Starting phenix.real_space_refine on Tue Feb 11 06:37:11 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8k19_36789/02_2025/8k19_36789.cif Found real_map, /net/cci-nas-00/data/ceres_data/8k19_36789/02_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_36789/02_2025/8k19_36789.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8k19_36789/02_2025/8k19_36789.map" model { file = "/net/cci-nas-00/data/ceres_data/8k19_36789/02_2025/8k19_36789.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8k19_36789/02_2025/8k19_36789.cif" } resolution = 3.88 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= 0.002 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): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/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: 3.07, per 1000 atoms: 0.95 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: 0.77 Conformation dependent library (CDL) restraints added in 443.3 milliseconds 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: 0.46 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: 0.91 Time building geometry restraints manager: 0.94 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: 1.980 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.030 Construct map_model_manager: 0.000 Extract box with map and model: 0.130 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 13.280 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.680 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.210 ------------------------------------------------------------------------------- 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 3303 Z= 0.874 Angle : 1.836 8.239 4484 Z= 1.215 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.84 (0.37), 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 TRP 0.080 0.026 TRP A 36 HIS 0.052 0.012 HIS B 93 PHE 0.078 0.013 PHE E 497 TYR 0.137 0.031 TYR A 59 ARG 0.037 0.005 ARG A 35 *********************** 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 : 0.346 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: 0.3055 time to fit residues: 10.1873 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 : 0.373 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 32 optimal weight: 10.0000 chunk 29 optimal weight: 3.9990 chunk 16 optimal weight: 6.9990 chunk 10 optimal weight: 6.9990 chunk 19 optimal weight: 20.0000 chunk 15 optimal weight: 6.9990 chunk 30 optimal weight: 4.9990 chunk 11 optimal weight: 6.9990 chunk 18 optimal weight: 10.0000 chunk 22 optimal weight: 4.9990 chunk 35 optimal weight: 30.0000 overall best weight: 5.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 93 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 394 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3922 r_free = 0.3922 target = 0.032536 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.020124 restraints weight = 51011.606| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.020335 restraints weight = 48011.028| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.020277 restraints weight = 44999.263| |-----------------------------------------------------------------------------| r_work (final): 0.3222 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8320 moved from start: 0.3306 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.068 3303 Z= 0.258 Angle : 0.659 6.946 4484 Z= 0.353 Chirality : 0.045 0.140 483 Planarity : 0.005 0.036 581 Dihedral : 5.583 34.216 457 Min Nonbonded Distance : 2.614 Molprobity Statistics. All-atom Clashscore : 17.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.19 % Favored : 95.81 % Rotamer: Outliers : 0.00 % Allowed : 6.52 % Favored : 93.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.03 (0.39), residues: 406 helix: -2.67 (0.81), residues: 32 sheet: -0.81 (0.41), residues: 128 loop : -0.22 (0.38), residues: 246 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP A 109 HIS 0.003 0.001 HIS B 70 PHE 0.015 0.002 PHE B 49 TYR 0.014 0.002 TYR A 33 ARG 0.003 0.001 ARG E 454 *********************** 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 16 residues out of total 353 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 16 time to evaluate : 0.365 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 34 MET cc_start: 0.9329 (mpp) cc_final: 0.9044 (pmm) REVERT: A 82 MET cc_start: -0.0041 (mtm) cc_final: -0.0769 (mtt) outliers start: 0 outliers final: 0 residues processed: 16 average time/residue: 0.3047 time to fit residues: 5.8391 Evaluate side-chains 11 residues out of total 353 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 11 time to evaluate : 0.395 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 35 optimal weight: 8.9990 chunk 18 optimal weight: 9.9990 chunk 11 optimal weight: 0.9990 chunk 16 optimal weight: 8.9990 chunk 28 optimal weight: 20.0000 chunk 33 optimal weight: 10.0000 chunk 31 optimal weight: 8.9990 chunk 5 optimal weight: 0.9980 chunk 37 optimal weight: 0.0570 chunk 6 optimal weight: 5.9990 chunk 36 optimal weight: 1.9990 overall best weight: 2.0104 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 39 GLN B 38 HIS ** B 93 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 = 0.3956 r_free = 0.3956 target = 0.032625 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.020124 restraints weight = 49637.303| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.020256 restraints weight = 46367.037| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.020256 restraints weight = 45474.842| |-----------------------------------------------------------------------------| r_work (final): 0.3192 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8240 moved from start: 0.3691 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 3303 Z= 0.151 Angle : 0.557 5.538 4484 Z= 0.296 Chirality : 0.043 0.140 483 Planarity : 0.004 0.033 581 Dihedral : 4.748 19.415 457 Min Nonbonded Distance : 2.590 Molprobity Statistics. All-atom Clashscore : 13.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.20 % Favored : 96.80 % Rotamer: Outliers : 0.00 % Allowed : 6.52 % Favored : 93.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.58 (0.41), residues: 406 helix: -2.72 (0.83), residues: 32 sheet: -0.31 (0.42), residues: 127 loop : 0.03 (0.40), residues: 247 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 36 HIS 0.001 0.000 HIS A 104 PHE 0.011 0.001 PHE B 49 TYR 0.009 0.001 TYR A 79 ARG 0.004 0.000 ARG E 454 *********************** 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 14 residues out of total 353 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 14 time to evaluate : 0.401 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 78 MET cc_start: 0.8160 (ptt) cc_final: 0.7729 (ppp) REVERT: A 82 MET cc_start: -0.1479 (mtm) cc_final: -0.1817 (mtt) outliers start: 0 outliers final: 0 residues processed: 14 average time/residue: 0.3045 time to fit residues: 5.2467 Evaluate side-chains 12 residues out of total 353 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 12 time to evaluate : 0.383 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 19 optimal weight: 40.0000 chunk 34 optimal weight: 9.9990 chunk 0 optimal weight: 30.0000 chunk 22 optimal weight: 5.9990 chunk 9 optimal weight: 40.0000 chunk 26 optimal weight: 7.9990 chunk 36 optimal weight: 8.9990 chunk 18 optimal weight: 50.0000 chunk 15 optimal weight: 20.0000 chunk 8 optimal weight: 0.7980 chunk 16 optimal weight: 0.0050 overall best weight: 4.7600 ------------------------------------------------------------------------------- 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 = 0.3431 r_free = 0.3431 target = 0.024293 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3200 r_free = 0.3200 target = 0.017905 restraints weight = 72560.033| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 22)----------------| | r_work = 0.3200 r_free = 0.3200 target = 0.017904 restraints weight = 77972.279| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.3200 r_free = 0.3200 target = 0.017904 restraints weight = 78104.150| |-----------------------------------------------------------------------------| r_work (final): 0.3183 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8090 moved from start: 0.5051 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 3303 Z= 0.207 Angle : 0.559 5.287 4484 Z= 0.300 Chirality : 0.044 0.141 483 Planarity : 0.004 0.034 581 Dihedral : 4.818 21.457 457 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 18.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.17 % Favored : 94.83 % 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 (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: -0.79 (0.41), residues: 406 helix: -3.31 (0.63), residues: 44 sheet: -0.33 (0.41), residues: 142 loop : 0.12 (0.43), residues: 220 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP A 109 HIS 0.003 0.001 HIS B 38 PHE 0.013 0.002 PHE B 49 TYR 0.017 0.002 TYR E 380 ARG 0.005 0.001 ARG E 454 *********************** 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 13 residues out of total 353 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 12 time to evaluate : 0.446 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 82 MET cc_start: -0.2930 (mtm) cc_final: -0.3343 (mtt) outliers start: 1 outliers final: 0 residues processed: 13 average time/residue: 0.3207 time to fit residues: 5.1512 Evaluate side-chains 11 residues out of total 353 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 11 time to evaluate : 0.495 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 24 optimal weight: 0.0010 chunk 29 optimal weight: 20.0000 chunk 13 optimal weight: 3.9990 chunk 34 optimal weight: 6.9990 chunk 33 optimal weight: 5.9990 chunk 30 optimal weight: 1.9990 chunk 27 optimal weight: 20.0000 chunk 0 optimal weight: 30.0000 chunk 32 optimal weight: 20.0000 chunk 8 optimal weight: 3.9990 chunk 5 optimal weight: 9.9990 overall best weight: 3.1994 ------------------------------------------------------------------------------- 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 = 0.3418 r_free = 0.3418 target = 0.024289 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3189 r_free = 0.3189 target = 0.017958 restraints weight = 72778.736| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 22)----------------| | r_work = 0.3189 r_free = 0.3189 target = 0.017958 restraints weight = 76719.865| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.3189 r_free = 0.3189 target = 0.017958 restraints weight = 76719.865| |-----------------------------------------------------------------------------| r_work (final): 0.3132 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8480 moved from start: 0.5318 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 3303 Z= 0.162 Angle : 0.547 8.087 4484 Z= 0.287 Chirality : 0.043 0.140 483 Planarity : 0.004 0.031 581 Dihedral : 4.679 21.793 457 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 15.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 0.28 % Allowed : 8.50 % 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 (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: -0.72 (0.41), residues: 406 helix: -3.40 (0.60), residues: 44 sheet: -0.09 (0.43), residues: 134 loop : 0.05 (0.42), residues: 228 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 109 HIS 0.002 0.001 HIS B 38 PHE 0.012 0.002 PHE E 456 TYR 0.012 0.001 TYR E 380 ARG 0.003 0.000 ARG E 454 *********************** 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 12 residues out of total 353 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 11 time to evaluate : 0.361 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 78 MET cc_start: 0.8301 (ptt) cc_final: 0.7154 (ppp) REVERT: A 82 MET cc_start: -0.1542 (mtm) cc_final: -0.2217 (mtt) outliers start: 1 outliers final: 0 residues processed: 12 average time/residue: 0.3252 time to fit residues: 4.8811 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 : 0.382 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 18 optimal weight: 40.0000 chunk 19 optimal weight: 30.0000 chunk 11 optimal weight: 40.0000 chunk 20 optimal weight: 20.0000 chunk 14 optimal weight: 7.9990 chunk 38 optimal weight: 6.9990 chunk 4 optimal weight: 20.0000 chunk 17 optimal weight: 20.0000 chunk 16 optimal weight: 6.9990 chunk 25 optimal weight: 7.9990 chunk 32 optimal weight: 7.9990 overall best weight: 7.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 70 HIS E 394 ASN E 493 GLN ** E 505 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.023933 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3156 r_free = 0.3156 target = 0.017466 restraints weight = 73984.001| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3154 r_free = 0.3154 target = 0.017436 restraints weight = 79129.499| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3153 r_free = 0.3153 target = 0.017407 restraints weight = 81330.949| |-----------------------------------------------------------------------------| r_work (final): 0.3098 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8490 moved from start: 0.6815 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 3303 Z= 0.276 Angle : 0.633 5.787 4484 Z= 0.340 Chirality : 0.044 0.139 483 Planarity : 0.005 0.041 581 Dihedral : 5.188 22.263 457 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 28.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.91 % Favored : 94.09 % Rotamer: Outliers : 1.13 % Allowed : 9.92 % Favored : 88.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.87 (0.42), residues: 406 helix: -3.66 (0.56), residues: 44 sheet: -0.41 (0.42), residues: 142 loop : 0.16 (0.44), residues: 220 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP A 109 HIS 0.005 0.002 HIS E 505 PHE 0.016 0.002 PHE E 347 TYR 0.017 0.002 TYR E 380 ARG 0.005 0.001 ARG E 454 *********************** 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 14 residues out of total 353 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 10 time to evaluate : 0.411 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 34 MET cc_start: 0.9200 (mpp) cc_final: 0.8855 (mpp) REVERT: A 78 MET cc_start: 0.8392 (ptt) cc_final: 0.7061 (ppp) outliers start: 4 outliers final: 0 residues processed: 14 average time/residue: 0.2496 time to fit residues: 4.4862 Evaluate side-chains 9 residues out of total 353 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 9 time to evaluate : 0.409 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 21 optimal weight: 0.0770 chunk 24 optimal weight: 8.9990 chunk 0 optimal weight: 30.0000 chunk 12 optimal weight: 50.0000 chunk 23 optimal weight: 5.9990 chunk 30 optimal weight: 20.0000 chunk 33 optimal weight: 4.9990 chunk 31 optimal weight: 6.9990 chunk 8 optimal weight: 5.9990 chunk 26 optimal weight: 4.9990 chunk 22 optimal weight: 20.0000 overall best weight: 4.4146 ------------------------------------------------------------------------------- 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 = 0.3403 r_free = 0.3403 target = 0.023488 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3158 r_free = 0.3158 target = 0.017096 restraints weight = 73835.172| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 19)----------------| | r_work = 0.3158 r_free = 0.3158 target = 0.017092 restraints weight = 77825.568| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.3158 r_free = 0.3158 target = 0.017092 restraints weight = 78116.559| |-----------------------------------------------------------------------------| r_work (final): 0.3098 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8495 moved from start: 0.6837 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 3303 Z= 0.200 Angle : 0.565 8.122 4484 Z= 0.302 Chirality : 0.043 0.140 483 Planarity : 0.004 0.035 581 Dihedral : 4.998 20.533 457 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 21.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.17 % Favored : 94.83 % Rotamer: Outliers : 1.13 % Allowed : 11.05 % Favored : 87.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.83 (0.43), residues: 406 helix: -3.46 (0.62), residues: 44 sheet: -0.40 (0.43), residues: 141 loop : 0.15 (0.44), residues: 221 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 47 HIS 0.003 0.001 HIS B 38 PHE 0.011 0.002 PHE B 49 TYR 0.020 0.002 TYR E 380 ARG 0.002 0.000 ARG E 454 *********************** 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 13 residues out of total 353 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 9 time to evaluate : 0.362 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 78 MET cc_start: 0.8557 (ptt) cc_final: 0.7160 (ppp) outliers start: 4 outliers final: 1 residues processed: 13 average time/residue: 0.2137 time to fit residues: 3.7007 Evaluate side-chains 10 residues out of total 353 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 9 time to evaluate : 0.371 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 20 optimal weight: 2.9990 chunk 28 optimal weight: 0.0980 chunk 19 optimal weight: 50.0000 chunk 35 optimal weight: 0.9990 chunk 4 optimal weight: 8.9990 chunk 10 optimal weight: 30.0000 chunk 0 optimal weight: 30.0000 chunk 31 optimal weight: 20.0000 chunk 18 optimal weight: 50.0000 chunk 11 optimal weight: 0.2980 chunk 34 optimal weight: 3.9990 overall best weight: 1.6786 ------------------------------------------------------------------------------- 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 = 0.3394 r_free = 0.3394 target = 0.023314 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3151 r_free = 0.3151 target = 0.016977 restraints weight = 74524.976| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 22)----------------| | r_work = 0.3151 r_free = 0.3151 target = 0.016976 restraints weight = 79505.385| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.3151 r_free = 0.3151 target = 0.016976 restraints weight = 79534.184| |-----------------------------------------------------------------------------| r_work (final): 0.3095 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8521 moved from start: 0.6652 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 3303 Z= 0.139 Angle : 0.526 8.338 4484 Z= 0.278 Chirality : 0.044 0.140 483 Planarity : 0.004 0.034 581 Dihedral : 4.731 20.339 457 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 15.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.17 % Favored : 94.83 % Rotamer: Outliers : 1.13 % Allowed : 10.76 % Favored : 88.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.74 (0.42), residues: 406 helix: -3.46 (0.63), residues: 44 sheet: -0.24 (0.43), residues: 136 loop : 0.14 (0.44), residues: 226 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 47 HIS 0.002 0.001 HIS B 70 PHE 0.010 0.001 PHE E 456 TYR 0.009 0.001 TYR A 33 ARG 0.002 0.000 ARG A 35 *********************** 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 13 residues out of total 353 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 9 time to evaluate : 0.360 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 78 MET cc_start: 0.8586 (ptt) cc_final: 0.7368 (ppp) REVERT: E 430 MET cc_start: 0.9291 (tpt) cc_final: 0.8958 (tpp) outliers start: 4 outliers final: 2 residues processed: 13 average time/residue: 0.2222 time to fit residues: 3.8313 Evaluate side-chains 11 residues out of total 353 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 9 time to evaluate : 0.405 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 92 ASP 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 29 optimal weight: 20.0000 chunk 8 optimal weight: 40.0000 chunk 22 optimal weight: 7.9990 chunk 9 optimal weight: 50.0000 chunk 34 optimal weight: 5.9990 chunk 11 optimal weight: 20.0000 chunk 2 optimal weight: 9.9990 chunk 28 optimal weight: 2.9990 chunk 12 optimal weight: 6.9990 chunk 14 optimal weight: 50.0000 chunk 19 optimal weight: 30.0000 overall best weight: 6.7990 ------------------------------------------------------------------------------- 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 = 0.3373 r_free = 0.3373 target = 0.023132 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3132 r_free = 0.3132 target = 0.016811 restraints weight = 74235.435| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3131 r_free = 0.3131 target = 0.016776 restraints weight = 78974.019| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 19)----------------| | r_work = 0.3129 r_free = 0.3129 target = 0.016748 restraints weight = 81537.631| |-----------------------------------------------------------------------------| r_work (final): 0.3068 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8511 moved from start: 0.7585 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.079 3303 Z= 0.255 Angle : 0.585 8.344 4484 Z= 0.317 Chirality : 0.043 0.144 483 Planarity : 0.005 0.035 581 Dihedral : 5.064 22.710 457 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 25.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.14 % Favored : 92.86 % Rotamer: Outliers : 0.57 % Allowed : 12.46 % 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 (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: -0.80 (0.43), residues: 406 helix: -3.45 (0.63), residues: 44 sheet: -0.41 (0.42), residues: 142 loop : 0.22 (0.46), residues: 220 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 47 HIS 0.003 0.001 HIS B 38 PHE 0.014 0.002 PHE E 347 TYR 0.016 0.002 TYR E 380 ARG 0.003 0.001 ARG E 454 *********************** 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 11 residues out of total 353 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 9 time to evaluate : 0.369 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 78 MET cc_start: 0.8628 (ptt) cc_final: 0.7187 (ppp) outliers start: 2 outliers final: 1 residues processed: 11 average time/residue: 0.2741 time to fit residues: 3.9351 Evaluate side-chains 10 residues out of total 353 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 9 time to evaluate : 0.361 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 23 optimal weight: 0.0870 chunk 36 optimal weight: 1.9990 chunk 14 optimal weight: 40.0000 chunk 27 optimal weight: 6.9990 chunk 7 optimal weight: 10.0000 chunk 17 optimal weight: 50.0000 chunk 25 optimal weight: 6.9990 chunk 21 optimal weight: 7.9990 chunk 19 optimal weight: 30.0000 chunk 4 optimal weight: 20.0000 chunk 5 optimal weight: 3.9990 overall best weight: 4.0166 ------------------------------------------------------------------------------- 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 = 0.3394 r_free = 0.3394 target = 0.023197 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.018928 restraints weight = 74013.389| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3230 r_free = 0.3230 target = 0.018350 restraints weight = 132408.324| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3221 r_free = 0.3221 target = 0.018175 restraints weight = 167946.621| |-----------------------------------------------------------------------------| r_work (final): 0.3213 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8016 moved from start: 0.7546 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 3303 Z= 0.180 Angle : 0.548 8.042 4484 Z= 0.294 Chirality : 0.043 0.143 483 Planarity : 0.004 0.036 581 Dihedral : 4.938 20.839 457 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 20.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.68 % Favored : 95.32 % Rotamer: Outliers : 0.57 % Allowed : 12.46 % 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 (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: -0.77 (0.43), residues: 406 helix: -3.38 (0.66), residues: 44 sheet: -0.36 (0.41), residues: 143 loop : 0.20 (0.46), residues: 219 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 47 HIS 0.003 0.001 HIS B 38 PHE 0.013 0.002 PHE E 456 TYR 0.014 0.001 TYR E 380 ARG 0.002 0.000 ARG E 454 ********************** 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 11 residues out of total 353 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 9 time to evaluate : 0.360 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 78 MET cc_start: 0.7583 (ptt) cc_final: 0.6481 (ppp) REVERT: A 100 MET cc_start: 0.1889 (ttt) cc_final: 0.1350 (ttt) outliers start: 2 outliers final: 1 residues processed: 11 average time/residue: 0.2405 time to fit residues: 3.5131 Evaluate side-chains 10 residues out of total 353 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 9 time to evaluate : 0.418 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 31 optimal weight: 7.9990 chunk 30 optimal weight: 20.0000 chunk 12 optimal weight: 0.9980 chunk 35 optimal weight: 20.0000 chunk 16 optimal weight: 2.9990 chunk 9 optimal weight: 40.0000 chunk 21 optimal weight: 8.9990 chunk 10 optimal weight: 8.9990 chunk 18 optimal weight: 20.0000 chunk 11 optimal weight: 0.0020 chunk 20 optimal weight: 7.9990 overall best weight: 3.9994 ------------------------------------------------------------------------------- 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 = 0.3383 r_free = 0.3383 target = 0.022971 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.019130 restraints weight = 76437.483| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3213 r_free = 0.3213 target = 0.018399 restraints weight = 163175.401| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3224 r_free = 0.3224 target = 0.018334 restraints weight = 206098.241| |-----------------------------------------------------------------------------| r_work (final): 0.3233 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7968 moved from start: 0.7844 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 3303 Z= 0.180 Angle : 0.552 8.343 4484 Z= 0.290 Chirality : 0.043 0.137 483 Planarity : 0.004 0.036 581 Dihedral : 4.773 21.739 457 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 19.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.67 % Favored : 94.33 % Rotamer: Outliers : 0.28 % Allowed : 13.03 % 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 (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: -0.78 (0.43), residues: 406 helix: -3.50 (0.64), residues: 44 sheet: -0.33 (0.41), residues: 143 loop : 0.20 (0.46), residues: 219 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 47 HIS 0.003 0.001 HIS B 38 PHE 0.012 0.002 PHE B 49 TYR 0.017 0.002 TYR E 380 ARG 0.002 0.000 ARG A 103 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1618.98 seconds wall clock time: 29 minutes 38.10 seconds (1778.10 seconds total)