Starting phenix.real_space_refine on Tue Feb 11 05:51:17 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8j1t_35932/02_2025/8j1t_35932.cif Found real_map, /net/cci-nas-00/data/ceres_data/8j1t_35932/02_2025/8j1t_35932.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8j1t_35932/02_2025/8j1t_35932.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8j1t_35932/02_2025/8j1t_35932.map" model { file = "/net/cci-nas-00/data/ceres_data/8j1t_35932/02_2025/8j1t_35932.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8j1t_35932/02_2025/8j1t_35932.cif" } resolution = 3.3 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= 0.001 sd= 0.016 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 1374 atoms to isotropic. 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 17 5.16 5 C 2035 2.51 5 N 543 2.21 5 O 609 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 5 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib" Total number of atoms: 3204 Number of models: 1 Model: "" Number of chains: 3 Chain: "H" Number of atoms: 874 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 874 Classifications: {'peptide': 115} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 111} Chain: "K" Number of atoms: 825 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 825 Classifications: {'peptide': 108} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 101} Chain: "F" Number of atoms: 1505 Number of conformers: 1 Conformer: "" Number of residues, atoms: 188, 1505 Classifications: {'peptide': 188} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 11, 'TRANS': 176} Chain breaks: 1 Time building chain proxies: 3.96, per 1000 atoms: 1.24 Number of scatterers: 3204 At special positions: 0 Unit cell: (63.05, 64.02, 92.15, 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 17 16.00 O 609 8.00 N 543 7.00 C 2035 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS H 23 " - pdb=" SG CYS H 96 " distance=2.04 Simple disulfide: pdb=" SG CYS K 23 " - pdb=" SG CYS K 88 " distance=2.04 Simple disulfide: pdb=" SG CYS F 336 " - pdb=" SG CYS F 361 " distance=2.03 Simple disulfide: pdb=" SG CYS F 379 " - pdb=" SG CYS F 432 " distance=2.03 Simple disulfide: pdb=" SG CYS F 391 " - pdb=" SG CYS F 525 " distance=2.03 Simple disulfide: pdb=" SG CYS F 480 " - pdb=" SG CYS F 488 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.72 Conformation dependent library (CDL) restraints added in 429.6 milliseconds 806 Ramachandran restraints generated. 403 Oldfield, 0 Emsley, 403 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 748 Finding SS restraints... Secondary structure from input PDB file: 7 helices and 7 sheets defined 10.2% alpha, 23.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.42 Creating SS restraints... Processing helix chain 'H' and resid 29 through 33 removed outlier: 3.895A pdb=" N ASN H 33 " --> pdb=" O VAL H 30 " (cutoff:3.500A) Processing helix chain 'H' and resid 61 through 65 removed outlier: 3.670A pdb=" N ARG H 65 " --> pdb=" O ASP H 62 " (cutoff:3.500A) Processing helix chain 'F' and resid 337 through 343 Processing helix chain 'F' and resid 366 through 372 removed outlier: 3.851A pdb=" N ASN F 370 " --> pdb=" O SER F 366 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N PHE F 371 " --> pdb=" O VAL F 367 " (cutoff:3.500A) Processing helix chain 'F' and resid 384 through 388 removed outlier: 4.094A pdb=" N ASN F 388 " --> pdb=" O THR F 385 " (cutoff:3.500A) Processing helix chain 'F' and resid 405 through 410 removed outlier: 4.573A pdb=" N SER F 408 " --> pdb=" O ASN F 405 " (cutoff:3.500A) Processing helix chain 'F' and resid 416 through 422 removed outlier: 3.632A pdb=" N TYR F 421 " --> pdb=" O ASN F 417 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'H' and resid 4 through 8 removed outlier: 3.884A pdb=" N GLN H 4 " --> pdb=" O SER H 26 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N SER H 22 " --> pdb=" O SER H 8 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'H' and resid 11 through 13 removed outlier: 6.178A pdb=" N GLY H 11 " --> pdb=" O THR H 115 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N VAL H 114 " --> pdb=" O ALA H 92 " (cutoff:3.500A) removed outlier: 4.770A pdb=" N TYR H 34 " --> pdb=" O ASP H 99 " (cutoff:3.500A) removed outlier: 6.700A pdb=" N MET H 35 " --> pdb=" O VAL H 51 " (cutoff:3.500A) removed outlier: 4.399A pdb=" N VAL H 51 " --> pdb=" O MET H 35 " (cutoff:3.500A) removed outlier: 6.459A pdb=" N TRP H 37 " --> pdb=" O VAL H 49 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'K' and resid 4 through 6 removed outlier: 3.932A pdb=" N VAL K 19 " --> pdb=" O ILE K 75 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N PHE K 71 " --> pdb=" O CYS K 23 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'K' and resid 45 through 48 removed outlier: 5.799A pdb=" N LEU K 46 " --> pdb=" O GLN K 37 " (cutoff:3.500A) removed outlier: 6.101A pdb=" N GLN K 37 " --> pdb=" O LEU K 46 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'F' and resid 354 through 355 removed outlier: 3.585A pdb=" N ASN F 354 " --> pdb=" O SER F 399 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N SER F 399 " --> pdb=" O ASN F 354 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'F' and resid 391 through 392 Processing sheet with id=AA7, first strand: chain 'F' and resid 452 through 454 76 hydrogen bonds defined for protein. 183 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: 0.80 Time building geometry restraints manager: 0.87 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 1029 1.34 - 1.46: 859 1.46 - 1.58: 1377 1.58 - 1.70: 0 1.70 - 1.82: 22 Bond restraints: 3287 Sorted by residual: bond pdb=" CA ILE K 29 " pdb=" CB ILE K 29 " ideal model delta sigma weight residual 1.553 1.538 0.015 7.40e-03 1.83e+04 4.28e+00 bond pdb=" CB ASN F 343 " pdb=" CG ASN F 343 " ideal model delta sigma weight residual 1.516 1.548 -0.032 2.50e-02 1.60e+03 1.63e+00 bond pdb=" CA ILE H 107 " pdb=" CB ILE H 107 " ideal model delta sigma weight residual 1.540 1.526 0.014 1.36e-02 5.41e+03 1.03e+00 bond pdb=" CA VAL H 49 " pdb=" CB VAL H 49 " ideal model delta sigma weight residual 1.545 1.536 0.009 9.10e-03 1.21e+04 9.38e-01 bond pdb=" CB PHE F 400 " pdb=" CG PHE F 400 " ideal model delta sigma weight residual 1.502 1.480 0.022 2.30e-02 1.89e+03 8.92e-01 ... (remaining 3282 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.03: 4162 1.03 - 2.07: 244 2.07 - 3.10: 39 3.10 - 4.14: 18 4.14 - 5.17: 3 Bond angle restraints: 4466 Sorted by residual: angle pdb=" C GLN K 89 " pdb=" CA GLN K 89 " pdb=" CB GLN K 89 " ideal model delta sigma weight residual 111.17 106.80 4.37 1.96e+00 2.60e-01 4.98e+00 angle pdb=" C SER K 93 " pdb=" CA SER K 93 " pdb=" CB SER K 93 " ideal model delta sigma weight residual 111.71 106.94 4.77 2.23e+00 2.01e-01 4.58e+00 angle pdb=" CA ALA F 411 " pdb=" C ALA F 411 " pdb=" N PRO F 412 " ideal model delta sigma weight residual 117.62 119.65 -2.03 1.03e+00 9.43e-01 3.88e+00 angle pdb=" N GLN K 89 " pdb=" CA GLN K 89 " pdb=" CB GLN K 89 " ideal model delta sigma weight residual 111.46 114.42 -2.96 1.54e+00 4.22e-01 3.70e+00 angle pdb=" CA GLY K 28 " pdb=" C GLY K 28 " pdb=" O GLY K 28 " ideal model delta sigma weight residual 122.61 120.22 2.39 1.28e+00 6.10e-01 3.47e+00 ... (remaining 4461 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.68: 1761 15.68 - 31.35: 129 31.35 - 47.03: 31 47.03 - 62.70: 6 62.70 - 78.38: 3 Dihedral angle restraints: 1930 sinusoidal: 747 harmonic: 1183 Sorted by residual: dihedral pdb=" CB CYS F 480 " pdb=" SG CYS F 480 " pdb=" SG CYS F 488 " pdb=" CB CYS F 488 " ideal model delta sinusoidal sigma weight residual 93.00 171.38 -78.38 1 1.00e+01 1.00e-02 7.67e+01 dihedral pdb=" CA ASN H 84 " pdb=" C ASN H 84 " pdb=" N SER H 85 " pdb=" CA SER H 85 " ideal model delta harmonic sigma weight residual -180.00 -151.42 -28.58 0 5.00e+00 4.00e-02 3.27e+01 dihedral pdb=" CB CYS F 391 " pdb=" SG CYS F 391 " pdb=" SG CYS F 525 " pdb=" CB CYS F 525 " ideal model delta sinusoidal sigma weight residual 93.00 125.38 -32.38 1 1.00e+01 1.00e-02 1.49e+01 ... (remaining 1927 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.034: 288 0.034 - 0.067: 133 0.067 - 0.100: 32 0.100 - 0.134: 16 0.134 - 0.167: 5 Chirality restraints: 474 Sorted by residual: chirality pdb=" CA SER K 93 " pdb=" N SER K 93 " pdb=" C SER K 93 " pdb=" CB SER K 93 " both_signs ideal model delta sigma weight residual False 2.51 2.68 -0.17 2.00e-01 2.50e+01 7.01e-01 chirality pdb=" CA VAL H 51 " pdb=" N VAL H 51 " pdb=" C VAL H 51 " pdb=" CB VAL H 51 " both_signs ideal model delta sigma weight residual False 2.44 2.59 -0.15 2.00e-01 2.50e+01 5.28e-01 chirality pdb=" CA ILE F 402 " pdb=" N ILE F 402 " pdb=" C ILE F 402 " pdb=" CB ILE F 402 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.14 2.00e-01 2.50e+01 5.24e-01 ... (remaining 471 not shown) Planarity restraints: 582 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASN F 343 " -0.011 2.00e-02 2.50e+03 2.10e-02 4.40e+00 pdb=" C ASN F 343 " 0.036 2.00e-02 2.50e+03 pdb=" O ASN F 343 " -0.014 2.00e-02 2.50e+03 pdb=" N ALA F 344 " -0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR F 396 " 0.011 2.00e-02 2.50e+03 7.76e-03 1.20e+00 pdb=" CG TYR F 396 " -0.018 2.00e-02 2.50e+03 pdb=" CD1 TYR F 396 " 0.001 2.00e-02 2.50e+03 pdb=" CD2 TYR F 396 " 0.001 2.00e-02 2.50e+03 pdb=" CE1 TYR F 396 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 TYR F 396 " 0.000 2.00e-02 2.50e+03 pdb=" CZ TYR F 396 " 0.003 2.00e-02 2.50e+03 pdb=" OH TYR F 396 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C TYR H 53 " 0.018 5.00e-02 4.00e+02 2.74e-02 1.20e+00 pdb=" N PRO H 54 " -0.047 5.00e-02 4.00e+02 pdb=" CA PRO H 54 " 0.014 5.00e-02 4.00e+02 pdb=" CD PRO H 54 " 0.015 5.00e-02 4.00e+02 ... (remaining 579 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.76: 469 2.76 - 3.29: 2996 3.29 - 3.83: 4905 3.83 - 4.36: 5946 4.36 - 4.90: 10335 Nonbonded interactions: 24651 Sorted by model distance: nonbonded pdb=" OH TYR K 36 " pdb=" OE1 GLN K 89 " model vdw 2.220 3.040 nonbonded pdb=" O GLN K 38 " pdb=" OG1 THR K 85 " model vdw 2.243 3.040 nonbonded pdb=" OE1 GLN K 6 " pdb=" OG1 THR K 104 " model vdw 2.266 3.040 nonbonded pdb=" O ASN F 439 " pdb=" OG SER F 443 " model vdw 2.339 3.040 nonbonded pdb=" OD1 ASN F 388 " pdb=" N ASP F 389 " model vdw 2.343 3.120 ... (remaining 24646 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=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: 3.330 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.030 Construct map_model_manager: 0.000 Extract box with map and model: 0.140 Check model and map are aligned: 0.020 Set scattering table: 0.040 Process input model: 14.450 Find NCS groups from input model: 0.030 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:2.820 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.870 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7043 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 : 0.004 0.032 3287 Z= 0.275 Angle : 0.585 5.169 4466 Z= 0.321 Chirality : 0.044 0.167 474 Planarity : 0.004 0.027 582 Dihedral : 11.734 66.984 1164 Min Nonbonded Distance : 2.220 Molprobity Statistics. All-atom Clashscore : 8.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.20 % Favored : 92.80 % Rotamer: Outliers : 0.00 % Allowed : 0.29 % Favored : 99.71 % 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: -1.87 (0.39), residues: 403 helix: -3.01 (0.65), residues: 33 sheet: -0.44 (0.47), residues: 134 loop : -1.47 (0.36), residues: 236 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP F 353 HIS 0.005 0.001 HIS H 100 PHE 0.009 0.001 PHE F 338 TYR 0.018 0.002 TYR F 396 ARG 0.004 0.000 ARG F 355 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 806 Ramachandran restraints generated. 403 Oldfield, 0 Emsley, 403 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 806 Ramachandran restraints generated. 403 Oldfield, 0 Emsley, 403 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 59 residues out of total 347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 59 time to evaluate : 0.373 Fit side-chains revert: symmetry clash REVERT: K 63 SER cc_start: 0.6549 (t) cc_final: 0.6239 (t) REVERT: F 453 TYR cc_start: 0.8207 (p90) cc_final: 0.7912 (p90) outliers start: 0 outliers final: 0 residues processed: 59 average time/residue: 0.1633 time to fit residues: 11.8226 Evaluate side-chains 58 residues out of total 347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 58 time to evaluate : 0.361 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 32 optimal weight: 1.9990 chunk 29 optimal weight: 0.8980 chunk 16 optimal weight: 0.1980 chunk 10 optimal weight: 0.8980 chunk 19 optimal weight: 0.6980 chunk 15 optimal weight: 0.6980 chunk 30 optimal weight: 0.9990 chunk 11 optimal weight: 0.5980 chunk 18 optimal weight: 2.9990 chunk 22 optimal weight: 0.9990 chunk 35 optimal weight: 0.6980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 40 GLN F 354 ASN ** F 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3816 r_free = 0.3816 target = 0.139734 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3593 r_free = 0.3593 target = 0.123104 restraints weight = 4404.740| |-----------------------------------------------------------------------------| r_work (start): 0.3589 rms_B_bonded: 2.17 r_work: 0.3477 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.3301 rms_B_bonded: 4.55 restraints_weight: 0.2500 r_work (final): 0.3301 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7471 moved from start: 0.1008 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.028 3287 Z= 0.295 Angle : 0.592 5.261 4466 Z= 0.322 Chirality : 0.046 0.151 474 Planarity : 0.004 0.032 582 Dihedral : 5.182 37.556 458 Min Nonbonded Distance : 2.570 Molprobity Statistics. All-atom Clashscore : 7.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.70 % Favored : 93.30 % Rotamer: Outliers : 0.86 % Allowed : 6.34 % Favored : 92.80 % 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: -1.88 (0.39), residues: 403 helix: -3.10 (0.66), residues: 33 sheet: -0.26 (0.49), residues: 120 loop : -1.53 (0.35), residues: 250 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP F 436 HIS 0.004 0.001 HIS H 100 PHE 0.010 0.001 PHE F 338 TYR 0.015 0.002 TYR K 49 ARG 0.003 0.000 ARG K 61 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 806 Ramachandran restraints generated. 403 Oldfield, 0 Emsley, 403 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 806 Ramachandran restraints generated. 403 Oldfield, 0 Emsley, 403 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 56 residues out of total 347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 53 time to evaluate : 0.311 Fit side-chains revert: symmetry clash outliers start: 3 outliers final: 3 residues processed: 53 average time/residue: 0.1384 time to fit residues: 9.2999 Evaluate side-chains 56 residues out of total 347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 53 time to evaluate : 0.337 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 57 SER Chi-restraints excluded: chain K residue 31 SER Chi-restraints excluded: chain F residue 393 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 36 optimal weight: 0.9980 chunk 34 optimal weight: 0.2980 chunk 12 optimal weight: 1.9990 chunk 10 optimal weight: 0.9980 chunk 11 optimal weight: 0.9980 chunk 13 optimal weight: 5.9990 chunk 16 optimal weight: 3.9990 chunk 33 optimal weight: 0.4980 chunk 17 optimal weight: 1.9990 chunk 20 optimal weight: 0.7980 chunk 15 optimal weight: 0.2980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** K 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 343 ASN F 354 ASN F 417 ASN F 422 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3809 r_free = 0.3809 target = 0.139096 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3586 r_free = 0.3586 target = 0.122553 restraints weight = 4432.791| |-----------------------------------------------------------------------------| r_work (start): 0.3582 rms_B_bonded: 2.18 r_work: 0.3465 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.3290 rms_B_bonded: 4.57 restraints_weight: 0.2500 r_work (final): 0.3290 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7482 moved from start: 0.1277 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.029 3287 Z= 0.287 Angle : 0.570 5.175 4466 Z= 0.309 Chirality : 0.045 0.154 474 Planarity : 0.004 0.032 582 Dihedral : 5.025 28.064 458 Min Nonbonded Distance : 2.580 Molprobity Statistics. All-atom Clashscore : 6.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.44 % Favored : 92.56 % Rotamer: Outliers : 1.73 % Allowed : 8.93 % Favored : 89.34 % 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: -1.89 (0.39), residues: 403 helix: -3.08 (0.75), residues: 27 sheet: -0.37 (0.46), residues: 133 loop : -1.60 (0.36), residues: 243 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP F 436 HIS 0.003 0.001 HIS H 100 PHE 0.012 0.002 PHE F 377 TYR 0.013 0.002 TYR F 423 ARG 0.004 0.000 ARG F 355 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 806 Ramachandran restraints generated. 403 Oldfield, 0 Emsley, 403 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 806 Ramachandran restraints generated. 403 Oldfield, 0 Emsley, 403 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 55 residues out of total 347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 49 time to evaluate : 0.272 Fit side-chains revert: symmetry clash outliers start: 6 outliers final: 5 residues processed: 51 average time/residue: 0.1387 time to fit residues: 8.8582 Evaluate side-chains 57 residues out of total 347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 52 time to evaluate : 0.322 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 57 SER Chi-restraints excluded: chain K residue 31 SER Chi-restraints excluded: chain K residue 96 SER Chi-restraints excluded: chain F residue 343 ASN Chi-restraints excluded: chain F residue 393 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 10 optimal weight: 0.9980 chunk 9 optimal weight: 0.9990 chunk 33 optimal weight: 0.6980 chunk 15 optimal weight: 0.3980 chunk 14 optimal weight: 0.9990 chunk 12 optimal weight: 1.9990 chunk 25 optimal weight: 0.6980 chunk 31 optimal weight: 0.6980 chunk 27 optimal weight: 0.0770 chunk 37 optimal weight: 0.7980 chunk 32 optimal weight: 0.8980 overall best weight: 0.5138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** K 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 354 ASN ** F 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3814 r_free = 0.3814 target = 0.139419 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3585 r_free = 0.3585 target = 0.122633 restraints weight = 4446.370| |-----------------------------------------------------------------------------| r_work (start): 0.3586 rms_B_bonded: 2.23 r_work: 0.3466 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.3291 rms_B_bonded: 4.64 restraints_weight: 0.2500 r_work (final): 0.3291 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7478 moved from start: 0.1461 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.025 3287 Z= 0.263 Angle : 0.566 5.802 4466 Z= 0.303 Chirality : 0.045 0.154 474 Planarity : 0.004 0.032 582 Dihedral : 4.980 27.159 458 Min Nonbonded Distance : 2.596 Molprobity Statistics. All-atom Clashscore : 7.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.69 % Favored : 92.31 % Rotamer: Outliers : 1.44 % Allowed : 10.37 % Favored : 88.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -1.92 (0.39), residues: 403 helix: -3.17 (0.74), residues: 27 sheet: -0.36 (0.45), residues: 133 loop : -1.63 (0.36), residues: 243 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP F 436 HIS 0.004 0.001 HIS H 100 PHE 0.009 0.001 PHE F 377 TYR 0.014 0.001 TYR F 423 ARG 0.003 0.000 ARG F 355 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 806 Ramachandran restraints generated. 403 Oldfield, 0 Emsley, 403 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 806 Ramachandran restraints generated. 403 Oldfield, 0 Emsley, 403 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 57 residues out of total 347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 52 time to evaluate : 0.342 Fit side-chains revert: symmetry clash REVERT: F 343 ASN cc_start: 0.8032 (t0) cc_final: 0.7729 (t0) REVERT: F 355 ARG cc_start: 0.8674 (ttt90) cc_final: 0.8455 (ttt90) outliers start: 5 outliers final: 5 residues processed: 54 average time/residue: 0.1370 time to fit residues: 9.3505 Evaluate side-chains 57 residues out of total 347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 52 time to evaluate : 0.324 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 57 SER Chi-restraints excluded: chain K residue 31 SER Chi-restraints excluded: chain K residue 96 SER Chi-restraints excluded: chain F residue 393 THR Chi-restraints excluded: chain F residue 415 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 13 optimal weight: 0.9990 chunk 4 optimal weight: 0.8980 chunk 25 optimal weight: 0.7980 chunk 2 optimal weight: 0.9990 chunk 31 optimal weight: 0.2980 chunk 37 optimal weight: 0.2980 chunk 26 optimal weight: 0.9980 chunk 35 optimal weight: 0.5980 chunk 30 optimal weight: 0.5980 chunk 32 optimal weight: 2.9990 chunk 5 optimal weight: 0.0980 overall best weight: 0.3780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** K 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 354 ASN ** F 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3829 r_free = 0.3829 target = 0.140565 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3601 r_free = 0.3601 target = 0.123606 restraints weight = 4424.303| |-----------------------------------------------------------------------------| r_work (start): 0.3601 rms_B_bonded: 2.25 r_work: 0.3478 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.3298 rms_B_bonded: 4.69 restraints_weight: 0.2500 r_work (final): 0.3298 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7467 moved from start: 0.1587 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 3287 Z= 0.205 Angle : 0.534 5.128 4466 Z= 0.285 Chirality : 0.044 0.154 474 Planarity : 0.003 0.032 582 Dihedral : 4.734 24.507 458 Min Nonbonded Distance : 2.612 Molprobity Statistics. All-atom Clashscore : 6.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.44 % Favored : 92.56 % Rotamer: Outliers : 1.73 % Allowed : 10.66 % Favored : 87.61 % 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: -1.84 (0.39), residues: 403 helix: -3.12 (0.75), residues: 27 sheet: -0.25 (0.45), residues: 133 loop : -1.60 (0.36), residues: 243 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP F 436 HIS 0.004 0.001 HIS H 100 PHE 0.009 0.001 PHE F 377 TYR 0.015 0.001 TYR F 423 ARG 0.002 0.000 ARG F 355 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 806 Ramachandran restraints generated. 403 Oldfield, 0 Emsley, 403 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 806 Ramachandran restraints generated. 403 Oldfield, 0 Emsley, 403 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 59 residues out of total 347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 53 time to evaluate : 0.316 Fit side-chains revert: symmetry clash REVERT: F 343 ASN cc_start: 0.8227 (t0) cc_final: 0.7849 (t0) REVERT: F 406 GLU cc_start: 0.8295 (OUTLIER) cc_final: 0.8039 (tt0) outliers start: 6 outliers final: 4 residues processed: 55 average time/residue: 0.1381 time to fit residues: 9.5911 Evaluate side-chains 58 residues out of total 347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 53 time to evaluate : 0.333 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 57 SER Chi-restraints excluded: chain K residue 31 SER Chi-restraints excluded: chain K residue 96 SER Chi-restraints excluded: chain F residue 393 THR Chi-restraints excluded: chain F residue 406 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 7 optimal weight: 0.9990 chunk 28 optimal weight: 0.5980 chunk 21 optimal weight: 0.1980 chunk 8 optimal weight: 0.6980 chunk 23 optimal weight: 0.3980 chunk 17 optimal weight: 5.9990 chunk 14 optimal weight: 0.9980 chunk 13 optimal weight: 0.9990 chunk 25 optimal weight: 0.9980 chunk 30 optimal weight: 0.8980 chunk 38 optimal weight: 0.0970 overall best weight: 0.3978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** K 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 354 ASN ** F 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3807 r_free = 0.3807 target = 0.139769 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3585 r_free = 0.3585 target = 0.122602 restraints weight = 4580.003| |-----------------------------------------------------------------------------| r_work (start): 0.3578 rms_B_bonded: 2.25 r_work: 0.3468 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.3304 rms_B_bonded: 4.53 restraints_weight: 0.2500 r_work (final): 0.3304 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7415 moved from start: 0.1710 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 3287 Z= 0.219 Angle : 0.539 5.056 4466 Z= 0.290 Chirality : 0.045 0.185 474 Planarity : 0.003 0.033 582 Dihedral : 4.732 24.558 458 Min Nonbonded Distance : 2.610 Molprobity Statistics. All-atom Clashscore : 6.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.70 % Favored : 93.30 % Rotamer: Outliers : 2.02 % Allowed : 11.24 % Favored : 86.74 % 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: -1.82 (0.40), residues: 403 helix: -3.16 (0.74), residues: 27 sheet: -0.27 (0.45), residues: 139 loop : -1.59 (0.37), residues: 237 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP F 436 HIS 0.003 0.001 HIS H 100 PHE 0.009 0.001 PHE F 377 TYR 0.011 0.001 TYR K 49 ARG 0.001 0.000 ARG F 355 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 806 Ramachandran restraints generated. 403 Oldfield, 0 Emsley, 403 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 806 Ramachandran restraints generated. 403 Oldfield, 0 Emsley, 403 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 59 residues out of total 347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 52 time to evaluate : 0.288 Fit side-chains revert: symmetry clash REVERT: F 343 ASN cc_start: 0.8218 (t0) cc_final: 0.7818 (t0) REVERT: F 406 GLU cc_start: 0.8208 (OUTLIER) cc_final: 0.7880 (tt0) outliers start: 7 outliers final: 6 residues processed: 54 average time/residue: 0.1367 time to fit residues: 9.4182 Evaluate side-chains 59 residues out of total 347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 52 time to evaluate : 0.317 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 57 SER Chi-restraints excluded: chain K residue 4 MET Chi-restraints excluded: chain K residue 31 SER Chi-restraints excluded: chain K residue 96 SER Chi-restraints excluded: chain F residue 393 THR Chi-restraints excluded: chain F residue 406 GLU Chi-restraints excluded: chain F residue 415 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 37 optimal weight: 0.9980 chunk 8 optimal weight: 0.9980 chunk 6 optimal weight: 0.9990 chunk 14 optimal weight: 0.9990 chunk 12 optimal weight: 0.9990 chunk 16 optimal weight: 2.9990 chunk 15 optimal weight: 0.0470 chunk 3 optimal weight: 0.9990 chunk 10 optimal weight: 0.9990 chunk 35 optimal weight: 0.9990 chunk 11 optimal weight: 0.7980 overall best weight: 0.7680 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** K 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 354 ASN ** F 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3778 r_free = 0.3778 target = 0.137679 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.3556 r_free = 0.3556 target = 0.120610 restraints weight = 4489.852| |-----------------------------------------------------------------------------| r_work (start): 0.3547 rms_B_bonded: 2.21 r_work: 0.3436 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.3271 rms_B_bonded: 4.47 restraints_weight: 0.2500 r_work (final): 0.3271 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7480 moved from start: 0.1816 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.046 3287 Z= 0.375 Angle : 0.608 5.353 4466 Z= 0.328 Chirality : 0.047 0.159 474 Planarity : 0.004 0.036 582 Dihedral : 5.143 29.817 458 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 7.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.94 % Favored : 92.06 % Rotamer: Outliers : 2.59 % Allowed : 12.10 % Favored : 85.30 % 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: -1.94 (0.39), residues: 403 helix: -3.32 (0.70), residues: 27 sheet: -0.18 (0.46), residues: 133 loop : -1.75 (0.36), residues: 243 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP F 436 HIS 0.004 0.001 HIS H 100 PHE 0.008 0.002 PHE F 338 TYR 0.015 0.002 TYR K 49 ARG 0.002 0.000 ARG F 498 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 806 Ramachandran restraints generated. 403 Oldfield, 0 Emsley, 403 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 806 Ramachandran restraints generated. 403 Oldfield, 0 Emsley, 403 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 62 residues out of total 347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 53 time to evaluate : 0.332 Fit side-chains revert: symmetry clash REVERT: H 77 ASN cc_start: 0.7961 (t0) cc_final: 0.7592 (t0) REVERT: F 343 ASN cc_start: 0.8216 (t0) cc_final: 0.7863 (t0) REVERT: F 406 GLU cc_start: 0.8177 (OUTLIER) cc_final: 0.7900 (tt0) outliers start: 9 outliers final: 7 residues processed: 58 average time/residue: 0.1385 time to fit residues: 10.2107 Evaluate side-chains 61 residues out of total 347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 53 time to evaluate : 0.324 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 57 SER Chi-restraints excluded: chain H residue 116 VAL Chi-restraints excluded: chain K residue 4 MET Chi-restraints excluded: chain K residue 31 SER Chi-restraints excluded: chain K residue 96 SER Chi-restraints excluded: chain F residue 393 THR Chi-restraints excluded: chain F residue 406 GLU Chi-restraints excluded: chain F residue 415 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 30 optimal weight: 0.6980 chunk 32 optimal weight: 2.9990 chunk 13 optimal weight: 0.0670 chunk 0 optimal weight: 1.9990 chunk 8 optimal weight: 0.9980 chunk 15 optimal weight: 0.8980 chunk 3 optimal weight: 0.5980 chunk 23 optimal weight: 0.0770 chunk 9 optimal weight: 0.3980 chunk 22 optimal weight: 0.2980 chunk 10 optimal weight: 0.5980 overall best weight: 0.2876 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 103 HIS ** K 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 422 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3832 r_free = 0.3832 target = 0.140979 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3608 r_free = 0.3608 target = 0.124083 restraints weight = 4390.717| |-----------------------------------------------------------------------------| r_work (start): 0.3609 rms_B_bonded: 2.23 r_work: 0.3487 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.3308 rms_B_bonded: 4.68 restraints_weight: 0.2500 r_work (final): 0.3308 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7460 moved from start: 0.1937 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 3287 Z= 0.179 Angle : 0.542 5.152 4466 Z= 0.289 Chirality : 0.044 0.157 474 Planarity : 0.003 0.034 582 Dihedral : 4.744 23.022 458 Min Nonbonded Distance : 2.570 Molprobity Statistics. All-atom Clashscore : 7.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.46 % Favored : 94.54 % Rotamer: Outliers : 2.59 % Allowed : 12.97 % Favored : 84.44 % 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: -1.78 (0.40), residues: 403 helix: -3.22 (0.73), residues: 27 sheet: 0.00 (0.47), residues: 131 loop : -1.68 (0.36), residues: 245 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP F 436 HIS 0.003 0.001 HIS H 100 PHE 0.013 0.001 PHE F 377 TYR 0.009 0.001 TYR K 36 ARG 0.001 0.000 ARG F 355 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 806 Ramachandran restraints generated. 403 Oldfield, 0 Emsley, 403 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 806 Ramachandran restraints generated. 403 Oldfield, 0 Emsley, 403 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 62 residues out of total 347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 53 time to evaluate : 0.431 Fit side-chains revert: symmetry clash REVERT: H 77 ASN cc_start: 0.7939 (t0) cc_final: 0.7576 (t0) REVERT: F 343 ASN cc_start: 0.8261 (t0) cc_final: 0.7874 (t0) REVERT: F 406 GLU cc_start: 0.8273 (OUTLIER) cc_final: 0.8013 (tt0) outliers start: 9 outliers final: 7 residues processed: 59 average time/residue: 0.1573 time to fit residues: 11.4357 Evaluate side-chains 61 residues out of total 347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 53 time to evaluate : 0.343 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 57 SER Chi-restraints excluded: chain H residue 116 VAL Chi-restraints excluded: chain K residue 31 SER Chi-restraints excluded: chain K residue 96 SER Chi-restraints excluded: chain F residue 393 THR Chi-restraints excluded: chain F residue 406 GLU Chi-restraints excluded: chain F residue 415 THR Chi-restraints excluded: chain F residue 422 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 34 optimal weight: 0.0670 chunk 25 optimal weight: 0.5980 chunk 3 optimal weight: 0.9990 chunk 15 optimal weight: 0.0970 chunk 28 optimal weight: 0.9990 chunk 2 optimal weight: 0.0060 chunk 30 optimal weight: 0.5980 chunk 35 optimal weight: 0.9990 chunk 18 optimal weight: 0.7980 chunk 12 optimal weight: 0.5980 chunk 9 optimal weight: 0.7980 overall best weight: 0.2732 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 422 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3809 r_free = 0.3809 target = 0.139874 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3585 r_free = 0.3585 target = 0.122672 restraints weight = 4501.354| |-----------------------------------------------------------------------------| r_work (start): 0.3584 rms_B_bonded: 2.27 r_work: 0.3479 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.3314 rms_B_bonded: 4.56 restraints_weight: 0.2500 r_work (final): 0.3314 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7422 moved from start: 0.2015 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 3287 Z= 0.178 Angle : 0.538 5.492 4466 Z= 0.287 Chirality : 0.044 0.157 474 Planarity : 0.003 0.034 582 Dihedral : 4.658 22.796 458 Min Nonbonded Distance : 2.603 Molprobity Statistics. All-atom Clashscore : 6.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.70 % Favored : 93.30 % Rotamer: Outliers : 2.59 % Allowed : 13.54 % Favored : 83.86 % 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: -1.77 (0.39), residues: 403 helix: -3.20 (0.73), residues: 27 sheet: 0.06 (0.48), residues: 121 loop : -1.64 (0.36), residues: 255 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP F 436 HIS 0.003 0.001 HIS H 100 PHE 0.013 0.001 PHE F 377 TYR 0.012 0.001 TYR F 421 ARG 0.002 0.000 ARG F 355 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 806 Ramachandran restraints generated. 403 Oldfield, 0 Emsley, 403 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 806 Ramachandran restraints generated. 403 Oldfield, 0 Emsley, 403 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 62 residues out of total 347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 53 time to evaluate : 0.343 Fit side-chains revert: symmetry clash REVERT: H 77 ASN cc_start: 0.7891 (t0) cc_final: 0.7531 (t0) REVERT: F 343 ASN cc_start: 0.8229 (t0) cc_final: 0.7858 (t0) REVERT: F 406 GLU cc_start: 0.8182 (OUTLIER) cc_final: 0.7869 (tt0) outliers start: 9 outliers final: 8 residues processed: 59 average time/residue: 0.1544 time to fit residues: 11.2209 Evaluate side-chains 62 residues out of total 347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 53 time to evaluate : 0.376 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 57 SER Chi-restraints excluded: chain H residue 116 VAL Chi-restraints excluded: chain K residue 31 SER Chi-restraints excluded: chain K residue 96 SER Chi-restraints excluded: chain K residue 104 THR Chi-restraints excluded: chain F residue 393 THR Chi-restraints excluded: chain F residue 406 GLU Chi-restraints excluded: chain F residue 415 THR Chi-restraints excluded: chain F residue 422 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 8 optimal weight: 1.9990 chunk 29 optimal weight: 0.3980 chunk 14 optimal weight: 1.9990 chunk 16 optimal weight: 0.9980 chunk 37 optimal weight: 0.6980 chunk 4 optimal weight: 0.5980 chunk 23 optimal weight: 0.6980 chunk 31 optimal weight: 0.8980 chunk 38 optimal weight: 0.4980 chunk 17 optimal weight: 3.9990 chunk 32 optimal weight: 0.5980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 37 GLN ** K 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 422 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3792 r_free = 0.3792 target = 0.138669 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3572 r_free = 0.3572 target = 0.121707 restraints weight = 4468.037| |-----------------------------------------------------------------------------| r_work (start): 0.3564 rms_B_bonded: 2.20 r_work: 0.3456 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.3291 rms_B_bonded: 4.46 restraints_weight: 0.2500 r_work (final): 0.3291 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7455 moved from start: 0.2024 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 3287 Z= 0.284 Angle : 0.572 5.738 4466 Z= 0.305 Chirality : 0.046 0.160 474 Planarity : 0.004 0.035 582 Dihedral : 4.839 25.383 458 Min Nonbonded Distance : 2.601 Molprobity Statistics. All-atom Clashscore : 8.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.70 % Favored : 93.30 % Rotamer: Outliers : 2.88 % Allowed : 13.83 % Favored : 83.29 % 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: -1.86 (0.39), residues: 403 helix: -3.30 (0.70), residues: 27 sheet: -0.07 (0.47), residues: 123 loop : -1.68 (0.36), residues: 253 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP F 436 HIS 0.004 0.001 HIS H 100 PHE 0.010 0.001 PHE F 377 TYR 0.017 0.002 TYR F 423 ARG 0.001 0.000 ARG H 67 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 806 Ramachandran restraints generated. 403 Oldfield, 0 Emsley, 403 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 806 Ramachandran restraints generated. 403 Oldfield, 0 Emsley, 403 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 60 residues out of total 347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 50 time to evaluate : 0.359 Fit side-chains revert: symmetry clash REVERT: H 77 ASN cc_start: 0.7917 (t0) cc_final: 0.7579 (t0) REVERT: F 343 ASN cc_start: 0.8229 (t0) cc_final: 0.7869 (t0) REVERT: F 406 GLU cc_start: 0.8145 (OUTLIER) cc_final: 0.7882 (tt0) REVERT: F 453 TYR cc_start: 0.8412 (p90) cc_final: 0.8029 (p90) outliers start: 10 outliers final: 8 residues processed: 58 average time/residue: 0.1511 time to fit residues: 10.9336 Evaluate side-chains 59 residues out of total 347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 50 time to evaluate : 0.313 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 57 SER Chi-restraints excluded: chain H residue 116 VAL Chi-restraints excluded: chain K residue 31 SER Chi-restraints excluded: chain K residue 96 SER Chi-restraints excluded: chain K residue 104 THR Chi-restraints excluded: chain F residue 393 THR Chi-restraints excluded: chain F residue 406 GLU Chi-restraints excluded: chain F residue 415 THR Chi-restraints excluded: chain F residue 422 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 2 optimal weight: 0.0050 chunk 0 optimal weight: 0.5980 chunk 11 optimal weight: 0.9980 chunk 1 optimal weight: 0.9990 chunk 4 optimal weight: 0.8980 chunk 23 optimal weight: 0.2980 chunk 33 optimal weight: 0.6980 chunk 30 optimal weight: 0.0770 chunk 7 optimal weight: 0.5980 chunk 26 optimal weight: 0.9990 chunk 10 optimal weight: 0.0970 overall best weight: 0.2150 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 422 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3810 r_free = 0.3810 target = 0.140063 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3597 r_free = 0.3597 target = 0.123627 restraints weight = 4471.653| |-----------------------------------------------------------------------------| r_work (start): 0.3584 rms_B_bonded: 2.08 r_work: 0.3478 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.3314 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.3314 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7422 moved from start: 0.2068 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 3287 Z= 0.159 Angle : 0.534 5.392 4466 Z= 0.285 Chirality : 0.044 0.155 474 Planarity : 0.003 0.034 582 Dihedral : 4.631 22.386 458 Min Nonbonded Distance : 2.614 Molprobity Statistics. All-atom Clashscore : 7.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.96 % Favored : 94.04 % Rotamer: Outliers : 2.88 % Allowed : 13.54 % Favored : 83.57 % 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: -1.73 (0.40), residues: 403 helix: -3.16 (0.73), residues: 27 sheet: 0.06 (0.48), residues: 121 loop : -1.60 (0.36), residues: 255 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP F 436 HIS 0.003 0.001 HIS H 100 PHE 0.013 0.001 PHE F 377 TYR 0.010 0.001 TYR F 423 ARG 0.002 0.000 ARG F 355 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2158.75 seconds wall clock time: 38 minutes 51.32 seconds (2331.32 seconds total)