Starting phenix.real_space_refine on Mon Feb 10 19:30:55 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7tpk_26058/02_2025/7tpk_26058.cif Found real_map, /net/cci-nas-00/data/ceres_data/7tpk_26058/02_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_26058/02_2025/7tpk_26058.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7tpk_26058/02_2025/7tpk_26058.map" model { file = "/net/cci-nas-00/data/ceres_data/7tpk_26058/02_2025/7tpk_26058.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7tpk_26058/02_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-5592/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: 3.70, per 1000 atoms: 2.49 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: 0.35 Conformation dependent library (CDL) restraints added in 185.3 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: 0.21 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: 0.35 Time building geometry restraints manager: 0.43 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: 7.220 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.060 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 11.560 Find NCS groups from input model: 0.020 Set up NCS constraints: 0.000 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.700 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.600 ------------------------------------------------------------------------------- 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 : 0.011 0.060 1528 Z= 0.711 Angle : 1.403 7.313 2084 Z= 0.955 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 *********************** 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 : 0.169 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: 0.1937 time to fit residues: 7.0692 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 : 0.166 ------------------------------------------------------------------------------- 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: 0.3980 chunk 9 optimal weight: 0.4980 chunk 5 optimal weight: 0.0970 chunk 11 optimal weight: 0.4980 chunk 17 optimal weight: 0.6980 chunk 18 optimal weight: 0.8980 chunk 15 optimal weight: 0.2980 chunk 13 optimal weight: 0.9980 overall best weight: 0.2616 ------------------------------------------------------------------------------- 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 = 0.3815 r_free = 0.3815 target = 0.164737 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3654 r_free = 0.3654 target = 0.150324 restraints weight = 2023.263| |-----------------------------------------------------------------------------| r_work (start): 0.3650 rms_B_bonded: 1.83 r_work: 0.3570 rms_B_bonded: 2.21 restraints_weight: 0.5000 r_work: 0.3452 rms_B_bonded: 3.96 restraints_weight: 0.2500 r_work (final): 0.3452 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7673 moved from start: 0.2987 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 1528 Z= 0.219 Angle : 0.560 5.466 2084 Z= 0.298 Chirality : 0.045 0.131 223 Planarity : 0.004 0.032 269 Dihedral : 5.345 35.555 238 Min Nonbonded Distance : 2.584 Molprobity Statistics. All-atom Clashscore : 3.18 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: -1.68 (0.54), residues: 192 helix: -4.00 (0.52), residues: 31 sheet: 0.87 (0.77), residues: 39 loop : -1.00 (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 497 TYR 0.010 0.001 TYR E 351 ARG 0.002 0.000 ARG E 457 *********************** 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 : 0.165 Fit side-chains outliers start: 1 outliers final: 1 residues processed: 26 average time/residue: 0.2019 time to fit residues: 5.8581 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 : 0.158 ------------------------------------------------------------------------------- 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: 0.0770 chunk 6 optimal weight: 0.9990 chunk 4 optimal weight: 0.2980 chunk 3 optimal weight: 0.0970 chunk 18 optimal weight: 0.4980 chunk 9 optimal weight: 0.2980 chunk 2 optimal weight: 0.5980 chunk 7 optimal weight: 0.0980 chunk 10 optimal weight: 0.3980 chunk 11 optimal weight: 0.9980 chunk 12 optimal weight: 0.4980 overall best weight: 0.1736 ------------------------------------------------------------------------------- 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 = 0.3782 r_free = 0.3782 target = 0.162197 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3630 r_free = 0.3630 target = 0.148312 restraints weight = 2032.922| |-----------------------------------------------------------------------------| r_work (start): 0.3629 rms_B_bonded: 1.71 r_work: 0.3550 rms_B_bonded: 2.14 restraints_weight: 0.5000 r_work: 0.3433 rms_B_bonded: 3.85 restraints_weight: 0.2500 r_work (final): 0.3433 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7742 moved from start: 0.3692 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.020 1528 Z= 0.139 Angle : 0.471 3.856 2084 Z= 0.255 Chirality : 0.043 0.121 223 Planarity : 0.004 0.027 269 Dihedral : 4.341 26.054 238 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 2.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 1.44 % Allowed : 10.79 % Favored : 87.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -1.48 (0.54), residues: 192 helix: -3.73 (0.51), residues: 31 sheet: 1.39 (0.82), residues: 37 loop : -1.02 (0.50), residues: 124 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP E 436 PHE 0.008 0.001 PHE E 497 TYR 0.008 0.001 TYR E 351 ARG 0.004 0.001 ARG E 457 *********************** 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 : 0.171 Fit side-chains REVERT: E 506 GLN cc_start: 0.7265 (mm-40) cc_final: 0.6954 (mp10) outliers start: 2 outliers final: 2 residues processed: 24 average time/residue: 0.2003 time to fit residues: 5.4125 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 : 0.168 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 373 SER Chi-restraints excluded: chain E residue 407 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 19 random chunks: chunk 5 optimal weight: 0.3980 chunk 8 optimal weight: 0.9990 chunk 13 optimal weight: 0.9990 chunk 2 optimal weight: 0.9980 chunk 14 optimal weight: 0.4980 chunk 16 optimal weight: 0.9980 chunk 9 optimal weight: 0.3980 chunk 18 optimal weight: 0.8980 chunk 6 optimal weight: 0.5980 chunk 7 optimal weight: 0.6980 chunk 10 optimal weight: 0.3980 overall best weight: 0.4580 ------------------------------------------------------------------------------- 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 = 0.3672 r_free = 0.3672 target = 0.151797 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.138773 restraints weight = 2047.314| |-----------------------------------------------------------------------------| r_work (start): 0.3531 rms_B_bonded: 1.63 r_work: 0.3441 rms_B_bonded: 2.20 restraints_weight: 0.5000 r_work: 0.3326 rms_B_bonded: 3.94 restraints_weight: 0.2500 r_work (final): 0.3326 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7873 moved from start: 0.4338 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 1528 Z= 0.294 Angle : 0.554 6.209 2084 Z= 0.288 Chirality : 0.045 0.129 223 Planarity : 0.004 0.028 269 Dihedral : 4.966 28.561 238 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 2.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.65 % Favored : 96.35 % Rotamer: Outliers : 2.88 % Allowed : 11.51 % Favored : 85.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -3.58 (0.59), residues: 31 sheet: 1.76 (0.87), residues: 37 loop : -1.18 (0.48), residues: 124 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP E 436 PHE 0.011 0.002 PHE E 429 TYR 0.010 0.001 TYR E 351 ARG 0.002 0.001 ARG E 509 *********************** 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 25 residues out of total 167 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 21 time to evaluate : 0.172 Fit side-chains outliers start: 4 outliers final: 4 residues processed: 23 average time/residue: 0.1566 time to fit residues: 4.1535 Evaluate side-chains 22 residues out of total 167 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 18 time to evaluate : 0.136 ------------------------------------------------------------------------------- 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 Chi-restraints excluded: chain E residue 438 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 19 random chunks: chunk 11 optimal weight: 0.5980 chunk 13 optimal weight: 0.9980 chunk 16 optimal weight: 0.9990 chunk 12 optimal weight: 0.4980 chunk 10 optimal weight: 0.7980 chunk 5 optimal weight: 0.3980 chunk 7 optimal weight: 0.3980 chunk 15 optimal weight: 0.4980 chunk 6 optimal weight: 0.0980 chunk 0 optimal weight: 0.9990 chunk 1 optimal weight: 0.3980 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 = 0.3685 r_free = 0.3685 target = 0.153694 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.140985 restraints weight = 2022.461| |-----------------------------------------------------------------------------| r_work (start): 0.3546 rms_B_bonded: 1.55 r_work: 0.3464 rms_B_bonded: 1.98 restraints_weight: 0.5000 r_work: 0.3355 rms_B_bonded: 3.47 restraints_weight: 0.2500 r_work (final): 0.3355 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7854 moved from start: 0.4716 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 1528 Z= 0.234 Angle : 0.501 4.480 2084 Z= 0.265 Chirality : 0.044 0.125 223 Planarity : 0.004 0.028 269 Dihedral : 4.868 29.054 238 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 1.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 2.88 % Allowed : 11.51 % Favored : 85.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -1.46 (0.55), residues: 192 helix: -3.11 (0.71), residues: 31 sheet: 1.83 (0.89), residues: 37 loop : -1.35 (0.46), 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 377 TYR 0.008 0.001 TYR E 351 ARG 0.003 0.001 ARG E 457 *********************** 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: 4 poor density : 27 time to evaluate : 0.183 Fit side-chains outliers start: 4 outliers final: 3 residues processed: 29 average time/residue: 0.1680 time to fit residues: 5.4775 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: 0.9980 chunk 10 optimal weight: 0.6980 chunk 13 optimal weight: 0.9980 chunk 16 optimal weight: 0.0970 chunk 6 optimal weight: 0.7980 chunk 0 optimal weight: 0.9990 chunk 5 optimal weight: 0.0870 chunk 1 optimal weight: 0.3980 chunk 4 optimal weight: 0.7980 chunk 2 optimal weight: 0.5980 overall best weight: 0.3756 ------------------------------------------------------------------------------- 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 = 0.3660 r_free = 0.3660 target = 0.150658 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.138031 restraints weight = 2080.494| |-----------------------------------------------------------------------------| r_work (start): 0.3515 rms_B_bonded: 1.64 r_work: 0.3420 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.3304 rms_B_bonded: 3.93 restraints_weight: 0.2500 r_work (final): 0.3304 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7902 moved from start: 0.5035 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 1528 Z= 0.243 Angle : 0.498 4.708 2084 Z= 0.262 Chirality : 0.044 0.131 223 Planarity : 0.004 0.028 269 Dihedral : 4.911 29.961 238 Min Nonbonded Distance : 2.584 Molprobity Statistics. All-atom Clashscore : 2.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 2.16 % Allowed : 12.95 % Favored : 84.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -1.56 (0.53), residues: 192 helix: -3.03 (0.70), residues: 31 sheet: 1.64 (0.87), residues: 37 loop : -1.43 (0.45), residues: 124 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 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 *********************** 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 24 residues out of total 167 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 21 time to evaluate : 0.158 Fit side-chains outliers start: 3 outliers final: 3 residues processed: 22 average time/residue: 0.1753 time to fit residues: 4.3941 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 : 0.159 ------------------------------------------------------------------------------- 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: 0.9990 chunk 6 optimal weight: 0.5980 chunk 12 optimal weight: 0.0870 chunk 11 optimal weight: 0.0970 chunk 8 optimal weight: 0.1980 chunk 7 optimal weight: 0.2980 chunk 9 optimal weight: 0.2980 chunk 17 optimal weight: 0.7980 chunk 15 optimal weight: 0.6980 chunk 0 optimal weight: 0.9990 chunk 18 optimal weight: 0.6980 overall best weight: 0.1956 ------------------------------------------------------------------------------- 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 = 0.3702 r_free = 0.3702 target = 0.155513 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3564 r_free = 0.3564 target = 0.143078 restraints weight = 2027.274| |-----------------------------------------------------------------------------| r_work (start): 0.3560 rms_B_bonded: 1.54 r_work: 0.3480 rms_B_bonded: 1.99 restraints_weight: 0.5000 r_work: 0.3366 rms_B_bonded: 3.59 restraints_weight: 0.2500 r_work (final): 0.3366 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7854 moved from start: 0.5097 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 1528 Z= 0.151 Angle : 0.455 3.947 2084 Z= 0.239 Chirality : 0.043 0.127 223 Planarity : 0.004 0.028 269 Dihedral : 4.606 28.837 238 Min Nonbonded Distance : 2.598 Molprobity Statistics. All-atom Clashscore : 1.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 0.72 % Allowed : 15.11 % Favored : 84.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -1.49 (0.54), residues: 192 helix: -3.06 (0.68), residues: 31 sheet: 1.64 (0.88), residues: 37 loop : -1.33 (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 377 TYR 0.007 0.001 TYR E 351 ARG 0.002 0.000 ARG E 457 *********************** 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 25 residues out of total 167 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 24 time to evaluate : 0.132 Fit side-chains outliers start: 1 outliers final: 1 residues processed: 24 average time/residue: 0.1857 time to fit residues: 5.0517 Evaluate side-chains 23 residues out of total 167 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 22 time to evaluate : 0.130 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 367 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 19 random chunks: chunk 13 optimal weight: 0.0470 chunk 9 optimal weight: 0.9990 chunk 1 optimal weight: 0.1980 chunk 15 optimal weight: 0.5980 chunk 12 optimal weight: 0.5980 chunk 11 optimal weight: 0.6980 chunk 3 optimal weight: 0.9980 chunk 0 optimal weight: 0.7980 chunk 10 optimal weight: 0.0370 chunk 17 optimal weight: 0.7980 chunk 7 optimal weight: 0.5980 overall best weight: 0.2956 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3659 r_free = 0.3659 target = 0.150502 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3516 r_free = 0.3516 target = 0.138027 restraints weight = 2067.461| |-----------------------------------------------------------------------------| r_work (start): 0.3525 rms_B_bonded: 1.61 r_work: 0.3429 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.3313 rms_B_bonded: 4.01 restraints_weight: 0.2500 r_work (final): 0.3313 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7912 moved from start: 0.5206 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 1528 Z= 0.200 Angle : 0.473 4.093 2084 Z= 0.248 Chirality : 0.044 0.134 223 Planarity : 0.004 0.029 269 Dihedral : 4.720 30.177 238 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 1.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.65 % Favored : 96.35 % Rotamer: Outliers : 1.44 % Allowed : 15.83 % Favored : 82.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -1.51 (0.54), residues: 192 helix: -2.92 (0.72), residues: 31 sheet: 1.55 (0.86), residues: 37 loop : -1.36 (0.46), residues: 124 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP E 436 PHE 0.007 0.001 PHE E 377 TYR 0.008 0.001 TYR E 351 ARG 0.002 0.001 ARG E 466 *********************** 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 24 residues out of total 167 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 22 time to evaluate : 0.131 Fit side-chains REVERT: E 466 ARG cc_start: 0.7937 (ttm-80) cc_final: 0.7184 (ttm-80) outliers start: 2 outliers final: 2 residues processed: 23 average time/residue: 0.1848 time to fit residues: 4.8000 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 : 0.145 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 367 VAL Chi-restraints excluded: chain E residue 373 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 19 random chunks: chunk 16 optimal weight: 0.8980 chunk 4 optimal weight: 0.7980 chunk 3 optimal weight: 0.6980 chunk 18 optimal weight: 0.0040 chunk 14 optimal weight: 0.9980 chunk 10 optimal weight: 0.0970 chunk 15 optimal weight: 0.6980 chunk 2 optimal weight: 0.5980 chunk 5 optimal weight: 0.2980 chunk 13 optimal weight: 0.0770 chunk 17 optimal weight: 0.1980 overall best weight: 0.1348 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3707 r_free = 0.3707 target = 0.154687 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.142141 restraints weight = 2070.169| |-----------------------------------------------------------------------------| r_work (start): 0.3565 rms_B_bonded: 1.55 r_work: 0.3479 rms_B_bonded: 2.09 restraints_weight: 0.5000 r_work: 0.3368 rms_B_bonded: 3.70 restraints_weight: 0.2500 r_work (final): 0.3368 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7832 moved from start: 0.5261 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.017 1528 Z= 0.126 Angle : 0.438 3.751 2084 Z= 0.231 Chirality : 0.043 0.125 223 Planarity : 0.004 0.030 269 Dihedral : 4.387 28.301 238 Min Nonbonded Distance : 2.558 Molprobity Statistics. All-atom Clashscore : 1.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 1.44 % Allowed : 15.83 % Favored : 82.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.90 (0.55), residues: 192 helix: -2.29 (1.12), residues: 18 sheet: 1.67 (0.88), residues: 37 loop : -1.09 (0.46), residues: 137 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP E 436 PHE 0.005 0.001 PHE E 400 TYR 0.006 0.001 TYR E 351 ARG 0.003 0.000 ARG E 457 *********************** 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 27 residues out of total 167 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 25 time to evaluate : 0.171 Fit side-chains outliers start: 2 outliers final: 2 residues processed: 26 average time/residue: 0.1861 time to fit residues: 5.4000 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 : 0.170 ------------------------------------------------------------------------------- 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: 1.9990 chunk 12 optimal weight: 0.6980 chunk 4 optimal weight: 0.4980 chunk 17 optimal weight: 0.9980 chunk 16 optimal weight: 0.7980 chunk 3 optimal weight: 0.6980 chunk 5 optimal weight: 0.8980 chunk 11 optimal weight: 0.9980 chunk 10 optimal weight: 0.9990 chunk 0 optimal weight: 0.5980 chunk 6 optimal weight: 0.5980 overall best weight: 0.6180 ------------------------------------------------------------------------------- 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 = 0.3619 r_free = 0.3619 target = 0.147514 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.135238 restraints weight = 2113.489| |-----------------------------------------------------------------------------| r_work (start): 0.3476 rms_B_bonded: 1.58 r_work: 0.3390 rms_B_bonded: 2.09 restraints_weight: 0.5000 r_work: 0.3274 rms_B_bonded: 3.75 restraints_weight: 0.2500 r_work (final): 0.3274 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7943 moved from start: 0.5317 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 1528 Z= 0.369 Angle : 0.545 5.231 2084 Z= 0.286 Chirality : 0.047 0.135 223 Planarity : 0.005 0.028 269 Dihedral : 5.265 34.045 238 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 2.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.17 % Favored : 95.83 % Rotamer: Outliers : 2.16 % Allowed : 15.11 % Favored : 82.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -1.68 (0.53), residues: 192 helix: -2.75 (0.77), residues: 31 sheet: 1.42 (0.85), residues: 37 loop : -1.57 (0.45), residues: 124 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP E 436 PHE 0.013 0.002 PHE E 429 TYR 0.009 0.001 TYR E 453 ARG 0.002 0.001 ARG E 357 ********************** 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 27 residues out of total 167 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 24 time to evaluate : 0.170 Fit side-chains outliers start: 3 outliers final: 3 residues processed: 25 average time/residue: 0.2032 time to fit residues: 5.6582 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 : 0.172 ------------------------------------------------------------------------------- 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 19 random chunks: chunk 14 optimal weight: 0.9990 chunk 7 optimal weight: 0.3980 chunk 5 optimal weight: 0.0870 chunk 16 optimal weight: 0.5980 chunk 15 optimal weight: 0.0570 chunk 8 optimal weight: 0.0980 chunk 11 optimal weight: 0.8980 chunk 4 optimal weight: 0.0870 chunk 0 optimal weight: 0.9990 chunk 18 optimal weight: 0.0980 chunk 12 optimal weight: 0.0000 overall best weight: 0.0658 ------------------------------------------------------------------------------- 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 = 0.3690 r_free = 0.3690 target = 0.154037 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.141784 restraints weight = 2132.246| |-----------------------------------------------------------------------------| r_work (start): 0.3552 rms_B_bonded: 1.60 r_work: 0.3463 rms_B_bonded: 2.18 restraints_weight: 0.5000 r_work: 0.3350 rms_B_bonded: 3.92 restraints_weight: 0.2500 r_work (final): 0.3350 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7856 moved from start: 0.5411 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 1528 Z= 0.131 Angle : 0.467 3.873 2084 Z= 0.246 Chirality : 0.043 0.122 223 Planarity : 0.004 0.028 269 Dihedral : 4.843 29.801 238 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 1.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 1.44 % Allowed : 16.55 % 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: -1.11 (0.55), residues: 192 helix: -2.47 (0.88), residues: 25 sheet: 1.56 (0.86), residues: 37 loop : -1.14 (0.47), residues: 130 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP E 436 PHE 0.006 0.001 PHE E 392 TYR 0.005 0.001 TYR E 351 ARG 0.003 0.000 ARG E 457 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1676.32 seconds wall clock time: 30 minutes 32.36 seconds (1832.36 seconds total)