Starting phenix.real_space_refine on Fri Oct 10 12:00:35 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8k19_36789/10_2025/8k19_36789.cif Found real_map, /net/cci-nas-00/data/ceres_data/8k19_36789/10_2025/8k19_36789.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.88 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8k19_36789/10_2025/8k19_36789.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8k19_36789/10_2025/8k19_36789.map" model { file = "/net/cci-nas-00/data/ceres_data/8k19_36789/10_2025/8k19_36789.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8k19_36789/10_2025/8k19_36789.cif" } resolution = 3.88 write_initial_geo_file = False refinement { macro_cycles = 10 } 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= 0.002 sd= 0.021 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 1446 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 19 5.16 5 C 2041 2.51 5 N 546 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 9 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5842/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 3224 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 906 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 906 Classifications: {'peptide': 119} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 114} Chain: "B" Number of atoms: 818 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 818 Classifications: {'peptide': 107} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 4, 'TRANS': 100} Chain: "E" Number of atoms: 1500 Number of conformers: 1 Conformer: "" Number of residues, atoms: 188, 1500 Classifications: {'peptide': 188} Link IDs: {'PTRANS': 10, 'TRANS': 177} Chain breaks: 1 Time building chain proxies: 0.99, per 1000 atoms: 0.31 Number of scatterers: 3224 At special positions: 0 Unit cell: (61.48, 69.96, 94.34, 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 19 16.00 O 618 8.00 N 546 7.00 C 2041 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 E 336 " - pdb=" SG CYS E 361 " distance=2.03 Simple disulfide: pdb=" SG CYS E 379 " - pdb=" SG CYS E 432 " distance=2.05 Simple disulfide: pdb=" SG CYS E 391 " - pdb=" SG CYS E 525 " distance=2.04 Simple disulfide: pdb=" SG CYS E 480 " - pdb=" SG CYS E 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: 0.25 Conformation dependent library (CDL) restraints added in 130.9 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 812 Ramachandran restraints generated. 406 Oldfield, 0 Emsley, 406 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: 10 helices and 9 sheets defined 12.8% alpha, 38.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.14 Creating SS restraints... Processing helix chain 'A' and resid 28 through 32 Processing helix chain 'A' and resid 61 through 64 removed outlier: 3.507A pdb=" N LYS A 64 " --> pdb=" O ASP A 61 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 61 through 64' Processing helix chain 'A' and resid 86 through 90 Processing helix chain 'B' and resid 79 through 83 removed outlier: 3.877A pdb=" N ILE B 83 " --> pdb=" O PRO B 80 " (cutoff:3.500A) Processing helix chain 'E' and resid 338 through 343 Processing helix chain 'E' and resid 349 through 353 Processing helix chain 'E' and resid 365 through 370 Processing helix chain 'E' and resid 405 through 410 Processing helix chain 'E' and resid 416 through 422 Processing helix chain 'E' and resid 502 through 505 Processing sheet with id=AA1, first strand: chain 'A' and resid 4 through 7 removed outlier: 3.539A pdb=" N VAL A 5 " --> pdb=" O ALA A 23 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N LEU A 80 " --> pdb=" O LEU A 20 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 57 through 59 removed outlier: 6.826A pdb=" N TRP A 36 " --> pdb=" O VAL A 48 " (cutoff:3.500A) removed outlier: 4.517A pdb=" N ASP A 50 " --> pdb=" O MET A 34 " (cutoff:3.500A) removed outlier: 6.747A pdb=" N MET A 34 " --> pdb=" O ASP A 50 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N VAL A 108 " --> pdb=" O ARG A 97 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 57 through 59 removed outlier: 6.826A pdb=" N TRP A 36 " --> pdb=" O VAL A 48 " (cutoff:3.500A) removed outlier: 4.517A pdb=" N ASP A 50 " --> pdb=" O MET A 34 " (cutoff:3.500A) removed outlier: 6.747A pdb=" N MET A 34 " --> pdb=" O ASP A 50 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 4 through 7 removed outlier: 3.939A pdb=" N HIS B 70 " --> pdb=" O SER B 67 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 10 through 13 removed outlier: 3.788A pdb=" N ALA B 84 " --> pdb=" O VAL B 104 " (cutoff:3.500A) removed outlier: 6.681A pdb=" N TRP B 35 " --> pdb=" O LEU B 47 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'E' and resid 354 through 358 removed outlier: 3.658A pdb=" N GLU E 354 " --> pdb=" O SER E 399 " (cutoff:3.500A) removed outlier: 4.177A pdb=" N VAL E 395 " --> pdb=" O ILE E 358 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N GLY E 431 " --> pdb=" O TYR E 380 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'E' and resid 354 through 358 removed outlier: 3.658A pdb=" N GLU E 354 " --> pdb=" O SER E 399 " (cutoff:3.500A) removed outlier: 4.177A pdb=" N VAL E 395 " --> pdb=" O ILE E 358 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N PHE E 392 " --> pdb=" O VAL E 524 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N VAL E 524 " --> pdb=" O PHE E 392 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'E' and resid 452 through 454 Processing sheet with id=AA9, first strand: chain 'E' and resid 473 through 474 122 hydrogen bonds defined for protein. 300 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: 0.50 Time building geometry restraints manager: 0.35 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 782 1.33 - 1.46: 737 1.46 - 1.58: 1757 1.58 - 1.70: 1 1.70 - 1.82: 26 Bond restraints: 3303 Sorted by residual: bond pdb=" CB ASP B 1 " pdb=" CG ASP B 1 " ideal model delta sigma weight residual 1.516 1.631 -0.115 2.50e-02 1.60e+03 2.13e+01 bond pdb=" N GLY E 476 " pdb=" CA GLY E 476 " ideal model delta sigma weight residual 1.446 1.476 -0.030 9.50e-03 1.11e+04 1.01e+01 bond pdb=" CD2 HIS A 104 " pdb=" NE2 HIS A 104 " ideal model delta sigma weight residual 1.374 1.407 -0.033 1.10e-02 8.26e+03 8.78e+00 bond pdb=" CZ ARG B 61 " pdb=" NH2 ARG B 61 " ideal model delta sigma weight residual 1.330 1.292 0.038 1.30e-02 5.92e+03 8.56e+00 bond pdb=" N VAL E 382 " pdb=" CA VAL E 382 " ideal model delta sigma weight residual 1.455 1.490 -0.034 1.18e-02 7.18e+03 8.51e+00 ... (remaining 3298 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.65: 2953 1.65 - 3.30: 1198 3.30 - 4.94: 279 4.94 - 6.59: 41 6.59 - 8.24: 13 Bond angle restraints: 4484 Sorted by residual: angle pdb=" CA ASP A 107 " pdb=" CB ASP A 107 " pdb=" CG ASP A 107 " ideal model delta sigma weight residual 112.60 119.22 -6.62 1.00e+00 1.00e+00 4.39e+01 angle pdb=" OD1 ASN E 334 " pdb=" CG ASN E 334 " pdb=" ND2 ASN E 334 " ideal model delta sigma weight residual 122.60 116.66 5.94 1.00e+00 1.00e+00 3.53e+01 angle pdb=" CB HIS B 93 " pdb=" CG HIS B 93 " pdb=" CD2 HIS B 93 " ideal model delta sigma weight residual 131.20 123.49 7.71 1.30e+00 5.92e-01 3.52e+01 angle pdb=" OE1 GLN A 39 " pdb=" CD GLN A 39 " pdb=" NE2 GLN A 39 " ideal model delta sigma weight residual 122.60 117.01 5.59 1.00e+00 1.00e+00 3.12e+01 angle pdb=" OE1 GLN A 13 " pdb=" CD GLN A 13 " pdb=" NE2 GLN A 13 " ideal model delta sigma weight residual 122.60 117.11 5.49 1.00e+00 1.00e+00 3.02e+01 ... (remaining 4479 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 25.54: 1886 25.54 - 51.07: 63 51.07 - 76.61: 6 76.61 - 102.15: 1 102.15 - 127.68: 1 Dihedral angle restraints: 1957 sinusoidal: 765 harmonic: 1192 Sorted by residual: dihedral pdb=" C GLU A 26 " pdb=" N GLU A 26 " pdb=" CA GLU A 26 " pdb=" CB GLU A 26 " ideal model delta harmonic sigma weight residual -122.60 -138.49 15.89 0 2.50e+00 1.60e-01 4.04e+01 dihedral pdb=" CA ARG A 97 " pdb=" C ARG A 97 " pdb=" N PRO A 98 " pdb=" CA PRO A 98 " ideal model delta harmonic sigma weight residual 180.00 152.15 27.85 0 5.00e+00 4.00e-02 3.10e+01 dihedral pdb=" CA ASN A 32 " pdb=" C ASN A 32 " pdb=" N TYR A 33 " pdb=" CA TYR A 33 " ideal model delta harmonic sigma weight residual 180.00 153.59 26.41 0 5.00e+00 4.00e-02 2.79e+01 ... (remaining 1954 not shown) Histogram of chiral volume deviations from ideal: 0.001 - 0.112: 370 0.112 - 0.223: 105 0.223 - 0.334: 6 0.334 - 0.444: 1 0.444 - 0.555: 1 Chirality restraints: 483 Sorted by residual: chirality pdb=" CA GLU A 26 " pdb=" N GLU A 26 " pdb=" C GLU A 26 " pdb=" CB GLU A 26 " both_signs ideal model delta sigma weight residual False 2.51 1.96 0.56 2.00e-01 2.50e+01 7.71e+00 chirality pdb=" CA ASN E 487 " pdb=" N ASN E 487 " pdb=" C ASN E 487 " pdb=" CB ASN E 487 " both_signs ideal model delta sigma weight residual False 2.51 2.17 0.34 2.00e-01 2.50e+01 2.90e+00 chirality pdb=" CB THR E 523 " pdb=" CA THR E 523 " pdb=" OG1 THR E 523 " pdb=" CG2 THR E 523 " both_signs ideal model delta sigma weight residual False 2.55 2.27 0.28 2.00e-01 2.50e+01 2.00e+00 ... (remaining 480 not shown) Planarity restraints: 581 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB HIS B 93 " 0.135 2.00e-02 2.50e+03 1.07e-01 1.70e+02 pdb=" CG HIS B 93 " -0.115 2.00e-02 2.50e+03 pdb=" ND1 HIS B 93 " -0.115 2.00e-02 2.50e+03 pdb=" CD2 HIS B 93 " -0.078 2.00e-02 2.50e+03 pdb=" CE1 HIS B 93 " 0.121 2.00e-02 2.50e+03 pdb=" NE2 HIS B 93 " 0.052 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLU B 105 " -0.057 2.00e-02 2.50e+03 1.20e-01 1.43e+02 pdb=" CD GLU B 105 " 0.207 2.00e-02 2.50e+03 pdb=" OE1 GLU B 105 " -0.075 2.00e-02 2.50e+03 pdb=" OE2 GLU B 105 " -0.075 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 59 " -0.137 2.00e-02 2.50e+03 7.20e-02 1.04e+02 pdb=" CG TYR A 59 " 0.057 2.00e-02 2.50e+03 pdb=" CD1 TYR A 59 " 0.084 2.00e-02 2.50e+03 pdb=" CD2 TYR A 59 " 0.047 2.00e-02 2.50e+03 pdb=" CE1 TYR A 59 " 0.004 2.00e-02 2.50e+03 pdb=" CE2 TYR A 59 " 0.034 2.00e-02 2.50e+03 pdb=" CZ TYR A 59 " 0.004 2.00e-02 2.50e+03 pdb=" OH TYR A 59 " -0.093 2.00e-02 2.50e+03 ... (remaining 578 not shown) Histogram of nonbonded interaction distances: 1.50 - 2.18: 1 2.18 - 2.86: 956 2.86 - 3.54: 4394 3.54 - 4.22: 7933 4.22 - 4.90: 12972 Nonbonded interactions: 26256 Sorted by model distance: nonbonded pdb=" CD2 LEU E 455 " pdb=" OE1 GLN E 493 " model vdw 1.496 3.460 nonbonded pdb=" CZ PHE E 456 " pdb=" NE2 GLN E 493 " model vdw 2.507 3.420 nonbonded pdb=" OG1 THR A 56 " pdb=" OD2 ASP E 420 " model vdw 2.538 3.040 nonbonded pdb=" OD1 ASP E 442 " pdb=" OH TYR E 451 " model vdw 2.580 3.040 nonbonded pdb=" N PHE B 49 " pdb=" O PHE B 49 " model vdw 2.586 2.496 ... (remaining 26251 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.910 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.020 Construct map_model_manager: 0.000 Extract box with map and model: 0.040 Check model and map are aligned: 0.000 Set scattering table: 0.010 Process input model: 5.270 Find NCS groups from input model: 0.010 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:1.240 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 9.510 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5336 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 : 0.014 0.115 3309 Z= 0.792 Angle : 1.836 8.239 4496 Z= 1.214 Chirality : 0.095 0.555 483 Planarity : 0.027 0.136 581 Dihedral : 13.091 127.681 1183 Min Nonbonded Distance : 1.496 Molprobity Statistics. All-atom Clashscore : 4.27 Ramachandran Plot: Outliers : 0.74 % Allowed : 4.68 % Favored : 94.58 % Rotamer: Outliers : 0.57 % Allowed : 3.12 % Favored : 96.32 % Cbeta Deviations : 0.53 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.84 (0.37), residues: 406 helix: -4.57 (0.30), residues: 24 sheet: -1.18 (0.39), residues: 122 loop : -0.87 (0.36), residues: 260 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.037 0.005 ARG A 35 TYR 0.137 0.031 TYR A 59 PHE 0.078 0.013 PHE E 497 TRP 0.080 0.026 TRP A 36 HIS 0.052 0.012 HIS B 93 Details of bonding type rmsd covalent geometry : bond 0.01360 ( 3303) covalent geometry : angle 1.83568 ( 4484) SS BOND : bond 0.00853 ( 6) SS BOND : angle 1.97784 ( 12) hydrogen bonds : bond 0.25137 ( 107) hydrogen bonds : angle 10.11466 ( 300) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 812 Ramachandran restraints generated. 406 Oldfield, 0 Emsley, 406 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 812 Ramachandran restraints generated. 406 Oldfield, 0 Emsley, 406 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 29 residues out of total 353 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 27 time to evaluate : 0.134 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 82 MET cc_start: -0.0555 (mtm) cc_final: -0.1670 (mtt) outliers start: 2 outliers final: 0 residues processed: 29 average time/residue: 0.1336 time to fit residues: 4.4835 Evaluate side-chains 13 residues out of total 353 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 13 time to evaluate : 0.145 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 24 optimal weight: 4.9990 chunk 26 optimal weight: 5.9990 chunk 2 optimal weight: 7.9990 chunk 16 optimal weight: 6.9990 chunk 32 optimal weight: 10.0000 chunk 31 optimal weight: 9.9990 chunk 25 optimal weight: 7.9990 chunk 19 optimal weight: 20.0000 chunk 30 optimal weight: 0.9990 chunk 22 optimal weight: 0.9990 chunk 37 optimal weight: 4.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 39 GLN ** B 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 37 GLN B 38 HIS ** B 93 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 394 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3958 r_free = 0.3958 target = 0.033463 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.020734 restraints weight = 49830.532| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.020796 restraints weight = 47936.202| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.020858 restraints weight = 44875.224| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.020916 restraints weight = 42440.892| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.020919 restraints weight = 40909.749| |-----------------------------------------------------------------------------| r_work (final): 0.3246 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8271 moved from start: 0.2868 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 3309 Z= 0.136 Angle : 0.615 6.963 4496 Z= 0.330 Chirality : 0.045 0.138 483 Planarity : 0.005 0.035 581 Dihedral : 5.431 35.323 457 Min Nonbonded Distance : 2.624 Molprobity Statistics. All-atom Clashscore : 14.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 0.00 % Allowed : 5.67 % Favored : 94.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.94 (0.39), residues: 406 helix: -2.77 (0.76), residues: 32 sheet: -0.59 (0.40), residues: 130 loop : -0.23 (0.39), residues: 244 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG E 454 TYR 0.015 0.002 TYR A 33 PHE 0.014 0.002 PHE B 49 TRP 0.008 0.001 TRP E 436 HIS 0.002 0.001 HIS B 91 Details of bonding type rmsd covalent geometry : bond 0.00309 ( 3303) covalent geometry : angle 0.61404 ( 4484) SS BOND : bond 0.00267 ( 6) SS BOND : angle 0.87391 ( 12) hydrogen bonds : bond 0.03302 ( 107) hydrogen bonds : angle 7.05585 ( 300) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 812 Ramachandran restraints generated. 406 Oldfield, 0 Emsley, 406 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 812 Ramachandran restraints generated. 406 Oldfield, 0 Emsley, 406 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 17 residues out of total 353 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 17 time to evaluate : 0.125 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 34 MET cc_start: 0.9304 (mpp) cc_final: 0.9008 (pmm) REVERT: A 82 MET cc_start: -0.0476 (mtm) cc_final: -0.1048 (mtt) REVERT: B 4 MET cc_start: 0.9037 (mtm) cc_final: 0.8828 (ptp) outliers start: 0 outliers final: 0 residues processed: 17 average time/residue: 0.1429 time to fit residues: 2.8685 Evaluate side-chains 10 residues out of total 353 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 10 time to evaluate : 0.102 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 22 optimal weight: 4.9990 chunk 2 optimal weight: 20.0000 chunk 23 optimal weight: 8.9990 chunk 11 optimal weight: 8.9990 chunk 21 optimal weight: 1.9990 chunk 17 optimal weight: 20.0000 chunk 31 optimal weight: 20.0000 chunk 30 optimal weight: 9.9990 chunk 26 optimal weight: 9.9990 chunk 0 optimal weight: 2.9990 chunk 15 optimal weight: 50.0000 overall best weight: 5.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 93 HIS ** 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 = 0.3453 r_free = 0.3453 target = 0.024860 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.019933 restraints weight = 72161.045| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 22)----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.019933 restraints weight = 79849.856| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.019933 restraints weight = 79883.123| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.019933 restraints weight = 79883.308| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.019933 restraints weight = 79886.496| |-----------------------------------------------------------------------------| r_work (final): 0.3243 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8210 moved from start: 0.4543 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 3309 Z= 0.160 Angle : 0.616 6.003 4496 Z= 0.331 Chirality : 0.044 0.140 483 Planarity : 0.005 0.032 581 Dihedral : 5.124 22.183 457 Min Nonbonded Distance : 2.562 Molprobity Statistics. All-atom Clashscore : 19.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.93 % Favored : 95.07 % Rotamer: Outliers : 0.28 % Allowed : 7.65 % Favored : 92.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.93 (0.40), residues: 406 helix: -3.54 (0.59), residues: 44 sheet: -0.30 (0.43), residues: 124 loop : -0.07 (0.40), residues: 238 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG E 454 TYR 0.014 0.002 TYR A 79 PHE 0.012 0.002 PHE E 377 TRP 0.008 0.002 TRP A 109 HIS 0.004 0.002 HIS E 505 Details of bonding type rmsd covalent geometry : bond 0.00355 ( 3303) covalent geometry : angle 0.61463 ( 4484) SS BOND : bond 0.00342 ( 6) SS BOND : angle 1.04757 ( 12) hydrogen bonds : bond 0.03089 ( 107) hydrogen bonds : angle 6.81936 ( 300) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 812 Ramachandran restraints generated. 406 Oldfield, 0 Emsley, 406 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 812 Ramachandran restraints generated. 406 Oldfield, 0 Emsley, 406 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 13 residues out of total 353 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 12 time to evaluate : 0.145 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 82 MET cc_start: -0.2677 (mtm) cc_final: -0.2908 (mtt) outliers start: 1 outliers final: 0 residues processed: 13 average time/residue: 0.1157 time to fit residues: 1.8200 Evaluate side-chains 10 residues out of total 353 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 10 time to evaluate : 0.096 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 17 optimal weight: 30.0000 chunk 9 optimal weight: 9.9990 chunk 12 optimal weight: 40.0000 chunk 15 optimal weight: 1.9990 chunk 8 optimal weight: 50.0000 chunk 0 optimal weight: 9.9990 chunk 1 optimal weight: 6.9990 chunk 28 optimal weight: 8.9990 chunk 19 optimal weight: 7.9990 chunk 33 optimal weight: 20.0000 chunk 24 optimal weight: 6.9990 overall best weight: 6.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 93 HIS ** E 505 HIS ** 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 = 0.3407 r_free = 0.3407 target = 0.024155 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3263 r_free = 0.3263 target = 0.019408 restraints weight = 71787.842| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3255 r_free = 0.3255 target = 0.019240 restraints weight = 91610.994| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 15)----------------| | r_work = 0.3255 r_free = 0.3255 target = 0.019240 restraints weight = 107172.154| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.3255 r_free = 0.3255 target = 0.019240 restraints weight = 107172.217| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3255 r_free = 0.3255 target = 0.019240 restraints weight = 107172.772| |-----------------------------------------------------------------------------| r_work (final): 0.3211 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8104 moved from start: 0.5816 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 3309 Z= 0.185 Angle : 0.609 5.076 4496 Z= 0.332 Chirality : 0.044 0.139 483 Planarity : 0.005 0.037 581 Dihedral : 5.285 26.188 457 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 22.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.93 % Favored : 95.07 % Rotamer: Outliers : 0.00 % Allowed : 8.78 % Favored : 91.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.87 (0.41), residues: 406 helix: -3.45 (0.60), residues: 44 sheet: -0.20 (0.43), residues: 137 loop : -0.07 (0.42), residues: 225 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG E 454 TYR 0.019 0.002 TYR E 380 PHE 0.015 0.002 PHE B 49 TRP 0.015 0.002 TRP A 109 HIS 0.004 0.002 HIS B 70 Details of bonding type rmsd covalent geometry : bond 0.00396 ( 3303) covalent geometry : angle 0.60702 ( 4484) SS BOND : bond 0.00393 ( 6) SS BOND : angle 1.02330 ( 12) hydrogen bonds : bond 0.03188 ( 107) hydrogen bonds : angle 6.95475 ( 300) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 812 Ramachandran restraints generated. 406 Oldfield, 0 Emsley, 406 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 812 Ramachandran restraints generated. 406 Oldfield, 0 Emsley, 406 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 10 residues out of total 353 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 10 time to evaluate : 0.146 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 10 average time/residue: 0.1368 time to fit residues: 1.7079 Evaluate side-chains 10 residues out of total 353 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 10 time to evaluate : 0.129 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 5 optimal weight: 30.0000 chunk 19 optimal weight: 30.0000 chunk 4 optimal weight: 50.0000 chunk 21 optimal weight: 6.9990 chunk 8 optimal weight: 20.0000 chunk 27 optimal weight: 30.0000 chunk 7 optimal weight: 7.9990 chunk 13 optimal weight: 6.9990 chunk 6 optimal weight: 0.9990 chunk 11 optimal weight: 7.9990 chunk 12 optimal weight: 0.9980 overall best weight: 4.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 70 HIS E 493 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.024033 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3260 r_free = 0.3260 target = 0.019068 restraints weight = 71890.955| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 22)----------------| | r_work = 0.3260 r_free = 0.3260 target = 0.019068 restraints weight = 81243.389| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 18)----------------| | r_work = 0.3260 r_free = 0.3260 target = 0.019068 restraints weight = 81245.251| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 16)----------------| | r_work = 0.3260 r_free = 0.3260 target = 0.019068 restraints weight = 81246.018| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3260 r_free = 0.3260 target = 0.019068 restraints weight = 81246.307| |-----------------------------------------------------------------------------| r_work (final): 0.3206 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8230 moved from start: 0.6222 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 3309 Z= 0.143 Angle : 0.559 7.173 4496 Z= 0.299 Chirality : 0.043 0.143 483 Planarity : 0.004 0.034 581 Dihedral : 5.035 19.610 457 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 20.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.68 % Favored : 95.32 % Rotamer: Outliers : 0.85 % Allowed : 9.92 % Favored : 89.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.91 (0.42), residues: 406 helix: -3.48 (0.62), residues: 44 sheet: -0.31 (0.43), residues: 144 loop : -0.01 (0.44), residues: 218 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG E 454 TYR 0.016 0.002 TYR E 380 PHE 0.012 0.002 PHE E 374 TRP 0.008 0.002 TRP A 36 HIS 0.003 0.001 HIS B 38 Details of bonding type rmsd covalent geometry : bond 0.00312 ( 3303) covalent geometry : angle 0.55797 ( 4484) SS BOND : bond 0.00272 ( 6) SS BOND : angle 0.93091 ( 12) hydrogen bonds : bond 0.02638 ( 107) hydrogen bonds : angle 6.49752 ( 300) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 812 Ramachandran restraints generated. 406 Oldfield, 0 Emsley, 406 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 812 Ramachandran restraints generated. 406 Oldfield, 0 Emsley, 406 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 13 residues out of total 353 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 10 time to evaluate : 0.157 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 4 MET cc_start: 0.8990 (ptp) cc_final: 0.8753 (ptp) outliers start: 3 outliers final: 1 residues processed: 13 average time/residue: 0.0906 time to fit residues: 1.5230 Evaluate side-chains 11 residues out of total 353 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 10 time to evaluate : 0.151 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 446 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 8 optimal weight: 40.0000 chunk 31 optimal weight: 10.0000 chunk 4 optimal weight: 50.0000 chunk 33 optimal weight: 20.0000 chunk 37 optimal weight: 7.9990 chunk 16 optimal weight: 8.9990 chunk 12 optimal weight: 50.0000 chunk 22 optimal weight: 4.9990 chunk 20 optimal weight: 9.9990 chunk 18 optimal weight: 9.9990 chunk 5 optimal weight: 20.0000 overall best weight: 8.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 37 GLN ** B 93 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 394 ASN ** E 505 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.023532 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3129 r_free = 0.3129 target = 0.017004 restraints weight = 76150.109| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 22)----------------| | r_work = 0.3129 r_free = 0.3129 target = 0.017004 restraints weight = 82742.766| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.3129 r_free = 0.3129 target = 0.017004 restraints weight = 82742.894| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.3129 r_free = 0.3129 target = 0.017004 restraints weight = 82742.894| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3129 r_free = 0.3129 target = 0.017004 restraints weight = 82742.894| |-----------------------------------------------------------------------------| r_work (final): 0.3134 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8237 moved from start: 0.7791 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.075 3309 Z= 0.231 Angle : 0.675 7.660 4496 Z= 0.364 Chirality : 0.046 0.150 483 Planarity : 0.005 0.041 581 Dihedral : 5.621 25.095 457 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 32.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.39 % Favored : 92.61 % Rotamer: Outliers : 1.98 % Allowed : 11.05 % Favored : 86.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.13 (0.42), residues: 406 helix: -3.56 (0.60), residues: 44 sheet: -0.50 (0.43), residues: 136 loop : -0.16 (0.44), residues: 226 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG E 454 TYR 0.018 0.002 TYR E 365 PHE 0.018 0.003 PHE E 347 TRP 0.009 0.002 TRP A 109 HIS 0.005 0.002 HIS B 70 Details of bonding type rmsd covalent geometry : bond 0.00500 ( 3303) covalent geometry : angle 0.66977 ( 4484) SS BOND : bond 0.00707 ( 6) SS BOND : angle 1.82258 ( 12) hydrogen bonds : bond 0.03818 ( 107) hydrogen bonds : angle 7.75391 ( 300) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 812 Ramachandran restraints generated. 406 Oldfield, 0 Emsley, 406 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 812 Ramachandran restraints generated. 406 Oldfield, 0 Emsley, 406 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 16 residues out of total 353 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 9 time to evaluate : 0.129 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 100 MET cc_start: 0.4649 (ttt) cc_final: 0.3850 (ttt) outliers start: 7 outliers final: 3 residues processed: 16 average time/residue: 0.0899 time to fit residues: 1.8304 Evaluate side-chains 12 residues out of total 353 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 9 time to evaluate : 0.130 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 THR Chi-restraints excluded: chain B residue 92 ASP Chi-restraints excluded: chain E residue 446 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 29 optimal weight: 30.0000 chunk 17 optimal weight: 9.9990 chunk 34 optimal weight: 10.0000 chunk 20 optimal weight: 9.9990 chunk 16 optimal weight: 10.0000 chunk 36 optimal weight: 5.9990 chunk 38 optimal weight: 5.9990 chunk 15 optimal weight: 7.9990 chunk 2 optimal weight: 10.0000 chunk 21 optimal weight: 0.0170 chunk 26 optimal weight: 10.0000 overall best weight: 6.0026 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 32 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 = 0.3384 r_free = 0.3384 target = 0.023310 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3128 r_free = 0.3128 target = 0.016762 restraints weight = 76437.573| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 22)----------------| | r_work = 0.3128 r_free = 0.3128 target = 0.016762 restraints weight = 80920.691| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.3128 r_free = 0.3128 target = 0.016762 restraints weight = 80920.691| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.3128 r_free = 0.3128 target = 0.016762 restraints weight = 80920.691| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3128 r_free = 0.3128 target = 0.016762 restraints weight = 80920.691| |-----------------------------------------------------------------------------| r_work (final): 0.3074 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8496 moved from start: 0.7801 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 3309 Z= 0.170 Angle : 0.616 8.634 4496 Z= 0.328 Chirality : 0.045 0.147 483 Planarity : 0.004 0.037 581 Dihedral : 5.376 20.194 457 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 25.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.16 % Favored : 93.84 % Rotamer: Outliers : 2.55 % Allowed : 11.05 % Favored : 86.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.14 (0.43), residues: 406 helix: -3.43 (0.64), residues: 44 sheet: -0.48 (0.44), residues: 135 loop : -0.23 (0.45), residues: 227 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG E 454 TYR 0.021 0.002 TYR E 380 PHE 0.013 0.002 PHE E 347 TRP 0.006 0.001 TRP A 47 HIS 0.003 0.001 HIS B 38 Details of bonding type rmsd covalent geometry : bond 0.00377 ( 3303) covalent geometry : angle 0.60855 ( 4484) SS BOND : bond 0.00520 ( 6) SS BOND : angle 1.90494 ( 12) hydrogen bonds : bond 0.02927 ( 107) hydrogen bonds : angle 7.20148 ( 300) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 812 Ramachandran restraints generated. 406 Oldfield, 0 Emsley, 406 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 812 Ramachandran restraints generated. 406 Oldfield, 0 Emsley, 406 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 18 residues out of total 353 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 9 time to evaluate : 0.127 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 438 THR cc_start: 0.8470 (OUTLIER) cc_final: 0.8181 (p) outliers start: 9 outliers final: 5 residues processed: 18 average time/residue: 0.1096 time to fit residues: 2.4190 Evaluate side-chains 15 residues out of total 353 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 9 time to evaluate : 0.142 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 THR Chi-restraints excluded: chain B residue 92 ASP Chi-restraints excluded: chain E residue 368 LEU Chi-restraints excluded: chain E residue 438 THR Chi-restraints excluded: chain E residue 439 ARG Chi-restraints excluded: chain E residue 446 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 19 optimal weight: 50.0000 chunk 24 optimal weight: 9.9990 chunk 33 optimal weight: 2.9990 chunk 38 optimal weight: 9.9990 chunk 23 optimal weight: 7.9990 chunk 34 optimal weight: 4.9990 chunk 32 optimal weight: 9.9990 chunk 7 optimal weight: 6.9990 chunk 14 optimal weight: 10.0000 chunk 29 optimal weight: 9.9990 chunk 27 optimal weight: 5.9990 overall best weight: 5.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.022959 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3097 r_free = 0.3097 target = 0.016346 restraints weight = 78309.014| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 14)----------------| | r_work = 0.3097 r_free = 0.3097 target = 0.016344 restraints weight = 81817.041| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3097 r_free = 0.3097 target = 0.016339 restraints weight = 81985.134| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 12)----------------| | r_work = 0.3097 r_free = 0.3097 target = 0.016339 restraints weight = 82311.565| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3097 r_free = 0.3097 target = 0.016339 restraints weight = 82316.978| |-----------------------------------------------------------------------------| r_work (final): 0.3047 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8513 moved from start: 0.8055 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 3309 Z= 0.164 Angle : 0.582 7.520 4496 Z= 0.313 Chirality : 0.044 0.144 483 Planarity : 0.004 0.038 581 Dihedral : 5.249 21.451 457 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 24.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.91 % Favored : 94.09 % Rotamer: Outliers : 1.98 % Allowed : 11.33 % Favored : 86.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.20 (0.43), residues: 406 helix: -3.44 (0.64), residues: 44 sheet: -0.67 (0.43), residues: 137 loop : -0.15 (0.45), residues: 225 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG E 454 TYR 0.014 0.002 TYR E 380 PHE 0.015 0.002 PHE E 347 TRP 0.007 0.001 TRP A 47 HIS 0.004 0.002 HIS B 38 Details of bonding type rmsd covalent geometry : bond 0.00368 ( 3303) covalent geometry : angle 0.58081 ( 4484) SS BOND : bond 0.00366 ( 6) SS BOND : angle 0.82997 ( 12) hydrogen bonds : bond 0.03037 ( 107) hydrogen bonds : angle 6.81009 ( 300) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 812 Ramachandran restraints generated. 406 Oldfield, 0 Emsley, 406 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 812 Ramachandran restraints generated. 406 Oldfield, 0 Emsley, 406 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 16 residues out of total 353 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 9 time to evaluate : 0.080 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 438 THR cc_start: 0.8479 (OUTLIER) cc_final: 0.8215 (p) outliers start: 7 outliers final: 4 residues processed: 16 average time/residue: 0.1117 time to fit residues: 2.1943 Evaluate side-chains 14 residues out of total 353 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 9 time to evaluate : 0.140 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 THR Chi-restraints excluded: chain B residue 92 ASP Chi-restraints excluded: chain E residue 368 LEU Chi-restraints excluded: chain E residue 438 THR Chi-restraints excluded: chain E residue 446 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 21 optimal weight: 0.9980 chunk 1 optimal weight: 6.9990 chunk 12 optimal weight: 1.9990 chunk 10 optimal weight: 6.9990 chunk 15 optimal weight: 10.0000 chunk 3 optimal weight: 40.0000 chunk 5 optimal weight: 4.9990 chunk 16 optimal weight: 7.9990 chunk 30 optimal weight: 4.9990 chunk 35 optimal weight: 40.0000 chunk 11 optimal weight: 20.0000 overall best weight: 3.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.022940 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3117 r_free = 0.3117 target = 0.016495 restraints weight = 76388.713| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 22)----------------| | r_work = 0.3117 r_free = 0.3117 target = 0.016495 restraints weight = 80750.651| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.3117 r_free = 0.3117 target = 0.016495 restraints weight = 80751.042| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.3117 r_free = 0.3117 target = 0.016495 restraints weight = 80751.508| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 21)----------------| | r_work = 0.3117 r_free = 0.3117 target = 0.016495 restraints weight = 80751.702| |-----------------------------------------------------------------------------| r_work (final): 0.3118 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8229 moved from start: 0.8069 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 3309 Z= 0.140 Angle : 0.559 6.669 4496 Z= 0.299 Chirality : 0.044 0.140 483 Planarity : 0.005 0.069 581 Dihedral : 5.072 22.003 457 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 23.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.42 % Favored : 94.58 % Rotamer: Outliers : 1.13 % Allowed : 13.03 % Favored : 85.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.02 (0.43), residues: 406 helix: -3.49 (0.63), residues: 44 sheet: -0.40 (0.43), residues: 137 loop : -0.10 (0.46), residues: 225 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG E 439 TYR 0.013 0.001 TYR E 380 PHE 0.012 0.002 PHE E 347 TRP 0.007 0.001 TRP A 47 HIS 0.004 0.002 HIS E 505 Details of bonding type rmsd covalent geometry : bond 0.00319 ( 3303) covalent geometry : angle 0.55903 ( 4484) SS BOND : bond 0.00307 ( 6) SS BOND : angle 0.69391 ( 12) hydrogen bonds : bond 0.02667 ( 107) hydrogen bonds : angle 6.39278 ( 300) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 812 Ramachandran restraints generated. 406 Oldfield, 0 Emsley, 406 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 812 Ramachandran restraints generated. 406 Oldfield, 0 Emsley, 406 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 13 residues out of total 353 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 9 time to evaluate : 0.129 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 4 outliers final: 3 residues processed: 13 average time/residue: 0.1055 time to fit residues: 1.7514 Evaluate side-chains 12 residues out of total 353 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 9 time to evaluate : 0.080 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 THR Chi-restraints excluded: chain E residue 368 LEU Chi-restraints excluded: chain E residue 446 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 36 optimal weight: 0.0070 chunk 29 optimal weight: 20.0000 chunk 2 optimal weight: 8.9990 chunk 15 optimal weight: 20.0000 chunk 5 optimal weight: 30.0000 chunk 11 optimal weight: 0.1980 chunk 26 optimal weight: 0.0170 chunk 17 optimal weight: 30.0000 chunk 30 optimal weight: 40.0000 chunk 22 optimal weight: 20.0000 chunk 13 optimal weight: 7.9990 overall best weight: 3.4440 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.022855 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3117 r_free = 0.3117 target = 0.016423 restraints weight = 74736.593| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3115 r_free = 0.3115 target = 0.016390 restraints weight = 77731.442| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.3115 r_free = 0.3115 target = 0.016390 restraints weight = 80096.712| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.3115 r_free = 0.3115 target = 0.016390 restraints weight = 80097.257| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3115 r_free = 0.3115 target = 0.016390 restraints weight = 80097.258| |-----------------------------------------------------------------------------| r_work (final): 0.3067 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8508 moved from start: 0.8085 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 3309 Z= 0.120 Angle : 0.531 5.615 4496 Z= 0.284 Chirality : 0.043 0.135 483 Planarity : 0.005 0.058 581 Dihedral : 4.835 20.721 457 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 21.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.17 % Favored : 94.83 % Rotamer: Outliers : 0.85 % Allowed : 13.03 % Favored : 86.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.94 (0.43), residues: 406 helix: -3.59 (0.61), residues: 44 sheet: -0.34 (0.42), residues: 137 loop : -0.01 (0.46), residues: 225 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG E 439 TYR 0.015 0.001 TYR E 380 PHE 0.011 0.001 PHE B 49 TRP 0.008 0.001 TRP A 47 HIS 0.003 0.001 HIS B 38 Details of bonding type rmsd covalent geometry : bond 0.00273 ( 3303) covalent geometry : angle 0.53038 ( 4484) SS BOND : bond 0.00268 ( 6) SS BOND : angle 0.67879 ( 12) hydrogen bonds : bond 0.02545 ( 107) hydrogen bonds : angle 6.09045 ( 300) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 812 Ramachandran restraints generated. 406 Oldfield, 0 Emsley, 406 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 812 Ramachandran restraints generated. 406 Oldfield, 0 Emsley, 406 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 13 residues out of total 353 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 10 time to evaluate : 0.141 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 430 MET cc_start: 0.9327 (tpt) cc_final: 0.9019 (tpp) outliers start: 3 outliers final: 3 residues processed: 13 average time/residue: 0.0998 time to fit residues: 1.6887 Evaluate side-chains 13 residues out of total 353 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 10 time to evaluate : 0.135 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 THR Chi-restraints excluded: chain B residue 92 ASP Chi-restraints excluded: chain E residue 368 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 0 optimal weight: 40.0000 chunk 28 optimal weight: 0.2980 chunk 3 optimal weight: 40.0000 chunk 22 optimal weight: 0.3980 chunk 20 optimal weight: 20.0000 chunk 35 optimal weight: 8.9990 chunk 37 optimal weight: 7.9990 chunk 8 optimal weight: 9.9990 chunk 2 optimal weight: 7.9990 chunk 30 optimal weight: 10.0000 chunk 7 optimal weight: 4.9990 overall best weight: 4.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.022814 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3241 r_free = 0.3241 target = 0.018640 restraints weight = 75607.028| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 22)----------------| | r_work = 0.3241 r_free = 0.3241 target = 0.018638 restraints weight = 158672.716| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 65)----------------| | r_work = 0.3174 r_free = 0.3174 target = 0.017677 restraints weight = 160121.043| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3174 r_free = 0.3174 target = 0.017679 restraints weight = 177605.906| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3175 r_free = 0.3175 target = 0.017652 restraints weight = 189465.720| |-----------------------------------------------------------------------------| r_work (final): 0.3170 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8058 moved from start: 0.8367 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 3309 Z= 0.133 Angle : 0.537 5.537 4496 Z= 0.288 Chirality : 0.043 0.140 483 Planarity : 0.005 0.053 581 Dihedral : 4.794 21.002 457 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 22.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.16 % Favored : 93.84 % Rotamer: Outliers : 0.85 % Allowed : 13.03 % Favored : 86.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.92 (0.44), residues: 406 helix: -3.53 (0.62), residues: 44 sheet: -0.34 (0.42), residues: 137 loop : -0.00 (0.47), residues: 225 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG A 103 TYR 0.013 0.001 TYR E 380 PHE 0.013 0.002 PHE E 347 TRP 0.007 0.001 TRP A 47 HIS 0.004 0.001 HIS B 38 Details of bonding type rmsd covalent geometry : bond 0.00301 ( 3303) covalent geometry : angle 0.53657 ( 4484) SS BOND : bond 0.00252 ( 6) SS BOND : angle 0.64688 ( 12) hydrogen bonds : bond 0.02641 ( 107) hydrogen bonds : angle 6.09025 ( 300) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 916.56 seconds wall clock time: 16 minutes 28.33 seconds (988.33 seconds total)