Starting phenix.real_space_refine on Fri Dec 27 07:18:26 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7wee_32448/12_2024/7wee_32448.cif Found real_map, /net/cci-nas-00/data/ceres_data/7wee_32448/12_2024/7wee_32448.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7wee_32448/12_2024/7wee_32448.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7wee_32448/12_2024/7wee_32448.map" model { file = "/net/cci-nas-00/data/ceres_data/7wee_32448/12_2024/7wee_32448.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7wee_32448/12_2024/7wee_32448.cif" } resolution = 4.0 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= 0.003 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 14 5.16 5 C 2139 2.51 5 N 560 2.21 5 O 637 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 10 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/chem_data/mon_lib" Total number of atoms: 3350 Number of models: 1 Model: "" Number of chains: 3 Chain: "E" Number of atoms: 1612 Number of conformers: 1 Conformer: "" Number of residues, atoms: 201, 1612 Classifications: {'peptide': 201} Link IDs: {'PTRANS': 12, 'TRANS': 188} Chain: "H" Number of atoms: 938 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 938 Classifications: {'peptide': 119} Link IDs: {'PTRANS': 7, 'TRANS': 111} Chain: "L" Number of atoms: 800 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 800 Classifications: {'peptide': 109} Link IDs: {'PTRANS': 5, 'TRANS': 103} Time building chain proxies: 3.58, per 1000 atoms: 1.07 Number of scatterers: 3350 At special positions: 0 Unit cell: (87.74, 66.34, 100.58, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 14 16.00 O 637 8.00 N 560 7.00 C 2139 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, 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=2.03 Simple disulfide: pdb=" SG CYS E 391 " - pdb=" SG CYS E 525 " distance=2.03 Simple disulfide: pdb=" SG CYS E 480 " - pdb=" SG CYS E 488 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 97 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 91 " distance=2.04 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: 0.84 Conformation dependent library (CDL) restraints added in 442.3 milliseconds 846 Ramachandran restraints generated. 423 Oldfield, 0 Emsley, 423 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 792 Finding SS restraints... Secondary structure from input PDB file: 7 helices and 8 sheets defined 8.2% alpha, 31.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.47 Creating SS restraints... Processing helix chain 'E' and resid 338 through 343 Processing helix chain 'E' and resid 349 through 353 removed outlier: 3.842A pdb=" N TRP E 353 " --> pdb=" O VAL E 350 " (cutoff:3.500A) Processing helix chain 'E' and resid 383 through 387 Processing helix chain 'E' and resid 405 through 407 No H-bonds generated for 'chain 'E' and resid 405 through 407' Processing helix chain 'E' and resid 438 through 443 removed outlier: 3.911A pdb=" N SER E 443 " --> pdb=" O ASN E 439 " (cutoff:3.500A) Processing helix chain 'H' and resid 88 through 92 removed outlier: 3.727A pdb=" N THR H 92 " --> pdb=" O PRO H 89 " (cutoff:3.500A) Processing helix chain 'L' and resid 82 through 86 Processing sheet with id=AA1, first strand: chain 'E' and resid 354 through 358 removed outlier: 4.321A pdb=" N ASN E 354 " --> pdb=" O SER E 399 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N SER E 399 " --> pdb=" O ASN E 354 " (cutoff:3.500A) removed outlier: 6.461A pdb=" N CYS E 361 " --> pdb=" O CYS E 525 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'E' and resid 354 through 358 removed outlier: 4.321A pdb=" N ASN E 354 " --> pdb=" O SER E 399 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N SER E 399 " --> pdb=" O ASN E 354 " (cutoff:3.500A) removed outlier: 4.860A pdb=" N ASN E 394 " --> pdb=" O GLU E 516 " (cutoff:3.500A) removed outlier: 4.218A pdb=" N GLU E 516 " --> pdb=" O ASN E 394 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N CYS E 432 " --> pdb=" O LEU E 513 " (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 Processing sheet with id=AA5, first strand: chain 'H' and resid 3 through 7 Processing sheet with id=AA6, first strand: chain 'H' and resid 11 through 12 removed outlier: 3.984A pdb=" N ALA H 51 " --> pdb=" O TRP H 38 " (cutoff:3.500A) removed outlier: 6.532A pdb=" N ARG H 40 " --> pdb=" O TRP H 49 " (cutoff:3.500A) removed outlier: 5.029A pdb=" N TRP H 49 " --> pdb=" O ARG H 40 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N ARG H 60 " --> pdb=" O LEU H 52 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'L' and resid 10 through 12 removed outlier: 7.354A pdb=" N VAL L 11 " --> pdb=" O LEU L 109 " (cutoff:3.500A) removed outlier: 6.631A pdb=" N GLN L 40 " --> pdb=" O LEU L 49 " (cutoff:3.500A) removed outlier: 6.086A pdb=" N LEU L 49 " --> pdb=" O GLN L 40 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'L' and resid 19 through 24 97 hydrogen bonds defined for protein. 228 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: 0.91 Time building geometry restraints manager: 0.99 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 1057 1.34 - 1.46: 864 1.46 - 1.58: 1503 1.58 - 1.69: 1 1.69 - 1.81: 16 Bond restraints: 3441 Sorted by residual: bond pdb=" CG PRO H 9 " pdb=" CD PRO H 9 " ideal model delta sigma weight residual 1.503 1.344 0.159 3.40e-02 8.65e+02 2.18e+01 bond pdb=" CB PRO H 9 " pdb=" CG PRO H 9 " ideal model delta sigma weight residual 1.492 1.672 -0.180 5.00e-02 4.00e+02 1.30e+01 bond pdb=" N PRO H 9 " pdb=" CD PRO H 9 " ideal model delta sigma weight residual 1.473 1.509 -0.036 1.40e-02 5.10e+03 6.63e+00 bond pdb=" N PRO H 9 " pdb=" CA PRO H 9 " ideal model delta sigma weight residual 1.469 1.448 0.021 1.28e-02 6.10e+03 2.71e+00 bond pdb=" CA ASN H 86 " pdb=" CB ASN H 86 " ideal model delta sigma weight residual 1.527 1.542 -0.015 1.61e-02 3.86e+03 8.50e-01 ... (remaining 3436 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.22: 4664 3.22 - 6.45: 21 6.45 - 9.67: 2 9.67 - 12.90: 1 12.90 - 16.12: 2 Bond angle restraints: 4690 Sorted by residual: angle pdb=" CA PRO H 9 " pdb=" N PRO H 9 " pdb=" CD PRO H 9 " ideal model delta sigma weight residual 112.00 95.88 16.12 1.40e+00 5.10e-01 1.33e+02 angle pdb=" N PRO H 9 " pdb=" CD PRO H 9 " pdb=" CG PRO H 9 " ideal model delta sigma weight residual 103.20 91.07 12.13 1.50e+00 4.44e-01 6.54e+01 angle pdb=" N ILE E 418 " pdb=" CA ILE E 418 " pdb=" C ILE E 418 " ideal model delta sigma weight residual 113.53 108.95 4.58 9.80e-01 1.04e+00 2.19e+01 angle pdb=" CA PRO H 9 " pdb=" CB PRO H 9 " pdb=" CG PRO H 9 " ideal model delta sigma weight residual 104.50 96.01 8.49 1.90e+00 2.77e-01 2.00e+01 angle pdb=" N PRO H 9 " pdb=" CA PRO H 9 " pdb=" CB PRO H 9 " ideal model delta sigma weight residual 103.25 99.58 3.67 1.05e+00 9.07e-01 1.22e+01 ... (remaining 4685 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.10: 1760 14.10 - 28.20: 193 28.20 - 42.29: 61 42.29 - 56.39: 12 56.39 - 70.49: 1 Dihedral angle restraints: 2027 sinusoidal: 782 harmonic: 1245 Sorted by residual: dihedral pdb=" CB CYS L 23 " pdb=" SG CYS L 23 " pdb=" SG CYS L 91 " pdb=" CB CYS L 91 " ideal model delta sinusoidal sigma weight residual 93.00 22.51 70.49 1 1.00e+01 1.00e-02 6.39e+01 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 93.00 130.56 -37.56 1 1.00e+01 1.00e-02 1.99e+01 dihedral pdb=" CA LEU E 517 " pdb=" C LEU E 517 " pdb=" N LEU E 518 " pdb=" CA LEU E 518 " ideal model delta harmonic sigma weight residual 180.00 158.07 21.93 0 5.00e+00 4.00e-02 1.92e+01 ... (remaining 2024 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.039: 358 0.039 - 0.079: 114 0.079 - 0.118: 37 0.118 - 0.157: 6 0.157 - 0.197: 2 Chirality restraints: 517 Sorted by residual: chirality pdb=" CB THR E 333 " pdb=" CA THR E 333 " pdb=" OG1 THR E 333 " pdb=" CG2 THR E 333 " both_signs ideal model delta sigma weight residual False 2.55 2.35 0.20 2.00e-01 2.50e+01 9.68e-01 chirality pdb=" CA PRO H 9 " pdb=" N PRO H 9 " pdb=" C PRO H 9 " pdb=" CB PRO H 9 " both_signs ideal model delta sigma weight residual False 2.72 2.54 0.18 2.00e-01 2.50e+01 7.89e-01 chirality pdb=" CA ASN H 86 " pdb=" N ASN H 86 " pdb=" C ASN H 86 " pdb=" CB ASN H 86 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.15 2.00e-01 2.50e+01 5.93e-01 ... (remaining 514 not shown) Planarity restraints: 600 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLY H 8 " 0.056 5.00e-02 4.00e+02 7.59e-02 9.21e+00 pdb=" N PRO H 9 " -0.131 5.00e-02 4.00e+02 pdb=" CA PRO H 9 " 0.033 5.00e-02 4.00e+02 pdb=" CD PRO H 9 " 0.042 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP H 88 " -0.034 5.00e-02 4.00e+02 5.09e-02 4.14e+00 pdb=" N PRO H 89 " 0.088 5.00e-02 4.00e+02 pdb=" CA PRO H 89 " -0.026 5.00e-02 4.00e+02 pdb=" CD PRO H 89 " -0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE E 490 " 0.023 5.00e-02 4.00e+02 3.46e-02 1.91e+00 pdb=" N PRO E 491 " -0.060 5.00e-02 4.00e+02 pdb=" CA PRO E 491 " 0.018 5.00e-02 4.00e+02 pdb=" CD PRO E 491 " 0.019 5.00e-02 4.00e+02 ... (remaining 597 not shown) Histogram of nonbonded interaction distances: 2.12 - 2.67: 50 2.67 - 3.23: 3069 3.23 - 3.79: 4699 3.79 - 4.34: 6398 4.34 - 4.90: 10716 Nonbonded interactions: 24932 Sorted by model distance: nonbonded pdb=" OG1 THR L 95 " pdb=" O SER L 98 " model vdw 2.116 3.040 nonbonded pdb=" OG1 THR H 104 " pdb=" OD1 ASP H 107 " model vdw 2.212 3.040 nonbonded pdb=" OG SER E 349 " pdb=" O LEU E 452 " model vdw 2.266 3.040 nonbonded pdb=" OG SER L 70 " pdb=" OG1 THR L 73 " model vdw 2.276 3.040 nonbonded pdb=" OG SER H 7 " pdb=" OG1 THR H 21 " model vdw 2.285 3.040 ... (remaining 24927 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.550 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.140 Check model and map are aligned: 0.020 Set scattering table: 0.040 Process input model: 15.100 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.020 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:3.320 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.250 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7807 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 : 0.005 0.180 3441 Z= 0.345 Angle : 0.720 16.124 4690 Z= 0.408 Chirality : 0.044 0.197 517 Planarity : 0.005 0.076 600 Dihedral : 12.682 54.785 1217 Min Nonbonded Distance : 2.116 Molprobity Statistics. All-atom Clashscore : 8.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.49 % Favored : 95.51 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % 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: -1.60 (0.40), residues: 423 helix: -3.73 (0.83), residues: 21 sheet: -0.23 (0.42), residues: 141 loop : -1.33 (0.38), residues: 261 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP E 436 HIS 0.005 0.001 HIS L 41 PHE 0.011 0.001 PHE L 65 TYR 0.011 0.001 TYR E 501 ARG 0.005 0.000 ARG L 45 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 846 Ramachandran restraints generated. 423 Oldfield, 0 Emsley, 423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 846 Ramachandran restraints generated. 423 Oldfield, 0 Emsley, 423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 64 residues out of total 371 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 64 time to evaluate : 0.402 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 389 ASP cc_start: 0.7649 (p0) cc_final: 0.6915 (p0) outliers start: 0 outliers final: 0 residues processed: 64 average time/residue: 0.1131 time to fit residues: 9.6884 Evaluate side-chains 52 residues out of total 371 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 52 time to evaluate : 0.398 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 34 optimal weight: 9.9990 chunk 31 optimal weight: 5.9990 chunk 17 optimal weight: 7.9990 chunk 10 optimal weight: 2.9990 chunk 20 optimal weight: 9.9990 chunk 16 optimal weight: 2.9990 chunk 32 optimal weight: 6.9990 chunk 12 optimal weight: 0.8980 chunk 19 optimal weight: 0.9980 chunk 23 optimal weight: 9.9990 chunk 37 optimal weight: 9.9990 overall best weight: 2.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7994 moved from start: 0.1538 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.076 3441 Z= 0.407 Angle : 0.694 8.465 4690 Z= 0.368 Chirality : 0.048 0.149 517 Planarity : 0.005 0.050 600 Dihedral : 5.436 26.740 470 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 8.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.75 % Favored : 91.25 % Rotamer: Outliers : 1.62 % Allowed : 11.86 % Favored : 86.52 % 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: -1.60 (0.41), residues: 423 helix: -3.45 (0.85), residues: 26 sheet: -0.18 (0.40), residues: 152 loop : -1.38 (0.41), residues: 245 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP E 436 HIS 0.002 0.001 HIS L 100 PHE 0.017 0.002 PHE E 429 TYR 0.015 0.002 TYR L 52 ARG 0.002 0.000 ARG E 454 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 846 Ramachandran restraints generated. 423 Oldfield, 0 Emsley, 423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 846 Ramachandran restraints generated. 423 Oldfield, 0 Emsley, 423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 58 residues out of total 371 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 52 time to evaluate : 0.392 Fit side-chains REVERT: E 389 ASP cc_start: 0.7935 (p0) cc_final: 0.7334 (p0) REVERT: E 474 GLN cc_start: 0.7318 (pp30) cc_final: 0.6918 (pp30) REVERT: H 45 LYS cc_start: 0.8493 (ptmm) cc_final: 0.8128 (ptmm) REVERT: L 108 LYS cc_start: 0.8018 (tppt) cc_final: 0.7628 (tptt) outliers start: 6 outliers final: 4 residues processed: 54 average time/residue: 0.1341 time to fit residues: 9.3160 Evaluate side-chains 53 residues out of total 371 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 49 time to evaluate : 0.377 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 47 LEU Chi-restraints excluded: chain H residue 71 ILE Chi-restraints excluded: chain L residue 40 GLN Chi-restraints excluded: chain L residue 63 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 20 optimal weight: 5.9990 chunk 11 optimal weight: 6.9990 chunk 30 optimal weight: 1.9990 chunk 25 optimal weight: 0.6980 chunk 10 optimal weight: 0.9990 chunk 37 optimal weight: 9.9990 chunk 40 optimal weight: 6.9990 chunk 33 optimal weight: 5.9990 chunk 36 optimal weight: 5.9990 chunk 12 optimal weight: 0.8980 chunk 29 optimal weight: 4.9990 overall best weight: 1.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7987 moved from start: 0.1782 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 3441 Z= 0.285 Angle : 0.637 7.303 4690 Z= 0.333 Chirality : 0.045 0.146 517 Planarity : 0.005 0.052 600 Dihedral : 5.394 27.347 470 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 7.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.09 % Favored : 92.91 % Rotamer: Outliers : 2.43 % Allowed : 16.71 % Favored : 80.86 % 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: -1.53 (0.40), residues: 423 helix: -3.62 (0.92), residues: 20 sheet: -0.14 (0.40), residues: 152 loop : -1.38 (0.40), residues: 251 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP E 436 HIS 0.002 0.001 HIS E 505 PHE 0.014 0.002 PHE L 103 TYR 0.014 0.002 TYR L 52 ARG 0.002 0.000 ARG E 466 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 846 Ramachandran restraints generated. 423 Oldfield, 0 Emsley, 423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 846 Ramachandran restraints generated. 423 Oldfield, 0 Emsley, 423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 63 residues out of total 371 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 54 time to evaluate : 0.409 Fit side-chains revert: symmetry clash REVERT: E 389 ASP cc_start: 0.8027 (p0) cc_final: 0.7512 (p0) REVERT: E 474 GLN cc_start: 0.7260 (pp30) cc_final: 0.6847 (pp30) REVERT: H 45 LYS cc_start: 0.8428 (ptmm) cc_final: 0.8166 (ptmm) REVERT: L 108 LYS cc_start: 0.8128 (tppt) cc_final: 0.7866 (tptp) outliers start: 9 outliers final: 8 residues processed: 60 average time/residue: 0.1123 time to fit residues: 8.9607 Evaluate side-chains 64 residues out of total 371 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 56 time to evaluate : 0.425 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 430 THR Chi-restraints excluded: chain E residue 503 VAL Chi-restraints excluded: chain H residue 3 THR Chi-restraints excluded: chain H residue 47 LEU Chi-restraints excluded: chain H residue 71 ILE Chi-restraints excluded: chain L residue 30 VAL Chi-restraints excluded: chain L residue 40 GLN Chi-restraints excluded: chain L residue 63 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 36 optimal weight: 0.4980 chunk 28 optimal weight: 5.9990 chunk 19 optimal weight: 2.9990 chunk 4 optimal weight: 0.2980 chunk 17 optimal weight: 0.7980 chunk 25 optimal weight: 3.9990 chunk 37 optimal weight: 9.9990 chunk 39 optimal weight: 7.9990 chunk 35 optimal weight: 8.9990 chunk 10 optimal weight: 0.8980 chunk 33 optimal weight: 8.9990 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7947 moved from start: 0.1876 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 3441 Z= 0.198 Angle : 0.599 7.610 4690 Z= 0.310 Chirality : 0.044 0.144 517 Planarity : 0.005 0.056 600 Dihedral : 5.088 26.561 470 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 7.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.38 % Favored : 93.62 % Rotamer: Outliers : 2.70 % Allowed : 19.14 % Favored : 78.17 % 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: -1.51 (0.41), residues: 423 helix: -3.56 (0.80), residues: 27 sheet: -0.13 (0.40), residues: 153 loop : -1.28 (0.41), residues: 243 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP E 436 HIS 0.001 0.001 HIS L 41 PHE 0.013 0.001 PHE L 65 TYR 0.011 0.001 TYR E 380 ARG 0.001 0.000 ARG E 466 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 846 Ramachandran restraints generated. 423 Oldfield, 0 Emsley, 423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 846 Ramachandran restraints generated. 423 Oldfield, 0 Emsley, 423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 371 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 63 time to evaluate : 0.385 Fit side-chains revert: symmetry clash REVERT: E 389 ASP cc_start: 0.8016 (p0) cc_final: 0.7442 (p0) REVERT: E 474 GLN cc_start: 0.7230 (pp30) cc_final: 0.6753 (pp30) REVERT: H 45 LYS cc_start: 0.8338 (ptmm) cc_final: 0.8110 (ptmm) REVERT: L 108 LYS cc_start: 0.8098 (tppt) cc_final: 0.7897 (tptp) outliers start: 10 outliers final: 8 residues processed: 70 average time/residue: 0.1118 time to fit residues: 10.4615 Evaluate side-chains 66 residues out of total 371 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 58 time to evaluate : 0.403 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 333 THR Chi-restraints excluded: chain E residue 430 THR Chi-restraints excluded: chain E residue 503 VAL Chi-restraints excluded: chain H residue 3 THR Chi-restraints excluded: chain H residue 47 LEU Chi-restraints excluded: chain L residue 30 VAL Chi-restraints excluded: chain L residue 40 GLN Chi-restraints excluded: chain L residue 63 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 22 optimal weight: 3.9990 chunk 0 optimal weight: 3.9990 chunk 29 optimal weight: 0.6980 chunk 16 optimal weight: 0.9990 chunk 33 optimal weight: 6.9990 chunk 27 optimal weight: 3.9990 chunk 20 optimal weight: 10.0000 chunk 35 optimal weight: 4.9990 chunk 10 optimal weight: 4.9990 chunk 13 optimal weight: 0.8980 chunk 7 optimal weight: 0.9990 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7971 moved from start: 0.2109 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 3441 Z= 0.238 Angle : 0.609 6.961 4690 Z= 0.318 Chirality : 0.045 0.154 517 Planarity : 0.005 0.061 600 Dihedral : 5.176 26.366 470 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 6.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.62 % Favored : 93.38 % Rotamer: Outliers : 3.23 % Allowed : 22.91 % Favored : 73.85 % 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: -1.43 (0.41), residues: 423 helix: -3.52 (0.81), residues: 26 sheet: 0.04 (0.41), residues: 149 loop : -1.31 (0.41), residues: 248 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP E 436 HIS 0.001 0.001 HIS L 42 PHE 0.010 0.001 PHE H 24 TYR 0.012 0.001 TYR L 52 ARG 0.002 0.000 ARG E 454 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 846 Ramachandran restraints generated. 423 Oldfield, 0 Emsley, 423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 846 Ramachandran restraints generated. 423 Oldfield, 0 Emsley, 423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 69 residues out of total 371 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 57 time to evaluate : 0.364 Fit side-chains revert: symmetry clash REVERT: E 389 ASP cc_start: 0.7991 (p0) cc_final: 0.7501 (p0) REVERT: E 474 GLN cc_start: 0.7158 (pp30) cc_final: 0.6684 (pp30) REVERT: E 518 LEU cc_start: 0.4543 (OUTLIER) cc_final: 0.4313 (tp) outliers start: 12 outliers final: 10 residues processed: 66 average time/residue: 0.1138 time to fit residues: 10.0436 Evaluate side-chains 65 residues out of total 371 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 54 time to evaluate : 0.409 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 333 THR Chi-restraints excluded: chain E residue 430 THR Chi-restraints excluded: chain E residue 503 VAL Chi-restraints excluded: chain E residue 518 LEU Chi-restraints excluded: chain H residue 3 THR Chi-restraints excluded: chain H residue 47 LEU Chi-restraints excluded: chain H residue 71 ILE Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 30 VAL Chi-restraints excluded: chain L residue 40 GLN Chi-restraints excluded: chain L residue 63 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 23 optimal weight: 5.9990 chunk 9 optimal weight: 4.9990 chunk 39 optimal weight: 9.9990 chunk 32 optimal weight: 7.9990 chunk 18 optimal weight: 0.6980 chunk 3 optimal weight: 0.6980 chunk 13 optimal weight: 1.9990 chunk 20 optimal weight: 5.9990 chunk 38 optimal weight: 5.9990 chunk 4 optimal weight: 3.9990 chunk 22 optimal weight: 0.9990 overall best weight: 1.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 111 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7985 moved from start: 0.2264 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 3441 Z= 0.255 Angle : 0.623 7.639 4690 Z= 0.324 Chirality : 0.045 0.166 517 Planarity : 0.005 0.053 600 Dihedral : 5.261 26.753 470 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 7.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.33 % Favored : 92.67 % Rotamer: Outliers : 4.04 % Allowed : 24.26 % Favored : 71.70 % 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 (0.41), residues: 423 helix: -3.53 (0.81), residues: 26 sheet: 0.09 (0.43), residues: 143 loop : -1.38 (0.40), residues: 254 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP E 436 HIS 0.001 0.001 HIS E 505 PHE 0.012 0.001 PHE E 515 TYR 0.013 0.001 TYR L 52 ARG 0.002 0.000 ARG E 454 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 846 Ramachandran restraints generated. 423 Oldfield, 0 Emsley, 423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 846 Ramachandran restraints generated. 423 Oldfield, 0 Emsley, 423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 74 residues out of total 371 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 59 time to evaluate : 0.420 Fit side-chains REVERT: E 379 CYS cc_start: 0.5818 (m) cc_final: 0.5552 (m) REVERT: E 389 ASP cc_start: 0.8037 (p0) cc_final: 0.7544 (p0) REVERT: E 474 GLN cc_start: 0.7183 (pp30) cc_final: 0.6802 (pp30) REVERT: L 103 PHE cc_start: 0.4385 (OUTLIER) cc_final: 0.3634 (m-10) outliers start: 15 outliers final: 11 residues processed: 71 average time/residue: 0.0975 time to fit residues: 9.2716 Evaluate side-chains 65 residues out of total 371 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 53 time to evaluate : 0.401 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 333 THR Chi-restraints excluded: chain E residue 335 LEU Chi-restraints excluded: chain E residue 430 THR Chi-restraints excluded: chain E residue 503 VAL Chi-restraints excluded: chain H residue 3 THR Chi-restraints excluded: chain H residue 47 LEU Chi-restraints excluded: chain H residue 71 ILE Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 30 VAL Chi-restraints excluded: chain L residue 40 GLN Chi-restraints excluded: chain L residue 63 ASN Chi-restraints excluded: chain L residue 103 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 28 optimal weight: 6.9990 chunk 22 optimal weight: 2.9990 chunk 33 optimal weight: 20.0000 chunk 39 optimal weight: 10.0000 chunk 24 optimal weight: 5.9990 chunk 18 optimal weight: 0.9980 chunk 15 optimal weight: 0.2980 chunk 23 optimal weight: 0.8980 chunk 11 optimal weight: 4.9990 chunk 7 optimal weight: 0.9990 chunk 25 optimal weight: 0.9990 overall best weight: 0.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7938 moved from start: 0.2349 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 3441 Z= 0.173 Angle : 0.614 11.435 4690 Z= 0.311 Chirality : 0.044 0.171 517 Planarity : 0.004 0.056 600 Dihedral : 5.016 24.444 470 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 8.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.44 % Favored : 94.56 % Rotamer: Outliers : 2.70 % Allowed : 25.61 % Favored : 71.70 % 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: -1.43 (0.41), residues: 423 helix: -3.52 (0.79), residues: 26 sheet: 0.09 (0.43), residues: 146 loop : -1.33 (0.40), residues: 251 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP E 436 HIS 0.001 0.001 HIS L 42 PHE 0.011 0.001 PHE H 24 TYR 0.010 0.001 TYR E 501 ARG 0.001 0.000 ARG E 509 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 846 Ramachandran restraints generated. 423 Oldfield, 0 Emsley, 423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 846 Ramachandran restraints generated. 423 Oldfield, 0 Emsley, 423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 68 residues out of total 371 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 58 time to evaluate : 0.388 Fit side-chains revert: symmetry clash REVERT: E 389 ASP cc_start: 0.7963 (p0) cc_final: 0.7482 (p0) REVERT: E 474 GLN cc_start: 0.7142 (pp30) cc_final: 0.6658 (pp30) REVERT: L 103 PHE cc_start: 0.3808 (OUTLIER) cc_final: 0.2924 (m-10) outliers start: 10 outliers final: 7 residues processed: 65 average time/residue: 0.1015 time to fit residues: 8.9214 Evaluate side-chains 64 residues out of total 371 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 56 time to evaluate : 0.393 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 333 THR Chi-restraints excluded: chain E residue 430 THR Chi-restraints excluded: chain H residue 47 LEU Chi-restraints excluded: chain H residue 71 ILE Chi-restraints excluded: chain L residue 30 VAL Chi-restraints excluded: chain L residue 40 GLN Chi-restraints excluded: chain L residue 63 ASN Chi-restraints excluded: chain L residue 103 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 26 optimal weight: 6.9990 chunk 19 optimal weight: 0.7980 chunk 3 optimal weight: 2.9990 chunk 31 optimal weight: 8.9990 chunk 35 optimal weight: 4.9990 chunk 37 optimal weight: 0.3980 chunk 34 optimal weight: 4.9990 chunk 36 optimal weight: 4.9990 chunk 22 optimal weight: 10.0000 chunk 16 optimal weight: 3.9990 chunk 28 optimal weight: 8.9990 overall best weight: 2.6386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8044 moved from start: 0.2674 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.035 3441 Z= 0.373 Angle : 0.706 11.415 4690 Z= 0.367 Chirality : 0.047 0.172 517 Planarity : 0.005 0.055 600 Dihedral : 5.674 25.763 470 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 9.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.22 % Favored : 90.78 % Rotamer: Outliers : 3.50 % Allowed : 25.61 % Favored : 70.89 % 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: -1.55 (0.40), residues: 423 helix: -3.71 (0.89), residues: 20 sheet: 0.06 (0.43), residues: 143 loop : -1.50 (0.38), residues: 260 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP H 38 HIS 0.002 0.001 HIS E 505 PHE 0.015 0.002 PHE E 515 TYR 0.017 0.002 TYR L 52 ARG 0.003 0.000 ARG E 454 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 846 Ramachandran restraints generated. 423 Oldfield, 0 Emsley, 423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 846 Ramachandran restraints generated. 423 Oldfield, 0 Emsley, 423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 62 residues out of total 371 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 49 time to evaluate : 0.369 Fit side-chains revert: symmetry clash REVERT: E 389 ASP cc_start: 0.8144 (p0) cc_final: 0.7655 (p0) REVERT: E 474 GLN cc_start: 0.7255 (pp30) cc_final: 0.6746 (pp30) REVERT: L 103 PHE cc_start: 0.4582 (OUTLIER) cc_final: 0.3545 (m-10) outliers start: 13 outliers final: 10 residues processed: 59 average time/residue: 0.1085 time to fit residues: 8.7512 Evaluate side-chains 59 residues out of total 371 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 48 time to evaluate : 0.387 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 333 THR Chi-restraints excluded: chain E residue 335 LEU Chi-restraints excluded: chain E residue 430 THR Chi-restraints excluded: chain H residue 47 LEU Chi-restraints excluded: chain H residue 71 ILE Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 30 VAL Chi-restraints excluded: chain L residue 40 GLN Chi-restraints excluded: chain L residue 63 ASN Chi-restraints excluded: chain L residue 101 ILE Chi-restraints excluded: chain L residue 103 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 11 optimal weight: 4.9990 chunk 33 optimal weight: 2.9990 chunk 34 optimal weight: 4.9990 chunk 36 optimal weight: 3.9990 chunk 24 optimal weight: 6.9990 chunk 38 optimal weight: 6.9990 chunk 23 optimal weight: 5.9990 chunk 18 optimal weight: 0.8980 chunk 27 optimal weight: 5.9990 chunk 40 optimal weight: 5.9990 chunk 37 optimal weight: 2.9990 overall best weight: 3.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8079 moved from start: 0.3059 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.041 3441 Z= 0.442 Angle : 0.767 12.141 4690 Z= 0.400 Chirality : 0.049 0.162 517 Planarity : 0.005 0.055 600 Dihedral : 6.222 27.935 470 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 10.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.11 % Favored : 88.89 % Rotamer: Outliers : 3.77 % Allowed : 25.88 % Favored : 70.35 % 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: 423 helix: -3.84 (0.86), residues: 20 sheet: 0.42 (0.46), residues: 125 loop : -1.98 (0.36), residues: 278 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP H 49 HIS 0.003 0.001 HIS E 519 PHE 0.017 0.002 PHE E 429 TYR 0.024 0.002 TYR L 52 ARG 0.003 0.000 ARG L 45 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 846 Ramachandran restraints generated. 423 Oldfield, 0 Emsley, 423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 846 Ramachandran restraints generated. 423 Oldfield, 0 Emsley, 423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 64 residues out of total 371 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 50 time to evaluate : 0.367 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 389 ASP cc_start: 0.8161 (p0) cc_final: 0.7632 (p0) REVERT: E 474 GLN cc_start: 0.7305 (pp30) cc_final: 0.6866 (pp30) REVERT: L 103 PHE cc_start: 0.4464 (OUTLIER) cc_final: 0.3307 (m-10) outliers start: 14 outliers final: 11 residues processed: 62 average time/residue: 0.1232 time to fit residues: 9.9570 Evaluate side-chains 59 residues out of total 371 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 47 time to evaluate : 0.415 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 333 THR Chi-restraints excluded: chain E residue 430 THR Chi-restraints excluded: chain E residue 503 VAL Chi-restraints excluded: chain H residue 47 LEU Chi-restraints excluded: chain H residue 71 ILE Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 30 VAL Chi-restraints excluded: chain L residue 40 GLN Chi-restraints excluded: chain L residue 42 HIS Chi-restraints excluded: chain L residue 63 ASN Chi-restraints excluded: chain L residue 101 ILE Chi-restraints excluded: chain L residue 103 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 32 optimal weight: 10.0000 chunk 3 optimal weight: 0.0770 chunk 25 optimal weight: 0.9980 chunk 19 optimal weight: 0.6980 chunk 34 optimal weight: 5.9990 chunk 9 optimal weight: 0.6980 chunk 29 optimal weight: 7.9990 chunk 4 optimal weight: 3.9990 chunk 13 optimal weight: 0.8980 chunk 33 optimal weight: 10.0000 chunk 6 optimal weight: 1.9990 overall best weight: 0.6738 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7946 moved from start: 0.2784 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 3441 Z= 0.165 Angle : 0.637 10.486 4690 Z= 0.323 Chirality : 0.045 0.163 517 Planarity : 0.004 0.052 600 Dihedral : 5.246 24.069 470 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 8.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.15 % Favored : 93.85 % Rotamer: Outliers : 2.70 % Allowed : 26.95 % Favored : 70.35 % 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: -1.79 (0.40), residues: 423 helix: -3.54 (0.78), residues: 26 sheet: -0.06 (0.43), residues: 146 loop : -1.68 (0.39), residues: 251 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP E 353 HIS 0.001 0.000 HIS E 519 PHE 0.011 0.001 PHE H 24 TYR 0.012 0.001 TYR E 380 ARG 0.001 0.000 ARG L 64 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 846 Ramachandran restraints generated. 423 Oldfield, 0 Emsley, 423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 846 Ramachandran restraints generated. 423 Oldfield, 0 Emsley, 423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 68 residues out of total 371 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 58 time to evaluate : 0.529 Fit side-chains revert: symmetry clash REVERT: E 389 ASP cc_start: 0.7985 (p0) cc_final: 0.7517 (p0) REVERT: E 425 LEU cc_start: 0.9228 (mp) cc_final: 0.9024 (mp) REVERT: E 474 GLN cc_start: 0.7099 (pp30) cc_final: 0.6606 (pp30) REVERT: L 54 VAL cc_start: 0.5788 (m) cc_final: 0.5514 (m) REVERT: L 103 PHE cc_start: 0.4071 (OUTLIER) cc_final: 0.3081 (m-10) outliers start: 10 outliers final: 9 residues processed: 66 average time/residue: 0.1194 time to fit residues: 10.6450 Evaluate side-chains 67 residues out of total 371 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 57 time to evaluate : 0.457 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 333 THR Chi-restraints excluded: chain E residue 430 THR Chi-restraints excluded: chain E residue 503 VAL Chi-restraints excluded: chain H residue 47 LEU Chi-restraints excluded: chain H residue 71 ILE Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 30 VAL Chi-restraints excluded: chain L residue 40 GLN Chi-restraints excluded: chain L residue 63 ASN Chi-restraints excluded: chain L residue 103 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 28 optimal weight: 7.9990 chunk 1 optimal weight: 3.9990 chunk 23 optimal weight: 5.9990 chunk 37 optimal weight: 10.0000 chunk 21 optimal weight: 3.9990 chunk 27 optimal weight: 2.9990 chunk 26 optimal weight: 5.9990 chunk 24 optimal weight: 0.8980 chunk 16 optimal weight: 4.9990 chunk 15 optimal weight: 1.9990 chunk 40 optimal weight: 0.5980 overall best weight: 2.0986 ------------------------------------------------------------------------------- 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 = 0.3724 r_free = 0.3724 target = 0.124738 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.098639 restraints weight = 6795.692| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.095948 restraints weight = 10506.604| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.093778 restraints weight = 9358.202| |-----------------------------------------------------------------------------| r_work (final): 0.3266 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7975 moved from start: 0.2892 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.030 3441 Z= 0.316 Angle : 0.702 10.764 4690 Z= 0.354 Chirality : 0.046 0.150 517 Planarity : 0.005 0.052 600 Dihedral : 5.536 24.916 470 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 9.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.46 % Favored : 90.54 % Rotamer: Outliers : 2.70 % Allowed : 27.76 % Favored : 69.54 % 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: -1.75 (0.40), residues: 423 helix: -3.73 (0.87), residues: 20 sheet: 0.00 (0.44), residues: 143 loop : -1.70 (0.38), residues: 260 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP E 436 HIS 0.002 0.001 HIS E 505 PHE 0.012 0.002 PHE E 429 TYR 0.012 0.002 TYR L 52 ARG 0.002 0.000 ARG E 454 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1132.98 seconds wall clock time: 21 minutes 54.13 seconds (1314.13 seconds total)