Starting phenix.real_space_refine on Fri Dec 27 06:42:36 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7wcu_32429/12_2024/7wcu_32429.cif Found real_map, /net/cci-nas-00/data/ceres_data/7wcu_32429/12_2024/7wcu_32429.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.09 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7wcu_32429/12_2024/7wcu_32429.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7wcu_32429/12_2024/7wcu_32429.map" model { file = "/net/cci-nas-00/data/ceres_data/7wcu_32429/12_2024/7wcu_32429.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7wcu_32429/12_2024/7wcu_32429.cif" } resolution = 3.09 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= 0.038 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 15 5.16 5 C 2053 2.51 5 N 553 2.21 5 O 627 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 26 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: 3248 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 926 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 926 Classifications: {'peptide': 119} Link IDs: {'PTRANS': 3, 'TRANS': 115} Chain: "B" Number of atoms: 826 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 826 Classifications: {'peptide': 109} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 103} Chain: "R" Number of atoms: 1496 Number of conformers: 1 Conformer: "" Number of residues, atoms: 188, 1496 Classifications: {'peptide': 188} Link IDs: {'PTRANS': 9, 'TRANS': 178} Chain breaks: 1 Time building chain proxies: 3.79, per 1000 atoms: 1.17 Number of scatterers: 3248 At special positions: 0 Unit cell: (85.32, 63.72, 87.48, 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 15 16.00 O 627 8.00 N 553 7.00 C 2053 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS A 22 " - pdb=" SG CYS A 95 " distance=2.03 Simple disulfide: pdb=" SG CYS B 23 " - pdb=" SG CYS B 88 " distance=2.04 Simple disulfide: pdb=" SG CYS R 336 " - pdb=" SG CYS R 361 " distance=2.03 Simple disulfide: pdb=" SG CYS R 379 " - pdb=" SG CYS R 432 " distance=2.06 Simple disulfide: pdb=" SG CYS R 391 " - pdb=" SG CYS R 525 " distance=2.04 Simple disulfide: pdb=" SG CYS R 480 " - pdb=" SG CYS R 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: 0.73 Conformation dependent library (CDL) restraints added in 389.5 milliseconds 816 Ramachandran restraints generated. 408 Oldfield, 0 Emsley, 408 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 756 Finding SS restraints... Secondary structure from input PDB file: 9 helices and 8 sheets defined 11.8% alpha, 33.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.44 Creating SS restraints... Processing helix chain 'A' and resid 28 through 32 removed outlier: 3.561A pdb=" N ARG A 31 " --> pdb=" O ILE A 28 " (cutoff:3.500A) Processing helix chain 'A' and resid 86 through 90 removed outlier: 3.864A pdb=" N THR A 90 " --> pdb=" O VAL A 87 " (cutoff:3.500A) Processing helix chain 'B' and resid 79 through 83 removed outlier: 3.505A pdb=" N ASP B 82 " --> pdb=" O GLN B 79 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N SER B 83 " --> pdb=" O SER B 80 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 79 through 83' Processing helix chain 'R' and resid 338 through 343 Processing helix chain 'R' and resid 365 through 370 Processing helix chain 'R' and resid 405 through 410 removed outlier: 4.107A pdb=" N ARG R 408 " --> pdb=" O ASP R 405 " (cutoff:3.500A) Processing helix chain 'R' and resid 417 through 422 Processing helix chain 'R' and resid 438 through 443 removed outlier: 3.609A pdb=" N SER R 443 " --> pdb=" O ASN R 439 " (cutoff:3.500A) Processing helix chain 'R' and resid 502 through 505 Processing sheet with id=AA1, first strand: chain 'A' and resid 3 through 7 removed outlier: 4.022A pdb=" N GLN A 3 " --> pdb=" O SER A 25 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N LEU A 80 " --> pdb=" O LEU A 20 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 11 through 12 removed outlier: 4.296A pdb=" N TYR A 33 " --> pdb=" O ASP A 98 " (cutoff:3.500A) removed outlier: 6.789A pdb=" N MET A 34 " --> pdb=" O VAL A 50 " (cutoff:3.500A) removed outlier: 4.533A pdb=" N VAL A 50 " --> pdb=" O MET A 34 " (cutoff:3.500A) removed outlier: 6.525A pdb=" N TRP A 36 " --> pdb=" O VAL A 48 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 11 through 12 removed outlier: 7.067A pdb=" N CYS A 95 " --> pdb=" O TRP A 107 " (cutoff:3.500A) removed outlier: 4.869A pdb=" N TRP A 107 " --> pdb=" O CYS A 95 " (cutoff:3.500A) removed outlier: 6.939A pdb=" N ARG A 97 " --> pdb=" O ASP A 105 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N TYR A 103 " --> pdb=" O TYR A 99 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 5 through 6 removed outlier: 6.813A pdb=" N THR B 69 " --> pdb=" O ALA B 25 " (cutoff:3.500A) removed outlier: 10.710A pdb=" N GLN B 27 " --> pdb=" O SER B 67 " (cutoff:3.500A) removed outlier: 10.166A pdb=" N SER B 67 " --> pdb=" O GLN B 27 " (cutoff:3.500A) removed outlier: 11.398A pdb=" N VAL B 29 " --> pdb=" O SER B 65 " (cutoff:3.500A) removed outlier: 11.419A pdb=" N SER B 65 " --> pdb=" O VAL B 29 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 10 through 13 removed outlier: 6.894A pdb=" N LEU B 33 " --> pdb=" O TYR B 49 " (cutoff:3.500A) removed outlier: 5.190A pdb=" N TYR B 49 " --> pdb=" O LEU B 33 " (cutoff:3.500A) removed outlier: 6.522A pdb=" N TRP B 35 " --> pdb=" O LEU B 47 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'R' and resid 354 through 358 removed outlier: 3.596A pdb=" N GLY R 431 " --> pdb=" O TYR R 380 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N TYR R 380 " --> pdb=" O GLY R 431 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N VAL R 433 " --> pdb=" O LYS R 378 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N LYS R 378 " --> pdb=" O VAL R 433 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'R' and resid 452 through 454 Processing sheet with id=AA8, first strand: chain 'R' and resid 473 through 474 99 hydrogen bonds defined for protein. 240 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: 0.84 Time building geometry restraints manager: 0.88 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 1053 1.34 - 1.47: 918 1.47 - 1.60: 1335 1.60 - 1.73: 0 1.73 - 1.86: 18 Bond restraints: 3324 Sorted by residual: bond pdb=" CG TYR B 91 " pdb=" CD1 TYR B 91 " ideal model delta sigma weight residual 1.389 1.317 0.072 2.10e-02 2.27e+03 1.17e+01 bond pdb=" CA THR R 430 " pdb=" CB THR R 430 " ideal model delta sigma weight residual 1.529 1.564 -0.035 1.38e-02 5.25e+03 6.41e+00 bond pdb=" CE2 TYR B 91 " pdb=" CZ TYR B 91 " ideal model delta sigma weight residual 1.378 1.335 0.043 2.40e-02 1.74e+03 3.14e+00 bond pdb=" CB GLN R 498 " pdb=" CG GLN R 498 " ideal model delta sigma weight residual 1.520 1.573 -0.053 3.00e-02 1.11e+03 3.14e+00 bond pdb=" CB ASP A 98 " pdb=" CG ASP A 98 " ideal model delta sigma weight residual 1.516 1.472 0.044 2.50e-02 1.60e+03 3.12e+00 ... (remaining 3319 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.74: 4352 2.74 - 5.49: 132 5.49 - 8.23: 19 8.23 - 10.98: 3 10.98 - 13.72: 3 Bond angle restraints: 4509 Sorted by residual: angle pdb=" CA CYS R 432 " pdb=" CB CYS R 432 " pdb=" SG CYS R 432 " ideal model delta sigma weight residual 114.40 128.12 -13.72 2.30e+00 1.89e-01 3.56e+01 angle pdb=" N ASP A 101 " pdb=" CA ASP A 101 " pdb=" C ASP A 101 " ideal model delta sigma weight residual 111.81 104.16 7.65 1.54e+00 4.22e-01 2.47e+01 angle pdb=" CB MET B 4 " pdb=" CG MET B 4 " pdb=" SD MET B 4 " ideal model delta sigma weight residual 112.70 99.26 13.44 3.00e+00 1.11e-01 2.01e+01 angle pdb=" CA PRO A 14 " pdb=" N PRO A 14 " pdb=" CD PRO A 14 " ideal model delta sigma weight residual 112.00 106.09 5.91 1.40e+00 5.10e-01 1.78e+01 angle pdb=" CB GLN R 498 " pdb=" CG GLN R 498 " pdb=" CD GLN R 498 " ideal model delta sigma weight residual 112.60 119.40 -6.80 1.70e+00 3.46e-01 1.60e+01 ... (remaining 4504 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.69: 1691 14.69 - 29.38: 202 29.38 - 44.07: 57 44.07 - 58.75: 5 58.75 - 73.44: 5 Dihedral angle restraints: 1960 sinusoidal: 763 harmonic: 1197 Sorted by residual: dihedral pdb=" CA ASN A 73 " pdb=" C ASN A 73 " pdb=" N SER A 74 " pdb=" CA SER A 74 " ideal model delta harmonic sigma weight residual 180.00 149.82 30.18 0 5.00e+00 4.00e-02 3.64e+01 dihedral pdb=" CA TYR B 91 " pdb=" C TYR B 91 " pdb=" N ASN B 92 " pdb=" CA ASN B 92 " ideal model delta harmonic sigma weight residual -180.00 -150.25 -29.75 0 5.00e+00 4.00e-02 3.54e+01 dihedral pdb=" CB CYS R 379 " pdb=" SG CYS R 379 " pdb=" SG CYS R 432 " pdb=" CB CYS R 432 " ideal model delta sinusoidal sigma weight residual 93.00 44.38 48.62 1 1.00e+01 1.00e-02 3.25e+01 ... (remaining 1957 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.057: 320 0.057 - 0.115: 122 0.115 - 0.172: 31 0.172 - 0.229: 5 0.229 - 0.286: 2 Chirality restraints: 480 Sorted by residual: chirality pdb=" CG LEU B 21 " pdb=" CB LEU B 21 " pdb=" CD1 LEU B 21 " pdb=" CD2 LEU B 21 " both_signs ideal model delta sigma weight residual False -2.59 -2.30 -0.29 2.00e-01 2.50e+01 2.05e+00 chirality pdb=" CB THR B 56 " pdb=" CA THR B 56 " pdb=" OG1 THR B 56 " pdb=" CG2 THR B 56 " both_signs ideal model delta sigma weight residual False 2.55 2.29 0.26 2.00e-01 2.50e+01 1.73e+00 chirality pdb=" CA CYS R 432 " pdb=" N CYS R 432 " pdb=" C CYS R 432 " pdb=" CB CYS R 432 " both_signs ideal model delta sigma weight residual False 2.51 2.31 0.20 2.00e-01 2.50e+01 1.02e+00 ... (remaining 477 not shown) Planarity restraints: 588 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C TYR A 52 " -0.050 5.00e-02 4.00e+02 7.71e-02 9.52e+00 pdb=" N PRO A 53 " 0.133 5.00e-02 4.00e+02 pdb=" CA PRO A 53 " -0.040 5.00e-02 4.00e+02 pdb=" CD PRO A 53 " -0.043 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLN A 13 " 0.051 5.00e-02 4.00e+02 7.38e-02 8.71e+00 pdb=" N PRO A 14 " -0.127 5.00e-02 4.00e+02 pdb=" CA PRO A 14 " 0.036 5.00e-02 4.00e+02 pdb=" CD PRO A 14 " 0.041 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TYR B 91 " -0.022 2.00e-02 2.50e+03 1.81e-02 6.59e+00 pdb=" CG TYR B 91 " 0.045 2.00e-02 2.50e+03 pdb=" CD1 TYR B 91 " -0.007 2.00e-02 2.50e+03 pdb=" CD2 TYR B 91 " -0.006 2.00e-02 2.50e+03 pdb=" CE1 TYR B 91 " -0.003 2.00e-02 2.50e+03 pdb=" CE2 TYR B 91 " -0.003 2.00e-02 2.50e+03 pdb=" CZ TYR B 91 " -0.003 2.00e-02 2.50e+03 pdb=" OH TYR B 91 " -0.000 2.00e-02 2.50e+03 ... (remaining 585 not shown) Histogram of nonbonded interaction distances: 2.29 - 2.81: 995 2.81 - 3.33: 2674 3.33 - 3.86: 5563 3.86 - 4.38: 6357 4.38 - 4.90: 11331 Nonbonded interactions: 26920 Sorted by model distance: nonbonded pdb=" O ASN R 439 " pdb=" OG SER R 443 " model vdw 2.289 3.040 nonbonded pdb=" O ARG A 31 " pdb=" OH TYR R 473 " model vdw 2.336 3.040 nonbonded pdb=" OG SER A 35 " pdb=" O SER A 49 " model vdw 2.336 3.040 nonbonded pdb=" OH TYR A 33 " pdb=" O LEU R 455 " model vdw 2.339 3.040 nonbonded pdb=" OE2 GLU R 406 " pdb=" OH TYR R 495 " model vdw 2.352 3.040 ... (remaining 26915 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: 2.680 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: 13.520 Find NCS groups from input model: 0.040 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:3.030 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.490 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8034 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 : 0.009 0.072 3324 Z= 0.564 Angle : 1.153 13.722 4509 Z= 0.624 Chirality : 0.064 0.286 480 Planarity : 0.007 0.077 588 Dihedral : 13.760 73.442 1186 Min Nonbonded Distance : 2.289 Molprobity Statistics. All-atom Clashscore : 6.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.84 % Favored : 92.16 % Rotamer: Outliers : 0.29 % Allowed : 0.86 % Favored : 98.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.25 % 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: -2.63 (0.39), residues: 408 helix: -4.49 (0.52), residues: 26 sheet: -1.34 (0.43), residues: 145 loop : -1.67 (0.38), residues: 237 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.003 TRP A 107 PHE 0.027 0.003 PHE A 102 TYR 0.045 0.003 TYR B 91 ARG 0.018 0.002 ARG R 454 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 816 Ramachandran restraints generated. 408 Oldfield, 0 Emsley, 408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 816 Ramachandran restraints generated. 408 Oldfield, 0 Emsley, 408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 89 time to evaluate : 0.402 Fit side-chains revert: symmetry clash REVERT: A 31 ARG cc_start: 0.7766 (ptm160) cc_final: 0.7031 (ptm160) outliers start: 1 outliers final: 0 residues processed: 90 average time/residue: 0.2522 time to fit residues: 25.7699 Evaluate side-chains 73 residues out of total 350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 73 time to evaluate : 0.409 ------------------------------------------------------------------------------- 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: 2.9990 chunk 29 optimal weight: 0.7980 chunk 16 optimal weight: 1.9990 chunk 10 optimal weight: 0.9980 chunk 19 optimal weight: 0.9980 chunk 15 optimal weight: 0.0980 chunk 30 optimal weight: 0.5980 chunk 11 optimal weight: 0.0170 chunk 18 optimal weight: 0.7980 chunk 22 optimal weight: 0.5980 chunk 35 optimal weight: 4.9990 overall best weight: 0.4218 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 42 GLN R 394 ASN R 474 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8000 moved from start: 0.1733 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 3324 Z= 0.199 Angle : 0.678 7.751 4509 Z= 0.346 Chirality : 0.047 0.153 480 Planarity : 0.005 0.059 588 Dihedral : 5.781 26.261 467 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 9.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.37 % Favored : 93.63 % Rotamer: Outliers : 1.14 % Allowed : 11.43 % Favored : 87.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % 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: -2.55 (0.38), residues: 408 helix: -4.48 (0.50), residues: 27 sheet: -1.29 (0.43), residues: 137 loop : -1.60 (0.36), residues: 244 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP R 436 PHE 0.011 0.001 PHE B 71 TYR 0.013 0.001 TYR B 91 ARG 0.009 0.001 ARG B 18 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 816 Ramachandran restraints generated. 408 Oldfield, 0 Emsley, 408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 816 Ramachandran restraints generated. 408 Oldfield, 0 Emsley, 408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 79 time to evaluate : 0.353 Fit side-chains outliers start: 4 outliers final: 3 residues processed: 82 average time/residue: 0.2303 time to fit residues: 21.6424 Evaluate side-chains 74 residues out of total 350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 71 time to evaluate : 0.301 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 ILE Chi-restraints excluded: chain A residue 17 SER Chi-restraints excluded: chain R residue 425 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 19 optimal weight: 1.9990 chunk 10 optimal weight: 1.9990 chunk 29 optimal weight: 0.4980 chunk 24 optimal weight: 1.9990 chunk 9 optimal weight: 1.9990 chunk 35 optimal weight: 2.9990 chunk 38 optimal weight: 0.6980 chunk 31 optimal weight: 0.7980 chunk 12 optimal weight: 0.5980 chunk 28 optimal weight: 0.5980 chunk 26 optimal weight: 0.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 42 GLN B 89 GLN ** R 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8018 moved from start: 0.1912 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 3324 Z= 0.221 Angle : 0.647 7.267 4509 Z= 0.330 Chirality : 0.046 0.151 480 Planarity : 0.005 0.059 588 Dihedral : 5.434 27.146 467 Min Nonbonded Distance : 2.601 Molprobity Statistics. All-atom Clashscore : 8.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.62 % Favored : 93.38 % Rotamer: Outliers : 2.57 % Allowed : 12.86 % Favored : 84.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % 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: -2.41 (0.39), residues: 408 helix: -4.37 (0.53), residues: 26 sheet: -1.33 (0.42), residues: 139 loop : -1.42 (0.38), residues: 243 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP R 436 PHE 0.014 0.002 PHE R 377 TYR 0.012 0.001 TYR A 94 ARG 0.004 0.001 ARG B 18 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 816 Ramachandran restraints generated. 408 Oldfield, 0 Emsley, 408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 816 Ramachandran restraints generated. 408 Oldfield, 0 Emsley, 408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 74 time to evaluate : 0.392 Fit side-chains REVERT: A 31 ARG cc_start: 0.7718 (ptm160) cc_final: 0.7425 (ptm160) REVERT: A 98 ASP cc_start: 0.7832 (OUTLIER) cc_final: 0.7461 (m-30) outliers start: 9 outliers final: 7 residues processed: 79 average time/residue: 0.2457 time to fit residues: 22.2323 Evaluate side-chains 79 residues out of total 350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 71 time to evaluate : 0.348 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 ILE Chi-restraints excluded: chain A residue 17 SER Chi-restraints excluded: chain A residue 43 THR Chi-restraints excluded: chain A residue 98 ASP Chi-restraints excluded: chain R residue 345 THR Chi-restraints excluded: chain R residue 408 ARG Chi-restraints excluded: chain R residue 425 LEU Chi-restraints excluded: chain R residue 427 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 18 optimal weight: 2.9990 chunk 3 optimal weight: 1.9990 chunk 16 optimal weight: 3.9990 chunk 23 optimal weight: 3.9990 chunk 35 optimal weight: 0.4980 chunk 37 optimal weight: 3.9990 chunk 33 optimal weight: 0.9980 chunk 10 optimal weight: 0.9990 chunk 31 optimal weight: 0.9980 chunk 21 optimal weight: 0.9980 chunk 0 optimal weight: 3.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 394 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8042 moved from start: 0.2091 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 3324 Z= 0.281 Angle : 0.663 7.790 4509 Z= 0.339 Chirality : 0.046 0.145 480 Planarity : 0.005 0.056 588 Dihedral : 5.410 26.570 467 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 9.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.86 % Favored : 93.14 % Rotamer: Outliers : 4.29 % Allowed : 14.00 % Favored : 81.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % 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: -2.48 (0.38), residues: 408 helix: -4.05 (0.46), residues: 33 sheet: -1.40 (0.41), residues: 139 loop : -1.38 (0.39), residues: 236 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP R 436 PHE 0.024 0.002 PHE R 377 TYR 0.018 0.001 TYR R 369 ARG 0.005 0.001 ARG B 18 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 816 Ramachandran restraints generated. 408 Oldfield, 0 Emsley, 408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 816 Ramachandran restraints generated. 408 Oldfield, 0 Emsley, 408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 76 time to evaluate : 0.401 Fit side-chains REVERT: A 31 ARG cc_start: 0.7711 (ptm160) cc_final: 0.7206 (ptm160) REVERT: A 98 ASP cc_start: 0.8101 (OUTLIER) cc_final: 0.7869 (m-30) outliers start: 15 outliers final: 13 residues processed: 83 average time/residue: 0.2421 time to fit residues: 22.8720 Evaluate side-chains 88 residues out of total 350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 74 time to evaluate : 0.369 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 ILE Chi-restraints excluded: chain A residue 17 SER Chi-restraints excluded: chain A residue 43 THR Chi-restraints excluded: chain A residue 63 VAL Chi-restraints excluded: chain A residue 98 ASP Chi-restraints excluded: chain B residue 11 LEU Chi-restraints excluded: chain B residue 56 THR Chi-restraints excluded: chain B residue 78 LEU Chi-restraints excluded: chain R residue 345 THR Chi-restraints excluded: chain R residue 394 ASN Chi-restraints excluded: chain R residue 408 ARG Chi-restraints excluded: chain R residue 425 LEU Chi-restraints excluded: chain R residue 483 VAL Chi-restraints excluded: chain R residue 500 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 28 optimal weight: 0.4980 chunk 15 optimal weight: 0.9990 chunk 32 optimal weight: 4.9990 chunk 26 optimal weight: 0.0020 chunk 0 optimal weight: 3.9990 chunk 19 optimal weight: 0.9990 chunk 33 optimal weight: 0.7980 chunk 9 optimal weight: 1.9990 chunk 12 optimal weight: 0.0980 chunk 7 optimal weight: 0.0070 chunk 22 optimal weight: 0.9990 overall best weight: 0.2806 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7977 moved from start: 0.2422 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 3324 Z= 0.159 Angle : 0.601 7.575 4509 Z= 0.310 Chirality : 0.045 0.160 480 Planarity : 0.005 0.058 588 Dihedral : 5.057 25.754 467 Min Nonbonded Distance : 2.582 Molprobity Statistics. All-atom Clashscore : 8.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.37 % Favored : 93.63 % Rotamer: Outliers : 2.57 % Allowed : 15.14 % Favored : 82.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % 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: -2.58 (0.38), residues: 408 helix: -3.98 (0.44), residues: 39 sheet: -1.41 (0.40), residues: 141 loop : -1.43 (0.40), residues: 228 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP R 436 PHE 0.017 0.001 PHE R 377 TYR 0.021 0.001 TYR R 369 ARG 0.010 0.001 ARG B 18 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 816 Ramachandran restraints generated. 408 Oldfield, 0 Emsley, 408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 816 Ramachandran restraints generated. 408 Oldfield, 0 Emsley, 408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 75 time to evaluate : 0.396 Fit side-chains REVERT: A 31 ARG cc_start: 0.7569 (ptm160) cc_final: 0.7068 (ptm160) REVERT: B 79 GLN cc_start: 0.7585 (mp10) cc_final: 0.7020 (mp10) outliers start: 9 outliers final: 5 residues processed: 79 average time/residue: 0.2566 time to fit residues: 23.0874 Evaluate side-chains 78 residues out of total 350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 73 time to evaluate : 0.399 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 ILE Chi-restraints excluded: chain A residue 17 SER Chi-restraints excluded: chain B residue 56 THR Chi-restraints excluded: chain R residue 408 ARG Chi-restraints excluded: chain R residue 425 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 9 optimal weight: 2.9990 chunk 37 optimal weight: 3.9990 chunk 31 optimal weight: 3.9990 chunk 17 optimal weight: 6.9990 chunk 3 optimal weight: 0.7980 chunk 12 optimal weight: 0.0980 chunk 19 optimal weight: 0.6980 chunk 36 optimal weight: 0.0870 chunk 4 optimal weight: 0.7980 chunk 21 optimal weight: 0.8980 chunk 27 optimal weight: 0.6980 overall best weight: 0.4758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 394 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7989 moved from start: 0.2574 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 3324 Z= 0.182 Angle : 0.595 7.358 4509 Z= 0.306 Chirality : 0.044 0.150 480 Planarity : 0.005 0.053 588 Dihedral : 4.925 25.098 467 Min Nonbonded Distance : 2.581 Molprobity Statistics. All-atom Clashscore : 8.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.62 % Favored : 93.38 % Rotamer: Outliers : 3.71 % Allowed : 14.29 % Favored : 82.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % 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: -2.44 (0.39), residues: 408 helix: -3.87 (0.49), residues: 39 sheet: -1.29 (0.41), residues: 141 loop : -1.36 (0.40), residues: 228 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP R 436 PHE 0.012 0.001 PHE R 377 TYR 0.019 0.001 TYR R 369 ARG 0.010 0.001 ARG B 18 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 816 Ramachandran restraints generated. 408 Oldfield, 0 Emsley, 408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 816 Ramachandran restraints generated. 408 Oldfield, 0 Emsley, 408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 77 time to evaluate : 0.410 Fit side-chains REVERT: A 86 ARG cc_start: 0.6443 (mmp-170) cc_final: 0.6203 (mmm160) REVERT: A 98 ASP cc_start: 0.8016 (OUTLIER) cc_final: 0.7768 (m-30) outliers start: 13 outliers final: 10 residues processed: 82 average time/residue: 0.2344 time to fit residues: 22.1356 Evaluate side-chains 85 residues out of total 350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 74 time to evaluate : 0.401 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 SER Chi-restraints excluded: chain A residue 98 ASP Chi-restraints excluded: chain B residue 56 THR Chi-restraints excluded: chain B residue 78 LEU Chi-restraints excluded: chain B residue 91 TYR Chi-restraints excluded: chain R residue 345 THR Chi-restraints excluded: chain R residue 425 LEU Chi-restraints excluded: chain R residue 427 ASP Chi-restraints excluded: chain R residue 430 THR Chi-restraints excluded: chain R residue 432 CYS Chi-restraints excluded: chain R residue 500 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 21 optimal weight: 2.9990 chunk 31 optimal weight: 0.7980 chunk 37 optimal weight: 2.9990 chunk 23 optimal weight: 3.9990 chunk 22 optimal weight: 1.9990 chunk 17 optimal weight: 7.9990 chunk 15 optimal weight: 0.9990 chunk 11 optimal weight: 0.0570 chunk 7 optimal weight: 0.2980 chunk 25 optimal weight: 0.9980 chunk 18 optimal weight: 0.6980 overall best weight: 0.5698 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8000 moved from start: 0.2726 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 3324 Z= 0.205 Angle : 0.617 7.127 4509 Z= 0.319 Chirality : 0.045 0.158 480 Planarity : 0.004 0.053 588 Dihedral : 4.949 25.546 467 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 9.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.37 % Favored : 93.63 % Rotamer: Outliers : 5.43 % Allowed : 13.43 % Favored : 81.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % 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: -2.35 (0.39), residues: 408 helix: -3.91 (0.48), residues: 39 sheet: -1.17 (0.41), residues: 139 loop : -1.32 (0.40), residues: 230 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP R 436 PHE 0.010 0.001 PHE A 27 TYR 0.015 0.001 TYR R 369 ARG 0.006 0.001 ARG B 18 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 816 Ramachandran restraints generated. 408 Oldfield, 0 Emsley, 408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 816 Ramachandran restraints generated. 408 Oldfield, 0 Emsley, 408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 74 time to evaluate : 0.397 Fit side-chains REVERT: A 31 ARG cc_start: 0.7543 (ptm160) cc_final: 0.7316 (ptm160) REVERT: A 98 ASP cc_start: 0.8087 (OUTLIER) cc_final: 0.7880 (m-30) REVERT: B 75 ILE cc_start: 0.8560 (OUTLIER) cc_final: 0.8338 (mm) outliers start: 19 outliers final: 14 residues processed: 84 average time/residue: 0.2391 time to fit residues: 23.1939 Evaluate side-chains 89 residues out of total 350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 73 time to evaluate : 0.364 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 ILE Chi-restraints excluded: chain A residue 17 SER Chi-restraints excluded: chain A residue 43 THR Chi-restraints excluded: chain A residue 87 VAL Chi-restraints excluded: chain A residue 98 ASP Chi-restraints excluded: chain B residue 56 THR Chi-restraints excluded: chain B residue 75 ILE Chi-restraints excluded: chain B residue 78 LEU Chi-restraints excluded: chain B residue 91 TYR Chi-restraints excluded: chain R residue 345 THR Chi-restraints excluded: chain R residue 425 LEU Chi-restraints excluded: chain R residue 427 ASP Chi-restraints excluded: chain R residue 430 THR Chi-restraints excluded: chain R residue 432 CYS Chi-restraints excluded: chain R residue 483 VAL Chi-restraints excluded: chain R residue 500 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 3 optimal weight: 2.9990 chunk 29 optimal weight: 1.9990 chunk 34 optimal weight: 2.9990 chunk 36 optimal weight: 0.8980 chunk 32 optimal weight: 3.9990 chunk 35 optimal weight: 1.9990 chunk 21 optimal weight: 0.5980 chunk 15 optimal weight: 1.9990 chunk 27 optimal weight: 0.8980 chunk 10 optimal weight: 0.9990 chunk 31 optimal weight: 2.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 79 GLN ** R 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8055 moved from start: 0.2638 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 3324 Z= 0.325 Angle : 0.681 7.473 4509 Z= 0.347 Chirality : 0.046 0.145 480 Planarity : 0.005 0.051 588 Dihedral : 5.293 26.968 467 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 10.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.11 % Favored : 92.89 % Rotamer: Outliers : 4.57 % Allowed : 14.86 % Favored : 80.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % 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: -2.27 (0.40), residues: 408 helix: -3.77 (0.54), residues: 39 sheet: -1.15 (0.42), residues: 139 loop : -1.26 (0.41), residues: 230 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP A 47 PHE 0.015 0.002 PHE A 27 TYR 0.015 0.002 TYR R 369 ARG 0.006 0.001 ARG B 18 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 816 Ramachandran restraints generated. 408 Oldfield, 0 Emsley, 408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 816 Ramachandran restraints generated. 408 Oldfield, 0 Emsley, 408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 74 time to evaluate : 0.383 Fit side-chains REVERT: A 31 ARG cc_start: 0.7715 (ptm160) cc_final: 0.7445 (ptm160) outliers start: 16 outliers final: 13 residues processed: 83 average time/residue: 0.2166 time to fit residues: 20.8384 Evaluate side-chains 87 residues out of total 350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 74 time to evaluate : 0.394 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 SER Chi-restraints excluded: chain A residue 43 THR Chi-restraints excluded: chain A residue 87 VAL Chi-restraints excluded: chain B residue 11 LEU Chi-restraints excluded: chain B residue 20 THR Chi-restraints excluded: chain B residue 56 THR Chi-restraints excluded: chain B residue 78 LEU Chi-restraints excluded: chain R residue 345 THR Chi-restraints excluded: chain R residue 425 LEU Chi-restraints excluded: chain R residue 430 THR Chi-restraints excluded: chain R residue 432 CYS Chi-restraints excluded: chain R residue 483 VAL Chi-restraints excluded: chain R residue 500 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 33 optimal weight: 0.6980 chunk 34 optimal weight: 0.8980 chunk 23 optimal weight: 0.8980 chunk 37 optimal weight: 2.9990 chunk 22 optimal weight: 0.5980 chunk 17 optimal weight: 4.9990 chunk 25 optimal weight: 0.7980 chunk 38 optimal weight: 0.0040 chunk 35 optimal weight: 0.9980 chunk 30 optimal weight: 0.9990 chunk 3 optimal weight: 0.5980 overall best weight: 0.5392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 79 GLN ** R 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8007 moved from start: 0.2777 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 3324 Z= 0.218 Angle : 0.663 7.132 4509 Z= 0.341 Chirality : 0.045 0.145 480 Planarity : 0.005 0.066 588 Dihedral : 4.988 25.163 467 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 9.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.62 % Favored : 93.38 % Rotamer: Outliers : 3.43 % Allowed : 17.14 % Favored : 79.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % 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: -2.23 (0.40), residues: 408 helix: -3.72 (0.55), residues: 39 sheet: -1.03 (0.42), residues: 141 loop : -1.30 (0.40), residues: 228 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP R 436 PHE 0.010 0.001 PHE A 27 TYR 0.017 0.001 TYR B 91 ARG 0.015 0.001 ARG B 18 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 816 Ramachandran restraints generated. 408 Oldfield, 0 Emsley, 408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 816 Ramachandran restraints generated. 408 Oldfield, 0 Emsley, 408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 75 time to evaluate : 0.381 Fit side-chains REVERT: A 31 ARG cc_start: 0.7578 (ptm160) cc_final: 0.7358 (ptm160) outliers start: 12 outliers final: 12 residues processed: 81 average time/residue: 0.2150 time to fit residues: 20.1851 Evaluate side-chains 85 residues out of total 350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 73 time to evaluate : 0.390 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 ILE Chi-restraints excluded: chain A residue 17 SER Chi-restraints excluded: chain A residue 43 THR Chi-restraints excluded: chain A residue 87 VAL Chi-restraints excluded: chain B residue 56 THR Chi-restraints excluded: chain B residue 91 TYR Chi-restraints excluded: chain R residue 345 THR Chi-restraints excluded: chain R residue 425 LEU Chi-restraints excluded: chain R residue 430 THR Chi-restraints excluded: chain R residue 432 CYS Chi-restraints excluded: chain R residue 483 VAL Chi-restraints excluded: chain R residue 500 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 23 optimal weight: 0.6980 chunk 18 optimal weight: 2.9990 chunk 24 optimal weight: 0.5980 chunk 32 optimal weight: 5.9990 chunk 9 optimal weight: 0.8980 chunk 28 optimal weight: 0.9980 chunk 4 optimal weight: 0.6980 chunk 8 optimal weight: 0.8980 chunk 30 optimal weight: 2.9990 chunk 12 optimal weight: 0.5980 chunk 31 optimal weight: 0.8980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 79 GLN ** R 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8025 moved from start: 0.2824 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 3324 Z= 0.251 Angle : 0.664 7.157 4509 Z= 0.339 Chirality : 0.046 0.143 480 Planarity : 0.006 0.091 588 Dihedral : 5.068 26.316 467 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 10.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.60 % Favored : 92.40 % Rotamer: Outliers : 2.86 % Allowed : 17.14 % Favored : 80.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % 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: -2.20 (0.40), residues: 408 helix: -3.71 (0.55), residues: 39 sheet: -1.00 (0.43), residues: 139 loop : -1.30 (0.40), residues: 230 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 107 PHE 0.011 0.001 PHE A 27 TYR 0.018 0.001 TYR B 91 ARG 0.023 0.001 ARG B 18 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 816 Ramachandran restraints generated. 408 Oldfield, 0 Emsley, 408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 816 Ramachandran restraints generated. 408 Oldfield, 0 Emsley, 408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 73 time to evaluate : 0.454 Fit side-chains REVERT: A 31 ARG cc_start: 0.7581 (ptm160) cc_final: 0.7360 (ptm160) outliers start: 10 outliers final: 10 residues processed: 78 average time/residue: 0.2327 time to fit residues: 21.0558 Evaluate side-chains 82 residues out of total 350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 72 time to evaluate : 0.404 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 SER Chi-restraints excluded: chain A residue 87 VAL Chi-restraints excluded: chain B residue 56 THR Chi-restraints excluded: chain B residue 91 TYR Chi-restraints excluded: chain R residue 345 THR Chi-restraints excluded: chain R residue 425 LEU Chi-restraints excluded: chain R residue 430 THR Chi-restraints excluded: chain R residue 432 CYS Chi-restraints excluded: chain R residue 483 VAL Chi-restraints excluded: chain R residue 500 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 3 optimal weight: 0.8980 chunk 5 optimal weight: 1.9990 chunk 27 optimal weight: 0.7980 chunk 1 optimal weight: 0.0070 chunk 22 optimal weight: 0.9980 chunk 35 optimal weight: 0.0470 chunk 20 optimal weight: 0.9990 chunk 26 optimal weight: 0.5980 chunk 24 optimal weight: 0.7980 chunk 23 optimal weight: 0.7980 chunk 15 optimal weight: 1.9990 overall best weight: 0.4496 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3576 r_free = 0.3576 target = 0.099362 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.086068 restraints weight = 7497.544| |-----------------------------------------------------------------------------| r_work (start): 0.3350 rms_B_bonded: 2.84 r_work: 0.3242 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.3242 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8134 moved from start: 0.2959 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 3324 Z= 0.207 Angle : 0.651 7.059 4509 Z= 0.334 Chirality : 0.045 0.143 480 Planarity : 0.005 0.087 588 Dihedral : 4.872 24.973 467 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 9.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.11 % Favored : 92.89 % Rotamer: Outliers : 3.43 % Allowed : 16.86 % Favored : 79.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % 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: -2.14 (0.40), residues: 408 helix: -3.71 (0.55), residues: 39 sheet: -0.88 (0.43), residues: 141 loop : -1.31 (0.40), residues: 228 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP R 436 PHE 0.009 0.001 PHE A 27 TYR 0.017 0.001 TYR B 91 ARG 0.021 0.001 ARG B 18 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1422.41 seconds wall clock time: 26 minutes 38.41 seconds (1598.41 seconds total)