: 0.5000 r_work: 0.3338 rms_B_bonded: 3.54 restraints_weight: 0.2500 r_work (final): 0.3338 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7887 moved from start: 0.5184 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= 0.130 Angle : 0.496 4.081 2095 Z= 0.260 Chirality : 0.044 0.132 223 Planarity : 0.004 0.029 269 Dihedral : 4.948 29.789 238 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 1.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 2.16 % Allowed : 12.95 % Favored : 84.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.63 (0.53), residues: 192 helix: -2.91 (0.69), residues: 31 sheet: 1.56 (0.87), residues: 37 loop : -1.52 (0.45), residues: 124 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP E 436 PHE 0.006 0.001 PHE E 429 TYR 0.008 0.001 TYR E 351 ARG 0.003 0.001 ARG E 457 Details of bonding type rmsd link_NAG-ASN : bond 0.00020 ( 1) link_NAG-ASN : angle 2.28261 ( 3) hydrogen bonds : bond 0.03666 ( 44) hydrogen bonds : angle 6.58503 ( 105) SS BOND : bond 0.00176 ( 4) SS BOND : angle 1.05541 ( 8) covalent geometry : bond 0.00309 ( 1528) covalent geometry : angle 0.48552 ( 2084) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 384 Ramachandran restraints generated. 192 Oldfield, 0 Emsley, 192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 384 Ramachandran restraints generated. 192 Oldfield, 0 Emsley, 192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 26 residues out of total 167 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 23 time to evaluate : 0.169 Fit side-chains outliers start: 3 outliers final: 3 residues processed: 24 average time/residue: 0.1838 time to fit residues: 4.9937 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 : 0.172 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 367 VAL Chi-restraints excluded: chain E residue 373 SER Chi-restraints excluded: chain E residue 407 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 19 random chunks: chunk 13 optimal weight: 0.6980 chunk 6 optimal weight: 0.9980 chunk 12 optimal weight: 0.5980 chunk 11 optimal weight: 0.5980 chunk 8 optimal weight: 0.5980 chunk 7 optimal weight: 0.1980 chunk 9 optimal weight: 0.0970 chunk 17 optimal weight: 0.2980 chunk 15 optimal weight: 0.4980 chunk 0 optimal weight: 0.9990 chunk 18 optimal weight: 0.5980 overall best weight: 0.3378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3651 r_free = 0.3651 target = 0.150336 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3516 r_free = 0.3516 target = 0.138097 restraints weight = 2091.637| |-----------------------------------------------------------------------------| r_work (start): 0.3512 rms_B_bonded: 1.55 r_work: 0.3424 rms_B_bonded: 2.08 restraints_weight: 0.5000 r_work: 0.3310 rms_B_bonded: 3.71 restraints_weight: 0.2500 r_work (final): 0.3310 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7901 moved from start: 0.5328 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 1533 Z= 0.137 Angle : 0.502 4.289 2095 Z= 0.262 Chirality : 0.044 0.133 223 Planarity : 0.004 0.029 269 Dihedral : 4.936 30.406 238 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 1.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.17 % Favored : 95.83 % Rotamer: Outliers : 2.16 % Allowed : 15.83 % Favored : 82.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.67 (0.53), residues: 192 helix: -2.90 (0.68), residues: 31 sheet: 1.46 (0.87), residues: 37 loop : -1.52 (0.45), residues: 124 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP E 436 PHE 0.007 0.001 PHE E 497 TYR 0.008 0.001 TYR E 351 ARG 0.003 0.001 ARG E 357 Details of bonding type rmsd link_NAG-ASN : bond 0.00023 ( 1) link_NAG-ASN : angle 2.29088 ( 3) hydrogen bonds : bond 0.03719 ( 44) hydrogen bonds : angle 6.57400 ( 105) SS BOND : bond 0.00139 ( 4) SS BOND : angle 1.08936 ( 8) covalent geometry : bond 0.00327 ( 1528) covalent geometry : angle 0.49101 ( 2084) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 384 Ramachandran restraints generated. 192 Oldfield, 0 Emsley, 192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 384 Ramachandran restraints generated. 192 Oldfield, 0 Emsley, 192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 26 residues out of total 167 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 23 time to evaluate : 0.148 Fit side-chains REVERT: E 449 TYR cc_start: 0.6976 (m-80) cc_final: 0.6665 (m-80) outliers start: 3 outliers final: 3 residues processed: 24 average time/residue: 0.1720 time to fit residues: 4.6781 Evaluate side-chains 25 residues out of total 167 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 22 time to evaluate : 0.149 ------------------------------------------------------------------------------- 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: 0.5980 chunk 9 optimal weight: 0.5980 chunk 1 optimal weight: 0.8980 chunk 15 optimal weight: 0.7980 chunk 12 optimal weight: 0.5980 chunk 11 optimal weight: 1.9990 chunk 3 optimal weight: 0.5980 chunk 0 optimal weight: 0.0980 chunk 10 optimal weight: 0.5980 chunk 17 optimal weight: 0.5980 chunk 7 optimal weight: 0.7980 overall best weight: 0.4980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3626 r_free = 0.3626 target = 0.148070 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.135468 restraints weight = 2071.760| |-----------------------------------------------------------------------------| r_work (start): 0.3485 rms_B_bonded: 1.60 r_work: 0.3389 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.3273 rms_B_bonded: 3.97 restraints_weight: 0.2500 r_work (final): 0.3273 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7967 moved from start: 0.5457 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.033 1533 Z= 0.186 Angle : 0.543 4.984 2095 Z= 0.284 Chirality : 0.046 0.136 223 Planarity : 0.004 0.028 269 Dihedral : 5.319 32.954 238 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 2.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 2.16 % Allowed : 17.27 % Favored : 80.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.85 (0.52), residues: 192 helix: -2.73 (0.73), residues: 31 sheet: 1.27 (0.86), residues: 37 loop : -1.72 (0.45), residues: 124 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP E 436 PHE 0.010 0.001 PHE E 429 TYR 0.010 0.001 TYR E 351 ARG 0.003 0.001 ARG E 466 Details of bonding type rmsd link_NAG-ASN : bond 0.00137 ( 1) link_NAG-ASN : angle 2.47905 ( 3) hydrogen bonds : bond 0.03974 ( 44) hydrogen bonds : angle 6.69212 ( 105) SS BOND : bond 0.00187 ( 4) SS BOND : angle 1.31230 ( 8) covalent geometry : bond 0.00455 ( 1528) covalent geometry : angle 0.53006 ( 2084) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 384 Ramachandran restraints generated. 192 Oldfield, 0 Emsley, 192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 384 Ramachandran restraints generated. 192 Oldfield, 0 Emsley, 192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 25 residues out of total 167 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 22 time to evaluate : 0.195 Fit side-chains outliers start: 3 outliers final: 3 residues processed: 23 average time/residue: 0.1965 time to fit residues: 5.1861 Evaluate side-chains 24 residues out of total 167 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 21 time to evaluate : 0.183 ------------------------------------------------------------------------------- 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 16 optimal weight: 0.8980 chunk 4 optimal weight: 0.1980 chunk 3 optimal weight: 0.6980 chunk 18 optimal weight: 0.5980 chunk 14 optimal weight: 0.9990 chunk 10 optimal weight: 0.6980 chunk 15 optimal weight: 0.0970 chunk 2 optimal weight: 0.9990 chunk 5 optimal weight: 0.0670 chunk 13 optimal weight: 0.0870 chunk 17 optimal weight: 0.4980 overall best weight: 0.1894 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3674 r_free = 0.3674 target = 0.152150 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.139599 restraints weight = 2066.483| |-----------------------------------------------------------------------------| r_work (start): 0.3531 rms_B_bonded: 1.60 r_work: 0.3438 rms_B_bonded: 2.21 restraints_weight: 0.5000 r_work: 0.3320 rms_B_bonded: 3.92 restraints_weight: 0.2500 r_work (final): 0.3320 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7892 moved from start: 0.5514 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= 0.106 Angle : 0.503 3.361 2095 Z= 0.264 Chirality : 0.044 0.129 223 Planarity : 0.004 0.030 269 Dihedral : 5.051 30.578 238 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 2.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.65 % Favored : 96.35 % Rotamer: Outliers : 1.44 % Allowed : 17.27 % Favored : 81.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.76 (0.52), residues: 192 helix: -2.77 (0.71), residues: 31 sheet: 1.27 (0.86), residues: 37 loop : -1.60 (0.45), residues: 124 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP E 436 PHE 0.006 0.001 PHE E 497 TYR 0.007 0.001 TYR E 351 ARG 0.003 0.001 ARG E 466 Details of bonding type rmsd link_NAG-ASN : bond 0.00068 ( 1) link_NAG-ASN : angle 2.25295 ( 3) hydrogen bonds : bond 0.03411 ( 44) hydrogen bonds : angle 6.59252 ( 105) SS BOND : bond 0.00280 ( 4) SS BOND : angle 1.54309 ( 8) covalent geometry : bond 0.00245 ( 1528) covalent geometry : angle 0.48778 ( 2084) *********************** 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 24 residues out of total 167 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 22 time to evaluate : 0.150 Fit side-chains outliers start: 2 outliers final: 2 residues processed: 23 average time/residue: 0.1912 time to fit residues: 4.9503 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 : 0.180 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 367 VAL Chi-restraints excluded: chain E residue 373 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 19 random chunks: chunk 2 optimal weight: 0.8980 chunk 12 optimal weight: 0.0470 chunk 4 optimal weight: 0.5980 chunk 17 optimal weight: 0.8980 chunk 16 optimal weight: 0.2980 chunk 3 optimal weight: 0.9990 chunk 5 optimal weight: 0.0370 chunk 11 optimal weight: 0.7980 chunk 10 optimal weight: 0.9980 chunk 0 optimal weight: 0.1980 chunk 6 optimal weight: 0.5980 overall best weight: 0.2356 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3679 r_free = 0.3679 target = 0.152538 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.140991 restraints weight = 2082.402| |-----------------------------------------------------------------------------| r_work (start): 0.3540 rms_B_bonded: 1.48 r_work: 0.3458 rms_B_bonded: 1.98 restraints_weight: 0.5000 r_work: 0.3347 rms_B_bonded: 3.55 restraints_weight: 0.2500 r_work (final): 0.3347 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7867 moved from start: 0.5530 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 1533 Z= 0.108 Angle : 0.482 3.364 2095 Z= 0.252 Chirality : 0.044 0.132 223 Planarity : 0.004 0.029 269 Dihedral : 4.813 29.878 238 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 2.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.17 % Favored : 95.83 % Rotamer: Outliers : 1.44 % Allowed : 17.99 % Favored : 80.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.62 (0.53), residues: 192 helix: -2.68 (0.73), residues: 31 sheet: 1.40 (0.86), residues: 37 loop : -1.51 (0.46), residues: 124 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP E 436 PHE 0.006 0.001 PHE E 497 TYR 0.006 0.001 TYR E 351 ARG 0.002 0.000 ARG E 457 Details of bonding type rmsd link_NAG-ASN : bond 0.00069 ( 1) link_NAG-ASN : angle 2.11738 ( 3) hydrogen bonds : bond 0.03247 ( 44) hydrogen bonds : angle 6.43364 ( 105) SS BOND : bond 0.00224 ( 4) SS BOND : angle 1.26592 ( 8) covalent geometry : bond 0.00255 ( 1528) covalent geometry : angle 0.47028 ( 2084) ********************** 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: 2 poor density : 24 time to evaluate : 0.148 Fit side-chains outliers start: 2 outliers final: 2 residues processed: 25 average time/residue: 0.2147 time to fit residues: 6.0042 Evaluate side-chains 25 residues out of total 167 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 23 time to evaluate : 0.199 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 367 VAL Chi-restraints excluded: chain E residue 373 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 19 random chunks: chunk 14 optimal weight: 0.9980 chunk 7 optimal weight: 0.6980 chunk 5 optimal weight: 0.0980 chunk 16 optimal weight: 0.6980 chunk 15 optimal weight: 0.8980 chunk 8 optimal weight: 0.5980 chunk 11 optimal weight: 0.7980 chunk 4 optimal weight: 0.6980 chunk 0 optimal weight: 0.9990 chunk 18 optimal weight: 0.9980 chunk 12 optimal weight: 0.4980 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3635 r_free = 0.3635 target = 0.148477 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.136075 restraints weight = 2165.762| |-----------------------------------------------------------------------------| r_work (start): 0.3489 rms_B_bonded: 1.60 r_work: 0.3400 rms_B_bonded: 2.14 restraints_weight: 0.5000 r_work: 0.3285 rms_B_bonded: 3.78 restraints_weight: 0.2500 r_work (final): 0.3285 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7925 moved from start: 0.5592 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.034 1533 Z= 0.193 Angle : 0.557 4.721 2095 Z= 0.290 Chirality : 0.046 0.138 223 Planarity : 0.004 0.031 269 Dihedral : 5.399 33.774 238 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 3.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.17 % Favored : 95.83 % Rotamer: Outliers : 1.44 % Allowed : 18.71 % Favored : 79.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.86 (0.52), residues: 192 helix: -2.66 (0.75), residues: 31 sheet: 1.20 (0.86), residues: 37 loop : -1.73 (0.45), residues: 124 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP E 436 PHE 0.010 0.001 PHE E 429 TYR 0.008 0.001 TYR E 351 ARG 0.003 0.001 ARG E 357 Details of bonding type rmsd link_NAG-ASN : bond 0.00106 ( 1) link_NAG-ASN : angle 2.45612 ( 3) hydrogen bonds : bond 0.03924 ( 44) hydrogen bonds : angle 6.61336 ( 105) SS BOND : bond 0.00232 ( 4) SS BOND : angle 1.63548 ( 8) covalent geometry : bond 0.00472 ( 1528) covalent geometry : angle 0.54123 ( 2084) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1807.31 seconds wall clock time: 31 minutes 43.60 seconds (1903.60 seconds total)