Starting phenix.real_space_refine on Sat Apr 26 19:37:23 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8xe9_38283/04_2025/8xe9_38283.cif Found real_map, /net/cci-nas-00/data/ceres_data/8xe9_38283/04_2025/8xe9_38283.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8xe9_38283/04_2025/8xe9_38283.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8xe9_38283/04_2025/8xe9_38283.map" model { file = "/net/cci-nas-00/data/ceres_data/8xe9_38283/04_2025/8xe9_38283.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8xe9_38283/04_2025/8xe9_38283.cif" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.020 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 2079 2.51 5 N 554 2.21 5 O 618 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/chem_data/mon_lib" Total number of atoms: 3266 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 888 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 888 Classifications: {'peptide': 117} Link IDs: {'PTRANS': 4, 'TRANS': 112} Chain: "B" Number of atoms: 821 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 821 Classifications: {'peptide': 107} Link IDs: {'PCIS': 2, 'PTRANS': 4, 'TRANS': 100} Chain: "C" Number of atoms: 1557 Number of conformers: 1 Conformer: "" Number of residues, atoms: 196, 1557 Classifications: {'peptide': 196} Link IDs: {'PTRANS': 13, 'TRANS': 182} Time building chain proxies: 2.90, per 1000 atoms: 0.89 Number of scatterers: 3266 At special positions: 0 Unit cell: (61.56, 76.95, 89.91, 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 618 8.00 N 554 7.00 C 2079 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=2.03 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.03 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.03 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.03 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 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: 0.70 Conformation dependent library (CDL) restraints added in 384.4 milliseconds 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 768 Finding SS restraints... Secondary structure from input PDB file: 5 helices and 10 sheets defined 6.2% alpha, 27.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.42 Creating SS restraints... Processing helix chain 'A' and resid 86 through 90 Processing helix chain 'C' and resid 349 through 353 removed outlier: 3.681A pdb=" N TRP C 353 " --> pdb=" O VAL C 350 " (cutoff:3.500A) Processing helix chain 'C' and resid 383 through 387 removed outlier: 3.724A pdb=" N LEU C 387 " --> pdb=" O PRO C 384 " (cutoff:3.500A) Processing helix chain 'C' and resid 406 through 410 removed outlier: 3.556A pdb=" N ILE C 410 " --> pdb=" O VAL C 407 " (cutoff:3.500A) Processing helix chain 'C' and resid 417 through 422 removed outlier: 3.801A pdb=" N TYR C 421 " --> pdb=" O ASN C 417 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 3 through 7 Processing sheet with id=AA2, first strand: chain 'A' and resid 11 through 12 removed outlier: 6.771A pdb=" N MET A 34 " --> pdb=" O VAL A 50 " (cutoff:3.500A) removed outlier: 4.496A pdb=" N VAL A 50 " --> pdb=" O MET A 34 " (cutoff:3.500A) removed outlier: 6.832A pdb=" N TRP A 36 " --> pdb=" O VAL A 48 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N VAL A 48 " --> pdb=" O TRP A 36 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 11 through 12 Processing sheet with id=AA4, first strand: chain 'B' and resid 4 through 6 Processing sheet with id=AA5, first strand: chain 'B' and resid 4 through 6 Processing sheet with id=AA6, first strand: chain 'B' and resid 53 through 54 removed outlier: 6.453A pdb=" N TRP B 35 " --> pdb=" O LEU B 47 " (cutoff:3.500A) removed outlier: 4.605A pdb=" N TYR B 49 " --> pdb=" O LEU B 33 " (cutoff:3.500A) removed outlier: 6.659A pdb=" N LEU B 33 " --> pdb=" O TYR B 49 " (cutoff:3.500A) removed outlier: 5.954A pdb=" N TYR B 91 " --> pdb=" O THR B 98 " (cutoff:3.500A) removed outlier: 8.020A pdb=" N THR B 98 " --> pdb=" O TYR B 91 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N ASP B 93 " --> pdb=" O LEU B 96 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 379 through 380 Processing sheet with id=AA8, first strand: chain 'C' and resid 400 through 402 removed outlier: 3.535A pdb=" N VAL C 510 " --> pdb=" O PHE C 400 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AB1, first strand: chain 'C' and resid 473 through 474 87 hydrogen bonds defined for protein. 180 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: 0.78 Time building geometry restraints manager: 0.86 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: 1046 1.34 - 1.46: 873 1.46 - 1.58: 1416 1.58 - 1.70: 0 1.70 - 1.82: 18 Bond restraints: 3353 Sorted by residual: bond pdb=" CB PRO C 445 " pdb=" CG PRO C 445 " ideal model delta sigma weight residual 1.492 1.559 -0.067 5.00e-02 4.00e+02 1.78e+00 bond pdb=" CA GLY B 68 " pdb=" C GLY B 68 " ideal model delta sigma weight residual 1.514 1.530 -0.016 1.41e-02 5.03e+03 1.23e+00 bond pdb=" C ILE C 418 " pdb=" O ILE C 418 " ideal model delta sigma weight residual 1.231 1.242 -0.011 1.02e-02 9.61e+03 1.06e+00 bond pdb=" N GLY B 68 " pdb=" CA GLY B 68 " ideal model delta sigma weight residual 1.449 1.464 -0.015 1.45e-02 4.76e+03 1.06e+00 bond pdb=" CG PRO B 95 " pdb=" CD PRO B 95 " ideal model delta sigma weight residual 1.512 1.486 0.026 2.70e-02 1.37e+03 9.21e-01 ... (remaining 3348 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.10: 4342 1.10 - 2.20: 155 2.20 - 3.29: 45 3.29 - 4.39: 16 4.39 - 5.49: 2 Bond angle restraints: 4560 Sorted by residual: angle pdb=" C SER C 486 " pdb=" CA SER C 486 " pdb=" CB SER C 486 " ideal model delta sigma weight residual 110.42 115.91 -5.49 1.99e+00 2.53e-01 7.60e+00 angle pdb=" N VAL C 524 " pdb=" CA VAL C 524 " pdb=" C VAL C 524 " ideal model delta sigma weight residual 106.72 110.81 -4.09 1.59e+00 3.96e-01 6.62e+00 angle pdb=" CA PRO C 445 " pdb=" N PRO C 445 " pdb=" CD PRO C 445 " ideal model delta sigma weight residual 112.00 108.80 3.20 1.40e+00 5.10e-01 5.21e+00 angle pdb=" C VAL C 362 " pdb=" N ALA C 363 " pdb=" CA ALA C 363 " ideal model delta sigma weight residual 121.97 125.54 -3.57 1.73e+00 3.34e-01 4.25e+00 angle pdb=" C GLY B 50 " pdb=" N ALA B 51 " pdb=" CA ALA B 51 " ideal model delta sigma weight residual 121.54 125.36 -3.82 1.91e+00 2.74e-01 4.00e+00 ... (remaining 4555 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.86: 1785 17.86 - 35.72: 161 35.72 - 53.58: 23 53.58 - 71.45: 5 71.45 - 89.31: 2 Dihedral angle restraints: 1976 sinusoidal: 765 harmonic: 1211 Sorted by residual: dihedral pdb=" CB CYS A 22 " pdb=" SG CYS A 22 " pdb=" SG CYS A 95 " pdb=" CB CYS A 95 " ideal model delta sinusoidal sigma weight residual 93.00 153.06 -60.06 1 1.00e+01 1.00e-02 4.81e+01 dihedral pdb=" CA ARG A 97 " pdb=" C ARG A 97 " pdb=" N ASP A 98 " pdb=" CA ASP A 98 " ideal model delta harmonic sigma weight residual -180.00 -159.64 -20.36 0 5.00e+00 4.00e-02 1.66e+01 dihedral pdb=" CB CYS C 336 " pdb=" SG CYS C 336 " pdb=" SG CYS C 361 " pdb=" CB CYS C 361 " ideal model delta sinusoidal sigma weight residual -86.00 -52.42 -33.58 1 1.00e+01 1.00e-02 1.60e+01 ... (remaining 1973 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.027: 261 0.027 - 0.054: 143 0.054 - 0.081: 47 0.081 - 0.108: 23 0.108 - 0.134: 13 Chirality restraints: 487 Sorted by residual: chirality pdb=" CA VAL C 401 " pdb=" N VAL C 401 " pdb=" C VAL C 401 " pdb=" CB VAL C 401 " both_signs ideal model delta sigma weight residual False 2.44 2.58 -0.13 2.00e-01 2.50e+01 4.51e-01 chirality pdb=" CA ILE B 48 " pdb=" N ILE B 48 " pdb=" C ILE B 48 " pdb=" CB ILE B 48 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.45e-01 chirality pdb=" CA ILE C 468 " pdb=" N ILE C 468 " pdb=" C ILE C 468 " pdb=" CB ILE C 468 " both_signs ideal model delta sigma weight residual False 2.43 2.55 -0.12 2.00e-01 2.50e+01 3.58e-01 ... (remaining 484 not shown) Planarity restraints: 591 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LYS C 444 " 0.065 5.00e-02 4.00e+02 9.75e-02 1.52e+01 pdb=" N PRO C 445 " -0.169 5.00e-02 4.00e+02 pdb=" CA PRO C 445 " 0.051 5.00e-02 4.00e+02 pdb=" CD PRO C 445 " 0.053 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TRP B 94 " -0.026 5.00e-02 4.00e+02 3.95e-02 2.50e+00 pdb=" N PRO B 95 " 0.068 5.00e-02 4.00e+02 pdb=" CA PRO B 95 " -0.022 5.00e-02 4.00e+02 pdb=" CD PRO B 95 " -0.020 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS C 462 " 0.021 5.00e-02 4.00e+02 3.20e-02 1.64e+00 pdb=" N PRO C 463 " -0.055 5.00e-02 4.00e+02 pdb=" CA PRO C 463 " 0.016 5.00e-02 4.00e+02 pdb=" CD PRO C 463 " 0.018 5.00e-02 4.00e+02 ... (remaining 588 not shown) Histogram of nonbonded interaction distances: 2.27 - 2.79: 786 2.79 - 3.32: 2757 3.32 - 3.85: 5147 3.85 - 4.37: 6163 4.37 - 4.90: 11124 Nonbonded interactions: 25977 Sorted by model distance: nonbonded pdb=" OD2 ASP C 398 " pdb=" OH TYR C 423 " model vdw 2.265 3.040 nonbonded pdb=" NH2 ARG A 102 " pdb=" O SER C 490 " model vdw 2.311 3.120 nonbonded pdb=" NH2 ARG C 454 " pdb=" O SER C 469 " model vdw 2.316 3.120 nonbonded pdb=" NH1 ARG A 102 " pdb=" OE1 GLN C 493 " model vdw 2.351 3.120 nonbonded pdb=" OH TYR A 33 " pdb=" O LEU C 455 " model vdw 2.362 3.040 ... (remaining 25972 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: 1.700 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: 0.150 Check model and map are aligned: 0.020 Set scattering table: 0.040 Process input model: 12.780 Find NCS groups from input model: 0.030 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:2.800 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.550 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7991 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 : 0.003 0.067 3359 Z= 0.122 Angle : 0.557 5.488 4572 Z= 0.299 Chirality : 0.042 0.134 487 Planarity : 0.005 0.097 591 Dihedral : 13.283 89.308 1190 Min Nonbonded Distance : 2.265 Molprobity Statistics. All-atom Clashscore : 6.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.49 % Favored : 92.51 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % 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: -2.10 (0.41), residues: 414 helix: -4.97 (0.25), residues: 27 sheet: -1.46 (0.53), residues: 116 loop : -0.94 (0.37), residues: 271 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP C 436 HIS 0.001 0.000 HIS C 339 PHE 0.010 0.001 PHE C 456 TYR 0.009 0.001 TYR B 91 ARG 0.004 0.000 ARG C 457 Details of bonding type rmsd hydrogen bonds : bond 0.24663 ( 78) hydrogen bonds : angle 11.45155 ( 180) SS BOND : bond 0.00194 ( 6) SS BOND : angle 0.52474 ( 12) covalent geometry : bond 0.00279 ( 3353) covalent geometry : angle 0.55666 ( 4560) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 353 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 90 time to evaluate : 0.424 Fit side-chains revert: symmetry clash REVERT: A 35 THR cc_start: 0.8623 (m) cc_final: 0.8423 (t) outliers start: 0 outliers final: 0 residues processed: 90 average time/residue: 0.1921 time to fit residues: 20.2493 Evaluate side-chains 58 residues out of total 353 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 58 time to evaluate : 0.385 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 33 optimal weight: 3.9990 chunk 30 optimal weight: 0.0670 chunk 16 optimal weight: 0.0050 chunk 10 optimal weight: 4.9990 chunk 20 optimal weight: 0.0470 chunk 31 optimal weight: 3.9990 chunk 12 optimal weight: 3.9990 chunk 19 optimal weight: 1.9990 chunk 23 optimal weight: 5.9990 chunk 36 optimal weight: 3.9990 chunk 11 optimal weight: 0.9990 overall best weight: 0.6234 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 3 GLN A 39 GLN B 38 GLN B 89 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3082 r_free = 0.3082 target = 0.065017 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 23)----------------| | r_work = 0.2809 r_free = 0.2809 target = 0.052673 restraints weight = 9118.777| |-----------------------------------------------------------------------------| r_work (start): 0.2790 rms_B_bonded: 3.96 r_work: 0.2654 rms_B_bonded: 4.19 restraints_weight: 0.5000 r_work (final): 0.2654 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7990 moved from start: 0.2624 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 3359 Z= 0.125 Angle : 0.640 7.772 4572 Z= 0.334 Chirality : 0.044 0.190 487 Planarity : 0.005 0.065 591 Dihedral : 4.342 20.184 464 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 7.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.97 % Favored : 92.03 % Rotamer: Outliers : 2.55 % Allowed : 12.75 % Favored : 84.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.78 (0.41), residues: 414 helix: -4.89 (0.26), residues: 26 sheet: -0.76 (0.52), residues: 118 loop : -0.98 (0.37), residues: 270 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 35 HIS 0.001 0.000 HIS C 519 PHE 0.017 0.001 PHE C 392 TYR 0.017 0.001 TYR B 91 ARG 0.003 0.000 ARG C 457 Details of bonding type rmsd hydrogen bonds : bond 0.03486 ( 78) hydrogen bonds : angle 6.79630 ( 180) SS BOND : bond 0.00816 ( 6) SS BOND : angle 2.83857 ( 12) covalent geometry : bond 0.00287 ( 3353) covalent geometry : angle 0.62403 ( 4560) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 353 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 66 time to evaluate : 0.373 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 104 GLU cc_start: 0.7728 (tm-30) cc_final: 0.7011 (tm-30) REVERT: B 17 GLU cc_start: 0.8858 (mm-30) cc_final: 0.8652 (mm-30) REVERT: B 32 ASN cc_start: 0.8569 (m-40) cc_final: 0.8335 (t0) REVERT: B 57 ASP cc_start: 0.8036 (t0) cc_final: 0.7807 (t0) REVERT: B 69 THR cc_start: 0.8444 (t) cc_final: 0.8243 (m) REVERT: B 70 GLU cc_start: 0.7721 (mm-30) cc_final: 0.7391 (mm-30) REVERT: C 357 ARG cc_start: 0.9295 (ttt-90) cc_final: 0.9066 (ttt-90) REVERT: C 471 GLU cc_start: 0.8820 (tp30) cc_final: 0.8535 (tp30) REVERT: C 516 GLU cc_start: 0.7950 (tt0) cc_final: 0.7626 (pt0) outliers start: 9 outliers final: 5 residues processed: 71 average time/residue: 0.1393 time to fit residues: 12.3879 Evaluate side-chains 65 residues out of total 353 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 60 time to evaluate : 0.377 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 98 ASP Chi-restraints excluded: chain A residue 99 LEU Chi-restraints excluded: chain A residue 101 ILE Chi-restraints excluded: chain B residue 105 VAL Chi-restraints excluded: chain B residue 107 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 11 optimal weight: 4.9990 chunk 5 optimal weight: 0.0030 chunk 33 optimal weight: 4.9990 chunk 3 optimal weight: 3.9990 chunk 36 optimal weight: 4.9990 chunk 37 optimal weight: 3.9990 chunk 10 optimal weight: 5.9990 chunk 31 optimal weight: 2.9990 chunk 12 optimal weight: 0.8980 chunk 17 optimal weight: 8.9990 chunk 28 optimal weight: 1.9990 overall best weight: 1.9796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 3 GLN ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2978 r_free = 0.2978 target = 0.059466 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2688 r_free = 0.2688 target = 0.047247 restraints weight = 9417.120| |-----------------------------------------------------------------------------| r_work (start): 0.2680 rms_B_bonded: 3.90 r_work: 0.2542 rms_B_bonded: 4.10 restraints_weight: 0.5000 r_work (final): 0.2542 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8412 moved from start: 0.4669 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.039 3359 Z= 0.237 Angle : 0.650 7.139 4572 Z= 0.343 Chirality : 0.044 0.145 487 Planarity : 0.005 0.050 591 Dihedral : 4.679 25.154 464 Min Nonbonded Distance : 2.595 Molprobity Statistics. All-atom Clashscore : 7.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.45 % Favored : 91.55 % Rotamer: Outliers : 3.97 % Allowed : 13.60 % Favored : 82.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.85 (0.41), residues: 414 helix: -4.97 (0.21), residues: 26 sheet: -0.66 (0.50), residues: 130 loop : -1.11 (0.38), residues: 258 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP C 436 HIS 0.001 0.001 HIS C 519 PHE 0.014 0.001 PHE C 392 TYR 0.016 0.002 TYR A 79 ARG 0.002 0.000 ARG C 457 Details of bonding type rmsd hydrogen bonds : bond 0.03521 ( 78) hydrogen bonds : angle 5.99446 ( 180) SS BOND : bond 0.00617 ( 6) SS BOND : angle 2.67934 ( 12) covalent geometry : bond 0.00557 ( 3353) covalent geometry : angle 0.63603 ( 4560) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 353 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 65 time to evaluate : 0.362 Fit side-chains REVERT: A 104 GLU cc_start: 0.8118 (tm-30) cc_final: 0.7434 (tm-30) REVERT: B 3 VAL cc_start: 0.9340 (t) cc_final: 0.9036 (p) REVERT: B 17 GLU cc_start: 0.8994 (mm-30) cc_final: 0.8751 (mm-30) REVERT: B 57 ASP cc_start: 0.8192 (t0) cc_final: 0.7811 (t0) REVERT: B 69 THR cc_start: 0.8228 (t) cc_final: 0.8012 (m) REVERT: B 70 GLU cc_start: 0.7932 (mm-30) cc_final: 0.7664 (mm-30) REVERT: C 436 TRP cc_start: 0.7620 (OUTLIER) cc_final: 0.7021 (m-10) REVERT: C 471 GLU cc_start: 0.9029 (tp30) cc_final: 0.8654 (tp30) REVERT: C 516 GLU cc_start: 0.8172 (tt0) cc_final: 0.7867 (pt0) outliers start: 14 outliers final: 10 residues processed: 72 average time/residue: 0.1423 time to fit residues: 12.6887 Evaluate side-chains 69 residues out of total 353 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 58 time to evaluate : 0.363 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 THR Chi-restraints excluded: chain A residue 98 ASP Chi-restraints excluded: chain A residue 99 LEU Chi-restraints excluded: chain A residue 101 ILE Chi-restraints excluded: chain B residue 105 VAL Chi-restraints excluded: chain B residue 107 ILE Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 395 VAL Chi-restraints excluded: chain C residue 436 TRP Chi-restraints excluded: chain C residue 503 VAL Chi-restraints excluded: chain C residue 511 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 35 optimal weight: 1.9990 chunk 13 optimal weight: 3.9990 chunk 23 optimal weight: 4.9990 chunk 33 optimal weight: 1.9990 chunk 4 optimal weight: 0.8980 chunk 14 optimal weight: 1.9990 chunk 10 optimal weight: 3.9990 chunk 39 optimal weight: 3.9990 chunk 34 optimal weight: 1.9990 chunk 20 optimal weight: 0.9990 chunk 37 optimal weight: 0.3980 overall best weight: 1.2586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 90 GLN ** 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 = 0.3057 r_free = 0.3057 target = 0.062763 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2778 r_free = 0.2778 target = 0.049575 restraints weight = 9656.920| |-----------------------------------------------------------------------------| r_work (start): 0.2764 rms_B_bonded: 4.07 r_work: 0.2622 rms_B_bonded: 4.16 restraints_weight: 0.5000 r_work (final): 0.2622 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8552 moved from start: 0.4968 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 3359 Z= 0.161 Angle : 0.613 6.653 4572 Z= 0.320 Chirality : 0.043 0.149 487 Planarity : 0.005 0.045 591 Dihedral : 4.351 22.267 464 Min Nonbonded Distance : 2.574 Molprobity Statistics. All-atom Clashscore : 7.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.45 % Favored : 91.55 % Rotamer: Outliers : 3.97 % Allowed : 16.15 % Favored : 79.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % 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 (0.41), residues: 414 helix: -4.95 (0.21), residues: 26 sheet: -0.51 (0.50), residues: 130 loop : -1.09 (0.37), residues: 258 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 436 HIS 0.001 0.001 HIS C 505 PHE 0.009 0.001 PHE C 392 TYR 0.013 0.001 TYR B 36 ARG 0.008 0.001 ARG B 24 Details of bonding type rmsd hydrogen bonds : bond 0.02931 ( 78) hydrogen bonds : angle 5.57463 ( 180) SS BOND : bond 0.00246 ( 6) SS BOND : angle 2.42920 ( 12) covalent geometry : bond 0.00380 ( 3353) covalent geometry : angle 0.60095 ( 4560) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 353 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 58 time to evaluate : 0.408 Fit side-chains REVERT: A 104 GLU cc_start: 0.8188 (tm-30) cc_final: 0.7557 (tm-30) REVERT: B 3 VAL cc_start: 0.9420 (t) cc_final: 0.9134 (p) REVERT: B 4 MET cc_start: 0.8776 (mtp) cc_final: 0.8300 (mtp) REVERT: B 17 GLU cc_start: 0.8963 (mm-30) cc_final: 0.8693 (mm-30) REVERT: B 24 ARG cc_start: 0.8338 (ttm110) cc_final: 0.7923 (mtp-110) REVERT: B 30 ASN cc_start: 0.9124 (p0) cc_final: 0.8649 (p0) REVERT: B 57 ASP cc_start: 0.8204 (t0) cc_final: 0.7886 (t0) REVERT: B 70 GLU cc_start: 0.7965 (mm-30) cc_final: 0.7734 (mm-30) REVERT: B 81 GLU cc_start: 0.9139 (OUTLIER) cc_final: 0.8420 (tm-30) REVERT: C 471 GLU cc_start: 0.9080 (tp30) cc_final: 0.8671 (tp30) REVERT: C 516 GLU cc_start: 0.8341 (tt0) cc_final: 0.7981 (pt0) outliers start: 14 outliers final: 10 residues processed: 65 average time/residue: 0.1588 time to fit residues: 12.8440 Evaluate side-chains 67 residues out of total 353 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 56 time to evaluate : 0.401 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 THR Chi-restraints excluded: chain A residue 98 ASP Chi-restraints excluded: chain A residue 99 LEU Chi-restraints excluded: chain A residue 101 ILE Chi-restraints excluded: chain B residue 13 VAL Chi-restraints excluded: chain B residue 81 GLU Chi-restraints excluded: chain B residue 105 VAL Chi-restraints excluded: chain B residue 107 ILE Chi-restraints excluded: chain C residue 383 SER Chi-restraints excluded: chain C residue 395 VAL Chi-restraints excluded: chain C residue 434 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 32 optimal weight: 1.9990 chunk 4 optimal weight: 0.6980 chunk 0 optimal weight: 6.9990 chunk 7 optimal weight: 5.9990 chunk 22 optimal weight: 3.9990 chunk 6 optimal weight: 3.9990 chunk 14 optimal weight: 4.9990 chunk 11 optimal weight: 4.9990 chunk 1 optimal weight: 2.9990 chunk 33 optimal weight: 2.9990 chunk 29 optimal weight: 0.9980 overall best weight: 1.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 6 GLN ** B 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3012 r_free = 0.3012 target = 0.060695 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2727 r_free = 0.2727 target = 0.047436 restraints weight = 9818.359| |-----------------------------------------------------------------------------| r_work (start): 0.2719 rms_B_bonded: 4.01 r_work: 0.2577 rms_B_bonded: 4.11 restraints_weight: 0.5000 r_work (final): 0.2577 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8599 moved from start: 0.5319 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.035 3359 Z= 0.228 Angle : 0.637 7.266 4572 Z= 0.335 Chirality : 0.044 0.148 487 Planarity : 0.004 0.040 591 Dihedral : 4.436 23.138 464 Min Nonbonded Distance : 2.564 Molprobity Statistics. All-atom Clashscore : 6.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.97 % Favored : 92.03 % Rotamer: Outliers : 5.67 % Allowed : 14.73 % Favored : 79.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % 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: -1.70 (0.41), residues: 414 helix: -4.84 (0.24), residues: 26 sheet: -0.48 (0.50), residues: 130 loop : -1.06 (0.37), residues: 258 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 436 HIS 0.001 0.000 HIS C 339 PHE 0.019 0.002 PHE C 400 TYR 0.017 0.001 TYR B 36 ARG 0.005 0.000 ARG B 24 Details of bonding type rmsd hydrogen bonds : bond 0.03042 ( 78) hydrogen bonds : angle 5.42825 ( 180) SS BOND : bond 0.00352 ( 6) SS BOND : angle 2.57805 ( 12) covalent geometry : bond 0.00532 ( 3353) covalent geometry : angle 0.62421 ( 4560) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 353 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 55 time to evaluate : 0.382 Fit side-chains REVERT: A 104 GLU cc_start: 0.8186 (tm-30) cc_final: 0.7534 (tm-30) REVERT: B 3 VAL cc_start: 0.9450 (t) cc_final: 0.9185 (p) REVERT: B 4 MET cc_start: 0.8871 (mtp) cc_final: 0.8306 (mtp) REVERT: B 24 ARG cc_start: 0.8335 (ttm110) cc_final: 0.8060 (mtp-110) REVERT: B 57 ASP cc_start: 0.8324 (t0) cc_final: 0.8009 (t0) REVERT: B 81 GLU cc_start: 0.9158 (pt0) cc_final: 0.8554 (tm-30) REVERT: C 436 TRP cc_start: 0.7755 (OUTLIER) cc_final: 0.7137 (m-10) REVERT: C 471 GLU cc_start: 0.9154 (tp30) cc_final: 0.8699 (tp30) REVERT: C 516 GLU cc_start: 0.8353 (tt0) cc_final: 0.8024 (pt0) outliers start: 20 outliers final: 16 residues processed: 66 average time/residue: 0.1529 time to fit residues: 12.4588 Evaluate side-chains 72 residues out of total 353 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 55 time to evaluate : 0.394 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 TRP Chi-restraints excluded: chain A residue 68 THR Chi-restraints excluded: chain A residue 98 ASP Chi-restraints excluded: chain A residue 99 LEU Chi-restraints excluded: chain A residue 101 ILE Chi-restraints excluded: chain B residue 5 THR Chi-restraints excluded: chain B residue 13 VAL Chi-restraints excluded: chain B residue 105 VAL Chi-restraints excluded: chain B residue 107 ILE Chi-restraints excluded: chain C residue 364 ASP Chi-restraints excluded: chain C residue 383 SER Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 395 VAL Chi-restraints excluded: chain C residue 436 TRP Chi-restraints excluded: chain C residue 456 PHE Chi-restraints excluded: chain C residue 503 VAL Chi-restraints excluded: chain C residue 511 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 24 optimal weight: 0.4980 chunk 28 optimal weight: 0.0170 chunk 14 optimal weight: 3.9990 chunk 16 optimal weight: 1.9990 chunk 20 optimal weight: 0.8980 chunk 1 optimal weight: 4.9990 chunk 7 optimal weight: 3.9990 chunk 26 optimal weight: 0.6980 chunk 10 optimal weight: 4.9990 chunk 0 optimal weight: 5.9990 chunk 31 optimal weight: 0.7980 overall best weight: 0.5818 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 109 GLN ** B 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3071 r_free = 0.3071 target = 0.063404 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2829 r_free = 0.2829 target = 0.050615 restraints weight = 9937.775| |-----------------------------------------------------------------------------| r_work (start): 0.2814 rms_B_bonded: 3.80 r_work: 0.2676 rms_B_bonded: 3.96 restraints_weight: 0.5000 r_work (final): 0.2676 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8560 moved from start: 0.5461 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 3359 Z= 0.111 Angle : 0.591 6.207 4572 Z= 0.309 Chirality : 0.043 0.146 487 Planarity : 0.004 0.040 591 Dihedral : 4.127 19.304 464 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 6.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.97 % Favored : 92.03 % Rotamer: Outliers : 4.25 % Allowed : 17.28 % Favored : 78.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % 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 (0.41), residues: 414 helix: -4.75 (0.29), residues: 26 sheet: -0.37 (0.52), residues: 124 loop : -0.93 (0.37), residues: 264 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 36 HIS 0.000 0.000 HIS C 339 PHE 0.021 0.001 PHE C 400 TYR 0.013 0.001 TYR B 36 ARG 0.004 0.000 ARG B 24 Details of bonding type rmsd hydrogen bonds : bond 0.02567 ( 78) hydrogen bonds : angle 5.02091 ( 180) SS BOND : bond 0.00243 ( 6) SS BOND : angle 2.18593 ( 12) covalent geometry : bond 0.00265 ( 3353) covalent geometry : angle 0.58152 ( 4560) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 353 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 57 time to evaluate : 0.416 Fit side-chains REVERT: A 88 ASP cc_start: 0.9282 (m-30) cc_final: 0.9040 (p0) REVERT: A 104 GLU cc_start: 0.8156 (tm-30) cc_final: 0.7556 (tm-30) REVERT: B 3 VAL cc_start: 0.9419 (t) cc_final: 0.9153 (p) REVERT: B 4 MET cc_start: 0.8774 (mtp) cc_final: 0.8188 (mtp) REVERT: B 17 GLU cc_start: 0.8880 (mm-30) cc_final: 0.8677 (mm-30) REVERT: B 30 ASN cc_start: 0.9017 (p0) cc_final: 0.8536 (p0) REVERT: B 57 ASP cc_start: 0.8196 (t0) cc_final: 0.7865 (t0) REVERT: B 70 GLU cc_start: 0.8244 (mm-30) cc_final: 0.7987 (mm-30) REVERT: B 81 GLU cc_start: 0.9144 (pt0) cc_final: 0.8501 (tm-30) REVERT: B 106 GLU cc_start: 0.8040 (tp30) cc_final: 0.7765 (tp30) REVERT: C 471 GLU cc_start: 0.9086 (tp30) cc_final: 0.8652 (tp30) REVERT: C 516 GLU cc_start: 0.8259 (tt0) cc_final: 0.7958 (pt0) outliers start: 15 outliers final: 9 residues processed: 66 average time/residue: 0.1612 time to fit residues: 13.0822 Evaluate side-chains 64 residues out of total 353 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 55 time to evaluate : 0.396 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 TRP Chi-restraints excluded: chain A residue 98 ASP Chi-restraints excluded: chain A residue 101 ILE Chi-restraints excluded: chain B residue 5 THR Chi-restraints excluded: chain B residue 107 ILE Chi-restraints excluded: chain C residue 364 ASP Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 395 VAL Chi-restraints excluded: chain C residue 456 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 16 optimal weight: 0.7980 chunk 9 optimal weight: 5.9990 chunk 28 optimal weight: 1.9990 chunk 3 optimal weight: 1.9990 chunk 13 optimal weight: 0.5980 chunk 36 optimal weight: 5.9990 chunk 5 optimal weight: 0.7980 chunk 0 optimal weight: 6.9990 chunk 33 optimal weight: 2.9990 chunk 2 optimal weight: 0.9990 chunk 7 optimal weight: 0.9990 overall best weight: 0.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 90 GLN ** 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 = 0.3063 r_free = 0.3063 target = 0.063036 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2821 r_free = 0.2821 target = 0.050265 restraints weight = 9661.635| |-----------------------------------------------------------------------------| r_work (start): 0.2809 rms_B_bonded: 3.74 r_work: 0.2670 rms_B_bonded: 3.91 restraints_weight: 0.5000 r_work (final): 0.2670 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8586 moved from start: 0.5542 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 3359 Z= 0.128 Angle : 0.599 6.489 4572 Z= 0.313 Chirality : 0.042 0.146 487 Planarity : 0.005 0.052 591 Dihedral : 4.053 19.267 464 Min Nonbonded Distance : 2.580 Molprobity Statistics. All-atom Clashscore : 7.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.73 % Favored : 92.27 % Rotamer: Outliers : 3.68 % Allowed : 17.28 % Favored : 79.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % 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: 414 helix: -4.55 (0.43), residues: 26 sheet: -0.14 (0.52), residues: 122 loop : -0.97 (0.37), residues: 266 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 36 HIS 0.000 0.000 HIS C 519 PHE 0.019 0.001 PHE C 400 TYR 0.016 0.001 TYR B 36 ARG 0.014 0.001 ARG B 24 Details of bonding type rmsd hydrogen bonds : bond 0.02589 ( 78) hydrogen bonds : angle 4.92666 ( 180) SS BOND : bond 0.00193 ( 6) SS BOND : angle 2.28597 ( 12) covalent geometry : bond 0.00304 ( 3353) covalent geometry : angle 0.58797 ( 4560) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 69 residues out of total 353 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 56 time to evaluate : 0.375 Fit side-chains REVERT: A 88 ASP cc_start: 0.9288 (m-30) cc_final: 0.9057 (p0) REVERT: A 104 GLU cc_start: 0.8139 (tm-30) cc_final: 0.7526 (tm-30) REVERT: B 3 VAL cc_start: 0.9420 (t) cc_final: 0.9154 (p) REVERT: B 17 GLU cc_start: 0.8902 (mm-30) cc_final: 0.8687 (mm-30) REVERT: B 30 ASN cc_start: 0.9029 (p0) cc_final: 0.8517 (p0) REVERT: B 57 ASP cc_start: 0.8202 (t0) cc_final: 0.7877 (t0) REVERT: B 70 GLU cc_start: 0.8253 (mm-30) cc_final: 0.7891 (mm-30) REVERT: B 81 GLU cc_start: 0.9118 (OUTLIER) cc_final: 0.8484 (tm-30) REVERT: C 471 GLU cc_start: 0.9114 (tp30) cc_final: 0.8681 (tp30) REVERT: C 516 GLU cc_start: 0.8272 (tt0) cc_final: 0.7965 (pt0) outliers start: 13 outliers final: 11 residues processed: 62 average time/residue: 0.1579 time to fit residues: 12.1112 Evaluate side-chains 66 residues out of total 353 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 54 time to evaluate : 0.397 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 TRP Chi-restraints excluded: chain A residue 98 ASP Chi-restraints excluded: chain A residue 101 ILE Chi-restraints excluded: chain B residue 13 VAL Chi-restraints excluded: chain B residue 81 GLU Chi-restraints excluded: chain B residue 107 ILE Chi-restraints excluded: chain C residue 383 SER Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 391 CYS Chi-restraints excluded: chain C residue 395 VAL Chi-restraints excluded: chain C residue 434 ILE Chi-restraints excluded: chain C residue 456 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 23 optimal weight: 4.9990 chunk 33 optimal weight: 3.9990 chunk 39 optimal weight: 0.5980 chunk 1 optimal weight: 0.9990 chunk 6 optimal weight: 0.9980 chunk 37 optimal weight: 0.9980 chunk 30 optimal weight: 3.9990 chunk 19 optimal weight: 0.6980 chunk 14 optimal weight: 0.9990 chunk 9 optimal weight: 5.9990 chunk 28 optimal weight: 1.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 90 GLN ** 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 = 0.3060 r_free = 0.3060 target = 0.062935 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2815 r_free = 0.2815 target = 0.050050 restraints weight = 9772.666| |-----------------------------------------------------------------------------| r_work (start): 0.2804 rms_B_bonded: 3.79 r_work: 0.2668 rms_B_bonded: 3.94 restraints_weight: 0.5000 r_work (final): 0.2668 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8580 moved from start: 0.5623 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 3359 Z= 0.131 Angle : 0.612 6.425 4572 Z= 0.320 Chirality : 0.043 0.147 487 Planarity : 0.004 0.038 591 Dihedral : 4.050 19.270 464 Min Nonbonded Distance : 2.563 Molprobity Statistics. All-atom Clashscore : 7.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.73 % Favored : 92.27 % Rotamer: Outliers : 3.40 % Allowed : 18.70 % Favored : 77.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % 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: -1.36 (0.41), residues: 414 helix: -4.48 (0.48), residues: 26 sheet: -0.02 (0.52), residues: 122 loop : -0.96 (0.37), residues: 266 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 36 HIS 0.000 0.000 HIS C 519 PHE 0.017 0.001 PHE C 400 TYR 0.011 0.001 TYR B 36 ARG 0.002 0.000 ARG B 24 Details of bonding type rmsd hydrogen bonds : bond 0.02662 ( 78) hydrogen bonds : angle 4.85950 ( 180) SS BOND : bond 0.00255 ( 6) SS BOND : angle 2.29042 ( 12) covalent geometry : bond 0.00311 ( 3353) covalent geometry : angle 0.60143 ( 4560) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 353 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 54 time to evaluate : 0.402 Fit side-chains REVERT: A 88 ASP cc_start: 0.9277 (m-30) cc_final: 0.9071 (p0) REVERT: A 104 GLU cc_start: 0.8128 (tm-30) cc_final: 0.7489 (tm-30) REVERT: B 3 VAL cc_start: 0.9483 (t) cc_final: 0.9237 (p) REVERT: B 17 GLU cc_start: 0.8895 (mm-30) cc_final: 0.8664 (mm-30) REVERT: B 30 ASN cc_start: 0.9020 (p0) cc_final: 0.8500 (p0) REVERT: B 57 ASP cc_start: 0.8247 (t0) cc_final: 0.7916 (t0) REVERT: B 81 GLU cc_start: 0.9092 (OUTLIER) cc_final: 0.8505 (tm-30) REVERT: C 471 GLU cc_start: 0.9106 (tp30) cc_final: 0.8678 (tp30) REVERT: C 516 GLU cc_start: 0.8311 (tt0) cc_final: 0.8017 (pt0) outliers start: 12 outliers final: 11 residues processed: 59 average time/residue: 0.1689 time to fit residues: 12.1581 Evaluate side-chains 64 residues out of total 353 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 52 time to evaluate : 0.385 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 TRP Chi-restraints excluded: chain A residue 98 ASP Chi-restraints excluded: chain A residue 101 ILE Chi-restraints excluded: chain B residue 13 VAL Chi-restraints excluded: chain B residue 81 GLU Chi-restraints excluded: chain B residue 107 ILE Chi-restraints excluded: chain C residue 383 SER Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 391 CYS Chi-restraints excluded: chain C residue 395 VAL Chi-restraints excluded: chain C residue 434 ILE Chi-restraints excluded: chain C residue 456 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 1 optimal weight: 1.9990 chunk 35 optimal weight: 0.0570 chunk 11 optimal weight: 0.5980 chunk 36 optimal weight: 1.9990 chunk 29 optimal weight: 0.0970 chunk 23 optimal weight: 4.9990 chunk 22 optimal weight: 3.9990 chunk 4 optimal weight: 0.0270 chunk 32 optimal weight: 4.9990 chunk 30 optimal weight: 1.9990 chunk 21 optimal weight: 1.9990 overall best weight: 0.5556 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 90 GLN ** 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 = 0.3078 r_free = 0.3078 target = 0.064140 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2819 r_free = 0.2819 target = 0.050752 restraints weight = 9876.731| |-----------------------------------------------------------------------------| r_work (start): 0.2830 rms_B_bonded: 4.05 r_work: 0.2688 rms_B_bonded: 4.16 restraints_weight: 0.5000 r_work (final): 0.2688 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8640 moved from start: 0.5718 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 3359 Z= 0.110 Angle : 0.598 6.354 4572 Z= 0.313 Chirality : 0.042 0.147 487 Planarity : 0.004 0.038 591 Dihedral : 3.936 18.064 464 Min Nonbonded Distance : 2.564 Molprobity Statistics. All-atom Clashscore : 7.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.97 % Favored : 92.03 % Rotamer: Outliers : 3.68 % Allowed : 18.70 % Favored : 77.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % 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: -1.22 (0.42), residues: 414 helix: -4.30 (0.62), residues: 26 sheet: 0.14 (0.53), residues: 122 loop : -0.91 (0.37), residues: 266 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 36 HIS 0.001 0.000 HIS C 339 PHE 0.017 0.001 PHE C 400 TYR 0.009 0.001 TYR B 49 ARG 0.001 0.000 ARG A 102 Details of bonding type rmsd hydrogen bonds : bond 0.02576 ( 78) hydrogen bonds : angle 4.70222 ( 180) SS BOND : bond 0.00228 ( 6) SS BOND : angle 2.07416 ( 12) covalent geometry : bond 0.00258 ( 3353) covalent geometry : angle 0.58930 ( 4560) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 68 residues out of total 353 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 55 time to evaluate : 0.371 Fit side-chains REVERT: A 104 GLU cc_start: 0.8165 (tm-30) cc_final: 0.7554 (tm-30) REVERT: B 3 VAL cc_start: 0.9466 (t) cc_final: 0.9212 (p) REVERT: B 17 GLU cc_start: 0.8876 (mm-30) cc_final: 0.8644 (mm-30) REVERT: B 24 ARG cc_start: 0.8494 (ttm-80) cc_final: 0.7822 (ttm110) REVERT: B 30 ASN cc_start: 0.9020 (p0) cc_final: 0.8494 (p0) REVERT: B 57 ASP cc_start: 0.8189 (t0) cc_final: 0.7901 (t0) REVERT: B 70 GLU cc_start: 0.8374 (mm-30) cc_final: 0.8091 (mm-30) REVERT: B 81 GLU cc_start: 0.9082 (OUTLIER) cc_final: 0.8540 (tm-30) REVERT: C 471 GLU cc_start: 0.9048 (tp30) cc_final: 0.8667 (tp30) REVERT: C 516 GLU cc_start: 0.8309 (tt0) cc_final: 0.8016 (pt0) outliers start: 13 outliers final: 11 residues processed: 60 average time/residue: 0.1705 time to fit residues: 12.6508 Evaluate side-chains 64 residues out of total 353 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 52 time to evaluate : 0.366 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 MET Chi-restraints excluded: chain A residue 98 ASP Chi-restraints excluded: chain A residue 101 ILE Chi-restraints excluded: chain B residue 13 VAL Chi-restraints excluded: chain B residue 81 GLU Chi-restraints excluded: chain B residue 107 ILE Chi-restraints excluded: chain C residue 383 SER Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 391 CYS Chi-restraints excluded: chain C residue 395 VAL Chi-restraints excluded: chain C residue 434 ILE Chi-restraints excluded: chain C residue 456 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 29 optimal weight: 0.0980 chunk 17 optimal weight: 4.9990 chunk 37 optimal weight: 3.9990 chunk 22 optimal weight: 3.9990 chunk 13 optimal weight: 5.9990 chunk 38 optimal weight: 1.9990 chunk 18 optimal weight: 0.9980 chunk 23 optimal weight: 7.9990 chunk 34 optimal weight: 0.2980 chunk 30 optimal weight: 0.8980 chunk 25 optimal weight: 2.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 90 GLN ** 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 = 0.3048 r_free = 0.3048 target = 0.060549 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2811 r_free = 0.2811 target = 0.050082 restraints weight = 9572.548| |-----------------------------------------------------------------------------| r_work (start): 0.2816 rms_B_bonded: 3.67 r_work: 0.2682 rms_B_bonded: 3.85 restraints_weight: 0.5000 r_work (final): 0.2682 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8622 moved from start: 0.5770 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 3359 Z= 0.130 Angle : 0.617 6.509 4572 Z= 0.320 Chirality : 0.043 0.149 487 Planarity : 0.004 0.038 591 Dihedral : 4.001 19.495 464 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 8.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.97 % Favored : 92.03 % Rotamer: Outliers : 3.40 % Allowed : 19.26 % Favored : 77.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % 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: -1.23 (0.42), residues: 414 helix: -4.22 (0.68), residues: 26 sheet: 0.16 (0.53), residues: 122 loop : -0.94 (0.37), residues: 266 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 36 HIS 0.001 0.000 HIS C 339 PHE 0.010 0.001 PHE C 400 TYR 0.019 0.001 TYR B 36 ARG 0.002 0.000 ARG B 24 Details of bonding type rmsd hydrogen bonds : bond 0.02516 ( 78) hydrogen bonds : angle 4.72281 ( 180) SS BOND : bond 0.00205 ( 6) SS BOND : angle 2.13233 ( 12) covalent geometry : bond 0.00307 ( 3353) covalent geometry : angle 0.60818 ( 4560) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 65 residues out of total 353 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 53 time to evaluate : 0.379 Fit side-chains REVERT: A 104 GLU cc_start: 0.8171 (tm-30) cc_final: 0.7533 (tm-30) REVERT: B 3 VAL cc_start: 0.9460 (t) cc_final: 0.9198 (p) REVERT: B 24 ARG cc_start: 0.8476 (ttm-80) cc_final: 0.7883 (ttm110) REVERT: B 30 ASN cc_start: 0.8999 (p0) cc_final: 0.8479 (p0) REVERT: B 57 ASP cc_start: 0.8163 (t0) cc_final: 0.7871 (t0) REVERT: B 70 GLU cc_start: 0.8343 (mm-30) cc_final: 0.8040 (mm-30) REVERT: B 81 GLU cc_start: 0.9058 (OUTLIER) cc_final: 0.8539 (tm-30) REVERT: C 471 GLU cc_start: 0.9038 (tp30) cc_final: 0.8697 (tp30) REVERT: C 516 GLU cc_start: 0.8320 (tt0) cc_final: 0.8028 (pt0) outliers start: 12 outliers final: 11 residues processed: 57 average time/residue: 0.1633 time to fit residues: 11.6753 Evaluate side-chains 66 residues out of total 353 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 54 time to evaluate : 0.424 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 MET Chi-restraints excluded: chain A residue 98 ASP Chi-restraints excluded: chain A residue 101 ILE Chi-restraints excluded: chain B residue 13 VAL Chi-restraints excluded: chain B residue 81 GLU Chi-restraints excluded: chain B residue 107 ILE Chi-restraints excluded: chain C residue 383 SER Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 391 CYS Chi-restraints excluded: chain C residue 395 VAL Chi-restraints excluded: chain C residue 434 ILE Chi-restraints excluded: chain C residue 456 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 14 optimal weight: 2.9990 chunk 13 optimal weight: 5.9990 chunk 25 optimal weight: 2.9990 chunk 12 optimal weight: 0.7980 chunk 3 optimal weight: 3.9990 chunk 24 optimal weight: 0.8980 chunk 0 optimal weight: 6.9990 chunk 10 optimal weight: 3.9990 chunk 5 optimal weight: 0.9980 chunk 32 optimal weight: 0.0170 chunk 29 optimal weight: 2.9990 overall best weight: 1.1420 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 6 GLN ** B 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3029 r_free = 0.3029 target = 0.060098 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2754 r_free = 0.2754 target = 0.048410 restraints weight = 9721.049| |-----------------------------------------------------------------------------| r_work (start): 0.2780 rms_B_bonded: 3.94 r_work: 0.2640 rms_B_bonded: 4.05 restraints_weight: 0.5000 r_work (final): 0.2640 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8669 moved from start: 0.5813 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 3359 Z= 0.151 Angle : 0.629 7.056 4572 Z= 0.324 Chirality : 0.043 0.147 487 Planarity : 0.004 0.037 591 Dihedral : 4.093 21.196 464 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 8.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.21 % Favored : 91.79 % Rotamer: Outliers : 3.68 % Allowed : 18.98 % Favored : 77.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % 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: -1.23 (0.42), residues: 414 helix: -4.20 (0.72), residues: 26 sheet: 0.13 (0.53), residues: 122 loop : -0.92 (0.37), residues: 266 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 436 HIS 0.001 0.000 HIS C 339 PHE 0.007 0.001 PHE C 392 TYR 0.023 0.001 TYR B 36 ARG 0.002 0.000 ARG B 24 Details of bonding type rmsd hydrogen bonds : bond 0.02609 ( 78) hydrogen bonds : angle 4.77662 ( 180) SS BOND : bond 0.00239 ( 6) SS BOND : angle 2.20841 ( 12) covalent geometry : bond 0.00356 ( 3353) covalent geometry : angle 0.61965 ( 4560) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1927.30 seconds wall clock time: 33 minutes 48.92 seconds (2028.92 seconds total)